bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of social environment on bird song: listener-specific expression of a sexual signal
Authors: Jablonszky Mónika , Zsebők Sándor , Laczi Miklós , Nagy Gergely , Vaskuti Éva , Garamszegi László Zsolt 
Published: November 2020

Abstract
Animal signals should consistently differ among individuals to convey distinguishable information about the signalers. However, behavioral display signals, such as bird song are also loaded with considerable within-individual variance with mostly unknown function. We hypothesized that the immediate social environment may play a role in mediating such variance component, and investigated in the collared flycatcher (Ficedula albicollis) if the identity and quality of listeners could affect song production in signalers. After presenting territorial males with either a female or male social stimulus, we found in the subsequent song recordings that the among-stimulus effects corresponded to non-zero variance components in several acoustic traits indicating that singing males are able to plastically adjust their songs according to stimulus identity. Male and female stimuli elicited different responses as the identity of the female stimuli affected song complexity only, while the identity of male stimuli altered also song length, maximum frequency, and song rate. The stimulus-specific effect on song in some cases decreased with time, being particularly detectable right after the removal of the stimulus and ceasing later, but this pattern varied across the sex of the stimulus and the song traits. We were able to identify factors that can explain the among-stimulus effects (e.g., size and quality of the stimuli) with roles that also varied among song traits. Our results confirm that the variable social environment can raise considerable variation in song performance, highlighting that within-individual plasticity of bird song can play important roles in sexual signaling.
Ready, Set, Go: Community Science Field Campaign Reveals Habitat Preferences of Nonnative Asian Earthworms in an Urban Landscape
Authors: Ziter Carly D , Herrick Bradley M , Johnston Marie R , Turner Monica G 
Published: November 2020

AbstractAsian pheretimoid earthworms of the genera Amynthas and Metaphire (jumping worms) are leading a new wave of coinvasion into Northeastern and Midwestern states, with potential consequences for native organisms and ecosystem processes. However, little is known about their distribution, abundance, and habitat preferences in urban landscapes—areas that will likely influence their range expansion via human-driven spread. We led a participatory field campaign to assess jumping worm distribution and abundance in Madison, Wisconsin, in the United States. By compressing 250 person-hours of sampling effort into a single day, we quantified the presence and abundance of three jumping worm species across different land-cover types (forest, grassland, open space, and residential lawns and gardens), finding that urban green spaces differed in invasibility. We show that community science can be powerful for researching invasive species while engaging the public in conservation. This approach was particularly effective in the present study, where broad spatial sampling was required within a short temporal window.
Modulation of Nogo receptor 1 expression orchestrates myelin-associated infiltration of glioblastoma
Authors: Hong Jun-Hee , Kang Sangjo , Sa Jason K , Park Gunwoo , Oh Young Taek , Kim Tae Hoon , Yin Jinlong , Kim Sung Soo , D’Angelo Fulvio , Koo Harim , You Yeonhee , Park Saewhan , Kwon Hyung Joon , Kim Chan Il , Ryu Haseo , Lin Weiwei , Park Eun Jung , Kim Youn-Jae , Park Myung-Jin , Kim Hyunggee , Kim Mi-Suk , Chung Seok , Park Chul-Kee , Park Sung-Hye , Kang Yun Hee , Kim Jong Heon , Saya Hideyuki , Nakano Ichiro , Gwak Ho-Shin , Yoo Heon , Lee Jeongwu , Hur Eun-Mi , Shi Bingyang , Nam Do-Hyun , Iavarone Antonio , Lee Seung-Hoon , Park Jong Bae 
Published: November 2020

