bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulsar candidate identification using semi-supervised generative adversarial networks
Authors: Balakrishnan Vishnu , Champion David , Barr Ewan , Kramer Michael , Sengar Rahul , Bailes Matthew 
Published: May 2021

ABSTRACT
Machine learning methods are increasingly helping astronomers identify new radio pulsars. However, they require a large amount of labelled data, which is time consuming to produce and biased. Here, we describe a Semi-supervised generative adversarial network, which achieves better classification performance than the standard supervised algorithms using majority unlabelled data sets. We achieved an accuracy and mean F-Score of 94.9 per cent trained on only 100 labelled candidates and 5000 unlabelled candidates compared to our standard supervised baseline which scored at 81.1 per cent and 82.7 per cent, respectively. Our final model trained on a much larger labelled data set achieved an accuracy and mean F-score value of 99.2 per cent and a recall rate of 99.7 per cent. This technique allows for high-quality classification during the early stages of pulsar surveys on new instruments when limited labelled data are available. We open-source our work along with a new pulsar-candidate data set produced from the High Time Resolution Universe – South Low Latitude Survey. This data set has the largest number of pulsar detections of any public data set and we hope it will be a valuable tool for benchmarking future machine learning models.
Zinc stable isotope analysis reveals Zn dyshomeostasis in benign tumours, breast cancer, and adjacent histologically normal tissue
Authors: Sullivan Kaj V , Moore Rebekah E T , Capper Miles S , Schilling Kathrin , Goddard Kate , Ion Charlotte , Layton-Matthews Daniel , Leybourne Matthew I , Coles Barry , Kreissig Katharina , Antsygina Olga , Coombes R Charles , Larner Fiona , Rehkämper Mark 
Published: May 2021

Abstract
The disruption of Zn homeostasis has been linked with breast cancer development and progression. To enhance our understanding of changes in Zn homeostasis both inside and around the tumour microenvironment, Zn concentrations and isotopic compositions (δ66Zn) were determined in benign (BT) and malignant (MT) tumours, healthy tissue from reduction mammoplasty (HT), and histologically normal tissue adjacent to benign (NAT(BT)) and malignant tumours (NAT(MT)). Mean Zn concentrations in NAT(BT) are 5.5 µg g−1 greater than in NAT(MT) (p = 0.00056) and 5.1 µg g−1 greater than in HT (p = 0.0026). Zinc concentrations in MT are 12.9 µg g−1 greater than in HT (p = 0.00012) and 13.3 µg g−1 greater than in NAT(MT) (p &lt; 0.0001), whereas δ66Zn is 0.17‰ lower in MT than HT (p = 0.017). Benign tumour Zn concentrations are also elevated compared to HT (p = 0.00013), but are not significantly elevated compared to NAT(BT) (p = 0.32). The δ66Zn of BT is 0.15‰ lower than in NAT(BT) (p = 0.045). The similar light δ66Zn of BT and MT compared to HT and NAT may be related to the isotopic compensation of increased metallothionein (64Zn-rich) expression by activated matrix metalloproteinase (66Zn-rich) in MT, and indicates a resultant 66Zn-rich reservoir may exist in patients with breast tumours. Zinc isotopic compositions thus show promise as a potential diagnostic tool for the detection of breast tumours. The revealed differences of Zn accumulation in healthy and tumour-adjacent tissues require additional investigation.
YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria
Authors: D’Souza Aaron R , Van Haute Lindsey , Powell Christopher A , Mutti Christian D , Páleníková Petra , Rebelo-Guiomar Pedro , Rorbach Joanna , Minczuk Michal 
Published: May 2021

Abstract
Mitochondria contain their own translation apparatus which enables them to produce the polypeptides encoded in their genome. The mitochondrially-encoded RNA components of the mitochondrial ribosome require various post-transcriptional processing steps. Additional protein factors are required to facilitate the biogenesis of the functional mitoribosome. We have characterized a mitochondrially-localized protein, YbeY, which interacts with the assembling mitoribosome through the small subunit. Loss of YbeY leads to a severe reduction in mitochondrial translation and a loss of cell viability, associated with less accurate mitochondrial tRNASer(AGY) processing from the primary transcript and a defect in the maturation of the mitoribosomal small subunit. Our results suggest that YbeY performs a dual, likely independent, function in mitochondria being involved in precursor RNA processing and mitoribosome biogenesis. Issue Section: Nucleic Acid Enzymes.
noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise
Authors: Moutsopoulos Ilias , Maischak Lukas , Lauzikaite Elze , Vasquez Urbina Sergio A , Williams Eleanor C , Drost Hajk-Georg , Mohorianu Irina I 
Published: May 2021

