bluuebunny/crossref_metadata_2025_split huggingface dataset:
Upper circulation in Bone Bay and its relation to biogeochemical distribution: from observation and model
Authors: Widyastuti P , Atmadipoera A S , Nurjaya I W , Natih N M , Priatna A 
Published: May 2019

AbstractThe surrounding waters and the physical mechanisms within the ocean are playing a major role to bring nutrients to Bone Bay, field observation in October 2014 and analysis of numerical modeling were conducted in order to understand the pattern of water circulation, as well as the variability of seawater transport and its impacts to the biogeochemical distribution. The results of the observation show that the distribution of salinity is lower in locations closest to the gulf (Transect A) and higher towards the furthest locations from the gulf (Transect D), followed by the pattern of other parameters (temperature, dissolved oxygen, and chlorophyll-a). This happened due to the low current speed in the Flores Sea during the time of observation hence no water flowed into the gulf which was dominated by freshwater from rivers. It is confirmed by the transport model that shows that seawater is transported strongly to the north from January to March and due to the topography at the mouth of the gulf, the water accumulates and forms an eddy which transports water to the south in April until the next few months. This explains the distribution of phytoplankton and zooplankton inside the gulf from January to March.
Blood Pressure Instability in Persons With SCI: Evidence From a 30-Day Home Monitoring Observation
Authors: Katzelnick Caitlyn G , Weir Joseph P , Jones April , Galea Marinella , Dyson-Hudson Trevor A , Kirshblum Steven C , Wecht Jill M 
Published: May 2019

Abstract

Background
To determine the degree of blood pressure instability over a 30-day home observation in participants with spinal cord injury grouped by level of injury pertaining to cardiovascular autonomic regulation.

Methods
This is an observational study completed at the Kessler Foundation and James J. Peters Veterans Medical Center. Seventy-two participants with tetraplegia (C1–T1), 13 with high thoracic (T2–T4), and 28 with low thoracic (T5–T12) injury participated in this study. Participants were asked to record their blood pressure using an ambulatory blood pressure monitor three times a day for 30 days.

Results
The number of blood pressure fluctuations was significantly increased in the tetraplegia group compared with the paraplegia groups. Age and duration of injury contributed to an increase in the observation of 30-day blood pressure instability; however, completeness of injury did not.

Conclusion
The data indicate significant blood pressure instability that may not be exclusive to persons with tetraplegia; in fact, individuals with low thoracic injuries demonstrated severe blood pressure fluctuations. The use of a monitor at home for an extended period may help document dangerous and extreme fluctuations in blood pressure and should be considered an important adjunctive clinical practice for tracking of the secondary consequences in the spinal cord injury population.
TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification
Authors: Sayyari Erfan , Kawas Ban , Mirarab Siavash 
Published: May 2019

AbstractMotivationLearning associations of traits with the microbial composition of a set of samples is a fundamental goal in microbiome studies. Recently, machine learning methods have been explored for this goal, with some promise. However, in comparison to other fields, microbiome data are high-dimensional and not abundant; leading to a high-dimensional low-sample-size under-determined system. Moreover, microbiome data are often unbalanced and biased. Given such training data, machine learning methods often fail to perform a classification task with sufficient accuracy. Lack of signal is especially problematic when classes are represented in an unbalanced way in the training data; with some classes under-represented. The presence of inter-correlations among subsets of observations further compounds these issues. As a result, machine learning methods have had only limited success in predicting many traits from microbiome. Data augmentation consists of building synthetic samples and adding them to the training data and is a technique that has proved helpful for many machine learning tasks.ResultsIn this paper, we propose a new data augmentation technique for classifying phenotypes based on the microbiome. Our algorithm, called TADA, uses available data and a statistical generative model to create new samples augmenting existing ones, addressing issues of low-sample-size. In generating new samples, TADA takes into account phylogenetic relationships between microbial species. On two real datasets, we show that adding these synthetic samples to the training set improves the accuracy of downstream classification, especially when the training data have an unbalanced representation of classes.Availability and implementationTADA is available at https://github.com/tada-alg/TADA.Supplementary informationSupplementary data are available at Bioinformatics online.
Benchmarking of 4C-seq pipelines based on real and simulated data
Authors: Walter Carolin , Schuetzmann Daniel , Rosenbauer Frank , Dugas Martin 
Published: May 2019

