bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preinfection Neutralizing Antibodies, Omicron BA.5 Breakthrough Infection, and Long COVID: A Propensity Score-Matched Analysis
Authors: Yamamoto Shohei , Matsuda Kouki , Maeda Kenji , Horii Kumi , Okudera Kaori , Oshiro Yusuke , Inamura Natsumi , Nemoto Takashi , Takeuchi Junko S , Li Yunfei , Konishi Maki , Tsuchiya Kiyoto , Gatanaga Hiroyuki , Oka Shinichi , Mizoue Tetsuya , Sugiyama Haruhito , Aoyanagi Nobuyoshi , Mitsuya Hiroaki , Sugiura Wataru , Ohmagari Norio 
Published: September 2023

Abstract

Background
Data are limited on the role of preinfection humoral immunity protection against Omicron BA.5 infection and long coronavirus disease (COVID) development.

Methods
We conducted nested case-control analysis among tertiary hospital staff in Tokyo who donated blood samples in June 2022 (1 month before Omicron BA.5 wave), approximately 6 months after receiving a third dose of COVID-19 mRNA vaccine. We measured live virus-neutralizing antibody titers against wild type and Omicron BA.5, and anti–receptor-binding domain (RBD) antibody titers at preinfection, and compared them between cases and propensity-matched controls. Among the breakthrough cases, we examined association between preinfection antibody titers and incidence of long COVID.

Results
Preinfection anti-RBD and neutralizing antibody titers were lower in cases than controls. Neutralizing titers against wild type and Omicron BA.5 were 64% (95% confidence interval [CI], 42%–77%) and 72% (95% CI, 53%–83%) lower, respectively, in cases than controls. Individuals with previous Omicron BA.1/BA.2 infections were more frequent among controls than cases (10.3% vs 0.8%), and their Omicron BA.5 neutralizing titers were 12.8-fold higher than infection-naive individuals. Among cases, preinfection antibody titers were not associated with incidence of long COVID.

Conclusions
Preinfection immunogenicity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may play a role in protecting against the Omicron BA.5 infection but not preventing long COVID.
Antiviral Susceptibility of Highly Pathogenic Avian Influenza A(H5N1) Viruses Circulating Globally in 2022–2023
Authors: Andreev Konstantin , Jones Jeremy C , Seiler Patrick , Kandeil Ahmed , Turner Jasmine C M , Barman Subrata , Rubrum Adam M , Webby Richard J , Govorkova Elena A 
Published: September 2023

Abstract
The antiviral susceptibility of currently circulating (2022–2023) highly pathogenic avian influenza (HPAI) A(H5N1) viruses was assessed by genotypic and phenotypic approaches. The frequency was low for neuraminidase (NA) and polymerase acidic (PA) substitutions associated with reduced inhibition by NA inhibitors (21/2698, 0.78%) or the PA inhibitor baloxavir (14/2600, 0.54%). Phenotypic testing of 22 clade 2.3.2.1a and 2.3.4.4b viruses revealed broad susceptibility to NA inhibitors and baloxavir for a conclusion that most contemporary HPAI A(H5N1) viruses retain susceptibility to antiviral drugs. Novel NA-K432E and NA-T438I substitutions (N2 numbering) were identified at elevated frequencies (104/2698, 3.85%) and caused reduced zanamivir and peramivir inhibition.
Improving the quality of hospital sterilization process using failure modes and effects analysis, fuzzy logic, and machine learning: experience in tertiary dental centre
Authors: En-Naaoui Amine , Aguezzoul Aicha , Kaicer Mohammed 
Published: September 2023

