bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel artificial intelligence network to assess the prognosis of gastrointestinal cancer to immunotherapy based on genetic mutation features
Authors: Ye Bicheng , Li Zhongyan , Wang Qiqi 
Published: June 2024

BackgroundImmune checkpoint inhibitors (ICIs) have revolutionized gastrointestinal cancer treatment, yet the absence of reliable biomarkers hampers precise patient response prediction.MethodsWe developed and validated a genomic mutation signature (GMS) employing a novel artificial intelligence network to forecast the prognosis of gastrointestinal cancer patients undergoing ICIs therapy. Subsequently, we explored the underlying immune landscapes across different subtypes using multiomics data. Finally, UMI-77 was pinpointed through the analysis of drug sensitization data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. The sensitivity of UMI-77 to the AGS and MKN45 cell lines was evaluated using the cell counting kit-8 (CCK8) assay and the plate clone formation assay.ResultsUsing the artificial intelligence network, we developed the GMS that independently predicts the prognosis of gastrointestinal cancer patients. The GMS demonstrated consistent performance across three public cohorts and exhibited high sensitivity and specificity for 6, 12, and 24-month overall survival (OS) in receiver operating characteristic (ROC) curve analysis. It outperformed conventional clinical and molecular features. Low-risk samples showed a higher presence of cytolytic immune cells and enhanced immunogenic potential compared to high-risk samples. Additionally, we identified the small molecule compound UMI-77. The half-maximal inhibitory concentration (IC50) of UMI-77 was inversely related to the GMS. Notably, the AGS cell line, classified as high-risk, displayed greater sensitivity to UMI-77, whereas the MKN45 cell line, classified as low-risk, showed less sensitivity.ConclusionThe GMS developed here can reliably predict survival benefit for gastrointestinal cancer patients on ICIs therapy.
Prognostic prediction and comparison of three staging programs for patients with advanced (T2-T4) esophageal squamous carcinoma after radical resection
Authors: Wang Zhongshuai , Li Feng , Zhu Mingchuang , Lu Tao , Wen Linqi , Yang Shengzhao , Zhuang Xiaofei , Zhang Shuangping , Ma Yong , Lian Jianhong 
Published: June 2024

PurposeLymph node-based staging protocols are frequently employed to evaluate the prognosis of esophageal cancer, yet their accuracy remains contentious. The present study was conducted to assess the prognostic significance of three lymph node staging systems, namely N stage, lymph node rate (LNR), and log odds of positive lymph nodes (LODDS), in patients diagnosed with advanced (T2-T4) esophageal squamous cell carcinoma (ESCC).MethodsThis cohort comprised 319 eligible patients, with an additional 409 individuals retrieved from the Surveillance, Epidemiology, and End Results (SEER) database, forming the validation cohort. Differences in overall survival (OS) of patients between groups were assessed using the log-rank test. Prognostic independent risk variables were identified, and lymph nodes (LN) prognostic models were built using multivariate Cox regression analysis. Besides, the predictive accuracy of each model was evaluated utilizing the (-2) log-likelihood ratio (-2LLR), the likelihood ratio χ2 score (LRχ2), the Akaike information criterion (AIC), and Harrell’s concordance index (C-index). To further evaluate the potential superiority of the model, a nomogram was constructed for comparison with the conventional Tumor Node Metastasis (TNM) staging approach.ResultsIndependent prognostic factors for advanced ESCC include the N stage, LNR, and LODDS. Herein, LODDS presented higher values for C-index and LRχ2, and lower values for AIC and -2LLR in OS compared to the others. Consequently, a nomogram was constructed based on LODDS. Calibration curves exhibited strong agreement, and assessment through C-index, receiver operating characteristic (ROC) curves, and clinical decision curve analysis (DCA) demonstrated promising clinical applicability.ConclusionLODDS emerges as a promising future prognostic indicator. After surgery, the proposed model holds the potential to provide valuable treatment recommendations for patients with advanced ESCC.
Value of intralesional and perilesional radiomics for predicting the bioactivity of hepatic alveolar echinococcosis
Authors: Zhang Simiao , Hou Juan , Xia Wenwen , Zhao Zicheng , Xu Min , Li Shouxian , Xu Chunhui , Zhang Tieliang , Liu Wenya 
Published: June 2024

