bluuebunny/crossref_metadata_2025_split huggingface dataset:
VoteDock: Consensus docking method for prediction of protein–ligand interactions
Authors: Plewczynski Dariusz , Łażniewski Michał , Grotthuss Marcin Von , Rychlewski Leszek , Ginalski Krzysztof 
Published: September 2010

AbstractMolecular recognition plays a fundamental role in all biological processes, and that is why great efforts have been made to understand and predict protein–ligand interactions. Finding a molecule that can potentially bind to a target protein is particularly essential in drug discovery and still remains an expensive and time‐consuming task. In silico, tools are frequently used to screen molecular libraries to identify new lead compounds, and if protein structure is known, various protein–ligand docking programs can be used. The aim of docking procedure is to predict correct poses of ligand in the binding site of the protein as well as to score them according to the strength of interaction in a reasonable time frame. The purpose of our studies was to present the novel consensus approach to predict both protein–ligand complex structure and its corresponding binding affinity. Our method used as the input the results from seven docking programs (Surflex, LigandFit, Glide, GOLD, FlexX, eHiTS, and AutoDock) that are widely used for docking of ligands. We evaluated it on the extensive benchmark dataset of 1300 protein–ligands pairs from refined PDBbind database for which the structural and affinity data was available. We compared independently its ability of proper scoring and posing to the previously proposed methods. In most cases, our method is able to dock properly approximately 20% of pairs more than docking methods on average, and over 10% of pairs more than the best single program. The RMSD value of the predicted complex conformation versus its native one is reduced by a factor of 0.5 Å. Finally, we were able to increase the Pearson correlation of the predicted binding affinity in comparison with the experimental value up to 0.5. © 2010 Wiley Periodicals, Inc. J Comput Chem 32: 568–581, 2011
Live cell imaging and systems biology
Authors: Sung Myong‐Hee , McNally James G. 
Published: September 2010

AbstractMuch of the experimental data used to construct mathematical models of molecular networks are derived from in vitro measurements. However, there is increasing evidence that in vitro measurements fail to capture both the complexity and the individuality found in single, living cells. These limitations can be overcome by live cell microscopy which is evolving to enable in vivo biochemistry. Here, we survey the current capabilities of live cell microscopy and illustrate how a number of different imaging approaches could be applied to analyze a specific molecular network. We argue that incorporation of such quantitative live‐cell imaging methods is critical for the progress of systems biology. WIREs Syst Biol Med 2011 3 167–182 DOI: 10.1002/wsbm.108This article is categorized under:

Biological Mechanisms > Cell Signaling
Laboratory Methods and Technologies > Imaging
Physiology > Mammalian Physiology in Health and Disease
Adhesion Awareness: A National Survey of Surgeons
Authors: Schreinemacher Marc H. F. , ten Broek Richard P. , Bakkum Erica A. , van Goor Harry , Bouvy Nicole D. 
Published: September 2010

AbstractBackgroundPostoperative adhesions are the most frequent complication of abdominal surgery, leading to high morbidity, mortality, and costs. However, the problem seems to be neglected by surgeons for largely unknown reasons.MethodsA survey assessing knowledge and personal opinion about the extent and impact of adhesions was sent to all Dutch surgeons and surgical trainees. The informed‐consent process and application of antiadhesive agents were questioned in addition.ResultsThe response rate was 34.4%. Two thirds of all respondents (67.7%) agreed that adhesions exert a clinically relevant, negative effect. A negative perception of adhesions correlated with a positive attitude regarding adhesion prevention (ρ = 0.182, p < 0.001). However, underestimation of the extent and impact of adhesions resulted in low knowledge scores (mean test score 37.6%). Lower scores correlated with more uncertainty about indications for antiadhesive agents which, in turn, correlated with never having used any of these agents (ρ = 0.140, p = 0.002; ρ = 0.095, p = 0.035; respectively). Four in 10 respondents (40.9%) indicated that they never inform patients on adhesions and only 9.8% informed patients routinely. A majority of surgeons (55.9%) used antiadhesive agents in the past, but only a minority (13.4%) did in the previous year. Of trainees, 82.1% foresaw an increase in the use of antiadhesive agents compared to 64.5% of surgeons (p < 0.001).ConclusionsThe magnitude of the problem of postoperative adhesions is underestimated and informed consent is provided inadequately by Dutch surgeons. Exerting adhesion prevention is related to the perception of and knowledge about adhesions.
Neurocognitive functioning in school‐aged cystinosis patients
Authors: Besouw M. T. P. , Hulstijn‐Dirkmaat G. M. , van der Rijken R. E. A. , Cornelissen E. A. M. , van Dael C. M. , Vande Walle J. , Lilien M. R. , Levtchenko E. N. 
Published: September 2010

