bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics
Authors: Pham Thang V. , Piersma Sander R. , Warmoes Marc , Jimenez Connie R. 
Published: December 2009

AbstractMotivation: Spectral count data generated from label-free tandem mass spectrometry-based proteomic experiments can be used to quantify protein's abundances reliably. Comparing spectral count data from different sample groups such as control and disease is an essential step in statistical analysis for the determination of altered protein level and biomarker discovery. The Fisher's exact test, the G-test, the t-test and the local-pooled-error technique (LPE) are commonly used for differential analysis of spectral count data. However, our initial experiments in two cancer studies show that the current methods are unable to declare at 95% confidence level a number of protein markers that have been judged to be differential on the basis of the biology of the disease and the spectral count numbers. A shortcoming of these tests is that they do not take into account within- and between-sample variations together. Hence, our aim is to improve upon existing techniques by incorporating both the within- and between-sample variations.Result: We propose to use the beta-binomial distribution to test the significance of differential protein abundances expressed in spectral counts in label-free mass spectrometry-based proteomics. The beta-binomial test naturally normalizes for total sample count. Experimental results show that the beta-binomial test performs favorably in comparison with other methods on several datasets in terms of both true detection rate and false positive rate. In addition, it can be applied for experiments with one or more replicates, and for multiple condition comparisons. Finally, we have implemented a software package for parameter estimation of two beta-binomial models and the associated statistical tests.Availability and implementation: A software package implemented in R is freely available for download at http://www.oncoproteomics.nl/.Contact: t.pham@vumc.nlSupplementary information: Supplementary data are available at Bioinformatics online.
A novel method for accurate one-dimensional protein structure prediction based on fragment matching
Authors: Zhou Tuping , Shu Nanjiang , Hovmöller Sven 
Published: December 2009

Abstract
Motivation: The precise prediction of one-dimensional (1D) protein structure as represented by the protein secondary structure and 1D string of discrete state of dihedral angles (i.e. Shape Strings) is a prerequisite for the successful prediction of three-dimensional (3D) structure as well as protein–protein interaction. We have developed a novel 1D structure prediction method, called Frag1D, based on a straightforward fragment matching algorithm and demonstrated its success in the prediction of three sets of 1D structural alphabets, i.e. the classical three-state secondary structure, three- and eight-state Shape Strings.
Results: By exploiting the vast protein sequence and protein structure data available, we have brought secondary-structure prediction closer to the expected theoretical limit. When tested by a leave-one-out cross validation on a non-redundant set of PDB cutting at 30% sequence identity containing 5860 protein chains, the overall per-residue accuracy for secondary-structure prediction, i.e. Q3 is 82.9%. The overall per-residue accuracy for three- and eight-state Shape Strings are 85.1 and 71.5%, respectively. We have also benchmarked our program with the latest version of PSIPRED for secondary structure prediction and our program predicted 0.3% better in Q3 when tested on 2241 chains with the same training set. For Shape Strings, we compared our method with a recently published method with the same dataset and definition as used by that method. Our program predicted at 2.2% better in accuracy for three-state Shape Strings. By quantitatively investigating the effect of data base size on 1D structure prediction we show that the accuracy increases by ∼1% with every doubling of the database size.
Availability: The program is available for download at http://www.fos.su.se/∼nanjiang/Frag1D/download. Supplementary data are available at http://www.fos.su.se/∼nanjiang/Frag1D/supplement/suppl.html
Contact: svenh@struc.su.se
Supplementary information: Supplementary data are available at Bioinformatics online.
ConceptGen: a gene set enrichment and gene set relation mapping tool
Authors: Sartor Maureen A. , Mahavisno Vasudeva , Keshamouni Venkateshwar G. , Cavalcoli James , Wright Zachary , Karnovsky Alla , Kuick Rork , Jagadish H.V. , Mirel Barbara , Weymouth Terry , Athey Brian , Omenn Gilbert S. 
Published: December 2009