Abstract
As the clinical failure of glioblastoma treatment is attributed by multiple components, including myelin-associated infiltration, assessment of the molecular mechanisms underlying such process and identification of the infiltrating cells have been the primary objectives in glioblastoma research. Here, we adopted radiogenomic analysis to screen for functionally relevant genes that orchestrate the process of glioma cell infiltration through myelin and promote glioblastoma aggressiveness. The receptor of the Nogo ligand (NgR1) was selected as the top candidate through Differentially Expressed Genes (DEG) and Gene Ontology (GO) enrichment analysis. Gain and loss of function studies on NgR1 elucidated its underlying molecular importance in suppressing myelin-associated infiltration in vitro and in vivo. The migratory ability of glioblastoma cells on myelin is reversibly modulated by NgR1 during differentiation and dedifferentiation process through deubiquitinating activity of USP1, which inhibits the degradation of ID1 to downregulate NgR1 expression. Furthermore, pimozide, a well-known antipsychotic drug, upregulates NgR1 by post-translational targeting of USP1, which sensitizes glioma stem cells to myelin inhibition and suppresses myelin-associated infiltration in vivo. In primary human glioblastoma, downregulation of NgR1 expression is associated with highly infiltrative characteristics and poor survival. Together, our findings reveal that loss of NgR1 drives myelin-associated infiltration of glioblastoma and suggest that novel therapeutic strategies aimed at reactivating expression of NgR1 will improve the clinical outcome of glioblastoma patients.
Triglyceride-Rich Lipoprotein Remnants and Cardiovascular Disease
Authors: Duran Edward K , Pradhan Aruna D 
Published: November 2020

AbstractBackgroundTriglycerides, cholesterol, and their metabolism are linked due to shared packaging and transport within circulating lipoprotein particles. While a case for a causal role of cholesterol-carrying low-density lipoproteins (LDLs) in atherosclerosis is well made, the body of scientific evidence for a causal role of triglyceride-rich lipoproteins (TRLs) is rapidly growing, with multiple lines of evidence (old and new) providing robust support.ContentThis review will discuss current perspectives and accumulated evidence that an overabundance of remnant lipoproteins stemming from intravascular remodeling of nascent TRLs—chylomicrons and very low-density lipoproteins (VLDL)—results in a proatherogenic milieu that augments cardiovascular risk. Basic mechanisms of TRL metabolism and clearance will be summarized, assay methods reviewed, and pivotal clinical studies highlighted.SummaryRemnant lipoproteins are rendered highly atherogenic by their high cholesterol content, altered apolipoprotein composition, and physicochemical properties. The aggregate findings from multiple lines of evidence suggest that TRL remnants play a central role in residual cardiovascular risk.
OGDA: a comprehensive organelle genome database for algae
Authors: Liu Tao , Cui Yutong , Jia Xuli , Zhang Jing , Li Ruoran , Yu Yahui , Jia Shangang , Qu Jiangyong , Wang Xumin 
Published: November 2020

Abstract
Algae are the oldest taxa on Earth, with an evolutionary relationship that spans prokaryotes (Cyanobacteria) and eukaryotes. A long evolutionary history has led to high algal diversity. Their organelle DNAs are characterized by uniparental inheritance and a compact genome structure compared with nuclear genomes; thus, they are efficient molecular tools for the analysis of gene structure, genome structure, organelle function and evolution. However, an integrated organelle genome database for algae, which could enable users to both examine and use relevant data, has not previously been developed. Therefore, to provide an organelle genome platform for algae, we have developed a user-friendly database named Organelle Genome Database for Algae (OGDA, http://ogda.ytu.edu.cn/). OGDA contains organelle genome data either retrieved from several public databases or sequenced in our laboratory (Laboratory of Genetics and Breeding of Marine Organism [MOGBL]), which are continuously updated. The first release of OGDA contains 1055 plastid genomes and 755 mitochondrial genomes. Additionally, a variety of applications have been integrated into this platform to analyze the structural characteristics, collinearity and phylogeny of organellar genomes for algae. This database represents a useful tool for users, enabling the rapid retrieval and analysis of information related to organellar genomes for biological discovery.
Quantitative levels of serumN-glycans in type 1 diabetes and their association with kidney disease
Authors: Colombo Marco , Asadi Shehni Akram , Thoma Ioanna , McGurnaghan Stuart J , Blackbourn Luke A K , Wilkinson Hayden , Collier Andrew , Patrick Alan W , Petrie John R , McKeigue Paul M , Saldova Radka , Colhoun Helen M ,   the Scottish Diabetes Research Network (SDRN) Type 1 Bioresource Investigators
Published: November 2020

