bluuebunny/crossref_metadata_2025_split huggingface dataset:
Silica hydrogels as a carbon-free solid media for the culture of diverse organisms
Authors: Vaid Druhi , Zubir Alisa , Hanak Alistair , Qi Tanda , Delneri Daniela , Wong Lu Shin 
Published: December 2024

Abstract
Bacteriological agar plates are commonly used to carry out experiments for the selective growth of microorganisms and the isolation of single-strain colonies. However, the presence of agar itself may be a confounding factor since it may serve as a source of carbon and energy. Moreover, there have been ongoing constraints on the production and sourcing of agar. These concerns have led to an interest in the development of agar substitutes. Silica hydrogels are entirely inorganic carbon-free polymeric materials that lack any source of micronutrients. Herein, a revised method for the preparation of silica hydrogels as a solid culture medium is reported. These gels can be formulated with a range of nutrient-rich or minimal media supplemented with various carbon sources, and can be manipulated in the same manner as agar gels. Their use for the culture and isolation of diverse microorganisms, including both Gram-positive and Gram-negative bacteria, yeast, and filamentous fungi is demonstrated. These silica hydrogels supplemented with either antibiotics or other molecules of interest can also be used for microbial selection experiments.
TAT-1, a phosphatidylserine flippase, affects molting and regulates membrane trafficking in the epidermis of Caenorhabditis elegans
Authors: Milne Shae M , Edeen Philip T , Fay David S 
Published: December 2024

Abstract
Membrane trafficking is a conserved process required for the import, export, movement, and distribution of proteins and other macromolecules within cells. The Caenorhabditis elegans NIMA-related kinases NEKL-2 (human NEK8/9) and NEKL-3 (human NEK6/7) are conserved regulators of membrane trafficking and are required for the completion of molting. Using a genetic approach, we identified reduction-of-function mutations in tat-1 that suppress nekl-associated molting defects. tat-1 encodes the C. elegans ortholog of mammalian ATP8A1/2, a phosphatidylserine flippase that promotes the asymmetric distribution of phosphatidylserine on the cytosolic leaflet of lipid membrane bilayers. CHAT-1 (human CDC50), a conserved chaperone, was required for the correct localization of TAT-1, and chat-1 inhibition strongly suppressed nekl defects. Using a phosphatidylserine sensor, we found that TAT-1 was required for the normal localization of phosphatidylserine at apical endosomes and that loss of TAT-1 led to aberrant endosomal morphologies. Consistent with these data, TAT-1 localized to early endosomes and to recycling endosomes marked with RME-1, the C. elegans ortholog of the human EPS15 homology domain-containing protein, EHD1. TAT-1, phosphatidylserine biosynthesis, and the phosphatidylserine-binding protein RFIP-2 (human RAB11-FIP2) were all required for the normal localization of RME-1 to apical endosomes. Consistent with these proteins functioning together, inhibition of RFIP-2 or RME-1 led to the partial suppression of nekl molting defects, as did inhibition of phosphatidylserine biosynthesis. We propose that TAT-1 flippase activity, in conjunction with RFIP-2, promotes the recruitment of RME-1 to apical recycling endosomes and that inhibition of TAT-1–RFIP-2–RME-1 can compensate for a reduction in NEKL activities.
Mentorship advances antimicrobial use surveillance systems in low- and middle-income countries
Authors: Bajracharya Kiran Sunder , Luu Susan , Cheah Ron , KC Santosh , Mushtaq Atifa , Elijah Marjorie , Poudel Bhupendra Kumar , Cham Celeste Fernandes Xavier , Mandal Shyamu , Muhi Stephen , Buising Kirsty 
Published: December 2024