AbstractIntroductionCystinosis is an autosomal recessive disorder leading to intralysosomal cystine accumulation in various tissues. It causes renal Fanconi syndrome and end stage renal failure around the age of 10 years if not treated with cysteamine. Children with cystinosis seem to have a normal intelligence but frequently show learning difficulties. These problems may be due to specific neurocognitive deficits rather than impaired renal function. Whether cysteamine treatment can improve cognitive functioning of cystinosis patients is thus far unknown. We aim to analyze neurocognitive functioning of school‐aged cystinosis patients treated with cysteamine in order to identify specific deficits that can lead to learning difficulties.Patients and methodsFourteen Dutch and Belgian school‐aged cystinosis patients were included. Glomerular filtration rate was estimated using the Schwartz formula. Children were tested for general intelligence, visual‐motor integration, inhibition, interference, sustained attention, accuracy, planning, visual memory, processing speed, motor planning, fluency and speed, and behavioural and emotional functioning using standardized methods.ResultsGlomerular filtration rate ranged from 22 to 120 ml min−1 1.73 m−2. Median full‐scale intelligence was below the average of a normal population (87, range 60–132), with a discrepancy between verbal (median 95, range 60–125) and performance (median 87, range 65–130) intelligence. Over 50% of the patients scored poorly on visual‐motor integration, sustained attention, visual memory, planning, or motor speed. The other tested areas showed no differences between patients’ and normal values.ConclusionNeurocognitive diagnostics are indicated in cystinosis patients. Early recognition of specific deficits and supervision from special education services might reduce learning difficulties and improve school careers.
The genotypic and phenotypic spectrum of pyridoxine‐dependent epilepsy due to mutations in ALDH7A1
Authors: Scharer Gunter , Brocker Chad , Vasiliou Vasilis , Creadon‐Swindell Geralyn , Gallagher Renata C. , Spector Elaine , Van Hove Johan L. K. 
Published: September 2010

AbstractPyridoxine‐dependent epilepsy is a disorder associated with severe seizures that may be caused by deficient activity of α‐aminoadipic semialdehyde dehydrogenase, encoded by the ALDH7A1 gene, with accumulation of α‐aminoadipic semialdehyde and piperideine‐6‐carboxylic acid. The latter reacts with pyridoxal‐phosphate, explaining the effective treatment with pyridoxine. We report the clinical phenotype of three patients, their mutations and those of 12 additional patients identified in our clinical molecular laboratory. There were six missense, one nonsense, and five splice‐site mutations, and two small deletions. Mutations c.1217_1218delAT, I431F, IVS‐1(+2)T > G, IVS‐2(+1)G > A, and IVS‐12(+1)G > A are novel. Some disease alleles were recurring: E399Q (eight times), G477R (six times), R82X (two times), and c.1217_1218delAT (two times). A systematic review of mutations from the literature indicates that missense mutations cluster around exons 14, 15, and 16. Nine mutations represent 61% of alleles. Molecular modeling of missense mutations allows classification into three groups: those that affect NAD+ binding or catalysis, those that affect the substrate binding site, and those that affect multimerization. There are three clinical phenotypes: patients with complete seizure control with pyridoxine and normal developmental outcome (group 1) including our first patient; patients with complete seizure control with pyridoxine but with developmental delay (group 2), including our other two patients; and patients with persistent seizures despite pyridoxine treatment and with developmental delay (group 3). There is preliminary evidence for a genotype‐phenotype correlation with patients from group 1 having mutations with residual activity. There is evidence from patients with similar genotypes for nongenetic factors contributing to the phenotypic spectrum.
The MoS2 Nanotubes with Defect-Controlled Electric Properties
Authors: Remskar Maja , Mrzel Ales , Virsek Marko , Godec Matjaz , Krause Matthias , Kolitsch Andreas , Singh Amol , Seabaugh Alan 
Published: September 2010

