bluuebunny/crossref_metadata_2025_split huggingface dataset:
High level of correspondence across different news domain quality rating sets
Authors: Lin Hause , Lasser Jana , Lewandowsky Stephan , Cole Rocky , Gully Andrew , Rand David G , Pennycook Gordon 
Published: September 2023

Abstract
One widely used approach for quantifying misinformation consumption and sharing is to evaluate the quality of the news domains that a user interacts with. However, different media organizations and fact-checkers have produced different sets of news domain quality ratings, raising questions about the reliability of these ratings. In this study, we compared six sets of expert ratings and found that they generally correlated highly with one another. We then created a comprehensive set of domain ratings for use by the research community (github.com/hauselin/domain-quality-ratings), leveraging an ensemble “wisdom of experts” approach. To do so, we performed imputation together with principal component analysis to generate a set of aggregate ratings. The resulting rating set comprises 11,520 domains—the most extensive coverage to date—and correlates well with other rating sets that have more limited coverage. Together, these results suggest that experts generally agree on the relative quality of news domains, and the aggregate ratings that we generate offer a powerful research tool for evaluating the quality of news consumed or shared and the efficacy of misinformation interventions.
Evaporation of a nonsingular Reissner–Nordström black hole and the information loss problem
Authors: Sueto Kensuke , Yoshino Hirotaka 
Published: September 2023

Abstract
One of the attractive solutions to the information loss problem is that the event horizon does not appear in the process of gravitational collapse and subsequent evaporation once the spacetime singularity is regularized by some mechanism, as pointed out by Hayward and Frolov. In this paper, we examine whether this Hayward–Frolov scenario holds for the evaporation of a charged black hole. The process of collapse and evaporation is modeled with the charged Vaidya spacetime and two kinds of regularization of the central singularity are considered. Analyzing the spacetime structure of the evaporating black hole, we find that the appropriately regularized evaporating Reissner–Nordström “black hole” has no event and Cauchy horizons, indicating the possibility that the Hayward–Frolov scenario may have sufficient generality as the solution to the information loss problem. In addition, the properties of the nonsingular evaporating Reissner–Nordström black hole are examined in detail.
Gas clumping in the outskirts of galaxy clusters, an assessment of the sensitivity ofSTAR-X
Authors: Norseth Christian T , Wik Daniel R , ZuHone John A , Miller Eric D , Bautz Marshall W , McDonald Michael 
Published: September 2023

AbstractIn the outskirts of galaxy clusters, entropy profiles measured from X-ray observations of the hot intracluster medium (ICM) drops off unexpectedly. One possible explanation for this effect is gas clumping, where pockets of cooler and denser structures within the ICM are present. Current observatories are unable to directly detect these hypothetical gas clumps. One of the science drivers of the proposed STAR-X observatory is to resolve these or similar structures. Its high spatial resolution, large effective area, and low instrumental background make STAR-X ideal for directly detecting and characterizing clumps and diffuse emission in cluster outskirts. The aim of this work is to simulate observations of clumping in clusters to determine how well STAR-X will be able to detect clumps, as well as what clumping properties reproduce observed entropy profiles. This is achieved by using yt, pyXSIM, SOXS, and other tools to inject ideally modelled clumps into 3D models derived from actual clusters using their observed profiles from other X-ray missions. Radial temperature and surface brightness profiles are then extracted from mock observations using concentric annuli. We find that in simulated observations for STAR-X, a parameter space of clump properties exists where gas clumps can be successfully identified using wavdetect and masked, and are able to recover the true cluster profiles. This demonstrates that STAR-X could be capable of detecting substructure in the outskirts of nearby clusters and that the properties of both the outskirts and the clumps will be revealed.
Optimal lameness induction model development using amphotericin B in meat goats
Authors: Weeder Mikaela M , Kleinhenz Michael D , Reppert Emily J , Fritz Bailey R , Viscardi Abbie V , Montgomery Shawnee R , Martin Miriam S , Curtis Andrew K , Leslie Alyssa A , Lou Maria E , Hall Madeline G , Coetzee Johann F 
Published: September 2023

