bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deployment of an Artificial Intelligence Histology Tool to Aid Qualitative Assessment of Histopathology Using the Nancy Histopathology Index in Ulcerative Colitis
Authors: Rubin David T , Kubassova Olga , Weber Christopher R , Adsul Shashi , Freire Marcelo , Biedermann Luc , Koelzer Viktor H , Bressler Brian , Xiong Wei , Niess Jan H , Matter Matthias S , Kopylov Uri , Barshack Iris , Mayer Chen , Magro Fernando , Carneiro Fatima , Maharshak Nitsan , Greenberg Ariel , Hart Simon , Dehmeshki Jamshid , Peyrin-Biroulet Laurent 
Published: September 2024

Abstract

Background
Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by increased stool frequency, rectal bleeding, and urgency. To streamline the quantitative assessment of histopathology using the Nancy Index in UC patients, we developed a novel artificial intelligence (AI) tool based on deep learning and tested it in a proof-of-concept trial. In this study, we report the performance of a modified version of the AI tool.

Methods
Nine sites from 6 countries were included. Patients were aged ≥18 years and had UC. Slides were prepared with hematoxylin and eosin staining. A total of 791 images were divided into 2 groups: 630 for training the tool and 161 for testing vs expert histopathologist assessment. The refined AI histology tool utilized a 4-neural network structure to characterize images into a series of cell and tissue type combinations and locations, and then 1 classifier module assigned a Nancy Index score.

Results
In comparison with the proof-of-concept tool, each feature demonstrated an improvement in accuracy. Confusion matrix analysis demonstrated an 80% correlation between predicted and true labels for Nancy scores of 0 or 4; a 96% correlation for a true score of 0 being predicted as 0 or 1; and a 100% correlation for a true score of 2 being predicted as 2 or 3. The Nancy metric (which evaluated Nancy Index prediction) was 74.9% compared with 72.3% for the proof-of-concept model.

Conclusions
We have developed a modified AI histology tool in UC that correlates highly with histopathologists’ assessments and suggests promising potential for its clinical application.
Uncrewed surface vehicles (USVs) as platforms for fisheries and plankton acoustics
Authors: Handegard Nils Olav , De Robertis Alex , Holmin Arne Johannes , Johnsen Espen , Lawrence Joshua , Le Bouffant Naig , O'Driscoll Richard , Peddie David , Pedersen Geir , Priou Pierre , Rogge Rabea , Samuelsen Mikal , Demer David A 
Published: September 2024

Abstract
Uncrewed surface vehicles (USVs) equipped with echosounders have the potential to replace or enhance acoustic observations from conventional research vessels (RVs), increase spatial and temporal coverage, and reduce cost and carbon emission. We discuss the objectives, system requirements, infrastructure, and regulations for using USVs with echosounders to conduct ecological experiments, acoustic-trawl surveys, and long-term monitoring. We present four example applications of USVs with lengths &lt;8 m, and highlight some advantages and disadvantages relative to RV-based data acquisitions. Sail-driven USVs operate continuously for months and are more mature than motorized USVs, but they are slower. To maintain the pace of an RV, multiple sail-powered USVs sample in coordination. In comparison, motorized USVs can travel as fast as RVs and therefore may facilitate a combined survey, interleaving USV and RV transects, with RV-based biological sampling. Important considerations for all USVs include platform design, noise and transducer motion mitigation, communications and operations infrastructure, onboard data processing, biological sampling approach, and legal requirements. This technology is evolving and applied in multiple disciplines, but further development and institutional commitment are needed to allow USVs equipped with echosounders to become ubiquitous and useful components of a worldwide network of autonomous ocean observation platforms.
Calibration and comparison of SIR, SEIR/SLIR and SLAIR models for influenza dynamics: insights from the 2016-2017 season in the Valencian Community, Spain
Authors: Adenane Rim , Andreu-Vilarroig Carlos , Avram Florin , Villanueva Rafael-Jacinto 
Published: September 2024

