bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stress and immunity in the pig.
Authors: Kick A. R. , Tompkins M. B. , Almond G. W. 
Published: August 2014

Abstract
One potential indication of decreased welfare in pigs is a greater prevalence of disease as a result of compromised immunity in 'stressed' animals. Various studies have endeavoured to assess the effects of stress on pigs. Stressors included social interactions from crowding or mixing pigs, ambient temperature variations, restraint, transportation, food deprivation, weaning and photoperiod manipulation. Typically, serum cortisol concentrations are used to quantify or confirm whether the animals were stressed; however, several methods were used to examine the influence of stress on immune function. The results of these studies varied in documenting whether the animals were stressed, what the general effects were on the porcine immune system and, in particular, which cells of the adaptive or innate immune systems were affected. This review is intended to provide an overview of previous methods of creating stressful conditions for pigs, techniques to assess immune function and finally, the interactions between stress and measurements of immune function in pigs. Emphasis is laid on the influence of stress on adaptive immunity.
Regulation of feed efficiency in dairy cattle.
Authors: Spurlock D. M. , VandeHaar M. 
Published: August 2014

Abstract
The efficiency with which dairy cows convert feed to milk impacts farm profitability and environmental stewardship. Thus, feed efficiency is a particularly critical trait to the dairy industry as feed costs increase. Feed efficiency is a complex trait influenced by many components, including milk output, nutrient intake, body weight and body weight change. Recent studies show that feed efficiency is low to moderately heritable, indicating it should respond to genetic selection. Progress is being made towards understanding the genetic regulation of feed efficiency, estimation of genomic breeding values and incorporation of feed efficiency into multi-trait selection programmes. However, underlying biological processes that contribute to variation in feed efficiency are poorly understood, particularly in lactating dairy cattle. Selection experiments in beef cattle, pigs, chickens and mice demonstrate that feed efficiency can be altered by selection. Heat production, activity or feeding behaviour, digestibility, muscle turnover and mitochondrial function are associated with variation in feed efficiency in many of these selection lines, but data from lactating dairy cows are currently lacking. A more detailed understanding of underlying biological processes and their relative importance to variation in feed efficiency is crucial for the development of novel strategies to further improve feed efficiency in dairy cattle. The objective of this review is to summarize our current understanding of the genetic and biological regulation of feed efficiency in lactating dairy cows. Insights from the evaluation of feed efficiency in beef cattle and other species are also considered.
Neosporosis in dogs.
Authors: Dubey J. P. 
Published: August 2014

Abstract

Neospora caninum
is a protozoan parasite of animals. Until 1988, it was misdiagnosed as
Toxoplasma gondii
. Since its first recognition in 1984 and the description of a new genus and species
N. caninum
in 1988, neosporosis has emerged as a serious disease of dogs and cattle worldwide. In addition, dog and other canids are the definitive hosts of the parasite that excrete the environmentally resistant oocysts in faeces. Neosporosis is a crippling disease of dogs, predominantly of Labradors and boxers. Currently available medicines do not eradicate the parasite from the body and some dogs die even after prolonged treatment. This paper reviews information on the life cycle, biology, clinical signs, diagnosis, treatment and control of neosporosis in dogs.
In vitro anticancer activity of loquat tea by inducing apoptosis in human leukemia cells
Authors: Zar Phyu Phyu Khine , Yano Satoshi , Sakao Kozue , Hashimoto Fumio , Nakano Takayuki , Fujii Makoto , Hou De-Xing 
Published: August 2014

