bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nasal and Plasma Severe Acute Respiratory Syndrome Coronavirus 2 RNA Levels Are Associated With Timing of Symptom Resolution in the ACTIV-2 Trial of Nonhospitalized Adults With Coronavirus Disease 2019
Authors: Li Yijia , Harrison Linda J , Chew Kara W , Currier Judy S , Wohl David A , Daar Eric S , Evering Teresa H , Wu Ryan , Giganti Mark , Ritz Justin , Javan Arzhang Cyrus , Coombs Robert W , Moser Carlee , Hughes Michael D , Eron Joseph J , Smith Davey M , Li Jonathan Z 
Published: October 2022

AbstractAcute Coronavirus Disease 2019 symptoms limit daily activities, but little is known about its association with severe acute respiratory syndrome coronavirus 2 viral burden. In this exploratory analysis of placebo recipients in the ACTIV-2/A5401 platform trial, we showed that high anterior nasal RNA levels and detectable plasma RNA were associated with delayed symptom improvement.Clinical Trials Registration. https://clinicaltrials.gov/ct2/show/NCT04518410.
miRNA analysis reveals novel dysregulated pathways in amyotrophic lateral sclerosis
Authors: Hur Junguk , Paez-Colasante Ximena , Figueroa-Romero Claudia , Lo Ting-wen , Barmada Sami J , Paulsen Michelle T , Ljungman Mats , Alakwaa Fadhl M , Savelieff Masha G , Goutman Stephen A , Feldman Eva L 
Published: October 2022

AbstractAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. Its complex pathogenesis and phenotypic heterogeneity hinder therapeutic development and early diagnosis. Altered RNA metabolism is a recurrent pathophysiologic theme, including distinct microRNA (miRNA) profiles in ALS tissues. We profiled miRNAs in accessible biosamples, including skin fibroblasts and whole blood and compared them in age- and sex-matched healthy controls versus ALS participants with and without repeat expansions to chromosome 9 open reading frame 72 (C9orf72; C9-ALS and nonC9-ALS), the most frequent ALS mutation. We identified unique and shared profiles of differential miRNA (DmiRNA) levels in each C9-ALS and nonC9-ALS tissues versus controls. Fibroblast DmiRNAs were validated by quantitative real-time PCR and their target mRNAs by 5-bromouridine and 5-bromouridine-chase sequencing. We also performed pathway analysis to infer biological meaning, revealing anticipated, tissue-specific pathways and pathways previously linked to ALS, as well as novel pathways that could inform future research directions. Overall, we report a comprehensive study of a miRNA profile dataset from C9-ALS and nonC9-ALS participants across two accessible biosamples, providing evidence of dysregulated miRNAs in ALS and possible targets of interest. Distinct miRNA patterns in accessible tissues may also be leveraged to distinguish ALS participants from healthy controls for earlier diagnosis. Future directions may look at potential correlations of miRNA profiles with clinical parameters.
Development of an Accessible and Scalable Quantitative Polymerase Chain Reaction Assay for Monkeypox Virus Detection
Authors: Porzucek Abigail J , Proctor Abigale M , Klinkhammer Katharina E , Tritsch Sarah R , Robertson Molly A , Bashor Jonathan P , Villani Jack , Sepulveda Jorge L , Mores Christopher N 
Published: October 2022

Abstract
During the 2022 monkeypox (MPX) outbreak, testing has been limited and results delayed, allowing ongoing transmission. Gold-standard quantitative polymerase chain reaction (qPCR) diagnostics are difficult to obtain. This research adapted the June 2022 CDC MPX qPCR assay for broad implementation. Validated using MPX stocks in a matrix with multiple sample types, MPX was detected with cycle threshold (Ct) values 17.46–35.59 and titer equivalents 8.01 × 106 to 2.45 × 100 plaque–forming unit (PFU)/mL. The detection limit was 3.59 PFU/mL. Sensitivity and specificity were both 100%. This qPCR assay can be quickly and broadly implemented in research and public health laboratories to increase diagnostic capacity amid the growing MPX outbreak.
Sniffing out Stingray Noses: The Functional Morphology of Batoid Olfaction
Authors: Rutledge K M 
Published: October 2022

