bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgical Hand Antisepsis With Alcohol-Based Hand Rub Comparison of Effectiveness After 1.5 and 3 Minutes of Application
Authors: Weber Walter P. , Reck Stefan , Neff Uschi , Saccilotto Ramon , Dangel Marc , Rotter Manfred L. , Frei Reno , Oertli Daniel , Marti Walter R. , Widmer Andreas F. 
Published: March 2009

Objective.Research has shown 1.5 minutes of surgical hand antisepsis with alcohol-based hand rub to be at least as effective under experimental conditions as the 3-minute reference disinfection recommended by European Norm 12791. The aim of the present study was to validate the effectiveness of 1.5 minutes of surgical hand antisepsis in a clinical setting by comparing the effectiveness of 1.5- and 3-minute applications of alcohol-based hand rub (45% vol/vol 2-propanol, 30% vol/vol 1-propanol, and 0.2% mecetronium ethylsulphate).Design.Prospective crossover trial in which each surgeon served as his or her own control, with individual randomization to the 1.5-or the 3-minute group during the first part of the trial.Setting.Basel University Hospital, Switzerland.Participants.Thirty-two surgeons with different levels of postdoctoral training.Methods.We measured the bactericidal effectiveness of 1.5 minutes and 3 minutes of surgical hand antisepsis with alcohol-based hand rub by assessing the mean (± SD) log10 number of colony-forming units before the application of hand rub (baseline), after the application of hand rub (immediate effect), and after surgery (sustained effect) so as to follow European Norm 12791 as closely as possible.Results.The immediate mean (± SD) log10 reduction in colony-forming units (cfu) was 2.66 ±1.13 log10 cfu for the 1.5-minute group and 3.01 ±1.06 log10 cfu for the 3-minute group (P = .204). Similarly, there was no statistically significant difference between the 2 groups with respect to the sustained effect; the mean ( ± SD) log10 increase in bacterial density during surgery was 1.08 ± 1.13 log10 cfu for the 1.5-minute group and 0.95 ± 1.27 log10 cfu for the 3-minute group (P = .708). No adverse effects were recorded.Conclusion.In this clinical trial, surgical hand antisepsis with alcohol-based hand rub resulted in a similar bacterial reduction, regardless of whether it was applied for 3 or 1.5 minutes, which confirms experimental data generated with healthy volunteers.
dCAS: a desktop application for cDNA sequence annotation
Authors: Guo Yongjian , Ribeiro Jose M. C. , Anderson Jennifer M. , Bour Stephan 
Published: March 2009

Abstract
Motivation: Understanding gene regulation and expression is the key to the advancement of biology. EST sequence assembly and analysis provide unique benefits in this regard. We have developed a standalone application, dCAS (Desktop cDNA Annotation System), which performs automated EST cleaning, clustering, assembly and annotation on a desktop computer. Compared with other available tools, dCAS provides a more convenient and user-friendly solution to biologists for extracting biological meaning from sequence data.
Availability: The dCAS package is distributed freely. A cross-platform installer and associated sequence databases can be downloaded at: http://exon.niaid.nih.gov/applications.html
Contact: guoyo@mail.nih.gov
Integrating shotgun proteomics and mRNA expression data to improve protein identification
Authors: Ramakrishnan Smriti R. , Vogel Christine , Prince John T. , Wang Rong , Li Zhihua , Penalva Luiz O. , Myers Margaret , Marcotte Edward M. , Miranker Daniel P. 
Published: March 2009

Abstract
Motivation: Tandem mass spectrometry (MS/MS) offers fast and reliable characterization of complex protein mixtures, but suffers from low sensitivity in protein identification. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other information available, e.g. the probability of a protein's presence is likely to correlate with its mRNA concentration.
Results: We develop a Bayesian score that estimates the posterior probability of a protein's presence in the sample given its identification in an MS/MS experiment and its mRNA concentration measured under similar experimental conditions. Our method, MSpresso, substantially increases the number of proteins identified in an MS/MS experiment at the same error rate, e.g. in yeast, MSpresso increases the number of proteins identified by ∼40%. We apply MSpresso to data from different MS/MS instruments, experimental conditions and organisms (Escherichia coli, human), and predict 19–63% more proteins across the different datasets. MSpresso demonstrates that incorporating prior knowledge of protein presence into shotgun proteomics experiments can substantially improve protein identification scores.
Availability and Implementation: Software is available upon request from the authors. Mass spectrometry datasets and supplementary information are available from http://www.marcottelab.org/MSpresso/.
Contact: marcotte@icmb.utexas.edu; miranker@cs.utexas.edu
Supplementary Information: Supplementary data website: http://www.marcottelab.org/MSpresso/.
An assessment of the functional variability of selected coastal ecosystems in the context of local environmental changes
Authors: Baird Dan 
Published: March 2009

