bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Endoscopic and Artificial Intelligence Diagnoses for Predicting the Histological Healing of Ulcerative Colitis in a Real-World Clinical Setting
Authors: Omori Teppei , Yamamoto Tomoko , Murasugi Shun , Koroku Miki , Yonezawa Maria , Nonaka Kouichi , Nagashima Yoji , Nakamura Shinichi , Tokushige Katsutoshi 
Published: January 2024

Abstract

Background
Artificial intelligence (AI)-assisted colonoscopy systems with contact microscopy capabilities have been reported previously; however, no studies regarding the clinical use of a commercially available system in patients with ulcerative colitis (UC) have been reported. In this study, the diagnostic performance of an AI-assisted ultra-magnifying colonoscopy system for histological healing was compared with that of conventional light non-magnifying endoscopic evaluation in patients with UC.

Methods
The data of 52 patients with UC were retrospectively analyzed. The Mayo endoscopic score (MES) was determined by 3 endoscopists. Using the AI system, healing of the same spot assessed via MES was defined as a predicted Geboes score (GS) &lt; 3.1. The GS was then determined using pathology specimens from the same site.

Results
A total of 191 sites were evaluated, including 159 with a GS &lt; 3.1. The MES diagnosis identified 130 sites as MES0. A total of 120 sites were determined to have healed based on AI. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of MES0 for the diagnosis of GS &lt; 3.1 were 79.2%, 90.6%, 97.7%, 46.8%, and 81.2%, respectively. The AI system performed similarly to MES for the diagnosis of GS &lt; 3.1: sensitivity, 74.2%; specificity: 93.8%; PPV: 98.3%; NPV: 42.3%; and accuracy: 77.5%. The AI system also significantly identified a GS of &lt; 3.1 in the setting of MES1 (P = .0169).

Conclusions
The histological diagnostic yield the MES- and AI-assisted diagnoses was comparable. Healing decisions using AI may avoid the need for histological examinations.
Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences
Authors: Ramazi Shahin , Tabatabaei Seyed Amir Hossein , Khalili Elham , Nia Amirhossein Golshan , Motarjem Kiomars 
Published: January 2024

Abstract
The post-translational modifications occur as crucial molecular regulatory mechanisms utilized to regulate diverse cellular processes. Malonylation of proteins, a reversible post-translational modification of lysine/k residues, is linked to a variety of biological functions, such as cellular regulation and pathogenesis. This modification plays a crucial role in metabolic pathways, mitochondrial functions, fatty acid oxidation and other life processes. However, accurately identifying malonylation sites is crucial to understand the molecular mechanism of malonylation, and the experimental identification can be a challenging and costly task. Recently, approaches based on machine learning (ML) have been suggested to address this issue. It has been demonstrated that these procedures improve accuracy while lowering costs and time constraints. However, these approaches also have specific shortcomings, including inappropriate feature extraction out of protein sequences, high-dimensional features and inefficient underlying classifiers. As a result, there is an urgent need for effective predictors and calculation methods. In this study, we provide a comprehensive analysis and review of existing prediction models, tools and benchmark datasets for predicting malonylation sites in protein sequences followed by a comparison study. The review consists of the specifications of benchmark datasets, explanation of features and encoding methods, descriptions of the predictions approaches and their embedding ML or deep learning models and the description and comparison of the existing tools in this domain. To evaluate and compare the prediction capability of the tools, a new bunch of data has been extracted based on the most updated database and the tools have been assessed based on the extracted data. Finally, a hybrid architecture consisting of several classifiers including classical ML models and a deep learning model has been proposed to ensemble the prediction results. This approach demonstrates the better performance in comparison with all prediction tools included in this study (the source codes of the models presented in this manuscript are available in https://github.com/Malonylation).
Database URL: https://github.com/A-Golshan/Malonylation
The chromosome-level genome of the submerged plantCryptocoryne crispatulaprovides insights into the terrestrial–freshwater transition in Araceae
Authors: Qian Zhi-Hao , Li Wei , Wang Qing-Feng , Liang Shi-Chu , Wu Shuang , Li Zhi-Zhong , Chen Jin-Ming 
Published: January 2024