Abstract
High-throughput sequencing enables an unprecedented resolution in transcript quantification, at the cost of magnifying the impact of technical noise. The consistent reduction of random background noise to capture functionally meaningful biological signals is still challenging. Intrinsic sequencing variability introducing low-level expression variations can obscure patterns in downstream analyses. We introduce noisyR, a comprehensive noise filter to assess the variation in signal distribution and achieve an optimal information-consistency across replicates and samples; this selection also facilitates meaningful pattern recognition outside the background-noise range. noisyR is applicable to count matrices and sequencing data; it outputs sample-specific signal/noise thresholds and filtered expression matrices. We exemplify the effects of minimizing technical noise on several datasets, across various sequencing assays: coding, non-coding RNAs and interactions, at bulk and single-cell level. An immediate consequence of filtering out noise is the convergence of predictions (differential-expression calls, enrichment analyses and inference of gene regulatory networks) across different approaches.
HP1021 is a redox switch protein identified in Helicobacter pylori
Authors: Szczepanowski Piotr , Noszka Mateusz , Żyła-Uklejewicz Dorota , Pikuła Fabian , Nowaczyk-Cieszewska Malgorzata , Krężel Artur , Stingl Kerstin , Zawilak-Pawlik Anna 
Published: May 2021

Abstract
Helicobacter pylori is a gram-negative, microaerophilic, pathogenic bacterium and a widespread colonizer of humans. H. pylori has developed mechanisms that enable it to overcome the harsh environment of the human stomach, including reactive oxygen species (ROS). Interestingly, up to now no typical regulator dedicated to the oxidative-stress response has been discovered. In this work, we reveal that the inhibitor of replication initiation HP1021 functions as a redox switch protein in H. pylori and plays an important role in response to oxidative stress of the gastric pathogen. Each of the two predicted HP1021 domains contains three cysteine residues. We show that the cysteine residues of HP1021 are sensitive to oxidation both in vitro and in vivo, and we demonstrate that HP1021 DNA-binding activity to oriC depends on the redox state of the protein. Moreover, Zn2+ modulates HP1021 affinity towards oriC template DNA. Transcription analysis of selected H. pylori genes by RT-qPCR indicated that HP1021 is directly involved in the oxygen-dependent control of H. pylori fecA3 and gluP genes, which are implicated in response to oxidative stress. In conclusion, HP1021 is a redox switch protein and could be a target for H. pylori control strategies.
Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis
Authors: Durand Sylvain , Callan-Sidat Adam , McKeown Josie , Li Stephen , Kostova Gergana , Hernandez-Fernaud Juan R , Alam Mohammad Tauqeer , Millard Andrew , Allouche Delphine , Constantinidou Chrystala , Condon Ciarán , Denham Emma L 
Published: May 2021

Abstract
sRNAs are a taxonomically-restricted but transcriptomically-abundant class of post-transcriptional regulators. While of major importance for adaption to the environment, we currently lack global-scale methodology enabling target identification, especially in species without known RNA hub proteins (e.g. Hfq). Using psoralen RNA cross-linking and Illumina-sequencing we identify RNA–RNA interacting pairs in vivo in Bacillus subtilis, resolving previously well-described interactants. Although sRNA–sRNA pairings are rare (compared with sRNA–mRNA), we identify a robust example involving the conserved sRNA RoxS and an unstudied sRNA RosA (Regulator of sRNA A). We show RosA to be the first confirmed RNA sponge described in a Gram-positive bacterium. RosA interacts with at least two sRNAs, RoxS and FsrA. The RosA/RoxS interaction not only affects the levels of RoxS but also its processing and regulatory activity. We also found that the transcription of RosA is repressed by CcpA, the key regulator of carbon-metabolism in B. subtilis. Since RoxS is already known to be transcriptionally controlled by malate via the transcriptional repressor Rex, its post-transcriptional regulation by CcpA via RosA places RoxS in a key position to control central metabolism in response to varying carbon sources.
Genome-Wide Association Study Identifies Genetic Risk Factors for Spastic Cerebral Palsy
Authors: Hale Andrew T , Akinnusotu Oluwatoyin , He Jing , Wang Janey , Hibshman Natalie , Shannon Chevis N , Naftel Robert P 
Published: May 2021

Abstract

BACKGROUND
Although many clinical risk factors of spastic cerebral palsy (CP) have been identified, the genetic basis of spastic CP is largely unknown. Here, using whole-genome genetic information linked to a deidentified electronic health record (BioVU) with replication in the UK Biobank and FinnGen, we perform the first genome-wide association study (GWAS) for spastic CP.

