bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carry-over effects of resource competition and social environment on aggression
Authors: Kilgour R J , Norris D R , McAdam A G 
Published: September 2019

AbstractAggressive behavior is common in many species and is often adaptive because it enables individuals to gain access to limited resources. However, aggression is also highly plastic and the degree of plasticity could be influenced by factors such as resource limitation and the social environment. In this study, we examined how the effects of social experience and resource limitation could persist to affect future aggressive interactions. Using naturally inbred strains of Drosophila melanogaster that differ in aggressiveness, we manipulated the level of available resources by varying fly density (two treatments: high and low per capita resources) and group composition by varying strain frequency (five treatments: homogeneous strains, or mixed at 1:3, 1:1 or 3:1 ratios of the more aggressive to less-aggressive strain). For each treatment group, we measured aggression before and after flies were placed through a 4-day period of fixed resources. There was no consistent effect of resource competition on aggression. Instead, changes in aggression depended on resource availability in combination with group composition. In homogeneous groups made up of only one strain, all males became more aggressive following the fixed-resource period, regardless of fly density. In mixed-strain treatments at high density, we observed plastic shifts in aggression of males from both strains, but the direction of plastic responses depended on social composition. Our results show that aggression may not only be influenced by the intensity of previous competitive experiences caused by resource limitation, but also through social effects caused by the composition of the group.
Self-reported Sleep Problems Related to Amyloid Deposition in Cortical Regions with High HOMER1 Gene Expression
Authors: Fjell Anders M , Sederevicius Donatas , Sneve Markus H , de Lange Ann-Marie Glasø , Bråthen Anne CecilieSjøli , Idland Ane-Victoria , Watne Leiv Otto , Wang Yunpeng , Reinbold Céline , Dobricic Valerija , Kilpert Fabian , Blennow Kaj , Zetterbergj Henrik , Hong Shengjun , Bertram Lars , Walhovd Kristine B ,   for The Alzheimer’s Disease Neuroimaging Initiative
Published: September 2019

AbstractSleep problems are related to the elevated levels of the Alzheimer’s disease (AD) biomarker β-amyloid (Aβ). Hypotheses about the causes of this relationship can be generated from molecular markers of sleep problems identified in rodents. A major marker of sleep deprivation is Homer1a, a neural protein coded by the HOMER1 gene, which has also been implicated in brain Aβ accumulation. Here, we tested whether the relationship between cortical Aβ accumulation and self-reported sleep quality, as well as changes in sleep quality over 3 years, was stronger in cortical regions with high HOMER1 mRNA expression levels. In a sample of 154 cognitively healthy older adults, Aβ correlated with poorer sleep quality cross-sectionally and longitudinally (n = 62), but more strongly in the younger than in older individuals. Effects were mainly found in regions with high expression of HOMER1. The anatomical distribution of the sleep-Aβ relationship followed closely the Aβ accumulation pattern in 69 patients with mild cognitive impairment or AD. Thus, the results indicate that the relationship between sleep problems and Aβ accumulation may involve Homer1 activity in the cortical regions, where harbor Aβ deposits in AD. The findings may advance our understanding of the relationship between sleep problems and AD risk.
A Validated Ultra-Performance Liquid Chromatographic Method for the Simultaneous Determination of Nadifloxacin, Mometasone Furoate and Miconazole Nitrate in Their Combined Dosage Form and Spiked Human Plasma Samples
Authors: Tarek Mohamed , Wagdy Hebatallah A , Elzanfaly Eman S , Amer Sawsan M 
Published: September 2019

