bluuebunny/crossref_metadata_2025_split huggingface dataset:
Practical strategies for SARS-CoV-2 RT-PCR testing in resource-constrained settings
Authors: Muller Meredith S. , Chhetri Srijana Bhattarai , Basham Christopher , Rapp Tyler , Lin Feng-Chang , Lin Kelly , Westreich Daniel , Cerami Carla , Juliano Jonathan J. , Lin Jessica T. 
Published: February 2021

ABSTRACTBackgrounStandard nasopharyngeal swab testing for SARS-CoV-2 detection by PCR is not always feasible due to limitations in trained personnel, personal protective equipment, swabs, PCR reagents, and access to cold chain and biosafety hoods.MethodWe piloted the collection of nasal mid-turbinate swabs amenable to self-testing, including both standard polyester flocked swabs as well as 3D printed plastic lattice swabs, placed into either viral transport media or an RNA stabilization agent. Quantitative SARS-CoV-2 viral detection by RT-qPCR was compared to that obtained by nasopharyngeal sampling as the reference standard. Pooling specimens in the lab versus pooling swabs at the point of collection was also evaluated.ResultsAmong 275 participants, flocked nasal swabs identified 104/121 individuals who were PCR-positive for SARS-CoV-2 by nasopharyngeal sampling (sensitivity 87%, 95% CI 79-92%), mostly missing those with low viral load (<10^3 viral copies/uL). 3D-printed nasal swabs showed similar sensitivity. When nasal swabs were placed directly into an RNA stabilizer, the mean 1.4 log decrease in viral copies/uL compared to nasopharyngeal samples was reduced to <1 log, even when samples were left at room temperature for up to 7 days. Pooling sample specimens or swabs both successfully detected samples >102viral copies/uL.ConclusionsNasal swabs are likely adequate for clinical diagnosis of acute infections to help expand testing capacity in resource-constrained settings. When collected into an RNA preservative that also inactivates infectious virus, nasal swabs yielded quantitative viral loads approximating those obtained by nasopharyngeal sampling.
Causal effects from non-alcoholic fatty liver disease on kidney function: A Mendelian randomization study
Authors: Park Sehoon , Lee Soojin , Kim Yaerim , Cho Semin , Kim Kwangsoo , Kim Yong Chul , Han Seung Seok , Lee Hajeong , Lee Jung Pyo , Joo Kwon Wook , Lim Chun Soo , Kim Yon Su , Kim Dong Ki 
Published: February 2021

AbstractBackground & aimsAn observational association between nonalcoholic fatty liver disease (NAFLD) and kidney function impairment has been reported. A genetic variant linked to an increased risk of NAFLD, the G allele of rs738409, has been reported to be associated with a reduction in estimated glomerular filtration rate (eGFR).Approach & ResultsIn this Mendelian randomization (MR) study, we first performed single-variant MR with rs738409 as a genetic instrument to predict NAFLD. Another genetic instrument was developed from a previous genome-wide association study for the NAFLD phenotype in the Million Veteran Program cohort among individuals of European ancestry (68,725 cases and 95,472 controls). The eGFR outcome was assessed in individuals of white British ancestry included in the UK Biobank (N = 321,405). Further, the associations were reassessed in two negative control subgroups (body mass index < 25 kg/m2 and serum alanine aminotransferase level < 20 IU/mL) with a low probability of developing NAFLD. As a replication analysis, a summary-level MR was performed with the European ancestry CKDGen dataset (N = 567,460). In the UK Biobank dataset, a genetic predisposition for NAFLD, either by rs738409 or a group of variants, was significantly associated with a reduced eGFR even with adjustment for major metabolic disorders. Although the associations were not significant in the negative control subgroups with a low probability of developing NAFLD, they were significant in the subgroups with a remaining risk of NAFLD, suggesting the absence of a horizontal pleiotropic pathway. The summary-level MR from the CKDGen dataset supported the causal effects of NAFLD on reduced eGFR.ConclusionsThis MR analysis supports the causal reduction in kidney function by NAFLD.
Use of WATCH antibiotics prior to presentation to the hospital in rural Burkina Faso
Authors: Valia Daniel , Ingelbeen Brecht , Kaboré Bérenger , Karama Ibrahima , Peeters Marjan , Lompo Palpouguini , Vlieghe Erika , Post Annelies , Cox Janneke , de Mast Quirijn , Robert Annie , van der Sande Marianne A.B. , Villalobos Hector Rodriguez , van der Ven Andre , Tinto Halidou , Jacobs Jan 
Published: February 2021