Abstract
A shortage of trained personnel poses significant challenges to implementing antimicrobial use (AMU) surveillance systems in low- and middle-income countries (LMICs). Traditional training models, such as workshops, seminars and online courses, often lack the sustained engagement and support necessary for deep learning and skill mastery. This article advocates for mentorship as an effective training method for AMU professionals in LMICs. Drawing on our experiences as mentors and mentees from 1- to 2-year mentorship programmes in Nepal, Pakistan, Papua New Guinea and Timor-Leste between 2019 and 2023, we highlight the challenges and success factors of mentorship. Our insights demonstrate mentorship’s value in building expertise and sustaining capacity in AMU surveillance, offering a promising solution to address the personnel shortage in these regions.
Enhancing patient representation learning with inferred family pedigrees improves disease risk prediction
Authors: Huang Xiayuan , Arora Jatin , Erzurumluoglu Abdullah Mesut , Stanhope Stephen A , Lam Daniel ,   Boehringer Ingelheim—Global Computational Biology and Digital Sciences, Arora Jatin , Erzurumluoglu Abdullah Mesut , Lam Daniel , Khoueiry Pierre , Jensen Jan N , Cai James , Lawless Nathan , Kriegl Jan , Ding Zhihao , de Jong Johann , Zhao Hongyu , Ding Zhihao , Wang Zuoheng , de Jong Johann 
Published: December 2024

Abstract

Background
Machine learning and deep learning are powerful tools for analyzing electronic health records (EHRs) in healthcare research. Although family health history has been recognized as a major predictor for a wide spectrum of diseases, research has so far adopted a limited view of family relations, essentially treating patients as independent samples in the analysis.

Methods
To address this gap, we present ALIGATEHR, which models inferred family relations in a graph attention network augmented with an attention-based medical ontology representation, thus accounting for the complex influence of genetics, shared environmental exposures, and disease dependencies.

Results
Taking disease risk prediction as a use case, we demonstrate that explicitly modeling family relations significantly improves predictions across the disease spectrum. We then show how ALIGATEHR’s attention mechanism, which links patients’ disease risk to their relatives’ clinical profiles, successfully captures genetic aspects of diseases using longitudinal EHR diagnosis data. Finally, we use ALIGATEHR to successfully distinguish the 2 main inflammatory bowel disease subtypes with highly shared risk factors and symptoms (Crohn’s disease and ulcerative colitis).

Conclusion
Overall, our results highlight that family relations should not be overlooked in EHR research and illustrate ALIGATEHR’s great potential for enhancing patient representation learning for predictive and interpretable modeling of EHRs.
CARE-SD: classifier-based analysis for recognizing provider stigmatizing and doubt marker labels in electronic health records: model development and validation
Authors: Walker Andrew , Thorne Annie , Das Sudeshna , Love Jennifer , Cooper Hannah L F , Livingston Melvin , Sarker Abeed 
Published: December 2024

Abstract

Objective
To detect and classify features of stigmatizing and biased language in intensive care electronic health records (EHRs) using natural language processing techniques.

Materials and Methods
We first created a lexicon and regular expression lists from literature-driven stem words for linguistic features of stigmatizing patient labels, doubt markers, and scare quotes within EHRs. The lexicon was further extended using Word2Vec and GPT 3.5, and refined through human evaluation. These lexicons were used to search for matches across 18 million sentences from the de-identified Medical Information Mart for Intensive Care-III (MIMIC-III) dataset. For each linguistic bias feature, 1000 sentence matches were sampled, labeled by expert clinical and public health annotators, and used to supervised learning classifiers.

Results
Lexicon development from expanded literature stem-word lists resulted in a doubt marker lexicon containing 58 expressions, and a stigmatizing labels lexicon containing 127 expressions. Classifiers for doubt markers and stigmatizing labels had the highest performance, with macro F1-scores of 0.84 and 0.79, positive-label recall and precision values ranging from 0.71 to 0.86, and accuracies aligning closely with human annotator agreement (0.87).

Discussion
This study demonstrated the feasibility of supervised classifiers in automatically identifying stigmatizing labels and doubt markers in medical text and identified trends in stigmatizing language use in an EHR setting. Additional labeled data may help improve lower scare quote model performance.

