bluuebunny/crossref_metadata_2025 huggingface dataset:
Final thermal conditions override the effects of temperature history and dispersal in experimental communities
Authors: Limberger Romana , Low-Décarie Etienne , Fussmann Gregor F.
Published: September 2014

Predicting the effect of climate change on biodiversity is a multifactorial problem that is complicated by potentially interactive effects with habitat properties and altered species interactions. In a microcosm experiment with communities of microalgae, we analysed whether the effect of rising temperature on diversity depended on the initial or the final temperature of the habitat, on the rate of change, on dispersal and on landscape heterogeneity. We also tested whether the response of species to temperature measured in monoculture allowed prediction of the composition of communities under rising temperature. We found that the final temperature of the habitat was the primary driver of diversity in our experimental communities. Species richness declined faster at higher temperatures. The negative effect of warming was not alleviated by a slower rate of warming or by dispersal among habitats and did not depend on the initial temperature. The response of evenness, however, did depend on the rate of change and on the initial temperature. Community composition was not predictable from monoculture assays, but higher fitness inequality (as seen by larger variance in growth rate among species in monoculture at higher temperatures) explained the faster loss of biodiversity with rising temperature.
Global distribution and drivers of language extinction risk
Authors: Amano Tatsuya , Sandel Brody , Eager Heidi , Bulteau Edouard , Svenning Jens-Christian , Dalsgaard Bo , Rahbek Carsten , Davies Richard G. , Sutherland William J.
Published: September 2014

Many of the world's languages face serious risk of extinction. Efforts to prevent this cultural loss are severely constrained by a poor understanding of the geographical patterns and drivers of extinction risk. We quantify the global distribution of language extinction risk—represented by small range and speaker population sizes and rapid declines in the number of speakers—and identify the underlying environmental and socioeconomic drivers. We show that both small range and speaker population sizes are associated with rapid declines in speaker numbers, causing 25% of existing languages to be threatened based on criteria used for species. Language range and population sizes are small in tropical and arctic regions, particularly in areas with high rainfall, high topographic heterogeneity and/or rapidly growing human populations. By contrast, recent speaker declines have mainly occurred at high latitudes and are strongly linked to high economic growth. Threatened languages are numerous in the tropics, the Himalayas and northwestern North America. These results indicate that small-population languages remaining in economically developed regions are seriously threatened by continued speaker declines. However, risks of future language losses are especially high in the tropics and in the Himalayas, as these regions harbour many small-population languages and are undergoing rapid economic growth.
Nocturnality in synapsids predates the origin of mammals by over 100 million years
Authors: Angielczyk K. D. , Schmitz L.
Published: September 2014

Nocturnality is widespread among extant mammals and often considered the ancestral behavioural pattern for all mammals. However, mammals are nested within a larger clade, Synapsida, and non-mammalian synapsids comprise a rich phylogenetic, morphological and ecological diversity. Even though non-mammalian synapsids potentially could elucidate the early evolution of diel activity patterns and enrich the understanding of synapsid palaeobiology, data on their diel activity are currently unavailable. Using scleral ring and orbit dimensions, we demonstrate that nocturnal activity was not an innovation unique to mammals but a character that appeared much earlier in synapsid history, possibly several times independently. The 24 Carboniferous to Jurassic non-mammalian synapsid species in our sample featured eye morphologies consistent with all major diel activity patterns, with examples of nocturnality as old as the Late Carboniferous (ca300 Ma). Carnivores such asSphenacodon feroxandDimetrodon milleri, but also the herbivorous cynodontTritylodon longaevuswere likely nocturnal, whereas most of the anomodont herbivores are reconstructed as diurnal. Recognizing the complexity of diel activity patterns in non-mammalian synapsids is an important step towards a more nuanced picture of the evolutionary history of behaviour in the synapsid clade.
BoCluSt: bootstrap clustering stability algorithm for community detection in networks
Authors: Garcia Carlos
Published: September 2014

Background

The identification of modules or communities of related variables is a key step in the analysis and modelling of biological systems. Many module identification procedures are available, but few of these can determine the module partitions best fitting a given dataset in the absence of previous information, in an unsupervised way, and when the links between variables have different weights. Here I propose such a procedure, which uses the stability under bootstrap resampling of different alternative module structures as a criterion to identify the structure best fitting to a set of variables. In its present implementation, the procedure uses linear correlations as link weights.

Results

Computer simulations show that the procedure is useful for problems involving moderate numbers of variables, such as those commonly found in gene regulation cascades or metabolic pathways, and also that it can detect hierarchical network structures, in which modules are composed of smaller sub modules. The procedure becomes less practical as the number of variables increases, due to increases in processing time.