AbstractNadifloxacin, mometasone furoate and miconazole nitrate are formulated together as a topical antifungal dosage form. In this work, a reversed-phase ultra-performance liquid chromatographic method coupled with a diode array detector (RP-UPLC-DAD) was developed and validated to determine nadifloxacin, mometasone furoate and miconazole nitrate simultaneously in their bulk powder, in pharmaceutical preparation and in spiked human plasma samples. Separation was achieved on an ACQUITY UPLC C18 column of 2.2 μm particle size (2.1 × 100 mm) via isocratic elution using a mobile phase consisting of methanol, acetonitrile and water with ratio (50:20:30; v/v/v) and 0.1 g ammonium acetate, then pH was adjusted to (7.00) using acetic acid, flow rate 0.6 mL/min, temperature 30°C and UV detection at 220 nm. The method is linear in a range from 5 to 400 μg/mL for both nadifloxacin and miconazole nitrate and from 20 to 500 μg/mL for mometasone furoate. The method was validated according to the ICH guidelines then applied successfully to determine the mentioned drugs in their pharmaceutical preparation and spiked human plasma samples. For plasma samples, the results showed that the method can determine nadifloxacin, mometasone furoate and miconazole nitrate in human plasma samples with high accuracy and precision.
Risk Factors for Brain Abscess: A Nationwide, Population-Based, Nested Case-Control Study
Authors: Bodilsen Jacob , Dalager-Pedersen Michael , van de Beek Diederik , Brouwer Matthijs C , Nielsen Henrik 
Published: September 2019

Abstract

Background
Knowledge on risk factors for brain abscess is limited and relies on single-center cohort studies.

Methods
We accessed nationwide medical registries to conduct a population-based, nested case-control study of risk factors for brain abscess. We applied risk-set sampling for the selection of population controls (1:10), who were individually matched by age, sex, and area of residence. Conditional logistic regression was used to compute adjusted odds ratios (aOR) with 95% confidence intervals (CIs). Population-attributable fractions were calculated.

Results
We identified 1384 brain abscess patients in Denmark from 1982 through 2016, and 13 839 matched population controls. The median age of patients was 50 years (interquartile range 33–63) and 37% were female. Cases often had Charlson comorbidity scores &gt;2 (16%), compared with controls (3%). Our calculated aORs were 2.15 (95% CI 1.72–2.70) for head trauma; 19.3 (95% CI 14.3–26.0) for neurosurgery; 4.61 (95% CI 3.39–6.26) for dental infections; 2.57 (95% CI 1.71–3.84) for dental surgery; 3.81 (95% CI 3.11–4.67) for ear, nose, and throat infection; 2.85 (95% CI 2.21–3.70) for ear, nose, and throat surgery; 15.6 (95% CI 9.57–25.4) for congenital heart disease; 1.74 (95% CI 1.33–2.29) for diabetes mellitus; 2.22 (95% CI 1.58–3.11) for alcohol abuse; 2.37 (95% CI 1.53–3.68) for liver disease; 2.04 (95% CI 1.30–3.20) for kidney disease and 8.15 (95% CI 3.59–18.5) for lung abscess or bronchiectasis. The aORs were 4.12 (95% CI 3.37–5.04) for solid cancer; 8.77 (95% CI 5.66–13.6) for hematological cancer; 12.0 (95% CI 6.13–23.7) for human immunodeficiency virus; and 5.71 (95% CI 4.22–7.75) for immunomodulating treatments. Population-attributable fractions showed were substantial contributors to the occurrence of brain abscess neurosurgery (12%); solid cancer (11%); ear, nose, and throat infections (7%); and immunomodulating treatments (5%).

Conclusions
Important risk factors included neurosurgery; cancer; ear, nose, and throat infections; and immunomodulating treatments.
Vitamin K antagonist has a higher impact than heparin in preventing circuit clotting in chronic haemodialysis patients
Authors: Charles Pierre-Yves , Le Meur Yannick , Tanquerel Tugdual , Galinat Hubert 
Published: September 2019

Abstract

Background
In dialysis sessions, some data suggest that decreasing or even avoiding additional anticoagulation by heparin is possible among patients already treated with oral anticoagulation. However, the required dose of heparin may actually depend on the pre-dialysis international normalized ratio (INR), which varies from one session to another. The aim of our study was to determine the respective role of INR and heparin dosing in the risk of circuit clotting during chronic haemodialysis.