AbstractBaird, D. (2009) An assessment of the functional variability of selected coastal ecosystems in the context of local environmental changes. – ICES Journal of Marine Science, 66: 1520–1527. The functioning of coastal ecosystems is greatly dependent on a wide variety of external pulses (e.g. tides, freshwater influx, seasonal trends in temperature, nutrient input, etc.). Assessments of the effect of a selection of environmental characteristics driven by natural and/or anthropogenic forces on ecosystem function are given using selected ecosystem properties, such as total system throughput, system organization, productivity, recycling, and trophic efficiency, derived from ecological network analysis (ENA) of several coastal ecosystems on monthly, intra-seasonal, seasonal, and interdecadal scales. Each ecosystem was modelled depicting data of standing stocks, the flows between the constituent living and non-living components in the system, exports, and imports. Results from ENA revealed considerable differences of the same property (or properties) resulting from physical changes (e.g. temperature, salinity, oxygen, rate of freshwater inflow) over time. A small temperature increase in a Florida seagrass bed, for example, resulted in increases in system throughput, the P/B ratio, and in the rate of carbon recycling, but also in a significant decrease in system organization. The effect of seasonal increases in water temperature and of measured decrease/increase in river run-off to a few selected estuaries is discussed using ENA.
The comparative effects of habitat complexity on faunal assemblages of northern temperate artificial and natural reefs
Authors: Hunter W. R. , Sayer M. D. J. 
Published: March 2009

Abstract
Hunter, W. R., and Sayer, M. D. J. 2009. The comparative effects of habitat complexity on faunal assemblages of northern temperate artificial and natural reefs. – ICES Journal of Marine Science, 66: 691–698. Several north temperate marine species were recorded on subtidal hard-substratum reef sites selected to produce a gradient of structural complexity. The study employed an established scuba-based census method, the belt transect. The three types of reef examined, with a measured gradient of increasing structural complexity, were natural rocky reef, artificial reef constructed of solid concrete blocks, and artificial reef made of concrete blocks with voids. Surveys were undertaken monthly over a calendar year using randomly placed fixed rope transects. For a number of conspicuous species of fish and invertebrates, significant differences were found between the levels of habitat complexity and abundance. Overall abundance for many of the species examined was 2–3 times higher on the complex artificial habitats than on simple artificial or natural reef habitats. The enhanced habitat availability produced by the increased structural complexity delivered through specifically designed artificial reefs may have the potential to augment faunal abundance while promoting species diversity.
Infants with late breast milk acquisition of HIV-1 generate interferon-gamma responses more rapidly than infants with early peripartum acquisition
Authors: Lohman-Payne B , Slyker J A , Richardson B A , Farquhar C , Majiwa M , Maleche-Obimbo E , Mbori-Ngacha D , Overbaugh J , Rowland-Jones S , John-Stewart G 
Published: March 2009