Conclusions

The proposed procedure may be a valuable and robust network analysis tool. Because it is based on comparing the amount of evidence for different module partitions structures, this procedure may detect the existence of hierarchical network structures.
ProbAlign: a re-alignment method for long sequencing reads
Authors: Zeng Feng , Jiang Rui , Ji Guoli , Chen Ting
Published: September 2014

The incorrect alignments are a severe problem in variant calling, and remain as a challenge computational issue in Bioinformatics field. Although there have been some methods utilizing the re-alignment approach to tackle the misalignments, a standalone re-alignment tool for long sequencing reads is lacking. Hence, we present a standalone tool to correct the misalignments, called ProbAlign. It can be integrated into the pipelines of not only variant calling but also other genomic applications. We demonstrate the use of re-alignment in two diverse and important genomics fields: variant calling and viral quasispecies reconstruction. First, variant calling results in the Pacific Biosciences SMRT re-sequencing data of NA12878 show that false positives can be reduced by 43.5%, and true positives can be increased by 24.8% averagely, after re-alignment. Second, results in reconstructing a 5-virus-mix show that the viral population can be completely unraveled, and also the estimation of quasispecies frequencies has been improved, after re-alignment. ProbAlign is freely available in the PyroTools toolkit (https://github.com/homopolymer/PyroTools).
Linking signaling pathways to transcriptional programs in breast cancer
Authors: Osmanbeyoglu Hatice U. , Pelossof Raphael , Bromberg Jacqueline F. , Leslie Christina S.
Published: September 2014

Cancer cells acquire genetic and epigenetic alterations that often lead to dysregulation of oncogenic signal transduction pathways, which in turn alters downstream transcriptional programs. Numerous methods attempt to deduce aberrant signaling pathways in tumors from mRNA data alone, but these pathway analysis approaches remain qualitative and imprecise. In this study, we present a statistical method to link upstream signaling to downstream transcriptional response by exploiting reverse phase protein array (RPPA) and mRNA expression data in The Cancer Genome Atlas (TCGA) breast cancer project. Formally, we use an algorithm called affinity regression to learn an interaction matrix between upstream signal transduction proteins and downstream transcription factors (TFs) that explains target gene expression. The trained model can then predict the TF activity, given a tumor sample’s protein expression profile, or infer the signaling protein activity, given a tumor sample’s gene expression profile. Breast cancers are comprised of molecularly distinct subtypes that respond differently to pathway-targeted therapies. We trained our model on the TCGA breast cancer data set and identified subtype-specific and common TF regulators of gene expression. We then used the trained tumor model to predict signaling protein activity in a panel of breast cancer cell lines for which gene expression and drug response data was available. Correlations between inferred protein activities and drug responses in breast cancer cell lines grouped several drugs that are clinically used in combination. Finally, inferred protein activity predicted the clinical outcome within the METABRIC Luminal A cohort, identifying high- and low-risk patient groups within this heterogeneous subtype.
High-resolution synchrotron diffraction study of porous buffer InP(001) layers
Authors: Lomov Andrey A. , Punegov Vasily I. , Nohavica Dusan , Chuev Mikhail A. , Vasiliev Alexander L. , Novikov Dmitrii V.
Published: September 2014

X-ray reciprocal space mapping was used for quantitative investigation of porous layers in indium phosphide. A new theoretical model in the frame of the statistical dynamical theory for cylindrical pores was developed and applied for numerical data evaluation. The analysis of reciprocal space maps provided comprehensive information on a wide range of the porous layer parameters, for example, layer thickness and porosity, orientation, and correlation length of segmented pore structures. The results are in a good agreement with scanning electron microscopy data.
SynchLink: an iOS app for ISPyB
Authors: Ginn Helen Mary , Mostefaoui Ghita Kouadri , Levik Karl Erik , Grimes Jonathan Mark , Walsh Martin Austin , Ashton Alun William , Stuart David Ian
Published: September 2014

The macromolecular crystallography (MX) user experience at synchrotron radiation facilities continues to evolve, with the impact of developments in X-ray detectors, computer hardware and automation methods making it possible for complete data sets to be collected on timescales of tens of seconds. Data can be reduced in a couple of minutes and in favourable cases structures solved and refined shortly after. The information-rich database ISPyB, automatically populated by data acquisition software, data processing and structure solution pipelines at the Diamond Light Source beamlines, allows users to automatically track MX experiments in real time. In order to improve the synchrotron users' experience, efficient access to the data contained in ISPyB is now providedviaan iOS 6.0+ app for iPhones and iPads. This provides users, both local and remote, with a succinct summary of data collection, visualization of diffraction images and crystals, and key metrics for data quality in real time.
Scleroderma renal crisis following pericardial effusion in a Japanese female
Authors: Shu En , Kanoh Hiroyuki , Seishima Mariko
Published: September 2014

Scleroderma renal crisis (SRC) occurs in 4–5% of Japanese patients with systemic sclerosis (SSc) and is one of the most severe complications, along with interstitial pneumonia and pulmonary hypertension, which lead to a poor outcome. The factors predicting SRC include diffuse progressive skin thickening, a duration of SSc of 4 years or less, having autoantibodies against RNA polymerase III, systemic corticosteroid (CS) administration and recent cardiac events, including pericarditis. We herein report a female case of SRC preceded by pericardial effusion during the treatment with CS for rapidly progressive skin thickening. She had none of the known autoantibodies and was successfully treated with an angiotensin II receptor blocker.
The Effect of Light Exposure on the Degradation of Latent Fingerprints on Brass Surfaces: The Use of Silver Electroless Deposition as a Visualization Technique
Authors: Payne Imogen C. , McCarthy Imogen , Almond Matthew J. , Baum John V. , Bond John W.
Published: September 2014