Abstract:
Lameness continues to be a critical health and welfare concern associated with goat production. Amphotericin B (amp B) is an antimicrobial successful in inducing transient lameness for research purposes previously in livestock animals. The objectives of this study were to (1) identify which of three varying doses of amp B would be most effective in inducing lameness in meat type goats and (2) develop a facial grimace scale for goats. Lameness was produced by an intra-articular injection of amphotericin B into the left hind lateral claw distal interphalangeal joint with either a 5 mg/0.25 mL (high–low, 5 mg of amphotericin B in a volume of 0.25 mL), 5 mg/0.5 mL (high–high, 5 mg of amphotericin B in a volume of 0.5 mL), or a 2.5 mg/0.25 mL (low–low, 2.5 mg of amphotericin B in a volume of 0.25 mL). A saline treatment of 0.5 mL was used as control (0.9% sterile saline solution). Lameness response was analyzed by infrared thermography (IRT) at the induced joint, mechanical-nociception threshold (MNT), visual lameness scoring (VLS), a visual analogue scale (VAS), kinetic gait analysis (KGA), plasma cortisol (CORT), substance P (Sub P), and behavior scoring. The IRT and MNT values differed by timepoint (P ≤ 0.0001). Results from VLS showed the HL treatment was the most effective at inducing lameness (6/6 goats became lame compared to HH 4/6 and LL 2/6). At 24, 48, and 72 h, VAS scores were significantly higher when comparing HL to all other treatment groups (P = 0.0003). Both behavior observers (1 and 2) reported a significant time effect (P = 0.05), with goats exhibiting more facial grimacing at 24 h post-lameness induction. From these data, an optimal dose for a repeatable lameness induction model in goats was aquired. An effective Goat Grimace Scale (GGS) was also developed to evaluate pain responses in goats.
Effects of pretreating wheat middlings and sunflower meal with fiber degrading enzymes on components solubilization and utilization in broiler chickens
Authors: Njeri Felix M , Patterson Robert , Gachuiri Charles K , Kiarie Elijah G 
Published: September 2023

Abstract
Pretreating fibrous feedstuffs with exogenous enzymes may improve their utilization in broiler chickens. Pretreatment of wheat middlings (WM) and sunflower meal (SM) with fiber degrading enzymes (FDE) was investigated for 1) in vitro solubilization of crude protein (CP) and fiber-degrading (experiment 1), and 2) apparent retention (AR) of CP, neutral detergent fiber (NDF), nitrogen corrected apparent metabolizable energy (AMEn), as well as the concentration of ceca digesta metabolites in broiler chickens (experiment 2). In experiment 1, WM was pretreated with FDE and SM with FDE ± protease and incubated in a shaker for 24 or 48 h at 40°C and 200 rpm. Samples were centrifuged, and the supernatant used for assay of sugars and organic acids and pellet processed for determination of apparent disappearance (AD) of dry matter (DM), fiber, and CP solubilization. In experiment 2, WM and SM were pretreated with FDE for 24 h, oven-dried, and incorporated in iso-caloric and iso-nitrogenous experimental diets. Diets were: 1) a corn–soybean meal positive control (PC); 2) PC plus untreated WM and SM (negative control, NC), and diets 3, 4, 5, and 6 test diets, in which the untreated WM and SM in NC were replaced with pretreated WM and SM at 25% (N25), 50% (N50), 75% (N75), and 100% (N100), respectively. Diets were prepared in mash form in two phases (starter, days 0 to 21 and finisher, days 22 to 42) and had TiO2 (0.3%) as an indigestible marker. A total of 288 Ross708 d-old male broiler chicks were placed in cages based on body weights (6 birds/cage) and allocated diets (n = 8). Birds had free access to feed and water. Samples of excreta for AR and AMEn, and of ceca digesta for the concentration of short-chain fatty acids (SCFA) were collected at the end of each phase. Pretreatment with FDE increased (P &lt; 0.001) solubilization of CP, AD of NDF, and release of sugars and organic acids in the supernatant. The mixture of FDE and protease further increased (P &lt; 0.001) CP solubilization in SM. Feeding pretreated WM and SM had a linear response (P ≤ 0.038) on AMEn, and gross energy (GE) (day 21) and a quadratic response (P &lt; 0.05) on AR of components and AMEn (day 42) and concentration of total SCFA on day 42. On day 42, N25 and N50 had higher AR of DM, CP, NDF, and GE than N75 and N100. In conclusion, pretreatment of WM and SM with enzymes increased CP and fiber degradation. Incorporating moderate amounts (N25 and N50) of pretreated WM and SM in a corn–soybean meal diet fed to broiler chickens improved nutrient and energy utilization.
Triglyceride-glucose index as a biomarker to differentiate stroke subtypes: A hospital-based cross-sectional study
Authors: Daoussi Nizar , Zemni Imen , Saad Yasmin , Abbes Amal , Ben Dhia Rihab , Mhiri Mariem , Belghith-Sriha Asma , Frih-Ayed Mahbouba 
Published: September 2023