Conclusions
Classifiers developed in this study showed high model performance and can be applied to identify patterns and target interventions to reduce stigmatizing labels and doubt markers in healthcare systems.
The influence of crop and leaf position on thrips (Thysanoptera: Thripidae) oviposition in cotton, soybean, and peanut seedlings
Authors: Rossi Giovani , Mahas Jessica B , Chitturi Anitha , Graham Scott H , Jacobson Alana L 
Published: December 2024

Abstract
Thrips (Thysanoptera: Thripidae) can injure seedling cotton (Gossypium hirsutum L.), soybean (Glycine max (L.) Merr.), and peanut (Arachis hypogaea L.) crops in the southern United States. The planting window and timing of thrips infestations into these crops overlap in the region, but thrips preference for oviposition has not been investigated. We evaluated thrips preference for cotton, soybean, and peanut by counting eggs, immatures, and adults at the cotyledon to 4 true leaf stages. Peanut was significantly more attractive for oviposition than cotton and soybean. Oviposition in cotton was significantly higher in the cotyledons than the other leaves. The highest oviposition in soybeans also occurred in the cotyledons but differed only significantly from the fourth true leaf. In all crops, there was no significant difference among oviposition in the true leaves. The highest number of immatures were found on cotton, followed by peanut and then soybean, while adults were evenly distributed among crops. Our results suggest that while peanut is preferred for oviposition, this crop may not facilitate immature development and survival as effectively when compared with cotton. This study presents an initial examination of crop selection by thrips under field conditions and suggests peanut may be the preferred oviposition host.
Trained Immunity Enhances Host Resistance to Infection in Aged Mice
Authors: Hao Dan , Caja Katherine R , McBride Margaret A , Owen Allison M , Bohannon Julia K , Hernandez Antonio , Ali Sabah , Dalal Sujata , Williams David L , Sherwood Edward R 
Published: December 2024

Abstract
Aging significantly increases the incidence and severity of infections, with individuals aged 65 and above accounting for 65% of sepsis cases. Innate immune training, known as “trained immunity” or “innate immune memory”, has emerged as a potential strategy to enhance infection resistance by modulating the aging immune system. We investigated the impact of β-glucan-induced trained immunity on aged mice (18–20 months old) compared to young adult mice (10–12 weeks old). Our findings showed that β-glucan equally augmented the host resistance to infection in both young and aged mice. This enhancement was characterized by augmented bacterial clearance, enhanced leukocyte recruitment and decreased cytokine production in response to Pseudomonas aeruginosa infection. Furthermore, young and aged trained macrophages displayed heightened metabolic capacity and improved antimicrobial functions, including enhanced phagocytosis and respiratory burst. RNA-seq analysis showed a distinctive gene expression pattern induced by trained immunity in macrophages characterized by activation of pathways regulating inflammation and the host response to infection and suppression of pathways regulating cell division, which was consistently observed in both young and aged groups. As compared to macrophages from young mice, aged macrophages showed increased activation of gene ontology pathways regulating angiogenesis, connective tissue deposition and wound healing. Our results indicate that immune training can be effectively induced in aging mice, providing valuable insights into potential strategies for enhancing infection resistance in the elderly.
A family-based behavioral group obesity randomized control feasibility trial across a clinical trials network: a focus on contact hours
Authors: Davis Ann M , Darden Paul , Lancaster Brittany , Chang Di , Cushing Christopher C , Janicke David M , Lim Crystal S , Olalde Megan , Bullard Sarah , McCulloh Russell , Perry Danika , Pyles Lee , Staiano Amanda E , Serrano-Gonzalez Monica , Davis Deborah Winders , Jelalian Elissa 
Published: December 2024

Abstract

Objective
This ancillary study’s purpose is to describe the relationship between dose of treatment and body mass index (BMI) outcomes in a tele-behavioral health program delivered in the IDeA States Pediatric Clinical Trials Network to children and their families living in rural communities.

Methods
Participants randomized to the intervention were able to receive 26 contact hours (15 hr of group sessions and 11 hr of individual sessions) of material focused on nutrition, physical activity, and behavioral caregiver training delivered via interactive televideo. Dose of the intervention received by child/caregiver dyads (n = 52) from rural areas was measured as contact hours. The total doses of group, individual, and total contact hours were analyzed, and generalized linear mixed models were utilized to determine how dose received impacted BMI outcomes.