AbstractBackgroundIn low- and middle-income countries (LMIC), the prevalence of antimicrobial resistance (AMR) is increasing. WHO recommends monitoring antibiotic use, in particular Watch antibiotics, clinical important but at risk of becoming ineffective due to increasing AMR. We investigated antibiotic use at primary care or community-level in rural Burkina Faso.MethodsDuring 2016-2017, patients aged >3 months admitted with severe acute fever to the rural hospital of Nanoro Health District, Burkina Faso, reported antibiotic use in the two weeks prior to consultation or hospitalization, which we analysed using the WHO Access, Watch, Reserve (AWaRe) classification. Most Watch antibiotics, e.g. ceftriaxone, are not recommended at primary health center level, as is also the case for ciprofloxacin in children.ResultsOf 920 participants (63.0% ≤14 years), pre-admission antibiotic use was reported by 363 (39.5%) of whom 58 (16.0%) reported more than one antibiotic. Use was more frequent among health center referrals (231, 54.0%) than among self-referred patients (131, 26.7%, p<0.001). Of 424 antibiotics, 261 (61.6%) were Access and 159 (37.5%) Watch antibiotics. Watch antibiotics use was more frequent among >14 year olds (72, 51.1%) than 0-14 year olds (87, 30.7%) and among referrals (41, 28.1%) compared to self-referred patients (117, 42.2%). Most frequently used Watch antibiotics were ceftriaxone (114, 26.9%) and ciprofloxacin (32, 7.5%). Among antibiotics reported by referral patients, ceftriaxone and ciprofloxacin were respectively recorded 100 (36.1%) and 12 times (4.3%).ConclusionThe frequent use of Watch group antibiotics prior to presentation to the hospital in rural Burkina Faso highlights the need to address primary care, over-the-counter and informal community-level antibiotic use as part of antibiotic stewardship in LMIC, facilitating referral, access to qualified prescribers, or improving diagnostic tools in health centers.
Modelling seeding and neuroanatomic spread of pathology in amyotrophic lateral sclerosis
Authors: Pandya Sneha , Maia Pedro D. , Freeze Benjamin , Menke Ricarda A L , Talbot Kevin , Turner Martin R , Raj Ashish 
Published: February 2021

AbstractThe neurodegenerative disorder amyotrophic lateral sclerosis (ALS) is characterized by the progressive loss of upper and lower motor neurons, with pathological involvement of cerebral motor and, additionally, extra-motor areas, in a clinicopathological spectrum with frontotemporal dementia (FTD). A key unresolved question is whether the distribution of pathology in ALS is driven by molecular factors such as regional gene expression, by differential network vulnerability, or is a combination of both. A system of histopathological staging of ALS based on the regional burden of TDP-43 pathology observed inpost mortembrains has been supported to some extent by analysis of distribution ofin vivostructural MRI changes. In this paper, computational modelling using a Network Diffusion Model (NDM) was used to investigate whether a process of focal pathological ‘seeding’ followed by structural network-based spread recapitulatedpost mortemhistopathological staging and, secondly, whether this had any relationship to the pattern of expression of a panel of genes implicated in ALS across the healthy brain. Regionally parcellated T1-weighted MRI data from ALS patients (baseline n=79) was studied in relation to a healthy control structural connectome and a database of associated regional cerebral gene expression. The NDM provided strong support for a structural network-based basis for regional pathological spread in ALS, but no simple relationship to the spatial distribution of ALS-related genes in the healthy brain. Intriguingly, the critical seed regions for spread within the model were not within the primary motor cortex but basal ganglia, thalamus and insula, where NDM recapitulated aspects of thepost mortemhistopathological staging system. Within the ALS-FTD clinicopathological spectrum, non-primary motor structures may be among the earliest sites of cerebral pathology.
The Origins and Drivers of Neotropical Diversity
Authors: Meseguer Andrea S. , Michel Alice , Fabre Pierre-Henri , Pérez-Escobar Oscar A. , Chomicki Guillaume , Riina Ricarda , Antonelli Alexandre , Antoine Pierre-Olivier , Delsuc Frédéric , Condamine Fabien L. 
Published: February 2021

