bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical risk prediction using language models: benefits and considerations
Authors: Acharya Angeela , Shrestha Sulabh , Chen Anyi , Conte Joseph , Avramovic Sanja , Sikdar Siddhartha , Anastasopoulos Antonios , Das Sanmay 
Published: February 2024

Abstract

Objective
The use of electronic health records (EHRs) for clinical risk prediction is on the rise. However, in many practical settings, the limited availability of task-specific EHR data can restrict the application of standard machine learning pipelines. In this study, we investigate the potential of leveraging language models (LMs) as a means to incorporate supplementary domain knowledge for improving the performance of various EHR-based risk prediction tasks.

Methods
We propose two novel LM-based methods, namely “LLaMA2-EHR” and “Sent-e-Med.” Our focus is on utilizing the textual descriptions within structured EHRs to make risk predictions about future diagnoses. We conduct a comprehensive comparison with previous approaches across various data types and sizes.

Results
Experiments across 6 different methods and 3 separate risk prediction tasks reveal that employing LMs to represent structured EHRs, such as diagnostic histories, results in significant performance improvements when evaluated using standard metrics such as area under the receiver operating characteristic (ROC) curve and precision-recall (PR) curve. Additionally, they offer benefits such as few-shot learning, the ability to handle previously unseen medical concepts, and adaptability to various medical vocabularies. However, it is noteworthy that outcomes may exhibit sensitivity to a specific prompt.

Conclusion
LMs encompass extensive embedded knowledge, making them valuable for the analysis of EHRs in the context of risk prediction. Nevertheless, it is important to exercise caution in their application, as ongoing safety concerns related to LMs persist and require continuous consideration.
Effects of crude protease produced by Bacillus subtilis (MAFIC Y7) on growth performance, immune indices, and anti-inflammatory responses of broilers fed soybean meal- or cottonseed meal-based diets
Authors: Guo Xiangyue , Li Qianxi , Wang Lixue , Zhang Ying , Johnston Lee J , Levesque Crystal L , Cao Yunhe , Dong Bing 
Published: February 2024

Abstract
A strain of Bacillus subtilis (MAFIC Y7) was isolated from the intestine of Tibetan pigs and was able to express high protease activity. The aim of this study was to characterize the proteases produced by MAFIC Y7, and to investigate the effects of protease addition on growth performance, ileal amino acid digestibility, and serum immunoglobulin and immune factors of broilers fed SBM-based diets, or on growth performance, carcass characteristics, and intestinal morphology of broilers fed CSM-based diets. B. subtilis (MAFIC Y7) expressed protease showed its optimal enzyme activity at 50 °C and pH 7.0. The coated crude enzyme (CCE) showed greater stability at pH 3.0 than its uncoated counterpart. Experiment 1 was conducted with six diets based on three levels of crude protein (CP)—CPlow, CPmedium, and CPhigh—with or without CCE. In CPlow, CCE increased gain:feed (G:F) (days 1 to 21, days 1 to 42) by 8%, 3%, respectively, and enhanced apparent ileal digestibility (AID) of crude protein and lysine (on day 42) by 8.8%, 4.6%, respectively, compared with diets containing no CCE (P &lt; 0.05). CCE increased G:F from days 1 to 21 from 0.63 to 0.68, improved G:F and average daily gain (ADG) during days 1 to 42, and enhanced AID of crude protein, lysine, cysteine, and isoleucine on day 42 compared with the unsupplemented treatments (in CPmedium, P &lt; 0.05). CCE increased serum IgA (on day 21), serum IgA and IgG and increased serum IL-10 (on day 42), but decreased serum tumor necrosis factor-α (TNF-α; on day 21), and serum IL-8 and TNF-α (on day 42) compared with unsupplemented treatments. At CPhigh, CCE decreased serum levels of IL-6 and TNF-α (on day 21), and IL-8 and TNF-α (on day 42) compared with unsupplemented treatments (in CPhigh, P &lt; 0.05). In experiment 2, CSM-based diets with two lysine-to-protein ratios (5.2% or 5.5%) with or without CCE. In the high Lys diet (5.5% Lys:protein), CCE increased ADG and G:F, increased carcass, but decreased abdominal fat compared with the unsupplemented treatment (P &lt; 0.05). In the 5.2% Lys:protein dietary treatment, CCE improved duodenal villus height compared with the unsupplemented treatment (P &lt; 0.05). Supplementation of protease produced by MAFIC Y7 was associated with lower inflammatory responses in SBM diets (CPmedium or CPhigh) and improved ADG in broilers fed CPmedium or CPhigh. The proteases improved ADG and the efficiency of CSM use when the ratio of Lys to protein was 5.5%.
Earliest records of the Asian longhorned tick (Acari: Ixodidae) in Staten Island, New York, and subsequent population establishment, with a review of its potential medical and veterinary importance in the United States
Authors: Bajwa Waheed , Kennedy Ashley , Vincent Zachary , Heck Garrett , Riaj Shamim , Shah Zahir , Tsynman Leonid , Casal Cory , Haynes Scott , Cornman Hannah , Egizi Andrea , Stromdahl Ellen , Nadolny Robyn 
Published: February 2024

