bluuebunny/crossref_metadata_2025 huggingface dataset:
Discrimination and health: A cross-sectional study comparing Muslims with other-religious
Authors: Ishaq Bushra , Diaz Esperanza , Østby Lars
Published: March 2024

Aims:

The aim of this study is to report perceived discrimination among Muslims living in Norway and to address and compare associations between perceived discrimination and health among Muslims with an immigrant background and other-religious with an immigrant background.

Method:

A representative sample of individuals with an immigrant background in Norway was used in a cross-sectional study design that included 5484 respondents aged 16 to 74 years. The respondents were sub-grouped after religious affiliation, and as immigrants and Norwegian-born. This sample is from ‘The Survey on living conditions among persons with an immigrant background 2016’, conducted by Statistics Norway. Multivariate logistic regression analyses were conducted to investigate the relationship between perceived discrimination and self-rated health and between perceived discrimination and mental health problems.

Results:

Our findings show that Muslims with an immigrant background are more likely to report perceived discrimination than non-Muslims with an immigrant background. Perceived discrimination was associated with poor self-rated health and mental health problems among immigrant Muslims and Norwegian-born Muslims. Among other-religious with an immigrant background, perceived discrimination had an inverse relationship with mental health problems among immigrants, while an association between perceived discrimination and poor self-rated health was found among Norwegian-born.

Conclusions:

Our findings suggest that perceived discrimination does play a role in health among minorities with an immigrant background in Norway, regardless of religion. However, the association between perceived discrimination and poor health seems to be stronger among Muslims, especially Norwegian-born Muslims.
Warming up to Arctic shipping: Unique risk management challenges for marine insurers
Authors: Rebelo Pia , Uchenna Amaefule Cyril
Published: March 2024

Due to diminishing ice shelves in the Arctic, no doubt caused by climate change, previously unnavigable marine spaces are opening up, which in turn may provide new maritime routes. The shipping and maritime industry may capitalise on these routes more in the future as they provide shorter sailing times, and may assist with increasing oil and gas exploration and extraction in the region. However, increased maritime expansion in the Arctic comes with a number of unique risks and hazards for the insured and insurer. This opinion therefore seeks to discuss the implications of the multitude of risks that are associated with Arctic shipping from a marine insurance perspective and to highlight some of the gaps in existing regulatory frameworks. It is argued that marine insurers require improved data and risk management methodologies in order to better calculate the premiums of Hull & Machinery (H&M) and Protection & Indemnity (P&I) insurance policies for ships travelling through the Arctic. Until such time as these risks can be adequately assessed, evaluated, and managed by insurers; which of course is extremely difficult, due to the extreme environment, the unpredictability of climate change, a lack of key data, and the complexity of the various scenarios that can unfold in the Arctic environment, the practical viability of Arctic shipping remains doubtful. To date, insurers have paid out more in ship damage that has occurred in the Arctic than they have collected in premiums, which in itself is problematic. This situation may change in the future if Arctic shipping grows, and if it does the insurance market will no doubt, need to respond.
Vision-based detection of bolt tension considering non-rotatory loosening via a new calculation method of bolt flexibility coefficient
Authors: Zhao Yong , Lin Qingyuan , Liu Yuming , Pan Wei
Published: March 2024

Bolted joint is widely used in construction, vehicle, aerospace, and other engineering fields. Bolt tension is the most important performance index of bolted joints. The whole life cycle monitoring of bolt tension without contact and damage can be realized by vision-based method. The existing methods indirectly predict the change of bolt tension by calculating the rotary angle of the nut. This kind of method can judge the loosening caused by nut rotation but cannot deal with the non-rotary loosening. At the same time, the relationship between nut rotation angle and loosening must be obtained through calibration experiments. This paper proposes a vision-based method to measure the change of bolt tension considering the non-rotary loosening by detecting the change of bolt elongation. Based on VDI2230 and finite element analysis, a new calculation method of bolt flexibility coefficient is proposed. The experimental results show that this method can measure the change of bolt tension with high precision in the process of tightening and loosening.
Considering the sensory and social needs of disabled students in higher education: A call to return to the roots of universal design
Authors: Creaven Ann-Marie
Published: March 2024

Universal Design for Learning is a pedagogical approach that aims ‘to improve and optimize teaching and learning for all people based on scientific insights into how humans learn’ (CAST website, n.d.). Originating in the context of K12 education in the United States, the core principles involve the provision of multiple means of representation, engagement, and action/expression. Despite high instructor satisfaction with UDL, evidence of effectiveness for students’ learning is insufficient. Effectiveness aside, the purpose of this policy research note is to describe additional issues in UDL specifically relating to disabled students. First, I argue that the core tenet of UDL to meet all learners’ needs by emphasizing variability in approaches to learning (and consequently avoiding reference to ‘disability’) may inadvertently marginalize disabled students. Second, I argue that the focus on instructional design as a panacea to meet the needs of ‘all people’, including disabled students, is insufficient. This potentially distracts well-intentioned educators from more substantive challenges experienced by disabled students, relating to the built environment. Until the sensory and social needs of disabled students are met, instructional approaches like UDL cannot provide an equitable learning experience for many disabled students. Therefore, I argue that higher education leaders should attend to the sensory and social environments of university campuses before retrofitting inclusive pedagogies to the current typical university campus.
Associations Between Health Behaviors, Gastrointestinal Symptoms, and Gut Microbiota in a Cross-Sectional Sample of Cancer Survivors: Secondary Analysis from the Chemo-Gut Study
Authors: Deleemans Julie M. , Chleilat Faye , Reimer Raylene A. , Lawal Oluwaseyi A. , Baydoun Mohamad , Piedalue Katherine-Ann , Lowry Dana E. , Carlson Linda E.
Published: March 2024