We have studied the degradation of sebaceous fingerprints on brass surfaces using silver electroless deposition (SED) as a visualization technique. We have stored fingerprints on brass squares either (i) in a locked dark cupboard or (ii) in glass‐filtered natural daylight for periods of 3 h, 24 h, 1 week, 3 weeks, and 6 weeks. We find that fingerprints on brass surfaces degrade much more rapidly when kept in the light than they do under dark conditions with a much higher proportion of high‐quality prints found after 3 or 6 weeks of aging when stored in the dark. This process is more marked than for similar fingerprints on black PVC surfaces. Identifiable prints can be achieved on brass surfaces using both SED and cyanoacrylate fuming (CFM). SED is quick and straightforward to perform. CFM is more time‐consuming but is versatile and can be applied to a wider range of metal surfaces than SED, for example brass surfaces which have been coated by a lacquer.
Soybean aphid intrabiotype variability based on colonization of specific soybean genotypes
Authors: Pawlowski Michelle , Hill Curtis B. , Voegtlin David J. , Hartman Glen L.
Published: September 2014

The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), is one of the most destructive insect pests on soybeans in the United States. One method for managing this pest is through host plant resistance. Since its arrival in 2000, 4 aphid biotypes have been identified that are able to overcome soybean aphid resistance (Rag) genes. A soybean aphid isolate collected from Moline, Illinois readily colonized soybean plants with the soybean aphid resistance gene Rag2, unlike biotypes 1 and 2, but similar to soybean aphid biotype 3. Two no‐choice experiments compared the virulence of the Moline isolate with biotype 3. In both experiments, differences in aphid population counts were not significant (P > 0.05) on soybean genotypes LD08–12957a (Rag2) and LD11–5413a (Rag2), but the aphid counts for the Moline isolate were significantly (P < 0.05) lower than the aphid counts for the biotype 3 isolate on the soybean genotypes Dowling (Rag1), LD05–16611 (Rag1), LD11–4576a (Rag1), and PI 567598B (rag1b and rag3). The Moline isolate was a variant of aphid biotype 3, which is the first report showing that soybean aphid isolates classified as the same biotype, based on virulence against specific Rag genes, can differ in aggressiveness or ability to colonize specific host genotypes.
Fly‐In/Fly‐Out, Flexibility and the Future: Does Becoming a Regional FIFO Source Community Present Opportunity or Burden?
Authors: MCKENZIE FIONA , HASLAM MCKENZIE FIONA , HOATH AILEEN
Published: September 2014

The resources boom in Australia has resulted in considerable competition for labour, particularly in remote mining areas. Shortage of skilled labour has led mining companies to source workers from far afield, while the high incomes created by a tight labour market draw labour from across the country through long‐distance commuting arrangements such as fly‐in/fly‐out (FIFO). While much recent literature has focused on the impacts on receiving communities of these long‐distance commuters, less attention has been given to the experience of source communities. This paper compares the situation between two regional towns in which long‐distance commuters reside. The first, Busselton in Western Australia, is among several chosen by Rio Tinto to be labour source communities. The second, Stawell in Victoria, is looking to long‐distance commuting as a response to the impending closure of their existing gold mine. Hence the case studies offer not only insights into source communities' experience of long‐distance commuting, but also a comparison between the bottom‐up approach of Stawell in trying to establish FIFO with the experience of Busselton as an example of top‐down labour sourcing. This paper seeks to highlight some of the development challenges encountered by communities and offer solutions as to how these might be addressed for the future.
Large‐scale spatial analysis of ringing and re‐encounter data to infer movement patterns: A review including methodological perspectives
Authors: Thorup Kasper , Korner‐Nievergelt Fränzi , Cohen Emily B. , Baillie Stephen R.
Published: September 2014

A major aim of bird ringing is to provide information about the migration and movements of bird populations. However, in comparison with demographic studies, little research has been devoted to improving quantitative inferences through large‐scale spatial analyses. This represents a serious knowledge gap because robust information on geographical linkages of migratory populations throughout the annual cycle is necessary to understand the ecology and evolution of migrants and for the conservation and management of populations.

Here, we review recent developments and emerging opportunities for the quantitative study of movements of bird populations based on marked birds. Large‐scale spatial analyses of ringing data need to account for spatiotemporal variation in re‐encounter probability and the complexity of movement processes, including variability among individuals and populations in migration direction and distance.

We identify seven recent studies that used quantitative methods for large‐scale spatial analyses of ringing and re‐encounter data gathered by national ringing centres. In most cases, numbers ringed and recovered in a series of source and destination areas were used to derive estimates of the proportion of each source population travelling to each destination area. Where recovery data were sparse, precision was improved by incorporating information on re‐encounter probabilities of similar species. When numbers ringed were not available, inferences could sometimes be drawn based on local recapture data from the source areas.

