bluuebunny/crossref_metadata_2025_split huggingface dataset:
The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with infectious diseases
Authors: Yuan Lei , Zhu Qing , Chen Qiang , Lai Lan Min , Liu Peng , Liu Yang 
Published: June 2023

Abstract

Objective
Metagenomic next-generation sequencing (mNGS) can be used to detect pathogens in clinical infectious diseases through the sequencing analysis of microbial and host nucleic acids in clinical samples. This study aimed to assess the diagnostic performance of mNGS in patients with infections.

Methods
In this study, 641 patients with infectious diseases were enrolled. These patients simultaneously underwent pathogen detection by both mNGS and microbial culture. Through statistical analysis, we judged the diagnostic performance of mNGS and microbial culture on different pathogens.

Results
Among 641 patients, 276 cases of bacteria and 95 cases of fungi were detected by mNGS, whereas 108 cases of bacteria and 41 cases of fungi were detected by traditional cultures. Among all mixed infections, combined bacterial and viral infections were the highest (51%, 87/169), followed by combined bacterial with fungal infections (16.57%, 28/169) and mixed bacterial, fungal, and viral infections (13.61%, 23/169). Among all sample types, bronchoalveolar lavage fluid (BALF) samples had the highest positive rate (87.8%, 144/164), followed by sputum (85.4%, 76/89) and blood samples (61.2%, 158/258). For the culture method, sputum samples had the highest positive rate (47.2%, 42/89), followed by BALF (37.2%, 61/164). The positive rate of mNGS was 69.89% (448/641), which was significantly higher than that of traditional cultures (22.31% [143/641]) (P &lt; .05).

Conclusions
Our results show that mNGS is an effective tool for the rapid diagnosis of infectious diseases. Compared with traditional detection methods, mNGS also showed obvious advantages in mixed infections and infections with uncommon pathogens.
Red cell distribution width-to-albumin ratio is a predictor of survival in hepatitis B virus–associated decompensated cirrhosis
Authors: Mao WeiLin , Yuan ManChun , He Xia , Zhang Qiu 
Published: June 2023

Abstract

Objective
The aim of this study was to ascertain whether red cell distribution width-to-albumin ratio (RAR) is associated with survival in hepatitis B virus (HBV)–associated decompensated cirrhosis (DC) patients.

Methods
A cohort of 167 patients with confirmed HBV-DC was enrolled in our study. Demographic characteristics and laboratory data were obtained. The main endpoint was mortality at 30 days. The receiver operating characteristic curve and multivariable regression analysis were used to assess the power of RAR for predicting prognosis.

Results
Mortality at 30 days was 11.4% (19/167). The RAR levels were higher in the nonsurvivors than the survivors, and elevated RAR levels were clearly associated with poor prognosis. Moreover, the predictive powers of RAR and Model for End-Stage Liver Disease score were not obviously different.

Conclusion
Our data indicate that RAR is a novel potential prognostic biomarker of mortality in HBV-DC.
Comprehensive genomic analysis of the potential limitations of several published PCR primers targeting prfA-virulence gene cluster in Listeria species
Authors: Gao R M , Duceppe M-O , Kang M , Naushad S , Ogunremi D , Huang H 
Published: June 2023

Abstract
Polymerase chain reaction (PCR) is commonly used to detect Listeria monocytogenes, foodborne pathogen. This study conducted in silico genomic analysis to investigate the specificity and binding efficacy of four published pairs of PCR primers targeting Listeria prfA-virulence gene cluster (pVGC) based on Listeria sequences available. We first performed comprehensive genomic analyses of the pVGC, the main pathogenicity island in Listeria spp. In total, 2961 prfA, 642 plcB, 629 mpl, and 1181 hlyA gene sequences were retrieved from the NCBI database. Multiple sequence alignments and phylogenetic trees were generated using unique (non-identical or not-shared) sequences of each represented genes, targeting four pairs of PCR primers published previously, namely 202 prfA, 82 plcB, 150 mpl, and 176 hlyA unique gene sequences. Only the hlyA gene showed strong (over 94%) primer mapping results, while prfA, plcB, and mpl genes showed weak (&lt;50%) matching results. In addition, nucleotide variations were observed at the 3′ end of the primers, indicating non-binding to the targets could potentially cause false-negative results. Thus, we propose designing degenerate primers or multiple PCR primers based on as many isolates as possible to minimize the false-negative risk and reach the aim of low tolerable limits of detection.
Protothecosis in Veterinary Medicine: a minireview
Authors: Ely Valessa Lunkes , Espindola Julia Pires , Barasuol Bibiana Martins , Sangioni Luís Antônio , Pereira Daniela Brayer , Botton Sônia de Avila 
Published: June 2023