Abstract
Influenza and influenza-like illnesses pose significant challenges to healthcare systems globally. Mathematical models play a crucial role in understanding their dynamics, calibrating them to specific scenarios and making projections about their evolution over time. This study proposes a calibration process for three different but well-known compartmental models—SIR, SEIR/SLIR and SLAIR—using influenza data from the 2016–2017 season in the Valencian Community, Spain. The calibration process involves indirect calibration for the SIR and SLIR models, requiring post-processing to compare model output with data, while the SLAIR model is directly calibrated through direct comparison. Our calibration results demonstrate remarkable consistency between the SIR and SLIR models, with slight variations observed in the SLAIR model due to its unique design and calibration strategy. Importantly, all models align with existing evidence and intuitions found in the medical literature. Our findings suggest that at the onset of the epidemiological season, a significant proportion of the population (ranging from 29.08% to 43.75% of the total population) may have already entered the recovered state, likely due to immunization from the previous season. Additionally, we estimate that the percentage of infected individuals seeking healthcare services ranges from 5.7% to 12.2%. Through a well-founded and calibrated modeling approach, our study contributes to supporting, settling and quantifying current medical issues despite the inherent uncertainties involved in influenza dynamics. The full Mathematica code can be downloaded from https://munqu.webs.upv.es/software.html.
Oscillations in a tumor–immune system interaction model with immune response delay
Authors: Huo Zhaoxuan , Huang Jicai , Kuang Yang , Ruan Shigui , Zhang Yuyue 
Published: September 2024

Abstract
In this paper we consider a tumor–immune system interaction model with immune response delay, in which a nonmonotonic function is used to describe immune response to the tumor burden and a time delay is used to represent the time for the immune system to respond and take effect. It is shown that the model may have one, two or three tumor equilibria, respectively, under different conditions. Time delay can only affect the stability of the low tumor equilibrium, and local Hopf bifurcation occurs when the time delay passes through a critical value. The direction and stability of the bifurcating periodic solutions are also determined. Moreover, the global existence of periodic solutions is established by using a global Hopf bifurcation theorem. We also observe the existence of relaxation oscillations and complex oscillating patterns driven by the time delay. Numerical simulations are presented to illustrate the theoretical results.
Neisseria gonorrhoeae treatment failure to the recommended antibiotic regimen—Québec, Canada, 2015–19
Authors: Blouin Karine , Lefebvre Brigitte , Trudelle Annick , Defay Fannie , Perrault-Sullivan Gentiane , Gnimatin Jean-Pierre , Labbé Annie-Claude 
Published: September 2024

Abstract

Objective
To describe Neisseria gonorrhoeae treatment failure to the recommended antimicrobial regimens (azithromycin, cefixime and ceftriaxone).

Methods
Our study was a longitudinal analysis of treatment failures from an observational open cohort of gonococcal infection cases collected in Québec, Canada (n = 2547) between September 2015 and December 2019. Epidemiological and clinical data were collected using a self-administered questionnaire, direct case interviews and chart reviews. Antimicrobial susceptibility testing was performed using the agar dilution method. To be retained as a treatment failure, cases must have had (i) a laboratory-confirmed gonococcal infection; (ii) a documented treatment; (iii) a positive test of cure (TOC) performed within a defined period and (iv) no sexual contact (vaginal, oral or anal), even protected with a condom, between the beginning of treatment and the positive TOC. A broader definition, including suspected cases, was also examined.

Results
Among 1593 cases where a TOC was performed, 83 had a positive TOC: 11 were retained as treatment failure, and 6 were considered suspected cases (overall = 17/1593; 1.1%). Possible explanations for retained or suspected treatment failure included resistance to the antibiotics used for treatment (n = 1), pharyngeal infection (n = 9, of which 5 had been treated with ceftriaxone and 4 with other regimens); and azithromycin monotherapy (n = 1). Some cases had more than one potential explanation.

Conclusions
Treatment failure occurred in 1.1% of cases of Neisseria gonorrhoeae infection for which a TOC was performed, including some cases of pharyngeal infection treated with ceftriaxone.
Lodestar DX, an evaluation: loop-mediated isothermal amplification (LAMP) for the diagnosis of urinary tract infection in symptomatic adult females
Authors: Diggle Joanna , Van Der Goes Van Naters Ayako , Roula Mohammed Ali , Mitchell Shanine , Whiffen Dewi , Nieuwland Jeroen , Hayhurst Emma 
Published: September 2024

Abstract

Background
Over 404.6 million people are affected worldwide each year by urinary tract infections (UTIs), with ∼237 000 associated deaths globally in 2019. Much more common in women than men, acute UTI occurs in up to 50% of the female population. Despite this, there is a lack of good diagnostic tools for use at the point-of-care, and over- and under-diagnosis are common, leading to long-term complications and patient suffering, and driving the spread of antimicrobial resistance through insufficient appropriate antibiotic stewardship.