AbstractBackgroundA growing body of literature suggests that the triglyceride-glucose (TyG) index is linked to ischemic stroke in several ways. The usefulness of this biomarker to differentiate etiologic stroke subtypes has not been thoroughly studied. We aimed to figure out whether the TyG index differentiates cardioembolic (CE) from non-cardioembolic (NCE) strokes.MethodsA cross-sectional hospital-based study of consecutive stroke cases admitted to the University Hospital of Monastir in Tunisia from January 2018 to December 2022. The TyG index was calculated through the natural logarithm (Ln) of the product of triglyceride and glucose fasting levels. A binary logistic regression was performed to analyze the association between the TyG index and the studied stroke subtypes. We plotted the receiver operating characteristic curve (ROC curve) to determine the best cutoff point for the TyG index in differentiating between CE and NCE stroke subtypes.ResultsWe included 320 patients (mean age: 64.2 ±11.1 years; 65.3% males). The TyG index values were independently associated with the NCE subtype (OR=2.38; 95% CI=1.52-3.73; p<0.001) when analyzed as a continuous data variable. Logistic regression of quartile distribution showed that the probability of developing a NCE stroke increased proportionally with the TyG index quartiles. The ROC curve showed an area under the curve of 0.636 (95% CI=0.565-0.707; p<0.001) with a cutoff of 8.8 (sensitivity = 68.8%, specificity = 57%).ConclusionHigh levels of the TyG index are associated with a higher prevalence of NCE stroke while low values are associated with CE strokes. Thus, the TyG index can be a useful biomarker in the differentiation between CE and NCE stroke subtypes.
A proposed grading system for spinal cord arteriovenous shunts
Authors: Yu Jia-Xing , Lu Hao-Han , Bian Li-Song , Feng Yue-Shan , Li Jing-Wei , Yang Fan , Li Gui-Lin , He Chuan , Ye Ming , Hu Peng , Sun Li-Yong , Ma Yong-Jie , Ren Jian , Ling Feng , Hong Tao , Zhang Hong-Qi 
Published: September 2023

AbstractBackgroundThe clinical outcomes of microsurgery for spinal cord arteriovenous shunts (SCAVSs) exhibit fluctuations due to varying patient selection criteria, underscoring the importance of a standardized surgical grading system that can effectively stratify the feasibility of SCAVSs resection.MethodsA cohort of 308 consecutive patients with surgically treated SCAVSs was randomly divided into a modeling group and a validation group. The surgical grading system was developed based on the independent risk factors of incomplete resection identified in the modeling group and subsequently verified in the validation group. The system’s specificity and sensitivity were tested through Receiver Operating Characteristic (ROC) analyses.ResultsMultivariate analysis indicated that metameric AVSs (p=0.007), AVSs with maximum length ≥3 cm (p=0.017), embedded AVSs (p=0.032) and anterior sulcal artery supply (p=0.013) were independent risk factors of incomplete resection. Subsequently, each of the four parameters is assigned one point, and the SCAVSs grade is calculated by aggregating all parameter scores. The area under ROC curve (AUC) of modeling group and validation group was 0.856 (95% confidence interval [95% CI], 0.794-0.919) and 0.819 (95% CI, 0.747-0.892) respectively. Across the entire cohort, patients with scores ranging from 0 to 4 exhibited complete resection rates of 88.7%, 66.7%, 30.6%, 4.5% and 6.3%. The corresponding rates of severe treatment-related deterioration were found to be at levels of 6.0%, 12.0%, 12.9%, 31.8% and 25.0 %, respectively. Conclusion: The proposed grading system effectively stratifies the surgical feasibility of SCAVSs based on both the probability of achieving complete resection and the treatment risk. Its simplicity renders it a valuable tool for clinical decision-making, as well as a reference point for evaluating treatment outcomes across different centers and surgical techniques.
Large-scale annotated dataset for cochlear hair cell detection and classification
Authors: Buswinka Christopher J. , Rosenberg David B. , Simikyan Rubina G. , Osgood Richard T. , Fernandez Katharine , Nitta Hidetomi , Hayashi Yushi , Liberman Leslie W. , Nguyen Emily , Yildiz Erdem , Kim Jinkyung , Jarysta Amandine , Renauld Justine , Wesson Ella , Thapa Punam , Bordiga Pierrick , McMurtry Noah , Llamas Juan , Kitcher Siân R. , López-Porras Ana I. , Cui Runjia , Behnammanesh Ghazaleh , Bird Jonathan E. , Ballesteros Angela , Vélez-Ortega A. Catalina , Edge Albert SB , Deans Michael R. , Gnedeva Ksenia , Shrestha Brikha R. , Manor Uri , Zhao Bo , Ricci Anthony J. , Tarchini Basile , Basch Martin , Stepanyan Ruben S. , Landegger Lukas D. , Rutherford Mark , Liberman M. Charles , Walters Bradley J. , Kros Corné J. , Richardson Guy P. , Cunningham Lisa L. , Indzhykulian Artur A. 
Published: September 2023