SynopsisBatoid fishes (rays, skates, sawfishes, and guitarfishes) are macrosmatic, meaning they rely on their sense of smell as one of the primary senses for survival and reproduction. Olfaction is important for long-distance tracking and navigation, predator and prey recognition, and conspecific signaling. However, the mechanisms by which batoids harness odorants is unknown. Without a direct pump-like system, it is hypothesized that batoids irrigate their nostrils via one or a combination of the following: the motion pump, buccopharyngeal pump, pressure (ex. pitot-like mechanism), or a shearing force (ex. viscous entrainment). These mechanisms rely on the size, shape, and position of the nostrils with respect to the head and to each other. Batoids are united as a group by their dorsoventrally compressed body plans, with nostrils on the ventral side of their body. This position presents several challenges for odor capture and likely limits the effectivity of the motion pump. Batoid fishes display an expansive nasal morphology, with inlet nostrils ranging from thin, vertical slits to wide, horizontal ovals to protruding, tube-like funnels, and more. In this paper, a morphometric model is developed to quantify the vast diversity in batoid nose shapes, sizes, and positions on the head in an ecological and functional framework. Specifically, swimming mode, lifestyle, habitat, and diet are examined for correlations with observed nasal morphotypes. Morphometric measurements were taken on all 4 orders present in Batoidea to broadly encompass batoid nasal diversity (Rhinopristiformes 4/5 families; Rajiformes 2/4 families; Torpediniformes 4/4 families; Myliobatiformes 8/11 families). All batoid external nasal diversity was found to be categorized into 5 major morphological groups and were termed: flush nare [circle, comma, intermediate], open nare, and protruding nare. Several morphometric traits remained significant when accounting for shared ancestry, including the position and angle of the nostril on the head, the width of the inlet hole, and the spacing of the nostrils from each other. These measurements were found to be closely correlated and statistically significant with the swimming mode of the animal. This study provides the first crucial step in understanding batoid olfaction, by understanding the diversity of the morphology of the system. Because odor capture is a strictly hydrodynamic process, it may be that factors relating more directly to the fluid dynamics (i.e., swimming mode, velocity, Reynolds number) may be more important in shaping the evolution of the diversity of batoid noses than other ecological factors like habitat and diet.
Appropriateness of surgical antimicrobial prophylaxis in a teaching hospital in Ghana: findings and implications
Authors: Sefah Israel Abebrese , Denoo Edinam Yawo , Bangalee Varsha , Kurdi Amanj , Sneddon Jacqueline , Godman Brian 
Published: October 2022

Abstract

Background
Surgical site infections (SSIs) are among the most common infections seen in hospitalized patients in low- and middle-income countries (LMICs), accounting for up to 60% of hospital-acquired infections. Surgical antimicrobial prophylaxis (SAP) has shown to be an effective intervention for reducing SSIs and their impact. There are concerns of inappropriate use of SAP in Ghana and therefore our audit in this teaching hospital.

Methods
A retrospective cross sectional clinical audit of medical records of patients undergoing surgery over a 5 month duration from January to May 2021 in Ho Teaching Hospital. A data collection form was designed to collect key information including the age and gender of patients, type and duration of surgery, choice and duration of SAP. The collected data was assessed for the proportion of SAP compliance with Ghana Standard Treatment Guidelines (STGs) and any association with various patient, surgical wound and drug characteristics.

Results
Of the 597 medical records assessed, the mean age of patients was 35.6 ± 12.2 years with 86.8% (n = 518) female. Overall SAP compliance with the STG was 2.5% (n = 15). SAP compliance due to appropriate choice of antimicrobials was 67.0% (n = 400) and duration at 8.7% (n = 52). SAP compliance was predicted by duration of SAP (P &lt; 0.000) and postoperative hospitalization duration (P = 0.005).