Abstract
Protothecosis is an important infection caused by Prototheca spp., an alga that affect humans and animals. Prototheca spp. infections determine losses of production and quality of life for the affected animals. In this disease, prevention and early diagnosis are essential to avoid the spread of the agent to susceptible hosts. This review aimed to assemble the reported cases of protothecosis in Veterinary Medicine, highlighting Prototheca species involved in the infections, the main animal species affected, as well as the clinical manifestations, diagnosis, and treatment. Our findings showed that protothecosis has been reported in various domestic and wild animal species, presenting diverse clinical manifestations, including mastitis in cows, respiratory manifestations in goats and cats, and a wide range of clinical signs in dogs. The clinical diagnosis and treatment of Prototheca spp. infections are difficult and infected animals are frequently discarded or euthanized. Due to the importance of this infection, protothecosis must be considered an important differential diagnosis in routine clinical Veterinary Medicine.
Novelspatype and antimicrobial resistance gene profiles ofStaphylococcus aureusstrains isolated from bovine mastitis in Jordan
Authors: Gharaibeh Mohammad H , Abu-Qatouseh Luay F , Mashaqbah Sulieman A , Assaf Shehab-Aldeen J , Al Qudsi Farah R 
Published: June 2023

AbstractStaphylococcu aureus is the most prevalent microorganism associated with mastitis in cattle. This study was designed to determine the spa types of Staph. aureus and to assess the resistance genes profile of isolated strains in dairy farms in Jordan. In total, 747 milk samples of cattle suffering from subclinical mastitis were collected from 37 dairy farms and tested for Staph. aureus. To detect antimicrobial resistance genes, all 219 strains of Staph. aureus were tested. Furthermore, 21 isolates of Staph. aureus were typed using spa typing. As a result, different proportions of resistance genes were found for Staph. aureus. High resistance genes were in tetK 100%, blaZ 99%, and tetM 97%. Moderate resistance genes were in aac(6′)/aph(2′′ 52%, ant(4′)-Ia 48%, and ermC 41%. Low resistance genes were in ermA is 24%, aph(3′)-III is 15%, and mecA is 15%. The spa typing of 21 isolates revealed six spa types, of which five were previously known. For the first time, a novel spa type (t17158) was identified as the main cause of mastitis in dairy cows in Jordan. The identification of resistance genes and spa types is helpful in determining the most effective treatments for cows and plays a significant role in reducing the transmission of pathogens.
Neural innervation in adipose tissue, gut, pancreas, and liver
Authors: Sun Mengxue , Wan Yongwen , Shi Mengjie , Meng Zhuo-Xian , Zeng Wenwen 
Published: June 2023

Abstract
Efficient communication between the brain and peripheral organs is indispensable for regulating physiological function and maintaining energy homeostasis. The peripheral nervous system (PNS) in vertebrates, consisting of the autonomic and somatic nervous systems, bridges the peripheral organs and the central nervous system (CNS). Metabolic signals are processed by both vagal sensory nerves and somatosensory nerves. The CNS receives sensory inputs via ascending nerves, serves as the coordination and integration center, and subsequently controls internal organs and glands via descending nerves. The autonomic nervous system consists of sympathetic and parasympathetic branches that project peripheral nerves into various anatomical locations to regulate the energy balance. Sympathetic and parasympathetic nerves typically control the reflexive and involuntary functions in organs. In this review article, we outline the innervation of adipose tissue, gut, pancreas, and liver, to illustrate the neurobiological basis of central–peripheral interactions. We emphasize the importance of understanding the functional atlas of neural control of energy metabolism, and more importantly, provide potential avenues for further research in this area.
Some techniques for reasoning automatically on co-inductive data structures
Authors: Peltier Nicolas 
Published: June 2023

Abstract
Some techniques are proposed for reasoning on co-inductive structures. First, we devise a sound axiomatization of (conservative extensions) of such structures, thus reducing the problem of checking whether a formula admits a co-inductive model to a first-order satisfiability test. We devise a class of structures, called regularly co-inductive, for which the axiomatization is complete (for other co-inductive structures, the proposed axiomatization is sound, but not complete). Then, we propose proof calculi for reasoning on such structures. We first show that some of the axioms mentioned above can be omitted if the inference rules are able to handle rational terms. Furthermore, under some conditions, some other axioms may be replaced by an additional inference rule that computes the solutions of fixpoint equations. Finally, we show that a stronger completeness result can be established under some additional conditions on the signature.
On the study of acceptability in weighted argumentation frameworks through four-state labelling semantics
Authors: Bistarelli Stefano , Taticchi Carlo 
Published: June 2023