Abstract
Fresh loquat leaves have been used as folk health herb in Asian countries for long time, although the evidence supporting their functions is still minimal. This study aimed to clarify the chemopreventive effect of loquat tea extract (LTE) by investigating the inhibition on proliferation, and underlying mechanisms in human promyelocytic leukemia cells (HL-60). LTE inhibited proliferation of HL-60 in a dose-dependent manner. Molecular data showed that the isolated fraction of LTE induced apoptosis of HL-60 as characterized by DNA fragmentation; activation of caspase-3, -8, and -9; and inactivation of poly(ADP)ribose polymerase. Moreover, LTE fraction increased the ratio of pro-apoptotic Bcl-2-associated X protein (Bax)/anti-apoptotic myeloid cell leukemia 1 (Mcl-1) that caused mitochondrial membrane potential loss and cytochrome c released to cytosol. Thus, our data indicate that LTE might induce apoptosis in HL-60 cells through a mitochondrial dysfunction pathway. These findings enhance our understanding for chemopreventive function of loquat tea.
New series of avenanthramides in oat seed
Authors: Ishihara Atsushi , Kojima Kana , Fujita Takeshi , Yamamoto Yuya , Nakajima Hiromitsu 
Published: August 2014

Abstract
Avenanthramides are characteristic constituents of oat seeds. We analyzed the methanol extract of oat seeds by HPLC and detected three compounds 1, 2, and 3 eluted at retention times similar to avenanthramides. The three compounds were purified by column chromatography and HPLC. Spectroscopic analyses of 1, 2, and 3 suggested that they are amides of 4,5-dihydroxyanthranilic acid with caffeic, p-coumaric, and ferulic acids, respectively. Their identities were confirmed by comparing spectra and chromatographic behavior with compounds synthesized from 4,5-dihydroxyanthranilic acid and N-hyrdroxysuccinimide esters of hydroxycinnamic acids. LC-MS/MS analysis with multiple reaction monitoring showed that the amounts of 1, 2, and 3 were 16.5–26.9% of corresponding avenanthamides with 5-hydroxyanthranilic acid. Compounds 1, 2, and 3 showed stronger 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging activity than the corresponding avenanthramides with 5-hydroxyanthranilic acid, indicating the involvement of 4,5-dihydroxyanthranilic acid moiety in the scavenging of DPPH radicals.
Multi-digit Number Processing
Authors: Nuerk Hans-Christoph , Moeller Korbinian , Willmes Klaus 
Published: August 2014

Abstract
Only recently the focus in numerical cognition research has considered multi-digit number processing as a relatively new and yet understudied domain in mathematical cognition. In this chapter: (i) we argue that single-digit number processing is not sufficient to understand multi-digit number processing; (ii) provide an overview on which representations and effects have been investigated for multi-digit numbers; (iii) suggest a conceptual distinction between place-identification, place-value activation, and place-value computation; (iv) identify language influences on multi-digit number processing along that conceptual distinction; and (v) argue that for numerical development indices of multi-digit number processing may be more suitable predictors of later arithmetical performance than classical single-digit measure such as the distance effect or non-numerical variables (e.g., working memory). In the final section, we summarize the important issues in multi-digit number processing, outline future directions and try to encourage readers to contribute to a new, exciting, yet understudied domain of numerical cognition.
Patient Handoffs: Is Cross Cover or Night Shift Better?
Authors: Higgins Alanna , Brannen Melissa L. , Heiman Heather L. , Adler Mark D. 
Published: August 2014

Objectives
Studies show singular handoffs between health care providers to be risky. Few describe sequential handoffs or compare handoffs from different provider types. We investigated the transfer of information across 2 handoffs using a piloted survey instrument. We compared cross-cover (every fourth night call) with dedicated night-shift residents.

Methods
Surveys assessing provider knowledge of hospitalized patients were administered to pediatric residents. Primary teams were surveyed about their handoff upon completion of daytime coverage of a patient. Night-shift or cross-covering residents were surveyed about their handoff of the same patient upon completion of overnight coverage. Pediatric hospitalists rated the consistency of information between the surveys. Absolute difference was calculated between the 2 providers' rating of a patient’s (a) complexity and (b) illness severity. Scores were compared across provider type.