AbstractWe investigated associations of quantitative levels of N-glycans with hemoglobin A1c (HbA1c), renal function and renal function decline in type 1 diabetes. We measured 46 total N-glycan peaks (GPs) on 1565 serum samples from the Scottish Diabetes Research Network Type 1 Bioresource Study (SDRNT1BIO) and a pool of healthy donors. Quantitation of absolute abundance of each GP used 2AB-labeled mannose-3 as a standard. We studied cross-sectional associations of GPs and derived measures with HbA1c, albumin/creatinine ratio (ACR) and estimated glomerular filtration rate (eGFR), and prospective associations with incident albuminuria and final eGFR.All GPs were 1.4 to 3.2 times more abundant in SDRTN1BIO than in the healthy samples. Absolute levels of all GPs were slightly higher with higher HbA1c, with strongest associations for triantennary trigalactosylated disialylated, triantennary trigalactosylated trisialylated structures with core or outer arm fucose, and tetraantennary tetragalactosylated trisialylated glycans. Most GPs showed increased abundance with worsening ACR. Lower eGFR was associated with higher absolute GP levels, most significantly with biantennary digalactosylated disialylated glycans with and without bisect, triantennary trigalactosylated trisialylated glycans with and without outer arm fucose, and core fucosylated biantennary monogalactosylated monosialylated glycans. Although several GPs were inversely associated prospectively with final eGFR, cross-validated multivariable models did not improve prediction beyond clinical covariates.Elevated HbA1c is associated with an altered N-glycan profile in type 1 diabetes. Although we could not establish GPs to be prognostic of future renal function decline independently of HbA1c, further studies to evaluate their impact in the pathogenesis of diabetic kidney disease are warranted.
Genealogy from a distance: the media of correspondence and the Mormon church, 1910–45*
Authors: Hjorthén Adam 
Published: November 2020

Abstract
This article adopts a media historical approach to studying the modern history of genealogy, suggesting an alternative to both the dominant methodologies and periodization of the field. Empirically, it focuses on the ways in which correspondence was adopted as a tool for long-distance research by the Church of Jesus Christ of Latter-day Saints in 1910–45, examining in particular its research networks in Sweden. The article demonstrates that letter-writing was a research method dependent on record accessibility and interpersonal reliability. It also had the benefit of becoming its own resource, sustaining its relevance into the twenty-first century.
A metabarcoding comparison of taxonomic richness and composition between the water column and the benthic boundary layer
Authors: Parry H E , Atkinson A , Somerfield P J , Lindeque P K 
Published: November 2020

Abstract
Zooplankton monitoring in shelf seas predominantly uses nets that miss the benthic boundary layer (BBL) just above the seabed. However, this boundary between pelagic and benthic assemblages can be faunistically rich, having its own distinct hyperbenthic fauna and acting as a low-light refuge for overwintering or dielly migrating zooplankton. To compare species richness and composition between pelagic and BBL habitats, we sampled a long-term monitoring site in the Western English Channel seasonally. Metabarcoding methods applied to vertical net samples (top 50 m in a ∼54-m water column) and those from a hyperbenthic sledge generated &gt;100 000 sequences clustered into 294 operational taxonomic units. Of these, 215 were found in the BBL and 170 in the water column. Some key taxa (e.g. mysids) were native to the BBL; by contrast, other delicate taxa (e.g. ctenophores) seemed to avoid the BBL. The major contrasts in plankton composition related to the seasonal cycle rather than to pelagic-BBL differences, suggesting that the basic dynamics of the site are captured by our ongoing long-term weekly resolution monitoring. Overall, metabarcoding approaches, applied to both water column and BBL, provide an independent view of plankton dynamics, and augment existing traditional methods.
Recognition of ecosystem-based management principles in key documents of the seabed mining regime: implications and further recommendations
Authors: Guilhon Maila , Montserrat Francesc , Turra Alexander 
Published: November 2020

