bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photosynthetic cyclic electron transport provides ATP for homeostasis during trap closure in Dionaea muscipula
Authors: Maurer Daniel , Weber Daniel , Ballering Eva , Alfarraj Salah , Albasher Gada , Hedrich Rainer , Werner Christiane , Rennenberg Heinz 
Published: November 2019

Abstract

Background and Aims
The processes connected with prey capture and the early consumption of prey by carnivorous Dionaea muscipula require high amounts of energy. The aim of the present study was to identify processes involved in flytrap energy provision and ATP homeostasis under these conditions.

Methods
We determined photosynthetic CO2 uptake and chlorophyll fluorescence as well as the dynamics of ATP contents in the snap traps upon closure with and without prey.

Key Results
The results indicate that upon prey capture, a transient switch from linear to cyclic electron transport mediates a support of ATP homeostasis. Beyond 4 h after prey capture, prey resources contribute to the traps’ ATP pool and, 24 h after prey capture, export of prey-derived resources to other plant organs may become preferential and causes a decline in ATP contents.

Conclusions
Apparently, the energy demand of the flytrap for prey digestion and nutrient mining builds on both internal and prey-derived resources.
Machine learning approaches and databases for prediction of drug–target interaction: a survey paper
Authors: Bagherian Maryam , Sabeti Elyas , Wang Kai , Sartor Maureen A , Nikolovska-Coleska Zaneta , Najarian Kayvan 
Published: November 2019

AbstractThe task of predicting the interactions between drugs and targets plays a key role in the process of drug discovery. There is a need to develop novel and efficient prediction approaches in order to avoid costly and laborious yet not-always-deterministic experiments to determine drug–target interactions (DTIs) by experiments alone. These approaches should be capable of identifying the potential DTIs in a timely manner. In this article, we describe the data required for the task of DTI prediction followed by a comprehensive catalog consisting of machine learning methods and databases, which have been proposed and utilized to predict DTIs. The advantages and disadvantages of each set of methods are also briefly discussed. Lastly, the challenges one may face in prediction of DTI using machine learning approaches are highlighted and we conclude by shedding some lights on important future research directions.
EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI
Authors: Zheng Shijie C , Breeze Charles E , Beck Stephan , Dong Danyue , Zhu Tianyu , Ma Liangxiao , Ye Wei , Zhang Guoqing , Teschendorff Andrew E 
Published: November 2019

Abstract

Summary
It is well recognized that cell-type heterogeneity hampers the interpretation of Epigenome-Wide Association Studies (EWAS). Many tools have emerged to address this issue, including several R/Bioconductor packages that infer cell-type composition. Here we present a web application for cell-type deconvolution, which offers the functionality of our EpiDISH Bioconductor/R package in a user-friendly GUI environment. Users can upload their data to infer cell-type composition and differentially methylated cytosines in individual cell-types for a range of different tissues.

Availability and implementation
EpiDISH web server is implemented with Shiny in R, and is freely available at https://www.biosino.org/EpiDISH/.
Already at the bottom? Demographic declines are unlikely further to undermine genetic diversity of a large Arctic ungulate: muskox, Ovibos moschatus (Artiodactyla: Bovidae)
Authors: Prewer Erin , Kutz Susan , Leclerc Lisa Marie , Kyle Christopher J 
Published: November 2019