Abstract
Activities practiced in the hospital generate several types of risks. Therefore, performing the risk assessment is one of the quality improvement keys in the healthcare sector. For this reason, healthcare managers need to design and perform efficient risk assessment processes. Failure modes and effects analysis (FMEA) is one of the most used risk assessment methods. The FMEA is a proactive technique consisting of the evaluation of failure modes associated with a studied process using three factors: occurrence, non-detection, and severity, in order to obtain the risk priority number using fuzzy logic approach and machine learning algorithms, namely the support vector machine and the k-nearest neighbours. The proposed model is applied in the case of the central sterilization unit of a tertiary national reference centre of dental treatment, where its efficiency is evaluated compared to the classical approach. These comparisons are based on expert advice and machine learning performance metrics. Our developed model proved high effectiveness throughout the results of the expert’s vote (she agrees with 96% fuzzy-FMEA results against 6% with classical FMEA results). Furthermore, the machine learning metrics show a high level of accuracy in both training data (best rate is 96%) and testing data (90%). This study represents the first study that aims to perform artificial intelligence approach to risk management in the Moroccan healthcare sector. The perspective of this study is to promote the application of the artificial intelligence in Moroccan health management, especially in the field of quality and safety management.
Insights into bacterial community metatranscriptome and metabolome in river water influenced by palm oil mill effluent final discharge
Authors: Sharuddin Siti S , Ramli Norhayati , Yusoff Mohd Z M , Muhammad Nor A N , Ho Li S , Maeda Toshinari 
Published: September 2023

Abstract

Aims
This study aimed to investigate the effect of palm oil mill effluent (POME) final discharge on the active bacterial composition, gene expression, and metabolite profiles in the receiving rivers to establish a foundation for identifying potential biomarkers for monitoring POME pollution in rivers.

Methods and results
The POME final discharge, upstream (unpolluted by POME), and downstream (effluent receiving point) parts of the rivers from two sites were physicochemically characterized. The taxonomic and gene profiles were then evaluated using de novo metatranscriptomics, while the metabolites were detected using qualitative metabolomics. A similar bacterial community structure in the POME final discharge samples from both sites was recorded, but their composition varied. Redundancy analysis showed that several families, particularly Comamonadaceae and Burkholderiaceae [Pr(&gt;F) = 0.028], were positively correlated with biochemical oxygen demand (BOD5) and chemical oxygen demand (COD). The results also showed significant enrichment of genes regulating various metabolisms in the POME-receiving rivers, with methane, carbon fixation pathway, and amino acids among the predominant metabolisms identified (FDR &lt; 0.05, PostFC &gt; 4, and PPDE &gt; 0.95). This was further validated through qualitative metabolomics, whereby amino acids were detected as the predominant metabolites.

Conclusions
The results suggest that genes regulating amino acid metabolism have significant potential for developing effective biomonitoring and bioremediation strategies in river water influenced by POME final discharge, fostering a sustainable palm oil industry.
Supplementation with rumen-inert fat in the growing phase altered adipogenic gene expression and the size and number of adipocytes in Hanwoo steers
Authors: Bharanidharan Rajaraman , Thirugnanasambantham Krishnaraj , Kim Jayeon , Xaysana Panyavong , Viengsakoun Napasirth , Ibidhi Ridha , Oh Joonpyo , Kim Na-Yeon , Beak Seok-Hyeon , Smith Stephen B , Kim Kyoung Hoon 
Published: September 2023

Abstract
We hypothesized that the provision of rumen-inert fat (RIF) to growing cattle (9 to 13 mo of age) would affect the expression of genes involved in lipid metabolism and thereby affect the size and number of adipocytes of steers slaughtered at 30 mo of age. Thirty steers with an average initial body weight (BW) of 239 ± 25 kg were allocated to six pens, balanced for BW and genetic merit for marbling, and assigned to one of two treatment groups: control (only basal diet) or test diet (basal diet with 200 g of RIF per day, on an as-fed basis) for 5 mo. Biopsy samples of longissimus lumborum (LM) muscle were then collected for analysis of fatty acid composition and gene expression. Both groups were then fed the same basal diets during the early and late fattening phases, without RIF, until slaughter (average shrunk BW = 759 kg). Supplementation with RIF increased the longissimus thoracis (LT) intramuscular fatty acid concentration at slaughter (P = 0.087) and numerically increased the quality grade score (P = 0.106). The LM intramuscular relative mRNA expression of genes such as PPARα, ZFP423 and SREBP1, FASN, SCD, FABP4, GPAT1, and DGAT2 were downregulated (P &lt; 0.1) following RIF supplementation. Supplementation of RIF decreased (P &lt; 0.1) diameter and concomitantly increased intramuscular adipocytes per viewing section at slaughter. This likely was caused by promotion of triacylglycerol hydrolysis during the growing phase. Another possible explanation is that the relative mRNA expression of gene ATGL was upregulated by RIF supplementation during the growing (P &lt; 0.1) and the fattening phases (P &lt; 0.05), while the genes associated with fatty acid uptake (FABP4) and esterification (DGAT2) were downregulated during the growing phase and upregulated (P &lt; 0.1) during the fattening phase. This implies that the lipid turnover rate was higher for steers during the growing than fattening phase. This study demonstrated that RIF supplementation during the growing phase induced a carryover effect on the lipogenic transcriptional regulation involved in adipocyte lipid content of intramuscular adipose tissue; increased triacylglycerol hydrolysis during the growing phase subsequently was followed by increased lipid accumulation during the fattening phases.
Root and community inference on the latent growth process of a network
Authors: Crane Harry , Xu Min 
Published: September 2023