Background:

Health behaviors, such as diet and exercise, are actions individuals take that can potentially impact gastrointestinal (GI) symptoms and the gut microbiota. Little is known about how health behaviors impact GI symptoms and the gut microbiota after anti-cancer therapies.

Methods:

This is a secondary analysis of a cross-sectional study that investigated relationships between GI symptoms, gut microbiota, and patient-reported outcomes in adult cancer survivors. Gut microbiota was assessed from stool samples using 16 S rRNA gene sequencing. GI symptoms and health behaviors were measured via self-report. Descriptive statistics, multiple regression, and correlation analyses are reported.

Results:

A total of 334 cancer survivors participated, and a subsample of 17 provided stool samples. Most survivors rated their diet as moderately healthy (55.7%) and reported engaging in low intensity exercise (53.9%) for ≤5 h/week (69.1%). Antibiotic use was associated with more belly pain, constipation, and diarrhea ( P < .05). Survivors consuming a healthier diet had fewer symptoms of belly pain ( P = .03), gas/bloating ( P = .01), while higher protein consumption was associated with less belly pain ( P = .03). Better diet health was positively correlated with Lachnospiraceae abundance, and negatively with Bacteroides abundance ( P < .05). Greater exercise frequency positively correlated with abundance of Lachnospiraceae, Faecalibacterium, Bacteroides, Anaerostipes, Alistipes, and Subdoligranulum ( P < .05).

Conclusion:

Results provide evidence for associations between antibiotic use, probiotic use, dietary health behaviors, and GI symptoms. Diet and exercise behaviors are related to certain types of bacteria, but the direction of causality is unknown. Dietary-based interventions may be optimally suited to address survivors’ GI symptoms by influencing the gut microbiota. Larger trials are needed.
Anterograde Aortic Bypass Technique for Renal Preservation in Aneurysmal Repair With Horseshoe Kidney: A Novel Approach With Reduced Renal Ischemic Time
Authors: Palmier Mickael , Cherel Myriam , Plissonnier Didier
Published: March 2024

The purpose of this article is to highlight an innovative technique in the surgical management of aortic aneurysms in the presence of a horseshoe kidney. The technique involves an anterograde aortic bypass from the distal thoracic aorta to the major renal artery with the primary advantage to a significant reduction in renal ischemia time.
Pancreatic adenocarcinoma of the tail—Unveiling a rare presentation with venous thrombosis: A case report and literature review
Authors: Rabab Syeda Abiha , Zaidi Syeda Mahrukh Fatima , Amjad Ayesha , Paras  , Sattar Maryam
Published: March 2024

Pancreatic cancer is a silent and lethal adversary that often conceals its presence until advanced stages. This report elucidates a distinctive case of a 46-year-old patient with pancreatic tail adenocarcinoma presenting with venous thrombosis, a rare manifestation. The patient’s symptoms included severe left leg pain, swelling, and redness, accompanied by weight loss and decreased appetite. Laboratory findings indicated a prothrombotic state, whereas imaging revealed a substantial mass on the tail of the pancreas with hepatic metastasis. Elevated cancer antigen 19-9 and carcinoembryonic antigen supported the diagnosis which was confirmed by a liver biopsy. This case underscores the diagnostic challenges posed by pancreatic cancer, particularly in the tail, emphasizing the need for early detection. The intricate interplay between metastasis and thrombosis complicates the clinical landscape, requiring a comprehensive approach to management.
Online health information behaviour and its association with statin adherence in patients with high cardiovascular risk: A prospective cohort study
Authors: Lim Hooi Min , Ng Chirk Jenn , Abdullah Adina , Danee Mahmoud , Raubenheimer Jacques , Dunn Adam G.
Published: March 2024

Objective

Statins are effective for preventing cardiovascular disease. However, many patients decide not to take statins because of negative influences, such as online misinformation. Online health information may affect decisions on medication adherence, but measuring it is challenging. This study aimed to examine the associations between online health information behaviour and statin adherence in patients with high cardiovascular risk.

Methods

A prospective cohort study involving 233 patients with high cardiovascular risk was conducted at a primary care clinic in Malaysia. Participants used a digital information diary tool to record online health information they encountered for 2 months and completed a questionnaire about statin necessity, concerns and adherence at the end of the observation period. Data were analysed using structural equation modelling.

Results

The results showed that 55.8% (130 of 233 patients) encountered online health information. Patients who actively sought online health information (91 of 233 patients) had higher concerns about statin use ( β = 0.323, p = 0.023). Participants with higher concern about statin use were also more likely to be non-adherent ( β = -0.337, p < 0.001). Patients who actively sought online health information were more likely to have lower statin adherence, mediated by higher concerns about statin use (indirect effect, β = -0.109, p = 0.048).