Methods
From early 2012 to July 2016, we analysed the totality of dialysis sessions performed at Brest University Hospital among haemodialysis patients treated by vitamin K antagonists (VKA). We established a prediction of circuit clotting on the basis of a simplified score obtained by combining INR and heparin dosing.

Results
In total, 7184 dialysis sessions among chronic haemodialysis patients under VKA were identified, including 233 with clotting events. The mean INR without clotting events was 2.5 versus 1.8 with clotting events (P &lt; 0.001). Frequencies of circuit clotting were different according to INR group (INR &lt;2.0, INR 2.0–3.0, INR &gt;3.0; P &lt; 0.0001). The protective role of VKA was higher than heparin, as shown by discriminant factor analysis (P &lt; 0.0001).
Conclusion. Our study established a predictive model of thrombosis risk of dialysis circuits in patients treated by VKA for a given heparin dose and a given INR. This model shows a marginal contribution of heparin to protect against the risk of thrombosis compared with VKA. Moreover, heparin would not appear to be necessary for patients with an INR &gt;2.2.
Byte2vec: Malware Representation and Feature Selection for Android
Authors: Yousefi-Azar Mahmood , Hamey Len , Varadharajan Vijay , Chen Shiping 
Published: September 2019

AbstractMalware detection based on static features and without code disassembling is a challenging path of research. Obfuscation makes the static analysis of malware even more challenging. This paper extends static malware detection beyond byte level $n$-grams and detecting important strings. We propose a model (Byte2vec) with the capabilities of both binary file feature representation and feature selection for malware detection. Byte2vec embeds the semantic similarity of byte level codes into a feature vector (byte vector) and also into a context vector. The learned feature vectors of Byte2vec, using skip-gram with negative-sampling topology, are combined with byte-level term-frequency (tf) for malware detection. We also show that the distance between a feature vector and its corresponding context vector provides a useful measure to rank features. The top ranked features are successfully used for malware detection. We show that this feature selection algorithm is an unsupervised version of mutual information (MI). We test the proposed scheme on four freely available Android malware datasets including one obfuscated malware dataset. The model is trained only on clean APKs. The results show that the model outperforms MI in a low-dimensional feature space and is competitive with MI and other state-of-the-art models in higher dimensions. In particular, our tests show very promising results on a wide range of obfuscated malware with a false negative rate of only 0.3% and a false positive rate of 2.0%. The detection results on obfuscated malware show the advantage of the unsupervised feature selection algorithm compared with the MI-based method.
Foraging Site Selection by Nonbreeding White-Faced IBIS
Authors: Safran Rebecca J. , Colwell Mark A. , Isola Craig R. , Taft Oriane E. 
Published: September 2019

Abstract
We examined foraging site selection by White-faced Ibis (Plegadis chihi) wintering in the Grasslands Ecological Area, which contains the second largest population of nonbreeding ibis in California. We compared habitat variables at White-faced Ibis foraging sites with paired, random locations in managed wetlands of the Grasslands. We contrasted the density and biomass of benthic macroinvertebrates between a subsample of bird foraging locations and random sites. Compared to random locations, the foraging locations of White-faced Ibis were closer to emergent vegetation > 10 cm in height. Moreover, ibis selected foraging locations with significantly higher chironomid and lower oligochaete biomasses relative to random sites. These findings suggest that ibis foraged close to vegetation where prey abundance may be greater and illustrate the importance of maintaining the presence of emergent vegetation in freshwater wetlands.
Impaired NF-κB signalling underlies cyclophilin D-mediated mitochondrial permeability transition pore opening in doxorubicin cardiomyopathy
Authors: Dhingra Rimpy , Guberman Matthew , Rabinovich-Nikitin Inna , Gerstein Jonathon , Margulets Victoria , Gang Hongying , Madden Nicholas , Thliveris James , Kirshenbaum Lorrie A 
Published: September 2019

Abstract

Aims
The chemotherapy drug doxorubicin (Dox) is commonly used for treating a variety of human cancers; however, it is highly cardiotoxic and induces heart failure. We previously reported that the Bcl-2 mitochondrial death protein Bcl-2/19kDa interaction protein 3 (Bnip3), is critical for provoking mitochondrial perturbations and necrotic cell death in response to Dox; however, the underlying mechanisms had not been elucidated. Herein, we investigated mechanism that drives Bnip3 gene activation and downstream effectors of Bnip3-mediated mitochondrial perturbations and cell death in cardiac myocytes treated with Dox.