AbstractMotivation: The elucidation of biological concepts enriched with differentially expressed genes has become an integral part of the analysis and interpretation of genomic data. Of additional importance is the ability to explore networks of relationships among previously defined biological concepts from diverse information sources, and to explore results visually from multiple perspectives. Accomplishing these tasks requires a unified framework for agglomeration of data from various genomic resources, novel visualizations, and user functionality.Results: We have developed ConceptGen, a web-based gene set enrichment and gene set relation mapping tool that is streamlined and simple to use. ConceptGen offers over 20 000 concepts comprising 14 different types of biological knowledge, including data not currently available in any other gene set enrichment or gene set relation mapping tool. We demonstrate the functionalities of ConceptGen using gene expression data modeling TGF-beta-induced epithelial-mesenchymal transition and metabolomics data comparing metastatic versus localized prostate cancers.Availability: ConceptGen is part of the NIH's National Center for Integrative Biomedical Informatics (NCIBI) and is freely available at http://conceptgen.ncibi.org. For terms of use, visit http://portal.ncibi.org/gateway/pdf/Terms%20of%20use-web.pdfContact: conceptgen@umich.edu; sartorma@umich.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Oscillatory Growth in Lily Pollen Tubes Does Not Require Aerobic Energy Metabolism
Authors: Rounds Caleb M. , Hepler Peter K. , Fuller Sasha J. , Winship Lawrence J. 
Published: December 2009

AbstractOscillatory tip growth in pollen tubes depends on prodigious amounts of energy. We have tested the hypothesis that oscillations in the electron transport chain lead to growth oscillations in lily (Lilium formosanum). Using three respiratory inhibitors, oligomycin, antimycin A, and cyanide, we find that pollen tube growth is much less sensitive to respiratory inhibition than respiration is. All three block respiration at concentrations severalfold lower than necessary to inhibit growth. Mitochondrial NAD(P)H and potentiometric JC-1 fluorescence, employed as markers for electron transport chain activity, rise rapidly in response to oligomycin, as expected. Pollen tube growth stops for several minutes before resuming. Subsequent growth has a lower mean rate, but continues to oscillate, albeit with a longer period. NAD(P)H fluorescence no longer exhibits coherent oscillations, and mitochondria no longer congregate directly behind the apex: they distribute evenly throughout the cell. Postinhibition growth relies on aerobic fermentation for energy production as revealed by an increase in ethanol in the media. These data suggest that oscillatory growth depends not on a single oscillatory pacemaker but rather is an emergent property arising from a number of stable limit cycles.
DISC1 duplication in two brothers with autism and mild mental retardation
Authors: Crepel A , Breckpot J , Fryns J‐P , De la Marche W , Steyaert J , Devriendt K , Peeters H 
Published: December 2009

Crepel A, Breckpot J, Fryns J‐P, De la Marche W, Steyaert J, Devriendt K, Peeters H. DISC1 duplication in two brothers with autism and mild mental retardation.We describe the identification and delineation of an inherited 2.07 Mb microduplication in 1q42.2 in two brothers with autism and mild mental retardation. Since this duplication was not present in 1577 Belgian persons, we consider this as an extremely rare variant which has the potential to provide further insight into the genetics of autism. The duplication contains seven genes including the DISC1 gene, an interesting candidate gene that has been associated to schizophrenia, bipolar disorder, autism and Asperger syndrome. In this report we describe additional analyses undertaken to investigate the causal relationship of the duplication to the autism phenotype. We conclude that the 1q42.2 microduplication probably confers susceptibility to autism in the current family. This study is a typical illustration of the difficult interpretation of causality of a very rare variant in neuropsychiatric disease and the challenge of genetic counselling in a particular family.
Hand‐assisted versus total laparoscopic live donor nephrectomy: comparison and technique evolution at a single center in Taiwan
Authors: Lai I‐Rue , Yang Ching‐Yao , Yeh Chi‐Chuan , Tsai Meng‐Kun , Lee Po‐Huang 
Published: December 2009

