bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can resistant infections be perceptible in UK dairy farming?
Authors: Helliwell Richard , Morris Carol , Raman Sujatha 
Published: February 2019

AbstractThis paper interrogates the claim that antimicrobial-resistant infections are rarely encountered in animal agriculture. This has been widely reiterated by a range of academic, policy and industry stakeholders in the UK. Further support comes from the UK's Animal and Plant Health Agency’s (APHA) passive clinical surveillance regime, which relies on veterinarians to submit samples for analysis and similarly reports low levels of resistance amongst key animal pathogens. Building on social science work on knowledge-practices of animal health and disease, and insights from emerging literature on non-knowledge or ‘agnotology’, we investigate the conditions shaping what is known about antimicrobial-resistant infections on farms. In so doing, we find that how on-farm knowledge is produced about resistant infection is concurrently related to domains of imperceptibility or what cannot be known in the context of current practices. The paper discusses the findings of ethnographic research undertaken on an East Midlands dairy farm that highlight the following specific findings. First, farmers and veterinarians, when observing instances of treatment failure, draw on an experiential repertoire that effaces resistances and instead foregrounds the complexities of host-pathogen interaction, or failings in human behaviour, over pathogen-antibiotic interactions. Second, the knowledge-practices of both farmers and veterinarians, although adept at identifying and diagnosing infectious disease are not equipped to make resistance perceptible. Third, this imperceptibility has implications for antibiotic use practices. Most notably, veterinarians anticipate resistance when making antibiotic choices. However, because of the absence of farm level knowledge of resistance this anticipatory logic is informed through the prevalence of resistance ‘at large’. The analysis has implications for the existing passive resistance surveillance regime operating in the dairy sector, which relies on veterinarians and farmers voluntarily submitting samples for diagnostic and susceptibility testing. In effect this entrenches farm level imperceptibility and effacement by farmers and veterinarians within the national dairy surveillance regime. However, we also highlight opportunities for providing farm specific knowledge of resistance through the anticipatory logic of veterinarians and a more active regime of surveillance.
Universality of neutral models: decision process in politics
Authors: Hösel Volker , Müller Johannes , Tellier Aurelien 
Published: February 2019

AbstractPolitical elections exemplify complex decision processes in human populations. Data of proportional elections show a striking feature at different spatial scales, across years, and for several democracies: when ranking the parties according to their number of voters, the amount of votes grows exponentially with the party’s rank. We develop a mechanistic mathematical model of birth and death of parties and voter grouping based only on word of mouth and not on political contents, close to neutral models used in evolutionary biology (Ewens sampling formula), or Hubbell’s model of species biodiversity. Data and model agree strikingly well. The model explains, for instance, the steady loss of big-tent parties in France and Germany by the increasing number of parties standing for elections. A cannibalism effect (parties/candidates at a given rank systematically withdraw votes from others) can be identified. The interpretation and consequences of the rational or lack thereof of voters’ choices for modern democracies are discussed.
Decrease of citric acid produced by Aspergillus niger through disruption of the gene encoding a putative mitochondrial citrate-oxoglutarate shuttle protein
Authors: Kirimura Kohtaro , Kobayashi Keiichi , Yoshioka Isato 
Published: February 2019

ABSTRACT
The transporter that exports citric acid (CA) generated in mitochondria to the cytosol is an important component of the CA production machinery of Aspergillus niger. In this report, we cloned and identified the gene cocA, encoding a 33.7-kDa putative mitochondrial citrate-oxoglutarate shuttle protein of the CA hyper-producer A. niger WU-2223L. The amount of CA produced by a representative cocA disruptant (35 g/L) was significantly lower than that produced by strain WU-2223L (63 g/L) after culture for 12 days under CA production conditions, and the phenotype of the cocA disruptant differed in part from that of strain WU-2223L. A cocA disruptant complemented with cocA exhibited the same phenotypes as those of strain WU-2223L. This report is the first to show that cocA and its protein product clearly contribute to substantial CA production by A. niger, and provides a significant insight into microbial organic acid production by fermentation.
Abbreviations: CA: citric acid; CD medium: Czapek-Dox medium; CS: citrate synthase; CTP: citrate transport protein; HR: homologous recombination; MCF: mitochondrial carrier family; RT-PCR: reverse-transcription PCR; TCA: tricarboxylic acid
Approaches for Utilizing Insect Protein for Human Consumption: Effect of Enzymatic Hydrolysis on Protein Quality and Functionality
Authors: Liceaga Andrea M 
Published: February 2019

