bluuebunny/crossref_metadata_2025_split huggingface dataset:
The promise and challenge of cancer microbiome research
Authors: Manzoor Sumeed Syed , Doedens Annemiek , Burns Michael B. 
Published: June 2020

AbstractMany microbial agents have been implicated as contributors to cancer genesis and development, and the search to identify and characterize new cancer-related organisms is ongoing. Modern developments in methodologies, especially culture-independent approaches, have accelerated and driven this research. Recent work has shed light on the multifaceted role that the community of organisms in and on the human body plays in cancer onset, development, detection, treatment, and outcome. Much remains to be discovered, however, as methodological variation and functional testing of statistical correlations need to be addressed for the field to advance.
Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
Authors: Denisenko Elena , Guo Belinda B. , Jones Matthew , Hou Rui , de Kock Leanne , Lassmann Timo , Poppe Daniel , Clément Olivier , Simmons Rebecca K. , Lister Ryan , Forrest Alistair R. R. 
Published: June 2020

AbstractBackgroundSingle-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional profiles of individual cells. Multiple approaches for optimal sample dissociation and storage of single cells have been proposed as have single-nuclei profiling methods. What has been lacking is a systematic comparison of their relative biases and benefits.ResultsHere, we compare gene expression and cellular composition of single-cell suspensions prepared from adult mouse kidney using two tissue dissociation protocols. For each sample, we also compare fresh cells to cryopreserved and methanol-fixed cells. Lastly, we compare this single-cell data to that generated using three single-nucleus RNA sequencing workflows. Our data confirms prior reports that digestion on ice avoids the stress response observed with 37 °C dissociation. It also reveals cell types more abundant either in the cold or warm dissociations that may represent populations that require gentler or harsher conditions to be released intact. For cell storage, cryopreservation of dissociated cells results in a major loss of epithelial cell types; in contrast, methanol fixation maintains the cellular composition but suffers from ambient RNA leakage. Finally, cell type composition differences are observed between single-cell and single-nucleus RNA sequencing libraries. In particular, we note an underrepresentation of T, B, and NK lymphocytes in the single-nucleus libraries.ConclusionsSystematic comparison of recovered cell types and their transcriptional profiles across the workflows has highlighted protocol-specific biases and thus enables researchers starting single-cell experiments to make an informed choice.
Behavioural plasticity of Anopheles coluzzii and Anopheles arabiensis undermines LLIN community protective effect in a Sudanese-savannah village in Burkina Faso
Authors: Perugini Eleonora , Guelbeogo Wamdaogo Moussa , Calzetta Maria , Manzi Sara , Virgillito Chiara , Caputo Beniamino , Pichler Verena , Ranson Hilary , Sagnon N’Fale , della Torre Alessandra , Pombi Marco 
Published: June 2020

Abstract
Background
Despite the overall major impact of long-lasting insecticide treated nets (LLINs) in eliciting individual and collective protection to malaria infections, some sub-Saharan countries, including Burkina Faso, still carry a disproportionately high share of the global malaria burden. This study aims to analyse the possible entomological bases of LLIN limited impact, focusing on a LLIN-protected village in the Plateau Central region of Burkina Faso.

Methods
Human landing catches (HLCs) were carried out in 2015 for 12 nights both indoors and outdoors at different time windows during the highest biting activity phase for Anopheles gambiae (s.l.). Collected specimens were morphologically and molecularly identified and processed for Plasmodium detection and L1014F insecticide-resistance allele genotyping.

Results
Almost 2000 unfed An. gambiae (s.l.) (54% Anopheles coluzzii and 44% Anopheles arabiensis) females landing on human volunteers were collected, corresponding to a median number of 23.5 females/person/hour. No significant differences were observed in median numbers of mosquitoes collected indoors and outdoors, nor between sporozoite rates in An. coluzzii (6.1%) and An. arabiensis (5.5%). The estimated median hourly entomological inoculation rate (EIR) on volunteers was 1.4 infective bites/person/hour. Results do not show evidence of the biting peak during night hours typical for An. gambiae (s.l.) in the absence of bednet protection. The frequency of the L1014F resistant allele (n = 285) was 66% in An. coluzzii and 38% in An. arabiensis.