Abstract
Many statistical models for networks overlook the fact that most real-world networks are formed through a growth process. To address this, we introduce the Preferential Attachment Plus Erdős–Rényi model, where we let a random network G be the union of a preferential attachment (PA) tree T and additional Erdős–Rényi (ER) random edges. The PA tree captures the underlying growth process of a network where vertices/edges are added sequentially, while the ER component can be regarded as noise. Given only one snapshot of the final network G, we study the problem of constructing confidence sets for the root node of the unobserved growth process; the root node can be patient zero in an infection network or the source of fake news in a social network. We propose inference algorithms based on Gibbs sampling that scales to networks with millions of nodes and provide theoretical analysis showing that the size of the confidence set is small if the noise level of the ER edges is not too large. We also propose variations of the model in which multiple growth processes occur simultaneously, reflecting the growth of multiple communities; we use these models to provide a new approach to community detection.
Clonal aggregation of fluconazole-resistant Candida tropicalis isolated from sterile body fluid specimens from patients in Hefei, China
Authors: Wang Ying , Wan Xin , Zhao Li , Jin Peipei , Zhang Ju , Zhou Xin , Ye Naifang , Wang Xiaowei , Pan Yaping , Xu Liangfei 
Published: September 2023

Abstract
Candida tropicalis, a human conditionally pathogenic yeast, is distributed globally, especially in Asia-Pacific. The increasing morbidity and azole resistance of C. tropicalis have made clinical treatment difficult. The correlation between clonality and antifungal susceptibility of clinical C. tropicalis isolates has been reported. To study the putative correlation in C. tropicalis isolated from normally sterile body fluid specimens and explore the distinct clonal complex (CC) in Hefei, 256 clinical C. tropicalis isolates were collected from four teaching hospitals during 2016–2019, of which 30 were fluconazole-resistant (FR). Genetic profiles of 63 isolates, including 30 FR isolates and 33 fluconazole-susceptible (FS) isolates, were characterized using multilocus sequence typing (MLST). Phylogenetic analysis of the data was conducted using UPGMA (unweighted pair group method with arithmetic averages) and the minimum spanning tree algorithm. MLST clonal complexes (CCs) were analyzed using the goeBURST package. Among 35 differentiated diploid sequence types (DSTs), 16 DSTs and 1 genotype were identified as novel. A total of 35 DSTs were assigned to five major CCs based on goeBURST analysis. CC1 (containing DST376, 505, 507, 1221, 1222, 1223, 1226, and 1229) accounted for 86.7% (26/30) of the FR isolates. However, the genetic relationships among the FS isolates were relatively decentralized. The local FR CC1 belongs to a large fluconazole non-susceptible CC8 in global isolates, of which the putative founder genotype was DST225. The putative correlation between MLST types and antifungal susceptibility of clinical C. tropicalis isolates in Hefei showed that DSTs are closely related to FR clones.
Shared and unique antibody and B cell profiles in HIV-positive and HIV-negative individuals with cryptococcal meningoencephalitis
Authors: Yoon Hyunah , Nakouzi Antonio S , Duong Van Anh , Hung Le Quoc , Binh Tran Quang , Tung Nguyen Le Nhu , Day Jeremy N , Pirofski Liise-anne 
Published: September 2023