Studies to date illustrate that analyses of these large‐scale ringing data sets can provide robust quantitative inferences. Further work is needed to develop these modelling approaches and to test their sensitivity to key assumptions using both real and simulated data. Data for all birds that were marked, not only those re‐encountered, are often inaccessible and should be computerised in parallel with analytical developments. Further, there is great potential for the formal combination of re‐encounter data with information from additional data sources such as counts and detailed movement data from radiotracking or data loggers. Because data from bird ringing operations cover long periods of time and exist in large quantities, they hold great promise for inferring spatiotemporal migration patterns, including changes in relation to climate, land use change and other environmental drivers.
Damage functions and thermal requirements of Meloidogyne javanica and Meloidogyne incognita on watermelon
Authors: López‐Gómez M. , Gine A. , Vela M.D. , Ornat C. , Sorribas F.J. , Talavera M. , Verdejo‐Lucas S.
Published: September 2014

The relationship between the initial (Pi) and final (Pf) population densities of Meloidogyne javanica and yield of watermelon, Citrullus lanatus, cv. Sugar Baby were determined in pot and field experiments. In the pots, the maximum reproduction rate of the nematode was 14, and the equilibrium density was 49 400 eggs/100 cm3 of soil. Yield data represented as fresh top weight fitted the Seinhorst damage function (P < 0.001, R2 = 0.7), and the minimum relative yield (m) was 0.65 at Pi ≥ 3200 eggs/100 cm3 of soil and the tolerance limit (T) 74 eggs/100 cm3. In the field experiments (2011 and 2012), the maximum reproduction rate was 73 and 70, and the equilibrium density 32 and 35 second‐stage juveniles (J2)/100 cm3 soil. Yield data represented as fruit weight fitted the Seinhorst damage function in 2011 (P < 0.001, R2 = 0.92) and the m‐ and T‐values were 0.63 and 20 J2/100 cm3 of soil, respectively. Meloidogyne incognita and M. javanica needed similar length of time for development to egg‐laying females and life cycle completion at 24.4°C.
High‐dose rocuronium for rapid‐sequence induction and reversal with sugammadex in two myasthenic patients
Authors: CASAROTTI P. , MENDOLA C. , CAMMAROTA G. , DELLA CORTE F.
Published: September 2014

The anesthetic management of patients affected by myasthenia gravis is usually challenging in elective surgery and even more so in emergency procedures. The difficulties involved are several‐fold, ranging from the choice of an appropriate muscle relaxant (i.e. one that enables safe and rapid airway management) to neuromuscular monitoring and normal muscular recovery. Additionally, optimizing patient conditions – either pharmacologically or with plasmapheresis – before intervention is well beyond the realm of possibility. We discuss the anesthetic management of two myasthenic patients undergoing emergency surgery (for sigmoid perforation and upper gastrointestinal bleeding respectively). In both cases, we opted for rapid‐sequence induction with high‐dose rocuronium to prevent inhalation of gastric contents. We also report on the implication of neuromuscular monitoring. We found that the rocuronium–sugammadex combination was a useful and effective option in the emergency setting.
Molecular basis of reduced birth weight in smoking pregnant women: mitochondrial dysfunction and apoptosis
Authors: Garrabou Glòria , Hernàndez Ana‐Sandra , Catalán García Marc , Morén Constanza , Tobías Ester , Córdoba Sarai , López Marta , Figueras Francesc , Grau Josep M. , Cardellach Francesc
Published: September 2014

In utero exposure of fetuses to tobacco is associated with reduced birth weight. We hypothesized that this may be due to the toxic effect of carbon monoxide (CO) from tobacco, which has previously been described to damage mitochondria in non‐pregnant adult smokers. Maternal peripheral blood mononuclear cells (PBMCs), newborn cord blood mononuclear cells (CBMCs) and placenta were collected from 30 smoking pregnant women and their newborns and classified as moderate and severe smoking groups, and compared to a cohort of 21 non‐smoking controls. A biomarker for tobacco consumption (cotinine) was assessed by ELISA (enzyme‐linked immunosorbent assay). The following parameters were measured in all tissues: mitochondrial chain complex IV [cytochrome c oxidase (COX)] activity by spectrophotometry, mitochondrial DNA levels by reverse transcription polymerase chain reaction, oxidative stress by spectrophotometric lipid peroxide quantification, mitochondrial mass through citrate synthase spectrophotometric activity and apoptosis by Western blot parallelly confirmed by TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labelling) assay in placenta. Newborns from smoking pregnant women presented reduced birth weight by 10.75 percent. Materno‐fetal mitochondrial and apoptotic PBMC and CBMC parameters showed altered and correlated values regarding COX activity, mitochondrial DNA, oxidative stress and apoptosis. Placenta partially compensated this dysfunction by increasing mitochondrial number; even so ratios of oxidative stress and apoptosis were increased. A CO‐induced mitotoxic and apoptotic fingerprint is present in smoking pregnant women and their newborn, with a lack of filtering effect from the placenta. Tobacco consumption correlated with a reduction in birth weight and mitochondrial and apoptotic impairment, suggesting that both could be the cause of the reduced birth weight in smoking pregnant women.
Decomposition and nutrient release patterns of mistletoe litters in a semi‐arid savanna, southwest Zimbabwe
Authors: Ndagurwa Hilton G. T. , Dube John S. , Mlambo Donald
Published: September 2014

