Thu, 21 Aug 2008 01:47:31 BST CiteULike: Author Berman http://www.citeulike.org/author/Berman CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/group/5032/article/680 <i>Genome Biol, Vol. 5, No. 9. (2004)</i><br /><br />BACKGROUND: The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. RESULTS: We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. CONCLUSIONS: Measuring conservation of sequence features closely linked to function--such as binding-site clusterin--makes better use of comparative sequence data than commonly used methods that examine only sequence identity. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. BP Berman BD Pfeiffer TR Laverty SL Salzberg GM Rubin MB Eisen SE Celniker doi:10.1186/gb-2004-5-9-r61 Genome Biol, Vol. 5, No. 9. (2004) 2004-11-22T00:17:30-00:00 2004 Genome Biol 1465-6914 5 9 tfbs http://www.citeulike.org/user/granujilla/article/1250130 <i>Acta Crystallogr D Biol Crystallogr, Vol. 58, No. Pt 6 No 1. (June 2002), pp. 899-907.</i><br /><br />The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28, 235-242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules. Many secondary sources of information are derived from PDB data. It is the starting point for studies in structural bioinformatics. This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource. The reader should come away with an understanding of the scope of the PDB and what is provided by the resource. The Protein Data Bank. HM Berman T Battistuz TN Bhat WF Bluhm PE Bourne K Burkhardt Z Feng GL Gilliland L Iype S Jain P Fagan J Marvin D Padilla V Ravichandran B Schneider N Thanki H Weissig JD Westbrook C Zardecki Acta Crystallogr D Biol Crystallogr, Vol. 58, No. Pt 6 No 1. (June 2002), pp. 899-907. 2007-04-25T11:39:55-00:00 2002 Acta Crystallogr D Biol Crystallogr 0907-4449 58 Pt 6 No 1 899 907 no-tag http://www.citeulike.org/user/timg/article/255030 <i>Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 235-242.</i><br /><br />The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource. The Protein Data Bank. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne doi:10.1093/nar/28.1.235 Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 235-242. 2005-07-13T16:11:15-00:00 2000 Nucleic Acids Res 0305-1048 28 1 235 242 dataset http://www.citeulike.org/group/6322/article/3111856 <i>Genome biology, Vol. 3, No. 12. (2002)</i><br /><br />BACKGROUND: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences. RESULTS: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes. CONCLUSIONS: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. S Misra MA Crosby CJ Mungall BB Matthews KS Campbell P Hradecky Y Huang JS Kaminker GH Millburn SE Prochnik CD Smith JL Tupy EJ Whitfied L Bayraktaroglu BP Berman BR Bettencourt SE Celniker AD de Grey RA Drysdale NL Harris J Richter S Russo AJ Schroeder SQ Shu M Stapleton C Yamada M Ashburner WM Gelbart GM Rubin SE Lewis Genome biology, Vol. 3, No. 12. (2002) 2008-08-12T12:49:03-00:00 2002 Genome biology 1465-6914 3 12 annotation drosophila genome_sequence http://www.citeulike.org/group/6322/article/186930 <i>Science, Vol. 287, No. 5461. (24 March 2000), pp. 2185-2195.</i><br /><br />The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity. The genome sequence of Drosophila melanogaster. MD Adams SE Celniker RA Holt CA Evans JD Gocayne PG Amanatides SE Scherer PW Li RA Hoskins RF Galle RA George SE Lewis S Richards M Ashburner SN Henderson GG Sutton JR Wortman MD Yandell Q Zhang LX Chen RC Brandon YH Rogers RG Blazej M Champe BD Pfeiffer KH Wan C Doyle EG Baxter G Helt CR Nelson GL Gabor JF Abril A Agbayani HJ An C Andrews-Pfannkoch D Baldwin RM Ballew A Basu J Baxendale L Bayraktaroglu EM Beasley KY Beeson PV Benos BP Berman D Bhandari S Bolshakov D Borkova MR Botchan J Bouck P Brokstein P Brottier KC Burtis DA Busam H Butler E Cadieu A Center I Chandra JM Cherry S Cawley C Dahlke LB Davenport P Davies B de Pablos A Delcher Z Deng AD Mays I Dew SM Dietz K Dodson LE Doup M Downes S Dugan-Rocha BC Dunkov P Dunn KJ Durbin CC Evangelista C Ferraz S Ferriera W Fleischmann C Fosler AE Gabrielian NS Garg WM Gelbart K Glasser A Glodek F Gong JH Gorrell Z Gu P Guan M Harris NL Harris D Harvey TJ Heiman JR Hernandez J Houck D Hostin KA Houston TJ Howland MH Wei C Ibegwam M Jalali F Kalush GH Karpen Z Ke JA Kennison KA Ketchum BE Kimmel CD Kodira C Kraft S Kravitz D Kulp Z Lai P Lasko Y Lei AA Levitsky J Li Z Li Y Liang X Lin X Liu B Mattei TC McIntosh MP McLeod D McPherson G Merkulov NV Milshina C Mobarry J Morris A Moshrefi SM Mount M Moy B Murphy L Murphy DM Muzny DL Nelson DR Nelson KA Nelson K Nixon DR Nusskern JM Pacleb M Palazzolo GS Pittman S Pan J Pollard V Puri MG Reese K Reinert K Remington RD Saunders F Scheeler H Shen BC Shue I Sidén-Kiamos M Simpson MP Skupski T Smith E Spier AC Spradling M Stapleton R Strong E Sun R Svirskas C Tector R Turner E Venter AH Wang X Wang ZY Wang DA Wassarman GM Weinstock J Weissenbach SM Williams WoodageT KC Worley D Wu S Yang QA Yao J Ye RF Yeh JS Zaveri M Zhan G Zhang Q Zhao L Zheng XH Zheng FN Zhong W Zhong X Zhou S Zhu X Zhu HO Smith RA Gibbs EW Myers GM Rubin JC Venter Science, Vol. 287, No. 5461. (24 March 2000), pp. 2185-2195. 2005-05-09T16:56:36-00:00 2000 Science 0036-8075 287 5461 2185 2195 drosophila genome_sequence http://www.citeulike.org/user/chad_davis/article/142324 <i>Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 988-992.</i> PDBML: the representation of archival macromolecular structure data in XML Westbrook John Ito Nobutoshi Nakamura Haruki Henrick Kim M Berman doi:10.1093/bioinformatics/bti082 Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 988-992. 2005-03-28T20:02:50-00:00 2005 Bioinformatics 1367-4803 21 7 988 992 Oxford University Press database download structure toolkit http://www.citeulike.org/user/kas/article/3095952 <i>Physical Review B (Condensed Matter and Materials Physics), Vol. 78, No. 8. (2008)</i><br /><br />We calculate the dispersion equations for magnetoplasmons in a single layer, a pair of parallel layers, a graphite bilayer, and a superlattice of graphene layers in a perpendicular magnetic field. We demonstrate the feasibility of a drift-induced instability of magnetoplasmons. The magnetoplasmon instability in a superlattice is enhanced compared to a single graphene layer. The energies of the unstable magnetoplasmons could be in the terahertz (THz) part of the electromagnetic spectrum. The enhanced instability makes superlattice graphene a potential source of THz radiation. Magnetoplasmons in layered graphene structures Oleg Berman Godfrey Gumbs Yurii Lozovik doi:10.1103/PhysRevB.78.085401 Physical Review B (Condensed Matter and Materials Physics), Vol. 78, No. 8. (2008) 2008-08-07T14:11:52-00:00 2008 Physical Review B (Condensed Matter and Materials Physics) 78 8 APS bilayer graphene magnetic magnetoplasmon http://www.citeulike.org/user/monicadr/article/1681419 <i>Journal of Clinical Psychology, Vol. 62, No. 2. (2006), pp. 171-184.</i><br /><br />The patient who is at-risk for suicide is complex and is difficult to evaluate and treat effectively. Should suicidal behavior occur, the clinician faces the potential wrath of bereaved survivors and their externalized blame exercised through a malpractice suit. The clinician's duty of care to a patient is to act affirmatively to protect a patient from violent acts against self. A finding of malpractice is established if the court finds that this duty was breached, through an act of omission or commission relative to the standard of care, and that this breach was proximately related to the patient's suicidal behavior. This article discusses the standard of care and factors that determine liability in a suicide death of a patient. An extensive list of recommendations for competent caregiving for the at-risk patient and risk management guidelines are then presented. © 2005 Wiley Periodicals, Inc. J Clin Psychol: In Session 62: 171-184, 2006. Risk management with suicidal patients Alan Berman doi:10.1002/jclp.20221 Journal of Clinical Psychology, Vol. 62, No. 2. (2006), pp. 171-184. 