AbstractPlant terrestrialization (i.e. the transition to a terrestrial environment) is a significant evolutionary event that has been intensively studied. While certain plant lineages, particularly in angiosperms, have re-adapted to freshwater habitats after colonizing terrene, however, the molecular mechanism of the terrestrial–freshwater (T–F) transition remains limited. Here, the basal monocot Araceae was selected as the study object to explore the T–F transition adaptation mechanism by comparative genomic analysis. Our findings revealed that the substitution rates significantly increased in the lineage of freshwater Araceae, which may promote their adaptation to the freshwater habitat. Additionally, 20 gene sets across all four freshwater species displayed signs of positive selection contributing to tissue development and defense responses in freshwater plants. Comparative synteny analysis showed that genes specific to submerged plants were enriched in cellular respiration and photosynthesis. In contrast, floating plants were involved in regulating gene expression, suggesting that gene and genome duplications may provide the original material for plants to adapt to the freshwater environment. Our study provides valuable insights into the genomic aspects of the transition from terrestrial to aquatic environments in Araceae, laying the groundwork for future research in the angiosperm.
In-gallery social behaviors of the ambrosia beetle, Xylosandrus germanus (Coleoptera: Curculionidae)
Authors: Milbrath Lindsey R , Biazzo Jeromy , Mudrak Erika 
Published: January 2024

Abstract
The east Asian ambrosia beetle Xylosandrus germanus (Blanford) was first detected in the United States in 1932. It now occurs across much of eastern North America and parts of the Pacific Northwest. It attacks a broad range of stressed, woody hosts including ornamental and orchard species. The foundress tunnels into the sapwood of hosts where it cultures a symbiotic fungus as food for its offspring. A few other ambrosia beetles have been shown to possess a facultatively eusocial structure among gallery members, but this has not been described for Xylosandrus spp. Using a novel artificial diet arena, we quantified the behaviors of X. germanus larvae and adults (foundress and mature offspring) over 10 wk inside their galleries. Foundresses were responsible for constructing the gallery. They also initially tended the fungal garden and brood but eventually spent most of their time blocking the gallery entrance. Larvae were mainly observed to feed, crawl, or be inactive within the gallery, regardless of the absence or presence of adult siblings. Adult female offspring were primarily inactive, likely due to dormancy. Adult male offspring actively crawled and attempted to mate with their sisters before eventually dispersing out of the gallery. Cooperative hygienic behaviors (removal of frass, cannibalism of dead nest mates, grooming siblings) were observed but a division of labor among offspring was not clear. Rather, foundress behaviors were mostly distinct from offspring behaviors, particularly as the gallery aged. Because no overlap in generations occurred, X. germanus displays a quasisocial structure.
Calcific constrictive pericarditis following tumour necrosis factor-alpha inhibition
Authors: Cunneen Brian , Hussein Hafiz , O’Sullivan Jenna , Yearoo Ibrahim 
Published: January 2024

Abstract

Background
Tumour necrosis factor (TNF)-alpha inhibition is a core therapeutic avenue for a broad range of inflammatory and autoimmune disorders including rheumatoid arthritis and inflammatory bowel disease, as well as dermatological conditions such as hidradenitis suppurativa. Adalimumab has become one of the most common TNF-alpha–inhibiting agents, which is used for many of these conditions. Treatment with such agents is associated with numerous systemic side effects, though cardiac complications remain relatively rare. These include reports of pericarditis and pericardial effusions1–3.