Abstract
Host non-T cell markers to aid in the diagnosis of cryptococcal meningoencephalitis (CM) have not been identified. In this case-control study, we characterized antibody and B cell profiles in HIV-negative and HIV-positive Vietnamese individuals of the Kinh ethnicity recently diagnosed with CM and controls. The study included 60 HIV-negative with no known immunocompromising condition and 60 HIV-positive individuals, with 30 CM cases and 30 controls in each group. Participants were matched by age, sex, HIV serostatus, and CD4 count in the HIV-positive group. Plasma immunoglobulin (Ig) levels, including IgG1, IgG2, IgM, and IgA, Cryptococcus spp. glucuronoxylomannan (GXM)- and laminarin (branched ${\rm{\beta }}$-[1-3]-glucan)-binding IgG, IgM, IgA levels, and peripheral blood B cell subsets were measured. Logistic regression, principal component, and mediation analyses were conducted to assess associations between antibody, B cell levels, and CM. The results showed that GXM-IgG levels were higher and IgG1 and IgG2 were lower in CM cases than controls, regardless of HIV status. In HIV-negative individuals, IgG2 mediated an inverse association between CD19+CD27+CD43+CD5− (B-1b-like) cells and CM. In HIV-positive individuals, lower levels of IgA, laminarin-IgA, and CD19+CD27+IgM+IgD− (IgM+ memory B) cells were each associated with CM. The shared and distinct antibody and B cell profiles identified in HIV-negative and HIV-positive CM cases may inform the identification of non-T-cell markers of CM risk or unsuspected disease, particularly in HIV-negative individuals.
MF-Box: multifidelity and multiscale emulation for the matter power spectrum
Authors: Ho Ming-Feng , Bird Simeon , Fernandez Martin A , Shelton Christian R 
Published: September 2023

ABSTRACT
We introduce MF-Box, an extended version of MFEmulator, designed as a fast surrogate for power spectra, trained using N-body simulation suites from various box sizes and particle loads. To demonstrate MF-Box’s effectiveness, we design simulation suites that include low-fidelity (LF) suites (L1 and L2) at 256 and $100 \, \rm {Mpc\, ~}h^{-1}$, each with 1283 particles, and a high-fidelity (HF) suite with 5123 particles at $256 \, \rm {Mpc\, ~}h^{-1}$, representing a higher particle load compared to the LF suites. MF-Box acts as a probabilistic resolution correction function, learning most of the cosmological dependencies from L1 and L2 simulations and rectifying resolution differences with just three HF simulations using a Gaussian process. MF-Box successfully emulates power spectra from our HF testing set with a relative error of $\lt 3~{{\ \rm per\ cent}}$ up to $k \simeq 7 \, h\rm {Mpc}{^{-1}}$ at z ∈ [0, 3], while maintaining a cost similar to our previous multifidelity approach, which was accurate only up to z = 1. The addition of an extra LF node in a smaller box significantly improves emulation accuracy for MF-Box at $k \gt 2 \, h\rm {Mpc}{^{-1}}$, increasing it by a factor of 10. We conduct an error analysis of MF-Box based on computational budget, providing guidance for optimizing budget allocation per fidelity node. Our proposed MF-Box enables future surveys to efficiently combine simulation suites of varying quality, effectively expanding the range of emulation capabilities while ensuring cost efficiency.
Coverage dependent H2 desorption energy: a quantitative explanation based on encounter desorption mechanism
Authors: Meng Qingkuan , Chang Qiang , Zhao Gang , Quan Donghui , Tsuge Masashi , Zhang Xia , Zhang Yong , Li Xiao-Hu 
Published: September 2023

ABSTRACT
Recent experiments show that the desorption energy of H2 on a diamond-like carbon surface depends on the H2 coverage of the surface. We aim to quantitatively explain the coverage dependent H2 desorption energy measured by the experiments. We derive a math formula to calculate an effective H2 desorption energy based on the encounter desorption mechanism. The effective H2 desorption energy depends on two key parameters, the desorption energy of H2 on H2 substrate and the ratio of H2 diffusion barrier to its desorption energy. The calculated effective H2 desorption energy qualitatively agrees with the coverage dependent H2 desorption energy measured by the experiments if the values of these two parameters in literature are used in the calculations. We argue that the difference between the effective H2 desorption energy and the experimental results is due to the lack of knowledge about these two parameters. So, we recalculate these two parameters based on experimental data. Good agreement between theoretical and experimental results can be achieved if these two updated parameters are used in the calculations.
Long-term evolution of cyclotron line energy in an eclipsing pulsar 4U 1538−522
Authors: Tamang Ruchi , Ghising Manoj , Tobrej Mohammed , Rai Binay , Paul Bikash Chandra 
Published: September 2023