Abstract

Motivation
With its capacity for high-resolution data output in one region of interest, chromosome conformation capture combined with high-throughput sequencing (4C-seq) is a state-of-the-art next-generation sequencing technique that provides epigenetic insights, and regularly advances current medical research. However, 4C-seq data are complex and prone to biases, and while specialized programs exist, an unbiased, extensive benchmarking is still lacking. Furthermore, neither substantial datasets with fully characterized ground truth, nor simulation programs for realistic 4C-seq data have been published.

Results
We conducted a benchmarking study on 66 4C-seq samples from 20 datasets, and developed a novel 4C-seq simulation software, Basic4CSim, to allow for detailed comparisons of 4C-seq algorithms on 50 simulated datasets with 10–120 samples each. Simulations and benchmarking were adapted to address different characteristics of 4C-seq data. Simulated data were compared with published samples to validate simulation settings. We identified differences between 4C-seq algorithms in terms of precision, recall, interaction structure, and run time, and observed general trends. Novel differential pipeline versions of single-sample based 4C-seq algorithms were included in the benchmarking. While no single tool was optimally suited for both near-cis and far-cis, and both single-sample and differential analyses, choosing a high-performing algorithm variant did improve results considerably. For near-cis scenarios, r3Cseq, peakC and FourCSeq offered high precision, while fourSig demonstrated high overall F1 scores in far-cis analyses. Finally, 4C-seq simulations may aid in the development of improved analysis algorithms.

Availability and implementation
Basic4CSim is available at https://github.com/walter–ca/Basic4CSim.

Supplementary information
Supplementary data are available at Bioinformatics online.
Mating changes a male contestant from a loser to a winner in male–male competition in a wolf spider
Authors: Zhang Shichang , Ai Hui , Li Daiqin 
Published: May 2019

Abstract
Mating may change a male’s behaviour by increasing its motivation to engage in a contest, and enabling it to win in subsequent male–male contests. To test this hypothesis, we recorded male contests in the wolf spider, Venonia coruscans (Araneae: Lycosidae), testing a male’s motivation to fight under three different resource value conditions. First, we staged contests between two males in two different resource value conditions, on an egg-produced female’s web and then on a virgin female’s web, to test a male’s fighting ability. After determining each male’s fighting ability, we allowed each loser that lost its contests under both resource value conditions to mate with a virgin female and then introduced the previous contest winner to the web where the loser had mated. We found that without mating, the losers always lost their contests, regardless of the resource value conditions. However, once they had mated, the losers fiercely attacked the previous winners, and most won the contests back. Our study therefore provides evidence that a male’s motivation to fight can be changed under certain circumstances (e.g. mating) and can greatly influence contest outcomes in male–male competition in a mating context.
MALDI-TOF MS-based analysis of dried seed proteins immobilized on filter paper
Authors: Reeve Michael A , Pollard Kathryn M 
Published: May 2019