AbstractWe describe a two-step synthesis of pure multiwall MoS2 nanotubes with a high degree of homogeneity in size. The Mo6S4I6 nanowires grown directly from elements under temperature gradient conditions in hedgehog-like assemblies were used as precursor material. Transformation in argon-H2S/H2 mixture leads to the MoS2 nanotubes still grouped in hedgehog-like morphology. The described method enables a large-scale production of MoS2 nanotubes and their size control. X-ray diffraction, optical absorption and Raman spectroscopy, scanning electron microscopy with wave dispersive analysis, and transmission electron microscopy were used to characterize the starting Mo6S4I6 nanowires and the MoS2 nanotubes. The unit cell parameters of the Mo6S4I6 phase are proposed. Blue shift in optical absorbance and metallic behavior of MoS2 nanotubes in two-probe measurement are explained by a high defect concentration.
The Development of a Pressure Ulcer Risk‐Assessment Scale for Perioperative Patients
Authors: Munro Cassendra A. 
Published: September 2010

AbstractThe high incidence of pressure ulcer development in patients in the perioperative setting indicates the need for improved risk assessment and the use of preventive measures. A clinical nurse specialist used Dever's Epidemiological Model as the theoretical framework to develop a perioperative pressure ulcer risk‐assessment scale. The risk factors for the scale were based on findings from a review of the literature. The scale, along with a demographic questionnaire and an evaluation form, was distributed to 12 nurses and three anesthesiologists to obtain expert opinion to further the design of the scale. Twelve participants returned the forms. Only four of the participants had previous experience with a pressure ulcer risk‐assessment scale. The results indicated that diabetes should be included as a risk factor category and that preexisting skin ulcerations, breakdowns, and conditions should be addressed within the scale. The participants unanimously agreed that moisture is an important factor to assess. Validation of each risk factor is essential to improve the reliability of the scale before its implementation.
The effect of milk given at various temperatures on the oxygen consumption of young calves
Authors: Holmes C. W. 
Published: September 2010

SUMMARY1. Measurements of oxygen consumption and rectal temperature were made on young female calves at air temperatures of 9° and 20°C, before and after 4·5 kg milk was drunk at 23° and 39°C.2. When cool milk (23°C) was drunk at an air temperature of 9°C, vigorous shivering occurred, and during the 2-hr period after feeding, oxygen consumption was significantly higher than in the three other treatments.3. In all other treatments oxygen consumption increased considerably during the 30-min period which included drinking activity; the average increment, when no thermo-regulatory shivering occurred, was 1·9 ml O2 min−1kg−1.4. It was estimated that the 58 kcal ‘heat of warming’ required by milk at 23°C drunk at an air temperature of 9°C could be accounted for by the increment in heat production during the 2 hr after feeding and the fall in rectal temperature of 0-2-0-3°C which persisted after feeding in this treatment. These calculations suggested that the effect of a cool liquid on the energy balance of an animal would be less than that predicted from the ‘heat of warming’ required by the cool liquid.
A study of protein requirements of housed Scottish Blackface ewes during late pregnancy
Authors: McClelland T. H. , Forbes T. J. 
Published: September 2010

SUMMARYIn-lamb ewes were given 38, 58 and 82 g of digestible crude protein daily at a constant energy intake of 1600 kcal ME per head daily during the last 6 weeks of gestation. There were no significant differences between treatments in live-weight gain of the ewes, lamb birth weight or ewe net body-weight change (the difference between live-weight gain over the experimental period and live-weight loss at lambing).Digestibility coefficients for the diet components and nitrogen balances were determined on three ewes per treatment during weeks 15-16 and 19·20 of gestation. No differences in the apparent digestibility of the diet components were observed between the two periods. The apparent digestibility of crude protein increased significantly (P > 0·001) with increase in crude protein intake. A significant linear relationship (P<0·01) was found between digestible crude protein intake and nitrogen retention; daily N retention increased by 0·19 g per kg W0·73 for every 1 g per kg W0·73 of apparent digested nitrogen intake per day.
Aggressive behaviour in groups of domesticated pigs on removal and return of individuals
Authors: Ewbank R. , Meese G. B. 
Published: September 2010

