bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feeding of high-yielding bovines during transition phase.
Authors: Bakshi M. P. S. , Wadhwa M. , Makkar H. P. S. 
Published: April 2017

Abstract
Appropriate feeding during the pregnancy and post-pregnancy period determines both the milk production in the ensuing lactation as well as the reproductive efficiency of the animal. During this period, 3 weeks before and 3 weeks after parturition are very important because dramatic physiological and metabolic adaptations take place during this phase - called as the transition phase. Nutritional imbalances, caused by the low quality of desired nutritious rations, reduced appetite and low ingestion are responsible for depressed performance specifically during the transition period. The lack of knowledge and skill of farmers in feeding-management during this phase exacerbate the situation. The metabolic changes, metabolic adaptations and the nutritional-management strategies to ease out this phase are discussed in this review paper. With the advancement of gestation, the dry matter intake (DMI) of dairy cows declines and is at its lowest (1.7-2.0% of body weight) at parturition. The body condition score (BCS) parallels the DMI, but the aim should be not to lose more than one BCS (in the scale of 1-5) after calving. Simultaneously, with the growth of foetus the nutrient requirements increase and are at their peak before parturition as well as immediately after parturition. The milk production reaches its peak in about 5-8 weeks postpartum, while the diet consumption peaks at 10-14 weeks postpartum. Thus, dairy cows will typically suffer a 6-8-week period of negative energy balance during the postpartum period. The mammary energy requirements at 4-day postpartum are more than three times than that of uterus, with simultaneous increase in requirement of metabolizable protein, especially of methionine and lysine. The high incidence of metabolic and infectious diseases is responsible for the high incidence of inflammatory conditions, mostly immediately after calving. To prevent these diseases pro-inflammatory cytokine release should be avoided in postpartum. The mobilization of body reserves especially fat and protein; and hepatic gluconeogenesis takes place immediately after parturition leading to increased levels of ÃÂ²-hydroxy butyric acid and non-esterified fatty acids, which act as a gateway for a number of metabolic diseases. The transition phase can be eased by increasing DMI, feed conversion efficiency, density of ration, and protein supplements rich in rumen undegradable protein; by using anionic mineral mixture, optimizing roughage to concentrate (R:C) ratio, optimum physically effective fibre length of forages/silage/hay, dietary buffers, feed additives such as inflammation modulators, protected nutrients, glucogenic precursors and direct fed microbials/probiotics; and by following phased feeding programme.
Challenges of managing disease in tall orchard trees - pecan scab, a case study.
Authors: Bock C. H. , Brenneman T. B. , Wood B. W. , Stevenson K. L. 
Published: April 2017

Abstract

Managing disease in tall orchard trees presents unique issues not found in relatively shorter horticultural and agronomic crops, simply due to height Pecan scab (caused by
Venturia effusa
[G. Winter] Rossman & W.C. Allen) is used as an example of a major disease of one of the tallest orchard crops in the world (up to ∼44 m). This disease is a major issue for pecan (
Carya illinoinensis
[Wangenh.] K. Koch) notwithstanding ∼120 years of research aimed at improving management approaches. The historic and current use of host resistance, ground and aerial application of fungicides (and issues associated with their use) and possible benefits of tree management tools are discussed. The problems in obtaining maximum scab control are presented, and the research needs and the possibilities offered by new technologies, including use of unmanned aerial vehicles and genomics tools are presented. Better utilization of existing scab management options, applying new orchard management tools and incorporating new technologies should help ensure that pecan scab has less impact on pecan production in the coming decades.
Efficacy of an Acoustic Tag with Predation Detection Technology
Authors: Schultz Andrew A. , Afentoulis Virginia B. , Yip Curtis J. , Johnson Michele N. 
Published: April 2017