ObjectivesTo investigate the value of intralesional and perilesional radiomics based on computed tomography (CT) in predicting the bioactivity of hepatic alveolar echinococcosis (HAE).Materials and methodsIn this retrospective study, 131 patients who underwent surgical resection and diagnosed HAE in pathology were included (bioactive, n=69; bioinactive, n=62). All patients were randomly assigned to the training cohort (n=78) and validation cohort (n=53) in a 6:4 ratio. The gross lesion volume (GLV), perilesional volume (PLV), and gross combined perilesional volume (GPLV) radiomics features were extracted on CT images of portal vein phase. Feature selection was performed by intra-class correlation coefficient (ICC), univariate analysis, and least absolute shrinkage and selection operator (LASSO). Radiomics models were established by support vector machine (SVM). The Radscore of the best radiomics model and clinical independent predictors were combined to establish a clinical radiomics nomogram. Receiver operating characteristic curve (ROC) and decision curves were used to evaluate the predictive performance of the nomogram model.ResultsIn the training cohort, the area under the ROC curve (AUC) of the GLV, PLV, and GPLV radiomic models was 0.774, 0.729, and 0.868, respectively. GPLV radiomic models performed best among the three models in training and validation cohort. Calcification type and fibrinogen were clinical independent predictors (p&lt;0.05). The AUC of the nomogram-model-based clinical and GPLV radiomic signatures was 0.914 in the training cohort and 0.833 in the validation cohort. The decision curve analysis showed that the nomogram had greater benefits compared with the single radiomics model or clinical model.ConclusionThe nomogram model based on clinical and GPLV radiomic signatures shows the best performance in prediction of the bioactivity of HAE. Radiomics including perilesional tissue can significantly improve the prediction efficacy of HAE bioactivity.
Global prevalence of norovirus gastroenteritis after emergence of the GII.4 Sydney 2012 variant: a systematic review and meta-analysis
Authors: Zhang Pan , Hao Cai , Di Xie , Chuizhao Xue , Jinsong Li , Guisen Zheng , Hui Liu , Zhaojun Duan 
Published: June 2024

IntroductionNorovirus is widely recognized as a leading cause of both sporadic cases and outbreaks of acute gastroenteritis (AGE) across all age groups. The GII.4 Sydney 2012 variant has consistently prevailed since 2012, distinguishing itself from other variants that typically circulate for a period of 2–4 years.ObjectiveThis review aims to systematically summarize the prevalence of norovirus gastroenteritis following emergence of the GII.4 Sydney 2012 variant.MethodsData were collected from PubMed, Embase, Web of Science, and Cochrane databases spanning the period between January 2012 and August 2022. A meta-analysis was conducted to investigate the global prevalence and distribution patterns of norovirus gastroenteritis from 2012 to 2022.ResultsThe global pooled prevalence of norovirus gastroenteritis was determined to be 19.04% (16.66–21.42%) based on a comprehensive analysis of 70 studies, which included a total of 85,798 sporadic cases with acute gastroenteritis and identified 15,089 positive cases for norovirus. The prevalence rate is higher in winter than other seasons, and there are great differences among countries and age groups. The pooled attack rate of norovirus infection is estimated to be 36.89% (95% CI, 36.24–37.55%), based on a sample of 6,992 individuals who tested positive for norovirus out of a total population of 17,958 individuals exposed during outbreak events.ConclusionThe global prevalence of norovirus gastroenteritis is always high, necessitating an increased emphasis on prevention and control strategies with vaccine development for this infectious disease, particularly among the children under 5 years old and the geriatric population (individuals over 60 years old).
Trends in socioeconomic inequalities in life expectancy and lifespan variation in Chile
Authors: Silva-Illanes Nicolas 
Published: June 2024