Lai I‐R, Yang C‐Y, Yeh C‐C, Tsai M‐K, Lee P‐H. Hand‐assisted versus total laparoscopic live donor nephrectomy: comparison and technique evolution at a single center in Taiwan. Clin Transplant 2009 DOI: 10.1111/j.1399‐0012.2009.01173.x. © 2009 John Wiley & Sons A/S.Abstract:  Purpose:  To compare the outcome of hand‐assisted laparoscopic live donor nephrectomy (HLDN) and total laparoscopic live donor nephrectomy (TLDN) in a single center.Methods:  The demographics, complications, and outcomes were compared between successfully performed 51 HLDN and 42 TLDN.Results:  The patients’ demographics including body mass index were all similar. Four conversions were excluded for the outcome analysis. The operation time of HLDN group (188 ± 62 min) was shorter, although not significantly, than that of TLDN group’s (207 ± 30 min) (p = 0.065). However, the operation time of the first 24 cases (237 ± 66 min) was significantly longer than that of the later 69 performed (180 ± 35 min). The warm ischemia time was shorter in HLDN (2.5 ± 1.3 min) compared to that of TLDN (4.1 ± 1.7 min) (p < 0.01), but the serum creatinine values (mg/dL) of recipients were equivalent (HLDN/TLDN = 1.18 ± 0.3:1.14 ± 0.3, p = 0.587). There was no difference in the length of hospital stay (6.7 vs. 6.4 d, p = 0.475). There was no graft loss, but one ureter stricture (HLDN group) and one urinary leakage (TLDN group) were recorded.Conclusions:  Both HLDN and TLDN are effective and safe as reflected in graft functions and limited complications. There was a learning curve in establishing the technique of laparoscopic donor nephrectomy.
Salt Tolerance is Associated with Differences in Ion Accumulation, Biomass Allocation and Photosynthesis in Cowpea Cultivars
Authors: Praxedes S. C. , De Lacerda C. F. , DaMatta F. M. , Prisco J. T. , Gomes‐Filho E. 
Published: December 2009

AbstractCowpea is widely cultivated in arid and semi‐arid regions of the world where salinity is a major environmental stress that limits crop productivity. The effects of moderate salinity on growth and photosynthesis were examined during the vegetative phase of two cowpea cultivars previously classified as salt‐tolerant (Pitiúba) and salt‐sensitive (TVu). Two salt treatments (0 and 75 mm NaCl) were applied to 10‐day‐old plants grown in nutrient solution for 24 days. Salt stress caused decreases (59 % in Pitiúba and 72 % in TVu) in biomass accumulation at the end of the experiment. Photosynthetic rates per unit leaf mass, but not per unit leaf area, were remarkably impaired, particularly in TVu. This response was unlikely to have resulted from stomatal or photochemical constraints. Differences in salt tolerance between cultivars were unrelated to (i) variant patterns of Cl− and K+ tissue concentration, (ii) contrasting leaf water relations, or (iii) changes in relative growth rate and net assimilation rate. The relative advantage of Pitiúba over TVu under salt stress was primarily associated with (i) restricted Na+ accumulation in leaves paralleling an absolute increase in Na+ concentration in roots at early stages of salt treatment and (ii) improved leaf area (resulting from a larger leaf area ratio coupled with a larger leaf mass fraction and larger specific leaf area) and photosynthetic rates per unit leaf mass. Overall, these responses would allow greater whole‐plant carbon gain, thus contributing to a better agronomic performance of salt‐tolerant cowpea cultivars in salinity‐prone regions.
Effect of β‐Carotene Supply During Close‐up Dry Period on the Onset of First Postpartum Luteal Activity in Dairy Cows
Authors: Kawashima C , Nagashima S , Sawada K , Schweigert FJ , Miyamoto A , Kida K 
Published: December 2009

ContentsThe aim of this study was to examine the effect of β‐carotene supply during the close‐up dry period on the onset of first postpartum luteal activity in dairy cows. Twelve cows were supplied with 2000 mg of β‐carotene (20 g Rovimix®β‐Carotene containing 10%β‐carotene; DSM Nutrition Japan K.K., Tokyo, Japan) by oral administration daily from day 21 before expected calving date to parturition. Fourteen cows (control) did not receive β‐carotene supplementation. Blood samples were obtained on days 21, 14 and 7 before expected calving date and on days 1, 7, 14, 21 postpartum. When the plasma progesterone concentration exceeded 1 ng/ml by day 21 postpartum, luteal activity was assumed to have been initiated. The result showed that serum β‐carotene concentrations in the β‐carotene cows were higher than in the control cows during the experimental period (p < 0.01). The number of cows with the onset of luteal activity by day 21 postpartum was 9/12 in the β‐carotene cows and 4/14 in the control cows (p < 0.05). Retinol, certain metabolic parameters and metabolic hormones concentrations did not differ between β‐carotene and control cows. In addition, serum retinol concentration in β‐carotene cows without luteal activity was lower than in β‐carotene cows with luteal activity (p < 0.05), and serum gamma‐glutamyl transpeptidase concentration in β‐carotene cows with luteal activity (p < 0.05) and control cows without luteal activity (p < 0.01) was higher than in control cows with luteal activity. In conclusion, β‐carotene supply during the close‐up dry period may support the onset of luteal activity during early lactation in dairy cows.
Leukotrienes Affect Secretory Function of Ovarian Cells In Vitro*
Authors: Korzekwa AJ , Acosta TJ , Miklewicz M , Okuda K , Lee SH , Skarzynski DJ 
Published: December 2009