Conclusions

Our results suggest that patients with higher levels of concern about statins may be actively seeking online information about statins, and their concerns might influence how they search, what they find, and the potential to encounter misinformation. Our study highlights the importance of addressing patients’ concerns about medications to improve adherence.
GPT-4 as a Source of Patient Information for Anterior Cervical Discectomy and Fusion: A Comparative Analysis Against Google Web Search
Authors: Mastrokostas Paul G. , Mastrokostas Leonidas E. , Emara Ahmed K. , Wellington Ian J. , Ginalis Elizabeth , Houten John K. , Khalsa Amrit S. , Saleh Ahmed , Razi Afshin E. , Ng Mitchell K.
Published: March 2024

Study Design

Comparative study.

Objectives

This study aims to compare Google and GPT-4 in terms of (1) question types, (2) response readability, (3) source quality, and (4) numerical response accuracy for the top 10 most frequently asked questions (FAQs) about anterior cervical discectomy and fusion (ACDF).

Methods

“Anterior cervical discectomy and fusion” was searched on Google and GPT-4 on December 18, 2023. Top 10 FAQs were classified according to the Rothwell system. Source quality was evaluated using JAMA benchmark criteria and readability was assessed using Flesch Reading Ease and Flesch-Kincaid grade level. Differences in JAMA scores, Flesch-Kincaid grade level, Flesch Reading Ease, and word count between platforms were analyzed using Student’s t-tests. Statistical significance was set at the .05 level.

Results

Frequently asked questions from Google were varied, while GPT-4 focused on technical details and indications/management. GPT-4 showed a higher Flesch-Kincaid grade level (12.96 vs 9.28, P = .003), lower Flesch Reading Ease score (37.07 vs 54.85, P = .005), and higher JAMA scores for source quality (3.333 vs 1.800, P = .016). Numerically, 6 out of 10 responses varied between platforms, with GPT-4 providing broader recovery timelines for ACDF.

Conclusions

This study demonstrates GPT-4’s ability to elevate patient education by providing high-quality, diverse information tailored to those with advanced literacy levels. As AI technology evolves, refining these tools for accuracy and user-friendliness remains crucial, catering to patients’ varying literacy levels and information needs in spine surgery.
Multi-Level Mixed-Effects Analysis of Stunting Among 6 to 59 Months Children in Ethiopia: Evidenced from Analysis of Health and Demographic Survey, 2000 to 2019
Authors: Mezmur Haymanot , Tefera Maleda , Roba Aklilu Abrham , Başdaş Öznur
Published: March 2024

Background. Stunting remains a major public health issue in developing countries like Ethiopia. It is termed as a chronic malnutrition which leads to morbidity and mortality among children. This study aimed to assess the prevalence and factors associated with stunting among 6 to 59 months children in Ethiopia. Methods. A total weighted sample of 34 930 children aged 6 to 59 months was included in this study. A Multilevel Mixed-Effect logistic regression was carried out. The Median Odds Ratio (MOR) and the Intra class Correlation Coefficient (ICC) were calculated. An adjusted odds ratio along with a 95% confidence interval was reported and statistical significance was declared at a P-value ≤ .05. Results. The weighted prevalence of stunting in Ethiopia was 48.3% (95% CI: 47.8%, 48.8%). Being male, increased in age, having multiple births (twin), having less than 2 years birth interval, history of diarrhea, anemia, lack of maternal and paternal formal education, having poor and middle-wealth status, and living in rural areas were significantly associated with stunting. Conclusions. The prevalence of stunting is high in Ethiopia. The risk factors mentioned above increase the likely hood of stunting among children. Therefore, we recommend that responsible bodies place a greater emphasis and priority on promoting parental education, awareness on the impact of the birth interval on child nutrition, the prevention of childhood diarrhea and anemia, improving household economic status, and reducing rural-urban disparities.
Gentrification and Neighborhood Housing Wealth: How Gentrification Reproduces the Racial Stratification of Urban Neighborhoods
Authors: Beck Kevin
Published: March 2024

Few researchers have considered how gentrification affects inequalities of housing wealth between Black and White neighborhoods. Drawing on the U.S. census and the American Community Survey, I test the hypothesis that home values rise more slowly in gentrifying neighborhoods that are majority Black compared to those that are majority White. I find that home values appreciate more quickly in gentrifying neighborhoods that are majority Black, particularly those that are experiencing significant change in their racial-ethnic composition. The findings further suggest that Black gentrifying neighborhoods experiencing racial transition—a large increase in the proportion of White residents and a large decrease in the proportion of Black residents—experience higher rates of home value appreciation than those not experiencing racial transition. I argue that gentrification reproduces the racial stratification of urban neighborhoods because large increases to housing wealth tend to be coupled with the arrival of the White middle-class.
Are retention strategies used in National Institute for Health and Care Research, Health Technology Assessment trials supported by evidence for their effectiveness? A systematic mapping review
Authors: Way Rosalind , Parker Adwoa , Torgerson David J
Published: March 2024

Background and Aims

Poor retention of trial participants is common and can result in significant methodological, statistical, ethical, and financial challenges. To improve trial efficiency, we aimed to assess the extent to which commonly used strategies to retain participants within trials are supported by evidence for their effectiveness.