2007-09-21T03:16:32-00:00 2006 Journal of Clinical Psychology 62 2 171 184 review risk suicide http://www.citeulike.org/user/kas/article/3065638 <i>Physical Review B (Condensed Matter and Materials Physics), Vol. 78, No. 3. (2008)</i><br /><br />The Bose-Einstein condensation and superfluidity of quasi-two-dimensional spatially indirect magnetobiexcitons in a slab of superlattice with alternating electron and hole layers consisting from the semiconducting quantum wells (QWs) and graphene superlattice in high magnetic field are considered. The two different Hamiltonians of a dilute gas of magnetoexcitons with a dipole-dipole repulsion in superlattices, consisting of both QWs and graphene layers (GLs) in the limit of high magnetic field, have been reduced to one effective Hamiltonian—a dilute gas of two-dimensional excitons with the renormalized effective mass of the magnetoexciton, which depends on the magnetic field. This Hamiltonian does not include the vector potential. Moreover, for N excitons we have reduced the problem of 2N×2-dimensional space onto the problem of N×2-dimensional space by integrating over the coordinates of the relative motion of an electron and a hole. The instability of the ground state of the system of interacting two-dimensional indirect magnetoexcitons in a slab of superlattice with alternating electron and hole layers in high magnetic field is found. The stable system of indirect quasi-two-dimensional magnetobiexcitons, consisting of a pair of indirect excitons with opposite dipole moments, is considered. The density of the superfluid component ns(T) and the temperature of the Kosterlitz-Thouless phase transition to the superfluid state in the system of two-dimensional indirect magnetobiexcitons, interacting as electrical quadrupoles, are obtained for both the QW and graphene realizations. Collective properties of magnetobiexcitons in quantum wells and graphene superlattices Oleg Berman Roman Yurii Lozovik doi:10.1103/PhysRevB.78.035135 Physical Review B (Condensed Matter and Materials Physics), Vol. 78, No. 3. (2008) 2008-07-31T14:31:38-00:00 2008 Physical Review B (Condensed Matter and Materials Physics) 78 3 APS graphene superlattice http://www.citeulike.org/user/nishiokov/article/315921 <i>Cereb Cortex (20 July 2005)</i><br /><br />Brain processing of reward information is essential for complex functions such as learning and motivation. Recent primate electrophysiological studies using concepts from information, economic and learning theories indicate that the midbrain may code two statistical parameters of reward information: a transient reward error prediction signal that varies linearly with reward probability and a sustained signal that varies highly non-linearly with reward probability and that is highest with maximal reward uncertainty (reward probability = 0.5). Here, using event-related functional magnetic resonance imaging, we disentangled these two signals in humans using a novel paradigm that systematically varied monetary reward probability, magnitude and expected reward value. The midbrain was activated both transiently with the error prediction signal and in a sustained fashion with reward uncertainty. Moreover, distinct activity dynamics were observed in post-synaptic midbrain projection sites: the prefrontal cortex responded to the transient error prediction signal while the ventral striatum covaried with the sustained reward uncertainty signal. These data suggest that the prefrontal cortex may generate the reward prediction while the ventral striatum may be involved in motivational processes that are useful when an organism needs to obtain more information about its environment. Our results indicate that distinct functional brain networks code different aspects of the statistical properties of reward information in humans. Neural Coding of Distinct Statistical Properties of Reward Information in Humans. Jean-Claude Dreher Philip Kohn Karen Faith Berman Cereb Cortex (20 July 2005) 2005-09-12T15:00:31-00:00 2005 Cereb Cortex 1047-3211 fmri human reward http://www.citeulike.org/user/nishiokov/article/2176212 <i>Proceedings of the National Academy of Sciences, Vol. 104, No. 7. (13 February 2007), pp. 2465-2470.</i><br /><br />There is considerable evidence from animal studies that the mesolimbic and mesocortical dopamine systems are sensitive to circulating gonadal steroid hormones. Less is known about the influence of estrogen and progesterone on the human reward system. To investigate this directly, we used functional MRI and an event-related monetary reward paradigm to study women with a repeated-measures, counterbalanced design across the menstrual cycle. Here we show that during the midfollicular phase (days 4-8 after onset of menses) women anticipating uncertain rewards activated the orbitofrontal cortex and amygdala more than during the luteal phase (6-10 days after luteinizing hormone surge). At the time of reward delivery, women in the follicular phase activated the midbrain, striatum, and left fronto-polar cortex more than during the luteal phase. These data demonstrate augmented reactivity of the reward system in women during the midfollicular phase when estrogen is unopposed by progesterone. Moreover, investigation of between-sex differences revealed that men activated ventral putamen more than women during anticipation of uncertain rewards, whereas women more strongly activated the anterior medial prefrontal cortex at the time of reward delivery. Correlation between brain activity and gonadal steroid levels also revealed that the amygdalo-hippocampal complex was positively correlated with estradiol level, regardless of menstrual cycle phase. Together, our findings provide evidence of neurofunctional modulation of the reward system by gonadal steroid hormones in humans and establish a neurobiological foundation for understanding their impact on vulnerability to drug abuse, neuropsychiatric diseases with differential expression across males and females, and hormonally mediated mood disorders. 10.1073/pnas.0605569104 Menstrual cycle phase modulates reward-related neural function in women Jean-Claude Dreher Peter Schmidt Philip Kohn Daniella Furman David Rubinow Karen Berman doi:10.1073/pnas.0605569104 Proceedings of the National Academy of Sciences, Vol. 104, No. 7. (13 February 2007), pp. 2465-2470. 2007-12-28T02:55:06-00:00 2007 Proceedings of the National Academy of Sciences 104 7 2465 2470 dopamine fmri human reward http://www.citeulike.org/user/wolfe275/article/3043930 <i>Journal of the History of Sexuality, Vol. 6, No. 2. (1995), pp. 325-328.</i> Review: [The Language of Sex: Five Voices from Northern France around 1200] Constance Berman doi:10.2307/3704126 Journal of the History of Sexuality, Vol. 6, No. 2. (1995), pp. 325-328. 2008-07-26T00:15:38-00:00 1995 Journal of the History of Sexuality 6 2 325 328 University of Texas Press celibacy medieval http://www.citeulike.org/user/hsekiguc/article/227151 <i>Science, Vol. 287, No. 5461. (24 March 2000), pp. 2185-2195.