Nutrient loss from litter plays an essential role in carbon and nutrient cycling in nutrient‐constrained environments. However, the decomposition and nutrient dynamics of nutrient‐rich mistletoe litter remains unknown in semi‐arid savanna where productivity is nutrient limited. We studied the decomposition and nutrient dynamics (nitrogen: N, phosphorous; P, carbon: C) of litter of three mistletoe species, Erianthemum ngamicum, Plicosepalus kalachariensis, and Viscum verrucosum and N‐fixing Acacia karroo using the litter‐bag method in a semi‐arid savanna, southwest Zimbabwe. The temporal dynamics of the soil moisture content, microbial populations, and termite activity during decomposition were also assessed. Decay rates were slower for A. karroo litter (k = 0.63), but faster for the high quality mistletoe litters (mean k‐value = 0.79), which supports the premise that mistletoes can substantially influence nutrient availability to other plants. Nitrogen loss was between 1.3 and 3 times greater in E. ngamicum litter than in the other species. The litter of the mistletoes also lost C and P faster than A. karroo litter. However, soil moisture content and bacterial and fungal colony numbers changed in an opposite direction to changes in the decomposition rate. Additionally, there was little evidence of termite activity during the decay of all the species litters. This suggests that other factors such as photodegradation could be important in litter decomposition in semi‐arid savanna. In conclusion, the higher rate of decay and nutrient release of mistletoe than A. karroo litter indicate that mistletoes play an important role in carbon and nutrient fluxes in semi‐arid savanna.
A genome‐wide scan for selection signatures in Nellore cattle
Authors: Somavilla A. L. , Sonstegard T. S. , Higa R. H. , Rosa A. N. , Siqueira F. , Silva L. O. C. , Torres Júnior R. A. A. , Coutinho L. L. , Mudadu M. A. , Alencar M. M. , Regitano L. C. A.
Published: September 2014

Brazilian Nellore cattle (Bos indicus) have been selected for growth traits for over more than four decades. In recent years, reproductive and meat quality traits have become more important because of increasing consumption, exports and consumer demand. The identification of genome regions altered by artificial selection can potentially permit a better understanding of the biology of specific phenotypes that are useful for the development of tools designed to increase selection efficiency. Therefore, the aims of this study were to detect evidence of recent selection signatures in Nellore cattle using extended haplotype homozygosity methodology and BovineHD marker genotypes (>777 000 single nucleotide polymorphisms) as well as to identify corresponding genes underlying these signals. Thirty‐one significant regions (P < 0.0001) of possible recent selection signatures were detected, and 19 of these overlapped quantitative trait loci related to reproductive traits, growth, feed efficiency, meat quality, fatty acid profiles and immunity. In addition, 545 genes were identified in regions harboring selection signatures. Within this group, 58 genes were associated with growth, muscle and adipose tissue metabolism, reproductive traits or the immune system. Using relative extended haplotype homozygosity to analyze high‐density single nucleotide polymorphism marker data allowed for the identification of regions potentially under artificial selection pressure in the Nellore genome, which might be used to better understand autozygosity and the effects of selection on the Nellore genome.
A Practical Technique for Electron Microscopy of Buffy Coats in Dogs and Cats
Authors: Yabuki A. , Sawa M. , Chang H.‐S. , Yamato O.
Published: September 2014

Plastic hematocrit tubes (PHTs) are convenient tools for electron microscopy (EM) of peripheral blood buffy coats, and the PHT‐EM technique is expected to be a practical method for veterinary clinical medicine. In this study, fixatives composed of various concentrations of sucrose, glutaraldehyde, and phosphate buffer (PB) were tested for preparing canine and feline buffy coats. The highest quality images were obtained using a fixative consisting of 2.5% glutaraldehyde in 0.1 m PB, and it was concluded that this method allows clinicians who are inexperienced in histological techniques can conveniently transport buffy coat samples to diagnostic laboratories for analysis by EM.
Incidence of microcystin‐producing cyanobacteria in Lake Tana, the largest waterbody in Ethiopia
Authors: Mankiewicz‐Boczek Joanna , Gągała Ilona , Jurczak Tomasz , Urbaniak Magdalena , Negussie Yohannes Zerihun , Zalewski Maciej
Published: September 2014

The occurrence of toxic cyanobacterial blooms is a serious problem for fast‐developing countries in Africa, such as Ethiopia, that are struggling with significant degradation of the natural environment and limited access to water of good quality. Research undertaken on Lake Tana in Ethiopia between 2009 and 2011 was intended to assess the seasonal threat from cyanobacteria and to select methods for tracking of this threat in the future. The cyanobacterial genus Microcystis was found to be present throughout the monitoring period, and M. aeruginosa was determined as the dominant species. Moreover, in all samples, toxigenic cyanobacteria with the potential to produce microcystins were detected. High levels of microcystins, ranging from 0.58 to 2.65 μg L−1, were detected each November, which indicates that in the postrainy season, water usage should be limited. The correlation between concentrations of chlorophyll‐a and microcystins suggested that chlorophyll‐a could be used as an indicator of the potential presence of cyanobacterial‐derived hepatotoxins in Lake Tana in the future. Furthermore, for quick quantitative confirmation of the presence of microcystins, a simple and rapid ELISA test was recommended.
Surgical decision making in a teaching hospital: a linguistic analysis
Authors: Bezemer Jeff , Murtagh Ged , Cope Alexandra , Kneebone Roger
Published: September 2014

Background

The aim of the study was to gain insight in the involvement of non‐operating surgeons in intraoperative surgical decision making at a teaching hospital. The decision to proceed to clip and cut the cystic duct during laparoscopic cholecystectomy was investigated through direct observation of team work.