SUMMARYSeveral groups of eight fattening (18 kg to 91 kg) Large White pigs containing both immature female and castrated male animals were established, were fed twice a day on a commercial dry ration, were observed at feeding time and their social orders (linear dominance hierarchy) worked out. Individual pigs were removed, one at a time, from different places in the social order, isolated for varying periods of time, and then replaced in their groups. It was found that the removal of a pig from any rank in the dominance order altered neither the basic social hierarchy nor the amount of aggression within the remainder of the group. The duration of time that an animal could be removed, isolated and returned without being attacked by the rest of its group varied with its social rank. Top-ranking animals could be safely returned even after 25 days' isolation, but lowranking animals were severely attacked after only 3 days' absence.
Effect of winter environment on growth of young beef cattle 2. A note on the comparison of roofless cubicles with indoor cubicles for wintering 9-month-old Hereford × Shorthorn steers
Authors: McCarrick R. B. , Drennan M. J. 
Published: September 2010

SUMMARYLive-weight gains of two groups of 9-month-old Hereford × Shorthorn steers wintered in either roofless cubicles or indoor cubicles were compared during the winter of 1968/69, and during a subsequent 29 days at pasture. The animals were fed 1·82 kg concentrates per head daily and both treatment groups received equal quantities of silage.No significant difference was found between treatments in winter live-weight gains or subsequent weight changes at pasture. The health of all animals was excellent throughout.
A note on factors affecting lamb survival in Indian sheep
Authors: Malik R. C. , Acharya R. M. 
Published: September 2010

SUMMARYRecords on lamb survival were available for 757 lambs, the progeny of 33 rams. Purebred lambs were of the Nali and Lohi breeds and crossbred lambs were produced by mating Nali ewes to Nellore or Mandya rams, and Lohi ewes to Nellore rams. For the flock as a whole 93% of those born survived to 14 days of age and 86% to weaning. A least-squares analysis of variance showed that among the factors investigated only lamb's weight at birth significantly affected survival to 14 days of age, and lamb's weight at birth, ewe's weight at lambing and the year of birth had significant effects on lamb survival from 15 days to weaning. Heritability estimates for lamb survival were based on half sib correlations. For the period from birth to 14 days of age the estimates were 0·08 for pure Nali lambs and 0·03 for the whole flock, and for the period from 15 days to weaning the estimates were 0·10 and 0·26 for the two groups respectively.
A note on the effects of clipping pregnant ewes at housing
Authors: Rutter W. , Laird T. R. , Broadbent P. J. 
Published: September 2010

SUMMARYEighty pregnant ewes, housed in December approximately 14 weeks before lambing, were offered grass silage to appetite. The factors considered were breed (Greyface or North Country Cheviot), concentrate level during the final 7 weeks of pregnancy (‘normal’ or ‘high’) and clipping (clipped at housing or left undipped at housing). Silage intakes were affected by level of concentrate supplementation, the higher level tending to reduce intakes during the final weeks of pregnancy but no effect of clipping on silage intakes was detected. Level of concentrate had no effect on lambing performance, but ewes clipped at housing produced lambs which were 1 kg heavier (P<0·05) at birth than lambs from undipped ewes. Time of clipping had a significant effect on wool yields but no effect on wool grades.
Milk progesterone profiles and factors affecting post partum ovarian activity in beef cows
Authors: Peters A. R. , Riley G. M. 
Published: September 2010

ABSTRACTProgesterone concentration was measured in milk samples collected twice or three times weekly from 157 suckling beef cows in three herds during the period from parturition until the resumption of ovarian cycles. The length of the post partum acyclic period varied between cows from 11 to 125 days. The length of the acyclic period did not differ between cows suckling one or two calves or between the two breeds of cow studied. There were significant negative correlations between the length of the acyclic period and 1. body weight at calving (r = −0·394; P<0·001) and 2. days from calving to the next longest day of the year (r=−0·782; P<0·001). Cows calving between February and April were acyclic significantly longer (83 days) than those calving between August and December (44 days; s.e. of difference = 3·5; P < 0·001). In one herd there was a significant negative correlation between the length of the acyclic period and order of calving both in spring (r=−0·379; P<0·05)- and autumn/winter (r=− 0·349; P < 0·05)-calving cows. Of the 40 spring-calving cows in the same herd, 17 were served naturally prior to any rise in milk progesterone concentrations and 11 of these conceived to this service.
The influence of winter nutrition, grazing system and stocking rate on the performance of spring-calving Hereford × Friesian cows and their calves 2. Grazing system and stocking rate
Authors: Baker R. D. , Barker J. M. , Le Du Y. L. P. 
Published: September 2010