Case summary
A 63-year-old lady was referred to the outpatient respiratory clinic with a 1-year history of increasing breathlessness, on a background of 4 years of treatment with adalimumab for Stage III hidradenitis suppurativa. A high-resolution computed tomography (CT) thorax revealed evidence of pericardial calcification. Subsequent left and right heart catheterization study revealed equalization of intraventricular pressures, consistent with constrictive pericarditis. A QuantiFERON test was negative, and rheumatological serology was unremarkable. The patient was initially managed conservatively with close follow-up, before undergoing surgical pericardectomy when she developed signs of cardiac failure.

Discussion
Adalimumab is associated with a range of systemic side effects, though cardiac complications are relatively rare. This case highlights a potentially novel complication associated with prolonged adalimumab therapy. Given that there are reports in the literature of pericarditis and pericardial effusions associated with TNF-alpha inhibition1–3, it is reasonable to hypothesize that the calcific constrictive pericarditis seen in this case may demonstrate a novel cardiac phenomenon associated with this therapy, given the lack of any traditional aetiological factors.
Comparison of lactated Ringer's solution and Plasma-Lyte A as a base solution for del Nido cardioplegia: a prospective randomized trial
Authors: Kantathut Narongrit , Krathong Pimchanok , Khajarern Siam , Leelayana Parinya , Cherntanomwong Piya 
Published: January 2024

Abstract

OBJECTIVES
The use of del Nido cardioplegia has been increasing in popularity for adult cardiac surgery. However, the base solution, Plasma-Lyte A, is not always available in many countries. This prospective randomized controlled trial evaluated myocardial preservation and clinical outcomes when using lactated Ringer's solution (LRS) compared to Plasma-Lyte A as a base solution for del Nido cardioplegia.

METHODS
Adult patients undergoing first-time elective cardiac surgery for acquired heart disease, including isolated coronary artery bypass grafting, isolated valve surgery, combined valve surgery or concomitant coronary artery bypass grafting and valve surgery were randomized to receive either LRS (n = 100) or Plasma-Lyte A (n = 100).

RESULTS
There were no significant differences between the 2 groups in terms of age, comorbidities, Society of Thoracic Surgeons risk score and type of procedures. The primary outcome, postoperative troponin-T at 24 h, was similar in both groups (0.482 vs 0.524 ng/ml; P = 0.464). Other cardiac markers were also similar at all time points. The LRS group had a lower pH (7.228 vs 7.246; P = 0.005) and higher calcium levels (0.908 vs 0.358 mmol/l; P &lt; 0.001) in the delivered cardioplegia, but there were no significant differences in clinical outcomes, such as ventricular fibrillation, left ventricular ejection fraction, inotrope/vasopressor requirement, intra-aortic balloon pump support, intensive care unit stay, hospital stay, atrial fibrillation, red cell transfusion and complications.

CONCLUSIONS
The results suggest that LRS can be used as an alternative to Plasma-Lyte A as the base solution for del Nido cardioplegia, with similar myocardial preservation and clinical outcomes.
Evolutionary and empirical perspectives on ‘demand’ breastfeeding
Authors: Tracer David P 
Published: January 2024

Abstract

Background/Objectives
The concept of ‘demand’ breastfeeding is central in public health. A key feature of the concept is that the infant is the locus of control in the breastfeeding process; when the breast is demanded by the infant, it is given the opportunity to feed. This study questions this notion of the infant as the locus of control in demand breastfeeding for empirical and theoretical reasons. From an evolutionary perspective, infants are expected to seek maximal investment and, against this backdrop of maximal investment-seeking, parents decide how much investment to put into offspring.

Methodology
Focal follows were conducted among 113 mother–infant dyads in Papua New Guinea. During these follows, response times and types of responses, including breastfeeding to offspring fussing and crying, were recorded.

Results
Infants were breastfed an average of 3.6 times/hour for just over 2 min/feed. Fussing and crying were responded to quickly, with most response times under 1 min. When the mother responded, she breastfed the child approximately 52% of the time. The other 48% of the time, mothers responded to infants with other forms of pacification. Mothers were significantly less likely to respond to infants by breastfeeding if the child had been breastfed within the past 59–76 min.

