bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of dietary supplementation with Bacillus velezensis on the growth performance, body composition, antioxidant, immune-related gene expression, and histology of Pacific white shrimp, Litopenaeus vannamei
Authors: Abdelsamad Arwa E. M. , Said Rashad E. M. , Assas Mona , Gaafar Alkhateib Y. , Hamouda Awatef H. , Mahdy Aldoushy 
Published: August 2024

AbstractIn recent decades, probiotics have become an acceptable aquaculture strategy for shrimp growth promotion and immune modulation. This study aimed to evaluate the effect of Bacillus velezensis on Litopenaeus vannamei following a 60-day trial. L. vannamei (3 ± 0.4 g) were distributed into four groups with three replicates per group and fed an isonitrogenous diet supplemented with B. velezensis at 0, 1 × 107, 1 × 108, and 1 × 109 CFU/g, which were defined as the control, G1, G2, and G3 groups, respectively. B. velezensis significantly improved the growth, survival rate, and proximate body composition of L. vannamei (P < 0.05). All groups fed the B. velezensis diet showed significant increases in digestive enzymes (lipase, amylase, and protease), superoxide dismutase (SOD; G3), catalase (CAT; G3, G2, and G1), lysozyme activity (G3 and G2), immunoglobulin M (IgM), bactericidal activity BA%, alkaline phosphatase (AKP), and acid phosphatase (ACP) compared with the control group (P < 0.05). Malondialdehyde (MDA), triglycerides, cholesterol, high-density lipoprotein (HDL), low-density lipoprotein (LDL), aspartate aminotransferase (AST), and alanine aminotransferase (ALT) levels were significantly decreased in all groups fed B. velezensis diet compared with the control group (P < 0.05). The expression levels of SOD (G3), LZM, and serine proteinase genes were significantly higher in L. vannamei fed diets containing B. velezensis than in the control group (P < 0.05). This is the first study to address the effects of B. velezensis on the expression of the LZM and serine proteinase genes in L. vannamei. L. vannamei fed diet containing B. velezensis had more B and R cells in its hepatopancreas than did the control group. In conclusion, B. velezensis is a promising probiotic that can be safely added to the diet of L. vannamei with 1 × 109 CFU/g. Its application had a positive influence on the health status, survival rate, nutritional value, and immunity of L. vannamei.
Benchmarking computational methods for single-cell chromatin data analysis
Authors: Luo Siyuan , Germain Pierre-Luc , Robinson Mark D. , von Meyenn Ferdinand 
Published: August 2024

Abstract
Background
Single-cell chromatin accessibility assays, such as scATAC-seq, are increasingly employed in individual and joint multi-omic profiling of single cells. As the accumulation of scATAC-seq and multi-omics datasets continue, challenges in analyzing such sparse, noisy, and high-dimensional data become pressing. Specifically, one challenge relates to optimizing the processing of chromatin-level measurements and efficiently extracting information to discern cellular heterogeneity. This is of critical importance, since the identification of cell types is a fundamental step in current single-cell data analysis practices.

Results
We benchmark 8 feature engineering pipelines derived from 5 recent methods to assess their ability to discover and discriminate cell types. By using 10 metrics calculated at the cell embedding, shared nearest neighbor graph, or partition levels, we evaluate the performance of each method at different data processing stages. This comprehensive approach allows us to thoroughly understand the strengths and weaknesses of each method and the influence of parameter selection.

