bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of multidrug and extensive-drug resistant Gam-negative bacteria in skin and soft tissue infections
Authors: Brink Adrian J. , Richards Guy A. 
Published: January 2020

Purpose of review
Whereas Staphylococcus aureus remains the leading cause of skin and soft tissue infections (SSTI), Gram-negative bacilli (GNB) are increasingly reported as a cause of monomicrobial or polymicrobial infections. This review examines the expanding role of GNB in SSTI and discusses the risks for and the frequency of multidrug-resistance (MDR) and extensive drug-resistance (XDR) and the implications with regard to outcome and therapy.

Recent findings
Although the global epidemiology and role of GNB in SSTIs have not been studied systematically, complicated SSTIs caused by resistant GNB are increasing particularly in vulnerable patients with long-standing infections, those in long-term care facilities, and those with a history of recent hospitalization or prior antibiotic therapy. Mixed infections also occur in up to 25% of SSTIs, and inappropriate therapy occurs in 40% of cases. Prompt identification of the causative pathogen requires that patients with SSTI be risk stratified according to the likelihood of resistance to enable early recognition and swift initiation of appropriate therapy.

Summary
For individual treatment decisions in SSTIs, institutional diagnostic and treatment algorithms based on local epidemiology and risk factors are pivotal to reducing the incidence of treatment failure and improving outcomes associated with resistant GNB.
Complications After Reperitonealization of Mesh at Time of Sacrocolpopexy: A Retrospective Cohort Study
Authors: Glass Clark Stephanie M. , Shannon Megan B. , Gill Edward , Clark Michael D. , Lamb Elizabeth , Carroll Ashley 
Published: January 2020

Objectives
To determine if there is a difference in rates of surgical complications among patients who have reperitonealization of mesh versus no reperitonealization at time of sacrocolpopexy.

Methods
This was a retrospective cohort study of all patients who underwent sacrocolpopexy at an academic medical center between 2008 and 2017. The medical record was reviewed for the operative method of sacrocolpopexy, concomitant surgeries, intraoperative or postoperative complications, and readmissions. Groups were compared on whether mesh was reperitonealized under pelvic peritoneum or not.

Results
A total of 209 patients underwent sacrocolpopexy, with mesh reperitonealization performed in 115 (55%). Demographics were similar in both groups, except race/ethnicity and stage of prolapse. The majority (190 [91%]) of surgeries included concomitant procedures. A total of 18 intraoperative or postoperative complications (8.6%) were recorded. Relative risk of complication with mesh reperitonealization is 0.81 (95% confidence interval, 0.1–1.70). Complications for subjects without mesh reperitonealization included 4 cystostomies, 1 urethrotomy, 3 postoperative ileuses, and 1 small bowel obstruction. Among subjects with mesh reperitonealization, complications included 5 cystotomies, 2 proctotomies, 1 ureteral obstruction, and 1 small bowel obstruction. Rates of hospital readmission among both groups were not significantly different, with 3.2% of subjects without mesh reperitonealization versus 3.5% of mesh reperitonealization patients (P = 0.91) (relative risk, 1.09; 95% confidence interval, 0.38–2.56).

Conclusions
There is no significant difference in rates of complications or readmissions among patients with and without mesh reperitonealization at time of sacrocolpopexy. The only intraoperative complication solely attributed to mesh closure was a case with ureteral obstruction at time of reperitonealization.
Racial and Ethnic Differences in Urodynamic Parameters in Women With Overactive Bladder Symptoms
Authors: Zuo Stephanie W. , English Keara , Agalliu Ilir , Leegant Ava , Abraham Nitya 
Published: January 2020

Objectives
This study aimed to identify differences in severity of overactive bladder (OAB) symptoms in women of different races and ethnicities using urodynamic study (UDS) parameters.

Methods
We performed a 5-year retrospective chart review from January 2014 to January 2019 of women 18 years and older who endorsed OAB symptoms and underwent UDS at a racially and ethnically diverse academic urban medical center. Logistic and linear regressions were used to examine the associations of various UDS parameters between racial/ethnic groups, after adjusting for age, diabetes, and parity.