</i> The Genome Sequence of Drosophila melanogaster Mark Adams Susan Celniker Robert Holt Cheryl Evans Jeannine Gocayne Peter Amanatides Steven Scherer Peter Li Roger Hoskins Richard Galle Reed George Suzanna Lewis Stephen Richards Michael Ashburner Scott Henderson Granger Sutton Jennifer Wortman Mark Yandell Qing Zhang Lin Chen Rhonda Brandon Yu-Hui Rogers Robert Blazej Mark Champe Barret Pfeiffer Kenneth Wan Clare Doyle Evan Baxter Gregg Helt Catherine Nelson GL Gabor Josep Abril Anna Agbayani Hui-Jin An Cynthia Andrews-Pfannkoch Danita Baldwin Richard Ballew Anand Basu James Baxendale Leyla Bayraktaroglu Ellen Beasley Karen Beeson P Benos Benjamin Berman Deepali Bhandari Slava Bolshakov Dana Borkova Michael Botchan John Bouck Peter Brokstein Phillipe Brottier Kenneth Burtis Dana Busam Heather Butler Edouard Cadieu Angela Center Ishwar Chandra Michael Cherry Simon Cawley Carl Dahlke Lionel Davenport Peter Davies Beatriz Pablos Arthur Delcher Zuoming Deng Anne Mays Ian Dew Suzanne Dietz Kristina Dodson Lisa Doup Michael Downes Shannon Dugan-Rocha Boris Dunkov Patrick Dunn Kenneth Durbin Carlos Evangelista Concepcion Ferraz Steven Ferriera Wolfgang Fleischmann Carl Fosler Andrei Gabrielian Neha Garg William Gelbart Ken Glasser Anna Glodek Fangcheng Gong Harley Gorrell Zhiping Gu Ping Guan Michael Harris Nomi Harris Damon Harvey Thomas Heiman Judith Hernandez Jarrett Houck Damon Hostin Kathryn Houston Timothy Howland Ming-Hui Wei Chinyere Ibegwam Mena Jalali Francis Kalush Gary Karpen Zhaoxi Ke James Kennison Karen Ketchum Bruce Kimmel Chinnappa Kodira Cheryl Kraft Saul Kravitz David Kulp Zhongwu Lai Paul Lasko Yiding Lei Alexander Levitsky Jiayin Li Zhenya Li Yong Liang Xiaoying Lin Xiangjun Liu Bettina Mattei Tina Mcintosh Michael Mcleod Duncan Mcpherson Gennady Merkulov Natalia Milshina Clark Mobarry Joe Morris Ali Moshrefi Stephen Mount Mee Moy Brian Murphy Lee Murphy Donna Muzny David Nelson David Nelson Keith Nelson Katherine Nixon Deborah Nusskern Joanne Pacleb Michael Palazzolo Gjange Pittman Sue Pan John Pollard Vinita Puri Martin Reese Knut Reinert Karin Remington Robert Saunders Frederick Scheeler Hua Shen Bixiang Shue Inga Sidén-Kiamos Michael Simpson Marian Skupski Tom Smith Eugene Spier Allan Spradling Mark Stapleton Renee Strong Eric Sun Robert Svirskas Cyndee Tector Russell Turner Eli Venter Aihui Wang Xin Wang Zhen-Yuan Wang David Wassarman George Weinstock Jean Weissenbach Sherita Williams Trevor Woodage Kim Worley David Wu Song Yang Alison Yao Jane Ye Ru-Fang Yeh Jayshree Zaveri Ming Zhan Guangren Zhang Qi Zhao Liansheng Zheng Xiangqun Zheng Fei Zhong Wenyan Zhong Xiaojun Zhou Shiaoping Zhu Xiaohong Zhu Hamilton Smith Richard Gibbs Eugene Myers Gerald Rubin Craig Venter doi:10.1126/science.287.5461.2185 Science, Vol. 287, No. 5461. (24 March 2000), pp. 2185-2195. 2005-06-14T01:43:05-00:00 2000 Science 287 5461 2185 2195 genome http://www.citeulike.org/user/melvineloy/article/3038055 <i>(11 Oct 2002)</i><br /><br />We introduce simple and more advanced concepts that have played a key role in the development of supersymmetric systems. This is done by first describing various supersymmetric quantum mechanics models. Topics covered include the basic construction of supersymmetric field theories, the phase structure of supersymmetric systems with and without gauge particles, superconformal theories and infrared duality in both field theory and string theory. A discussion of the relation of conformal symmetry to a vanishing vacuum energy (cosmological constant) is included. Les Houches lectures on supersymmetric Gauge Theories DS Berman E Rabinovici (11 Oct 2002) 2008-07-24T01:06:31-00:00 2002 lectures les-houches supersymmetry http://www.citeulike.org/user/nishiokov/article/546682 <i>Cerebral Cortex, Vol. 16, No. 4. (April 2006), pp. 561-573.</i> Neural Coding of Distinct Statistical Properties of Reward Information in Humans Jean-Claude Dreher Philip Kohn Karen Berman doi:10.1093/cercor/bhj004 Cerebral Cortex, Vol. 16, No. 4. (April 2006), pp. 561-573. 2006-03-10T19:10:05-00:00 2006 Cerebral Cortex 1047-3211 16 4 561 573 Oxford University Press fmri human reward http://www.citeulike.org/user/djmonstermo/article/3019823 <i>The New England journal of medicine, Vol. 332, No. 23. (8 June 1995), pp. 1560-1565.</i> Otitis media in children. S Berman The New England journal of medicine, Vol. 332, No. 23. (8 June 1995), pp. 1560-1565. 2008-07-19T00:38:58-00:00 1995 The New England journal of medicine 0028-4793 332 23 1560 1565 peds http://www.citeulike.org/user/reyez/article/3017239 <i>Nucleic acids research, Vol. 35, No. Database issue. (January 2007)</i><br /><br />The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. The wwPDB website at http://www.wwpdb.org/ provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. H Berman K Henrick H Nakamura JL Markley Nucleic acids research, Vol. 35, No. Database issue. (January 2007) 2008-07-18T09:27:07-00:00 2007 Nucleic acids research 1362-4962 35 Database issue pdb wwpdb http://www.citeulike.org/user/reyez/article/2269007 <i>Nat Struct Mol Biol, Vol. 10, No. 12. (December 2003), pp. 980-980.</i> Announcing the worldwide Protein Data Bank Helen Berman Kim Henrick Haruki Nakamura doi:10.1038/nsb1203-980 Nat Struct Mol Biol, Vol. 10, No. 12. (December 2003), pp. 980-980. 2008-01-21T15:17:35-00:00 2003 Nat Struct Mol Biol 10 12 980 980 pdb wwpdb http://www.citeulike.org/user/reyez/article/1544653 <i>Nature Biotechnology, Vol. 25, No. 8., pp. 845-846.</i> Realism about PDB Helen Berman Kim Henrick Haruki Nakamura John Markley Philip Bourne John Westbrook doi:10.1038/nbt0807-845 Nature Biotechnology, Vol. 25, No. 8., pp. 845-846. 2007-08-09T00:39:25-00:00 Nature Biotechnology 1087-0156 25 8 845 846 Nature Publishing Group pdb wwpdb http://www.citeulike.org/user/djmonstermo/article/3016107 <i>MMWR. Recommendations and reports : Morbidity and mortality weekly report. Recommendations and reports / Centers for Disease Control, Vol. 55, No. RR-11. (4 August 2006), pp. 1-94.</i><br /><br />These guidelines for the treatment of persons who have sexually transmitted diseases (STDs) were developed by CDC after consultation with a group of professionals knowledgeable in the field of STDs who met in Atlanta, Georgia, during April 19-21, 2005. The information in this report updates the Sexually Transmitted Diseases Treatment Guidelines, 2002 (MMWR 2002;51[No. RR-6]). Included in these updated guidelines are an expanded diagnostic evaluation for cervicitis and trichomoniasis; new antimicrobial recommendations for trichomoniasis; additional data on the clinical efficacy of azithromycin for chlamydial infections in pregnancy; discussion of the role of Mycoplasma genitalium and trichomoniasis in urethritis/cervicitis and treatment-related implications; emergence of lymphogranuloma venereum protocolitis among men who have sex with men (MSM); expanded discussion of the criteria for spinal fluid examination to evaluate for neurosyphilis; the emergence of azithromycin- resistant Treponema pallidum; increasing prevalence of quinolone-resistant Neisseria gonorrhoeae in MSM; revised discussion concerning the sexual transmission of hepatitis C; postexposure prophylaxis after sexual assault; and an expanded discussion of STD prevention approaches. Sexually transmitted diseases treatment guidelines, 2006. KA Workowski SM Berman MMWR. Recommendations and reports : Morbidity and mortality weekly report. Recommendations and reports / Centers for Disease Control, Vol. 55, No. RR-11. (4 August 2006), pp. 1-94. 2008-07-18T01:46:35-00:00 2006 MMWR. Recommendations and reports : Morbidity and mortality weekly report. Recommendations and reports / Centers for Disease Control 1545-8601 55 RR-11 1 94 wh http://www.citeulike.org/user/LWelch/article/2973143 <i>(21 Jun 2008)</i><br /><br />We find that the quantum of gravity, the graviton, has time-varying mass (the gomidium), and radius (the somium); both vary with the inverse of R ; and its frequency is given by Hubble's parameter. Dark matter can be made of such gravitons. The number of gravitons varies with the square of R. The Machian radiated power of the Universe leads us to a "correct" energy density for the gravitons as dark matter. Gravitons, Dark Matter, and Classical Gravitation Marcelo Berman (21 Jun 2008) 2008-07-08T18:37:26-00:00 2008 graviton http://www.citeulike.org/user/achinerarias/article/2960398 <i>Am J Trop Med Hyg, Vol. 75, No. 3. (1 September 2006), pp. 430-433.