BackgroundSocioeconomic disparities in life expectancy are well-documented in various contexts, including Chile. However, there is a lack of research examining trends in life expectancy inequalities and lifespan variation over time. Addressing these gaps can provide crucial insights into the dynamics of health inequalities.MethodsThis study utilizes data from census records, population surveys, and death certificates to compare the life expectancy and the lifespan variation at age 26 of individuals according to their rank in the distribution of years of education within their own birth cohort. The analysis spans three periods (1991, 2002, and 2017) and focuses on two educational groups: individuals in the first (lowest) quintile and tenth (highest) decile of educational attainment. Changes in life expectancy are disaggregated by major causes of death to elucidate their contributions to overall trends.ResultsConsistent with existing literature, our findings confirm that individuals with lower education levels experience lower life expectancy and higher lifespan variation compared to their more educated counterparts. Notably, by 2017, life expectancy for individuals in the lowest quintile of education has caught up with that of the top decile in 1991, albeit with contrasting trends between genders. Among women, the gap has reduced, while it has increased for males. Moreover, lifespan variation decreased (increased) over time for individuals in the tenth decile (first quintile). The leading causes of death that explain the increase in life expectancy in women and men in the tenth decile as well as women in the first quintile are cardiovascular, cancer, respiratory and digestive diseases. In the case of males in the first quintile, few gains have been made in life expectancy resulting from cancer and a negative contribution is associated with digestive conditions.ConclusionsThis study underscores persistent socioeconomic disparities in life expectancy in Chile, emphasizing the importance of ongoing monitoring of health inequalities across different demographic segments. The gender-specific and educational gradient trends highlight areas for targeted interventions aimed at reducing health disparities and improving overall population health outcomes. Further research is warranted to delve into specific causes of death driving life expectancy differentials and to inform evidence-based policy interventions.
Observation and modeling of an unusual spatiotemporal pattern in bioacoustic chorusing
Authors: D’Spain Gerald L. , Rovner Galina L. , Batchelor Heidi , Rimington Dennis B. 
Published: June 2024

This paper describes an unusual underwater biological chorus recorded in the Southern California Bight and presents a numerical modeling approach that replicates aspects of the chorus. During one experiment, the evolution of the directionality of the chorusing region over time is suggestive of “The Wave”, the human waves performed by fans periodically standing and sitting in sports stadia around the world; here, the region of chorusing periodically propagated upcoast over 20 km of coastline at nearly 1.5 km/s. The chorus occurs predominantly at night in spring and summer, mostly in very shallow waters near the coast. It increases the underwater sound field levels within chorusing regions by 20–30 dB in the 50 Hz to 1 kHz frequency band. The chorus is composed of three parts; 1) a “sunset chorus” which is a 20-to-30 min continuous roar around sunset with received spectral levels up to 100 dB re 1 μPa2/Hz, 2) a “sunrise chorus” of lower level than the sunset chorus, and 3) an all-night-long cycling chorus. The cycling portion is made up of 15-to-20 s periods of higher received spectral levels (up to 90 dB re 1 μPa2/Hz within the chorusing region) each followed by a 10-to-20 s lull in which the spectral levels drop by 4–10 dB. This alternating pattern repeats every 30–40 s throughout the night. The numerical modeling approach is based on the physics of excitable media. A cellular automaton is used to model the two-dimensional spatial grid occupied by the calling animals (units), with each unit being either in the “resting”, “excitable”, or “active (calling)" state at each time step. Transition from resting to excitable and from active back to resting occurs automatically after a fixed period of time in the present state, whereas the probability of transitioning from excitable to active is determined not only by the elapsed time since entering the excitable state, but also by the received sound level at the unit location, creating a non-linear acoustics-based coupling between units. With appropriate inputs, many determined from measurements of the chorus properties and the individual animal calls themselves, simulations with the model can replicate the cycling levels in the night-long chorus, the continuous din of the sunset chorus, and (once properly initialized) the periodic upcoast evolution of the chorusing region (“The Wave”). When noise from a transiting ship is included in the simulations, the spatiotemporal characteristics of the chorus change appreciably, in ways similar to changes observed during the experiment.
Evaluating microbiological safety and associated handling practices of butchery-sold meat in Nairobi, Kenya
Authors: Koech Patricia Cherotich , Ogutu Winnie Aketch , Ochieng Linnet , Grace Delia , Gitao George , Bebora Lilly , Korir Max , Mutua Florence , Moodley Arshnee 
Published: June 2024