ContentsThe aim of this study was to determine which cells are the source of production and target for leukotriene (LTs) action within the bovine ovary. Luteal (CL, days 14–16 of the oestrous cycle), steroidogenic cells (LSC) and endothelial cells (LEC) of the bovine corpus luteum (CL), and granulosa cells (GC) were isolated enzymatically, cultured in a monolayer and incubated with LTC4, LTB4, Azelastine (an antagonist of LTC4) or Dapsone (an antagonist of LTB4). Then cells were collected for determination of mRNA expression for LT receptors (LTRs) and 5‐lipoxygenase (5‐LO) by real time RT‐PCR, and media were collected for determination of prostaglandin (PG)E2, F2α, progesterone (P4; LSC only), endothelin‐1 (ET‐1; LEC only) and 17‐β oestradiol (E2; GC only). The greatest mRNA expression for LTR‐II and 5‐LO were found in LEC, whereas LTR‐I mRNA expression did not differ among cell types. The level of PGE2 increased after LTs treatment in each type of ovarian cell, excluding LTC4 treatment in LEC. The secretion of PGF2α was also increased by LTs, but decreased after LTB4 treatment of LSC. In GC cultures, both LTs stimulated E2 secretion; in LEC cultures, LTB4 stimulated whereas LTC4 inhibited P4 secretion; in LEC cultures, LTC4 stimulated but LTB4 inhibited ET‐1 secretion. The results show that LTs are produced locally and are involved in PGs production/secretion in all examined cells (LSC, LEC and GC) of bovine ovary. Leukotriene treatment modulate secretion of E2, by GC, P4 by LSC and ET‐1 by LEC, which indicates that LTs are involved in regulation of ovarian secretory functions.
Sir William Mackenzie: sympathetic ophthalmia and glaucoma before ophthalmoscopy
Authors: Serpell Geoffrey 
Published: December 2009

AbstractOne of the practitioners of probably the oldest surgical specialty, ophthalmic, was the eminent Scottish ophthalmologist, Sir William Mackenzie. Educated in Edinburgh, he moved to Glasgow, and described and named sympathetic ophthalmia before the time of the ophthalmoscope, well defining his powers of observation and deduction. Founding the Glasgow Eye Infirmary, his ‘Practical Treatise on Diseases of the Eye’ appeared in English in four editions (1850–1884) and in French and German. In this also appears the first full and clear account of glaucoma. Both he and the illustrator of his book, Wharton Jones, moved to Glasgow because of rather indefinite connections with Robert Knox, the anatomist, who was allegedly helped by the bodysnatchers, Burke and Hare. Mackenzie and his book were highly regarded before the revolutionary ophthalmoscope. He was knighted and appointed Surgeon Oculist to the Queen in Scotland.
Plasticity of synaptic inhibition in mouse spinal cord lamina II neurons during early postnatal development and after inactivation of the glycine receptor α3 subunit gene
Authors: Rajalu M. , Müller U. C. , Caley A. , Harvey R. J. , Poisbeau P. 
Published: December 2009