</i><br /><br />Malarone was compared with placebo in a double-blind, randomized, placebo-controlled trial of prophylaxis of malaria in predominately Plasmodium vivax areas of Colombia. The study population consisted of 180 completely non-immune Colombian soldiers, male, average age 19 years, and average weight 63 kg. Twenty-four subjects were considered unevaluable because of compliance issues, including one Malarone subject (with no detectable drug levels) who became infected with P. vivax. Of the 97 evaluable subjects who received Malarone (250 mg atovaquone plus 100 mg proguanil hydrochloride) daily from 1 day before entering the endemic area to 7 days after leaving the endemic area, none became parasitemic. Of the 46 evaluable placebo subjects, 11 became infected with P. vivax and 2 became infected with Plasmodium falciparum. The protective efficacy of Malarone for all malaria and for P. vivax malaria was 100% (LL 95% CI = 63%) and 100% (LL 95% CI = 58%), respectively, and was 96% if the one case with undetectable blood levels was included. Malarone has high protective efficacy for P. vivax in Colombia. RANDOMIZED, DOUBLE-BLIND, PLACEBO-CONTROLLED STUDY OF MALARONE FOR MALARIA PROPHYLAXIS IN NON-IMMUNE COLOMBIAN SOLDIERS Jaime Soto Julia Toledo Magda Luzz Patricia Gutierrez Jonathan Berman Stephane Duparc Am J Trop Med Hyg, Vol. 75, No. 3. (1 September 2006), pp. 430-433. 2008-07-03T19:32:29-00:00 2006 Am J Trop Med Hyg 75 3 430 433 atovaquone malaria malarone primaquine proguanil prophylaxis http://www.citeulike.org/user/jyuh/article/2955969 <i>Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation, Vol. 14, No. 3. (July 2004), pp. 134-142.</i><br /><br />BACKGROUND: There is a direct relationship between age and serum parathyroid hormone (iPTH) in the normal population, but several studies suggest this relationship is reversed in maintenance hemodialysis (MHD) patients. The pathophysiologic basis of this age-related decline in serum iPTH levels remains unclear, although others have proposed that it is related to low dietary phosphorus intakes. METHODS: We conducted a prospective, cross-sectional evaluation of the relationship between age and serum iPTH levels and factors affecting this relationship. All participating subjects were asked to complete a 3-day food diary. The charts were reviewed to obtain routinely measured laboratory values over the preceding 3 months, and serum was collected to measure markers of systemic inflammation. RESULTS: Ninety-two MHD patients (47 men; age, 51.3+/-14.9 [standard deviation] years; median dialysis vintage, 25.8 months) were studied. Age was inversely correlated with both serum phosphorus and iPTH; these relationships remained significant even when the data were adjusted for diabetic status, dialysis vintage, and dietary nutrient intake. However, there were no associations of age, serum phosphorus, or iPTH with dietary intakes of protein, calories, phosphorus, or calcium either on univariate or multivariate analyses. Markers of systemic inflammation (serum C-reactive protein, and alpha1 acid glycoprotein) did not correlate with age, serum phosphorus, and iPTH or dietary nutrient intake. On the other hand, serum albumin, which may reflect long-term effects of inflammation, did correlate inversely with age and positively with serum phosphorus. CONCLUSIONS: Our cross-sectional study confirms that there are age-related lower levels of both serum phosphorus and iPTH in MHD patients. The mechanisms regarding the inverse relationship between serum phosphorus and age are unclear, but may not be caused by low phosphorus intake or systemic inflammation. In elderly MHD patients, the reduced responsiveness of parathyroid glands may be related to age-dependent accumulation of uremic toxins. Age-related decline in serum parathyroid hormone in maintenance hemodialysis patients is independent of inflammation and dietary nutrient intake. R Mehrotra O Supasyndh N Berman G Kaysen L Hurst M Leonardi D Das JD Kopple Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation, Vol. 14, No. 3. (July 2004), pp. 134-142. 2008-07-03T09:11:12-00:00 2004 Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation 1532-8503 14 3 134 142 aging diet hd inflammation pth http://www.citeulike.org/user/djmonstermo/article/2954910 <i>N Engl J Med (26 March 2007), NEJMoa070829.</i><br /><br />Background In patients with stable coronary artery disease, it remains unclear whether an initial management strategy of percutaneous coronary intervention (PCI) with intensive pharmacologic therapy and lifestyle intervention (optimal medical therapy) is superior to optimal medical therapy alone in reducing the risk of cardiovascular events. Methods We conducted a randomized trial involving 2287 patients who had objective evidence of myocardial ischemia and significant coronary artery disease at 50 U.S. and Canadian centers. Between 1999 and 2004, we assigned 1149 patients to undergo PCI with optimal medical therapy (PCI group) and 1138 to receive optimal medical therapy alone (medical-therapy group). The primary outcome was death from any cause and nonfatal myocardial infarction during a follow-up period of 2.5 to 7.0 years (median, 4.6). Results There were 211 primary events in the PCI group and 202 events in the medical-therapy group. The 4.6-year cumulative primary-event rates were 19.0% in the PCI group and 18.5% in the medical-therapy group (hazard ratio for the PCI group, 1.05; 95% confidence interval [CI], 0.87 to 1.27; P=0.62). There were no significant differences between the PCI group and the medical-therapy group in the composite of death, myocardial infarction, and stroke (20.0% vs. 19.5%; hazard ratio, 1.05; 95% CI, 0.87 to 1.27; P=0.62); hospitalization for acute coronary syndrome (12.4% vs. 11.8%; hazard ratio, 1.07; 95% CI, 0.84 to 1.37; P=0.56); or myocardial infarction (13.2% vs. 12.3%; hazard ratio, 1.13; 95% CI, 0.89 to 1.43; P=0.33). Conclusions As an initial management strategy in patients with stable coronary artery disease, PCI did not reduce the risk of death, myocardial infarction, or other major cardiovascular events when added to optimal medical therapy. (ClinicalTrials.gov number, NCT00007657 .) 10.1056/NEJMoa070829 Optimal Medical Therapy with or without PCI for Stable Coronary Disease William Boden Robert O'Rourke Koon Teo Pamela Hartigan David Maron William Kostuk Merril Knudtson Marcin Dada Paul Casperson Crystal Harris Bernard Chaitman Leslee Shaw Gilbert Gosselin Shah Nawaz Lawrence Title Gerald Gau Alvin Blaustein David Booth Eric Bates John Spertus Daniel Berman John Mancini William Weintraub The doi:10.1056/NEJMoa070829 N Engl J Med (26 March 2007), NEJMoa070829. 2008-07-03T04:00:58-00:00 2007 N Engl J Med NEJMoa070829 acs http://www.citeulike.org/user/heiko_reese/article/2944659 <i>(1995), pp. 14-14.</i> TRON: process-specific file protection for the UNIX operating system Andrew Berman Virgil Bourassa Erik Selberg (1995), pp. 14-14. 2008-06-30T13:50:28-00:00 1995 14 14 USENIX Association diplomarbeit tron unix http://www.citeulike.org/user/kas/article/2938308 <i>Physical Review B (Condensed Matter and Materials Physics), Vol. 77, No. 15. (2008)</i><br /><br />We propose experiments to observe Bose-Einstein condensation and superfluidity of quasi-two-dimensional spatially indirect magnetoexcitons in two-layer graphene. The energy spectrum of collective excitations, the sound spectrum, and the effective magnetic mass of magnetoexcitons are presented in the strong magnetic field regime. The superfluid density nS and the temperature of the Kosterlitz-Thouless phase transition Tc are shown to be increasing functions of the excitonic density n but decreasing functions of B and the interlayer separation D. Bose-Einstein condensation and superfluidity of magnetoexcitons in bilayer graphene Oleg Berman Yurii Lozovik Godfrey Gumbs doi:10.1103/PhysRevB.77.155433 Physical Review B (Condensed Matter and Materials Physics), Vol. 77, No. 15. (2008) 2008-06-27T21:20:33-00:00 2008 Physical Review B (Condensed Matter and Materials Physics) 77 15 APS bilayer graphene magnetic http://www.citeulike.org/user/reyez/article/2931252 <i>Acta Crystallographica Section D, Vol. 58, No. 6 Part 1. (Jun 2002), pp. 889-898.