Abstract
Humans have practiced entomophagy for thousands of years; yet until recently, interest from Western countries has emerged toward using insects as alternative proteins to feed the growing world population. Research shows that western cultures are in favor of consuming familiar foods formulated with insect protein. This has led to the productions of insect-derived flours, primarily from crickets and mealworms, which are now available in North American and European markets. Studies have shown limited functional properties of these insect flours. Food scientists have long used controlled enzymatic protein hydrolysis as means for improving the functionality of different animal and plant proteins. Consequently, the production of insect protein hydrolysates seems like a logical approach to improve the functionality and nutritional quality of insect flours. This article provides an overview of the application of controlled enzymatic hydrolysis to produce insect protein hydrolysates with improved protein functionality, as well as opportunities and challenges faced during their use in food and feed formulations.
How to Reply to Some Ethical Objections to Entomophagy
Authors: Fischer Bob 
Published: February 2019

Abstract
Some people have moral objections to insect consumption. After explaining the philosophical motivations for such objections, I discuss three of them, suggesting potential replies. The first is that insect consumption ignores the precautionary principle, which we can gloss here as “Don’t know, don’t farm.” In other words, although there might be evidence that insects are not conscious, we do not know that they are not; so, we should not take the moral risk associated with killing them en masse. The second concern is driven by a different way of assessing moral risk—namely, by calculating expected utility. The short version: even if it is incredibly unlikely that insects are conscious, farming them involves harming so many of them that it is better simply to grow plants instead. The third concern is about whether insects live “net negative lives,” with more pain than pleasure. The thought is that if they do, then their lives are not worth living overall, in which case it is wrong to bring them into existence. I conclude by considering the prospects for strategic alliances between animal advocates and those who promote insect consumption, in the even that they are unable to resolve their moral disagreements.
The Aldosterone/Renin Ratio Predicts Cardiometabolic Disorders in Subjects Without Classic Primary Aldosteronism
Authors: Vecchiola Andrea , Fuentes Cristóbal Andrés , Barros Eric Raúl , Martínez-Aguayo Alejandro , García Hernán , Allende Fidel , Solari Sandra , Olmos Roberto , Carvajal Cristian , Tapia-Castillo Alejandra , Campino Carmen , Kalergis Alexis Mikes , Baudrand Rene , Fardella Carlos Enrique 
Published: February 2019

Abstract

BACKGROUND
Aldosterone has been linked with obesity, metabolic syndrome (MetS), pro-inflammatory, and prothrombotic states; however, most studies relate these indicators with primary aldosteronism (PA), excluding non-PA patients.

OBJECTIVE
To determine whether aldosterone, renin, or the plasma aldosterone/renin ratio (ARR) are associated with metabolic disorders and inflammatory/vascular biomarkers in a non-PA population.

METHODS
We studied 275 patients including adolescents and adults of both genders and measured plasma and urinary aldosterone and determined the plasma renin activity. In all subjects, the presence of MetS was determined according to Adult Treatment Panel III. Renal, vascular, inflammatory, and mineralocorticoid activity biomarkers were evaluated.

RESULTS
The ARR correlated with the number of variables of MetS (r = 0.191, P = 0.002), body mass index (BMI; r = 0.136, P = 0.026), systolic blood pressure (r = 0.183, P = 0.002), diastolic blood pressure (r = 0.1917, P = 0.0014), potassium excreted fraction (r = 0.174, P = 0.004), low-density lipoprotein (r = 0.156, P = 0.01), plasminogen activator inhibitor type 1 (r = 0.158, P = 0.009), microalbuminuria (r = 0.136, P = 0.029), and leptin (r = 0.142, P = 0.019). In a linear regression model adjusted by age, BMI, and gender, only the ARR was still significant (r = 0.108, P = 0.05). In a logistic regression analysis, the ARR predicted MetS index (odds ratio (OR) = 1.07 [95% confidence interval (CI) = 1.011–1.131], P= 0.02) even after adjusting for age, BMI, and gender. On the other hand, aldosterone showed no association with MetS or inflammatory markers.