Summary
Infants infected with HIV-1 after the first month of life have a lower viral set-point and slower disease progression than infants infected before 1 month. We investigated the kinetics of HIV-1-specific CD8+ T lymphocyte secretion of interferon (IFN)-γ in infants infected before 1 month of life compared with those infected between months 1 and 12 (late infection). HIV-1 infection was assessed at birth and at months 1, 3, 6, 9 and 12 and timing of infection was determined by HIV-1 gag DNA from dried blood spots and verified by plasma HIV-1 RNA levels. HIV-1 peptide-specific IFN-γ responses were measured by enzyme-linked immunospot at months 1, 3, 6, 9 and 12. Timing of development of IFN-γ responses was compared using the log–rank test and Kaplan–Meier survival curves. Infants infected late developed HIV-1-specific CD8+ T cell responses 2·8 months sooner than infants infected peripartum: 2·3 versus 5·1 months after HIV-1 infection (n = 52, P = 0·04). Late-infected infants had more focused epitope recognition than early-infected infants (median 1 versus 2 peptides, P = 0·03); however, there were no differences in the strength of IFN-γ responses. In infants infected with HIV-1 after the first month of life, emergence of HIV-1-specific CD8+ IFN-γ responses is coincident with the decline in viral load, nearly identical to what is observed in adults and more rapid than in early-infected infants.
Out in the cold: physiological capacity influences behaviour in deer mice
Authors: Sears Michael W. , Hayes Jack P. , Banta Marilyn R. , McCormick Donna 
Published: March 2009

Summary

Understanding the links between physiological performance and fitness is key to predicting the responses of individuals to environmental change, especially that imposed by climate. Of particular interest are traits linked with metabolic performance. In particular, maximal metabolic rate (MMR; which describes the upper limit to heat production) and basal metabolic rate (BMR; which describes the lower limit to heat production for a normothermic endotherm) are important causal mechanisms that determine the physiological limits for activity under cold conditions.
Previous work with deer mice has shown important links between maximal metabolic performance and activity. Selection for elevated MMRs was detected in nature, and higher rates of above‐ground activity during periods of cold were associated with elevated MMRs. Here, we investigate further the links between activity and elevated MMRs.
We conducted a laboratory study to test whether BMR or MMR was correlated with activity and foraging behaviour of deer mice exposed to a series of cold temperatures (–5, –10 and –15 °C). Each mouse had access to a warm nest box, but needed to enter a cold environmental chamber to access food, ice chips and a running wheel. Behaviours were monitored for 2 days under these experimental conditions. Prior to the experimental trials, BMR and MMR were measured. MMR was also measured after the trials.
The amount of time that mice spent active in the cold was negatively correlated with ambient temperature. The duration of activity per bout (when mice were out of the nest box) decreased at colder temperatures, but the number of bouts did not. The total duration of activity and duration per bout increased with an individual's MMR and change in MMR over the course of the experiment. Body mass decreased at colder temperatures, and mice with higher MMR and greater increases in MMR consumed more food.
Our study suggests that mice with high MMR, or a capacity to increase MMR may be best able to tolerate cold environments. Thus, physiological capacity and behaviour can influence each other in response to environmental conditions.
Integrative studies between behaviour and physiology in an ecological context provide greater understanding of the potential responses of organisms to environmental change. With respect to climate, such responses will depend either on the ability of individuals to induce plastic (or acclamatory) responses to environmental stressors or on the structure of genetic variation for physiological traits within a particular population. Although, some effort has been directed at understanding the evolutionary significance of metabolic traits (particularly with respect to heritabilities), we suggest that priority should be given to studies that explicitly address the mechanistic links between physiology and fitness in light of ongoing climate change.
Cholesterol and desmosterol in two sperm populations separated on Sil‐Select gradient
Authors: Zalata A. , Hassan A. , Christophe A. , Comhaire F. , Mostafa T. 
Published: March 2009

SummarySperm lipids are important for sperm viability, maturity and function. This study aimed to identify cholesterol and desmosterol composition of human spermatozoa of two sperm populations separated on Sil‐Select gradient. Forty‐eight males were divided into four groups namely healthy men (n = 13), asthenozoospermia (n = 11), asthenoteratozoospermia (n = 10) and oligoasthenoteratozoospermia (n = 14). Sperm cholesterol and desmosterol were estimated in two human sperm population separated by centrifugation in a discontinuous Sil‐Select gradient. The results showed that cholesterol and desmosterol were the major sterols in human spermatozoa. Spermatozoa recovered from upper/lower layer interface (fraction I) had low fertilization potential, while those from the base (fraction II) had high fertilization potential. Median values of cholesterol and desmosterol in fraction I were 2.55 μmol and 0.77 μmol/109 spermatozoa and in fraction II were 1.16 μmol and 0.27 μmol/109 spermatozoa. Cholesterol/desmosterol ratio was significantly higher in fraction II than I (4.8 vs. 3.2, p < 0.01). Cholesterol, desmosterol, total phospholipids and sterols/phospholipids were negatively correlated with sperm concentrations, sperm motility, linear velocity, normal sperm morphology and acrosome reaction percentage whereas cholesterol/desmosterol ratio was positively correlated with these parameters. It is concluded that the difference in sterol composition of sperm subpopulations separated on Sil‐Select gradient suggests that composition of sterols is related to sperm functions.
Combined effect of the finasteride and doxazosin on rat ventral prostate morphology and physiology
Authors: Justulin Jr Luis A. , Acquaro Carolina , Carvalho Robson F. , Silva Maeli Dal Pai , Felisbino Sérgio L. 
Published: March 2009