Results
A total of 161 women with an average age of 59 years were included in the study. The racial/ethnic composition of the group was Hispanic (62%), black (24%), and white (11%). Symptoms on presentation included urgency and/or frequency (11.8%), urge incontinence (23.0%), or mixed urinary symptoms (65.2%). Black and Hispanic women presented with differing symptoms (urgency/frequency vs mixed urinary symptoms). Half of the patients (n = 82) had detrusor overactivity. Compared with whites, blacks were 3.4-fold more likely to have detrusor overactivity (95% confidence interval, 0.99–11.40) and had lower volumes at time of “strong desire” (−102.6 mL, P = 0.003). Hispanics had on average 75.88 mL less volume at sensation of “strong desire” (P = 0.016) than did whites.

Conclusions
Our study suggests that minority race and ethnicity may be associated with worse performance on certain UDS parameters. Future studies should aim to understand if these differences are due to genetic, disease-related, behavioral, and/or socioeconomic factors and whether these differences are associated with worse subjective OAB.
Caffeine stabilises fission yeast Wee1 in a Rad24-dependent manner but attenuates its expression in response to DNA damage identifying a putative role for TORC1 in mediating its effects on cell cycle progression
Authors: Alao John P. , Johansson-Sjölander Johanna , Rallis Charalampos , Sunnerhagen Per 
Published: January 2020

AbstractThe widely consumed neuroactive compound caffeine has generated much interest due to its ability to override the DNA damage and replication checkpoints. Previously Rad3 and its homologues was thought to be the target of caffeine’s inhibitory activity. Later findings indicate that the Target of Rapamycin Complex 1 (TORC1) is the preferred target of caffeine. Effective Cdc2 inhibition requires both the activation of the Wee1 kinase and inhibition of the Cdc25 phosphatase. The TORC1, DNA damage, and environmental stress response pathways all converge on Cdc25 and Wee1. We previously demonstrated that caffeine overrides DNA damage checkpoints by modulating Cdc25 stability. The effect of caffeine on cell cycle progression resembles that of TORC1 inhibition. Furthermore, caffeine activates the Sty1 regulated environmental stress response. Caffeine may thus modulate multiple signalling pathways that regulate Cdc25 and Wee1 levels, localisation and activity. Here we show that the activity of caffeine stabilises both Cdc25 and Wee1. The stabilising effect of caffeine and genotoxic agents on Wee1 was dependent on the Rad24 chaperone. Interestingly, caffeine inhibited the accumulation of Wee1 in response to DNA damage. Caffeine therefore modulates cell cycle progression contextually through increased Cdc25 activity and Wee1 repression following DNA damage via TORC1 inhibition.
Associations between dietary patterns and gene expression pattern in peripheral blood mononuclear cells: a cross-sectional study
Authors: Christensen Jacob J. , Ulven Stine M. , Thoresen Magne , Westerman Kenneth , Holven Kirsten B. , Andersen Lene F. 
Published: January 2020

AbstractBackgroundDiet may alter gene expression in immune cells involved in cardio-metabolic disease susceptibility. However, we still lack a robust understanding of the association between diet and immune cell-related gene expression in humans.ObjectiveOur objective was to examine the associations between dietary patterns (DPs) and gene expression profiles in peripheral blood mononuclear cells (PBMCs) in a population of healthy, Norwegian adults.MethodsWe used factor analysis to definea posterioriDPs from food frequency questionnaire-based dietary assessment data. In addition, we derived interpretable features from microarray-based gene expression data (13 967 transcripts) using two algorithms: CIBERSORT for estimation of cell subtype proportions, and weighted gene co-expression network analysis (WGCNA) for cluster discovery. Finally, we associated DPs with either CIBERSORT-predicted PBMC leukocyte distribution or WGCNA gene clusters using linear regression models. All analyses were gender-stratified (n = 130 women and 105 men).ResultsWe detected three DPs that broadly reflectedWestern, Vegetarian, andLow carbohydratediets. CIBERSORT-predicted percentage of monocytes associated strongly and negatively with theVegetarianDP in both women and men. For women, theVegetarianDP associated most strongly with a large gene cluster consisting of 600 genes mainly involved in regulation of DNA transcription. For men, theWesternDP inversely associated most strongly with a smaller cluster of 36 genes mainly involved in regulation of metabolic and inflammatory processes. In subsequent protein-protein interaction network analysis, the most importantdriver geneswithin these WGCNA gene clusters seemed to physically interact in biological networks.ConclusionsDPs may affect percentage monocytes and regulation of key biological processes within the PBMC pool. Although the present findings are exploratory, our analysis pipeline serves a useful framework for studying the association between diet and gene expression.
Shifts in gut microbiome and metabolome are associated with risk of recurrent atrial fibrillation
Authors: Zuo Kun , Li Jing , Zhang Jing , Wang Pan , Jiao Jie , Liu Zheng , Yin Xiandong , Liu Xiaoqing , Li Kuibao , Yang Xinchun 
Published: January 2020