AbstractLow genetic diversity is associated with low fitness and evolutionary potential, yet the demographic and life-history traits of some species contribute to low genetic diversity, without empirical evidence of negative impacts on fitness. Modelling past and future trajectories of genetic diversity under different demographic scenarios can provide insight into how genetic variation might impact population fitness. The muskox is an Arctic species that has undergone multiple population bottlenecks and, although populations have rebounded repeatedly, two large populations have recently declined by &gt; 50%. It is unclear how these demographic patterns influence muskox genetic diversity and fitness. We compared the genetic diversity of Canadian muskox populations undergoing opposing population trends. Genotyping 84 mainland and 244 Victoria Island individuals at ten microsatellite loci revealed low genetic variation (Victoria Island, mean allelic richness 1.66, expected heterozygosity 0.16; mainland, mean allelic richness 2.58, expected heterozygosity 0.41), with no evidence of further reductions in diversity subsequent to recent demographic declines. Bayesian modelling showed that a 1900s bottleneck contributed to the lack of diversity in contemporary populations, and forward-in-time simulations suggested little effect on genetic diversity over the next 100 years. Muskoxen might have reached a genetic diversity minimum, and additional research will be needed to determine their capacity to adapt to rapid changes in selective pressures in a rapidly changing Arctic.
Intersecting Epidemics: Incident Syphilis and Drug Use in Women Living With Human Immunodeficiency Virus in the United States (2005–2016)
Authors: Dionne-Odom Jodie , Westfall Andrew O , Dombrowski Julia C , Kitahata Mari M , Crane Heidi M , Mugavero Michael J , Moore Richard D , Karris Maile , Christopoulos Katerina , Geng Elvin , Mayer Kenneth H , Marrazzo Jeanne 
Published: November 2019

Abstract

Background
Rates of early syphilis in US women are steadily increasing, but predictors of infection in this group are not clearly defined.

Methods
This retrospective analysis focused on women enrolled in the US CFAR Network of Integrated Clinical Systems cohort between January 2005 and December 2016 with syphilis testing performed. The primary outcome of incident syphilis infection was defined serologically as a newly positive test with positive confirmatory testing after a negative test or a 2-dilution increase in rapid plasma regain titer. Infection rates were calculated for each woman-year in care with testing. Predictors of syphilis were sought among sociodemographics, clinical information, and self-reported behaviors. Multivariable logistic regression models were created; a subgroup analysis assessed predictors in women of reproductive age.

Results
The annual rate of incident syphilis among 4416 women engaged in human immunodeficiency virus (HIV) care and tested during the 12-year study period was 760/100 000 person-years. Independent predictors of infection were injection drug use as a risk factor for HIV acquisition (aOR, 2.2; 95% CI, 1.3–3.9), hepatitis C infection (aOR, 1.9; 95% CI, 1.1–3.4), black race (aOR, 2.2; 95% CI, 1.3–3.7 compared with white race), and more recent entry to care (since 2005 compared with 1994–2004). Predictors were similar in women aged 18–49.

Conclusions
Syphilis infection is common among US women in HIV care. Syphilis screening and prevention efforts should focus on women reporting drug use and with hepatitis C coinfection. Future studies should identify specific behaviors that mediate syphilis acquisition risk in women who use drugs.
Prognostic assessment of valvular surgery in active infective endocarditis: multicentric nationwide validation of a new score developed from a meta-analysis
Authors: Varela Barca Laura , Fernández-Felix Borja M , Navas Elorza Enrique , Mestres Carlos A , Muñoz Patricia , Cuerpo-Caballero Gregorio , Rodríguez-Abella Hugo , Montejo-Baranda Miguel , Rodríguez-Álvarez Regino , Gutiérrez Díez Francisco , Goenaga Miguel Angel , Quintana Eduard , Ojeda-Burgos Guillermo , de Alarcón Arístides , Vidal-Bonet Laura , Centella Hernández Tomasa , López-Menéndez Jose ,   on behalf of the Spanish Collaboration on Endocarditis—Grupo de Apoyo al Manejo de la Endocarditis infecciosa en ESpaña (GAMES)
Published: November 2019

Abstract

OBJECTIVES
Several risk prediction models have been developed to estimate the risk of mortality after valve surgery for active infective endocarditis (IE), but few external validations have been conducted to assess their accuracy. We previously developed a systematic review and meta-analysis of the impact of IE-specific factors for the in-hospital mortality rate after IE valve surgery, whose obtained pooled estimations were the basis for the development of a new score (APORTEI). The aim of the present study was to assess its prognostic accuracy in a nationwide cohort.