Conclusions
The observed biting rate and sporozoite rates are in line with the literature data available for An. gambiae (s.l.) in the same geographical area before LLIN implementation and highlight high levels of malaria transmission in the study village. Homogeneous biting rate throughout the night and lack of preference for indoor-biting activity, suggest the capacity of both An. coluzzii and An. arabiensis to adjust their host-seeking behaviour to bite humans despite bednet protection, accounting for the maintenance of high rates of mosquito infectivity and malaria transmission. These results, despite being limited to a local situation in Burkina Faso, represent a paradigmatic example of how high densities and behavioural plasticity in the vector populations may contribute to explaining the limited impact of LLINs on malaria transmission in holo-endemic Sudanese savannah areas in West Africa.
Draft genome sequence of “Candidatus Afipia apatlaquensis” sp. nov., IBT-C3, a potential strain for decolorization of textile dyes
Authors: Sánchez-Reyes Ayixon , Bretón-Deval Luz , Mangelson Hayley , Sanchez-Flores Alejandro 
Published: June 2020

Abstract
Objectives
In order to characterize a river-associated, enriched microbiome capable of degrading an anthraquinone dye from the oil blue family, as well as assessing its functional potential, we performed a taxa-specific metagenomic deconvolution analysis based on contact probability maps at the chromosomal level. This study will allow associating the genomic content of “Candidatus Afipia apatlaquensis” strain IBT-C3 with its phenotypic potential in the context of bioremediation of textile dyes. We anticipate that this resource will be very useful in comparative genomic clinical studies, contributing to understanding the genomic basis of Afipia pathogenicity.

Data description
Here, we report the first draft genome sequence of “Candidatus Afipia apatlaquensis” sp. nov., strain IBT-C3, obtained by deconvolution of a textile-dye degrader microbiome in Mexico. The genome composite was deconvoluted using a Hi-C proximity ligation method. Whole-genome-based comparisons and phylogenomics reconstruction indicate that strain IBT-C3 represents a new species of the genus Afipia. The assembly completeness was 92.5% with 5,604,749 bp in length and 60.72% G+C content. The genome complement of IBT-C3 suggests a functional potential for decolorization of textile dyes, contrasting with previous reports of Afipia genus focused on its pathogenic potential.
Androgens and the developing hippocampus
Authors: Kight Katherine E. , McCarthy Margaret M. 
Published: June 2020

AbstractThe hippocampus is central to spatial learning and stress responsiveness, both of which differ in form and function in males versus females, yet precisely how the hippocampus contributes to these sex differences is largely unknown. In reproductively mature individuals, sex differences in the steroid hormone milieu undergirds many sex differences in hippocampal-related endpoints. However, there is also evidence for developmental programming of adult hippocampal function, with a central role for androgens as well as their aromatized byproduct, estrogens. These include sex differences in cell genesis, synapse formation, dendritic arborization, and excitatory/inhibitory balance. Enduring effects of steroid hormone modulation occur during two developmental epochs, the first being the classic perinatal critical period of sexual differentiation of the brain and the other being adolescence and the associated hormonal changes of puberty. The cellular mechanisms by which steroid hormones enduringly modify hippocampal form and function are poorly understood, but we here review what is known and highlight where attention should be focused.
Identification of novel pig and human immunoglobulin G-binding proteins and characterization of the binding regions of enolase from Streptococcus suis serotype 2
Authors: Li Quan , Fu Yang , Guo Genglin , Wang Zhuohao , Zhang Wei 
Published: June 2020