Method

Eleven laparoscopic cholecystectomies performed by consultant surgeons and specialty trainees at a London teaching hospital were audio and video recorded. Talk among the surgical team was transcribed and subjected to linguistic analysis, in conjunction with observational analysis of the video material, sequentially marking the unfolding operation.

Results

Two components of decision making were identified, participation and rationalization. Participation refers to the degree to which agreement was sought within the surgical team prior to clipping the cystic duct. Rationalization refers to the degree to which the evidential grounds for clipping and cutting were verbalized.

Conclusion

The decision to clip and cut the cystic duct was jointly made by members of the surgical team, rather than a solitary surgeon in the majority of cases, involving verbal explication of clinical reasoning and verbal agreement. The extent of joint decision making appears to have been mitigated by two factors: trainee's level of training and duration of the case.
Effect of VRTN gene polymorphisms on Duroc pig production and carcass traits, and their genetic relationships
Authors: Nakano Hikaru , Sato Shuji , Uemoto Yoshinobu , Kikuchi Takashi , Shibata Tomoya , Kadowaki Hiroshi , Kobayashi Eiji , Suzuki Keiichi
Published: September 2014

The thoracic vertebral number is associated with body length and carcass traits, and represents one of the most important traits in the pig industry. Recent studies have shown that vertnin (VRTN) gene is associated with variations in the vertebral number in commercial European pigs. However, the genetic relationships and effect of this VRTN gene in pig production and carcass traits remain uncertain. Therefore, we investigated the genetic relationships among traits such as vertebral numbers, carcass weight and length‐related traits, and meat production traits, and the effect of VRTN gene polymorphisms on these traits in a Duroc purebred population selected for its meat production traits. Highly positive genetic correlations were obtained between the thoracic vertebral numbers and length‐related traits (0.56 to 0.84), whereas low correlations were obtained with production traits and carcass weight (−0.16 to 0.05). VRTN gene polymorphisms indicated that the number of thoracic vertebrae and length‐related traits were significantly associated with the VRTN genotype, but had no significant effect on production traits and carcass weight. The results indicate that VRTN gene may be used as an effective selection marker to obtain pigs with high thoracic vertebral numbers and length‐related traits, without adversely affecting meat production traits.
Genotype, production system and sex effects on fatty acid composition of meat from goat kids
Authors: Özcan Mustafa , Demirel Gulcan , Yakan Akın , Ekiz Bülent , Tölü Cemil , Savaş Türker
Published: September 2014

Two trials were performed to assess the meat fatty acid profile of goat kids from different genotypes, production systems and sex. In the first trial, genotype effect was determined in 24 suckling male kids from Turkish Saanen, Maltese and Gokceada breeds. In the second trial, male and female Gokceada Goat kids were used to compare the effect of extensive and semi‐intensive production systems on fatty acid composition of meat. Significant genotype effect was observed in the percentages of myristic acid (C14:0), palmitic acid (C16:0), oleic acid (C18:1 n‐9), linolenic acid (C18:3 n‐3), arachidonic acid (C20:4 n‐6) and docosahexaenoic acid (C22:6 n‐3), despite no differences on the ratios of polyunsaturated fatty acids to saturated fatty acids (PUFA/SFA) and n‐6/n‐3 (P > 0.05). The effect of production system had also significant effects on fatty acids, but sex only influenced significantly stearic acid (C18:0), C18:1 n‐9 and C18:3 n‐3 fatty acids and total PUFA level and PUFA/SFA ratio. This study confirms that dairy breeds are prone to produce higher levels of unsaturated fatty acids in their muscle. Meanwhile, meat from Gokceada goat kids, which is one of the indigenous breeds in Turkey, had similar PUFA/SFA and n‐6/n‐3 ratios to Turkish Saanen and Maltase.
Sex and age differences in meat composition of Yeso sika deer (Cervus nippon yesoensis) reared for a short period after capture in the wild
Authors: Hayashida Maki , Souma Kousaku , Sugo Kazuki , Araki Shin‐ichi , Ishizaka Fumiaki , Ueda Masami , Kasai Takamasa , Masuko Takayoshi
Published: September 2014

Yeso sika deer captured in winter around Lake Akan in Hokkaido were reared for 8–10 months at Tokyo University of Agriculture in Abashiri. Six 1‐year‐old females and males and six 2‐year‐old or older (adult) females and males were slaughtered and their carcasses were processed. The chemical composition, mineral contents and fatty acid composition of the loin were measured. No marked influence of gender or age was noted in the chemical composition of loin. In the mineral contents, significant differences were noted. The potassium and sulfur contents were lower and the sodium content was higher in adult deer meat (P < 0.05, respectively) and the potassium content was higher in male deer meat (P < 0.05). Arsenic, cadmium or lead were not detected. In the unsaturated fatty acid, a significant interaction was detected (P < 0.05), and it was high in 1‐year‐old female deer meat and low in 1‐year‐old male deer meat. Significant gender or age differences were noted only in the mineral contents in the loin of deer reared for a short period after capture.
Preventing Ultimate Harm as the Justification for Biomoral Modification
Authors: Murphy Timothy F.
Published: September 2014