Abstract
One of the most important assumptions in the use of data from an acoustically tagged fish is that the data are indeed from the fish that was originally tagged. However, there is likely to be some level of predation on the tagged subjects used in acoustic telemetry studies. When an acoustically tagged fish is consumed, the tag continues to emit the same signal even though the tagged fish is no longer alive. To assist in addressing this issue, a predation detection acoustic tag (PDAT) was developed to provide the functions of a typical acoustic tag with the added ability to indicate when a tagged fish has been consumed by a predator. Our goal was to test the efficacy and precision of this new technology. We implanted PDATs into live juvenile Chinook Salmon Oncorhynchus tshawytscha and fed them to adult Striped Bass Morone saxatilis under controlled conditions. Identifying when the PDATs “triggered” (i.e., changed their signal, indicating that the tag had been consumed) proved to be a simple process. The PDAT that we tested was effective 90% of the time in verifying that a tagged fish had been consumed. The mean elapsed time from the feeding event to the time of triggering (trigger time) was 59.2 h (SD = 28.1, range = 22.3–140.0). The PDAT has great potential to assist in more accurately interpreting acoustic data in the study of fish behavior and survival. Further testing of this technology is warranted and should include a broader range of the environmental factors likely to have a major influence on trigger time as well as trials under more natural conditions.
Received September 28, 2016; accepted January 27, 2017 Published online April 18, 2017
Safe and Competent Opioid Prescribing Education: Increasing Dissemination with a Train-The-Trainer Program
Authors: Zisblatt Lara , Hayes Sean M. , Lazure Patrice , Hardesty Ilana , White Julie L. , Alford Daniel P. 
Published: April 2017

Background: Due to the high prevalence of prescription opioid misuse, the US Food and Drug Administration (FDA) mandated a Risk Evaluation and Mitigation Strategy (REMS) requiring manufacturers of extended-release/long-acting (ER/LA) opioids to fund continuing education based on an FDA curricular Blueprint. This paper describes the Safe and Competent Opioid Prescribing Education ( SCOPE of Pain) train-the-trainer program and its impact on (1) disseminating the SCOPE of Pain curriculum and (2) knowledge, confidence, attitudes, and performance of the participants of trainer-led compared with expert-led meetings. Methods: SCOPE of Pain is a 3-hour ER/LA opioid REMS education. In addition to expert-led live statewide meetings, a 2-hour train-the-trainer (TTT) workshop was developed to increase dissemination nationally. The trainers were expected to conduct SCOPE of Pain meetings at their institutions. Participants of both the trainer-led and expert-led SCOPE of Pain programs were surveyed immediately post and 2 months post meetings to assess improvements in knowledge, confidence, attitudes, and self-reported safe opioid prescribing practices. Results: During 9 months (May 2013 to February 2014), 89 trainers were trained during 9 TTT workshops in 9 states. Over 24 months (May 2013 to April 2015), 33% of the trainers conducted at least 1 SCOPE of Pain training, with a total of 79 meetings that educated 1419 participants. The average number of meetings of those who conducted at least 1 meeting was 2.8 (range: 1–19). The participants of the trainer-led programs were significantly more likely to be practicing in rural settings than those who participated in the expert-led meetings (39% vs. 26%, P < .001). At 2 months post training, there were no significant differences in improvements in participant knowledge, confidence, attitudes, and performance between expert-led and trainer-led meetings. Conclusions: The SCOPE of Pain TTT program holds promise as an effective dissemination strategy to increase guideline-based safe opioid prescribing knowledge, confidence, attitudes, and self-reported practices.
Quinolone resistance-associated amino acid substitutions affect enzymatic activity of Mycobacterium leprae DNA gyrase
Authors: Yamaguchi Tomoyuki , Yokoyama Kazumasa , Nakajima Chie , Suzuki Yasuhiko 
Published: April 2017

Abstract
Quinolones are important antimicrobials for treatment of leprosy, a chronic infectious disease caused by Mycobacterium leprae. Although it is well known that mutations in DNA gyrase are responsible for quinolone resistance, the effect of those mutations on the enzymatic activity is yet to be studied in depth. Hence, we conducted in vitro assays to observe supercoiling reactions of wild type and mutated M. leprae DNA gyrases. DNA gyrase with amino acid substitution Ala91Val possessed the highest activity among the mutants. DNA gyrase with Gly89Cys showed the lowest level of activity despite being found in clinical strains, but it supercoiled DNA like the wild type does if applied at a sufficient concentration. In addition, patterns of time-dependent conversion from relaxed circular DNA into supercoiled DNA by DNA gyrases with clinically unreported Asp95Gly and Asp95Asn were observed to be distinct from those by the other DNA gyrases.
Alignment of dynamic networks
Authors: Vijayan V , Critchlow D , Milenković T 
Published: April 2017

Abstract

Motivation
Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems’ static network representations, as is currently done.

Results
For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface.

Availability and implementation
http://nd.edu/∼cone/DynaMAGNA++/.