CONCLUSION
These results suggest a continuum of cardiometabolic risk beyond the classic PA threshold screening. The ARR could be a more sensitive marker of obesity, MetS, and endothelial damage in non-PA patients than aldosterone or renin alone. Prospective studies are needed to develop future screening cutoff values.
Potential involvement of root auxins in drought tolerance by modulating nocturnal and daytime water use in wheat
Authors: Sadok Walid , Schoppach Rémy 
Published: February 2019

Abstract

Background and Aims
The ability of wheat genotypes to save water by reducing their transpiration rate (TR) at times of the day with high vapour pressure deficit (VPD) has been linked to increasing yields in terminal drought environments. Further, recent evidence shows that reducing nocturnal transpiration (TRN) could amplify water saving. Previous research indicates that such traits involve a root-based hydraulic limitation, but the contribution of hormones, particularly auxin and abscisic acid (ABA), has not been explored to explain the shoot–root link. In this investigation, based on physiological, genetic and molecular evidence gathered on a mapping population, we hypothesized that root auxin accumulation regulates whole-plant water use during both times of the day.

Methods
Eight double-haploid lines were selected from a mapping population descending from two parents with contrasting water-saving strategies and root hydraulic properties. These spanned the entire range of slopes of TR responses to VPD and TRN encountered in the population. We examined daytime/night-time auxin and ABA contents in the roots and the leaves in relation to hydraulic traits that included whole-plant TR, plant hydraulic conductance (KPlant), slopes of TR responses to VPD and leaf-level anatomical traits.

Key Results
Root auxin levels were consistently genotype-dependent in this group irrespective of experiments and times of the day. Daytime root auxin concentrations were found to be strongly and negatively correlated with daytime TR, KPlant and the slope of TR response to VPD. Night-time root auxin levels significantly and negatively correlated with TRN. In addition, daytime and night-time leaf auxin and ABA concentrations did not correlate with any of the examined traits.

Conclusions
The above results indicate that accumulation of auxin in the root system reduces daytime and night-time water use and modulates plant hydraulic properties to enable the expression of water-saving traits that have been associated with enhanced yields under drought.
Sub-Scarpa’s Lipectomy in Abdominoplasty: An Analysis of Risks and Rewards in 723 Consecutive Patients
Authors: Restifo Richard J 
Published: February 2019

Abstract

Background
During the course of performing abdominoplasties, a plastic surgeon will encounter a certain body habitus characterized by a thick, tethered, and excessively redundant upper skin flap. Often these patients also demonstrate diffuse and substantial fascial laxity. One approach to this problem involves direct thinning and release of the flap by resection of the sub-Scarpa’s fat pad. In theory, this resection should be safe from a flap perfusion standpoint. However, the safety of the sub-Scarpa’s resection has not been completely documented.

Objectives
The author sought to assess the safety and efficacy of sub-Scarpa’s lipectomy in abdominoplasty.

Methods
A total 723 patients were retrospectively examined and divided into 2 groups: those with (Group B) and those without (Group A) a sub-Scarpa’s lipectomy component to the abdominoplasty. Because of differences in the baseline characteristics between the 2 groups, data analysis was performed with a logistic regression model and with propensity score matching.

Results
The sub-Scarpa’s lipectomy technique allowed for substantial thinning of the flap: the average weight of the resected fat pad was 411 g. Wide undermining allowed for substantial fascial correction, and excellent results were obtainable even in challenging cases. The sub-Scarpa’s lipectomy group did not demonstrate an increase in either minor (&lt;5 cm2) or major (&gt;5 cm2) flap necrosis. However, there was a statistically significant increase in fat necrosis and seroma formation in Group B compared with Group A. In both groups, an increasing body mass index was a risk factor for fat necrosis and major flap necrosis.