Method

A systematic methodological review was carried out to identify commonly used retention strategies in National Institute for Health and Care Research (NIHR) Health Technology Assessment (HTA) trials (January 2020–June 2022). Strategies were then mapped to evidence for their effectiveness from the most recent Cochrane retention review (published 2021), and a future Study Within A Trial (SWAT) priority list was created.

Results

Amongst 80 trials, the most frequently reported retention strategies were: flexibility with data collection method/location (53%); participant diaries (38%); use of routine data (29%); PPI input (26%); telephone reminders for participants (26%); postal reminders for participants (25%); monitoring approaches (21%); offering flexibility with timing of data collection (20%); pre-paid return postage (18%); prioritising collection of key outcomes (15%); and participant newsletters (15%). Out of the 56 identified strategies, mostly no, very low or low evidence for their effectiveness was identified (64%; 14%; 13% respectively).

Discussion and Conclusions

Commonly used retention strategies are lacking good quality evidence for their effectiveness. The findings support the need for more SWATs and help identify priority areas for future SWAT research. These priorities could be used with other priority lists to inform future SWAT conduct.
Digital: The Promise of the Unlimited?
Authors: Paquienséguy Françoise
Published: March 2024

At the crossroads of notions of Technical and Human lies the notion of limits. Let us question the vocabulary: here, limits in the plural, boundaries, edges…, to be also nuanced with the meanings of bounded, limited. They seem negative: could limits be flaws, deficiencies, or challenges to overcome? Indeed, the Human appears to be limited by the body in the three dimensions of space and in that of time; therefore, there would be physical and material limits, or weaknesses, on which technology can certainly act concretely. But should we necessarily surpass them and seize upon technologies to achieve this? On the other hand, we have the impression that our mind, being more immaterial, could project itself infinitely and onto everything, including the technologies themselves. Could it be that humans are made of an unlimited spirit that creates technology, housed in a limited body served by it? The digital is omnipresent in our lives, and we must take the time to study the new technical-societal relationship developing with it. Guided by contemporary philosophers and thinkers, we will examine what defines a technique in its specific case: its lineage, technologies, dissemination, and interactions with humans. We will explore 1/how the digital represents a technical lineage, 2/how this technique and its technologies have evolved in contemporary societies, its widespread impact on communication and the construction of social bonds, 3/how humanity has adapted to these transformations by becoming hypermodern, 4/the new relationship between humans and time, and 5/why time becomes the place and moment of the social life to survive the digital regime and hypermodernity. Despite its theoretical content and level of abstraction, this paper speaks to us, inhabitants of a digital world, who continually use digital technologies and always desire more, faster, in an irresistible need for speed and unlimited.
Landscape of driver mutations and their clinical effects on Down syndrome–related myeloid neoplasms
Authors: Sato Tomohiko , Yoshida Kenichi , Toki Tsutomu , Kanezaki Rika , Terui Kiminori , Saiki Ryunosuke , Ojima Masami , Ochi Yotaro , Mizuno Seiya , Yoshihara Masaharu , Uechi Tamayo , Kenmochi Naoya , Tanaka Shiro , Matsubayashi Jun , Kisai Kenta , Kudo Ko , Yuzawa Kentaro , Takahashi Yuka , Tanaka Tatsuhiko , Yamamoto Yohei , Kobayashi Akie , Kamio Takuya , Sasaki Shinya , Shiraishi Yuichi , Chiba Kenichi , Tanaka Hiroko , Muramatsu Hideki , Hama Asahito , Hasegawa Daisuke , Sato Atsushi , Koh Katsuyoshi , Karakawa Shuhei , Kobayashi Masao , Hara Junichi , Taneyama Yuichi , Imai Chihaya , Hasegawa Daiichiro , Fujita Naoto , Yoshitomi Masahiro , Iwamoto Shotaro , Yamato Genki , Saida Satoshi , Kiyokawa Nobutaka , Deguchi Takao , Ito Masafumi , Matsuo Hidemasa , Adachi Souichi , Hayashi Yasuhide , Taga Takashi , Saito Akiko M. , Horibe Keizo , Watanabe Kenichiro , Tomizawa Daisuke , Miyano Satoru , Takahashi Satoru , Ogawa Seishi , Ito Etsuro
Published: March 2024