</i> The Nucleic Acid Database Helen Berman John Westbrook Zukang Feng Lisa Iype Bohdan Schneider Christine Zardecki doi:10.1107/S0907444902003487 Acta Crystallographica Section D, Vol. 58, No. 6 Part 1. (Jun 2002), pp. 889-898. 2008-06-26T14:58:59-00:00 2002 Acta Crystallographica Section D 58 6 Part 1 889 898 no-tag http://www.citeulike.org/user/reyez/article/841458 <i>Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)</i><br /><br />The Protein Data Bank (PDB) is the central worldwide repository for three-dimensional (3D) structure data of biological macromolecules. The Research Collaboratory for Structural Bioinformatics (RCSB) has completely redesigned its resource for the distribution and query of 3D structure data. The re-engineered site is currently in public beta test at http://pdbbeta.rcsb.org. The new site expands the functionality of the existing site by providing structure data in greater detail and uniformity, improved query and enhanced analysis tools. A new key feature is the integration and searchability of data from over 20 other sources covering genomic, proteomic and disease relationships. The current capabilities of the re-engineered site, which will become the RCSB production site at http://www.pdb.org in late 2005, are described. The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. N Deshpande KJ Addess WF Bluhm JC Merino-Ott W Townsend-Merino Q Zhang C Knezevich L Xie L Chen Z Feng RK Green JL Flippen-Anderson J Westbrook HM Berman PE Bourne Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005) 2006-09-12T23:56:52-00:00 2005 Nucleic Acids Res 1362-4962 33 Database issue no-tag http://www.citeulike.org/user/reyez/article/445762 <i>Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3450-3460.</i><br /><br />Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/. Tools for the automatic identification and classification of RNA base pairs Huanwang Yang Fabrice Jossinet Neocles Leontis Li Chen John Westbrook Helen Berman Eric Westhof Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3450-3460. 2005-12-21T00:37:45-00:00 2003 Nucl. Acids Res. 31 13 3450 3460 no-tag http://www.citeulike.org/user/reyez/article/833683 <i>RNA, Vol. 12, No. 4. (April 2006), pp. 533-541.</i><br /><br />The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework-an RNA Ontology (RO)-with a common, dynamic, controlled, and structured vocabulary to describe and characterize RNA sequences, secondary structures, three-dimensional structures, and dynamics pertaining to RNA function. The RO should produce tools for clear communication about RNA structure and function for multiple uses, including the integration of RNA electronic resources into the Semantic Web. These tools should allow the accurate description in computer-interpretable form of the coupling between RNA architecture, function, and evolution. The purposes for creating the RO are, therefore, (1) to integrate sequence and structural databases; (2) to allow different computational tools to interoperate; (3) to create powerful software tools that bring advanced computational methods to the bench scientist; and (4) to facilitate precise searches for all relevant information pertaining to RNA. For example, one initial objective of the ROC is to define, identify, and classify RNA structural motifs described in the literature or appearing in databases and to agree on a computer-interpretable definition for each of these motifs. To achieve these aims, the ROC will foster communication and promote collaboration among RNA scientists by coordinating frequent face-to-face workshops to discuss, debate, and resolve difficult conceptual issues. These meeting opportunities will create new directions at various levels of RNA research. The ROC will work closely with the PDB/NDB structural databases and the Gene, Sequence, and Open Biomedical Ontology Consortia to integrate the RO with existing biological ontologies to extend existing content while maintaining interoperability. The RNA Ontology Consortium: an open invitation to the RNA community. NB Leontis RB Altman HM Berman SE Brenner JW Brown DR Engelke SC Harvey SR Holbrook F Jossinet SE Lewis F Major DH Mathews JS Richardson JR Williamson E Westhof doi:10.1261/rna.2343206 RNA, Vol. 12, No. 4. (April 2006), pp. 533-541. 2006-09-07T16:26:19-00:00 2006 RNA 1355-8382 12 4 533 541 no-tag http://www.citeulike.org/user/lackaff/article/2924191 <i>Journal of Youth and Adolescence, Vol. 20, No. 4. (1991), pp. 427-440.</i><br /><br />The continued attachment to parents and peers in adults has been examined in two ways: the individual difference approach, examining characteristic attachment styles across relationships, and the general intensity approach, examining the salience of emotional and behavioral reactions to a particular separation. The present study examines the intensity of attachment to parents at the transition to college. This voluntary separation from parents was expected to elicit heightened attachment for college students, especially residential students, which would decrease over time. In addition, it was expected that high levels of parental attachment at the beginning of college would predispose students to later depression. Results indicate that parental attachment decreases during the first semester of college only for residential students. In addition, maternal attachment is significantly higher for females than for males. Finally, high levels of parental attachment in males at the beginning of college were predictive of high levels of depressed mood at the end of the first semester, while no relationship was found for females. Parental attachment and emotional distress in the transition to college William Berman Michael Sperling doi:10.1007/BF01537184 Journal of Youth and Adolescence, Vol. 20, No. 4. (1991), pp. 427-440. 2008-06-24T19:22:45-00:00 1991 Journal of Youth and Adolescence 20 4 427 440 attachment college longitudinal social support transition http://www.citeulike.org/user/jjray/article/2918995 <i>J. Bacteriol., Vol. 159, No. 2. (1 August 1984), pp. 750-756.</i><br /><br />We describe a simple method for selecting Escherichia coli mutants that carry gene fusions between a cloned gene and lacZ. We test this technique with the ompR gene, which codes for a positive regulatory factor in porin synthesis. A number of OmpR-LacZ hybrid proteins are examined, and several unusual phenotypes associated with these protein fusions are described. Evidence is presented to support the two-domain model for ompR proposed previously (Hall and Silhavy, J. Mol. Biol. 151:1-15). In addition, one of the ompR-lacZ fusions exhibits a dominant OmpR- phenotype. The utility of isolating a series of lacZ gene fusions to any target gene is discussed. Selection of lac gene fusions in vivo: ompR-lacZ fusions that define a functional domain of the ompR gene product. ML Berman DE Jackson J. Bacteriol., Vol. 159, No. 2. (1 August 1984), pp. 750-756. 2008-06-23T14:22:21-00:00 1984 J. Bacteriol. 159 2 750 756 bacteria operon salmonella translation two-component_system http://www.citeulike.org/user/kateeden/article/2908366 <i>The Journal of urology, Vol. 163, No. 3. (March 2000), pp. 888-893.