Abstract
Computational Argumentation provides tools for both modelling and reasoning with controversial information. Abstract Argumentation Frameworks represent the building blocks in this field and allow one to model the relationships between arguments with the ultimate goal of establishing their acceptability. Arguments can be evaluated through sets of criteria, called semantics, which distinguish among various justification states. For example, an argument may be accepted, rejected, ignored or even marked as undecided. This paper considers Weighted Argumentation Frameworks and proposes a novel labelling semantics that differentiates four states and generalizes existing approaches.
Novel Focused Ion Beam Liftouts for Spatial Characterization of Spherical Biominerals With Transmission Electron Microscopy
Authors: Zambare Neerja , Arey Bruce , Qafoku Odeta , Koirala Krishna Prasad , Kovarik Libor , Dohnalkova Alice 
Published: June 2023

Abstract
Focused ion beam (FIB) is frequently used to prepare electron- and X-ray-beam-transparent thin sections of samples, called lamellae. Typically, lamellae are prepared from only a subregion of a sample. In this paper, we present a novel approach for FIB lamella preparation of microscopic samples, wherein the entire cross-section of the whole sample can be investigated. The approach was demonstrated using spherical, porous, and often hollow microprecipitates of biologically precipitated calcium carbonate. The microprecipitate morphology made these biogenic samples more fragile and challenging than materials commonly investigated using FIB lamellae. Our method enables the appropriate orientation of the lamellae required for further electron/X-ray analyses after attachment to the transmission electron microscopy (TEM) grid post and facilitates more secure adhesion onto the grid post. We present evidence of autofluorescence in bacterially precipitated vaterite using this lamella preparation method coupled with TEM selected area diffraction. This innovative approach allows studying biomineralization at the micro to nano scales, which can provide novel insights into bacterial responses to microenvironmental conditions.
Multitechnique Characterization of Pigments Used in Paintings by Léon Pallière
Authors: do Nascimento Campos Guadalupe , Granato Marcus , Middea Antonieta , de Souza Gonçalves Vasques Fernando , da Fonseca Martins Gomes Otavio 
Published: June 2023

Abstract
This study provides a microanalytical characterization of pigment fragments from the painting “Allegory to the Arts” and two portraits, “Rubens” and “Tintoretto,” by Léon Pallière. The fragments were surface-analyzed using several near-surface methods to acquire information on the materials and determine the painting techniques utilized before the restoration. Scanning electron microscopy/energy-dispersive X-ray spectrometry (SEM/EDS), Raman spectroscopy coupled to an optical microscope (Raman microprobe), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR) revealed organic materials, hydrocerussite (Pb3(CO3)2(OH)2), cerussite (PbCO3), zincite (ZnO), chalcopyrite (CuFeS2), nepheline (K(Na,K)3AlSi4O16), calcite (CaCO3), brookite (TiO2), kinoshitalite (Ba3(Si2Al2)O10(OH)2), hematite (Fe2O3), barium magnesium silicate (Ba2Mg(Si2O7)), and aluminosilicates. Also identified were vermilion/cinnabar (HgS), copper phthalocyanine blue (C32H16CuN8), and mendipite (Pb3Cl2O2), in addition to the use of gold leaf in one of the artworks. SEM/EDS provided information on the chemical composition and surface morphology of the fragments, and XRD revealed crystalline raw materials (minerals or their synthetic analogs) used in the paintings. Raman microprobe was particularly useful in identifying pigments, providing a uniquely specific and sensitive means of identifying inorganic and organic compounds.
The Gulf War Illness and the Iraqi Population’s Forgotten Pain and Suffering
Authors: Moradi Faraidoun 
Published: June 2023