Most advocates of biogenetic modification hope to amplify existing human traits in humans in order to increase the value of such traits as intelligence and resistance to disease. These advocates defend such enhancements as beneficial for the affected parties. By contrast, some commentators recommend certain biogenetic modifications to serve social goals. As Ingmar Persson and Julian Savulescu see things, human moral psychology is deficient relative to the most important risks facing humanity as a whole, including the prospect of Ultimate Harm, the point at which worthwhile life is forever impossible on the planet. These risks can be mitigated, they say, by enhancing moral psychology in novel ways. Persson and Savulescu argue that some parents should modify the underlying biogenetics of their children's moral psychology, if such measures were safe and effective, but they admit these interventions may not decouple humanity from Ultimate Harm. Neither are these modifications the only options, they concede, for addressing risks to humanity. Even with these concessions, saving humanity from itself is a fairly poor reason to modify the moral psychology of children. In most ways, adults would be better candidates, morally speaking, for modifications of psychology. Even then, there is no direct link between morally enhanced human beings and the hoped‐for effect of better protection from Ultimate Harm. Asserting a general duty of all to contribute to the avoidance of Ultimate Harm is a better moral strategy than intervening in the moral psychology of some, even though meeting that duty may involve substantial interference with the free exercise of one's interests.
Patient Report of Guideline‐Congruent Gestational Weight Gain Advice From Prenatal Care Providers: Differences by Prepregnancy BMI
Authors: Waring Molly E. , Moore Simas Tiffany A. , Barnes Katharine C. , Terk Daniel , Baran Inna , Pagoto Sherry L. , Rosal Milagros C.
Published: September 2014

Background

Prenatal care provider weight gain advice consistent with the Institute of Medicine recommendations is related to guideline‐adherent gestational weight gain (GWG), yet many women may not receive guideline‐congruent advice. We examined pregnant women's recall of prenatal care provider GWG advice in relation to prepregnancy body mass index (BMI).

Methods

We conducted a prospective cohort study of women (n = 149) receiving prenatal care for a singleton pregnancy at a large academic medical center in 2010. Data were collected via a survey during late pregnancy and medical record abstraction.

Results

Thirty‐three percent of women did not recall receiving the provider GWG advice; 33 percent recalled advice consistent with 2009 Institute of Medicine recommendations. Recalled advice differed by prepregnancy BMI; 29 percent of normal weight, 26 percent of overweight, and 45 percent of obese women reported not receiving advice, and 6, 37, and 39 percent, respectively, recalled advice exceeding Institute of Medicine recommendations. Among the 62 percent who recalled that their provider had labeled their prepregnancy BMI, 100 percent of normal weight, 32 percent of overweight, and 23 percent of obese women recalled the labels “normal weight,” “overweight,” and “obese,” respectively.

Conclusions

Helping providers give their patients memorable and guideline‐consistent GWG advice is an actionable step toward preventing excessive GWG and associated maternal and child health consequences.
The Effect of Market Orientation on Learning, Innovativeness, and Performance in Primary Agriculture
Authors: Micheels Eric T. , Gow Hamish R.
Published: September 2014

Market awareness and innovativeness are important resources in any business environment. As customer needs and competitor responses change, performance may depend on the ability for firms to recognize and react to market shifts. Using survey data from beef farmers in Illinois, we examine the role market orientation, organizational learning, and innovativeness play on satisfaction with performance. We use a structural equation model to find that market‐oriented and innovative firms are more satisfied with their performance while controlling for structural and demographic variables. Results also show that while market‐oriented firms are more innovative, human capital resources moderate the ability to exploit innovations. We also find that an increase in experience correlates with less organizational learning.
Policy or Markets? An Analysis of Price Incentives and Disincentives for Rice and Cotton in Selected African Countries
Authors: Short Cameron , Barreiro‐Hurle Jesús , Balié Jean
Published: September 2014

African governments have intervened extensively in markets through regulations and other price, trade, or marketing policies to provide price incentives to farmers. Using data from the Monitoring and Analyzing Food and Agricultural Policies program, this paper reports nominal rates of protection (NRPs) for rice and cotton at wholesale and farm level in selected African countries between 2005 and 2010. Rice is an import that has received high levels of border protection by the governments concerned while cotton is a key export crop which has been the focus of direct and indirect public intervention. For both commodities, we provide evidence for both market and nonmarket failures. In the case of rice, these prevent border protection from reaching farmers while raising consumer prices. Cotton ginning and marketing is concentrated in a small number of private sector companies in most countries studied. The farm level NRPs provide evidence of market failure in these countries that may be mitigated by policies that set indicative prices and encourage competition. The NRPs indicate nonmarket failure in the two countries that maintain parastatal monopsonies for cotton.
A fungal perspective on conservation biology
Authors: Heilmann‐Clausen Jacob , Barron Elizabeth S. , Boddy Lynne , Dahlberg Anders , Griffith Gareth W. , Nordén Jenni , Ovaskainen Otso , Perini Claudia , Senn‐Irlet Beatrice , Halme Panu
Published: September 2014

Hitherto fungi have rarely been considered in conservation biology, but this is changing as the field moves from addressing single species issues to an integrative ecosystem‐based approach. The current emphasis on biodiversity as a provider of ecosystem services throws the spotlight on the vast diversity of fungi, their crucial roles in terrestrial ecosystems, and the benefits of considering fungi in concert with animals and plants. We reviewed the role of fungi in ecosystems and composed an overview of the current state of conservation of fungi. There are 5 areas in which fungi can be readily integrated into conservation: as providers of habitats and processes important for other organisms; as indicators of desired or undesired trends in ecosystem functioning; as indicators of habitats of conservation value; as providers of powerful links between human societies and the natural world because of their value as food, medicine, and biotechnological tools; and as sources of novel tools and approaches for conservation of megadiverse organism groups. We hope conservation professionals will value the potential of fungi, engage mycologists in their work, and appreciate the crucial role of fungi in nature.