ABSTRACTForty-eight Hereford × Friesian cows and their South Devon calves were paddock grazed at high or low stocking rates of 412 or 206 cows and calves per ha in experiment 1, and either paddock grazed or set stocked at high or low stocking rates of 4·12 or 2·74 cows and calves per ha in experiments 2 to 4.There was no significant effect of grazing system on milk yield, milk composition or calf growth but in experiment 2 paddock-grazed cows gained more weight than those set stocked. Cows at low stocking rates gained more weight than those at high stocking rates and, in general, gave more milk. Calf growth rates were also higher at low stocking rates in experiments 1, 3 and 4 but not in experiment 2. Milk composition was not significantly affected by stocking rate. There were substantial increases in calf live-weight gain per ha at the high stocking rate but, because of a lower gain by cows, the differences in total live-weight gains per ha for cows and calves were much smaller.
A note on the relationship between milk yield and reproductive performance in some British Friesian sire progeny groups
Authors: Wood P. D. P. , Frappell J. P. 
Published: September 2010

ABSTRACTThe 305-day lactation milk yields and the numbers of inseminations required to obtain a pregnancy during a particular lactation were obtained from 1475 lactations of 808 daughters of eight bulls, whose Improved Contemporary Comparisons spanned two genetic standard deviations of milk yield. All lactations were completed before September 1978. Cattle requiring more than one insemination for a pregnancy produced 173 (standard error of difference = 55) kg more milk in 305 days than those requiring only one. There was no correlation between the Improved Contemporary Comparisons of the sire and either the difference in yield, or the proportion of animals needing one or those needing more than one insemination per pregnancy.
High-fibre diets for ad libitum feeding of sows during lactation
Authors: Zoiopoulos P. E. , English P. R. , Topps J. H. 
Published: September 2010

ABSTRACT1. Two diets, containing either 400 g oat husks (OH) or 300 g straw (ST) per kg, given ad libitum during a 7-week lactation, were compared with a conventional control diet (C) given in restricted amounts. Eight sows per treatment were used in a randomized-block experiment.2. Mean daily intakes of dry matter during lactation were 4·87, 7·79 and 5·80 kg for the C, OH and ST diets respectively (P>0·001).3. There were no significant differences between diets in number or weights of piglets per litter either at 21 days of age or at weaning.4. Mean changes in live weight during lactation were –9·8, +5 1 and –16·8kg for sows on the C, OH and ST diets respectively (P<0·01). Sows that gained weight during lactation tended to lose more in the 7 days following weaning.5. There were no significant differences in either milk yield or composition. However, the fat content of milk tended to be higher for sows given the two fibrous diets.6. Mean apparent digestibility coefficients for dietary dry matter were 0·82, 0·63 and 0·59, and for nitrogen were 0·81, 0·75 and 0·63, in the C, OH and ST diets respectively. The rate of passage of the ST diet through the gut was significantly faster than that of the other two diets (P>0·001), which were similar.
The influence of the post-weaning social environment on the weaning to mating interval of the sow
Authors: Hemsworth P. H. , Salden N. T. C. J. , Hoogerbrugge A. 
Published: September 2010

ABSTRACTTwo studies were conducted at commercial farms on a total of 1117 sows to investigate the role of social environment on the weaning to mating interval of the sow. In one of the two studies, group housing and intense boar stimulation, achieved by daily introduction to a boar, were associated with significant reductions in the weaning to mating interval of the sow (P<0·05 and P<0·01, respectively): these two factors together produced increases of 0·18 and 0·22 in the proportion of sows mated within 10 and 28 days of weaning, respectively. In addition, parity and temperature during the week of weaning were significantly associated with the weaning to mating interval in both studies (P< 0·005 and P<005, respectively). It is concluded that the post-weaning social environment will influence the onset of oestrus in the sow.