Objectives
To evaluate the performance of a novel point-of-care testing platform, Lodestar DX, in comparison with standard laboratory processing of urine specimens.

Methods
A total of 199 fresh urine samples from symptomatic adult females suspected of having an acute UTI were tested using Lodestar DX and the results compared with standard laboratory methods performed at a local microbiology laboratory.

Results
Using standard laboratory methods, 129/199 samples produced a result and could be compared. Overall sensitivity and specificity of Lodestar DX were 88.1% (95% CI: 77.8%–94.7%) and 83.9% (95% CI: 72.3%–92.0%), respectively (n = 129), with a positive predictive value of 85.5% (95% CI: 76.9%–91.3%), a negative predictive value of 86.7% (95% CI: 77.1%–92.6%) and an overall accuracy of 86.1% (95% CI: 78.9%–91.5%).

Conclusions
The results show good correlation between Lodestar DX results and those of the standard laboratory method for this patient group. However, the platform would benefit from further testing to establish its true point-of-care compatibility and a direct comparison between this and other testing methods, such as urine dipstick testing.
The dynamic roles of intracellular vacuoles in heavy metal detoxification by Rhodotorula mucilaginosa
Authors: Shi Yixiao , Tang Lingyi , Shao Qi , Jiang Yizhou , Wang Zhijun , Peng Chao , Gu Tingting , Li Zhen 
Published: September 2024

Abstract

Aims
Rhodotorula mucilaginosa (Rho) can develop a range of strategies to resist the toxicity of heavy metals. This study aimed to investigate the physiological responses and transcriptomic regulation of the fungus under different heavy metal stresses.

Methods and results
This study applied transmission electron microscopy and RNA-seq to investigate the fungal resistance to Pb, Cd, and Cu stresses. Under Pb stress, the activated autophagy-related genes, vesicle-fusing ATPase, and vacuolar ATP synthase improved vacuolar sequestration. This offsets the loss of lipids. However, the metal sequestration by vacuoles was not improved under Cd stress. Vacuolar fusion was also inhibited following the interference of intravacuolar Ca2+ due to their similar ionic radii. Cu2+ showed the maximum toxic effects due to its lowest cellular sorption (as low as 7%) with respect to Pb2+ and Cd2+, although the efflux pumps and divalent metal ion transporters partially contributed to the detoxification.

Conclusions
Divalent cation transporters and vacuolar sequestration are the critical strategies for Rho to resist Pb stress. Superoxide dismutase (SOD) is the main strategy for Cd resistance in Rho. The intracellular Cu level was decreased by efflux pump and divalent metal ion transporters.
Exploring the impacts of fescue toxicosis on the pulmonary arterial pressure of angus cows
Authors: Rajo-Gomez E Benjamin , Giurgis Mariam , Pickworth Carrie L , Weaver Andrew R , Foster Derek M , Khanal Piush , Poole Daniel H 
Published: September 2024