Abstract
Three Asian longhorned ticks (Haemaphysalis longicornis) were collected on Staten Island, Richmond County, New York, in 2014–2015 as part of a tick-borne disease surveillance program conducted by the New York City Department of Health and Mental Hygiene and the Defense Centers of Public Health – Aberdeen Tick-Borne Disease Laboratory. These records mark the earliest known occurrence of H. longicornis in New York State outside of quarantine areas, predating previously reported detections by several years. Robust populations of H. longicornis were collected in subsequent years at the Staten Island site where these few ticks were found, demonstrating that small infestations have the potential to proliferate quickly. Haemaphysalis longicornis is a 3-host ixodid tick native to eastern Asia but now established in the United States, as well as Australasia and several Pacific islands. Although H. longicornis has not yet been associated with human disease transmission in the United States, it warrants attention as a potential vector, as it is demonstrated to harbor various pathogens of medical and veterinary interest across its native and introduced range.
Disentangling semantic and prosodic features of English poetry
Authors: Shang Wenyi , Underwood Ted 
Published: February 2024

Abstract
The distinction between genre and form is still contested in literary studies. While scholars associated with the New Formalism are criticized for perceiving everything as a form, digital humanists tend to argue that everything is a genre. In this research, we employed machine learning models to classify 36,635 English poems in the Chadwyck-Healey Literature Collections into twenty-seven categories, focusing on their semantic features (lexicons) and prosodic features (meters and rhymes) independently. Our findings reveal that different categories of poetry are distinguished by different groups of characteristics, without a clear-cut division between those driven predominantly by semantic features and those driven predominantly by prosodic features. Instead, poetry categories manifest a combination of semantic and prosodic elements, spanning a spectrum of different strengths in both domains. These findings suggest that the colloquial distinction between “genre” and “form” is based on real differences between poetic categories, although those differences may not be quite as crisply binary as the vocabulary implies.
Detecting anomalous proteins using deep representations
Authors: Michael-Pitschaze Tomer , Cohen Niv , Ofer Dan , Hoshen Yedid , Linial Michal 
Published: February 2024