Conclusions
Our analysis provides guidelines for choosing analysis methods for different datasets. Overall, feature aggregation, SnapATAC, and SnapATAC2 outperform latent semantic indexing-based methods. For datasets with complex cell-type structures, SnapATAC and SnapATAC2 are preferred. With large datasets, SnapATAC2 and ArchR are most scalable.
Towards an understanding of the ethics of electronic consent in clinical trials
Authors: Sahan Katherine , Wijesurendra Rohan , Preiss David , Mafham Marion , Sheehan Mark 
Published: August 2024

AbstractThere are good practical reasons to use electronic consent (e-consent) in randomised trials, especially when conducting large-scale clinical trials to answer population-level health research questions. However, determining ethical reasons for e-consent is not so clear and depends on a proper understanding of what e-consent means when used in clinical trials and its ethical significance. Here we focus on four features of ethical significance which give rise to a range of ethical considerations relating to e-consent and merit further focused ethics research.
Comparisons of magnetic resonance imaging, histopathological and Ki-67 labeling index findings in a single myxofibrosarcoma: a case report
Authors: Tsujimura Ryusuke , Uto Kenta , Nakano Noriyuki , Sato Yusuke , Kobashi Yuko , Kojima Toshio , Hao Hiroyuki 
Published: August 2024

Abstract
Background
Myxofibrosarcoma is a myxoid soft tissue sarcoma showing T2 high intensity on magnetic resonance imaging. However, myxofibrosarcoma is a heterogeneous sarcoma with both myxoid and cellular portions. Magnetic resonance imaging findings were obtained MRI findings for comparison with histological and Ki-67 immunohistochemical features, in different portions of one myxofibrosarcoma.

Case presentation
Magnetic resonance imaging observations were compared with gross pathological and microscopic findings of a myxofibrosarcoma from a 50-year-old Japanese female. The Ki-67 labeling indices of different portions of the tumor, that is, the myxoid, cellular, and histologically confirmed infiltrative margin portions (pathological tail sign), were compared. The T2 low intensity area was more cellular than the T2 high intensity area, while the cellular portion had a significantly higher Ki-67 index than the myxoid portion (p = 0.0313). The portions with the pathological tail sign had a significantly higher Ki-67 labeling index than those without this sign (p = 0.0313).

Conclusions
More cellular portions of a myxofibrosarcoma correspond to more areas of the tumor showing aggressive features. Furthermore, our data also support the hypothesis of high aggressiveness being associated with the pathological tail sign in myxofibrosarcoma. To our knowledge, this is the first case report to describe comparisons among the imaging findings, histological features, and Ki-67 immunohistochemistry results for different portions of one myxofibrosarcoma.
IQOS point-of-sale marketing: a comparison between Arab and Jewish neighborhoods in Israel
Authors: Khayat Amal , Levine Hagai , Berg Carla J. , Abroms Lorien C. , Duan Zongshuan , Wang Yan , LoParco Cassidy R. , Elbaz Daniel , Cui Yuxian , Bar-Zeev Yael 
Published: August 2024

Abstract
Background
Philip Morris International’s IQOS, with its heatsticks (HEETS), is the heated tobacco product with the largest global market share. IQOS and/or electronic cigarettes use rate is higher among Arabs vs. Jews in Israel. This paper aims to compare IQOS point-of-sale marketing strategies, and regulatory compliance in Arab vs. Jewish neighborhoods in Israel.

Methods
We integrated data from two separate studies including a cross-sectional survey with IQOS retailers (December 2020–April 2021) and audits of points-of-sale that sold IQOS/HEETS (April 2021–July 2021) in 5 large cities in Israel, after marketing restrictions including a points-of-sale display ban and plain packaging became effective in Israel (January 2020). The survey included 69 points-of-sale (21 Arab, 48 Jewish neighborhoods) and the audits included 129 points-of-sale (48 Arab, 81 Jewish neighborhoods). Comparisons of IQOS marketing strategies between points-of-sale in Arab and Jewish neighborhoods were conducted using Chi-Square test, Fisher’s exact test or Mann–Whitney test, as appropriate. Thematic analysis was used to analyze open-ended questions.