Results
Fifty-nine complete handoff pairs were obtained. Fourteen and 45 handoff surveys were completed by a cross-covering and a night-shift provider, respectively. There was no significant difference in information consistency between primary and night-shift (median, 4.0; interquartile range [IQR], 3–4) versus primary and cross-covering providers (median, 4.0; IQR, 3–4). There was no significant difference in median patient complexity ratings (night shift, 3.0; IQR, 1–5, versus cross cover, 3.5; IQR, 1–5) or illness severity ratings (night shift, 2.0; IQR, 1–4, versus cross-cover, 3.0; IQR, 1–6) when comparing provider types giving a handoff.

Conclusions
We did not find a difference in physicians' transfer of information during 2 handoffs among providers taking traditional call or on night shift. Development of tools to measure handoff consistency is needed.
Racial and Ethnic Disparities in Patient Safety
Authors: Okoroh Juliet Siena , Uribe Erika Flores , Weingart Saul 
Published: August 2014

Background
Although there is extensive evidence on disparities in the process and outcomes of health care, data on racial and ethnic disparities in patient safety remain inconclusive in the United States.

Objectives
The aims of this study were to (1) explore differences in reporting race/ethnicity in studies on disparities in patient safety; (2) assess adjustment for socioeconomic status, comorbidity, and disease severity; and (3) make recommendations on the inclusion of race/ethnicity for future studies on adverse events.

Methods
We searched PubMed database (for articles published from 1991 to May 1, 2013) using a predetermined criteria for studies on racial and ethnic disparities in patient safety. Only quantitative studies that used chart review or administrative data for the detection of adverse events were considered for eligibility. Two reviewers independently extracted data on inclusion of race/ethnicity in baseline characteristics and in stratification of outcomes.

Results
A total of 174 studies were initially obtained from the search. Of these, 24 met inclusion criteria and received full-text review. Meta-analysis was not performed because of the methodological and statistical heterogeneity between studies. Eight studies included race/ethnicity in baseline characteristics and adjusted for confounders. Hospital-level variations such teaching status and percentage of minorities served were infrequently analyzed.

Conclusions
To our knowledge, this is the first methodological review of racial/ethnic disparities in patient safety in the United States. The evidence on the existence of disparities in adverse events was mixed. Poor stratification of outcomes by race/ethnicity and consideration of geographic and hospital-level variations explain the inconclusive evidence; variations in the quality of care at hospitals should be considered in studies using national databases.
A codon model of nucleotide substitution with selection on synonymous codon usage
Authors: Kubatko Laura , Shah Premal , Herbei Radu , Gilchrist Michael A. 
Published: August 2014

ABSTRACTThe quality of phylogenetic inference made from protein-coding genes depends, in part, on the realism with which the codon substitution process is modeled. Here we propose a new mechanistic model that combines the standard M0 substitution model of Yang (1997) with a simplified model from Gilchrist (2007) that includes selection on synonymous substitutions as a function of codon-specific nonsense error rates. We tested the newly proposed model by applying it to 104 protein-coding genes in brewer’s yeast, and compared the fit of the new model to the standard M0 model and to the mutation-selection model of Yang and Nielsen (2008) using the AIC. Our new model provided significantly better fit in approximately 85% of the cases considered for the basic M0 model and in approximately 25% of the cases for the M0 model with estimated codon frequencies, but only in a few cases when the mutation-selection model was considered. However, our model includes a parameter that can be interpreted as a measure of the rate of protein production, and the estimates of this parameter were highly correlated with an independent measure of protein production for the yeast genes considered here. Finally, we found that in some cases the new model led to the preference of a different phylogeny for a subset of the genes considered, indicating that substitution model choice may have an impact on the estimated phylogeny.
Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming
Authors: Abdelsamad Ahmed , Pecinka Ales 
Published: August 2014