AbstractSynaptic inhibition mediated by GABAAreceptors and glycine receptors (GlyRs) in the outer laminae of the spinal cord dorsal horn efficiently filters ascending nociceptive messages, controlling pathological pain symptoms. However, although many studies have utilized transgenic models to study spinal nociceptive processing, very little is known about the development of functional inhibitory synapses onto these interneurons in mice. Here we report that most interneurons in lamina II are placed under phasic control by both GABAergic and glycinergic synapses, a number of which exhibit dual GABA/glycine co‐release. A developmental switch is also apparent: a subpopulation of lamina II interneurons controlled exclusively by either GABAergic or glycinergic synapses becomes detectable only after postnatal days 15 and 21, respectively. Using mice older than postnatal day 21, we also characterized the plastic changes in glycinergic transmission resulting from the inactivation of the GlyR α3 subunit gene, a key player in inflammatory pain pathways. This allowed us to demonstrate that synapses containing GlyR α3 contribute in large part to synaptic inhibition in lamina II. InGlra3knockout mice, we found that synaptic currents at the remaining glycinergic synapses, containing GlyR α1, showed faster decay kinetics with unchanged amplitudes but increased frequency. These findings explain the absence of any basal nociceptive hypersensitivity inGlra3knockout mice, as GlyR α1 is still available for mediating synaptic inhibition at lamina II synapses, but cannot be modulated by the prostaglandin–E‐prostanoid type 2 (EP2) receptor–protein kinase A signalling cascade. Our results clearly demonstrate that presynaptic GABA/glycine release properties are influenced by the nature and complexity of postsynaptic inhibitory receptor subtypes.
The glycine transporter GlyT1 controlsN‐methyl‐D‐aspartic acid receptor coagonist occupancy in the mouse retina
Authors: Reed Brian T. , Sullivan Steven J. , Tsai Guochuan , Coyle Joseph T. , Esguerra Manuel , Miller Robert F. 
Published: December 2009

AbstractWe examined the role of GlyT1, the high‐affinity glycine transporter, in the mouse retina with an emphasis on the role of glycine as a coagonist of N‐methyl‐D‐aspartic acid (NMDA) receptors. We pursued this objective by studying heterozygote mice deficient in the GlyT1 transporter (GlyT1−/+) and compared those results with wild‐type (WT) littermate controls (GlyT1+/+). Capillary electrophoresis was used to separate and quantitatively measure glycine release from isolated retina preparations; pharmacologically blocking GlyT1 with N‐[3‐([1,1‐biphenyl]‐4‐yloxy)‐3‐(4‐fluorophenyl)propyl]‐N‐methylglycine in the WT retina generated a significantly larger accumulation of glycine into the bathing environment when compared with the GlyT1−/+retinas. The relative occupancy state of the NMDA receptor coagonist sites was tested using whole‐cell recordings from ganglion cells while bath applying D‐serine or D‐serine + NMDA. The interpretation of these studies was simplified by blocking post‐synaptic inhibition with picrotoxinin and strychnine. NMDA receptor coagonist sites were more saturated and less enhanced by D‐serine in the GlyT1−/+mice compared with the WT controls. Immunoblots of NMDA receptor subunits (NR1, NR2A and NR2B) in WT and GlyT1−/+animals showed that the NR1 subunits were identical. These observations are discussed in view of contemporary issues about NMDA receptor coagonist function in the vertebrate retina and the role of glycine vs. D‐serine as the endogenous coagonist.
Genome‐wide gene expression profiling in GluR1 knockout mice: key role of the calcium signaling pathway in glutamatergically mediated hippocampal transmission
Authors: Zhou Rulun , Holmes Andrew , Du Jing , Malkesman Oz , Yuan Peixiong , Wang Yun , Damschroder‐Williams Patricia , Chen Guang , Guitart Xavier , Manji Husseini K. 
Published: December 2009

Abstractα‐Amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionic acid receptors (AMPARs) convey fast synaptic transmission in the CNS and mediate various forms of hippocampal plasticity. Disruption of glutamate receptor type 1 (GluR1), a member of the AMPAR family, causes synaptic alterations and learning/memory deficits in mice. To gain mechanistic insight into the synaptic and behavioral changes associated with GluR1 deletion, hippocampal genome‐wide expression profiling was conducted using groups of GluR1 knockout (KO) mice and their wild‐type littermates. Regulation of 38 genes was found to be altered more than 30% (P < 0.01, n = 8), and seven of these genes were studied with additional quantitative experiments. A large portion of the altered genes encoded molecules involved in calcium signaling, including calcium channel components, calcium‐binding proteins and calcium‐calmodulin‐dependent protein kinase II subunits. At the protein level, we further evaluated some genes in the calcium pathway that were altered in GluR1 KO mice. Protein levels of two key molecules in the calcium pathway – GluR, ionotropic, N‐methyl‐d‐aspartate‐1 and calcium/calmodulin‐dependent protein kinase II alpha – showed similar changes to those observed in mRNA levels. These findings raise the possibility that calcium signaling and other plasticity molecules may contribute to the hippocampal plasticity and behavioral deficits observed in GluR1 KO mice.