AbstractStreptococcus suis, a major emerging pathogen in swine and humans, expresses immunoglobulin G (IgG)-binding proteins (IBPs), which contribute to the ability of organism to evasion of host immune system. The objective of this study was to identify novel pig IgG (pIgG) and human IgG (hIgG)-binding proteins and characterize the binding regions of enolase from Streptococcus suis serotype 2 (S. suis 2). Here, four pIgG-binding proteins (pIBPs) and five hIgG-binding proteins (hIBPs) were identified from S. suis 2 surface proteins by 2D-Far-western blot assays. All the newly captured proteins were expressed and further confirmed their binding activity to pIgG or hIgG by Far-western blot and dot blot. In addition to previously identified factor H, fibronectin, collagen, fibrinogen, plasminogen and laminin, we also found that both pIgG and hIgG can specifically interact with enolase. Binding assays indicated that interactions of S. suis 2 enolase with pIgG and hIgG is primarily mediated by the enolase C-terminal portion (Enolase-C, a.a. 142–432). We found that hIgG exhibited stronger binding ability to Enolase-C than pIgG. Further analysis of the C-terminal regions of enolase (Enolase-C1 and Enolase-C2) suggested that the C-terminus possessed two different binding domains with distinct host IgG proteins. Strikingly, we confirmed that pIgG interacted with the Enolase-C1 (a.a. 142–271) and hIgG interacted with the Enolase-C2 (a.a. 271–432). These observations of enolase provide interesting insights in the pathogenesis of S. suis infection.
Organizational factors associated with adherence to low tidal volume ventilation: a secondary analysis of the CHECKLIST-ICU database
Authors:   for the CHECKLIST-ICU Investigators and the Brazilian Research in Intensive Care Network (BRICNet), Midega Thais Dias , Bozza Fernando A. , Machado Flávia Ribeiro , Guimarães Helio Penna , Salluh Jorge I. , Nassar Antonio Paulo , Normílio-Silva Karina , Schultz Marcus J. , Cavalcanti Alexandre Biasi , Serpa Neto Ary 
Published: June 2020

Abstract
Background
Survival benefit from low tidal volume (VT) ventilation (LTVV) has been demonstrated for patients with acute respiratory distress syndrome (ARDS), and patients not having ARDS could also benefit from this strategy. Organizational factors may play a role on adherence to LTVV. The present study aimed to identify organizational factors with an independent association with adherence to LTVV.

Methods
Secondary analysis of the database of a multicenter two-phase study (prospective cohort followed by a cluster-randomized trial) performed in 118 Brazilian intensive care units. Patients under mechanical ventilation at day 2 were included. LTVV was defined as a VT ≤ 8 ml/kg PBW on the second day of ventilation. Data on the type and number of beds of the hospital, teaching status, nursing, respiratory therapists and physician staffing, use of structured checklist, and presence of protocols were tested. A multivariable mixed-effect model was used to assess the association between organizational factors and adherence to LTVV.

Results
The study included 5719 patients; 3340 (58%) patients received LTVV. A greater number of hospital beds (absolute difference 7.43% [95% confidence interval 0.61–14.24%]; p = 0.038), use of structured checklist during multidisciplinary rounds (5.10% [0.55–9.81%]; p = 0.030), and presence of at least one nurse per 10 patients during all shifts (17.24% [0.85–33.60%]; p = 0.045) were the only three factors that had an independent association with adherence to LTVV.

Conclusions
Number of hospital beds, use of a structured checklist during multidisciplinary rounds, and nurse staffing are organizational factors associated with adherence to LTVV. These findings shed light on organizational factors that may improve ventilation in critically ill patients.
Optimal operation mode selection for energy-efficient light-weight multi-hop time synchronization in linear wireless sensor networks
Authors: Al Imran Md Abdullah , Dalveren Yaser , Tavli Bulent , Kara Ali 
Published: June 2020

AbstractWe explored the joint effect of synchronization window and offset/drift mode selection on the time synchronization of linear wireless sensor networks (LWSNs). Recent advances in the field along with the availability of capable hardware led to adoption of LWSNs in diverse areas like monitoring of roads, pipelines, and tunnels. The linear topology applications are susceptible to single point of failure; therefore, energy efficient operation of LWSNs is even more important than the traditional WSNs. To address the challenge, we investigate the time synchronization mode selection for the optimum operation of a multi-hop and low-overhead LWSN. We investigate two modes of synchronization: synchronization by using only offset and synchronization by using offset in addition to the clock drift. Furthermore, we investigate the effects of synchronization window size. Our experimental results reveal that computation of offset alone for smaller window sizes and resynchronization periods is sufficient in achieving acceptable degree of synchronization.
A crowdsourcing method for online social networks security assessment based on human-centric computing
Authors: Zhang Zhiyong , Jing Junchang , Wang Xiaoxue , Choo Kim-Kwang Raymond , Gupta Brij B. 
Published: June 2020

