bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparison framework for deep learning RFI detection algorithms
Authors: Du Toit Charl D , Grobler Trienko L , Ludick Danie J 
Published: March 2024

ABSTRACT
In the realm of radio astronomy, the detection of radio frequency interference (RFI) stands as a pivotal pursuit. This study performs a novel comparative analysis of deep learning methodologies and introduces a novel transfer learning method, called fine-tuning. We compare various aspects and factors relating to this problem, including supervised fully convolutional network (FCN) architectures used within the literature, loss functions, regularization techniques, and training methodologies, to establish the most effective strategies for RFI detection. Moreover, the relationship between parameters, FLOPS, and inference times are examined. Fine-tuning involves pre-training models with low-quality aoflagger reference outputs, a very popular and accessible RFI flagging software package, and thereafter re-training the models with high-quality reference outputs. We utilize two data sets: real observations from LOFAR and simulated data from HERA. The mean squared error (MSE) loss function emerges as a robust performer if a high recall is desired. In contrast, the binary cross-entropy (BCE) loss function excels in generalization but falls short in classification performance. The Dice loss function emerges as the top performer, maximizing the F1 score and thereby serving as the choice for our further investigations. Notably, we highlight the important role of data quality and model capacity. In particular, we find that low-capacity models exhibit resilience when trained with low-quality flags from aoflagger, showcasing their ability to mitigate overfitting and overflagging tendencies. In contrast, high-capacity models excel when trained with high-quality flags. Fine-tuning proved to be an effective method to unlearn the overflagging tendencies of aoflagger, whilst requiring very little data.
Galaxy triplets alignment in large-scale filaments
Authors: Rong Yu , Shen Jinzhi , Hua Zichen 
Published: March 2024

ABSTRACT
Leveraging the data sets of galaxy triplets and large-scale filaments obtained from the Sloan Digital Sky Survey, we scrutinize the alignment of the three sides of the triangles formed by galaxy triplets and the normal vectors of the triplet planes within observed large-scale filaments. Our statistical investigation reveals that the longest and median sides of the galaxy triplets exhibit a robust alignment with the spines of their host large-scale filaments, while the shortest sides show no or only weak alignment with the filaments. Additionally, the normal vectors of triplets tend to be perpendicular to the filaments. The alignment signal diminishes rapidly with the increasing distance from the triplet to the filament spine, and is primarily significant for triplets located within distances shorter than 0.2 Mpc$/h$, with a confidence level exceeding $20\sigma$. Moreover, in comparison to compact galaxy triplets, the alignment signal is more conspicuous among the loose triplets. This alignment analysis contributes to the formulation of a framework depicting the clustering and relaxation of galaxies within cosmological large-scale filament regimes, providing deeper insights into the intricate interactions between galaxies and their pivotal role in shaping galaxy groups.
Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts
Authors: Jackson Iseult , Woodman Peter , Dowd Marion , Fibiger Linda , Cassidy Lara M 
Published: March 2024

Abstract
Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.
Parietal theta burst TMS does not modulate bistable perception
Authors: Schauer Georg , Grassi Pablo Rodrigo , Gharabaghi Alireza , Bartels Andreas 
Published: March 2024

Abstract
The role of the parietal cortex in perceptual awareness and in resolving perceptual ambiguity is unsettled. Early influential transcranial magnetic stimulation studies have revealed differences in conscious perception following parietal stimulation, fuelling the notion that parietal cortex causally contributes to resolving perceptual ambiguity. However, central to this conclusion is the reliability of the method employed. Several prior studies have revealed opposing effects, such as shortening, lengthening, or no effect on multistable perceptual transitions following parietal stimulation. Here we addressed the reliability of continuous theta-burst stimulation (cTBS) on parietal cortex on the perception of bistable stimuli. We conducted three cTBS experiments that were matched to prior experiments in terms of stimuli, stimulation protocol, and target site, and used a higher number of participants. None of our cTBS experiments replicated prior cTBS results. The only experiment using individual functional localizers led to weak effects, while the two others led to null results. Individual variability of motor cortex cTBS did not predict parietal cTBS effects. In view of recent reports of highly variable cTBS effects over motor cortex, our results suggest that cTBS is particularly unreliable in modulating bistable perception when applied over parietal cortex.
INDUCER OF CBF EXPRESSION 1 promotes cold-enhanced immunity by directly activating salicylic acid signaling
Authors: Li Shaoqin , He Li , Yang Yongping , Zhang Yixin , Han Xiao , Hu Yanru , Jiang Yanjuan 
Published: March 2024