Results
The majority (64.4%) of participants received the target of at least 80% (20.8 hr) of the total intervention dose. Older children (9–11 years) achieved significantly less intervention dose than targeted (M = 19.7; p = .031); as did males (M = 17.2; p &lt; .001), children who identified as Black (M = 17.8; p &lt; .001), and children from Site 3 (M = 18.0; p &lt; .001). Dose was not significantly related to BMI outcomes in children or caregivers.

Conclusions
As this study is underpowered and took place during the early stages of the COVID-19 pandemic, results should be interpreted with caution, but contact hours did not predict health outcomes for families living in rural communities.
Robust evaluation of longitudinal surrogate markers with censored data
Authors: Agniel Denis , Parast Layla 
Published: December 2024

Abstract
The development of statistical methods to evaluate surrogate markers is an active area of research. In many clinical settings, the surrogate marker is not simply a single measurement but is instead a longitudinal trajectory of measurements over time, e.g. fasting plasma glucose measured every 6 months for 3 years. In general, available methods developed for the single-surrogate setting cannot accommodate a longitudinal surrogate marker. Furthermore, many of the methods have not been developed for use with primary outcomes that are time-to-event outcomes and/or subject to censoring. In this paper, we propose robust methods to evaluate a longitudinal surrogate marker in a censored time-to-event outcome setting. Specifically, we propose a method to define and estimate the proportion of the treatment effect on a censored primary outcome that is explained by the treatment effect on a longitudinal surrogate marker measured up to time t0. We accommodate both potential censoring of the primary outcome and of the surrogate marker. A simulation study demonstrates a good finite-sample performance of our proposed methods. We illustrate our procedures by examining repeated measures of fasting plasma glucose, a surrogate marker for diabetes diagnosis, using data from the diabetes prevention programme.
Understanding power grid network vulnerability through the stochastic lens of network motif evolution
Authors: Chen Yuzhou , Ng Hon Keung Tony , Gel Yulia R , Poor H Vincent 
Published: December 2024

Abstract
Modern cyber-physical systems must exhibit high reliability since their failures can lead to catastrophic cascading events. Enhancing our understanding of the mechanisms behind the functionality of such networks is a key to ensuring the resilience of many critical infrastructures. In this paper, we develop a novel stochastic model, based on topological measures of complex networks, as a framework within which to examine such functionality. The key idea is to evaluate the dynamics of network motifs as descriptors of the underlying network topology and its response to adverse events. Our experiments on multiple power grid networks show that the proposed approach offers a new competitive pathway for resilience quantification of complex systems.
Optimizing hematoma management in axillary osmidrosis surgery: the role of timely drainage and prevention of flap necrosis
Authors: Ho Wen-Tsao 
Published: December 2024

Abstract
Hematoma formation is a rare complication following axillary osmidrosis surgery, and its delayed liquefaction can pose significant risks to flap viability, leading to complications such as necrosis. This study examines two cases of postoperative hematomas, highlighting the importance of appropriate drainage management. In both cases, the initial hematomas were evacuated and treated with Penrose drains, but complications arose due to delayed liquefaction. The first case experienced delayed flap necrosis after premature removal of the drain, while the second case benefited from a proactive approach by reintroducing the drain on the sixth postoperative day. This strategy allowed for the prevention of toxic hematoma buildup, improving flap survival. The findings emphasize the need for vigilant postoperative monitoring and drainage management to minimize risks associated with hematoma liquefaction and optimize flap healing. Further research is required to establish standardized protocols for managing postoperative hematomas in axillary osmidrosis surgery.
Preduodenal portal vein: two distinct case reports with unique presentations and tailored surgical management strategies
Authors: Elnour Abdelrahman S , Taha Isam , Helali Mohamed , Nugud Faisal 
Published: December 2024

Abstract
Preduodenal portal vein (PDPV) is a rare congenital vascular malformation, which was first described by Knight in 1921 as an anomalous vein that lies in front of the duodenum, common bile duct, and hepatic artery instead of beneath them. This abnormal position may result in congenital duodenal obstruction and puts it in danger during operations around this region. PDPV is typically associated with other congenital anomalies, mainly intraabdominal and cardiac ones. The surgical management is usually determined intraoperatively based on evidence that the PDPV is the real cause of obstruction. We report two cases of PDPV each with a different presentation and management approach.
Successful retroperitoneal laparoscopic nephroureterectomy for thoracic kidney in a patient with ipsilateral ureteral cancer
Authors: Ogasawara Takuto , Tanaka Toshiaki , Shindo Tetsuya , Kyoda Yuki , Hashimoto Kohei , Kobayashi Ko , Masumori Naoya 
Published: December 2024