Results
The survey showed that most marketing strategies, such as promotions to customers, were uniform across points-of-sale in Arab and Jewish neighborhoods. The most noteworthy differences were that a higher proportion of retailers from Arab neighborhoods were invited to IQOS parties (47.6% vs. 21.7%, p < 0.05) and reported personal communication with a Philip Morris International’s representative (80.0% vs. 51.2%, p < 0.05). Additionally, Philip Morris International’s representatives assisted points-of-sale in both Arab and Jewish neighborhoods in implementing the display ban by providing free compliant cabinets and product placement instructions, and directly interacted with customers. The audits showed that points-of-sale in Arab neighborhoods were more compliant with the display ban (25.5% vs. 8.8%, p < 0.05), but less compliant with plain packaging (62.5% vs. 79.3%, p < 0.05).

Conclusions
There were not many notable differences in IQOS marketing across points-of-sale in Arab vs. Jewish neighborhoods, but Philip Morris International utilized marketing elements of cultural significance, especially for points-of-sale in Arab neighborhoods, such as more personal communication and invitation to social events. Continuous surveillance of tobacco points-of-sale marketing and legislation compliance is needed, with a special focus on demographic/location-based differences.
Mental health apps within the healthcare system: associations with stigma and mental health literacy
Authors: Fürtjes Sophia , Al-Assad Mariam , Kische Hanna , Beesdo-Baum Katja 
Published: August 2024

AbstractBackgroundMental health apps (MHA) as a new form of self-help have gained popularity over the last years. Tentative evidence has suggested that MHA might also present a first step into the help-seeking process, because their anonymity circumvents stigma. Using MHA might also increase mental health literacy and reduce stigma through psychoeducation, which could encourage formal help-seeking. To date, it remains unclear how MHA usage relates to stigma, mental health literacy, and utilization of professional help within the public healthcare system.MethodsWe conducted a cross-sectional survey withN = 1,263 individuals from the general population (mean age 32.56 ± 11.51, 58.2% female) and employed structural equation modeling to investigate associations between stigma (against individuals with psychological disorders and against help-seeking), mental health literacy, MHA usage, and service utilization within the public healthcare system for mental health problems.ResultsMHA usage is high within the general population (40.5% of participants). Results indicate that higher stigma against help-seeking is associated with and increased likelihood of MHA usage, which in turn is positively associated with increased likelihood of service utilization. Symptoms of psychological disorder were associated with higher likelihood of service utilization, but not MHA usage.ConclusionsIt can be concluded that MHA appeal especially to individuals with higher stigma against help-seeking and therefore might provide an opportunity to reach underserviced individuals. At the current time, MHA usage appears to take place mostly in a preventative manner or as a supplement to treatment. Better integration into the public healthcare system might help to exploit both preventative and interventional benefits of MHA.
Transcriptomic changes reveal hypoxic stress response in submerged seeds of maize (Zea mays L.)
Authors: Kim Ji Won , Hong Seongmin , Go Jiyun , Park Jin Seong , Yi Gibum 
Published: August 2024

AbstractMaize is highly sensitive to waterlogging stress, and seeds fail to germinate under hypoxic conditions induced by submergence, leading to severe yield losses. We conducted a comparative transcriptome analysis during the initial stages of seed germination, exploring aerobic and hypoxic conditions in two inbred lines, B73 and Okcheon Chal-1. Notably, significant differences emerged between aerobic and hypoxic conditions on the first day of germination, particularly in genes associated with fermentation and phytohormone regulation. However, consistent transcriptomic changes were observed in primary metabolic pathways such as glycolysis, the TCA cycle, and the pentose phosphate pathway. These differences strongly correlate with each other, illustrating the efficacy of the hypoxic response for survival in water. Furthermore, this suggests that germinating seeds serve as a promising model for studying plant hypoxia responses with controlled environmental conditions. Insights from this study contribute to understanding the fundamental mechanisms of hypoxia response and hold promise for developing strategies to cultivate waterlogging-tolerant maize cultivars.
Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn’s disease development
Authors: Luo Wanrong , Zhao Min , Dwidar Mohammed , Gao Yang , Xiang Liyuan , Wu Xueting , Medema Marnix H. , Xu Shu , Li Xiaozhi , Schäfer Hendrik , Chen Minhu , Feng Rui , Zhu Yijun 
Published: August 2024

Abstract
Background
H2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota.