Supplementary information
Supplementary data are available at Bioinformatics online.
MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs
Authors: Heinle Cassie Elizabeth , Gaultier Nicolas Paul Eugène , Miller Dana , Purbojati Rikky Wenang , Lauro Federico M. 
Published: April 2017

Abstract
Background: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. Findings: MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. Conclusions: MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers.
Infections in rheumatoid arthritis
Authors: Atzeni Fabiola , Masala Ignazio Francesco , di Franco Manuela , Sarzi-Puttini Piercarlo 
Published: April 2017

Purpose of review
The purpose of this review is to provide an update concerning recent advances in the evidence- based study of serious infections in patients with rheumatoid arthritis (RA) treated with biological drugs or conventional disease-modifying antirheumatic drugs (DMARDs), concentrating on studies published in the last 18 months.

Recent findings
New studies have further strengthened existing evidence relating the use of biological drugs to serious infections. The risk does not seem to be any different with short-term or long-term use. There is still a lack of conclusive studies identifying biomarkers, but it is plausible that the drugs have direct effects on cytokines and cell activity and then serious infections.

Summary
The frequent infections of patients with RA may be due to the disease itself (altered immunological function, disability, immobility, joint surgery), extra-articular manifestations or DMARDs, immunosuppressants and steroids. The use of biological drugs lead to the development of serious infections including tuberculosis. Patients should be informed of their increased risk, and physicians need to be aware of these complications and how to treat them.
Randomized Trial of Machine Perfusion Versus Cold Storage in Recipients of Deceased Donor Kidney Transplants With High Incidence of Delayed Graft Function
Authors: Tedesco-Silva Helio , Mello Offerni Juliano Chrystian , Ayres Carneiro Vanessa , Ivani de Paula Mayara , Neto Elias David , Brambate Carvalhinho Lemos Francine , Requião Moura Lúcio Roberto , Pacheco e Silva Filho Alvaro , de Morais Cunha Mirian de Fátima , Francisco da Silva Erica , Miorin Luiz Antonio , Demetrio Daniela Priscila , Luconi Paulo Sérgio , da Silva Luconi Waldere Tania , Bobbio Savina Adriana , kuschnaroff Liz Milstein , Noronha Irene Lourdes , Braga Sibele Lessa , Barsante Renata Cristina , Mendes Moreira João Cezar , Fernandes-Charpiot Ida Maria Maximina , Abbud-Filho Mario , Modelli de Andrade Luis Gustavo , Dalsoglio Garcia Paula , Tanajura Santamaria Saber Luciana , Fernandes Laurindo Alan , Chocair Pedro Renato , Cuvello Neto Américo Lourenço , Zanocco Juliana Aparecida , Duboc de Almeida Soares Filho Antonio Jose , Ferreira Aguiar Wilson , Medina Pestana Jose 
Published: April 2017

Background
This study compared the use of static cold storage versus continuous hypothermic machine perfusion in a cohort of kidney transplant recipients at high risk for delayed graft function (DGF).

Methods
In this national, multicenter, and controlled trial, 80 pairs of kidneys recovered from brain-dead deceased donors were randomized to cold storage or machine perfusion, transplanted, and followed up for 12 months. The primary endpoint was the incidence of DGF. Secondary endpoints included the duration of DGF, hospital stay, primary nonfunction, estimated glomerular filtration rate, acute rejection, and allograft and patient survivals.

Results
Mean cold ischemia time was high but not different between the 2 groups (25.6 ± 6.6 hours vs 25.05 ± 6.3 hours, 0.937). The incidence of DGF was lower in the machine perfusion compared with cold storage group (61% vs. 45%, P = 0.031). Machine perfusion was independently associated with a reduced risk of DGF (odds ratio, 0.49; 95% confidence interval, 0.26-0.95). Mean estimated glomerular filtration rate tended to be higher at day 28 (40.6 ± 19.9 mL/min per 1.73 m2 vs 49.0 ± 26.9 mL/min per 1.73 m2; P = 0.262) and 1 year (48.3 ± 19.8 mL/min per 1.73 m2 vs 54.4 ± 28.6 mL/min per 1.73 m2; P = 0.201) in the machine perfusion group. No differences in the incidence of acute rejection, primary nonfunction (0% vs 2.5%), graft loss (7.5% vs 10%), or death (8.8% vs 6.3%) were observed.