Abstract
Matrix-assisted laser-desorption and ionization time-of-flight mass spectroscopy (MALDI-TOF MS) is commonly used for the characterization of protein-containing biological samples. For this, we have previously developed sample-preparation methods that can be used for discrimination between Impatiens species and also between regional biotypes of Himalayan balsam (Impatiens glandulifera), initially using leaf samples and, more recently, using seed material. In the current article, we have developed a further MALDI-TOF MS-based method that can be used with seeds that uses only simple equipment and minimally hazardous reagents prior to storing and/or shipping dried seed proteins immobilized on filter paper for MALDI-TOF MS analysis. We have investigated I. glandulifera regional-biotype seeds originating from four different sites within the UK for which the parent plants differ in their susceptibility to the biological control agent Puccinia komarovii var. glanduliferae. Using a combination of time-course comparisons and principal-component analysis, we have demonstrated good MALDI-TOF MS spectral conservation, even after storage for 1 month at 35°C, of dried seed-protein samples immobilized on filter paper. This method may provide a further useful tool for the matching of biological control agents optimally to susceptible (regional) target-plant biotypes, and for seed characterization and/or identification in general.
Quantifying Facial Expression Intensity and Signal Use in Deaf Signers
Authors: Stoll Chloé , Rodger Helen , Lao Junpeng , Richoz Anne-Raphaëlle , Pascalis Olivier , Dye Matthew , Caldara Roberto 
Published: May 2019

Abstract
We live in a world of rich dynamic multisensory signals. Hearing individuals rapidly and effectively integrate multimodal signals to decode biologically relevant facial expressions of emotion. Yet, it remains unclear how facial expressions are decoded by deaf adults in the absence of an auditory sensory channel. We thus compared early and profoundly deaf signers (n = 46) with hearing nonsigners (n = 48) on a psychophysical task designed to quantify their recognition performance for the six basic facial expressions of emotion. Using neutral-to-expression image morphs and noise-to-full signal images, we quantified the intensity and signal levels required by observers to achieve expression recognition. Using Bayesian modeling, we found that deaf observers require more signal and intensity to recognize disgust, while reaching comparable performance for the remaining expressions. Our results provide a robust benchmark for the intensity and signal use in deafness and novel insights into the differential coding of facial expressions of emotion between hearing and deaf individuals.
Voluntarism, Corporatism and Path Dependency: The Metalworkers’ Unions Amalgamated Engineering Union and IG Metall and their Place in the History of British and German Industrial Relations
Authors: Hoffrogge Ralf 
Published: May 2019

Abstract
Germany and Britain have served as models of either corporatist or voluntarist industrial relations. The more recent typology of ‘varieties of capitalism’ then identified Britain as a model case of a ‘liberal market economy’ while Germany was portrayed as a (state) ‘co-ordinated market economy’. The mainstream of German-language labour history also tells this success story. Some research on the evolution of co-determination has portrayed its subject as a long-standing trait of German capitalism, with predecessors dating back as far as 1848. With its focus on the history of two key trade unions in core industries of Britain and Germany, the British metalworkers’ union the Amalgamated Society of Engineers / Amalgamated Engineering Union and the German Metal Workers’ Union / IG Metall, this article questions both exceptionalism and continuity. It argues that a path dependency exists in the structure of both unions and the industrial relations around them—but that this never came close to a linear evolution of voluntarism or corporatism. On closer examination, the history of both unions includes localist as well as centralist practices. From the 1890s both unions were part of collective bargaining with strong employers’ associations; especially after 1945 both were open to corporatist compromises. For West Germany only, such a compromise was found in the early 1950s, and not before, while in Britain that same compromise was attempted but failed during the crucial years between 1965 and 1979. Therefore, to quote Stefan Berger, this article argues that ‘similarities between the British and the German labour movements have been underestimated’.
Mendelian randomization analysis of celiac GWAS reveals a blood expression signature with diagnostic potential in absence of gluten consumption
Authors: Fernandez-Jimenez Nora , Bilbao Jose Ramon 
Published: May 2019