ABSTRACTSpecific alterations of gut microbiota (GM) in atrial fibrillation (AF) patients, including elevated microbial diversity, particularly perturbed composition, imbalanced microbial function, and associated metabolic pattern modifications have been described in our previous report. The current work aimed to assess the association of GM composition with AF recurrence (RAF) after ablation, and to construct a GM-based predictive model for RAF. Gut microbial composition and metabolic profiles were assessed based on metagenomic sequencing and metabolomic analyses. Compared with non-AF controls (50 individuals), GM composition and metabolomic profile were significantly altered between patients with recurrent AF (17 individuals) and the non-RAF group (23 individuals). Notably, discriminative taxa between the non-RAF and RAF groups, including the familiesNitrosomonadaceaeandLentisphaeraceae, the generaMarinitogaandRufibacter, and the speciesFaecalibacteriumsp. CAG:82,Bacillus gobiensis, andDesulfobacterales bacterium PC51MH44, were selected to construct a taxonomic scoring system based on LASSO analysis. An elevated area under curve (0.954) and positive net reclassification index (1.5601) for predicting RAF compared with traditional clinical scoring (AUC=0.6918) were obtained. The GM-based taxonomic scoring system theoretically improves the model performance. These data provide novel evidence that supports incorporating the GM factor into future recurrent risk stratification.
The incubation period of 2019-nCoV infections among travellers from Wuhan, China
Authors: Backer Jantien A. , Klinkenberg Don , Wallinga Jacco 
Published: January 2020

AbstractCurrently, a novel coronavirus 2019-nCoV causes an outbreak of viral pneumonia in Wuhan, China. Little is known about its epidemiological characteristics. Using the travel history and symptom onset of 88 confirmed cases that were detected outside Wuhan, we estimate the mean incubation period to be 6.4 (5.6 – 7.7, 95% CI) days, ranging from 2.1 to 11.1 days (2.5th to 97.5th percentile). These values help to inform case definitions for 2019-nCoV and appropriate durations for quarantine.
ctDNAtools: An R package to work with sequencing data of circulating tumor DNA
Authors: Alkodsi Amjad , Meriranta Leo , Pasanen Annika , Leppä Sirpa 
Published: January 2020

AbstractSummarySequencing of cell-free DNA (cfDNA) including circulating tumor DNA (ctDNA) in minimally-invasive liquid biopsies is rapidly maturing towards clinical utility for cancer diagnostics. However, the publicly available bioinformatics tools for the specialized analysis of ctDNA sequencing data are still scarce. Here, we present the ctDNAtools R package, which provides functionalities for testing minimal residual disease (MRD) and analyzing cfDNA fragmentation. MRD detection in ctDNAtools utilizes a Monte Carlo sampling approach to test ctDNA positivity through tracking a set of pre-detected reporter mutations in follow-up samples. Additionally, ctDNAtools includes various functionalities to study cfDNA fragment size histograms, profiles and fragment ends patterns.AvailabilityThe ctDNAtools package is freely available under MIT license athttps://github.com/alkodsi/ctDNAtools.
An analysis of Species Conservation Action Plans in Guinea
Authors: Couch Charlotte , Molmou Denise , Magassouba Sékou , Doumbouya Saïdou , Diawara Mamadou , Yaya Diallo Muhammad , Keita Sékou Moussa , Koné Falaye , Diallo Mahamadou Cellou , Kourouma Sékou , Diallo Mamadou Bella , Keita Mamady Sayba , Oulare Aboubacar , Darbyshire Iain , Nic Lughadha Eimear , Van Der Burgt Xander , Larridon Isabel , Cheek Martin 
Published: January 2020