IntroductionApproximately 70% of diarrheal cases in Kenya are attributed to ingestion of contaminated food and water and costs an estimated $ 1 billion USD due to morbidity and cost of treatment. This study aimed to assess the levels of microbiological contamination of meat sold in selected butcheries in Nairobi and the handling practices of butcher shop attendants.MethodsA cross-sectional study design was used during which 200 meat samples were collected, and meat handling practices were observed. Total coliforms and Escherichia coli were enumerated using 3M™ Petrifilm® count plates. Additionally, quantification of tetracycline- and cefotaxime-resistant Enterobacteriaceae was done on agar plates containing the respective antibiotics. Bacterial species were confirmed by Matrix-Assisted Laser Desorption/Ionization-Time of Flight mass spectrometry.Results and discussionSeventy two percent and 84% of the samples had E. coli and total coliforms respectively above the acceptable regulatory limits (i.e. E. coli &gt;100 CFU/g, Total coliforms &gt;361 CFU/g,) respectively as per the Kenya Bureau of Standards South African microbiological standards the European Union. Enterobacteriaceae resistant to tetracycline and cefotaxime were detected in 35% and 9.5% of the samples respectively. Eighty-five percent of the butcher shop attendants neither washed their hands before nor after handling the meat, 91% handled money while selling meat concurrently, and 99% did not wear gloves while handling meat. These poor meat handling practices coupled with the presence of microbial loads above the regulatory acceptable limits imply an increased risk of foodborne illness to consumers. Therefore, there is an urgent need for education of butcher shop attendants on appropriate handling of meat, highlighting the importance of good hygienic practices and their relationship to food safety, and provision of incentives for behavior change. This study is important and serves to inform policymakers in the identification of key control points for designing meat safety intervention(s).
Exploring positive welfare measures: preliminary findings from a prototype protocol in loose housing dairy cattle farms
Authors: Mattiello Silvana , Celozzi Stefania , Soli Federica Manila , Battini Monica 
Published: June 2024

IntroductionFollowing the increasing interest about the development of indicators of positive welfare and affective state in farm animals, the aim of this research is to present some preliminary results on the application of a prototype protocol based exclusively on positive welfare measures and to suggest potential benefits that can promote positive welfare.MethodsThe protocol was applied in 20 loose housing dairy cattle farms (6 on deep litter with straw, 14 in cubicles) and included only indicators of positive welfare and emotional states: feeding and resting synchronization, rumination during resting, comfortable lying postures, no visible eye white, relaxed ear postures, percentage of cow contacts with humans in the Avoidance Distance test. Potential benefits in terms of housing, feeding and management were then related to these variables (Mann-Whitney U test). Qualitative Behavior Assessment (QBA) was also carried out and analyzed by Principal Component Analysis to explore the effect of factors that were not evenly distributed in our sample (number of feed distributions, access to pasture, presence of paddock or environmental enrichments, automatic milking systems).ResultsWhen hay was included in the diet, higher feeding synchronization (93.7 ± 1.6 vs. 52.2 ± 4.7%; p &lt; 0.01), percentage of cows with relaxed ear postures (35.8 ± 5.4 vs. 15.5 ± 2.1%; p &lt; 0.01) and percentage of cows with no visible eye white (55.9 ± 17.0 vs. 36.6 ± 4.1%; n.s.) were recorded. A higher level of feeding synchronization was observed also when the feeding places/cow ratio was &gt; 1 (72.1 ± 9.9 vs. 53.8 ± 5.8%), although differences were not significant (p = 0.14). Deep litter had a more positive effect than cubicles on comfort at resting, with a significantly higher percentage of ruminating cows (65.8 ± 10.2 vs. 34.2 ± 3.7%; p &lt; 0.01), a higher percentage of cows with no visible eye white (55.6 ± 9.9 vs. 33.1 ± 3.7%; p &lt; 0.05) and a higher percentage of cows in a more comfortable posture, with stretched legs (14.3 ± 5.1 vs. 5.6 ± 1.6%; p = 0.09). QBA highlighted the most positive emotional state in the only farm that allowed access to pasture.ConclusionsThis study represents a first attempt to apply a protocol for on-farm welfare evaluation based exclusively on the use of positive welfare indicators and provides suggestions on possible benefits (e.g., deep litter, feeding places/cow ratio &gt; 1, hay in the diet and access to pasture) to enhance dairy cattle welfare.
Zoonotic pathogens in wild Asian primates: a systematic review highlighting research gaps
Authors: Patouillat Laurie , Hambuckers Alain , Adi Subrata Sena , Garigliany Mutien , Brotcorne Fany 
Published: June 2024