Abstract
Crowdsourcing and crowd computing are a trend that is likely to be increasingly popular, and there remain a number of research and operational challenges that need to be addressed. The human-centric computational abstraction called situation may be used to cope with these difficulties. In this paper, we focus on one such challenge, which is how to assign crowd assessment tasks about security and privacy in online social networks to the most appropriate users efficiently, effectively and accurately. Specifically, here we propose a novel task assignment method to facilitate crowd assessment, which improves the security and trustworthiness of social networking platforms, as well as a task assignment algorithm based on SocialSitu, which is a social-domain-focused situational analytics. Findings from our crowd assessment experiments on a real world social network Shareteches show that the precision and recall of the proposed method and algorithm are 0.491 and 0.538 higher than those of a random algorithm’s, as well as 0.336 and 0.366 higher than users’ theme-aware algorithm’s, respectively. Moreover, these results further suggest that our experimental evaluation enhance the security and privacy of online social networks.
Five-year change of prevalence and risk factors for infection and mortality of carbapenem-resistant Klebsiella pneumoniae bloodstream infection in a tertiary hospital in North China
Authors: Li Yuanyuan , Li Jihong , Hu Tong , Hu Jia , Song Ning , Zhang Yu , Chen Yuan 
Published: June 2020

Abstract
Background
There are few studies focused on carbapenem-resistant Klebsiella pneumoniae (CRKP) bloodstream infection (BSI). The aim of this study is to identify the prevalence and risk factors for infection and mortality of CRKP BSI.

Methods
Susceptibility of Klebsiella pneumoniae (KP) isolated from blood samples and the proportion of CRKP were recorded annually. One hundred sixty-four patients with CRKP and 328 with carbapenem-susceptible Klebsiella pneumoniae (CSKP) BSI were categorized as the case group and control group to identify risk factors for CRKP infection and mortality by univariable analysis and multivariable logistic-regression analysis.

Results
The proportion and mortality of CRKP BSI increased significantly, with the percentage of KP in BSI increasing from 7 to 12% from 2014 to 2019 with a concomitant resistance to meropenem increasing from 16.7 to 41.8%. Compared with CSKP group, patients in CRKP group had longer hospitalization time before bacteremia (median 14 vs 4, P < 0.001) and longer total hospitalization time (median 31 vs 19, P < 0.001). The proportion of admission to ICU was higher (70.7% vs 17.7%, P < 0.001), and APACHE II score was higher (median 12 vs 8, P < 0.001). The mortality in CRKP group was 43.9% (72/164), while 14.9% (49/328) in CSKP group (p < 0.001). KP detection in other sites(P = 0.036, OR 1.964), blood purification(P = 0.018, OR 3.326), bronchoscopy(P = 0.011, OR 5.423), surgery (P = 0.001, OR 3.084), carbapenem use(P = 0.001, OR 3.395), tigecycline use(P = 0.006, OR 4.595) were independent risk factors for CRKP BSI. Previous hospitalization (P = 0.048, OR 2.755), long hospitalization (P = 0.003, OR 1.035), bone marrow puncture (P = 0.037, OR3.856), use of β-lactamase inhibitor (P = 0.005, OR 3.890) were independent risk factors for mortality in CRKP BSI.

Conclusion
The prevalence and mortality of CRKP BSI are still increasing. Timely treatment of KP infection in other site, strengthening the hospital infection control of blood purification, bronchoscopy and surgery, control the use of carbapenem and tigecycline, may help to prevent CRKP BSI. More preventative hospital resources are needed for severely ill patients with prolonged hospitalizations and intensive care.
Potential utility of geomagnetic data for geolocation of demersal fishes in the North Pacific Ocean
Authors: Nielsen J. K. , Mueter F. J. , Adkison M. D. , Loher T. , McDermott S. F. , Seitz A. C. 
Published: June 2020

Abstract
Background
Archival tags that measure the Earth’s magnetic field could provide a new geolocation method for demersal fishes in the North Pacific Ocean. However, the presence of local magnetic field anomalies caused by geological formations such as volcanic rock and temporal fluctuations from solar storms could complicate its use in some high-latitude areas of the North Pacific Ocean. We assessed the potential value of adding geomagnetic data to a depth-based state-space model for geolocation of demersal fishes in Glacier Bay National Park, USA, a high-latitude magnetic anomaly area. We developed a high-resolution (100 m) magnetic field map of the study area and assessed in situ tag resolution by deploying 5 geomagnetic archival tags on a stationary mooring for 8 months. We compared performance of 4 theoretical geomagnetic tag measurement resolutions (low = ± 1000 nT, medium = ± 500 nT, high = ± 300 nT, and very high = ± 150 nT), 2 map resolutions (coarse- or fine-scale), and 5 methods of geomagnetic variance specification by estimating locations of simulated random walk trajectories under the different treatment scenarios using a hidden Markov model.