Abstract
Vasoconstriction of peripheral blood vessels is one of the hallmark symptoms of fescue toxicosis in cattle. Thus, it was hypothesized that exposure to ergot alkaloids would increase the pulmonary arterial pressure (PAP). The objectives of this study were to examine the relationship between PAP and different physiological parameters of cows grazing either endophyte-infected (EI) or novel-endophyte (EN) fescue, then evaluate changes in PAP and other physiological measurements in cows exposed to EI pastures and deemed as susceptible or tolerant based on animal performance. Pregnant Angus cows at 2 different locations grazed either EI or EN fescue pastures for 14 consecutive weeks starting in early April of 2022. Forage measurements were collected to assess ergot alkaloid exposure throughout the study. In addition to measuring PAP, weekly measurements and blood samples were collected to evaluate physiological responses to ergot alkaloid consumption. The Fescue Toxicosis Selection Method (FTSM) was used for a post hoc analysis to identify cattle as either tolerant (EI-TOL) or susceptible (EI-SUS) when challenged with ergot alkaloid exposure. Data were analyzed using a MIXED procedure of SAS with repeated measures. Cows grazing on EN pastures had greater mean PAP values than EI cows, (P &lt; 0.01), whereas a location effect was identified when comparing both EI-TOL and EI-SUS groups (P &lt; 0.01). Cows exposed to EN pastures had greater average daily gain (ADG) (P = 0.04) and progesterone (P4) concentrations (P &lt; 0.01), and lower hair shedding scores (HSS; P &lt; 0.01) than EI cows. The EI-TOL cows tended to have greater final body weight, ADG and had lower HSS (P &lt; 0.01) than EI-SUS cows. While cattle consuming EI tall fescue exhibited classical physiological changes, the decrease in PAP of cattle consuming EI fescue was unexpected and contradicted the initial hypothesis. Furthermore, the FTSM provides a means to identify animals with superior performance in spite of the chronic exposure to ergot alkaloids. Continued investigations examining the interaction between ergot alkaloid exposure and cardiovascular parameters will lead to a fuller understanding of the disease and are pivotal for developing innovative strategies that enhance best management practices to help guarantee the sustainability of the U.S. beef industry.
Benefits and harms of hepatocellular carcinoma screening outreach in patients with cirrhosis: a multicenter randomized clinical trial
Authors: Singal Amit G , Daher Darine , Narasimman Manasa , Yekkaluri Sruthi , Liu Yan , Cerda Vanessa , Banala Chaitra , Khan Aisha , Lee MinJae , Seif El Dahan Karim , Murphy Caitlin C , Kramer Jennifer R , Hernaez Ruben 
Published: September 2024

Abstract

Background
The value of hepatocellular carcinoma screening is defined by the balance of benefits from early tumor detection vs harms because of false-positive results. We evaluated the value of a mailed outreach strategy for hepatocellular carcinoma screening in patients with cirrhosis.

Methods
We conducted a multicenter pragmatic randomized clinical trial comparing mailed outreach for hepatocellular carcinoma screening (n = 1436) and usual care with visit-based screening (n = 1436) among patients with cirrhosis at 3 health systems from March 2018 to September 2021. Outcomes of interest were early stage hepatocellular carcinoma detection (ie, screening benefit) and diagnostic evaluation for false-positive or indeterminate results (ie, screening harm). Screening harm was categorized as mild, moderate, and severe based on number and type of diagnostic exams. All patients were included in intention-to-screen analyses.

Results
Of 125 patients diagnosed with hepatocellular carcinoma (67 outreach and 58 usual care), 71.2% were found at an early stage per the Milan criteria. Early tumor detection did not statistically significantly differ between the outreach and usual care arms (64.2% vs 79.3%; P = .06). The proportion of patients with physical harms also did not differ between the outreach and usual care arms (10.8% vs 10.7%; P = .95) with 5.9% in both arms having mild harms; 4.0% and 3.8%, respectively, with moderate harms; and 0.9% and 1.0%, respectively, with severe harms.

Conclusion
Most patients enrolled in hepatocellular carcinoma screening were detected at an early stage, and a minority experienced physical harms. A mailed outreach strategy did not increase early hepatocellular carcinoma detection or physical harms compared with usual care.

Clinical trials number
NCT02582918 and NCT03756051.
Spatial pattern and ecological adaptation of heterostylous and homostylous species of Primula in China
Authors: Li Shunqiu , Lyu Lisha , Lyu Tong , Dimitrov Dimitar , Wang Yunyun 
Published: September 2024