AbstractThe origins and evolution of the outstanding Neotropical biodiversity are still debated. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we evaluate four evolutionary scenarios assuming different diversification trajectories and drivers of Neotropical diversification, and assess their variation across Neotropical regions and taxa. Our analysis of 150 phylogenies (12,512 species) of seed plants and tetrapods reveals that Neotropical diversity has mostly expanded through time (70% of the clades), while scenarios of saturated and declining diversity also account for 21% and 9% of Neotropical diversity, respectively. We identify five biogeographic areas that represent distinctive units of long-term Neotropical evolution (Pan-Amazonia, Dry Diagonal, Bahama-Antilles, Galapagos, and an ‘elsewhere’ region) and find that diversity dynamics do not differ across these areas, suggesting no geographic structure in long-term Neotropical diversification. In contrast, diversification dynamics differ substantially across taxa: plant diversity mostly expanded through time (88%), while a substantial fraction (43%) of tetrapod diversity accumulated at a slower pace or declined toward the present. These opposite evolutionary patterns may reflect different capacities for plants and tetrapods to cope with climate change, with potential implications for future adaptation and ecosystem resilience.
Late-life fitness gains explain the absence of a selection shadow in ants
Authors: Nino Luisa M. Jaimes , Heinze Jürgen , Oettler Jan 
Published: February 2021

AbstractA key hypothesis for the occurrence of senescence is a decrease in the selection strength because of low late-life fitness – the so-called selection shadow. However, in social insects, aging is considered a plastic trait and senescence seems to be absent. By life-long tracking of 102 ant colonies, we find that queens increase the production of sexuals in late life regardless of their absolute lifespan or worker investment. This indicates a genetically accommodated adaptive shift towards increasingly queen-biased caste ratios over the course of a queens’ life. Furthermore, mortality decreased with age, supporting the hypothesis that aging is adaptive. We argue that selection for late life reproduction diminishes the selection shadow of old age and leads to the apparent absence of senescence in ants, in contrast to most iteroparous species.Significance StatementSocial insects are extraordinary with regard to the absolute age of queens of some species as well as the age differences between queens and short-lived workers. Yet, ultimate causes explaining these aging patterns remain poorly understood. By manipulating the investment ratio into queens and workers we studied the effect on lifespan and temporal reproductive investment of queens. We show that queens shift to the production of sexuals late in life, independent of social context (colony size) or individual quality (reproductive output and lifespan). Such late fitness gains result in maintenance in the selection strength with age, and thus explains the absence of senescence in queens.
Comparison study of sixteen differential abundance testing methods using two large Parkinson disease gut microbiome datasets
Authors: Wallen Zachary D. 
Published: February 2021