Conclusions
The implementation of a sub-Scarpa’s lipectomy during abdominoplasty is a useful technique to consider for selected abdominoplasty candidates. The risks of minor and major flap loss do not seem to be increased compared to the standard abdominoplasty, but the risks of fat necrosis and seroma formation may be greater.

Level of Evidence: 4
Finding de novo methylated DNA motifs
Authors: Ngo Vu , Wang Mengchi , Wang Wei 
Published: February 2019

Abstract

Motivation
Increasing evidence has shown that nucleotide modifications such as methylation and hydroxymethylation on cytosine would greatly impact the binding of transcription factors (TFs). However, there is a lack of motif finding algorithms with the function to search for motifs with modified bases. In this study, we expand on our previous motif finding pipeline Epigram to provide systematic de novo motif discovery and performance evaluation on methylated DNA motifs.

Results
mEpigram outperforms both MEME and DREME on finding modified motifs in simulated data that mimics various motif enrichment scenarios. Furthermore we were able to identify methylated motifs in Arabidopsis DNA affinity purification sequencing (DAP-seq) data that were previously demonstrated to contain such motifs. When applied to TF ChIP-seq and DNA methylome data in H1 and GM12878, our method successfully identified novel methylated motifs that can be recognized by the TFs or their co-factors. We also observed spacing constraint between the canonical motif of the TF and the newly discovered methylated motifs, which suggests operative recognition of these cis-elements by collaborative proteins.

Availability and implementation
The mEpigram program is available at http://wanglab.ucsd.edu/star/mEpigram.

Supplementary information
Supplementary data are available at Bioinformatics online.
Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability
Authors: Chang Jia-Ming , Floden Evan W , Herrero Javier , Gascuel Olivier , Di Tommaso Paolo , Notredame Cedric 
Published: February 2019

Abstract

Motivation
Most evolutionary analyses are based on pre-estimated multiple sequence alignment. Wong et al. established the existence of an uncertainty induced by multiple sequence alignment when reconstructing phylogenies. They were able to show that in many cases different aligners produce different phylogenies, with no simple objective criterion sufficient to distinguish among these alternatives.

Results
We demonstrate that incorporating MSA induced uncertainty into bootstrap sampling can significantly increase correlation between clade correctness and its corresponding bootstrap value. Our procedure involves concatenating several alternative multiple sequence alignments of the same sequences, produced using different commonly used aligners. We then draw bootstrap replicates while favoring columns of the more unique aligner among the concatenated aligners. We named this concatenation and bootstrapping method, Weighted Partial Super Bootstrap (wpSBOOT). We show on three simulated datasets of 16, 32 and 64 tips that our method improves the predictive power of bootstrap values. We also used as a benchmark an empirical collection of 853 one to one orthologous genes from seven yeast species and found wpSBOOT to significantly improve discrimination capacity between topologically correct and incorrect trees. Bootstrap values of wpSBOOT are comparable to similar readouts estimated using a single method. However, for reduced trees by 50 and 95% bootstrap thresholds, wpSBOOT comes out the lowest Type I error (less FP).

Availability and implementation
The automated generation of replicates has been implemented in the T-Coffee package, which is available as open source freeware available from www.tcoffee.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Structured crowdsourcing enables convolutional segmentation of histology images
Authors: Amgad Mohamed , Elfandy Habiba , Hussein Hagar , Atteya Lamees A , Elsebaie Mai A T , Abo Elnasr Lamia S , Sakr Rokia A , Salem Hazem S E , Ismail Ahmed F , Saad Anas M , Ahmed Joumana , Elsebaie Maha A T , Rahman Mustafijur , Ruhban Inas A , Elgazar Nada M , Alagha Yahya , Osman Mohamed H , Alhusseiny Ahmed M , Khalaf Mariam M , Younes Abo-Alela F , Abdulkarim Ali , Younes Duaa M , Gadallah Ahmed M , Elkashash Ahmad M , Fala Salma Y , Zaki Basma M , Beezley Jonathan , Chittajallu Deepak R , Manthey David , Gutman David A , Cooper Lee A D 
Published: February 2019

Abstract

Motivation
While deep-learning algorithms have demonstrated outstanding performance in semantic image segmentation tasks, large annotation datasets are needed to create accurate models. Annotation of histology images is challenging due to the effort and experience required to carefully delineate tissue structures, and difficulties related to sharing and markup of whole-slide images.