Conclusions
SAP compliance rate was suboptimal, principally due to a longer duration of prescription. Quality improvement measures such as education of front-line staff on guideline compliance, coupled with clinical audit and regular updates, are urgently needed to combat inappropriate prescribing and rising resistance rates.
Unique features of regulation of sulfate assimilation in monocots
Authors: Rahimzadeh Karvansara Parisa , Kelly Ciaran , Krone Raissa , Zenzen Ivan , Ristova Daniela , Silz Emely , Jobe Timothy O , Kopriva Stanislav 
Published: October 2022

Abstract
Sulfate assimilation is an essential pathway of plant primary metabolism, regulated by the demand for reduced sulfur (S). The S-containing tripeptide glutathione (GSH) is the key signal for such regulation in Arabidopsis, but little is known about the conservation of these regulatory mechanisms beyond this model species. Using two model monocot species, C3 rice (Oryza sativa) and C4Setaria viridis, and feeding of cysteine or GSH, we aimed to find out how conserved are the regulatory mechanisms described for Arabidopsis in these species. We showed that while in principle the regulation is similar, there are many species-specific differences. For example, thiols supplied by the roots are translocated to the shoots in rice but remain in the roots of Setaria. Cysteine and GSH concentrations are highly correlated in Setaria, but not in rice. In both rice and Setaria, GSH seems to be the signal for demand-driven regulation of sulfate assimilation. Unexpectedly, we observed cysteine oxidation to sulfate in both species, a reaction that does not occur in Arabidopsis. This reaction is dependent on sulfite oxidase, but the enzyme(s) releasing sulfite from cysteine still need to be identified. Altogether our data reveal a number of unique features in the regulation of S metabolism in the monocot species and indicate the need for using multiple taxonomically distinct models to better understand the control of nutrient homeostasis, which is important for generating low-input crop varieties.
Robust sampling for weak lensing and clustering analyses with the Dark Energy Survey
Authors: Lemos P , Weaverdyck N , Rollins R P , Muir J , Ferté A , Liddle A R , Campos A , Huterer D , Raveri M , Zuntz J , Valentino E Di , Fang X , Hartley W G , Aguena M , Allam S , Annis J , Bertin E , Bocquet S , Brooks D , Burke D L , Rosell A Carnero , Kind M Carrasco , Carretero J , Castander F J , Choi A , Costanzi M , Crocce M , da Costa L N , Pereira M E S , Dietrich J P , Everett S , Ferrero I , Frieman J , García-Bellido J , Gatti M , Gaztanaga E , Gerdes D W , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , James D J , Kuehn K , Kuropatkin N , Lima M , March M , Melchior P , Menanteau F , Miquel R , Morgan R , Palmese A , Paz-Chinchón F , Pieres A , Malagón A A Plazas , Porredon A , Sanchez E , Scarpine V , Schubnell M , Serrano S , Sevilla-Noarbe I , Smith M , Suchyta E , Swanson M E C , Tarle G , Thomas D , To C , Varga T N , Weller J ,   (DES Collaboration)
Published: October 2022

ABSTRACTRecent cosmological analyses rely on the ability to accurately sample from high-dimensional posterior distributions. A variety of algorithms have been applied in the field, but justification of the particular sampler choice and settings is often lacking. Here, we investigate three such samplers to motivate and validate the algorithm and settings used for the Dark Energy Survey (DES) analyses of the first 3 yr (Y3) of data from combined measurements of weak lensing and galaxy clustering. We employ the full DES Year 1 likelihood alongside a much faster approximate likelihood, which enables us to assess the outcomes from each sampler choice and demonstrate the robustness of our full results. We find that the ellipsoidal nested sampling algorithm multinest reports inconsistent estimates of the Bayesian evidence and somewhat narrower parameter credible intervals than the sliced nested sampling implemented in polychord. We compare the findings from multinest and polychord with parameter inference from the Metropolis–Hastings algorithm, finding good agreement. We determine that polychord provides a good balance of speed and robustness for posterior and evidence estimation, and recommend different settings for testing purposes and final chains for analyses with DES Y3 data. Our methodology can readily be reproduced to obtain suitable sampler settings for future surveys.
Full-shape galaxy power spectra and the curvature tension
Authors: Glanville Aaron , Howlett Cullan , Davis Tamara 
Published: October 2022