</i><br /><br />PURPOSE: Female sexual dysfunction is highly prevalent but not well defined or understood. We evaluated and revised existing definitions and classifications of female sexual dysfunction. MATERIALS AND METHODS: An interdisciplinary consensus conference panel consisting of 19 experts in female sexual dysfunction selected from 5 countries was convened by the Sexual Function Health Council of the American Foundation for Urologic Disease. A modified Delphi method was used to develop consensus definitions and classifications, and build on the existing framework of the International Classification of Diseases-10 and DSM-IV: Diagnostic and Statistical Manual of Mental Disorders of the American Psychiatric Association, which were limited to consideration of psychiatric disorders. RESULTS: Classifications were expanded to include psychogenic and organic causes of desire, arousal, orgasm and sexual pain disorders. An essential element of the new diagnostic system is the "personal distress" criterion. In particular, new definitions of sexual arousal and hypoactive sexual desire disorders were developed, and a new category of noncoital sexual pain disorder was added. In addition, a new subtyping system for clinical diagnosis was devised. Guidelines for clinical end points and outcomes were proposed, and important research goals and priorities were identified. CONCLUSIONS: We recommend use of the new female sexual dysfunction diagnostic and classification system based on physiological as well as psychological pathophysiologies, and a personal distress criterion for most diagnostic categories. Report of the international consensus development conference on female sexual dysfunction: definitions and classifications. R Basson J Berman A Burnett L Derogatis D Ferguson J Fourcroy I Goldstein A Graziottin J Heiman E Laan S Leiblum H Padma-Nathan R Rosen K Segraves RT Segraves R Shabsigh M Sipski G Wagner B Whipple The Journal of urology, Vol. 163, No. 3. (March 2000), pp. 888-893. 2008-06-19T17:49:33-00:00 2000 The Journal of urology 0022-5347 163 3 888 893 no-tag http://www.citeulike.org/user/jyuh/article/2905317 <i>The American journal of physiology, Vol. 270, No. 4 Pt 1. (April 1996)</i><br /><br />In many biological models, a relationship between variables may be modeled as a linear or polynomial function that changes abruptly when an independent variable obtains a threshold level. Usually, the transition point is unknown, and a major objective of the analysis is its estimation. This type of model is known as a segmented regression model. We present two methods, Gallant and Fuller's (J Am. Stat. Assoc. 68: 144-147, 1973) method and Tishler and Zang's (J. Am. Stat. Assoc. 76: 980-987, 1981) method, using nonlinear least-squares techniques for estimating the transition point. We give the following three examples: a hypoglycemia study, a testosterone study, and an estimate of age-cortisol relationship. Simulation techniques are used to compare the two methods. We conclude that these models provide useful information and that the two methods studied produce essentially equivalent results. We recommend that both methods be used to analyze a data set if possible to avoid problems due to local minima and that if the results do not agree, then evaluation of the likelihood function in the range of the estimates be used to determine the best estimate. Applications of segmented regression models for biomedical studies. NG Berman WK Wong S Bhasin E Ipp The American journal of physiology, Vol. 270, No. 4 Pt 1. (April 1996) 2008-06-18T12:58:01-00:00 1996 The American journal of physiology 0002-9513 270 4 Pt 1 changepoint http://www.citeulike.org/user/jmarkow/article/2902416 <i>Cereb. Cortex (27 February 2008), bhn004.</i><br /><br />Williams syndrome (WS) is a rare neurodevelopmental disorder caused by a 1.6 Mb microdeletion on chromosome 7q11.23 and characterized by hypersocial personality and prominent visuospatial construction impairments. Previous WS studies have identified functional and structural abnormalities in the hippocampal formation, prefrontal regions crucial for amygdala regulation and social cognition, and the dorsal visual stream, notably the intraparietal sulcus (IPS). Although aberrant ventral stream activation has not been found in WS, object-related visual information that is processed in the ventral stream is a critical source of input into these abnormal regions. The present study, therefore, examined neural interactions of ventral stream areas in WS. Using a passive face- and house-viewing paradigm, activation and functional connectivity of stimulus-selective regions in fusiform and parahippocampal gyri, respectively, were investigated. During house viewing, significant activation differences were observed between participants with WS and a matched control group in IPS. Abnormal functional connectivity was found between parahippocampal gyrus and parietal cortex and between fusiform gyrus and a network of brain regions including amygdala and portions of prefrontal cortex. These results indicate that abnormal upstream visual object processing may contribute to the complex cognitive/behavioral phenotype in WS and provide a systems-level characterization of genetically mediated abnormalities of neural interactions. 10.1093/cercor/bhn004 A Genetic Model for Understanding Higher Order Visual Processing: Functional Interactions of the Ventral Visual Stream in Williams Syndrome Deepak Sarpal Bradley Buchsbaum Philip Kohn Shane Kippenhan Carolyn Mervis Colleen Morris Andreas Meyer-Lindenberg Karen Berman doi:10.1093/cercor/bhn004 Cereb. Cortex (27 February 2008), bhn004. 2008-06-17T12:58:38-00:00 2008 Cereb. Cortex bhn004 amygdala fmri genetics ips it object object-recognition physiology williams-syndrome http://www.citeulike.org/user/Macroelectronics/article/2898816 <i>Thin Solid Films, Vol. 516, No. 12. (30 April 2008), pp. 4036-4039.</i><br /><br />Thin films of Al2O3 grown using atomic layer deposition (ALD) techniques can protect polymers from erosion by oxygen atoms. To quantify this protection, polyimide substrates with the same chemical repeat unit as Kapton® were applied to quartz crystal microbalance (QCM) sensors. Al2O3 ALD films with varying thicknesses were grown on the polyimide substrates. The ALD-coated polyimide materials were then exposed to a hyperthermal atomic-oxygen beam. The mass loss versus oxygen-atom exposure time was measured in situ by the QCM. Al2O3 ALD film thicknesses of ~ 35 Å were found to protect the polymer from erosion. Protection of polymer from atomic-oxygen erosion using Al2O3 atomic layer deposition coatings Russell Cooper Hari Upadhyaya Timothy Minton Michael Berman Xiaohua Du Steven George doi:10.1016/j.tsf.2007.07.150 Thin Solid Films, Vol. 516, No. 12. (30 April 2008), pp. 4036-4039. 2008-06-16T14:53:16-00:00 2008 Thin Solid Films 516 12 4036 4039 ald barrier-coating flexible-electronics macroelectronics http://www.citeulike.org/user/cchand/article/2889634 <i>Journal of neurotrauma, Vol. 25, No. 2. (February 2008), pp. 153-171.</i><br /><br />Considerable evidence indicates that outcomes from traumatic brain injury (TBI) are worse in the elderly, but there has been little preclinical research to explore potential mechanisms. In this study, we examined the age-related effects on outcome in a mouse model of controlled cortical impact (CCI) injury. We compared the responses of adult (5-6 months old) and aged (21-24 months old) male mice following a moderate lateral CCI injury to the sensorimotor cortex. Sensorimotor function was evaluated with the rotarod, gridwalk and spontaneous forelimb behavioral tests. Acute edema was assessed from hyperintensity on T2-weighted magnetic resonance images. Blood-brain barrier opening was measured using anti-mouse immunoglobulin G (IgG) immunohistochemistry. Neurodegeneration was assessed by amino-cupric silver staining, and lesion cavity volumes were measured from histological images. Indicators of injury were generally worse in the aged than the adult mice. Acute edema, measured at 24 and 48 h post-injury, resolved more slowly in the aged mice (p < 0.01). Rotarod recovery (p < 0.05) and gridwalk deficits (p < 0.01) were significantly worse in aged mice. There was greater (p < 0.01 at 3 days) and more prolonged post-acute opening of the blood-brain barrier in the aged mice. Neurodegeneration was greater in the aged mice (p < 0.01 at 3 days). In contrast, lesion cavity volumes, measured at 3 days post-injury, were not different between injured groups. These results suggest that following moderate controlled cortical impact injury, the aged brain is more vulnerable than the adult brain to neurodegeneration, resulting in greater loss of function. Tissue loss at the impact site does not explain the increased functional deficits seen in the aged animals. Prolonged acute edema, increased opening of the blood-brain barrier and increased neurodegeneration found in the aged animals implicate secondary processes in age-related differences in outcome. Detrimental effects of aging on outcome from traumatic brain injury: a behavioral, magnetic resonance imaging, and histological study in mice. G Onyszchuk YY He NE Berman WM Brooks doi:10.1089/neu.2007.0430 Journal of neurotrauma, Vol. 25, No. 2. (February 2008), pp. 153-171. 