Abstract
Many advances in biomedicine can be attributed to identifying unusual proteins and genes. Many of these proteins’ unique properties were discovered by manual inspection, which is becoming infeasible at the scale of modern protein datasets. Here, we propose to tackle this challenge using anomaly detection methods that automatically identify unexpected properties. We adopt a state-of-the-art anomaly detection paradigm from computer vision, to highlight unusual proteins. We generate meaningful representations without labeled inputs, using pretrained deep neural network models. We apply these protein language models (pLM) to detect anomalies in function, phylogenetic families, and segmentation tasks. We compute protein anomaly scores to highlight human prion-like proteins, distinguish viral proteins from their host proteome, and mark non-classical ion/metal binding proteins and enzymes. Other tasks concern segmentation of protein sequences into folded and unstructured regions. We provide candidates for rare functionality (e.g. prion proteins). Additionally, we show the anomaly score is useful in 3D folding-related segmentation. Our novel method shows improved performance over strong baselines and has objectively high performance across a variety of tasks. We conclude that the combination of pLM and anomaly detection techniques is a valid method for discovering a range of global and local protein characteristics.
Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean
Authors: Yuan Xiaobo , Jiang Xinyu , Zhang Mengzhu , Wang Longfei , Jiao Wu , Chen Huatao , Mao Junrong , Ye Wenxue , Song Qingxin 
Published: February 2024

Abstract
Synergistic optimization of key agronomic traits by traditional breeding has dramatically enhanced crop productivity in the past decades. However, the genetic basis underlying coordinated regulation of yield- and quality-related traits remains poorly understood. Here, we dissected the genetic architectures of seed weight and oil content by combining genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) using 421 soybean (Glycine max) accessions. We identified 26 and 33 genetic loci significantly associated with seed weight and oil content by GWAS, respectively, and detected 5,276 expression quantitative trait loci (eQTLs) regulating expression of 3,347 genes based on population transcriptomes. Interestingly, a gene module (IC79), regulated by two eQTL hotspots, exhibited significant correlation with both seed weigh and oil content. Twenty-two candidate causal genes for seed traits were further prioritized by TWAS, including Regulator of Weight and Oil of Seed 1 (GmRWOS1), which encodes a sodium pump protein. GmRWOS1 was verified to pleiotropically regulate seed weight and oil content by gene knockout and overexpression. Notably, allelic variations of GmRWOS1 were strongly selected during domestication of soybean. This study uncovers the genetic basis and network underlying regulation of seed weight and oil content in soybean and provides a valuable resource for improving soybean yield and quality by molecular breeding.
Arabidopsis as a model for translational research
Authors: Yaschenko Anna E , Alonso Jose M , Stepanova Anna N 
Published: February 2024

Abstract
Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage laboratory and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, and molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.
Nationwide estimation of daily ambient PM2.5 from 2008 to 2020 at 1 km2 in India using an ensemble approach
Authors: Mandal Siddhartha , Rajiva Ajit , Kloog Itai , Menon Jyothi S , Lane Kevin J , Amini Heresh , Walia Gagandeep K , Dixit Shweta , Nori-Sarma Amruta , Dutta Anubrati , Sharma Praggya , Jaganathan Suganthi , Madhipatla Kishore K , Wellenius Gregory A , de Bont Jeroen , Venkataraman Chandra , Prabhakaran Dorairaj , Prabhakaran Poornima , Ljungman Petter , Schwartz Joel 
Published: February 2024

AbstractHigh-resolution assessment of historical levels is essential for assessing the health effects of ambient air pollution in the large Indian population. The diversity of geography, weather patterns, and progressive urbanization, combined with a sparse ground monitoring network makes it challenging to accurately capture the spatiotemporal patterns of ambient fine particulate matter (PM2.5) pollution in India. We developed a model for daily average ambient PM2.5 between 2008 and 2020 based on monitoring data, meteorology, land use, satellite observations, and emissions inventories. Daily average predictions at each 1 km × 1 km grid from each learner were ensembled using a Gaussian process regression with anisotropic smoothing over spatial coordinates, and regression calibration was used to account for exposure error. Cross-validating by leaving monitors out, the ensemble model had an R2 of 0.86 at the daily level in the validation data and outperformed each component learner (by 5–18%). Annual average levels in different zones ranged between 39.7 μg/m3 (interquartile range: 29.8–46.8) in 2008 and 30.4 μg/m3 (interquartile range: 22.7–37.2) in 2020, with a cross-validated (CV)-R2 of 0.94 at the annual level. Overall mean absolute daily errors (MAE) across the 13 years were between 14.4 and 25.4 μg/m3. We obtained high spatial accuracy with spatial R2 greater than 90% and spatial MAE ranging between 7.3–16.5 μg/m3 with relatively better performance in urban areas at low and moderate elevation. We have developed an important validated resource for studying PM2.5 at a very fine spatiotemporal resolution, which allows us to study the health effects of PM2.5 across India and to identify areas with exceedingly high levels.
The Temporality of Intimate Partner Violence – How an Understanding of Time and Gendered Threats Can Foster Protection-Positive Outcomes
Authors: Aitchison Sharelle 
Published: February 2024