Transient abnormal myelopoiesis (TAM) is a common complication in newborns with Down syndrome (DS). It commonly progresses to myeloid leukemia (ML-DS) after spontaneous regression. In contrast to the favorable prognosis of primary ML-DS, patients with refractory/relapsed ML-DS have poor outcomes. However, the molecular basis for refractoriness and relapse and the full spectrum of driver mutations in ML-DS remain largely unknown. We conducted a genomic profiling study of 143 TAM, 204 ML-DS, and 34 non-DS acute megakaryoblastic leukemia cases, including 39 ML-DS cases analyzed by exome sequencing. Sixteen novel mutational targets were identified in ML-DS samples. Of these, inactivations of IRX1 (16.2%) and ZBTB7A (13.2%) were commonly implicated in the upregulation of the MYC pathway and were potential targets for ML-DS treatment with bromodomain-containing protein 4 inhibitors. Partial tandem duplications of RUNX1 on chromosome 21 were also found, specifically in ML-DS samples (13.7%), presenting its essential role in DS leukemia progression. Finally, in 177 patients with ML-DS treated following the same ML-DS protocol (the Japanese Pediatric Leukemia and Lymphoma Study Group acute myeloid leukemia -D05/D11), CDKN2A, TP53, ZBTB7A, and JAK2 alterations were associated with a poor prognosis. Patients with CDKN2A deletions (n = 7) or TP53 mutations (n = 4) had substantially lower 3-year event-free survival (28.6% vs 90.5%; P < .001; 25.0% vs 89.5%; P < .001) than those without these mutations. These findings considerably change the mutational landscape of ML-DS, provide new insights into the mechanisms of progression from TAM to ML-DS, and help identify new therapeutic targets and strategies for ML-DS.
Therapy-related chronic myelomonocytic leukemia does not have the high-risk features of a therapy-related neoplasm
Authors: Bataller Alex , Gener-Ricos Georgina , Almanza-Huante Emmanuel , Chien Kelly S. , Urrutia Samuel , Bazinet Alexandre , Rodriguez-Sevilla Juan Jose , Hammond Danielle , Sasaki Koji , Takahashi Koichi , DiNardo Courtney D. , Ravandi Farhad , Borthakur Gautam , Kadia Tapan M. , Kanagal-Shamanna Rashmi , Kantarjian Hagop M. , Garcia-Manero Guillermo , Montalban-Bravo Guillermo
Published: March 2024

Therapy-related myeloid neoplasms (t-MNs) arise after exposure to cytotoxic therapies and are associated with high-risk genetic features and poor outcomes. We analyzed a cohort of patients with therapy-related chronic myelomonocytic leukemia (tCMML; n = 71) and compared its features to that of de novo CMML (dnCMML; n = 461). Median time from cytotoxic therapy to tCMML diagnosis was 6.5 years. Compared with dnCMML, chromosome-7 abnormalities (4% vs 13%; P = .005) but not complex karyotype (3% vs 7%; P = .15), were more frequent in tCMML. tCMML was characterized by higher TP53 mutation frequency (4% vs 12%; P = .04) and lower NRAS (6% vs 22%, P = .007) and CBL (4% vs 12%, P = .04) mutation frequency. Prior therapy with antimetabolites (odd ratio [OR], 1.22; 95% confidence interval [CI], 1.05-1.42; P = .01) and mitotic inhibitors (OR, 1.24; 95% CI, 1.06-1.44; P = .009) was associated with NF1 and SETBP1 mutations whereas prior mitotic inhibitor therapy was associated with lower TET2 mutation frequency (OR, 0.71; 95% CI, 0.55-0.92; P = .01). Although no differences in median overall survival (OS) were observed among tCMML and dnCMML (34.7 months vs 35.9 months, P = .26), multivariate analysis for OS revealed that prior chemotherapy was associated with increased risk of death (hazard ratio, 1.76; 95% CI, 1.07-2.89; P = .026). Compared with a cohort of therapy-related myelodysplastic syndrome, tCMML had lower TP53 mutation frequency (12% vs 44.4%, P < .001) and less unfavorable outcomes. In summary, tCMML does not exhibit the high-risk features and poor outcomes of t-MNs.
Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness
Authors: Chowdhury H. M. A. Mohit , Boult Terrance , Oluwadare Oluwatosin
Published: March 2024

Background

Chromosome is one of the most fundamental part of cell biology where DNA holds the hierarchical information. DNA compacts its size by forming loops, and these regions house various protein particles, including CTCF, SMC3, H3 histone. Numerous sequencing methods, such as Hi-C, ChIP-seq, and Micro-C, have been developed to investigate these properties. Utilizing these data, scientists have developed a variety of loop prediction techniques that have greatly improved their methods for characterizing loop prediction and related aspects.

Results

In this study, we categorized 22 loop calling methods and conducted a comprehensive study of 11 of them. Additionally, we have provided detailed insights into the methodologies underlying these algorithms for loop detection, categorizing them into five distinct groups based on their fundamental approaches. Furthermore, we have included critical information such as resolution, input and output formats, and parameters. For this analysis, we utilized the GM12878 Hi-C datasets at 5 KB, 10 KB, 100 KB and 250 KB resolutions. Our evaluation criteria encompassed various factors, including memory usages, running time, sequencing depth, and recovery of protein-specific sites such as CTCF, H3K27ac, and RNAPII.

Conclusion

This analysis offers insights into the loop detection processes of each method, along with the strengths and weaknesses of each, enabling readers to effectively choose suitable methods for their datasets. We evaluate the capabilities of these tools and introduce a novel Biological, Consistency, and Computational robustness score ($$BCC_{score}$$

B
C

C

score

) to measure their overall robustness ensuring a comprehensive evaluation of their performance.
Cell4D: a general purpose spatial stochastic simulator for cellular pathways
Authors: Chan Donny , Cromar Graham L. , Taj Billy , Parkinson John
Published: March 2024

Background

With the generation of vast compendia of biological datasets, the challenge is how best to interpret ‘omics data alongside biochemical and other small-scale experiments to gain meaningful biological insights. Key to this challenge are computational methods that enable domain-users to generate novel hypotheses that can be used to guide future experiments. Of particular interest are flexible modeling platforms, capable of simulating a diverse range of biological systems with low barriers of adoption to those with limited computational expertise.