Conclusion/Implications
As predicted by evolutionary parental investment theory, infants make frequent demands on their parents for investment, but mothers are ultimately the locus of control in the investment process. The mother decides whether and how frequently to breastfeed her offspring against this backdrop of near-continuous investment demands.
Pulsed electric field, cryoballoon, and radiofrequency for paroxysmal atrial fibrillation ablation: a propensity score-matched comparison
Authors: Della Rocca Domenico G , Marcon Lorenzo , Magnocavallo Michele , Menè Roberto , Pannone Luigi , Mohanty Sanghamitra , Sousonis Vasileios , Sorgente Antonio , Almorad Alexandre , Bisignani Antonio , Głowniak Andrzej , Del Monte Alvise , Bala Gezim , Polselli Marco , Mouram Sahar , La Fazia Vincenzo Fazia , Ströker Erwin , Gianni Carola , Zeriouh Sarah , Bianchi Stefano , Sieira Juan , Combes Stephane , Sarkozy Andrea , Rossi Pietro , Boveda Serge , Natale Andrea , de Asmundis Carlo , Chierchia Gian-Battista ,   HRMC Investigators, Audiat Charles , Vetta Giampaolo , Cespón-Fernández María , Doundoulakis Ioannis , Monaco Cinzia , Overeinder Ingrid , Carette Gregory , Lombardo Ilenia , Nakasone Kazutaka , Eltzov Ivan , Meir Mark La 
Published: January 2024

Abstract

Aims
Pulsed field ablation (PFA) has emerged as a novel, non-thermal energy source to selectively ablate cardiac tissue. We describe a multicentre experience on pulmonary vein isolation (PVI) via the pentaspline Farapulse™ PFA system vs. thermal-based technologies in a propensity score-matched population of paroxysmal atrial fibrillation (PAF) patients.

Methods and results
Propensity score matching was adopted to compare PVI-only ablation outcomes via the Farawave™ system (Group PFA), cryoballoon (Group CRYO), or focal radiofrequency (Group RF) (PFA:CRYO:RF ratio = 1:2:2). Among 1572 (mean age: 62.4 ± 11.3 years; 42.5% females) PAF patients undergoing first time PVI with either PFA (n = 174), CRYO (n = 655), or RF (n = 743), propensity score matching yielded 174 PFA, 348 CRYO, and 348 RF patients. First-pass isolation was achieved in 98.8% of pulmonary veins (PVs) with PFA, 81.5% with CRYO, and 73.1% with RF (P &lt; 0.001). Procedural and dwell times were significantly shorter with PFA, whereas the availability of a 3D mapping system led to a significant reduction in X-ray exposure with RF. Overall complication rates were 3.4% (n = 6) with PFA, 8.6% (n = 30) with CRYO, and 5.5% (n = 19) with RF (P = 0.052). The 1-year Kaplan–Meier estimated freedom from any atrial tachyarrhythmia was 79.3% with PFA, 74.7% with CRYO, and 72.4% with RF (log-rank P-value: 0.24). Among 145 repeat ablation procedures, PV reconnection rate was 19.1% after PFA, 27.5% after CRYO, and 34.8% after RF (P = 0.01).

Conclusion
Pulsed field ablation contributed to significantly shorter procedural times. Follow-up data showed a similar arrhythmia freedom, although a higher rate of PV reconnection was documented in post-CRYO and post-RF redo procedures.
Harping on patriotism: female education meets Orléanist ambition in Jean-Antoine-Théodore Giroust’s The Harp Lesson (1791)
Authors: Freund Amy , Stammers Tom 
Published: January 2024