Methods and results
Nuclear factor-κB (NF-κB) signalling, which transcriptionally silences Bnip3 activation under basal states in cardiac myocytes was dramatically reduced following Dox treatment. This was accompanied by Bnip3 gene activation, mitochondrial injury including calcium influx, permeability transition pore (mPTP) opening, loss of nuclear high mobility group protein 1, reactive oxygen species production, and cell death. Interestingly, impaired NF-κB signalling in cells treated with Dox was accompanied by protein complexes between Bnip3 and cyclophilin D (CypD). Notably, Bnip3-mediated mPTP opening was suppressed by inhibition of CypD—demonstrating that CypD functionally operates downstream of Bnip3. Moreover, restoring IKKβ–NF-κB activity in cardiac myocytes treated with Dox suppressed Bnip3 expression, mitochondrial perturbations, and necrotic cell death.

Conclusions
The findings of the present study reveal a novel signalling pathway that functionally couples NF-κB and Dox cardiomyopathy to a mechanism that is mutually dependent upon and obligatorily linked to the transcriptional control of Bnip3. Our findings further demonstrate that mitochondrial injury and necrotic cell death induced by Bnip3 is contingent upon CypD. Hence, maintaining NF-κB signalling may prove beneficial in reducing mitochondrial dysfunction and heart failure in cancer patients undergoing Dox chemotherapy.
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus
Authors: Skwark Marcin J , Torres Pedro H M , Copoiu Liviu , Bannerman Bridget , Floto R Andres , Blundell Tom L 
Published: September 2019

AbstractMycobacterium abscessus, a rapid growing, multidrug resistant, nontuberculous mycobacteria, can cause a wide range of opportunistic infections, particularly in immunocompromised individuals. M. abscessus has emerged as a growing threat to patients with cystic fibrosis, where it causes accelerated inflammatory lung damage, is difficult and sometimes impossible to treat and can prevent safe transplantation. There is therefore an urgent unmet need to develop new therapeutic strategies. The elucidation of the M. abscessus genome in 2009 opened a wide range of research possibilities in the field of drug discovery that can be more effectively exploited upon the characterization of the structural proteome. Where there are no experimental structures, we have used the available amino acid sequences to create 3D models of the majority of the remaining proteins that constitute the M. abscessus proteome (3394 proteins and over 13 000 models) using a range of up-to-date computational tools, many developed by our own group. The models are freely available for download in an on-line database, together with quality data and functional annotation. Furthermore, we have developed an intuitive and user-friendly web interface (http://www.mabellinidb.science) that enables easy browsing, querying and retrieval of the proteins of interest. We believe that this resource will be of use in evaluating the prospective targets for design of antimicrobial agents and will serve as a cornerstone to support the development of new molecules to treat M. abscessus infections.
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery
Authors: Gourdine Jean-Philippe F , Brush Matthew H , Vasilevsky Nicole A , Shefchek Kent , Köhler Sebastian , Matentzoglu Nicolas , Munoz-Torres Monica C , McMurry Julie A , Zhang Xingmin Aaron , Robinson Peter N , Haendel Melissa A 
Published: September 2019