Results

We introduce Cell4D, a spatial-temporal modeling platform combining a robust simulation engine with integrated graphics visualization, a model design editor, and an underlying XML data model capable of capturing a variety of cellular functions. Cell4D provides an interactive visualization mode, allowing intuitive feedback on model behavior and exploration of novel hypotheses, together with a non-graphics mode, compatible with high performance cloud compute solutions, to facilitate generation of statistical data. To demonstrate the flexibility and effectiveness of Cell4D, we investigate the dynamics of CEACAM1 localization in T-cell activation. We confirm the importance of Ca2+ microdomains in activating calmodulin and highlight a key role of activated calmodulin on the surface expression of CEACAM1. We further show how lymphocyte-specific protein tyrosine kinase can help regulate this cell surface expression and exploit spatial modeling features of Cell4D to test the hypothesis that lipid rafts regulate clustering of CEACAM1 to promote trans-binding to neighbouring cells.

Conclusions

Through demonstrating its ability to test and generate hypotheses, Cell4D represents an effective tool to help integrate knowledge across diverse, large and small-scale datasets.
GNNMF: a multi-view graph neural network for ATAC-seq motif finding
Authors: Zhang Shuangquan , Wu Xiaotian , Lian Zhichao , Zuo Chunman , Wang Yan
Published: March 2024

Background

The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) utilizes the Transposase Tn5 to probe open chromatic, which simultaneously reveals multiple transcription factor binding sites (TFBSs) compared to traditional technologies. Deep learning (DL) technology, including convolutional neural networks (CNNs), has successfully found motifs from ATAC-seq data. Due to the limitation of the width of convolutional kernels, the existing models only find motifs with fixed lengths. A Graph neural network (GNN) can work on non-Euclidean data, which has the potential to find ATAC-seq motifs with different lengths. However, the existing GNN models ignored the relationships among ATAC-seq sequences, and their parameter settings should be improved.

Results

In this study, we proposed a novel GNN model named GNNMF to find ATAC-seq motifs via GNN and background coexisting probability. Our experiment has been conducted on 200 human datasets and 80 mouse datasets, demonstrated that GNNMF has improved the area of eight metrics radar scores of 4.92% and 6.81% respectively, and found more motifs than did the existing models.

Conclusions

In this study, we developed a novel model named GNNMF for finding multiple ATAC-seq motifs. GNNMF built a multi-view heterogeneous graph by using ATAC-seq sequences, and utilized background coexisting probability and the iterloss to find different lengths of ATAC-seq motifs and optimize the parameter sets. Compared to existing models, GNNMF achieved the best performance on TFBS prediction and ATAC-seq motif finding, which demonstrates that our improvement is available for ATAC-seq motif finding.
Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies
Authors: Kwon Daehong , Park Nayoung , Wy Suyeon , Lee Daehwan , Park Woncheoul , Chai Han-Ha , Cho In-Cheol , Lee Jongin , Kwon Kisang , Kim Heesun , Moon Youngbeen , Kim Juyeon , Kim Jaebum
Published: March 2024

Background

Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, the full genetic architecture of the trait still remains unclear in part because of the lack of accurate identification of related structural variations (SVs) which resulted from the shortage of target breeds, the limitations of sequencing data, and the incompleteness of genome assemblies. The recent generation of a new pig breed with superior meat quality, called Nanchukmacdon, and its chromosome-level genome assembly (the NCMD assembly) has provided new opportunities.

Results

By applying assembly-based SV calling approaches to various genome assemblies of pigs including Nanchukmacdon, the impact of SVs on meat quality was investigated. Especially, by checking the commonality of SVs with other pig breeds, a total of 13,819 Nanchukmacdon-specific SVs (NSVs) were identified, which have a potential effect on the unique meat quality of Nanchukmacdon. The regulatory potentials of NSVs for the expression of nearby genes were further examined using transcriptome- and epigenome-based analyses in different tissues.

Conclusions

Whole-genome comparisons based on chromosome-level genome assemblies have led to the discovery of SVs affecting meat quality in pigs, and their regulatory potentials were analyzed. The identified NSVs will provide new insights regarding genetic architectures underlying the meat quality in pigs. Finally, this study confirms the utility of chromosome-level genome assemblies and multi-omics analysis to enhance the understanding of unique phenotypes.
Overcoming barriers for left atrial appendage thrombus: a systematic review of left atrial appendage closure
Authors: Zhang Zixi , Zhou Jiabao , Lin Qiuzhen , Wang Cancan , Huang Yunying , Dai Yongguo , Zuo Wanyun , Liu Na , Xiao Yichao , Liu Qiming
Published: March 2024

Background

Approximately 90% of intracardial thrombi originate from the left atrial appendage in non-valvular atrial fibrillation patients. Even with anticoagulant therapy, left atrial appendage thrombus (LAAT) still occurs in 8% of patients. While left atrial appendage closure (LAAC) could be a promising alternative, the current consensus considers LAAT a contraindication to LAAC. However, the feasibility and safety of LAAC in patients with LAAT have yet to be determined.