ABSTRACTOur sense of hearing is mediated by cochlear hair cells, localized within the sensory epithelium called the organ of Corti. There are two types of hair cells in the cochlea, which are organized in one row of inner hair cells and three rows of outer hair cells. Each cochlea contains a few thousands of hair cells, and their survival is essential for our perception of sound because they are terminally differentiated and do not regenerate after insult. It is often desirable in hearing research to quantify the number of hair cells within cochlear samples, in both pathological conditions, and in response to treatment. However, the sheer number of cells along the cochlea makes manual quantification impractical. Machine learning can be used to overcome this challenge by automating the quantification process but requires a vast and diverse dataset for effective training. In this study, we present a large collection of annotated cochlear hair-cell datasets, labeled with commonly used hair-cell markers and imaged using various fluorescence microscopy techniques. The collection includes samples from mouse, human, pig and guinea pig cochlear tissue, from normal conditions and followingin-vivoandin-vitroototoxic drug application. The dataset includes over 90,000 hair cells, all of which have been manually identified and annotated as one of two cell types: inner hair cells and outer hair cells. This dataset is the result of a collaborative effort from multiple laboratories and has been carefully curated to represent a variety of imaging techniques. With suggested usage parameters and a well-described annotation procedure, this collection can facilitate the development of generalizable cochlear hair cell detection models or serve as a starting point for fine-tuning models for other analysis tasks. By providing this dataset, we aim to supply other groups within the hearing research community with the opportunity to develop their own tools with which to analyze cochlear imaging data more fully, accurately, and with greater ease.
Adrenergic and mesenchymal signatures are identifiable in cell-free DNA and correlate with metastatic disease burden in children with neuroblastoma
Authors: Vayani Omar R. , Kaufman Maria E. , Moore Kelley , Chennakesavalu Mohansrinivas , TerHaar Rachel , Chaves Gepoliano , Chlenski Alexandre , He Chuan , Cohn Susan L. , Applebaum Mark A. 
Published: September 2023