Abstract
One of the largest and most striking submissions to the 1791 Salon, The Harp Lesson by Jean-Antoine-Théodore Giroust was an ambitious but spectacularly ill-timed intervention in Revolutionary politics. It emerged from Félicité de Genlis’ remarkable educational project for the children of the duc d’Orléans, especially Princess Adélaïde, which mixed bold ideas about gender and civic virtue with specific political ambition. This article situates the painting within the experimental politics and sentimental crises of the Orléans household. It argues that Giroust, an intimate of this household, sought to exemplify some of Genlis’ boldest claims for the capacities and potential of the royal children in her care, especially at the expense of their biological mother. It demonstrates how Giroust engaged with the visual languages of recent Salon painting to create a domestic scene of female accomplishment that was also freighted with national purpose. The failure of the painting to resonate with the public illuminates the desperate gamble of different figures in the Orléanist camp as well as the unfulfilled possibilities of summer 1791.
Reconsidering the patient: pauvres malades and malades pauvres in eighteenth-century medical contexts
Authors: Rieder Philip , Vasset Sophie , Zanetti François 
Published: January 2024

Abstract
When humoral medicine gave way to more scientific approaches in the nineteenth century, the physician’s gaze changed. Amongst the epistemological transformations were representations and perceptions of the poor patient: the pauvre malade—a pauper who happened to be sick and was to be taken care of by traditional medical charities—became a malade pauvre, a sick person who happened to be poor and was to be treated in new institutions. This article explores these changes but in settings beyond the clinic. In three case studies, we explore the practice of the Genevan physician Louis Odier, the management of the poor in the French spa of Saint-Amand and, finally, treatises about British spas. The agency of physicians, administrators and the poor themselves are analysed. Physicians played an ambiguous role. Some resisted innovation and refused to consider the poor as suffering from the same diseases as the affluent; others made opportunistic use of case histories, including those of the poor, to convince richer patients of the benefits of specific treatments, thereby reinforcing ‘class-blind’ ontological conceptions of disease. Administrators, for their part, tended to see the poor foremost as patients and put pressure on physicians to arrive at precise diagnoses.
Chromosome-Level Assembly of Artemia franciscana Sheds Light on Sex Chromosome Differentiation
Authors: Bett Vincent Kiplangat , Macon Ariana , Vicoso Beatriz , Elkrewi Marwan 
Published: January 2024

Abstract
Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.
5-Aminolevulinic acid improves cold resistance through regulation of SlMYB4/SlMYB88-SlGSTU43 module to scavenge reactive oxygen species in tomato
Authors: Zhang Zhengda , Yuan Luqiao , Dang Jiao , Zhang Yuhui , Wen Yongshuai , Du Yu , Liang Yufei , Wang Ya , Liu Tao , Li Tianlai , Hu Xiaohui 
Published: January 2024

Abstract
Cold stress severely affects the growth and quality of tomato. 5-Aminolevulinic acid (ALA) can effectively improve tomato's cold stress tolerance. In this study, a tomato glutathione S-transferase gene, SlGSTU43, was identified. Results showed that ALA strongly induced the expression of SlGSTU43 under cold stress. SlGSTU43-overexpressing lines showed increased resistance to cold stress through an enhanced ability to scavenge reactive oxygen species. On the contrary, slgstu43 mutant lines were sensitive to cold stress, and ALA did not improve their cold stress tolerance. Thus, SlGSTU43 is a key gene in the process of ALA improving tomato cold tolerance. Through yeast library screening, SlMYB4 and SlMYB88 were preliminarily identified as transcription factors that bind to the SlGSTU43 promoter. Electrophoretic mobility shift, yeast one-hybrid, dual luciferase, and chromatin immunoprecipitation assays experiments verified that SlMYB4 and SlMYB88 can bind to the SlGSTU43 promoter. Further experiments showed that SlMYB4 and SlMYB88 are involved in the process of ALA-improving tomato's cold stress tolerance and they positively regulate the expression of SlGSTU43. The findings provide new insights into the mechanism by which ALA improves cold stress tolerance. SlGSTU43, as a valuable gene, could be added to the cold-responsive gene repository. Subsequently, it could be used in genetic engineering to enhance the cold tolerance of tomato.