Abstract
Floral syndrome is one of the key components of plant pollination syndromes, affecting variety of evolutionary and ecological processes in angiosperms. The evolutionary transition from self-incompatible heterostyly to self-compatible homostyly occurred repeatedly in angiosperm families. Although the evolution of heterostyly and homostyly has been deeply studied, our understanding on their differences in ecological strategies is still lacking. In this work, using the floral syndrome and distributions of the Primula in China we compared the spatial pattern of floral syndrome frequency and its climatic determinants. Our results reveal that distylous and homostylous Primula have similar primary centers of species diversity in southwest China, while distylous species have larger range size than homostylous ones. Temperature seasonality is the dominant climate factor of these geographic patterns, but its effect is much stronger in distylous than in homostylous Primula. Distylous species have larger flower size and number, and fruit size than homostylous ones. Climate, especially temperature seasonality mainly influenced species range size via its effects on floral syndrome. Our study suggests that homostyly is likely derived from heterostylous ancestors in similar geographical context, and larger reproductive investment in floral phenotype may provide compensatory mechanisms for obligate out-breeding heterostyly. Future investigations regarding the evolutionary history and tolerance or resistance to environmental change between distyly and homostyly may greatly advance our understanding of their spatial pattern and adaptative differences.
The association between initiation weekday of radiotherapy and local control in stage 1 glottic carcinoma: a retrospective analysis
Authors: Endo Masashi , Takahashi Satoru , Fukuda Yukiko , Okada Kohei , Ogawa Kazunari , Nakamura Michiko , Kawahara Masahiro , Akahane Keiko , Murakami Eri , Shibayama Chiaki , Onaga Ryutaro , Nagatomo Takafumi , Kanazawa Takeharu , Nishino Hiroshi , Mori Harushi , Shirai Katsuyuki 
Published: September 2024

Abstract
Radiotherapy is one of the definitive treatments for head and neck squamous cell carcinoma, especially early-stage glottic squamous cell carcinoma. Although there are several studies on the initiation weekday of cancer treatment, there are very few studies in the radiotherapy field. Thus, the present study investigated whether the initiation weekday of radiotherapy affects the local control rate for stage 1 glottic squamous cell carcinoma. A total of 105 patients with stage 1 glottic squamous cell carcinoma underwent definitive radiotherapy alone between 2007 and 2021. The group in which radiotherapy was started between Monday and Wednesday was compared with the group in which radiotherapy was started on Thursday or Friday. Sixty-seven patients started radiotherapy between Monday and Wednesday and 38 on Thursday or Friday. The 5-year local control rate was 98% (95% confidence interval: 94–100%) in the Monday–Wednesday group and 83% (95% confidence interval: 71–96%) in the Thursday–Friday group, with a significant difference (P = 0.005). On multivariate analysis including age, overall administration time (days), fractionation, irradiation field size and initiation weekday of radiotherapy, no factors other than initiation weekday affecting local control were identified. Radiotherapy toxicity did not differ between the two groups. For stage 1 glottic squamous cell carcinoma, starting radiotherapy on Thursday or Friday is associated with a lower local control rate; therefore, radiotherapy should be started by Wednesday.
Optimal risk-assessment scheduling for primary prevention of cardiovascular disease
Authors: Gasperoni Francesca , Jackson Christopher H , Wood Angela M , Sweeting Michael J , Newcombe Paul J , Stevens David , Barrett Jessica K 
Published: September 2024

Abstract
In this work, we introduce a personalized and age-specific net benefit function, composed of benefits and costs, to recommend optimal timing of risk assessments for cardiovascular disease (CVD) prevention. We extend the 2-stage landmarking model to estimate patient-specific CVD risk profiles, adjusting for time-varying covariates. We apply our model to data from the Clinical Practice Research Datalink, comprising primary care electronic health records from the UK. We find that people at lower risk could be recommended an optimal risk-assessment interval of 5 years or more. Time-varying risk factors are required to discriminate between more frequent schedules for high-risk people.
Gallstone ileus: report of two cases and a mini literature review
Authors: Gerasopoulos Georgios , Karagianni Foteini , Nikas Spyridon , Besikiaris Dimitrios , Veniadou Kalliopi , Chondri Maria , Routis Panagiotis , Zonitsa Sotiria , Sgouridi Despoina , Karaklas Aggelos 
Published: September 2024

Abstract
Gallstone ileus is a relatively rare complication of cholelithiasis, and an uncommon cause of small bowel obstruction most commonly seen in elderly and debilitated people with associated comorbidities. Symptoms of gallstone ileus are insidious and may be vague while the delay in diagnosis results in a high mortality rate. Herein we report two cases of gallstone ileus in elderly patients with complex medical history who presented at the emergency department with abdominal pain and distension, vomiting and fluid/electrolyte disorders due to cholecysto-enteric fistula and bowel obstruction.