Results
Our analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants ∆cysJ and ∆cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives.

Conclusions
Our study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD.
B cell academy of the gut: an update on gut associated germinal centre B cell dynamics
Authors: Wichmann Christopher , Wirthgen Elisa , Nowosad Carla R. , Däbritz Jan 
Published: August 2024

Abstract
Background
The gut is an environment in which the immune system closely interacts with a vast number of foreign antigens, both inert such as food and alive, from the viral, bacterial, fungal and protozoal microbiota. Within this environment, germinal centres, which are microanatomical structures where B cells affinity-mature, are chronically present and active.

Main Body
The functional mechanism by which gut-associated germinal centres contribute to gut homeostasis is not well understood. Additionally, the role of T cells in class switching to immunoglobulin A and the importance of B cell affinity maturation in homeostasis remains elusive. Here, we provide a brief overview of the dynamics of gut-associated germinal centres, T cell dependency in Immunoglobulin A class switching, and the current state of research regarding the role of B cell selection in germinal centres in the gut under steady-state conditions in gnotobiotic mouse models and complex microbiota, as well as in response to immunization and microbial colonization. Furthermore, we briefly link those processes to immune system maturation and relevant diseases.

Conclusion
B cell response at mucosal surfaces consists of a delicate interplay of many dynamic factors, including the microbiota and continuous B cell influx. The rapid turnover within gut-associated germinal centres and potential influences of an early-life window of immune system imprinting complicate B cell dynamics in the gut.
Internet of things and ensemble learning-based mental and physical fatigue monitoring for smart construction sites
Authors: Kim Bubryur , Sri Preethaa K. R. , Song Sujeen , Lukacs R. R. , An Jinwoo , Chen Zengshun , An Euijung , Kim Sungho 
Published: August 2024

AbstractThe construction industry substantially contributes to the economic growth of a country. However, it records a large number of workplace injuries and fatalities annually due to its hesitant adoption of automated safety monitoring systems. To address this critical concern, this study presents a real-time monitoring approach that uses the Internet of Things and ensemble learning. This study leverages wearable sensor technology, such as photoplethysmography and electroencephalography sensors, to continuously track the physiological parameters of construction workers. The sensor data is processed using an ensemble learning approach called the ChronoEnsemble Fatigue Analysis System (CEFAS), comprising deep autoregressive and temporal fusion transformer models, to accurately predict potential physical and mental fatigue. Comprehensive evaluation metrics, including mean square error, mean absolute scaled error, and symmetric mean absolute percentage error, demonstrated the superior prediction accuracy and reliability of the proposed model compared to standalone models. The ensemble learning model exhibited remarkable precision in predicting physical and mental fatigue, as evidenced by the mean square errors of 0.0008 and 0.0033, respectively. The proposed model promptly recognizes potential hazards and irregularities, considerably enhancing worker safety and reducing on-site risks.
A pilot feasibility study comparing large language models in extracting key information from ICU patient text records from an Irish population
Authors: Urquhart Emma , Ryan John , Hartigan Sean , Nita Ciprian , Hanley Ciara , Moran Peter , Bates John , Jooste Rachel , Judge Conor , Laffey John G. , Madden Michael G. , McNicholas Bairbre A. 
Published: August 2024

Abstract
Background
Artificial intelligence, through improved data management and automated summarisation, has the potential to enhance intensive care unit (ICU) care. Large language models (LLMs) can interrogate and summarise large volumes of medical notes to create succinct discharge summaries. In this study, we aim to investigate the potential of LLMs to accurately and concisely synthesise ICU discharge summaries.

Methods
Anonymised clinical notes from ICU admissions were used to train and validate a prompting structure in three separate LLMs (ChatGPT, GPT-4 API and Llama 2) to generate concise clinical summaries. Summaries were adjudicated by staff intensivists on ability to identify and appropriately order a pre-defined list of important clinical events as well as readability, organisation, succinctness, and overall rank.