METHODS
We analysed the prognostic utility of the APORTEI score using patient-level data from a multicentric national cohort. Patients who underwent surgery for active IE between 2008 and 2018 were included. Discrimination was evaluated using the area under the receiver operating characteristic curve, and the calibration was assessed using the calibration slope and the Hosmer–Lemeshow test. Agreement between the APORTEI and the EuroSCORE I was also analysed by Lin’s concordance correlation coefficient (CCC), the Bland–Altman agreement analysis and a scatterplot graph.

RESULTS
The 11 variables that comprised the APORTEI score were analysed in the sample. The APORTEI score was calculated in 1338 patients. The overall observed surgical mortality rate was 25.56%. The score demonstrated adequate discrimination (area under the receiver operating characteristic curve = 0.75; 95% confidence interval 0.72–0.77) and calibration (calibration slope = 1.03; Hosmer–Lemeshow test P = 0.389). We found a lack of agreement between the APORTEI and EuroSCORE I (concordance correlation coefficient = 0.55).

CONCLUSIONS
The APORTEI score, developed from a systematic review and meta-analysis, showed an adequate estimation of the risk of mortality after IE valve surgery in a nationwide cohort.
Testing sustained soil-to-soil contact as an approach for limiting the abiotic influence of source soils during experimental microbiome transfer
Authors: Trexler Ryan V , Bell Terrence H 
Published: November 2019

ABSTRACTExperimental separation of the biotic and abiotic components of soil will help in understanding the role of taxonomy and composition in soil microbiome function. The most common approach to soil microbiome transfer involves direct dilution of a non-sterile source soil into sterile recipient soils, introducing both microorganisms and soil compounds, leaving abiotic and biotic factors confounded. Here, we contrast microbiome transfer into sterile recipient soils through (i) direct soil transfer at two dilutions and (ii) a new approach, sustained contact between source and recipient soils. Sustained soil-to-soil contact retains separation between source and recipient soils, allows for multiple colonization events and increases confidence that microorganisms observed in recipient soils are active and growing. Each approach produced distinct microbiomes in recipient soils after 1 and 6 weeks of incubation, indicating that transfer method impacts microbial composition. The extent to which recipient microbiomes resembled source microbiomes varied by soil type, although in general, direct soil transfer appeared to most closely approximate source microbiomes. However, irrespective of transfer method, most bacterial sequences in recipient soils were from organisms transferred through all methods. We discuss the merits of each method for controlled soil microbiome studies.
Clinical Impacts and Outcomes With Possible Donor-Derived Infection in Infected Donor Liver Transplantation: A Single-Center Retrospective Study in China
Authors: Tong Li , Hu Xiao-Guang , Huang Fa , Huang Shun-Wei , Li Li-Fen , Tang Zhao-Xia , Yao Ji-You , Xu Jing-Hong , Zhu Yan-Ping , Chen Yin-Hua , He Xiao-Shun , Guan Xiang-Dong , Cai ChangJie 
Published: November 2019

Abstract

Background
Information on possible donor-derived transmission events in China is limited. We evaluated the impacts of liver transplantation from infected deceased-donors, analyzed possible donor-derived bacterial or fungal infection events in recipients, and evaluated the etiologic agents’ characteristics and cases outcomes.

Methods
A single-center observational study was performed from January 2015 to March 2017 to retrospectively collect data from deceased-donors diagnosed with infection. Clinical data were recorded for each culture-positive donor and the matched liver recipient. The microorganisms were isolated and identified, and antibiotic sensitivity testing was performed. The pathogens distribution and incidence of possible donor-derived infection (P-DDI) events were analyzed and evaluated.