AbstractTo achieve conservation success, we need to support the recovery of threatened species. Yet, <5% of plant species listed as threatened on the IUCN Red List have Species Conservation Action Plans (CAPs). If we are to move from a Red List to a Green List for threatened plant species, CAPs need to be devised and implemented. Guinea is one of the most botanically diverse countries in West Africa. Recent research found that nearly 4000 vascular plants occur in Guinea, a 30% increase from previous estimates. 273 of these plant species are now assessed as threatened with global extinction. There is increasing pressure on the environment from the extractive industry and a growing population. In parallel with implementation of an Important Plant Area programme in Guinea, CAPs were developed for 20 threatened plant species. These plans elaborate conservation efforts needed first to safeguard threatened species bothin situandex situand then to support their recovery. We document the approach used to assemble the Species Conservation Action Plans, and we discuss the importance of having up to date field information, IUCN Red List assessments, and use of a collaborative approach. The need for these plans is increasingly important with recent calculations suggesting a third of African plants are threatened with extinction. This paper outlines initial detailed plant conservation planning in Guinea and offers a template for conservation practitioners in other tropical African countries to follow.
The Role of Spatial Separation on Selective and Distributed Attention to Speech
Authors: Pinto Danna , Agmon Galit , Zion Golumbic Elana 
Published: January 2020

AbstractProcessing speech in multi-speaker environments poses substantial challenges to the human perceptual and attention system. Moreover, different contexts may require employing different listening strategies. For instance, in some cases individuals pay attentionSelectivelyto one speaker and attempt to ignore all other task-irrelevant sounds, whereas other contexts may require listeners toDistributetheir attention among several speakers. Spatial and spectral acoustic cues both play an important role in assisting listeners to segregate concurrent speakers. However, how these cues interact with varying demands for allocating top-down attention is less clear. In the current study, we test and compare how spatial cues are utilized to benefit performance on these different types of attentional tasks. To this end, participants listened to a concoction of two or four speakers, presented either as emanating from different locations in space or with no spatial separation. In separate trials, participants were required to employ different listening strategies, and detect a target-word spoken either by one pre-defined speaker (Selective Attention) or spoken by any of the speakers (Distributed Attention). Results indicate that the presence of spatial cues improved performance, particularly in the two-speaker condition, which is in line with the important role of spatial cues in stream segregation. However, spatial cues provided similar benefits to performance under Selective and Distributed attention. This pattern suggests that despite the advantage of spatial cues for stream segregation, they were nonetheless insufficient for directing a more focused ‘attentional spotlight’ towards the location of a designated speaker in the Selective attention condition.
Canine cognitive dysfunction (CCD) patients have reduced total hippocampal volume compared with aging control dogs: a comparative MRI study
Authors: Dewey Curtis Wells , Rishniw Mark , Platt Simon , Robinson Kelsey , Sackman Joseph , O’Donnell Marissa 
Published: January 2020

AbstractHippocampal atrophy is a key pathologic and MRI feature of human Alzheimer’s disease (AD). Hippocampal atrophy has not been documented via MRI in canine cognitive dysfunction (CCD), which is considered the dog model of human AD. The purpose of this retrospective comparative volumetric MRI study was to compare total hippocampal volumes between successfully aging (control) dogs and dogs diagnosed with CCD. Mimics®software was used to derive total hippocampal volumes and total brain volumes from the MRI studies of 42 aging dogs (≥ 9 years): 16 dogs diagnosed with CCD and 26 successfully aging controls. Total hippocampal volume normalized to total brain volume was significantly less for CCD patients compared with control dogs (p=0.04). The results of this study suggest that-similar to human AD-hippocampal atrophy is a pathological feature of CCD. This finding has potential importance for both investigating disease mechanisms related to dementia as well as future hippocampal-targeted therapies.
Genetic diversity, structure, and kinship analysis ofTrachemys venusta venustain Wildlife Management Units and wild populations in south Mexico. Implications for conservation and management
Authors: Recino-Reyes Elsi B. , Lesher-Gordillo Julia M. , Machkour-M’Rabet Salima , Gallardo-Alvárez Manuel I. , Zenteno-Ruiz Claudia E. , Olivera-Gómez León D. , Valdés-Marín Alejandra , Gómez-Carrasco Guadalupe , Ríos-Rodas Liliana , Barragán-Vázquez María del Rosario , Martínez Raymundo Hernández 
Published: January 2020