2008-06-12T16:19:16-00:00 2008 Journal of neurotrauma 0897-7151 25 2 153 171 no-tag http://www.citeulike.org/user/bertelsen/article/1271262 <i>BMC Bioinformatics, Vol. 8, No. 1. (2007)</i><br /><br />Pre-processing methods for two-sample long oligonucleotide arrays, specifically the Agilent technology, have not been extensively studied. The goal of this study is to quantify some of the sources of error that affect measurement of expression using Agilent arrays and to compare Agilent's Feature Extraction software with pre-processing methods that have become the standard for normalization of cDNA arrays. These include log transformation followed by loess normalization with or without background subtraction and often a between array scale normalization procedure. The larger goal is to define best study design and pre-processing practices for Agilent arrays, and we offer some suggestions. Simple loess normalization without background subtraction produced the lowest variability. However, without background subtraction, fold changes were biased towards zero, particularly at low intensities. ROC analysis of a spike-in experiment showed that differentially expressed genes are most reliably detected when background is not subtracted. Loess normalization and no background subtraction yielded an AUC of 99.7% compared with 88.8% for Agilent processed fold changes. All methods performed well when error was taken into account by t- or z-statistics, AUCs greater than 99.8%. A substantial proportion of genes showed dye effects, 43% (99% CI: 39%, 47%). However, these effects were generally small regardless of the pre-processing method. Simple loess normalization without background subtraction resulted in low variance fold changes that more reliably ranked gene expression than the other methods. While t-statistics and other measures that take variation into account, including Agilent's z-statistic, can also be used to reliably select differentially expressed genes, fold changes are a standard measure of differential expression for exploratory work, cross platform comparison, and biological interpretation and can not be entirely replaced. Although dye effects are small for most genes, many array features are affected. Therefore, an experimental design that incorporates dye swaps or a common reference could be valuable. Pre-processing Agilent microarray data Marianna Zahurak Giovanni Parmigiani Wayne Yu Robert Scharpf David Berman Edward Schaeffer Shabana Shabbeer Leslie Cope doi:10.1186/1471-2105-8-142 BMC Bioinformatics, Vol. 8, No. 1. (2007) 2007-05-02T09:41:17-00:00 2007 BMC Bioinformatics 8 1 agilent array cdna expression microarray pre-processing http://www.citeulike.org/user/dgoerlich/article/2875342 <i>The Quarterly Journal of Economics, Vol. 109, No. 2. (1994), pp. 367-397.</i><br /><br />This paper investigates the shift in demand away from unskilled and toward skilled labor in U.S. manufacturing over the 1980s. Production labor-saving technological change is the chief explanation for this shift. That conclusion is based on three facts: (1) the shift is due mostly to increased use of skilled workers within the 450 industries in U.S. manufacturing rather than to a reallocation of employment between industries, as would be implied by a shift in product demand due to trade or to a defense buildup; (2) trade- and defense-demand are associated with only small employment reallocation effects; (3) increased use of nonproduction workers is strongly correlated with investment in computers and in R&D. Changes in the Demand for Skilled Labor within U.S. Manufacturing: Evidence from the Annual Survey of Manufacturers Eli Berman John Bound Zvi Griliches doi:10.2307/2118467 The Quarterly Journal of Economics, Vol. 109, No. 2. (1994), pp. 367-397. 2008-06-09T11:18:31-00:00 1994 The Quarterly Journal of Economics 109 2 367 397 The MIT Press no-tag http://www.citeulike.org/user/Kyaita/article/2873260 <i>AJR. American journal of roentgenology, Vol. 148, No. 4. (April 1987), pp. 747-748.</i> Percutaneous decompression of cecal volvulus. D Patel E Ansari MD Berman AJR. American journal of roentgenology, Vol. 148, No. 4. (April 1987), pp. 747-748. 2008-06-08T08:12:18-00:00 1987 AJR. American journal of roentgenology 0361-803X 148 4 747 748 cecalvolvulus http://www.citeulike.org/user/garethclegg/article/2866381 <i>Experimental Neurology, Vol. 190, No. 1. (November 2004), pp. 70-78.</i><br /><br />Overload of intracellular calcium ([Ca2+]i) following traumatic brain injury (TBI) has been implicated in the pathogenesis of neuronal injury and death. Voltage-gated calcium channels (VGCCs) provide one of the major sources of Ca2+ entry into cells. Therefore, the potential neuroprotective activity of SNX-185, a specific N-type VGCC blocker, was tested in rats using the lateral fluid percussion (LFP) model of TBI. SNX-185 (50, 100, or 200 pmol) or vehicle was injected 5 min after injury into the CA2-3 subregion of the hippocampus ipsilateral to TBI. Acute neuronal degeneration was visualized in brain sections 24 h postinjury using the histofluorescent marker Fluoro-Jade (FJ), and the number of surviving neurons in the CA2-3 subregion of the hippocampus 42 days after injury was determined stereologically. Behavioral outcome after TBI and drug treatment was assessed in the beam walk test and Morris water maze. Direct injection of SNX-185 into the CA2-3 region of the hippocampus reduced neuronal injury 24 h after TBI and increased neuronal survival at 42 days at each of the three drug concentrations. Behavioral outcome in both the beam walk and Morris water maze were also improved by SNX-185, with 100 and 200 pmol, but not 50 pmol SNX-185 providing neuroprotection. These data support previous studies demonstrating substantial neuroprotection after TBI by treatment with N-type VGCC blockers. Neuroprotection in the rat lateral fluid percussion model of traumatic brain injury by SNX-185, an N-type voltage-gated calcium channel blocker Lillian Lee Ethel Galo Bruce Lyeth Paul Muizelaar Robert Berman doi:10.1016/j.expneurol.2004.07.003 Experimental Neurology, Vol. 190, No. 1. (November 2004), pp. 70-78. 2008-06-05T15:54:12-00:00 2004 Experimental Neurology 190 1 70 78 brain inflammation injury repair tbi http://www.citeulike.org/user/dekay23/article/2257653 <i>Functional Ecology, Vol. 22, No. 1. (February 2008), pp. 134-147.</i> Assessing functional diversity in the field methodology matters! Sandra Lavorel Karl Grigulis Sue Mcintyre Nick Williams Denys Garden Josh Dorrough Sandra Berman Fabien Quetier Aurelie Thebault Anne Bonis doi:10.1111/j.1365-2435.2007.01339.x Functional Ecology, Vol. 22, No. 1. (February 2008), pp. 134-147. 2008-01-19T17:44:34-00:00 2008 Functional Ecology 0269-8463 22 1 134 147 Blackwell Publishing ecology plant http://www.citeulike.org/user/reyez/article/2860806 <i>RNA, Vol. 14, No. 3. (March 2008), pp. 465-481.