Abstract
New human uses on the marine environment, such as deep-sea mining (DSM), have necessitated the adoption of more holistic approaches such as ecosystem-based management (EBM) to secure sustainable development. The United Nations Convention on the Law of the Sea (UNCLOS) and the rules, regulations, and procedures adopted by the International Seabed Authority (ISA) represent the main regulatory framework to govern DSM activities. This study aimed to examine whether UNCLOS and ISA documents include references to EBM principles, and if these references vary in documents through time. Following a literature review, 26 EBM principles were collated into 8 general categories, and their adherence to 5 key documents related to the DSM regime was analysed. Results demonstrated a trend in recognizing EBM principles in documents over time, especially in the Draft Regulations for Exploitation. However, the mere recognition of EBM principles in the regulatory framework does not guarantee that the approach will be clearly understood and appropriately incorporated by contractors throughout the process. For such, further clarification on the meaning of the Ecosystem Approach in the DSM context and building the capacity of the ISA Legal and Technical Commission are among the recommendations presented by this study.
The global burden of chronic hepatitis B virus infection: comparison of country-level prevalence estimates from four research groups
Authors: Schmit Nora , Nayagam Shevanthi , Thursz Mark R , Hallett Timothy B 
Published: November 2020

Abstract

Background
Progress towards viral hepatitis elimination goals relies on accurate estimates of chronic hepatitis B virus (HBV)-infection prevalence. We compared existing sources of country-level estimates from 2013 to 2017 to investigate the extent and underlying drivers of differences between them.

Methods
The four commonly cited sources of global-prevalence estimates, i.e. the Institute for Health Metrics and Evaluation, Schweitzer et al., the World Health Organization (WHO) and the CDA Foundation, were compared by calculating pairwise differences between sets of estimates and assessing their within-country variation. Differences in underlying empirical data and modelling methods were investigated as contributors to differences in sub-Saharan African estimates.

Results
The four sets of estimates across all ages were comparable overall and agreed on the global distribution of HBV burden. The WHO and the CDA produced the most similar estimates, differing by a median of 0.8 percentage points. Larger discrepancies were seen in estimates of prevalence in children under 5 years of age and in sub-Saharan African countries, where the median pairwise differences were 2.7 percentage and 2.4 percentage points for all-age prevalence and in children, respectively. Recency and representativeness of included data, and different modelling assumptions of the age distribution of HBV burden, seemed to contribute to these differences.

Conclusion
Current prevalence estimates, particularly those from the WHO and the CDA based on more recent empirical data, provide a useful resource to assess the population-level burden of chronic HBV-infection. However, further seroprevalence data in young children are needed particularly in sub-Saharan Africa. This is a priority, as monitoring progress towards elimination depends on improved knowledge of prevalence in this age group.
The Effect of IL-6 Inhibitors on Mortality Among Hospitalized COVID-19 Patients: A Multicenter Study
Authors: Sinha Pranay , Jafarzadeh S Reza , Assoumou Sabrina A , Bielick Catherine G , Carpenter Bethanne , Garg Shivani , Harleen Sahni , Neogi Tuhina , Nishio Midori Jane , Sagar Manish , Sharp Veronika , Kissin Eugene Y 
Published: November 2020

Abstract

Background
The effectiveness of interleukin-6 inhibitors (IL-6i) in ameliorating coronavirus disease 2019 (COVID-19) remains uncertain.