SummaryFinasteride (Fin) and Doxazosin (Dox), alone or in combination, have been widely used in treatment of benign prostatic hyperplasia (BPH) symptoms and recently have been suggested as potential drugs for prostate cancer (PCa)prevention and treatment. However, little is known about the effects of the combination therapy on prostate tissue morphology, physiology and matrix metalloproteinases (MMPs) activity, a special set of enzymes closely related to PCa progression and metastasis. In this study, adult Wistar rats were treated with Fin + Dox (25 mg/kg per day) and the ventral prostate (VP) was excised at days 3 and 30 of treatment to evaluate morphology, cell proliferation, death, transforming growth factor‐beta1 (TGF‐β1) protein expression, MMP‐2, MMP‐9 activities and MMP‐2, MMP‐9, TIMP‐1 and TIMP‐2 mRNA expression. Fin + Dox treatment induced a transient increase in testosterone (T) plasma concentration and a permanent reduction in dihydrotestosterone (DHT). The VP and epithelial cell proliferation were reduced and the stromal collagen fibre volume fraction and apoptosis of the epithelial cell were increased. Fin + Dox treatment also increased the TGF‐β1 immunoreaction in the epithelium and in the stroma. The mRNAs for MMP‐2, TIMPs‐1 and ‐2 expressions after 30 days of treatment were decreased. The mRNA for MMP‐9 was not detected in any of the groups analysed. Fin + Dox treatment for 30 days promoted a decrease in gelatinolytic activity of MMP‐2 and an increase in MMP‐9. In conclusion, combined treatment with Fin and Dox interferes in the epithelial cell behaviour and in the MMPs activity, potentially via TGF‐β1‐mediated and androgen pathways. Our results contribute to a better understanding of the clinical data and also of the molecular mechanisms behind isolated or combined Fin and Dox long‐term treatment.
Testing island biogeography theory with visitation rates of birds to British islands
Authors: Stracey Christine M. , Pimm Stuart L. 
Published: March 2009

AbstractAim  We consider three hypotheses – MacArthur and Wilson’s island biogeography theory (IBT), Lack’s habitat diversity idea and the ‘target effect’– that explain the pattern of decreased species richness on small and distant islands.Location  We evaluate these hypotheses using a detailed dataset on the occurrence and abundance of terrestrial birds on nine islands off the coast of Britain and the Republic of Ireland.Methods Unlike previous studies, we compile data on species that visit the islands, rather than just those that breed on them. We divided the species into five mutually exclusive categories based upon their migratory status and where they regularly breed: British residents, summer visitors to Britain, winter visitors to Britain, and vagrants from Europe or beyond Europe. For each species group on each island we calculated the average number of species visiting each year. We then regressed the average number of species against island area and distance to the mainland (all variables were log‐transformed). We also compared the average number of species visiting each island with the average number of species breeding on each island.Results Average number of visiting British residents decreased significantly with increasing island distance, but showed no relationship with island area. There was no significant relationship between island area or island distance and average number of summer or winter visitors. European and non‐European vagrants likewise showed no relationship between numbers of species visiting and island distance. However, the relationship between island area and number of visiting species was significant for both these categories; as island area increases so too does the number of visiting species.Main conclusions As predicted by IBT, there were fewer visiting species on more distant islands. There were substantially more visitors to each island than breeding species, supporting Lack’s argument that lower bird richness is not a result of varying immigration rates (as predicted by IBT) but rather a result of some other island property, e.g. fewer resources. Birds make a decision to either leave an island or stay and breed. The target effect was also clearly demonstrated by the increase in European and non‐European breeders with increasing island size.
Late Neogene history of the laurel tree (Laurus L., Lauraceae) based on phylogeographical analyses of Mediterranean and Macaronesian populations
Authors: Rodríguez‐Sánchez Francisco , Guzmán Beatriz , Valido Alfredo , Vargas Pablo , Arroyo Juan 
Published: March 2009