Results
Geomagnetic data improved model performance for both fine-scale and coarse-scale magnetic maps when tag resolutions were medium to very high and geomagnetic variance specification was based on error between measured and mapped values instead of study area attributes such as slope or roughness. Overall, the best model performance was observed for the highest tag resolution, the fine-scale map, and variance based on anomaly magnitudes. However, the coarse-scale map with a constant variance of 165 nT resulted in improvements over depth alone for all tag resolutions. In situ testing of mooring data suggests that the precision of the geomagnetic archival tags was comparable to the low and medium tag measurement resolutions tested in simulations, but variation in performance was high among tags.

Conclusions
Our results suggest that inclusion of geomagnetic data could improve geolocation of demersal fishes in the North Pacific Ocean, but improvements to geomagnetic tags and additional information on magnetic field values measured at the seafloor compared to the sea surface are needed to ensure its utility.
The big five personality traits, perfectionism and their association with mental health among UK students on professional degree programmes
Authors: Lewis Elisa G. , Cardwell Jacqueline M. 
Published: June 2020

Abstract
Background
In view of heightened rates of suicide and evidence of poor mental health among healthcare occupational groups, such as veterinarians, doctors, pharmacists and dentists, there has been increasing focus on the students aiming for careers in these fields. It is often proposed that a high proportion of these students may possess personality traits which render them vulnerable to mental ill-health.

Aim
To explore the relationship between the big five personality traits, perfectionism and mental health in UK students undertaking undergraduate degrees in veterinary medicine, medicine, pharmacy, dentistry and law.

Methods
A total of 1744 students studying veterinary medicine, medicine, dentistry, pharmacy and law in the UK completed an online questionnaire, which collected data on the big five personality traits (NEO-FFI), perfectionism (Frost Multidimensional Perfectionism Scale), wellbeing (Warwick-Edinburgh Mental Well-being Scale), psychological distress (General Health Questionnaire-12), depression (Beck Depression Inventory-II) and suicidal ideation and attempts.

Results
Veterinary, medical and dentistry students were significantly more agreeable than law students, while veterinary students had the lowest perfectionism scores of the five groups studied. High levels of neuroticism and low conscientiousness were predictive of increased mental ill-health in each of the student populations.

Conclusions
The study highlights that the prevailing anecdotal view of professional students possessing maladaptive personality traits that negatively impact on their mental health may be misplaced.
Four plus one dimensions of transferability: defining a framework for the application of a landscape characterization in the USA
Authors: Staniscia Stefania , Yuill Charles , Cribari Vincenzo 
Published: June 2020

AbstractThis perspective article presents considerations based on an attempt for initiating a landscape characterization in the United States using the Landscape Character Assessment (LCA) method initially developed in Great Britain. Literature on LCA underlines the issue of its transferability and the necessity to address, both theoretically and practically, its adaptation when the method is transplanted to other territories. The authors focus on the development of a theoretical framework for the adaptation of the method to a different cultural, geographical, social, political, and institutional context from the one it was designed for. The region of application are West Virginia southern coalfields where mountaintop removal coal mining coexists with rural landscapes, forested mountains, and scarcely inhabited valleys. The significance of conducting a landscape characterization in such an area is acknowledged as well as the necessity to address five dimensions of the question of transferability: physical, cultural, disciplinary, political, and social. In the article the authors examine the British and USA character-based approaches to landscape highlighting the main differences. The environmental history of West Virginia southern coalfields is introduced, and the current landscape is described. Finally, the authors discuss how the five dimensions of transferability can be addressed in the USA context stimulating further theoretical developments and practical attempts of landscape characterization.