Results
We recruited 25 participants, ranging in experience from senior pathologists to medical students, to delineate tissue regions in 151 breast cancer slides using the Digital Slide Archive. Inter-participant discordance was systematically evaluated, revealing low discordance for tumor and stroma, and higher discordance for more subjectively defined or rare tissue classes. Feedback provided by senior participants enabled the generation and curation of 20 000+ annotated tissue regions. Fully convolutional networks trained using these annotations were highly accurate (mean AUC=0.945), and the scale of annotation data provided notable improvements in image classification accuracy.

Availability and Implementation
Dataset is freely available at: https://goo.gl/cNM4EL.

Supplementary information
Supplementary data are available at Bioinformatics online.
KOnezumi: a web application for automating gene disruption strategies to generate knockout mice
Authors: Kuno Akihiro , Mizuno Seiya , Takahashi Satoru 
Published: February 2019

Abstract

Summary
Although gene editing using the CRISPR/Cas9 system enables the rapid generation of knockout mice, constructing an optimal gene disruption strategy is still labourious. Here, we propose KOnezumi, a simple and user-friendly web application, for use in automating the design of knockout strategies for multiple genes. Users only need to input gene symbols, and then KOnezumi returns target exons, gRNA candidates to delete the target exons, genotyping PCR primers, nucleotide sequences of the target exons and coding sequences of expected deletion products. KOnezumi enables users to easily and rapidly apply a rational strategy to accelerate the generation of KO mice using the CRISPR/Cas9 system.

Availability and implementation
This web application is freely available at http://www.md.tsukuba.ac.jp/LabAnimalResCNT/KOanimals/konezumi.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
‘The Perfect Murder’: An Exploratory Study of Staged Murder Scenes and Concealed Femicide
Authors: Bitton Yifat , Dayan Hava 
Published: February 2019

AbstractPresenting cases of criminologically unidentifiable circumstances, authors point to concealment susceptibility of some femicide cases, overlooked by both the criminal system and by scholars, rendering them ‘concealed femicides’. The paper presents descriptive and criminological analyses of Israeli cases whereby the woman’s murder was followed by scene staging. It extrapolates the common characteristics of femicide victims and perpetrators, offers a typology of homicide scene staging behaviour that facilitates domesticity-related femicide concealment and, eventually, introduces tools to enhance exposure of femicide.
The Vita Alcuini, Asser and Scholarly Service at the Court of Alfred the Great
Authors: Thomas Rebecca 
Published: February 2019

Abstract
Asser’s Life of King Alfred, a biography of Alfred the Great composed by a Welsh monk from St David’s in 893, is a key source for understanding connections between ninth-century Britain and the Continent. Asser’s biography draws on a variety of continental sources, the most famous and widely discussed being Einhard’s Vita Karoli. This article examines parallels between Asser’s Life of King Alfred and another, more obscure, continental source, the anonymous ninth-century Vita Alcuini, a text which has received little scholarly attention. Unlike many of his Carolingian counterparts, Asser’s biography features himself as a major character, providing an account of his journey to Alfred’s service. It has been noted by various scholars that this autobiographical section of the Life bears great similarity to the Vita Alcuini’s description of Alcuin entering the service of Charlemagne. This article provides a thorough examination of the two texts, assessing the possibility of a connection, and investigating the implications for our understanding of Asser and his agenda. As there is no manuscript evidence that the Vita Alcuini ever made it to Britain, this study has the potential to transform our understanding of its transmission and readership in the early Middle Ages, illuminating a further connection Britain England and the continent in the ninth century.