AbstractBackgroundWhen studying the relationship between the microbiome and a disease, a common question asked is what individual microbes are differentially abundant between a disease and healthy state. Numerous differential abundance (DA) testing methods exist and range from standard statistical tests to methods specifically designed for microbiome data. Comparison studies of DA testing methods have been performed, but none were performed on microbiome datasets collected for the study of real, complex disease. Due to this, we performed DA testing of microbial genera using 16 DA methods in two large, uniformly collected gut microbiome datasets on Parkinson disease (PD), and compared their results.ResultsPairwise concordances between methods ranged from 46%-99% similarity. Average pairwise concordance per dataset was 76%, and dropped to 62% when taking replication of signals across datasets into account. Certain methods consistently resulted in above average concordances (e.g. Kruskal-Wallis, ALDEx2, GLM with centered-log-ratio transform), while others consistently resulted in lower than average concordances (e.g. edgeR, fitZIG). Overall, ∼80% of genera tested were detected as differentially abundant by at least one method in each dataset. Requiring associations to replicate across datasets reduced significant signals by almost half. Further requirement of signals to be replicated by the majority of methods (≥8) yielded 19 associations. Only one genus (Agathobacter) was replicated by all methods. Use of hierarchical clustering revealed three groups of DA signatures that were (1) replicated by the majority of methods and included genera previously associated with PD, (2) replicated by few or no methods, and (3) replicated by a subset of methods and included rarer genera, all enriched in PD.ConclusionsDifferential abundance tests yielded varied results. Using one method on one dataset may find true associations, but may also detect non-reproducible signals, adding to inconsistency in the literature. To help lower false positives, one might analyze data with two or more DA methods to gauge concordance, and use a built-in replication dataset to show reproducibility. This study corroborated previously reported microorganism associations in PD, and revealed a potential new group of microorganisms whose abundance is significantly elevated in PD, and might be worth pursuing in future investigations.
SIMILE enables alignment of fragmentation mass spectra with statistical significance
Authors: Treen Daniel G.C. , Northen Trent R. , Bowen Benjamin P. 
Published: February 2021

AbstractInterrelating compounds according to their aligned fragmentation spectra is central to tandem mass spectrometry-based metabolomics. However, current alignment algorithms do not provide statistical significance and compounds that have multiple delocalized structural differences often fail to have their fragment ions aligned. Significant Interrelation of MS/MS Ions via Laplacian Embedding (SIMILE) is a new tool inspired by protein sequence alignment for aligning fragmentation spectra with statistical significance and allowance for multiple chemical differences. We found SIMILE yields 550% more pairs of structurally similar compounds than commonly used cosine-based scoring algorithms, and anticipate SIMILE will fill an important role by also providing p-values for fragmentation spectra alignments to explore structural relationships between compounds.
Identification of biomarkers and candidate inhibitors for multiple myeloma
Authors: Gu Hanming , Wang Wei , Yuan Gongsheng 
Published: February 2021

AbstractMultiple myeloma (MM) is a plasma cell malignancy that causes the overabundance of monoclonal paraprotein (M protein) and organ damages. In our study, we aim to identify biological markers and processes of MM using a bioinformatics method to elucidate their potential pathogenesis. The gene expression profiles of the GSE153626 datasets were originally produced by using the high-throughput Illumina HiSeq 4000 (Mus musculus). The functional categories and biochemical pathways were identified and analyzed by the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG), Gene Ontology (GO), and Reactom enrichment. KEGG and GO results showed the biological pathways related to immune dysfunction and signal transduction are mostly affected in the development of MM. Moreover, we identified several genes including Gngt2, Foxp3, and Cd3g were involved in the regulation of immune cells. We further predicted new inhibitors that have the ability to block the progression of MM based on the L1000fwd analysis. Therefore, this study provides further insights into the underlying pathogenesis of MM.
Modeling of fuel flow-rate of commercial aircraft for the descent flight using particle swarm optimization
Authors: Oruc Ridvan , Baklacioglu Tolga 
Published: February 2021

Purpose
The purpose of this paper is to create a new fuel flow rate model for the descent phase of the flight using particle swarm optimization (PSO).

Design/methodology/approach
A new fuel flow rate model was developed for the descent phase of the B737-800 aircraft, which is frequently used in commercial air transport using PSO method. For the analysis, the actual flight data records (FDRs) data containing the fuel flow rate, speed, altitude, engine speed, time and many more data were used. In this regard, an empirical formula has been created that gives real fuel flow rate values as a function of altitude and true airspeed. In addition, in the fuel flow rate predictions made for the descent phase of the specified aircraft, a different model has been created that can be used without any optimization process when FDR data are not available for a specific aircraft take-off weight condition.

Findings
The error analysis applied to the models showed that both models predict real fuel flow rate values with high precision.

Practical implications
Because of the high accuracy of the PSO model, it is thought to be useful in air traffic management, decision support systems, models used for trajectory prediction, aircraft performance models, strategies used to reduce fuel consumption and emissions because of fuel consumption.