AbstractAim  The post‐glacial range dynamics of many European plant species have been widely investigated, but information rapidly diminishes as one moves further back in time. Here we infer the historical range shifts of Laurus, a paradigmatic tree of the Tethyan flora that has covered southern Eurasia since the Oligo‐Miocene, by means of phylogenetic and phylogeographical analyses.Location  Mediterranean Basin, Black Sea and Macaronesian archipelagos (Azores, Madeira, Canary Islands).Methods  We analysed plastid DNA (cpDNA) sequence (trnK–matK, trnD–trnT) variation in 57 populations of Laurus and three Lauraceae genera. Phylogenetic methods (maximum parsimony and Bayesian inference) and statistical parsimony networks were used to reconstruct relationships among haplotypes. These results were contrasted with the fossil record and bioclimatic niche‐based model predictions of past distributions to infer the migration routes and location of refugia.Results  The phylogenetic tree revealed monophyly for Laurus. Overall sequence variability was low within Laurus, but six different haplotypes were distinguished and a single network retrieved, portraying three lineages primarily related to geography. A strongly divergent eastern lineage occupied Turkey and the Near East, a second clade was located in the Aegean region and, lastly, a western clade grouped all Macaronesian and central and western Mediterranean populations. A close relationship was observed between the Macaronesian populations of L. azorica and the western populations of L. nobilis.Main conclusions  The phylogeographical structure of Laurus preserves the imprints of an ancient contraction and break‐up of the range that resulted in the evolution of separate cpDNA lineages in its western‐ and easternmost extremes. Intense range dynamics in the western Mediterranean and multiple glacial refugia contributed to the generation and long‐term conservation of this phylogeographical pattern, as shown by the fit between the haplotype ranges and past suitable areas inferred from bioclimatic models. Finally, our results challenge the taxonomic separation of Laurus into two distinct species.
Biogeography of Aphodiinae dung beetles based on the regional composition and distribution patterns of genera
Authors: Cabrero‐Sañudo Francisco J. , Lobo Jorge M. 
Published: March 2009

AbstractAim  To examine current biogeographical patterns of Aphodiinae dung beetles (Coleoptera: Scarabaeoidea: Scarabaeidae) in order to reveal relationships among regions and their potential impact on the diversification of this group.Location  Worldwide.Methods  Information about all Aphodiinae genera was obtained from the literature. An occurrence matrix was built for the six worldwide biogeographical regions, and their faunas were characterized through simple statistics. Regional variations and similarities were further explored using co‐occurrence and nestedness analyses, sequential agglomerative, hierarchical and nested clustering (SAHN), and a parsimony analysis of endemicity (PAE). Mantel tests were also employed to assess the relationships between several characteristics of the regions and their faunas.Results  The Palaearctic and Palaeotropical regions showed the highest total numbers of Aphodiinae genera and the greatest generic endemism. Both these regions and the Oriental also showed higher numbers of genera than would be expected according to their size. Co‐occurrence and nestedness analyses confirmed the non‐randomness of the distribution of genera. Clustering and PAE showed that the Palaearctic and Oriental regions are the most similar, followed by the Palaeotropical region. Regional dissimilarity in genera composition was related to biological and historical traits, but not to ecoregions.Main conclusions  A structured geographical pattern for Aphodiinae was confirmed. Land continuity and proximity in the long term could have played a unifying role in regional faunas. We suggest that the different biogeographical regions have acted as either macroevolutionary sources (basically the Palaearctic and the Palaeotropical regions) or sink regions, according to their role as diversification centres. We review the processes and events that could account for current patterns of Aphodiinae diversity.