Methods

This systematic review synthesizes published data to explore the feasibility and safety of LAAC for patients with LAAT.

Results

This study included a total of 136 patients with LAATs who underwent successful LAAC. The Amulet Amplatzer device was the most frequently utilized device (48.5%). Among these patients, 77 (56.6%) had absolute contraindications to anticoagulation therapy. Cerebral protection devices were utilized by 47 patients (34.6%). Transesophageal echocardiography (TEE) is the primary imaging technique used during the procedure. Warfarin and novel oral anticoagulants were the main anticoagulant medications used prior to the procedure, while dual antiplatelet therapy was primarily used post-procedure. During a mean follow-up period of 13.2 ± 11.5 months, there was 1 case of fatality, 1 case of stroke, 3 major bleeding events, 3 instances of device-related thrombus, and 8 cases of peri-device leakage.

Conclusions

This review highlights the preliminary effectiveness and safety of the LAAC procedure in patients with persistent LAAT. Future large-scale RCTs with varied LAAT characteristics and LAAC device types are essential for evidence-based decision-making in clinical practice.
Development of the multivariate administrative data cystectomy model and its impact on misclassification bias
Authors: Ross James , Lavallee Luke T. , Hickling Duane , van Walraven Carl
Published: March 2024

Background

Misclassification bias (MB) is the deviation of measured from true values due to incorrect case assignment. This study compared MB when cystectomy status was determined using administrative database codes vs. predicted cystectomy probability.

Methods

We identified every primary cystectomy-diversion type at a single hospital 2009–2019. We linked to claims data to measure true association of cystectomy with 30 patient and hospitalization factors. Associations were also measured when cystectomy status was assigned using billing codes and by cystectomy probability from multivariate logistic regression model with covariates from administrative data. MB was the difference between measured and true associations.

Results

500 people underwent cystectomy (0.12% of 428 677 hospitalizations). Sensitivity and positive predictive values for cystectomy codes were 97.1% and 58.6% for incontinent diversions and 100.0% and 48.4% for continent diversions, respectively. The model accurately predicted cystectomy-incontinent diversion (c-statistic [C] 0.999, Integrated Calibration Index [ICI] 0.000) and cystectomy-continent diversion (C:1.000, ICI 0.000) probabilities. MB was significantly lower when model-based predictions was used to impute cystectomy-diversion type status using for both incontinent cystectomy (F = 12.75; p < .0001) and continent cystectomy (F = 11.25; p < .0001).

Conclusions

A model using administrative data accurately returned the probability that cystectomy by diversion type occurred during a hospitalization. Using this model to impute cystectomy status minimized MB. Accuracy of administrative database research can be increased by using probabilistic imputation to determine case status instead of individual codes.
Perioperative outcomes of the surgical management of achalasia in two tertiary Cameroonian hospitals: a cohort study
Authors: Kamla Joël Igor , Bang Guy Aristide , Tochie Joel Noutakdie , Bwelle George Motto , Oumarou Blondel Nana , Nonga Bernadette Ngo
Published: March 2024

Introduction

Achalasia is a rare esophageal disease with potentially lethal complications. Knowledge of the outcomes of the different surgical treatment modalities for achalasia by Heller’s cardiomyotomy (HCM) helps to choose the safest and most effective option. However, data on the management of achalsia using a Heller myotomy is limited in Africa. Thus, our aim was to determine the perioperative morbidity, mortality and short-term functional outcomes of HCM in Cameroon.

Methodology

We conducted a cohort study throughout a 10-year chart review of patients who underwent HCM for achalasia and were followed up postoperatively for at least three months at two tertiary health centers in Cameroon. We analyzed demographic data, preoperative clinical and imaging data, treatment details, and outcomes at three to twelve months after HCM using the Eckardt score.

Results

We enrolled 29 patients with achalasia having a mean age of 24 ± 16 years and predominantly females (M/F of 1/3.8). The mean symptom duration was 51 ± 20 months. In 80% of cases, the diagnosis was made through a conventional x-ray contrast imaging or “barium swallow test” (93%) and/or an upper gastrointestinal endoscopy (86%). The gold standard diagnostic method via esophageal manometry was unavailable. Preoperatievly, all patients had symptoms suggestive of an active achalasia. HCM was performed via laparotomy in 75% as opposed to 25% laparoscopic HCM procedures. Dor’s anterior partial fundoplication was the main anti-reflux procedure performed (59%). Mucosal perforations were the only intraoperative complications in eight patients (2 during laparoscopy vs. 6 during laparotomy; p > 0.5) and were managed successfully by simple sutures. Postoperative complications were non-severe and occurred in 10% of patients all operated via laparotomy. The mean postoperative length of hospital stay was 7 ± 3 days for laparotomy vs. 5 ± 2 days for laparoscopy; p > 0.5. The perioperative mortality rate was nil. Overall, the short-term postoperative functional outcome was rated excellent; average Eckardt score of 1.5 ± 0.5 (vs. preoperative Eckardt Score of 9 ± 1; p < 0.0001).