Originality/value
This study is the first fuel flow rate model for descent flight using PSO algorithm. The use of real FDR data in the analysis shows the originality of this study.
Impacts of monetary instruments on overnight spread under the interest rate corridor framework: evidence from China
Authors: Chang Chiu-Lan , Fang Ming , Hong Bin , Ho Kung-Cheng 
Published: February 2021

PurposeTo verify the effectiveness of the monetary policy, the impacts of monetary instruments on overnight spread under the interest rate corridor (IRC) are examined. The People's Bank of China (PBC) has operated the IRC since 2014. To understand the impacts of monetary instruments on overnight spread before and after the IRC framework, the complete samples are divided into two periods.Design/methodology/approachTo model the overnight spread, an exponential GARCH (EGARCH) approach is used which can examine the interbank market interest rates for monetary policy purposes. The overnight money market plays an important role in the implementation of monetary policy.FindingsChinese interest rate liberalization and the implementation of IRC affect the overnight spread in the short-term financing market. Before the implementation of the IRC, the key factor to affect the overnight spread is mainly affected by the PBC's monetary policy control on the liquidity supply side. After the implementation of IRC, the overnight spread can be the largest part explained by the liquidity demand side and the PBC's multiple monetary instruments have significant impacts on the reduction of overnight spread.Originality/valueThe overnight spread has recently been influenced by various factors that are directly or closely related to the monetary policy instruments and the interest rate policy of the PBC. Chinese interest rate liberalization and the implementation of interest rate corridor policy affect the overnight spread in the short-term financing market.
Multiple-input multiple-output antenna for dual-band applications with a novel radiating patch and enhanced feeding network
Authors: Zehforoosh Yashar , Alemi Payam 
Published: February 2021

Purpose
An Elephant trunk shape (ETS) radiating element is used to achieve the two covering bands of multi-input multi-output (MIMO) antenna. These frequency bands can be controlled by the length of a slot embedded in ETS. The slot length in ETS plays a defining role in controlling the impedance bandwidth (IBW) of the MIMO antenna, and its diligent adjustment of it leads to cover the frequency range of Bluetooth and Wireless Local Area Network systems.

Design/methodology/approach
A new MIMO antenna is introduced in this paper in conjunction with an enhanced Wilkinson power divider feeding platform.

Findings
These frequency bands can be controlled by the length of a slot embedded in ETS. The slot length in ETS plays a defining role in controlling the IBW of the MIMO antenna, and its diligent adjustment leads to covering the frequency range of Bluetooth and WLAN systems.

Originality/value
The proposed MIMO antenna benefits from good isolation between ports for both frequency bands. The proposed MIMO antenna is constructed on FR4 substrate with a volume of 90 × 134 × 1.6 mm3.
Factors influencing scholarly publication productivity: a systematic review
Authors: Wahid Nazia , Warraich Nosheen Fatima , Tahira Muzammil 
Published: February 2021

Purpose
The importance of scientific publications has enhanced the research activities at all aggregate levels. The purpose of this paper is to conduct an in-depth review of studies examined the factors that influence the publication productivity among researchers, institutions and countries.

Design/methodology/approach
This paper uses a systematic literature review approach that is based on relevant literature retrieved from two authentic and well-known databases named Web of Science and SCOPUS. Kitchenham protocol of systematic review was applied, and relevant studies were searched by selected keywords search. Inclusion and exclusion criteria were used to select high quality studies. A rigorous study selection procedure was designed.

Findings
Findings reveal that several factors play a significant role in the publication productivity growth. All of the identified factors were grouped into three categories. Most of the factors belong to personal category while two top dominant factors, funding and collaboration fall into situational category. Other most influential factors, time, academic rank and academic qualification are personal. Findings highlight that publication output at individual level is strongly influenced by personal factors while few environmental and situational factors also affect the number of publications. Publication productivity of institutes and countries is affected by environmental and situational factors.

Originality/value
This paper contributes by providing a detailed review to explore the influencing factors of scholarly publication of researchers, institutions and countries. This study will be supportive for researchers and policymakers for making strategies to stimulate the research publication practices at researchers, institutions and national level.