ABSTRACT
We present the timing and spectral analysis of the high-mass X-ray binary source 4U 1538−522 using Nuclear Spectroscopic Telescope Array (NuSTAR) observations. One of the observations partially covers the X-ray eclipse of the source along with eclipse ingress. The source is found to spin down at the rate of 0.163 ± 0.002 s yr−1 between ∼54973 and 58603 MJD. It is evident that at time ∼58620 MJD, a torque reversal occurred; thereafter, the source exhibited a spin-up trend at the rate −(0.305 ± 0.018) s yr−1 until 59275 MJD. A recent NuSTAR observation finds the pulse period of the source: (526.2341 ± 0.0041) s. The pulse profile exhibits a transition from double-peaked to single-peaked nature above ∼30 keV. We analysed the overall trend of the temporal evolution of fundamental cyclotron resonance scattering feature, Ecyc, incorporating recent NuSTAR measurements. Initially, during the time span ∼50452.16–55270.8 MJD, the cyclotron line energy is found to increase at a rate of 0.11 ± 0.03 keV yr−1, which is further followed by a decrease at a rate −0.14 ± 0.01 keV yr−1 between 55270.8 and 59267 MJD. The combined measurements in the time span 50452.16–59267 MJD reveal that the cyclotron line energy is increasing linearly at a rate of 0.08 ± 0.02 keV yr−1.
Magnetic field effects on nucleosynthesis and kilonovae from neutron star merger remnants
Authors: de Haas Sebastiaan , Bosch Pablo , Mösta Philipp , Curtis Sanjana , Schut Nathanyel 
Published: September 2023

ABSTRACT
We investigate the influence of parametric magnetic field configurations of a hypermassive neutron star (HMNS) on the outflow properties, nucleosynthesis yields, and kilonova light curves. We perform three-dimensional dynamical space–time general-relativistic magnetohydrodynamic simulations, including a neutrino leakage scheme, microphysical finite-temperature equation of state, and an initial poloidal magnetic field. We find that varying the magnetic field strength and falloff impacts the formation of magnetized winds or mildly relativistic jetted outflows, which in turn has profound effects on the outflow properties. All of the evolved configurations collapse to a black hole ∼38–40 ms after coalescence, where the ones forming jetted outflows seem more effective at redistributing angular momentum, which result in earlier collapse times. Larger mass ejecta rates and radial velocities of unbound material characterize the systems that form jetted outflows. The bolometric light curves of the kilonovae and r-process yields that are produced by the post-merger remnant system change considerably with different magnetic field parameters. We conclude that the magnetic field strength and falloff have robust effects on the outflow properties and electromagnetic observables. This can be particularly important as the total ejecta mass from our simulations (≃10−3 M⊙) makes the ejecta from HMNS a compelling source to power kilonova through radioactive decay of r-process elements.
Optimized temporal binning of comparison star measurements for differential photometry
Authors: Hartley Kathryn E , Wilson R W 
Published: September 2023

ABSTRACT
Ground-based, high precision observations of the light curves of objects such as transiting exoplanets rely on the application of differential photometry. The flux of the target object is measured relative to a comparison star in the same field, allowing correction for systematic trends in the light curve, mainly due to atmospheric effects including the variation of extinction with airmass. However, the precision of the light curve is then limited by the random noise for the measurements of both the target object and the comparison star. For time-resolved photometry using short exposure times of up to a few tens of seconds, the time-scale of the systematic variations due to atmospheric (or other) effects can be much longer than the cadence of the observations. In this case, the overall signal-to-noise ratio of the observation may be improved significantly by applying some temporal binning to the measurements of the comparison star, before comparison with the target object, without reducing the cadence of the overall light curve. In this paper, we will describe a data reduction pipeline for implementing this method which optimizes the number of frames to be binned for the comparison star, and we present example results for time-resolved photometric data. An example of applying the technique on an exoplanet transit light curve of WASP-166b is presented using four comparison stars of different magnitudes.