Abstract
Cold stress affects plant immune responses, and this process may involve the salicylic acid (SA) signaling pathway. However, the underlying mechanism by which low-temperature signals coordinate with SA signaling to regulate plant immunity remains unclear. Here, we found that low temperatures enhanced the disease resistance of Arabidopsis thaliana against Pseudomonas syringae pv. tomato DC3000. This process required INDUCER OF CBF EXPRESSION 1 (ICE1), the core transcription factor in cold-signal cascades. ICE1 physically interacted with NONEXPRESSER OF PATHOGENESIS-RELATED GENES 1 (NPR1), the master regulator of the SA signaling pathway. Enrichment of ICE1 on the PATHOGENESIS-RELATED GENE 1 (PR1) promoter and its ability to transcriptionally activate PR1 were enhanced by NPR1. Further analyses revealed that cold stress signals cooperate with SA signals to facilitate plant immunity against pathogen attack in an ICE1-dependent manner. Cold treatment promoted interactions of NPR1 and TGACG-BINDING FACTOR 3 (TGA3) with ICE1 and increased the ability of the ICE1–TGA3 complex to transcriptionally activate PR1. Together, our results characterize a critical role of ICE1 as an indispensable regulatory node linking low-temperature-activated and SA-regulated immunity. Understanding this crucial role of ICE1 in coordinating multiple signals associated with immunity broadens our understanding of plant–pathogen interactions.
Autophagosome biogenesis and organelle homeostasis in plant cells
Authors: Zhuang Xiaohong , Li Baiying , Jiang Liwen 
Published: March 2024

Abstract
Autophagy is one of the major highly inducible degradation processes in response to plant developmental and environmental signals. In response to different stimuli, cellular materials, including proteins and organelles, can be sequestered into a double membrane autophagosome structure either selectively or nonselectively. The formation of an autophagosome as well as its delivery into the vacuole involves complex and dynamic membrane processes. The identification and characterization of the conserved autophagy-related (ATG) proteins and their related regulators have greatly advanced our understanding of the molecular mechanism underlying autophagosome biogenesis and function in plant cells. Autophagosome biogenesis is tightly regulated by the coordination of multiple ATG and non-ATG proteins and by selective cargo recruitment. This review updates our current knowledge of autophagosome biogenesis, with special emphasis on the core molecular machinery that drives autophagosome formation and autophagosome-organelle interactions under abiotic stress conditions.
Concurrent Validity and Reliability of Video-Based Approach to Assess Physical Function in Adults With Knee Osteoarthritis
Authors: Aily Jéssica B , da Silva Alyssa Conte , de Noronha Marcos , White Daniel K , Mattiello Stela M 
Published: March 2024

Abstract

Objectives
The aim of this study was to determine the concurrent validity and reliability of the Osteoarthritis Research Society International recommended performance-based tests delivered by video-based in adults with knee osteoarthritis.

Methods
Thirty-two participants (aged 40–70 years; 15 men) undertook assessments of 4 performance-based tests via both video-based (real-time and recorded) and face-to-face approaches, on the same day. Outcome measures were performance-based test and the number of technical issues encountered. The performance-based tests included the 40-Meter Fast-Paced Walk Test (velocity, m/s), the 30-Second Chair Stand Test (number of repetitions), the Stair Climb Test (time, seconds), and the Timed “Up & Go” Test (time, seconds). The Bland–Altman limit of agreement measures, standard error of measurement (SEM), coefficient of variation (CV), minimal detectable changes, and bias (mean difference) were employed to analyze the concurrent validity between video-based and face-to-face approaches of the performance-based tests. Reliability was measured using intraclass correlation coefficients, CV, and SEM.

Results
A high degree of concurrent validity for the Timed “Up & Go” Test (bias = −0.22), the 30-Second Chair Stand Test (bias = −0.22), the Stair Climb Test (bias = −0.31), and the 40-Meter Fast-Paced Walk Test (bias = −0.06) was found. SEM and CV values were within the acceptable level for concurrent validity. There was a high degree of reliability demonstrated for all tests analyzed. Intraclass correlation coefficient measures ranged from 0.95 to 1.00 for intrarater reliability, and from 0.95 to 0.99 for interrater reliability.

Conclusions
Video-based assessment of physical performance tests is a valid and reliable tool for measuring physical function among adults with knee osteoarthritis via Microsoft Teams (Microsoft Corp, Redmond, WA, USA).