Una Perspectiva Micótica de la Biología de la Conservación
Histological insights into the pathogenesis of post‐Roux‐en‐Y hyperinsulinaemic hypoglycaemia
Authors: Lash R. W. , Giordano T. J. , Moraitis A. G. , Hodish I.
Published: September 2014

Background

β‐cell hyperplasia has been implicated in the aetiology of post Roux‐en‐Y gastric bypass hyperinsulinaemic hypoglycaemia, but the pathogenesis of this condition is still unclear.

Case report

We report a case of a 52‐year‐old man with post‐Roux‐en‐Y gastric bypass hyperinsulinaemic hypoglycaemia who underwent distal pancreatectomy to alleviate his symptoms. Pancreatic histopathology showed chronic pancreatitis with a corresponding loss of exocrine tissue and islet retention. Amyloid deposition was found in pancreatic islets. These features are more typically associated with Type 2 diabetes.

Discussion

This case highlights the potential multifactorial pathogenesis of symptomatic hypoglycaemia after Roux‐en‐Y gastric bypass.
Estimated insulin sensitivity predicts regression of albuminuria in Type 1 diabetes
Authors: Bjornstad P. , Maahs D. M. , Johnson R. J. , Rewers M. , Snell‐Bergeon J. K.
Published: September 2014

Aim

To test the hypothesis that greater baseline insulin sensitivity would predict regression of albuminuria over 6 years in adults with Type 1 diabetes.

Method

We enrolled 81 people aged 30–48 years with albuminuria at baseline in the present study and re‐examined them 6 years later. Urinary albumin excretion rate was measured and albuminuria was defined as urinary albumin excretion rate ≥ 20 μg/min. Regression of albuminuria was defined as normoalbuminuria (urinary albumin excretion rate  < 20 μg/min) at follow‐up. Predictors of regression of albuminuria were examined in stepwise logistic regression. The variables age, diabetes duration, sex, serum uric acid, HbA1c, systolic blood pressure, LDL cholesterol, HDL cholesterol, BMI, baseline albumin excretion rate, estimated insulin sensitivity at baseline, change in estimated insulin sensitivity from baseline to follow‐up and angiotensin‐converting enzyme inhibitor/angiotensin receptor blocker use were considered for inclusion in the model.

Results

Estimated insulin sensitivity was significantly higher at both baseline (4.6 ± 1.2 vs 3.4 ± 1.7; P = 0.002) and follow‐up (5.2 ± 1.9 vs. 3.5 ± 1.7; P < 0.0001) in people who had regression of albuminuria vs those who did not. HbA1c (odds ratio 0.4, 95% CI 0.2–0.8; P = 0.006), estimated insulin sensitivity (odds ratio 2.5, 95% CI 1.3–4.9; P = 0.006) at baseline and change in estimated insulin sensitivity from baseline to follow‐up (odds ratio 2.7, 95% CI 1.4–5.3; P = 0.003) were independently associated with regression of albuminuria in a multivariable stepwise model.

Conclusions

In conclusion, over 6 years, higher baseline estimated insulin sensitivity and change in estimated insulin sensitivity independently predicted regression of albuminuria. Improving insulin sensitivity in people with Type 1 diabetes is a potential therapeutic target to increase rates of regression of albuminuria.
Disparities in diabetes prevalence and preventable hospitalizations in people with intellectual and developmental disability: a population‐based study
Authors: Balogh R. S. , Lake J. K. , Lin E. , Wilton A. , Lunsky Y.
Published: September 2014

Aims

To describe and compare population‐level aspects of diabetes and diabetes primary care among people with and without intellectual and developmental disabilities.

Methods

Administrative health data accessed from the Institute for Clinical Evaluative Sciences was used to identify a cohort of Ontarians with and without intellectual and developmental disabilities between the ages of 30 and 69 years (n = 28 567). These people were compared with a random sample of people without intellectual and developmental disabilities (n = 2 261 919) according to diabetes prevalence, incidence, age, sex, rurality, neighbourhood income and morbidity. To measure diabetes primary care, we also studied hospitalizations for diabetes‐related ambulatory care‐sensitive conditions.

Results

Adults with intellectual and developmental disabilities had a consistently higher prevalence and incidence of diabetes than those without intellectual and developmental disabilities. Disparities in prevalence between those with and without intellectual and developmental disabilities were most notable among women, younger adults and those residing in rural or high income neighbourhoods. In terms of hospitalizations for diabetes‐related ambulatory care‐sensitive conditions, people with intellectual and developmental disabilities were 2.6 times more likely to be hospitalized.

Conclusions

Adults with intellectual and developmental disabilities are at high risk of developing and being hospitalized for diabetes. The findings of the present study have a number of important implications related to the early detection, prevention and proper management of diabetes among adults with intellectual and developmental disabilities.