Conclusions
In this cohort of recipients of deceased donor kidneys with high mean cold ischemia time and high incidence of DGF, the use of continuous machine perfusion was associated with a reduced risk of DGF compared with the traditional cold storage preservation method.
Alterations in cortical thickness and structural connectivity are associated with symptom severity in bulimia nervosa
Authors: Westwater Margaret L. , Seidlitz Jakob , Diederen Kelly M.J. , Fischer Sarah , Thompson James C. 
Published: April 2017

AbstractBulimia nervosa (BN) is a serious psychiatric illness defined by preoccupation with weight and shape, episodic binge-eating and compensatory behaviors. Although diagnosed BN has been associated with diffuse grey matter volume reductions, characterization of brain structure alterations in women with a range of BN symptoms has yet to be made. This study examined whether changes in cortical thickness (CT) scaled with BN symptom severity in a sample of 33 adult women (n = 10 BN; n = 5 EDNOS-BN). Our second objective was to assess global structural connectivity (SC) of CT and to determine if individual differences in global SC relate to BN symptom severity. We used the validated Eating Disorder Examination Questionnaire (EDE-Q; Fairburn & Beglin, 1994) as a continuous measure of BN symptom severity. Increased EDE-Q score was negatively related to global CT and local CT in the left middle frontal gyrus, right superior frontal gyrus and bilateral orbitofrontal cortex (OFC) and temporoparietal regions. Moreover, analysis of global SC indicated that BN-related cortical thinning preferentially occurred in regions with high global connectivity. Finally, we showed that individuals’ contribution to global SC at the group level were significantly related to EDE-Q score, where increased EDE-Q score correlated with reduced connectivity of the left OFC and middle temporal cortex and increased connectivity of the right superior parietal lobule. Our findings offer novel insight into CT alterations in BN and further suggest that the combination of CT and structural connectivity measures may be sensitive to individual differences in BN symptom severity.
The causal effect of educational attainment on Alzheimer’s disease: A two-sample Mendelian randomization study
Authors: Anderson Emma L , Wade Kaitlin H , Hemani Gibran , Bowden Jack , Korologou-Linden Roxanna , Smith George Davey , Ben-Shlomo Yoav , Howe Laura D , Stergiakouli Evie 
Published: April 2017

ABSTRACTBackgroundObservational evidence suggests that higher educational attainment is protective for Alzheimer’s disease (AD). It is unclear whether this association is causal or confounded by demographic and socioeconomic characteristics. We examined the causal effect of educational attainment on AD in a two-sample MR framework.MethodsWe extracted all available effect estimates of the 74 single nucleotide polymorphisms (SNPs) associated with years of schooling from the largest genome-wide association study (GWAS) of educational attainment (N=293,723) and the GWAS of AD conducted by the International Genomics of Alzheimer’s Project (n=17,008 AD cases and 37,154 controls). SNP-exposure and SNP-outcome coefficients were combined using an inverse variance weighted approach, providing an estimate of the causal effect of each SD increase in years of schooling on AD. We also performed appropriate sensitivity analyses examining the robustness of causal effect estimates to the various assumptions and conducted simulation analyses to examine potential survival bias of MR analyses.FindingsWith each SD increase in years of schooling (3.51 years), the odds of AD were, on average, reduced by approximately one third (odds ratio= 0.63, 95% confidence interval [CI]: 0.48 to 0.83, p<0.001). Causal effect estimates were consistent when using causal methods with varying MR assumptions or different sets of SNPs for educational attainment, lending confidence to the magnitude and direction of effect in our main findings. There was also no evidence of survival bias in our study.InterpretationOur findings support a causal role of educational attainment on AD, whereby an additional ∼3.5 years of schooling reduces the odds of AD by approximately one third.
The impact of human resources practices on consumers’ investment intentions
Authors: Ferreira Aristides I. , Martinez Luis F. , Rodrigues Rosa I. , Ilhéu Carla 
Published: April 2017

PurposeResearch has shown that corporate policies affect customers’ decisions. The purpose of this paper is to focus on the influence of human resources (HR) practices on investment intentions in the financial sector.Design/methodology/approachData were obtained from 548 managers and management students. Participants were presented real news regarding two banks with contrasting HR practices. Subsequently, they had to choose – from a given virtual amount – their investment allocations.FindingsResults primarily showed that participants decided to invest more money in the bank which was more profitable to them, regardless of that bank’s HR practice. But, most importantly, when the news was specifically addressed to the in-group (managers), participants decided to invest more money in the bank with the HR practice by which they identified more, although being less profitable to them.Originality/valueThe findings demonstrate the urgency for organizations to manage effectively their HR practices, as they serve as a vehicle to corporate reputation, thus affecting the relationship with the stakeholders and investors’ decisions.