Impact
Video-based assessment is a promising public health tool to measure physical function in adults with knee osteoarthritis.
Igniting the Fire of Discovery: Creating Partnerships Between Research, Education, and Practice
Authors: Dusing Stacey C 
Published: March 2024

Abstract
In the 28th H.P. Maley Lecture, Stacey Dusing, PT, PhD, FAPTA, shares a perspective on the importance of clinician–scientists in bridging the chasm that currently exists between scholarship and clinical practice. Describing herself as a clinician–scientist, or a qualified health care professional who functions mainly as a career scientist with the other portion of time dedicated to clinical practice, Dusing highlights the potential impact of limited training for clinician–scientists in the physical therapist profession and its impact on the future of physical therapy. She challenges all physical therapists to consider the impact of Commission on Accreditation in Physical Therapy Education requirements on scholarship and the lack of requirement for clinical practice while also recognizing that training programs for clinician–scientists are quite limited. Reviewing some historical data and highlighting possible areas for growth, Dusing calls physical therapists to action in 4 areas. This paper calls all physical therapists, especially educators and administrators, to consider the role of clinician–scientist in promoting physical therapy and knowledge translation. The author challenges the profession to consider whether we are helping to train or embed clinician–scientists in our clinical workplaces to promote knowledge translation. Suggestions are made to improve research and clinical training programs to increase the number of clinician–scientists in physical therapy.
Excitatory cerebellar transcranial direct current stimulation boosts the leverage of prior knowledge for predicting actions
Authors: Oldrati Viola , Butti Niccolò , Ferrari Elisabetta , Cattaneo Zaira , Urgesi Cosimo , Finisguerra Alessandra 
Published: March 2024

Abstract
The cerebellum causally supports social processing by generating internal models of social events based on statistical learning of behavioral regularities. However, whether the cerebellum is only involved in forming or also in using internal models for the prediction of forthcoming actions is still unclear. We used cerebellar transcranial Direct Current Stimulation (ctDCS) to modulate the performance of healthy adults in using previously learned expectations in an action prediction task. In a first learning phase of this task, participants were exposed to different levels of associations between specific actions and contextual elements, to induce the formation of either strongly or moderately informative expectations. In a following testing phase, which assessed the use of these expectations for predicting ambiguous (i.e. temporally occluded) actions, we delivered ctDCS. Results showed that anodic, compared to sham, ctDCS boosted the prediction of actions embedded in moderately, but not strongly, informative contexts. Since ctDCS was delivered during the testing phase, that is after expectations were established, our findings suggest that the cerebellum is causally involved in using internal models (and not just in generating them). This encourages the exploration of the clinical effects of ctDCS to compensate poor use of predictive internal models for social perception.
High Hepatitis C Cure Rates Among Patients With Alcohol Use at a Safety-Net Hepatitis C Clinic
Authors: Heiman Erica , Alexander Meghan , Zhang Rebecca , Zheng Ziduo , Miller Lesley S. 
Published: March 2024

Objectives
We set out to examine several aspects of the relationship between alcohol use and hepatitis C virus (HCV) among a cohort of patients treated at an HCV clinic within a safety net hospital. We examined (1) the prevalence of alcohol use among patients treated for HCV, (2) the likelihood of being started on treatment among patients who reported drinking alcohol compared with those who did not, and (3) the associations between alcohol use and HCV cure.

Methods
We performed a retrospective chart abstraction study using data from the Grady Liver Clinic, a specialty HCV clinic colocated in Grady Memorial Hospital's primary care clinic and run by general internists.

Results
Nine hundred fifty-four patients were included. The sustained virologic response rate among those with 12-week posttreatment measurement was 99.2%, with only 5 patients experiencing virologic failure. None of the alcohol use indicators significantly impacted sustained virologic response or loss to follow-up. Estimates of alcohol use ranged from 28.9% (by International Classification of Diseases, Tenth Revision, code) to 48.9% (clinician documentation). Treatment initiation rates were the same among those who did and did not report alcohol use.

Conclusions
Alcohol use was not associated with decreased HCV cure rates. Our findings validate the inclusion of patients with alcohol use in HCV treatment programs.
Timelines for Return to Different Sports Types After Eight Cervical Spine Fractures in Recreational and Elite Athletes
Authors: Hung Nicole J. , McClellan Robert Trigg , Hsu Wellington , Hu Serena S. , Clark Aaron J. , Theologis Alekos A. 
Published: March 2024

Study Design:
Prospective cross-sectional survey.

Objective:
To identify timelines for when athletes may be considered safe to return to varying athletic activities after sustaining cervical spine fractures.

Background:
While acute management and detection of cervical spine fractures have been areas of comprehensive investigation, insight into timelines for when athletes may return to different athletic activities after sustaining such fractures is limited.

Methods:
A web-based survey was administered to members of the Association for Collaborative Spine Research that consisted of surgeon demographic information and questions asking when athletes (recreational vs elite) with one of 8 cervical fractures would be allowed to return to play noncontact, contact, and collision sports treated nonoperatively or operatively. The third part queried whether the decision to return to sports was influenced by the type of fixation or the presence of radiculopathy.