Abstract
This article brings together temporality and gender in the refugee process and examines how refugee determination bodies and courts have interpreted gendered threats, as a specific form of intimate partner violence. A case law review of jurisdictions (that include Australia, Canada, New Zealand, and the UK) is conducted, revealing a flawed temporal phenomenon where decision-makers have focused primarily on the exogenous aspect of threats, namely, whether there is a real chance of a threat being actuated in the future, and have largely failed to assess the endogenous, psychological dimension of the threat, that encompasses past, present, and future aspects of time. The practice of treating threats of violence as a potential future harm rather than an already occurring harm exhibits an obvious privileging of the future over the present that is not rooted in the empirical evidence on intimate partner violence. Further, the predominant focus by decision-makers on isolated future events as harm fails to accommodate the broad temporal dimensions of systemic intimate partner violence, best suited to a predicament-based model of being persecuted. This article explores the temporal shortcomings and gendered interpretations that underpin this erroneous practice in case law, finding that the temporal governance of refugee law is still largely shaped by the male gaze and conceptualisations of masculinity and femininity, which contributes to the limited recognition of threats as a form of harm in themselves.
Updates on interstitial lung disease and other selected extra-articular manifestations of rheumatoid arthritis
Authors: Myasoedova Elena , Matteson Eric L. 
Published: February 2024

Purpose of review
To discuss changes in epidemiology, recent advances in understanding of the pathogenesis and management of selected extraarticular manifestations of rheumatoid arthritis (ExRA).

Recent findings
The incidence of ExRA overall and subcutaneous rheumatoid nodules in particular is declining after 2000. These trends reflect improved RA disease activity with early effective immunosuppressive treatments; changing environmental risk factors can be contributing. ExRA continues to carry a two-fold increased mortality risk. RA-associated interstitial lung disease (RA-ILD) is a major contributor to mortality, with no decline in incidence and scant therapeutic options. Individualized risk stratification for RA-ILD based on patient-level risk factors and biomarker profile is evolving with MUC5B as a major genetic risk factor. Clinical trials are underway to evaluate the benefits of novel antifibrotic therapies and targeted therapies for RA-ILD. The risk of cardiovascular disease in RA is generally amendable to treatment with disease-modifying antirheumatic drugs, although cardiovascular risk associated with JAK inhibition is not fully understood.

Summary
Despite reduction in incidence of ExRA overall, the incidence of RA-ILD shows no significant decline and remains a major therapeutic challenge. The use of novel antifibrotics and immunosuppressive drugs shows promise in slowing the progression of RA-ILD.
Intraoperative Epiphyseal Perfusion Monitoring Does Not Reliably Predict Osteonecrosis Following Treatment of Unstable SCFE
Authors: Ellsworth Bridget K. , Lee Julianna Y. , Batley Morgan G. , Sankar Wudbhav N. 
Published: February 2024

Background:
Avascular necrosis (AVN) remains the most dreaded complication of unstable slipped capital femoral epiphysis (SCFE) treatment. Newer closed reduction techniques (with perfusion monitoring) have emerged as a technically straightforward means to address residual SCFE deformity while still minimizing the risk of osteonecrosis. However, limited data exists regarding the reliability of intraoperative epiphyseal perfusion monitoring to predict the development of AVN. The purpose of this study was to evaluate its reliability.