Results
Information from 211 donors was collected. Of these, 82 donors were infected and classified as the donation after brain death category. Overall, 149 and 138 pathogens were isolated from 82 infected donors and 82 matched liver recipients, respectively. Gram-positive bacteria, Gram-negative bacteria, and fungi accounted for 42.3% (63 of 149), 46.3% (69 of 149), and 11.4% (17 of 149) of pathogens in infected donors. The incidence of multidrug-resistant bacteria was high and Acinetobacter baumannii was the most concerning species. Infections occurred within the first 2 weeks after liver transplantation with an organ from an infected donor. Compared with the noninfection recipient group, the infection recipient group experienced a longer mechanical ventilation time (P = .004) and intensive care unit stay (P = .003), a higher incidence of renal dysfunction (P = .026) and renal replacement therapy (P = .001), and higher hospital mortality (P = .015). Possible donor-derived infection was observed in 14.6% of cases. Recipients with acute-on-chronic liver failure were more prone to have P-DDI than recipients with other diseases (P = .007; odds ratio = 0.114; 95% confidence interval, .025–.529).

Conclusions
When a liver recipient receives a graft from an infected deceased-donor, the postoperative incidence of infection is high and the infection interval is short. In addition, when a possible donor-derived, drug-resistant bacterial infection occurs, recipients may have serious complications and poor outcomes.
Gillespie-Lindenmayer systems for stochastic simulation of morphogenesis
Authors: Cieslak Mikolaj , Prusinkiewicz Przemyslaw 
Published: November 2019

Abstract
Lindenmayer systems (L-systems) provide a useful framework for modelling the development of multicellular structures and organisms. The parametric extension of L-systems allows for incorporating molecular-level processes into the models. Until now, the dynamics of these processes has been expressed using differential equations, implying continuously valued concentrations of the substances involved. This assumption is not satisfied, however, when the numbers of molecules are small. A further extension that accounts for the stochastic effects arising in this case is thus needed. We integrate L-systems and the Gillespie’s Stochastic Simulation Algorithm to simulate stochastic processes in fixed and developing linear structures. We illustrate the resulting formalism with stochastic implementations of diffusion-decay, reaction-diffusion and auxin-transport-driven morphogenetic processes. Our method and software can be used to simulate molecular and higher-level spatially explicit stochastic processes in static and developing structures, and study their behaviour in the presence of stochastic perturbations.
MRI Evaluation of the Contralateral Breast in Women with Recently Diagnosed Breast Cancer: 2-Year Follow-up
Authors: Debruhl Nanette D , Lee Su-Ju , Mahoney Mary C , Hanna Lucy , Tuite Catherine , Gatsonis Constantine A , Lehman Constance 
Published: November 2019

Abstract

Objective
The American College of Radiology Imaging Network Trial 6667 showed that MRI can detect cancer in the contralateral breast that is missed by mammography and clinical examination at the time of the initial breast cancer diagnosis, based on 1-year follow-up. This study is a continuation of the trial that evaluates the diagnostic accuracy of MRI for contralateral breast cancer after 2 years of follow-up.

Methods
In total, 969 women with a diagnosis of unilateral breast cancer and no clinical or imaging abnormalities in the contralateral breast underwent breast MRI. The cancer status of all participants was monitored for 2 years after the initial MRI. Follow-up included documentation of any clinical, imaging, or interventional procedures performed. A study participant was considered positive for cancer if she had a tissue diagnosis of in situ or invasive breast cancer in the contralateral breast within 730 days of her initial MRI.

Results
Three additional cancers were diagnosed in the study population in the second year of the trial. The diagnostic yield for MRI for the 2-year period was 3% (31/969). After 2 years of follow-up, breast MRI has a sensitivity of 86% and specificity of 88% for detection of contralateral breast cancer. Its negative predictive value was 99%, and its positive predictive value was 22%. These values did not change significantly from the 1-year data.