Results:
Thirty-three responses were included for analysis. For all 8 cervical spine fractures treated nonoperatively and operatively, significantly longer times to return to sports for athletes playing contact or collision sports compared with recreational and elite athletes playing noncontact sports, respectively (P < 0.05), were felt to be more appropriate. Comparing collision sports with contact sports for recreational and elite athletes, similar times for return to sports for nearly all fractures treated nonoperatively or operatively were noted. In the setting of associated radiculopathy, the most common responses for safe return to play were “when only motor deficits resolve completely” and “when both motor and sensory deficits resolve completely.”

Conclusions:
In this survey of spine surgeons from the Association for Collaborative Spine Research, reasonable timeframes for return to play for athletes with 8 different cervical spine fractures treated nonoperatively or operatively varied based on fracture subtype and level of sporting physicality.
The association between mean arterial pressure and acute kidney injury reversal among patients with decompensated cirrhosis
Authors: Cullaro Giuseppe , Allegretti Andrew S. , Fenton Cynthia , Ge Jin , Patidar Kavish R. , Rubin Jessica , Sharma Arjun , Lai Jennifer C. 
Published: March 2024

Background and Aims:
This study informs how mean arterial pressure (MAP) impacts acute kidney injury (AKI) recovery among all patients hospitalized with cirrhosis, regardless of etiology.

Approach and Results:
We identified incident AKI episodes among subjects in our cohort of patients with decompensated cirrhosis. AKI was defined as a ≥50% increase in creatinine from an outpatient baseline (≥7 days prior) that required hospitalization. Linear mixed effects models were completed to determine the impact between AKI recovery, MAP, and time. To determine the impact of MAP on AKI reversal, we completed time-dependent Cox regression models with time beginning at the time of peak creatinine and ending at death, discharge, or AKI reversal, among those hospitalized with AKI and those with persistent AKI (≥48 h) We identified 702 hospitalized patients with cirrhosis with AKI. We found those with AKI reversal had, on average, higher MAP (2.1 mm Hg, p<0.05) and a greater increase in MAP over time (0.1 mm Hg per hour, p<0.001). Among all 702 hospitalized patients with AKI and adjusted for confounders, each 5 mm Hg increase in MAP was associated with 1.07× the hazard of AKI reversal (p<0.01). Similarly, among those with persistent AKI after adjusting for confounders, each 5 mm Hg increase in MAP was associated with a 1.19× greater likelihood of AKI reversal (p<0.001).

Discussion:
Our data demonstrate that MAP significantly increases the likelihood of AKI recovery regardless of severity or injury or AKI phenotype. We believe these data highlight the importance of MAP as a clinical tool to promote kidney function recovery among patients with cirrhosis hospitalized with AKI.
Feasibility of Liver Transplantation after 90Y Radioembolization: Lessons from a Radiation Protection Incident
Authors: Soret Marine , Maisonobe Jacques-Antoine , Maksud Philippe , Payen Stéphane , Allaire Manon , Savier Eric , Roux Charles , Lussey-Lepoutre Charlotte , Kas Aurélie 
Published: March 2024

Abstract
Radioembolization using 90Y is a growing procedure in nuclear medicine for treating hepatocellular carcinoma. Current guidelines suggest postponing liver transplantation or surgical resection for a period of 14 to 30 d after radioembolization to minimize surgeons’ exposure to ionizing radiation. In light of a radiation protection incident, we reevaluated the minimum delay required between radioembolization and subsequent liver transplantation. A patient with a hepatocellular carcinoma underwent a liver transplantation 44 h after undergoing radioembolization using 90Y (860 MBq SIR-Spheres). No specific radioprotection measures were followed during surgery and pathological analysis. We subsequently (1) evaluated the healthcare professionals' exposure to ionizing radiation by conducting dose rate measurements from removed liver tissue and (2) extrapolated the recommended interval to be observed between radioembolization and surgery/transplantation to ensure compliance with the radiation dose limits for worker safety. The surgeons involved in the transplantation procedure experienced the highest radiation exposure, with whole-body doses of 2.4 mSv and extremity doses of 24 mSv. The recommended delay between radioembolization and liver transplantation was 8 d when using SIR-Spheres and 15 d when injecting TheraSphere. This delay can be reduced further when considering the specific 90Y activity administered during radioembolization. This dosimetric study suggests the feasibility of shortening the delay for liver transplantation/surgery after radioembolization from the 8th or 15th day after using SIR-Spheres or TheraSphere, respectively. This delay can be decreased further when adjusted to the administrated activity while upholding radiation protection standards for healthcare professionals.