ABSTRACT
Exposure to chemical warfare agents results in long-term biopsychosocial complaints. A recent study has revealed an association between exposure to a low dose of Sarin and Gulf War illness in American veterans from the Gulf War. The prevalence of Gulf War illness has not been studied in the Iraqi population. In light of recent research results, Iraqi chemical warfare agent survivors’ multiple physical and mental illnesses should be highlighted. For this reason, establishing both legislation and medical commissions is most needed.
Two warm Neptunes transiting HIP 9618 revealed by TESS and Cheops
Authors: Osborn H P , Nowak G , Hébrard G , Masseron T , Lillo-Box J , Pallé E , Bekkelien A , Florén H-G , Guterman P , Simon A E , Adibekyan V , Bieryla A , Borsato L , Brandeker A , Ciardi D R , Collier Cameron A , Collins K A , Egger J A , Gandolfi D , Hooton M J , Latham D W , Lendl M , Matthews E C , Tuson A , Ulmer-Moll S , Vanderburg A , Wilson T G , Ziegler C , Alibert Y , Alonso R , Anglada G , Arnold L , Asquier J , Barrado y Navascues D , Baumjohann W , Beck T , Belinski A A , Benz W , Biondi F , Boisse I , Bonfils X , Broeg C , Buchhave L A , Bárczy T , Barros S C C , Cabrera J , Cardona Guillen C , Carleo I , Castro-González A , Charnoz S , Christiansen J , Cortes-Zuleta P , Csizmadia S , Dalal S , Davies M B , Deleuil M , Delfosse X , Delrez L , Demory B-O , Dunlavey A B , Ehrenreich D , Erikson A , Fernandes R B , Fortier A , Forveille T , Fossati L , Fridlund M , Gillon M , Goeke R F , Goliguzova M V , Gonzales E J , Günther M N , Güdel M , Heidari N , Henze C E , Howell S , Hoyer S , Frey J I , Isaak K G , Jenkins J M , Kiefer F , Kiss L , Korth J , Maxted P F L , Laskar J , Lecavelier des Etangs A , Lovis C , Lund M B , Luque R , Magrin D , Almenara J M , Martioli E , Mecina M , Medina J V , Moldovan D , Morales-Calderón M , Morello G , Moutou C , Murgas F , Jensen E L N , Nascimbeni V , Olofsson G , Ottensamer R , Pagano I , Peter G , Piotto G , Pollacco D , Queloz D , Ragazzoni R , Rando N , Rauer H , Ribas I , Ricker G , Demangeon O D S , Smith A M S , Santos N , Scandariato G , Seager S , Sousa S G , Steller M , Szabó G M , Ségransan D , Thomas N , Udry S , Ulmer B , Van Grootel V , Vanderspek R , Walton N , Winn J N 
Published: June 2023

ABSTRACT
HIP 9618 (HD 12572, TOI-1471, TIC 306263608) is a bright (G = 9.0 mag) solar analogue. TESS photometry revealed the star to have two candidate planets with radii of 3.9 ± 0.044 R⊕ (HIP 9618 b) and 3.343 ± 0.039 R⊕ (HIP 9618 c). While the 20.77291 d period of HIP 9618 b was measured unambiguously, HIP 9618 c showed only two transits separated by a 680-d gap in the time series, leaving many possibilities for the period. To solve this issue, CHEOPS performed targeted photometry of period aliases to attempt to recover the true period of planet c, and successfully determined the true period to be 52.56349 d. High-resolution spectroscopy with HARPS-N, SOPHIE, and CAFE revealed a mass of 10.0 ± 3.1M⊕ for HIP 9618 b, which, according to our interior structure models, corresponds to a $6.8\pm 1.4~{{\ \rm per\ cent}}$ gas fraction. HIP 9618 c appears to have a lower mass than HIP 9618 b, with a 3-sigma upper limit of &lt;18M⊕. Follow-up and archival RV measurements also reveal a clear long-term trend which, when combined with imaging and astrometric information, reveal a low-mass companion ($0.08^{+0.12}_{-0.05} M_\odot$) orbiting at $26.0^{+19.0}_{-11.0}$ au. This detection makes HIP 9618 one of only five bright (K &lt; 8 mag) transiting multiplanet systems known to host a planet with P &gt; 50 d, opening the door for the atmospheric characterization of warm (Teq &lt; 750 K) sub-Neptunes.
The Alcock–Paczyński effect from Lyman-α forest correlations: analysis validation with synthetic data
Authors: Cuceu Andrei , Font-Ribera Andreu , Martini Paul , Joachimi Benjamin , Nadathur Seshadri , Rich James , González-Morales Alma X , du Mas des Bourboux Hélion , Farr James 
Published: June 2023