ABSTRACTBackgroundCell free DNA (cfDNA) profiles of 5-hydroxymethylcytosine (5-hmC), an epigenetic marker of open chromatin and active gene expression, are correlated with metastatic disease burden in patients with neuroblastoma. Neuroblastoma tumors are comprised of adrenergic (ADRN) and mesenchymal (MES) cells, and the relative abundance of each in tumor biopsies has prognostic implications. We hypothesized that ADRN and MES specific signatures could be quantified in cfDNA 5-hmC profiles and would augment the detection of metastatic burden in patients with neuroblastoma.MethodsWe previously performed an integrative analysis to identify ADRN and MES specific genes (n=373 and n=159, respectively). Purified DNA from cell lines was serial diluted with healthy donor cfDNA. Using Gene Set Variation Analysis (GSVA), ADRN and MES signatures were optimized. We then quantified signature scores, and our prior neuroblastoma signature, in cfDNA from 84 samples from 46 high-risk patients including 21 patients with serial samples.ResultsSamples from patients with higher metastatic burden had increased GSVA scores for both ADRN and MES gene signatures (p < 0.001). While ADRN and MES signature scores tracked together in serially collected samples, we identified instances of patients with increases in either MES or ADRN score at relapse.ConclusionsWhile it is feasible to identify ADRN and MES signatures using 5-hmC profiles of cfDNA from neuroblastoma patients and correlate these signatures to metastatic burden, additional data are needed to determine the optimal strategies for clinical implementation. Prospective evaluation in larger cohorts is ongoing.
White spot syndrome virus endogenous viral elements (EVE) revealed by circular viral copy DNA (cvcDNA) in shrimp
Authors: Taengchaiyaphum Suparat , Srisala Jiraporn , Wongkhaluang Prapatsorn , Sukthaworn Suchitraporn , Macias Joaquin , Udin Iman Ihsan , Chokkara Madhu Babu , Athikkavil Mohammed Musthafa , Alday-Sanz Victoria , Flegel Timothy W. , Sritunyalucksana Kallaya 
Published: September 2023

ABSTRACTCircular, viral copy DNA (cvcDNA) can reveal the existence of endogenous viral elements (EVE) in shrimp genomic DNA. Here we describe isolation and sequencing of cvcDNA from a breeding stock of the whiteleg shrimpPenaeus vannamei. The stock was developed by onward breeding and selection for white spot syndrome virus (WSSV)-free individual survivors of white spot disease outbreaks. The stock exhibits high tolerance to WSSV. A pool of DNA extracted from 10 shrimp from this stock was subjected to cvcDNA isolation and amplification followed by high throughput sequencing. This revealed DNA fragments corresponding to locations covering much of the 300,000 bp WSSV genome. However, high frequency-read-fragments (HFRF) mapped to a surprisingly small region of approximately 1,400 bp. We hypothesized that the HFRF reflected their selection due to provision of tolerance to WSSV. Four PCR primer sets were designed to cover the 1,365 bp mapped region. One pair (Set 1) targeted the whole 1,365 bp mapped region, while another 3 primer sets (Set 2-4), targeted regions within the 1,365 bp target. All 4 primer sets were used with DNA samples from each of 36 shrimp from the same breeding stock (including the 10 used for cvcDNA preparation). Individual positive PCR results varied widely from shrimp to shrimp, ranging from only 1 primer set up to 4 primer sets. Only 1 specimen gave an amplicon of 1,365 bp, while others gave single to multiple positive amplicons in both continuous and discontinuous regions. This indicated that the amplicons did not arise from contiguous targets and might vary in insertion length. The results also confirmed that none of the shrimp were infected with WSSV. Sequencing of the PCR amplicons of expected sizes revealed sequence identity to extant WSSV genomes. This data will be used to screen the breeding stock for EVE that provide WSSV tolerance.
Benchmarking of PROTAC docking and virtual screening tools
Authors: Rovers Evianne , Schapira Matthieu 
Published: September 2023

AbstractProteolysis targeting chimeras (PROTACs) are bifunctional compounds that recruit an E3 ligase to a target protein to induce ubiquitination and degradation of the target and are pioneer molecules in the field of proximity pharmacology. Rational PROTAC design is a challenging process and novel computational tools have emerged that attempt to predict the ternary complexes created by PROTACs and identify PROTAC candidates. To compare the performance of recent PROTAC design and screening methods, a benchmark was developed to test the ability of these tools to 1) predict the ternary complexes observed in crystal structures and 2) dissociate active from inactive PROTACs. Unlike traditional protein-protein complex prediction software, the PROTAC virtual screening methods often generate successfully PROTAC-induced protein complex structures observed crystallographically, but these experimentally validated predictions are not dissociated from dozens or more of other predicted structures. PROTAC virtual screening efficiency is unclear and highly variable, in part due to the limited size of experimental datasets and the low number of negative controls. Defining ubiquitination zones within cullin-RING complexes does not improve predictions, but conformational arrangements can sometimes be found that are exclusively associated with active PROTACs. Computer assisted PROTAC design is still in its infancy. Pioneering tools highlight the promises and challenges in the field and may be more valuable when guided by clear structural and biophysical data and validated on specific chemical series.