ABSTRACT
With recent evidence for a possible ‘curvature tension’ among early and late universe cosmological probes, Effective Field Theories of Large Scale Structure (EFTofLSS) have emerged as a promising new framework to generate constraints on Ωk that are independent of both CMB measurements, and some of the assumptions of flatness that enter into other large-scale structure analyses. In this work we use EFTofLSS to simultaneously constrain measurements from the 6dFGS, BOSS, and eBOSS catalogues, representing the most expansive full-shape investigation of curvature to date. Using the Bayesian evidence ratio our full-shape data assigns betting odds of 2:1 in favour of curvature, indicating present measurements remain broadly compatible with both flat and curved cosmological models. When our full-shape sample is combined with Planck 2018 CMB measurements, we break the geometric degeneracy and recover a joint fit on Ωk of $-0.0037^{+0.0025}_{-0.0026}$. Using the suspiciousness statistic we find evidence for a moderate tension between Planck 2018 and our suite of full-shape measurements, at a significance of $1.86 ^{+0.13}_{-0.11} \sigma$ (p ∼ 0.06 ± 0.02). These results demonstrate the usefulness of full-shape clustering measurements as a CMB independent probe of curvature in the ongoing curvature tension debate.
Grantecan spectroscopic observations and confirmations of planetary nebulae candidates in the Northern Galactic Plane
Authors: Ritter Andreas , Parker Q A , Sabin L , Le Dû P , Mulato L , Patchick D 
Published: October 2022

ABSTRACT
We present Gran Telescopio Canarias (GTC) spectroscopic confirmations of 55 faint Planetary Nebulae (PNe) candidates discovered largely in the INT Photometric H α Survey (IPHAS) of the Northern Galactic Plane by our pro-am collaboration. We confirm 46 of them as ‘True’ (T), 4 as ‘Likely’ (L), and 5 as ‘Possible’ (P) PNe and including 5 new PNe central star (CSPN) discoveries. This was from observations of 62 new candidates yielding a maximum PN discovery success rate of 89 per cent. The sensitivity and longer wavelength coverage of IPHAS allows PNe to be found in regions of greater extinction and at these lower Galactic latitudes, including PNe in a more advanced evolutionary state and at larger distances compared to previously known Galactic PNe. We use a holistic set of observed characteristics and optical emission-line diagnostics to confirm candidates. Plasma properties have been determined in a self-consistent way using pyneb. This work is facilitated by the functionality of our powerful, multiwavelength database ‘HASH’ (Hong Kong, Australian Astronomical Observatory, Strasbourg Observatory H-alpha Planetary Nebula catalogue) that federates known imaging, spectroscopy, and other pertinent data for all Galactic T, L, P PNe, and the significant numbers of mimics. Reddenings, corrected radial velocities, and PNe electron density and temperature estimates are provided for these new PNe wherever possible.
Stochastic dynamical description of κ and ρ bursting classes of the microquasar GRS 1915+105
Authors: Alberti Tommaso , Massaro Enrico , Mineo Teresa , Feroci Marco 
Published: October 2022

ABSTRACT
We applied a stochastic analysis based on the Langevin equation to some bursting X-ray light curves of the bright microquasar GRS 1915+105. These time series, obtained with the PCA instrument onboard Rossi-XTE, are typical of the ρ and κ classes, which are characterized by several recurring bursts with different profiles and recurrence times. We computed the state functions which are able to capture the main dynamical properties of these light curves. In the case of the κ class, the state functions in four energy bands have a double-well structure (two stable states with an unstable one in between) and the system oscillates from one to the other minimum describing a typical hysteresis cycle, as in the case of a stochastic resonance under a forcing input. For the ρ class, the functions have only one stable state followed by an unstable interval, and the system describes a limit cycle. We also performed a new spectral analysis of these data with a multitemperature zero torque accretion disc model and used the resulting parameters for interpreting the main properties of the stochastic description.
Classification of local ultraluminous infrared galaxies and quasars with kernel principal component analysis
Authors: Papaefthymiou Evangelos S , Michos Ioannis , Pavlou Orestis , Papadopoulou Lesta Vicky , Efstathiou Andreas 
Published: October 2022