ABSTRACT
The three-dimensional distribution of the Ly α forest has been extensively used to constrain cosmology through measurements of the baryon acoustic oscillations (BAO) scale. However, more cosmological information could be extracted from the full shapes of the Ly α forest correlations through the Alcock–Paczyński (AP) effect. In this work, we prepare for a cosmological analysis of the full shape of the Ly α forest correlations by studying synthetic data of the extended Baryon Oscillation Spectroscopic Survey (eBOSS). We use a set of 100 eBOSS synthetic data sets in order to validate such an analysis. These mocks undergo the same analysis process as the real data. We perform a full-shape analysis on the mean of the correlation functions measured from the 100 eBOSS realizations, and find that our model of the Ly α correlations performs well on current data sets. We show that we are able to obtain an unbiased full-shape measurement of DM/DH(zeff), where DM is the transverse comoving distance, DH is the Hubble distance, and zeff is the effective redshift of the measurement. We test the fit over a range of scales, and decide to use a minimum separation of rmin = 25 h−1Mpc. We also study and discuss the impact of the main contaminants affecting Ly α forest correlations, and give recommendations on how to perform such analysis with real data. While the final eBOSS Ly α BAO analysis measured DM/DH(zeff = 2.33) with 4 per cent statistical precision, a full-shape fit of the same correlations could provide an $\sim 2~{{\ \rm per\ cent}}$ measurement.
Giant low surface brightness galaxies in TNG100
Authors: Zhu Qirong , Pérez-Montaño Luis Enrique , Rodriguez-Gomez Vicente , Cervantes Sodi Bernardo , Zjupa Jolanta , Marinacci Federico , Vogelsberger Mark , Hernquist Lars 
Published: June 2023

ABSTRACT
Giant low surface brightness (GLSB) galaxies, such as Malin 1 and UGC 1382, contain the largest stellar discs known. GLSB galaxies also often contain large masses of neutral hydrogen (H i). However, these extreme galaxies’ origin and properties remain poorly understood. Using the cosmological simulation IllustrisTNG 100, we identify and select a sample of ∼200 galaxies with extended ($R_{\rm {\rm H\,{\small I}}}\,\gt\, 50$ kpc) and well-defined H i discs, ∼6 per cent of the total galaxies in the same stellar mass range (10.2 &lt; log (M*/M⊙) &lt; 11.6). This GLSB sample is heterogeneous, with mixed galaxy morphologies ranging from the most disc-dominated systems to massive ellipticals. These simulated GLSB galaxies are located in massive haloes ($V_{\max }\, \gt \, 150\ \rm {km\ s^{-1}}$) and their properties, such as total H i content, stellar disc parameters, star formation rate, and rotation curves, agree with observed GLSB galaxies. We construct a paired control sample to contrast with the GLSB galaxies. The GLSB galaxies tend to have large galaxy spin parameters ($40{{\ \rm per\ cent}}$ larger) and larger ex situ stellar mass fractions than the paired control. We find evidence that aligned mergers promote the formation of extended discs and that isolated environments help the survival of those discs across cosmic time.
Measuring the X-ray luminosities of DESI groups from eROSITA Final Equatorial-Depth Survey – I. X-ray luminosity–halo mass scaling relation
Authors: Zheng Yun-Liang , Yang Xiaohu , He Min , Shen Shi-Yin , Li Qingyang , Li Xuejie 
Published: June 2023

ABSTRACT
We use the eROSITA Final Equatorial-Depth Survey (eFEDS) to measure the rest-frame 0.1–2.4 keV band X-ray luminosities of ∼600 000 DESI groups using two different algorithms in the overlap region of the two observations. These groups span a large redshift range of 0.0 ≤ zg ≤ 1.0 and group mass range of $10^{10.76}\, h^{-1}\, \mathrm{M}_{\odot } \le M_h \le 10^{15.0}\, h^{-1}\, \mathrm{M}_{\odot }$. (1) Using the blind detection pipeline of eFEDS, we find that 10932 X-ray emission peaks can be cross-matched with our groups, ∼38 per cent of which have a signal-to-noise ratio $\rm {S}/\rm {N} \ge 3$ in X-ray detection. Comparing to the numbers reported in previous studies, this matched sample size is a factor of ∼6 larger. (2) By stacking X-ray maps around groups with similar masses and redshifts, we measure the average X-ray luminosity of groups as a function of halo mass in five redshift bins. We find that in a wide halo mass range, the X-ray luminosity, LX, is roughly linearly proportional to Mh and quite independent to the redshift of the groups. (3) We use a Poisson distribution to model the X-ray luminosities obtained using two different algorithms and obtain the best-fit $L_{\rm X}=10^{28.46\pm 0.03}M_{\rm h}^{1.024\pm 0.002}$ and $L_{\rm X}=10^{26.73 \pm 0.04}M_{\rm h}^{1.140 \pm 0.003}$ scaling relations, respectively. The best-fit slopes are flatter than the results previously obtained but closer to a self-similar prediction.