AbstractThe Meso-American slider turtle (Trachemys venusta) is a freshwater turtle endemic to Mexico and Central America. Due to the overexploitation of its natural populations, it is in the at risk category formulated by the Official Mexican Standard NOM-059-ECOL-2010. In the state of Tabasco, Management Units for the Conservation of Wildlife (UMA) were created to reduce the impact of overexploitation of freshwater turtles. However, no genetic management plan was considered. This study presents the level of genetic diversity of the founder individuals in order to develop a management plan which will optimize reproduction in the UMA. Genetic diversity was compared between captive (n = 45) and wild (n = 86) individuals using 14 microsatellite molecular markers. Level of genetic diversity could be considered as low (He< 0.6) for a species of turtle and suggests that a higher level of protection is required for this particular species. Furthermore, values were slightly higher for the captive group reflecting the mix of genetic sources (founding individuals from different localities) and demonstrating that the captive population is genetically representative of natural populations. The genetic structure analysis revealed a relationship between captive and wild populations, indicating the influence of the two principal river basins in this region on the population of freshwater turtles. Finally, according to the results obtained from the analysis conducted using Stormand ML-Relateprograms, we recommend the use of 19 females and 13 males, generating a potential of 247 dyads with no relationship. These first results of genetic management in a Mexican UMA, demonstrate the importance of molecular approaches at the time of managing and conserving species in captivity.
Culex erythrothorax: Insecticide Susceptibility and Mosquito Control
Authors: Esterly AT , Alemayehu D , Rusmisel B , Busam J , Shelton TL , Sebay T , Zahiri N , Huston JW , Clausnitzer RJ , Haas-Stapleton EJ 
Published: January 2020

AbstractCulex erythrothoraxDyar is a West Nile virus (WNV) vector that breeds in wetland habitats with emergent vegetation. Urbanization and recreational activities near wetlands place humans and birds in close proximity toCx. erythrothorax, increasing the risk of WNV transmission. High adultCx. erythrothoraxabundance peaked in a marsh bordering the San Francisco Bay of California (USA) during the first 3 hours after sunset (5527 ± 4070 mosquitoes / trap night) during which adult mosquito control efforts are likely most effective. These adult mosquitoes were highly sensitive to permethrin, resmethrin, naled, and etofenprox insecticides when tested in a bottle bioassay (LC50 = 0.35, 0.68, 0.71, and 4.1 µg/bottle, respectively). The synergist piperonyl butoxide increased the sensitivity of the mosquitoes to a low concentration of permethrin (0.5 µg/bottle) while also reducing knock down time, but did not have similar effects with a higher permethrin concentration (2.0 µg/bottle). Biochemical enzyme assays measuring bulk mixed-function oxidase, alpha-esterase, or beta-esterase activities in mosquito homogenates were significantly higher inCx. erythrothoraxrelative to a strain ofCulex pipiensthat is sensitive to permethrin. Larvicide that was applied to the site had limited impact on reducing the abundance of adultCx. erythrothorax. Subsequent removal of emergent vegetation in concert with reduced daily temperature in the environment substantially reducedCx. erythrothoraxabundance. Land managers who have a need to controlCx. erythrothoraxin wetlands should consider vegetation removal over applying larvicide, while vector control agencies are likely to successfully control viremicCx. erythrothoraxthat enter nearby neighborhoods by applying insecticides that target the adult stage of the mosquito within 3 h of sunset.
Brain size predicts learning abilities in bees
Authors: Collado Miguel Á. , Montaner Cristina M. , Molina Francisco P. , Sol Daniel , Bartomeus Ignasi 
Published: January 2020

ABSTRACTA large brain is widely considered a distinctive feature of intelligence, a notion that mostly derives from studies in mammals. However, studies in insects demonstrates that cognitively sophisticated processes, such as social learning and tool use, are still possible with very small brains. Even after accounting for the allometric effect of body size, substantial variation in brain size still remains unexplained. A plausible advantage of a disproportionately larger brain might be an enhanced ability to learn new behaviors to cope with novel or complex challenges. While this hypothesis has received ample support from studies in birds and mammals, similar evidence is not available for small-brained animals like insects. Our objective is to compare the learning abilities of different bee species with their brain size investment. We conducted an experiment in which field-collected individuals had to associate an unconditioned stimulus (sucrose), with a conditioned stimulus (colored strip). We show that the probability of learning the reward-colour association was related to both absolute and relative brain size. This study shows that other bee species aside from the long studied honeybees and bumblebees, can be used in cognitive experiments and opens the door to explore the importance of relative brain sizes in cognitive tasks for insects and its consequences for species survival in a changing world.