ABSTRACT
We present a new diagnostic diagram for local ultraluminous infrared galaxies (ULIRGs) and quasars, analysing particularly the Spitzer Space Telescope’s infrared spectrograph spectra of 102 local ULIRGs and 37 Palomar Green quasars. Our diagram is based on a special non-linear mapping of these data, employing the kernel principal component analysis method. The novelty of this map lies in the fact that it distributes the galaxies under study on the surface of a well-defined ellipsoid, which, in turn, links basic concepts from geometry to physical properties of the galaxies. Particularly, we have found that the equatorial direction of the ellipsoid corresponds to the evolution of the power source of ULIRGs, starting from the pre-merger phase, moving through the starburst-dominated coalescing stage towards the active galactic nucleus-dominated phase, and finally terminating with the post-merger quasar phase. On the other hand, the meridian directions distinguish deeply obscured power sources of the galaxies from unobscured ones. These observations have also been verified by comparison with simulated ULIRGs and quasars using radiative transfer models. The diagram correctly identifies unique galaxies with extreme features that lie distinctly away from the main distribution of the galaxies. Furthermore, special two-dimensional projections of the ellipsoid recover almost monotonic variations of the two main physical properties of the galaxies, the silicate and polycyclic aromatic hydrocarbon features. This suggests that our diagram naturally extends the well-known Spoon diagram and it can serve as a diagnostic tool for existing and future infrared spectroscopic data, such as those provided by the James Webb Space Telescope.
CottonMD: a multi-omics database for cotton biological study
Authors: Yang Zhiquan , Wang Jing , Huang Yiming , Wang Shengbo , Wei Lulu , Liu Dongxu , Weng Yonglin , Xiang Jinhai , Zhu Qiang , Yang Zhaoen , Nie Xinhui , Yu Yu , Yang Zuoren , Yang Qing-Yong 
Published: October 2022

Abstract
Cotton is an important economic crop, and many loci for important traits have been identified, but it remains challenging and time-consuming to identify candidate or causal genes/variants and clarify their roles in phenotype formation and regulation. Here, we first collected and integrated the multi-omics datasets including 25 genomes, transcriptomes in 76 tissue samples, epigenome data of five species and metabolome data of 768 metabolites from four tissues, and genetic variation, trait and transcriptome datasets from 4180 cotton accessions. Then, a cotton multi-omics database (CottonMD, http://yanglab.hzau.edu.cn/CottonMD/) was constructed. In CottonMD, multiple statistical methods were applied to identify the associations between variations and phenotypes, and many easy-to-use analysis tools were provided to help researchers quickly acquire the related omics information and perform multi-omics data analysis. Two case studies demonstrated the power of CottonMD for identifying and analyzing the candidate genes, as well as the great potential of integrating multi-omics data for cotton genetic breeding and functional genomics research.
AntiSplodge: a neural-network-based RNA-profile deconvolution pipeline designed for spatial transcriptomics
Authors: Lund Jesper B , Lindberg Eric L , Maatz Henrike , Pottbaecker Fabian , Hübner Norbert , Lippert Christoph 
Published: October 2022

Abstract
With the current surge of spatial transcriptomics (ST) studies, researchers are exploring the deep interactive cell-play directly in tissues, in situ. However, with the current technologies, measurements consist of mRNA transcript profiles of mixed origin. Recently, applications have been proposed to tackle the deconvolution process, to gain knowledge about which cell types (SC) are found within. This is usually done by incorporating metrics from single-cell (SC) RNA, from similar tissues. Yet, most existing tools are cumbersome, and we found them hard to integrate and properly utilize. Therefore, we present AntiSplodge, a simple feed-forward neural-network-based pipeline designed to effective deconvolute ST profiles by utilizing synthetic ST profiles derived from real-life SC datasets. AntiSplodge is designed to be easy, fast and intuitive while still being lightweight. To demonstrate AntiSplodge, we deconvolute the human heart and verify correctness across time points. We further deconvolute the mouse brain, where spot patterns correctly follow that of the underlying tissue. In particular, for the hippocampus from where the cells originate. Furthermore, AntiSplodge demonstrates top of the line performance when compared to current state-of-the-art tools. Software availability: https://github.com/HealthML/AntiSplodge/.