OBJECTIVE
To define the genetic basis of spastic CP.

METHODS
Whole-genome data were obtained using the multi-ethnic genotyping array (MEGA) genotyping array capturing single-nucleotide polymorphisms (SNPs), minor allele frequency (MAF) > 0.01, and imputation quality score (r2) > 0.3, imputed based on the 1000 genomes phase 3 reference panel. Threshold for genome-wide significance was defined after Bonferroni correction for the total number of SNPs tested (P < 5.0 × 10–8). Replication analysis (defined as P < .05) was performed in the UK Biobank and FinnGen.

RESULTS
We identify 1 SNP (rs78686911) reaching genome-wide significance with spastic CP. Expression quantitative trait loci (eQTL) analysis suggests that rs78686911 decreases expression of GRIK4, a gene that encodes a high-affinity kainate glutamatergic receptor of largely unknown function. Replication analysis in the UK Biobank and FinnGen reveals additional SNPs in the GRIK4 loci associated with CP.

CONCLUSION
To our knowledge, we perform the first GWAS of spastic CP. Our study indicates that genetic variation contributes to CP risk.
Understanding Nonadherence to Tuberculosis Medications in India Using Urine Drug Metabolite Testing: A Cohort Study
Authors: Subbaraman Ramnath , Thomas Beena E , Kumar J Vignesh , Thiruvengadam Kannan , Khandewale Amit , Kokila S , Lubeck-Schricker Maya , Ranjith Kumar M , Gaurkhede Gunjan Rahul , Walgude Apurva Shashikant , Hephzibah Mercy J , Kumbhar Jagannath Dattatraya , Eliasziw Misha , Mayer Kenneth H , Haberer Jessica E 
Published: May 2021

Abstract

Background
Poor adherence to tuberculosis (TB) treatment is associated with disease recurrence and death. Little research has been conducted in India to understand TB medication nonadherence.

Methods
We enrolled adult drug-susceptible TB patients, approximately half of whom were people with human immunodeficiency virus (PWH), in Chennai, Vellore, and Mumbai. We conducted a single unannounced home visit to administer a survey assessing reasons for nonadherence and collect a urine sample that was tested for isoniazid content. We described patient-reported reasons for nonadherence and identified factors associated with nonadherence (ie, negative urine test) using multivariable logistic regression. We also assessed the association between nonadherence and treatment outcomes.

Results
Of 650 participants in the cohort, 77 (11.8%) had a negative urine test. Nonadherence was independently associated with daily wage labor (adjusted odds ratio [aOR], 2.7; confidence interval [CI], 1.1–6.5; P = .03), the late continuation treatment phase (aOR, 2.0; CI, 1.1–3.9; P = .03), smear-positive pulmonary disease (aOR, 2.1; CI, 1.1–3.9; P = .03), alcohol use (aOR, 2.5; CI, 1.2–5.2; P = .01), and spending ≥30 minutes collecting medication refills (aOR, 6.6; CI, 1.5–29.5; P = .01). People with HIV reported greater barriers to collecting medications than non-PWH. Among 167 patients reporting missing doses, reported reasons included traveling from home, forgetting, feeling depressed, and running out of pills. The odds of unfavorable treatment outcomes were 4.0 (CI, 2.1–7.6) times higher among patients with nonadherence (P &lt; .0001).

Conclusion
Addressing structural and psychosocial barriers will be critical to improve TB treatment adherence in India. Urine isoniazid testing may help identify nonadherent patients to facilitate early intervention during treatment.
Characterization of Bacterial and Fungal Infections in Hospitalized Patients With Coronavirus Disease 2019 and Factors Associated With Health Care-Associated Infections
Authors: Kubin Christine J , McConville Thomas H , Dietz Donald , Zucker Jason , May Michael , Nelson Brian , Istorico Elizabeth , Bartram Logan , Small-Saunders Jennifer , Sobieszczyk Magdalena E , Gomez-Simmonds Angela , Uhlemann Anne-Catrin 
Published: May 2021

Abstract

Background
Patients hospitalized with coronavirus disease 2019 (COVID-19) are at increased risk of health care–associated infections (HAIs), especially with prolonged hospital stays. We sought to identify incidence, antimicrobial susceptibilities, and outcomes associated with bacterial/fungal secondary infections in a large cohort of patients with COVID-19.