Conclusion

Achalasia is diagnosed late in this resource-limited setting. HCM yields satisfactory outcomes, especially via laparoscopic management. An improvement in diagnostic esophageal manometry and mini-invasive surgical infrastructure and the required surgical training/skills are needed for optimal achalasia care.
How does the SARS-CoV-2 reinfection rate change over time? The global evidence from systematic review and meta-analysis
Authors: Chen Ying , Zhu Wenhui , Han Xinyue , Chen Miaoshuang , Li Xin , Huang Haiping , Zhang Mengyuan , Wei Rongjie , Zhang Huadong , Yang Changhong , Zhang Tao
Published: March 2024

Background

There is a significant increase in the number of SARS-CoV-2 reinfection reports in various countries. However, the trend of reinfection rate over time is not clear.

Methods

We searched PubMed, Web of Science, Medline, Embase, Cochrane Central Register of Controlled Trials, China National Knowledge Infrastructure, and Wanfang for cohort studies, case-control studies, and cross-sectional studies up to March 16, 2023, to conduct a meta-analysis of global SARS-CoV-2 reinfection rate. Subgroup analyses were performed for age, country, study type, and study population, and time-varying reinfection rates of SARS-CoV-2 were estimated using meta-regression. The risk of bias was assessed using the Newcastle-Ottawa Scale and the Joanna Briggs Institute critical appraisal tool.

Result

A total of 55 studies involving 111,846 cases of SARS-CoV-2 reinfection were included. The pooled SARS-CoV-2 reinfection rate was 0.94% (95% CI: 0.65 -1.35%). In the subgroup analyses, there were statistically significant differences in the pooled reinfection rates by reinfection variant, and study type (P < 0.05). Based on meta-regression, the reinfection rate fluctuated with time.

Conclusion

Meta-regression analysis found that the overall reinfection rate increased and then decreased over time, followed by a period of plateauing and then a trend of increasing and then decreasing, but the peak of the second wave of reinfection rate was lower than the first wave. SARS-CoV-2 is at risk of reinfection and the Omicron variant has a higher reinfection rate than other currently known variants. The results of this study could help guide public health measures and vaccination strategies in response to the Coronavirus Disease 2019 (COVID-19) pandemic.
APOC1 is a prognostic biomarker associated with M2 macrophages in ovarian cancer
Authors: Yang Shimin , Du Jingxiao , Wang Wei , Zhou Dongmei , Xi Xiaowei
Published: March 2024

Background

Recent studies have demonstrated that APOC1 is associated with cancer progression, exerting cancer-promoting and immune infiltration-promoting effects. Nevertheless, there is currently no report on the presence of APOC1 in ovarian cancer (OV).

Method

In this study, we conducted data analysis using the GEO and TCGA databases. We conducted a thorough bioinformatics analysis to investigate the function of APOC1 in OV, utilizing various platforms including cBioPortal, STRING, GeneMANIA, LinkedOmics, GSCALite, TIMER, and CellMarker. Additionally, we performed immunohistochemical staining on tissue microarrays and conducted in vitro cellular assays to validate our findings.

Result

Our findings reveal that APOC1 expression is significantly upregulated in OV compared to normal tissues. Importantly, patients with high APOC1 levels show a significantly poorer prognosis. Furthermore, our study demonstrated that APOC1 exerted a crucial function in promoting the capacity of ovarian cancer cells to proliferate, migrate, and invade. Additionally, we have identified that genes co-expressed with APOC1 are primarily associated with adaptive immune responses. Notably, the levels of APOC1 in OV exhibit a correlation with the presence of M2 Tumor-associated Macrophages (TAMs).

Conclusion

APOC1 emerges as a promising prognostic biomarker for OV and exhibits a significant association with M2 TAMs in OV.
Dynamic stability evaluation of trunk accelerations during walking in blind and sighted individuals
Authors: Rasouli Kahaki Zeinab , Choobineh Alireza , Razeghi Mohsen , Karimi Mohammad Taghi , Safarpour Ali Reza
Published: March 2024

Background

Dynamic stability is a fundamental goal in standing activities. In this regard, monitoring, analysis, and interventions made to improve stability is a research topic investigated in the biomechanics of human movements. Vision has a major role to play in controlling human movement. Nonetheless, little is known about the effects of visual deprivation, especially from birth on dynamic gait stability.

Methods

The current study was conducted on 20 congenital blind and 10 sighted people (15–38 years). To evaluate the dynamic stability, descriptive data, harmonic ratio (HR), improved harmonic ratio (iHR), and root mean square (RMS), based on trunk acceleration data were measured in three axes: anteroposterior (AP), vertical (V), and mediolateral (ML) while participants walked an eight-meter straight path.

Results

In the comparison of blind and sighted people (eyes open), standard deviation, HR, iHR, and RMS indices were found to be significantly different in both AP and V directions. All the mentioned parameters were significantly lower in blind than in sighted participants. In the comparison of blind people and sighted ones with closed eyes, changes were observed in the maximum, range, standard deviation, and RMS only in the AP axis. In the comparison between eyes open and closed in sighted people, a significant difference was found only in the harmonic ratio of the vertical axis.

Conclusion

Visual deprivation led to a decrease in dynamic stability parameters in the AP and V axes. Even the movement of sighted people in unchallenged conditions is dependent on visual information.