Abstract
While abnormalities related to carbohydrates (glycans) are frequent for patients with rare and undiagnosed diseases as well as in many common diseases, these glycan-related phenotypes (glycophenotypes) are not well represented in knowledge bases (KBs). If glycan-related diseases were more robustly represented and curated with glycophenotypes, these could be used for molecular phenotyping to help to realize the goals of precision medicine. Diagnosis of rare diseases by computational cross-species comparison of genotype–phenotype data has been facilitated by leveraging ontological representations of clinical phenotypes, using Human Phenotype Ontology (HPO), and model organism ontologies such as Mammalian Phenotype Ontology (MP) in the context of the Monarch Initiative. In this article, we discuss the importance and complexity of glycobiology and review the structure of glycan-related content from existing KBs and biological ontologies. We show how semantically structuring knowledge about the annotation of glycophenotypes could enhance disease diagnosis, and propose a solution to integrate glycophenotypes and related diseases into the Unified Phenotype Ontology (uPheno), HPO, Monarch and other KBs. We encourage the community to practice good identifier hygiene for glycans in support of semantic analysis, and clinicians to add glycomics to their diagnostic analyses of rare diseases.
Experimental evolution of gallium resistance in Escherichia coli
Authors: Graves Joseph L , Ewunkem Akamu J , Ward Jason , Staley Constance , Thomas Misty D , Rhinehardt Kristen L , Han Jian , Harrison Scott H 
Published: September 2019

AbstractBackground and ObjectivesMetallic antimicrobial materials are of growing interest due to their potential to control pathogenic and multidrug-resistant bacteria. Yet we do not know if utilizing these materials can lead to genetic adaptations that produce even more dangerous bacterial varieties.MethodologyHere we utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.ResultsBy day 10 of evolution, increased gallium resistance was evident in populations cultured in medium containing a sublethal concentration of gallium. Furthermore, these populations showed increased resistance to ionic silver and iron (III), but not iron (II) and no increase in traditional antibiotic resistance compared with controls and the ancestral strain. In contrast, the control populations showed increased resistance to rifampicin relative to the gallium-resistant and ancestral population. Genomic analysis identified hard selective sweeps of mutations in several genes in the gallium (III)-resistant lines including: fecA (iron citrate outer membrane transporter), insl1 (IS30 tranposase) one intergenic mutations arsC →/→ yhiS; (arsenate reductase/pseudogene) and in one pseudogene yedN ←; (iapH/yopM family). Two additional significant intergenic polymorphisms were found at frequencies &gt; 0.500 in fepD ←/→ entS (iron-enterobactin transporter subunit/enterobactin exporter, iron-regulated) and yfgF ←/→ yfgG (cyclic-di-GMP phosphodiesterase, anaerobic/uncharacterized protein). The control populations displayed mutations in the rpoB gene, a gene associated with rifampicin resistance.ConclusionsThis study corroborates recent results observed in experiments utilizing pathogenic Pseudomonas strains that also showed that Gram-negative bacteria can rapidly evolve resistance to an atom that mimics an essential micronutrient and shows the pleiotropic consequences associated with this adaptation.Lay summaryWe utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.
Factors associated with improving diet and physical activity among persons with excess body weight
Authors: Reile Rainer , Leinsalu Mall 
Published: September 2019

Abstract

Background
As overweight and obesity are highly prevalent in Eastern Europe, the study examined the trends and factors associated with self-reported weight reducing behaviours among individuals with excess body weight in Estonia.

Methods
Study used nationally representative cross-sectional data from 2006 to 2016 including 4302 men and 3627 women aged 20–64 years with excess body weight (BMI ≥ 25). Trends in the prevalence of changing eating habits and physical activity and their sociodemographic and health-related correlates were studied using descriptive statistics and multivariable logistic regression.

Results
Among overweight or obese respondents, 41% of men and 48% of women reported improvements in dietary habits and 19% of men and women reported increase in physical activity during the past 12 months in 2016. Positive trend for 2006–2016 regarding both outcomes was observed for men whereas no statistically significant differences were found for women. Women and those with lower than tertiary education had higher odds for reporting change in eating habits whereas older age and smoking or excessive alcohol consumption reduced the odds. Improvement in physical activity was more likely among younger respondents, women, ethnic Estonians and those with tertiary education, whereas poorer health and smoking reduced the odds. Weight-related advice from health professionals or family had strong effect on both outcomes.

Conclusion
Socio-demographic and health profiles differentiate the self-reported behavioural change among persons with excess body weight. Advice from either health professionals or family may have a potential to facilitate positive changes in eating habits and physical activity among those individuals.