Methods
We evaluated adult patients diagnosed with COVID-19 between 2 March and 31 May 2020 and hospitalized &gt;24 hours. Data extracted from medical records included diagnoses, vital signs, laboratory results, microbiological data, and antibiotic use. Microbiologically confirmed bacterial and fungal pathogens from clinical cultures were evaluated to characterize community- and health care–associated infections, including describing temporal changes in predominant organisms on presentation and throughout hospitalization. Univariable and multivariable logistic regression analyses were performed to investigate risk factors for HAIs.

Results
A total of 3028 patients were included and accounted for 899 positive clinical cultures. Overall, 516 (17%) patients with positive cultures met criteria for infection. Community-associated coinfections were identified in 183 (6%) patients, whereas HAIs occurred in 350 (12%) patients. Fifty-seven percent of HAIs were caused by gram-negative bacteria and 19% by fungi. Antibiotic resistance increased with longer hospital stays, with incremental increases in the proportion of vancomycin resistance among enterococci and ceftriaxone and carbapenem resistance among Enterobacterales. Intensive care unit stay, invasive mechanical ventilation, and steroids were associated with HAIs.

Conclusions
HAIs occur in a small proportion of patients hospitalized with COVID-19 and are most often caused by gram-negative and fungal pathogens. Antibiotic resistance is more prevalent with prolonged hospital stays. Antimicrobial stewardship is imperative in this population to minimize unnecessary broad-spectrum antibiotic use.
The genomic revolution and species delimitation in birds (and other organisms): Why phenotypes should not be overlooked
Authors: Cadena Carlos Daniel , Zapata Felipe 
Published: May 2021

Abstract
Given the availability of genomic data to identify separately evolving groups of organisms, many researchers establish species limits based on assessments of the extent of gene flow among populations and often use analytical approaches to identify species in which gene flow is explicitly disallowed. Strictly considering lack of—or limited—gene flow as the main or only criterion to delimit species involves two main complications in practice. First, approaches often used to analyze genome-wide data cannot by themselves distinguish species limits from within-species population structure, particularly in allopatric organisms. Second, recognizing as species only those lineages one can identify using such approaches fails to embrace the role of other evolutionary forces (i.e. various forms of selection) in defining evolutionary lineages. Using examples from various groups of birds, we call for the importance of considering evolutionary forces additional to gene flow in species delimitation and explain why genomic approaches commonly used in taxonomic studies may be insufficient by themselves to properly uncover species limits. By considering the processes that structure genotypic and phenotypic variation during speciation, we argue that rigorous analyses of phenotypic variation remain crucial for species delimitation in the genomics era because phenotypes uniquely inform us about the role of selection maintaining the cohesion of evolutionary lineages. Evolutionary theory describing the roles of gene flow, genetic drift and natural and sexual selection in the origin and maintenance of species calls for an integration of genomics with phenomics in avian species delimitation.
Synthesis and structural characterizations of HAp–NaOH–Al2O3 composites for liquid petroleum gas sensing applications
Authors: Avinashi Sarvesh Kumar , Hussain Ajaz , Kumar Kuldeep , Yadav Bal Chandra , Gautam Chandkiram 
Published: May 2021

Abstract
The main objective of present work was to synthesize sodium doped polycrystalline hydroxyapatite NaHAp (NaOH-HAp) powder by employing wet chemical precipitation method and its composites with alumina (Al2O3; 0, 10, 40, 70 wt%) using a scalable solid-state reaction method. Detailed investigations of NaHAp and its composites using X-ray powder diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, Raman spectroscopy, UV–visible spectroscopy, scanning electron microscopy followed by energy-dispersive X-ray spectroscopy and sensing behaviour is carefully described. XRD results exhibited major and minor phase of HAp, Ca2P2O7 and NaOH for NaHAp sample while for all fabricated composites of HAp–NaOH–Al2O3 and revealed the major phase of hibonite CaO(Al2O3)6 along with secondary phases of Ca2P2O7, Na4[Al(PO4)2(OH)], Na3Al(OH)(HPO4)(PO4), NaAl3(PO4)2(OH)4 and NaOH. The crystallite size of NaHAp-based composites was also determined and lies in the range of 200–2800 nm, which is larger than that of Al2O3. FTIR and Raman spectroscopic studies reveal the bonding formation of P–O, O–P–O and Al–O due to intramolecular interaction of Na4(Al(PO4)2(OH)), Na3Al(OH)(HPO4)(PO4) and NaAl3(PO4)2(OH)4 in the HAp–NaOH–Al2O3 composite, while bonding formation of Al–O–H recognized to intermolecular interaction in between Al with H atoms of Na4(Al(PO4)2(OH)), Na3Al(OH)(HPO4)(PO4) and NaAl3(PO4)2(OH)4. The SEM and energy dispersive spectroscopy analysis revealed the presence of all constituent elements of used chemicals which also validate the purity of used materials. It is concluded that the fabricated sensor (60 NaHAp–40 Al2O3) shows lowest response and recovery time, 4 and 3 s for the 0.5 vol.% concentration of the LPG. Therefore, among all composites, this fabricated composite can be used for LPG gas sensing applications.
Structural and biochemical analyses of concanavalin A circular permutation by jack bean asparaginyl endopeptidase
Authors: Nonis Samuel G. , Haywood Joel , Schmidberger Jason W. , Mackie Emily R. R. , Soares da Costa Tatiana P. , Bond Charles S. , Mylne Joshua S. 
Published: May 2021