Abstract
A thoracic kidney is a scarce type of ectopic kidney. We report the case of a 76-year-old man who developed cancer of the ureter, ipsilateral to the thoracic kidney. He presented with abdominal pain in the right upper quadrant. Computed tomography revealed a right hydronephrotic kidney located in the thorax with elevation of the diaphragm. Further examination uncovered a cT2N0M0 ureteral cancer in the right upper ureter. A laparoscopic radical right nephroureterectomy was performed using a retroperitoneal approach. The retroperitoneal space was created for the usual port placement. A port between the 11th and 12th ribs was added to facilitate handling the suprahilar area, specifically the dissection of the superior aspect and separation of the kidney without accompanying pneumothorax. To our knowledge, this is the first report of a successful complete laparoscopic surgery via the retroperitoneal approach for a malignant disease associated with a thoracic kidney.
Uncovering topologically associating domains from three-dimensional genome maps with TADGATE
Authors: Dang Dachang , Zhang Shao-Wu , Dong Kangning , Duan Ran , Zhang Shihua 
Published: December 2024

Abstract
Topologically associating domains (TADs) are essential components of three-dimensional (3D) genome organization and significantly influence gene transcription regulation. However, accurately identifying TADs from sparse chromatin contact maps and exploring the structural and functional elements within TADs remain challenging. To this end, we develop TADGATE, a graph attention auto-encoder that can generate imputed maps from sparse Hi-C contact maps while adaptively preserving or enhancing the underlying topological structures, thereby facilitating TAD identification. TADGATE captures specific attention patterns with two types of units within TADs and demonstrates TAD organization relates to chromatin compartmentalization with diverse biological properties. We identify many structural and functional elements within TADs, with their abundance reflecting the overall properties of these domains. We applied TADGATE to sparse and noisy Hi-C contact maps from 21 human tissues or cell lines. That improved the clarity of TAD structures, allowing us to investigate conserved and cell-type-specific boundaries and uncover cell-type-specific transcriptional regulatory mechanisms associated with topological domains. We also demonstrated TADGATE’s capability to fill in sparse single-cell Hi-C contact maps and identify TAD-like domains within them, revealing the specific domain boundaries with distinct heterogeneity and the shared backbone boundaries characterized by strong CTCF enrichment and high gene expression levels.
Autophosphorylation of the Tousled-like kinases TLK1 and TLK2 regulates recruitment to damaged chromatin via PCNA interaction
Authors: West Kirk L , Nguyen Tram T N , Tengler Kyle A , Kreiling Natasha , Raney Kevin D , Ghosal Gargi , Leung Justin W 
Published: December 2024

Abstract
Tousled-like kinases 1 and 2 (TLK1 and 2) are cell cycle-regulated serine/threonine kinases that are involved in multiple biological processes. Mutation of TLK1 and 2 confer neurodegenerative diseases. Recent studies demonstrate that TLK1 and 2 are involved in DNA repair. However, there is no direct evidence that TLK1 and 2 function at DNA damage sites. Here, we show that both TLK1 and TLK2 are hyper-autophosphorylated at their N-termini, at least in part, mediated by their homo- or hetero- dimerization. We found that TLK1 and 2 hyper-autophosphorylation suppresses their recruitment to damaged chromatin. Furthermore, both TLK1 and 2 associate with PCNA specifically through their evolutionarily conserved non-canonical PCNA-interacting protein (PIP) box at the N-terminus, and mutation of the PIP-box abolishes their recruitment to DNA damage sites. Mechanistically, the TLK1 and 2 hyper-autophosphorylation masks the PIP-box and negatively regulates their recruitment to the DNA damage site. Overall, our study dissects the detailed genetic regulation of TLK1 and 2 at damaged chromatin, which provides important insights into their emerging roles in DNA repair.