</i><br /><br />A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a quality-filtered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle delta epsilon zeta alpha beta gamma delta combinations empirically found favorable for the sugar-to-sugar "suite" unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for delta epsilon zeta and a lowercase letter for alpha beta gamma delta, this modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs. RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). JS Richardson B Schneider LW Murray GJ Kapral RM Immormino JJ Headd DC Richardson D Ham E Hershkovits LD Williams KS Keating AM Pyle D Micallef J Westbrook HM Berman doi:10.1261/rna.657708 RNA, Vol. 14, No. 3. (March 2008), pp. 465-481. 2008-06-04T11:15:21-00:00 2008 RNA 1469-9001 14 3 465 481 backbone consortium ontology rna http://www.citeulike.org/user/yylin/article/2860471 <i>Algorithms in Bioinformatics (2006), pp. 138-149.</i><br /><br />For a genomic region containing a tandem gene cluster, a proper set of alignments needs to align only orthologous segments, i.e., those separated by a speciation event. Otherwise, methods for finding regions under evolutionary selection will not perform properly. Conversely, the alignments should indicate every orthologous pair of genes or genomic segments. Attaining this goal in practice requires a technique for avoiding a combinatorial explosion in the number of local alignments. To better understand this process, we model it as a graph problem of finding a minimum cardinality set of cliques that contain all edges. We provide an upper bound for an important class of graphs (the problem is NP-hard and very difficult to approximate in the general case), and use the bound and computer simulations to evaluate two heuristic solutions. An implementation of one of them is evaluated on mammalian sequences from the α-globin gene cluster. Controlling Size When Aligning Multiple Genomic Sequences with Duplications Minmei Hou Piotr Berman Louxin Zhang Webb Miller doi:10.1007/11851561_13 Algorithms in Bioinformatics (2006), pp. 138-149. 2008-06-04T07:45:31-00:00 2006 Algorithms in Bioinformatics 138 149 no-tag http://www.citeulike.org/user/Mtorov/article/2855216 <i>Administration Society, Vol. 26, No. 2. (1 August 1994), pp. 185-203.</i><br /><br />This study compares the ethics management strategies of large cities and firms with the purpose of examining whether public-private sector differences that have been hypothesized in the literature are reflected in ethics management practices. The findings suggest that differences between the public and private sectors are minimal; however, cities use more regulatory-based strategies, and large firms use code-based strategies. Moral leadership by senior managers is the most important strategy for improving ethics in both sectors. Concerns about litigation, public complaints, and promoting good public relations are important reasons driving concern with ethics in both cities and firms. 10.1177/009539979402600204 Ethics Management in Municipal Governments and Large Firms: Exploring Similarities and Differences Evan Berman Jonathan West Anita Cava doi:10.1177/009539979402600204 Administration Society, Vol. 26, No. 2. (1 August 1994), pp. 185-203. 2008-06-01T17:58:53-00:00 1994 Administration Society 26 2 185 203 firms http://www.citeulike.org/user/fernan/article/2762170 <i>PLoS Biology, Vol. 6, No. 5. (1 May 2008), e110.</i><br /><br />Candida albicans has an elaborate, yet efficient, mating system that promotes conjugation between diploid a and α strains. The product of mating is a tetraploid a/α cell that must undergo a reductional division to return to the diploid state. Despite the presence of several “meiosis-specific” genes in the C. albicans genome, a meiotic program has not been observed. Instead, tetraploid products of mating can be induced to undergo efficient, random chromosome loss, often producing strains that are diploid, or close to diploid, in ploidy. Using SNP and comparative genome hybridization arrays we have now analyzed the genotypes of products from the C. albicans parasexual cycle. We show that the parasexual cycle generates progeny strains with shuffled combinations of the eight C. albicans chromosomes. In addition, several isolates had undergone extensive genetic recombination between homologous chromosomes, including multiple gene conversion events. Progeny strains exhibited altered colony morphologies on laboratory media, demonstrating that the parasexual cycle generates phenotypic variants of C. albicans. In several fungi, including Saccharomyces cerevisiae and Schizosaccharomyces pombe, the conserved Spo11 protein is integral to meiotic recombination, where it is required for the formation of DNA double-strand breaks. We show that deletion of SPO11 prevented genetic recombination between homologous chromosomes during the C. albicans parasexual cycle. These findings suggest that at least one meiosis-specific gene has been re-programmed to mediate genetic recombination during the alternative parasexual life cycle of C. albicans. We discuss, in light of the long association of C. albicans with warm-blooded animals, the potential advantages of a parasexual cycle over a conventional sexual cycle. The Parasexual Cycle in Candida albicans Provides an Alternative Pathway to Meiosis for the Formation of Recombinant Strains Anja Forche Kevin Alby Dana Schaefer Alexander Johnson Judith Berman Richard Bennett doi:10.1371/journal.pbio.0060110 PLoS Biology, Vol. 6, No. 5. (1 May 2008), e110. 2008-05-06T17:56:05-00:00 2008 PLoS Biology 6 5 e110 candida cycle parasexual recombinant strains http://www.citeulike.org/user/bschaeli/article/2834580 <i>Parallel and Distributed Processing Symposium., Proceedings 15th International (2001), 8 pp..</i><br /><br />The performance of supercomputer schedulers is influenced by the workloads that serve as their input. Realistic workloads are therefore critical to evaluate how supercomputer schedulers perform in practice. There has been much written in the literature about rigid parallel jobs, i.e. jobs that require partitions of a fixed size to run. However the majority of the parallel jobs in production today are moldable, i.e. jobs that can execute on a variety of partition sizes. In this paper we describe a workload model for moldable jobs, which is based on a user survey and good analytical models. Our model can serve as the basis for the development of performance-efficient strategies for selection of the job partition size, as well as the basis for enhancing supercomputer schedulers to directly accept moldable request A model for moldable supercomputer jobs W Cirne F Berman doi:10.1109/IPDPS.2001.925004 Parallel and Distributed Processing Symposium., Proceedings 15th International (2001), 8 pp.. 2008-05-26T14:08:49-00:00 2001 Parallel and Distributed Processing Symposium., Proceedings 15th International 8 pp. no-tag http://www.citeulike.org/user/yylin/article/1822341 <i>SIAM J. Discret. Math., Vol. 12, No. 3. (September 1999), pp. 289-297.</i> A 2-Approximation Algorithm for the Undirected Feedback Vertex Set Problem Vineet Bafna Piotr Berman Toshihiro Fujito doi:10.1137/S0895480196305124 SIAM J. Discret. Math., Vol. 12, No. 3. (September 1999), pp. 289-297. 2007-10-25T21:30:07-00:00 1999 SIAM J. Discret. Math. 0895-4801 12 3 289 297 Society for Industrial and Applied Mathematics no-tag http://www.citeulike.org/user/jyuh/article/2492401 <i>Nature Biotechnology, Vol. 26, No. 3. (07 March 2008), pp. 305-312.</i> Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE) Eric Deutsch Catherine Ball Jules Berman Steven Bova Alvis Brazma Roger Bumgarner David Campbell Helen Causton Jeffrey Christiansen Fabrice Daian Delphine Dauga Duncan Davidson Gregory Gimenez Young Goo Sean Grimmond Thorsten Henrich Bernhard Herrmann Michael Johnson Martin Korb Jason Mills Asa Oudes Helen Parkinson Laura Pascal Nicolas Pollet John Quackenbush Mi