Methods:
We retrospectively reviewed all patients with unstable SCFE who underwent closed or open reduction with epiphyseal perfusion monitoring using an intracranial pressure (ICP) probe from 2015 to 2023 at a single institution with a minimum 6-month radiographic follow-up. Demographic, clinical, and radiographic data were recorded, including duration of symptoms, type of reduction, capsulotomy performed, presence of a waveform on ICP monitoring after epiphyseal fixation, and development of AVN on follow-up radiographs.

Results:
Our cohort included 33 hips (32 patients), of which 60.6% (n=20) were male. The average age was 12.5±1.8 years, with a median follow-up of 15.8 months. Eleven hips were treated with open reduction using the modified Dunn technique (10 hips) or anterior approach (1 hip), and 22 hips were treated with inadvertent (5 hips) or purposeful closed reduction using the Leadbetter technique (17 hips). Overall, 8 of the 33 hips in our series (24.2%) developed AVN, 6 of which (20%) had a pulsatile waveform on intraoperative epiphyseal perfusion monitoring. The overall rate of AVN after closed reductions was 31.8% (7 of 22 hips); the incidence of AVN after closed reduction with a detectable waveform was 30% (6 of 20 hips). There was no significant association between time to surgery (P=0.416) or type of reduction (P=0.218) and the incidence of AVN.

Conclusions:
In this series, intraoperative epiphyseal perfusion monitoring did not reliably predict the development of osteonecrosis. To our knowledge, this is the first study to report AVN after demonstrable intraoperative epiphyseal perfusion following closed reduction of unstable slips.

Level of Evidence:
Level IV: case series—therapeutic study.
A prospective study on the relationship between polycystic ovary syndrome and age at natural menopause
Authors: Amiri Mina , Rahmati Maryam , Firouzi Faegheh , Azizi Fereidoun , Ramezani Tehran Fahimeh 
Published: February 2024

Abstract

Objective
This study aimed to determine whether polycystic ovary syndrome (PCOS) was associated with age at menopause, compared with women without PCOS, after adjusting for potential confounders.

Methods
A total of 1,696 reproductive-aged participants from the Tehran Lipid and Glucose Study were included in this population-based prospective study with a follow-up of approximately 20 years. Of these, 348 women with PCOS based on the Rotterdam criteria and 1,348 non-PCOS controls were followed to assess the age at which they reached menopause. An accelerated failure time survival regression model was used to identify the association between PCOS and the age at natural menopause (ANM), with and without adjustment for potential confounders.

Results
The unadjusted accelerated failure time survival model revealed a significant positive association between PCOS and ANM; PCOS women experienced time to menopause by a factor of 1.05 than non-PCOS controls (95% confidence interval, 1.02-1.06; P < 0.001). After adjusting for age at baseline, menarche age, history of hypertension, history of type 2 diabetes mellitus, parity, oral contraceptive use, body mass index, education level, physical activity, and smoking, the results remained significant (time ratio: 1.03; 95% confidence interval, 1.01-1.06; P = 0.002).

Conclusions
This study indicates that ANM is significantly associated with PCOS in women. Our study findings may have implications for the fertility and reproductive health of women with PCOS. However, further large longitudinal studies on diverse populations accounting for other relevant confounders are still needed to provide data on the actual difference in age at menopause and to elucidate the underlying mechanisms of this association.
High-Resolution Ultrasound for Diagnosis and Treatment of Filler-Related Septal Necrosis
Authors: Desyatnikova Stella , Barrera Patricia 
Published: February 2024

Summary:
Nonsurgical rhinoplasty using filler injections is a popular procedure; however, it carries risks of significant complications, including vascular occlusion, skin necrosis, blindness, and cerebral ischemia. We present a case of septal necrosis after nonsurgical rhinoplasty and describe management using ultrasound guidance. Awareness of this complication and high clinical index of suspicion are necessary for early diagnosis and treatment, crucial to minimizing permanent sequelae. We show that high-definition ultrasound can help to guide the management and improve the treatment outcomes.