Abstract
Celiac disease (CeD) is an immune-mediated enteropathy with a strong genetic component where the main environmental trigger is dietary gluten, and currently a correct diagnosis of the disease is impossible if gluten-free diet (GFD) has already been started. We hypothesized that merging different levels of genomic information through Mendelian randomization (MR) could help discover genetic biomarkers useful for CeD diagnosis. MR was performed using public databases of expression quantitative trait loci (QTL) and methylation QTL as exposures and the largest CeD genome-wide association study conducted to date as the outcome, in order to identify potential causal genes. As a result, we identified UBE2L3, an ubiquitin ligase located in a CeD-associated region. We interrogated the expression of UBE2L3 in an independent data set of peripheral blood mononuclear cells (PBMCs) and found that its expression is altered in CeD patients on GFD when compared to non-celiac controls. The relative expression of UBE2L3 isoforms predicts CeD with 100% specificity and sensitivity and could be used as a diagnostic marker, especially in the absence of gluten consumption. This approach could be applicable to other diseases where diagnosis of asymptomatic patients can be complicated.
Non-linearity in stock–recruitment relationships of Atlantic cod: insights from a multi-model approach
Authors: Sguotti Camilla , Otto Saskia A , Cormon Xochitl , Werner Karl M , Deyle Ethan , Sugihara George , Möllmann Christian 
Published: May 2019

Abstract
The stock–recruitment relationship is the basis of any stock prediction and thus fundamental for fishery management. Traditional parametric stock–recruitment models often poorly fit empirical data, nevertheless they are still the rule in fish stock assessment procedures. We here apply a multi-model approach to predict recruitment of 20 Atlantic cod (Gadus morhua) stocks as a function of adult biomass and environmental variables. We compare the traditional Ricker model with two non-parametric approaches: (i) the stochastic cusp model from catastrophe theory and (ii) multivariate simplex projections, based on attractor state-space reconstruction. We show that the performance of each model is contingent on the historical dynamics of individual stocks, and that stocks which experienced abrupt and state-dependent dynamics are best modelled using non-parametric approaches. These dynamics are pervasive in Western stocks highlighting a geographical distinction between cod stocks, which have implications for their recovery potential. Furthermore, the addition of environmental variables always improved the models’ predictive power indicating that they should be considered in stock assessment and management routines. Using our multi-model approach, we demonstrate that we should be more flexible when modelling recruitment and tailor our approaches to the dynamical properties of each individual stock.
Less invasive left ventricular assist device implantation may reduce right ventricular failure
Authors: Pasrija Chetan , Sawan Mariem A , Sorensen Erik , Voorhees Hannah , Shah Aakash , Strauss Erik , Ton Van-Khue , DiChiacchio Laura , Kaczorowski David J , Griffith Bartley P , Pham Si M , Kon Zachary N 
Published: May 2019

Abstract

OBJECTIVES
Right ventricular (RV) failure after left ventricular assist device (LVAD) implantation continues to be a morbid complication. In this study, we hypothesized that a less invasive approach to implantation would preserve RV function relative to a conventional sternotomy (CS) approach.

METHODS
All patients (2013–2017) who underwent LVAD implantation were reviewed. Patients were stratified by surgical approach: less invasive left thoracotomy with hemi-sternotomy (LTHS) and CS. The primary outcome was severe RV failure.

RESULTS
Eighty-three patients (LTHS: 37, CS: 46) were identified. The median Interagency Registry for Mechanically Assisted Circulatory Support (INTERMACS) score was significantly worse in the LTHS compared to the CS cohort, and there was a trend towards higher RV failure scores and HeartMate II mortality scores. Preoperative RV dysfunction, in pulmonary artery pulsatility index and RV stroke work index were similar between the 2 groups. Though operative time did not significantly differ between the 2 groups, cardiopulmonary bypass time was significantly shorter in the LTHS group (61 vs 95 min, P < 0.001). The incidence of postoperative severe RV failure was significantly reduced in the LTHS group (16% vs 39%, P = 0.030), along with the need for temporary right ventricular assist device (3% vs 26%, P = 0.005). Improvement in RV function, along with a change in pulmonary artery pulsatility index, was significantly greater in the LTHS cohort. There was a trend towards improved Kaplan–Meier 1-year survival in the LTHS cohort (91% vs 56%, P = 0.056).