Methods
We analyzed data for patients aged ≥18 years admitted with a positive severe acute respiratory syndrome coronavirus 2 polymerase chain reaction test at 4 safety-net hospital systems with diverse populations and high rates of medical comorbidities in 3 US regions. We used inverse probability of treatment weighting via machine learning for confounding adjustment by demographics, comorbidities, and disease severity markers. We estimated the average treatment effect, the odds of IL-6i effect on in-hospital mortality from COVID-19, using a logistic marginal structural model.

Results
Of 516 patients, 104 (20.1%) received IL-6i. Estimate of the average treatment effect adjusted for confounders suggested a 37% reduction in odds of in-hospital mortality in those who received IL-6i compared with those who did not, although the confidence interval included the null value of 1 (odds ratio = 0.63; 95% confidence interval, .29–1.38). A sensitivity analysis suggested that potential unmeasured confounding would require a minimum odds ratio of 2.55 to nullify our estimated IL-6i effect size.

Conclusions
Despite low precision, our findings suggested a relatively large effect size of IL-6i in reducing the odds of COVID-19–related in-hospital mortality.
The role of antimicrobial stewardship in preventing KPC-producing Klebsiella pneumoniae
Authors: Carrara Elena , Conti Michela , Meschiari Marianna , Mussini Cristina 
Published: November 2020

Abstract
Antimicrobial stewardship programmes are widely considered to be a core component of the response to the antimicrobial resistance threat. However, a positive impact of these interventions in terms of microbiological outcomes remains difficult to demonstrate, especially when focusing on specific resistant phenotypes. The first part of this review aims to explore the complex relationship between antibiotic exposure and resistance development in KPC-producing Klebsiella pneumoniae. In the second part we aim to summarize published examples of antimicrobial stewardship interventions intended to impact on the epidemiology of KPC-producing K. pneumoniae. For this purpose, a literature search was performed and seven studies were included in the review. Both restrictive and non-restrictive interventions were associated with an overall reduction in antibiotic consumption, and a decrease in carbapenem resistance rates was observed in five studies. The overall quality of the evidence was low, mainly due to the poor reporting of microbiological outcomes, lack of a control group and suboptimal study design. Although the link between antibiotic use and resistance development is supported by strong evidence, demonstrating the impact of antimicrobial stewardship interventions on microbiological outcomes remains difficult. Studies with adequate design and appropriate outcome measures are needed to further promote antimicrobial stewardship and elucidate which interventions are more successful for controlling the spread of KPC-producing K. pneumoniae.
Application of Bayesian networks to generate synthetic health data
Authors: Kaur Dhamanpreet , Sobiesk Matthew , Patil Shubham , Liu Jin , Bhagat Puran , Gupta Amar , Markuzon Natasha 
Published: November 2020

Abstract

Objective
This study seeks to develop a fully automated method of generating synthetic data from a real dataset that could be employed by medical organizations to distribute health data to researchers, reducing the need for access to real data. We hypothesize the application of Bayesian networks will improve upon the predominant existing method, medBGAN, in handling the complexity and dimensionality of healthcare data.

Materials and Methods
We employed Bayesian networks to learn probabilistic graphical structures and simulated synthetic patient records from the learned structure. We used the University of California Irvine (UCI) heart disease and diabetes datasets as well as the MIMIC-III diagnoses database. We evaluated our method through statistical tests, machine learning tasks, preservation of rare events, disclosure risk, and the ability of a machine learning classifier to discriminate between the real and synthetic data.

Results
Our Bayesian network model outperformed or equaled medBGAN in all key metrics. Notable improvement was achieved in capturing rare variables and preserving association rules.

Discussion
Bayesian networks generated data sufficiently similar to the original data with minimal risk of disclosure, while offering additional transparency, computational efficiency, and capacity to handle more data types in comparison to existing methods. We hope this method will allow healthcare organizations to efficiently disseminate synthetic health data to researchers, enabling them to generate hypotheses and develop analytical tools.

Conclusion
We conclude the application of Bayesian networks is a promising option for generating realistic synthetic health data that preserves the features of the original data without compromising data privacy.