Abstract
Duplications allow for gene functional diversification and accelerate genome evolution. Occasionally, the transposon amplification machinery reverse transcribes the mRNA of a gene, integrates it into the genome, and forms an RNA-duplicated copy: the retrogene. Although retrogenes have been found in plants, their biology and evolution are poorly understood. Here, we identified 251 (216 novel) retrogenes in Arabidopsis thaliana, corresponding to 1% of protein-coding genes. Arabidopsis retrogenes are derived from ubiquitously transcribed parents and reside in gene-rich chromosomal regions. Approximately 25% of retrogenes are cotranscribed with their parents and 3% with head-to-head oriented neighbors. This suggests transcription by novel promoters for 72% of Arabidopsis retrogenes. Many retrogenes reach their transcription maximum in pollen, the tissue analogous to animal spermatocytes, where upregulation of retrogenes has been found previously. This implies an evolutionarily conserved mechanism leading to this transcription pattern of RNA-duplicated genes. During transcriptional repression, retrogenes are depleted of permissive chromatin marks without an obvious enrichment for repressive modifications. However, this pattern is common to many other pollen-transcribed genes independent of their evolutionary origin. Hence, retroposition plays a role in plant genome evolution, and the developmental transcription pattern of retrogenes suggests an analogous regulation of RNA-duplicated genes in plants and animals.
Crystal structure of 7-bromo-4-oxo-4H-chromene-3-carbaldehyde
Authors: Ishikawa Yoshinobu 
Published: August 2014

In the title compound, C10H5BrO3, a brominated 3-formylchromone derivative, all atoms are essentially coplanar (r.m.s. = 0.0631 Å for the non-H atoms), with the largest deviation from the least-squares plane [0.215 (3) Å] being for the formyl O atom. In the crystal, molecules are linked into tapes through C—H...O hydrogen bonds and these tapes are assembled by stacking interactions [centroid–centroid distance between the pyran rings = 3.858 (3) Å] to form supramolecular layers that stack along thecaxis.
Does dexmedetomidine have a cardiac protective effect during non‐cardiac surgery? A randomised controlled trial
Authors: Xu Lili , Hu Zhiyong , Shen Jianjun , McQuillan Patrick M 
Published: August 2014

SummaryThis study was designed to determine the effects of dexmedetomidine on perioperative myocardial injury by observing peripheral circulatory changes in response to tracheal intubation and extubation, myocardial enzyme levels, myocardial ischaemia improvements, cardiovascular adverse events and cytokines in patients with coronary heart disease (CHD) undergoing non‐cardiac surgery. This study was a prospective, randomized, double‐blind trial. Eighty patients having CHD were scheduled for elective hip‐replacement surgery and randomly allocated to receive a loading dose of 1 μg/kg dexmedetomidine followed by a 0.2 μg/kg per h infusion (Dex group; n = 40) or normal saline (control group; n = 40). Systolic blood pressure, diastolic blood pressure, mean arterial pressure, heart rate, rate–pressure product and changes in ST‐T segment on the electrocardiogram were recorded every 5 min during surgery. Serum creatine kinase‐MB (CK‐MB), cardiac troponin I (cTnI), glycogen phosphorylase BB (GP‐BB), interleukin (IL)‐6 and tumour necrosis factor (TNF)‐α protein levels were determined preoperatively, at the end of surgery and 12 and 24 h after surgery. The improvement rate of myocardial ischaemia was higher in the Dex than control group (87.5% vs 32.5%, respectively; P < 0.05). In addition, the Dex group had lower serum CK‐MB, IL‐6, cTnI and GP‐BB concentrations than the control group (P < 0.05). There was no significance difference in TNF‐α between the two groups (P > 0.05). Dexmedetomidine can reduce myocardial injury and cytokine levels in patients with CHD undergoing non‐cardiac surgery.
Effects of phylogenetic reconstruction method on the robustness of species delimitation using single‐locus data
Authors: Tang Cuong Q. , Humphreys Aelys M. , Fontaneto Diego , Barraclough Timothy G. 
Published: August 2014

Summary

Coalescent‐based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non‐ultrametric (PTP) gene trees as input, intended for use mostly with single‐locus data such as DNA barcodes.

Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods.

The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification.

Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model‐based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.
Exome sequencing of three cases of familial exceptional longevity
Authors: Cash Timothy P. , Pita Guillermo , Domínguez Orlando , Alonso Maria R. , Moreno Leticia T. , Borrás Consuelo , Rodríguez‐Mañas Leocadio , Santiago Catalina , Garatachea Nuria , Lucia Alejandro , Avellana Juan A. , Viña Jose , González‐Neira Anna , Serrano Manuel 
Published: August 2014

SummaryExceptional longevity (EL) is a rare phenotype that can cluster in families, and co‐segregation of genetic variation in these families may point to candidate genes that could contribute to extended lifespan. In this study, for the first time, we have sequenced a total of seven exomes from exceptionally long‐lived siblings (probands ≥ 103 years and at least one sibling ≥ 97 years) that come from three separate families. We have focused on rare functional variants (RFVs) which have ≤ 1% minor allele frequency according to databases and that are likely to alter gene product function. Based on this, we have identified one candidate longevity gene carrying RFVs in all three families, APOB. Interestingly, APOB is a component of lipoprotein particles together with APOE, and variants in the genes encoding these two proteins have been previously associated with human longevity. Analysis of nonfamilial EL cases showed a trend, without reaching statistical significance, toward enrichment of APOB RFVs. We have also identified candidate longevity genes shared between two families (5–13) or within individual families (66–156 genes). Some of these genes have been previously linked to longevity in model organisms, such as PPARGC1A, NRG1, RAD52, RAD51, NCOR1, and ADCY5 genes. This work provides an initial catalog of genes that could contribute to exceptional familial longevity.
Emergence of chemoresistance in a metastatic basal cell carcinoma patient after complete response to hedgehog pathway inhibitor vismodegib (GDC‐0449)
Authors: Meani Rowena E , Lim Shueh‐Wen , Chang Anne Lynn S , Kelly John W 
Published: August 2014

AbstractVismodegib (GDC‐0449, Genentech, USA), a small molecule inhibitor of the Hedgehog signalling pathway, has potent anti‐tumour activity in advanced basal cell carcinoma (BCC). We report a case of a 67‐year‐old Australian man with metastatic BCC including pulmonary disease with malignant effusion who showed a dramatic complete response to vismodegib but subsequently experienced a recurrence of pulmonary disease, indicative of chemoresistance to vismodegib. This case is the first to illustrate chemoresistance in a patient with metastatic BCC, and demonstrates the need for closely monitoring metastatic BCC patients even after an apparently complete response.
Perineal outcome and the risk of pelvic floor dysfunction: A cohort study of primiparous women
Authors: Rikard‐Bell Joan , Iyer Jay , Rane Ajay 
Published: August 2014

BackgroundPelvic floor dysfunction (PFD) is the most common complication of childbirth. Assumptions have been made that perineal trauma increases the risk of PFD compared to an intact perineum, however the evidence for this is lacking. The aim of this study was to explore the relationship between perineal outcome and postpartum PFD.Materials and MethodsProspective cohort study design, with a self‐reported quality of life (QOL) questionnaire mailed to all primiparous women with a non‐instrumental delivery at The Townsville Hospital between 2011 and 2012 (n = 766). ANOVA was used to compare how the symptoms of PFD affect QOL in women with an intact perineum, episiotomy or spontaneous tear.ResultsSeventy‐nine percent of the population had perineal injury; 60% had a spontaneous tear and 19% had an episiotomy. Ninety‐seven percent of women who completed the questionnaire (n = 196) complained of PFD symptoms. Women with episiotomy had the best QOL, reporting the lowest levels of urinary dysfunction (statistically significant). No differences between the groups were found for symptoms of bowel, prolapse or sexual dysfunction.ConclusionsThis study shows a relationship between perineal outcome and PFD and suggests that an episiotomy is associated with the least morbidity due to symptoms of urinary incontinence. Additional large‐scale prospective research is required to further investigate and delineate the impact of childbirth on PFD.