IntroductionOngoing global changes, including natural land conversion for agriculture and urbanization, modify the dynamics of human–primate contacts, resulting in increased zoonotic risks. Although Asia shelters high primate diversity and experiences rapid expansion of human–primate contact zones, there remains little documentation regarding zoonotic surveillance in the primates of this region.MethodsUsing the PRISMA guidelines, we conducted a systematic review to compile an inventory of zoonotic pathogens detected in wild Asian primates, while highlighting the coverage of primate species, countries, and pathogen groups surveyed, as well as the diagnostic methods used across the studies. Moreover, we compared the species richness of pathogens harbored by primates across diverse types of habitats classified according to their degree of anthropization (i.e., urban vs. rural vs. forest habitats).Results and discussionSearches of Scopus, PubMed, and the Global Mammal Parasite Database yielded 152 articles on 39 primate species. We inventoried 183 pathogens, including 63 helminthic gastrointestinal parasites, two blood-borne parasites, 42 protozoa, 45 viruses, 30 bacteria, and one fungus. Considering each study as a sample, species accumulation curves revealed no significant differences in specific richness between habitat types for any of the pathogen groups analyzed. This is likely due to the insufficient sampling effort (i.e., a limited number of studies), which prevents drawing conclusive findings. This systematic review identified several publication biases, particularly the uneven representation of host species and pathogen groups studied, as well as a lack of use of generic diagnostic methods. Addressing these gaps necessitates a multidisciplinary strategy framed in a One Health approach, which may facilitate a broader inventory of pathogens and ultimately limit the risk of cross-species transmission at the human–primate interface. Strengthening the zoonotic surveillance in primates of this region could be realized notably through the application of more comprehensive diagnostic techniques such as broad-spectrum analyses without a priori selection.
Characterization of Lectin from Bauhinia holophylla Using Bioinformatics Tools
Authors: Camargos Ludmila Maria Gonçalves Godoi de , Lopes Débora de Oliveira , Castro Ana Hortência Fonseca 
Published: June 2024

Lectins are proteins of a non-immune nature with activity against microorganisms, insects, and tumor cells. The aim of this work was to predict the physicochemical characteristics, structure, and functional properties of a Bauhinia holophylla lectin (BhL), sequenced from genomic material obtained from calli cultures, through bioinformatics tools. The results showed a high similarity between the Bhl gene and nucleotide sequences that encode lectins expressed by Bauhinia species and a high identity between the protein sequence of BhL and lectins from B. forficata (90%), B. variegata (79.04%), B. purpurea (78.01%), and B. ungulata (85.27%). BhL has 289 amino acids, of which 30, 85, and 174 residues are related to α-helix, β-sheet, and disordered regions, respectively. Their estimated molecular weight is 31.9 kDa and the theoretical isoelectric point is 5.79. Bauhinia holophylla lectin possibly undergoes phosphorylation and glycosylation at specific sites. Conserved protein domains, catalytic sites, and conserved amino acids were observed in BhL, bringing it closer to lectin families from other legume species. The prediction signaled the presence of a sequence of 28 amino acids at the N-terminal end of BhL, with a high hydropathicity index and conceptualized as a signal peptide. The molecular function predicted for BhL was associated with carbohydrate recognition activity. BhL could be an extracellular protein, and its three-dimensional structure showed 78.82% identity with the B. purpurea lectin.