CONCLUSIONS
In this cohort, less invasive LVAD implantation appears to be associated with reduced postoperative RV failure, and equivalent or improved survival compared to conventional LVAD implantation.
Bacterial brothers in arms: cooperation of Staphylococcus aureus and Pseudomonas aeruginosa during antimicrobial exposure
Authors: Lenhard Justin R , Smith Nicholas M , Quach Christine D , Nguyen Tuan Q , Doan Linh H , Chau Jeanette 
Published: May 2019

Abstract

Objectives
The optimal selection of antibacterials during polymicrobial infections is poorly defined. The objective of the current investigation was to quantify the pharmacodynamics of relevant antimicrobials during co-culture of Pseudomonas aeruginosa with two separate Staphylococcus aureus phenotypes.

Methods
Time–kill experiments were conducted against co-cultures of the P. aeruginosa strain PA01 paired with either the normal phenotype (NP) MRSA isolate COL or the small colony variant phenotype (SCVP) MRSA isolate Ia48. The killing by levofloxacin, gentamicin, clindamycin, vancomycin and polymyxin B was evaluated to investigate drugs with activity against one or both pathogens. A Hill-type function and a mechanism-based model were used to describe bacterial killing.

Results
P. aeruginosa attenuated the activity of clindamycin against NP MRSA, with a reduction in the Emax (maximal killing) from 3.67 (95% CI 2.79–4.56) in monoculture to 1.86 (95% CI 1.35–2.37) during co-culture, whereas a significant protective effect was not observed for other antibacterials. The reduction in NP MRSA killing by clindamycin was described well by a mechanism-based model that generated a maximal killing rate constant of clindamycin against the susceptible NP MRSA subpopulation of 0.267 h−1 in monoculture and 0.0395 h−1 in the presence of P. aeruginosa. During exposure to gentamicin, P. aeruginosa was the dominant organism in co-culture experiments regardless of the drug concentration or S. aureus phenotype; however, the SCVP MRSA was able to dominate the joint population beginning at a levofloxacin concentration of 1.5 mg/L.

Conclusions
The anti-staphylococcal activity of clindamycin was attenuated by the presence of P. aeruginosa.
Oral antibiotics for neonatal infections: a systematic review and meta-analysis
Authors: Keij Fleur M , Kornelisse René F , Hartwig Nico G , Reiss Irwin K M , Allegaert Karel , Tramper-Stranders Gerdien A 
Published: May 2019

AbstractBackgroundWorldwide many neonates suffer from bacterial infections. Adequate treatment is important but is associated with prolonged hospitalization for intravenous administration. In older children, oral switch therapy has been proven effective and safe for several indications and is now standard care.ObjectivesTo evaluate the currently available evidence on pharmacokinetics, safety and efficacy of oral antibiotics and oral switch therapy in neonates (0–28 days old).MethodsWe performed systematic searches in Medline, Embase.com, Cochrane, Google Scholar and Web of Science. Studies were eligible if they described the use of oral antibiotics in neonates (0–28 days old), including antibiotic switch studies and pharmacological studies.ResultsThirty-one studies met the inclusion criteria. Compared with parenteral administration, oral antibiotics generally reach their maximum concentration later and have a lower bioavailability, but in the majority of cases adequate serum levels for bacterial killing are reached. Furthermore, studies on efficacy of oral antibiotics showed equal relapse rates (OR 0.95; 95% CI 0.79–1.16; I2 0%) or mortality (OR 1.11; 95% CI 0.72–1.72; I2 0%). Moreover, a reduction in hospital stay was observed.ConclusionsOral antibiotics administered to neonates are absorbed and result in adequate serum levels, judged by MICs of relevant pathogens, over time. Efficacy studies are promising but robust evidence is lacking, most importantly because in many cases clinical efficacy and safety are not properly addressed. Early oral antibiotic switch therapy in neonates could be beneficial for both families and healthcare systems. There is a need for additional well-designed trials in different settings.