Conclusion
A negative contralateral breast MRI has a very high and reliable negative predictive value over 2 years, and, therefore, is helpful in managing and counseling patients during the period of initial diagnosis and early treatment.
On the Epistemic Status of Prenatal Ultrasound: Are Ultrasound Scans Photographic Pictures?
Authors: Favaretto Maddalena , Vears Danya F , Borry Pascal 
Published: November 2019

AbstractMedical imaging is predominantly a visual field. In this context, prenatal ultrasound images assume intense social, ethical, and psychological significance by virtue of the subject they represent: the fetus. This feature, along with the sophistication introduced by three-dimensional (3D) ultrasound imaging that allows improved visualization of the fetus, has contributed to the common impression that prenatal ultrasound scans are like photographs of the fetus. In this article we discuss the consistency of such a comparison. First, we investigate the epistemic role of both analogic and digital photographic images as visual information-providing representations holding a high degree of objectivity. Second, we examine the structure and process of production of ultrasound scans and argue that a comparison between two-dimensional (2D) ultrasound and photography is justified. This is in contrast to 3D ultrasound images that, due to the intensive mathematical processing involved in their production, present some structural issues that obfuscate their ontological and epistemic status.
NATO's About-Face: Adaptation to Gender Mainstreaming in an Alliance Setting
Authors: Hardt Heidi , von Hlatky Stéfanie 
Published: November 2019

AbstractScholars in global security studies have only recently focused attention on how and why international security organizations (ISOs) adapt. Since the United Nations Security Council's issuance of Resolution 1325, some ISOs have enacted changes to implement gender mainstreaming. The concept involves incorporating gender-based analyses in policy and planning and increasing women's representation. Drawing on interviews with seventy-one elites and a dataset of ninety-seven NATO gender guidelines, this article introduces an original argument for why NATO adapted to gender mainstreaming. Such adaptation is surprising given the military's historical resistance to gender considerations and that civilian bodies typically enact reforms. Findings indicate that other ISOs were substantially influential in the process and that institutional incentives built into NATO's military bodies drove military officials to implement mainstreaming in practice. Additionally, military elites perceived a link between gender mainstreaming and operational effectiveness, which further consolidated organization-wide adaptation. This study challenges long-held assumptions about militaries’ resistance to gender-related changes. It also offers one of the first empirical assessments of gender mainstreaming in an ISO.
Description of Enteropathic Escherichia coli Species in Pediatric Patients at a Quaternary Children’s Hospital
Authors: Nycz Bryan T , Pretty Kristin , Gomez-Trujillo Angel , Sanchez Brenda , Dominguez Samuel R 
Published: November 2019

Abstract

Background
The epidemiology, demographics, clinical presentations, and outcomes associated with enteroaggregative Escherichia coli (EAEC), enteropathogenic E. coli (EPEC), and enterotoxigenic E. coli (ETEC) pathotypes in US children are not well understood.

Methods
This study was a retrospective chart review of all pediatric patients with a stool sample submitted to the Children’s Hospital Colorado clinical microbiology laboratory for testing with the BioFire FilmArray Gastrointestinal Pathogen Panel from October 2015 through October 2017.

Results
During the study period, 5692 patient stool samples were submitted; 679 (13%) were positive for EAEC, EPEC, or ETEC. Of note, 163/232 (70%) patients with EAEC, 282/493 (57%) with EPEC, and 49/58 (85%) with ETEC had detection of at least 1 other pathogen. Of all E. coli–positive stool samples, only 158/679 (23%) were from low-risk patients who were singly infected with EAEC, EPEC, or ETEC. In this cohort, most cases were associated with acute diarrhea (50%), abdominal pain (61%), and/or cramping (49%) and presented without fever (14%), emesis (28%), or lethargy (7%). Thirteen (8%) of these 158 patients received antibiotics at the time of their initial presentation to care. Of the 145 patients who did not receive antibiotics at their initial visit, 23 (16%) returned to care due to persistence of symptoms.

Conclusions
Our results suggest that the majority of patients singly infected with EAEC, EPEC, or ETEC present with mild, self-limited, gastrointestinal (GI) complaints. Further research is needed to determine what role these pathogens might play in children who present with chronic or inflammatory GI symptoms.