Results
In the development phase, text from five ICU episodes was used to develop a series of prompts to best capture clinical summaries. In the testing phase, a summary produced by each LLM from an additional six ICU episodes was utilised for evaluation. Overall ability to identify a pre-defined list of important clinical events in the summary was 41.5 ± 15.2% for GPT-4 API, 19.2 ± 20.9% for ChatGPT and 16.5 ± 14.1% for Llama2 (p = 0.002). GPT-4 API followed by ChatGPT had the highest score to appropriately order a pre-defined list of important clinical events in the summary as well as readability, organisation, succinctness, and overall rank, whilst Llama2 scored lowest for all. GPT-4 API produced minor hallucinations, which were not present in the other models.

Conclusion
Differences exist in large language model performance in readability, organisation, succinctness, and sequencing of clinical events compared to others. All encountered issues with narrative coherence and omitted key clinical data and only moderately captured all clinically meaningful data in the correct order. However, these technologies suggest future potential for creating succinct discharge summaries.
Successful pancreatectomy after conversion-intended chemotherapy using gemcitabine and nab-paclitaxel for unresectable adenosquamous carcinoma of the pancreas: a case report
Authors: Nakamura Kenichi , Nakagawa Mitsuru , Ariga Mizuki , Higashiguchi Takahiko , Chikaishi Yuko , Matsuo Kazuhiro , Nishijima Aki , Endo Tomoyoshi , Kikuchi Kenji , Morohara Koji , Katsuno Hidetoshi , Tachi Yoshihiko , Uyama Ichiro , Suda Koichi , Morise Zenichi 
Published: August 2024

Abstract
Background
Adenosquamous carcinoma of the pancreas (ASCP) accounts for only 1–4% of all pancreatic exocrine cancers and has a particularly poor prognosis. The efficacy of chemotherapy for ASCP remains unknown because of the small number of cases, and few studies have evaluated conversion-intended chemotherapy.

Case presentation
A 76-year-old woman was referred to our hospital because of epigastric pain and nausea. A preoperative contrast-enhanced multidetector row computed tomography (MDCT) scan revealed a 17 × 17 mm low-density tumor with an ill-defined margin at the arterial phase in the pancreatic head. The tumor involved the common hepatic artery, left hepatic artery bifurcated from the common hepatic artery, and gastroduodenal artery, and was in contact with the portal vein. Fluorodeoxyglucose-positron emission tomography (FDG-PET) showed an uptake in the pancreatic head but no evidence of distant metastasis. The tumor was diagnosed as an adenocarcinoma of the pancreatic head and staged unresectable because the common and left hepatic arteries were involved. Hence, the patient underwent seven courses of conversion-intended chemotherapy using gemcitabine and nab-paclitaxel for pancreatic ductal adenocarcinoma over 7 months. After chemotherapy, the tumor shrank to 10 × 10 mm on contrast-enhanced MDCT. Consequently, the boundary between the tumor and major vessels of the common and left hepatic arteries and the portal vein became clear, and the involvement of the arteries with the tumor was evaluated to be released. The contact of the tumor to the portal vein also reduced to less than half the circumference of the portal vein. FDG-PET showed decreased accumulation in the tumor. Hence, the tumor was judged resectable, and pancreaticoduodenectomy was performed. The tumor and major blood vessels were easily dissected and R0 resection was achieved. The patient experienced no major complications and was discharged on postoperative day 28. The tumor was revealed as ASCP via pathological examination. The patient is alive and recurrence-free seven months after surgery. This is the first report of successful R0 resection for an initially unresectable ASCP following conversion-intended chemotherapy using gemcitabine and nab-paclitaxel regimen.

Conclusions
Conversion-intended chemotherapy using gemcitabine and nab-paclitaxel regimen may be effective for ASCP.