AbstractOver 30 years ago, an intriguing posttranslational modification was found responsible for creating concanavalin A (conA), a carbohydrate-binding protein from jack bean (Canavalia ensiformis) seeds and a common carbohydrate chromatography reagent. ConA biosynthesis involves what was then an unprecedented rearrangement in amino-acid sequence, whereby the N-terminal half of the gene-encoded conA precursor (pro-conA) is swapped to become the C-terminal half of conA. Asparaginyl endopeptidase (AEP) was shown to be involved, but its mechanism was not fully elucidated. To understand the structural basis and consequences of circular permutation, we generated recombinant jack bean pro-conA plus jack bean AEP (CeAEP1) and solved crystal structures for each to 2.1 and 2.7 Å, respectively. By reconstituting conA biosynthesis in vitro, we prove CeAEP1 alone can perform both cleavage and cleavage-coupled transpeptidation to form conA. CeAEP1 structural analysis reveals how it is capable of carrying out both reactions. Biophysical assays illustrated that pro-conA is less stable than conA. This observation was explained by fewer intermolecular interactions between subunits in the pro-conA crystal structure and consistent with a difference in the prevalence for tetramerization in solution. These findings elucidate the consequences of circular permutation in the only posttranslation example known to occur in nature.
Role of the unitary correlation operator on high-momentum antisymmetrized molecular dynamics using the bare NN interaction for 3H and 4He
Authors: Zhao Qing , Isaka Masahiro , Myo Takayuki , Lyu Mengjiao , Toki Hiroshi , Horiuchi Hisashi , Takemoto Hiroki , Wan Niu 
Published: May 2021

Abstract
We extend high-momentum antisymmetrized molecular dynamics (HMAMD) by incorporating the short-range part of the unitary correlation operator method (UCOM) as the variational method of finite nuclei. In this HMAMD+UCOM calculation of light nuclei, HMAMD is mainly in charge of the tensor correlation with up to four-body correlation, while the short-range correlation is further improved by using UCOM. The binding energies of the $^3$H and $^4$He nuclei are calculated with HMAMD+UCOM using the AV8$'$ bare nucleon–nucleon ($NN$) interaction. The different roles of the short-range and tensor correlations from HMAMD and UCOM are analyzed in the numerical results. Compared with previous calculations based on different variational methods, this newly extended HMAMD+UCOM method can almost provide consistent results with ab initio results.
A review of health-related quality of life associated with pneumococcal disease: pooled estimates by age and type of disease
Authors: Tang Zhaoli , Matanock Almea , Jeon Seonghye , Leidner Andrew J 
Published: May 2021

Abstract

Background
Estimates in the research literature on the health-related quality of life (QOL) associated with pneumococcal disease exhibit variation. It complicates the selection of estimates in modeling projects that evaluate the health impact and economic value of the prevention and treatment. This study reviewed the literature and developed pooled QOL estimates associated with pneumococcal disease states.

Methods
We searched peer-reviewed literature for studies that reported pneumococcal disease-related QOL estimates. For each study, we extracted QOL estimates and categorized by age group and disease state. QOL estimates were converted to quality-adjusted life-years (QALYs). Pooled QALY estimates were calculated using simple average, sample-size weighting and inverse-variance weighting.

Results
From 18 studies, we organized QOL estimates into 20 groups based on age and disease state. We observed the largest within-disease state variations of QALY estimates in meningitis-related disease states compared to other disease states. Across all age–disease state categories, the pooled QALY estimates ranged from 0.39 for meningitis with long-term sequelae among 0- to 18-year-olds, to 1.00 for non-inpatient pneumonia among 0- to 18-year-olds.

Conclusions
Our results indicated disparities in QOL estimates associated with pneumococcal disease from the literature. Pooled estimates provided a source of consistency that can be used in future modeling efforts.