bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Quantitatively Differential Chromosomal Compartmentalization Changes and Their Biological Significance from Hi-C data using DARIC
Authors: Kai Yan , Liu Nan , Orkin Stuart H , Yuan Guo-Cheng 
Published: April 2023

Abstract
Background. Chromosomal compartmentalization plays a critical role in maintaining proper transcriptional programs in cell differentiation and oncogenesis. However, currently the prevalent method for comparative analysis of compartmentalization landscapes between different cell types is limited to the qualitative switched compartments.
Results. To identify genomic regions with quantitatively differential compartmentalization changes from genome-wide chromatin conformation data like Hi-C, we developed a computational framework named DARIC. DARIC includes three modules: compartmentalization quantification, normalization, and differential analysis. Comparing DARIC with the conventional compartment switching analysis reveals substantial regions characterized by quantitatively significant compartmentalization changes without switching. These changes are accompanied by changes in gene expression, chromatin accessibility, H3K27ac intensity, as well as the interactions with nuclear lamina proteins and nuclear positioning, highlighting the functional importance of such quantitative changes in gene regulation. We applied DARIC to dissect the quantitative compartmentalization changes during human cardiomyocyte differentiation and identified two distinct mechanisms for gene activation based on the association with compartmentalization changes. Using the quantitative compartmentalization measurement module from DARIC, we further dissected the compartment variability landscape in the human genome by analyzing a compendium of 32 Hi-C datasets from 4DN. We discovered an interesting correlation between compartmentalization variability and sub-compartments.
Conclusions. DARIC is a useful tool for analyzing quantitative compartmentalization changes and mining novel biological insights from increasing Hi-C data. Our results demonstrate the functional significance of quantitative compartmentalization changes in gene regulation, and provide new insights into the relationship between compartmentalization variability and sub-compartments in the human genome.
Comprehensive analysis of CCR7 as a biomarker for the diagnosis, prognosis, and immunity in pan-cancer
Authors: Chen Jianrui , Huang Haiyue , Zhang Qingfang , Zhu Yuxin , Xie Zhenzhen 
Published: April 2023

Abstract
Chemokine receptor 7 (CCR7), a member of the CCR family genes, encodes CCR to bind chemokines and exert multiple types of biological processes. It has been evident that CCR7 can play a crucial role in cancer development and progression. Our study has investigated the value of CCR7 expression in the diagnosis and prognosis and immunological signatures of CCR7. Through the utilization of The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx), The Human Protein Atlas (HPA), TIMER, TISIDB, GSEA, GeneMANIA, The Cancer single-cell state Atlas (CancerSEA), UALCAN, Shiny Methylation Analysis Resource Tool (SMART), MethSurv, and cBioPortal database, we used bioinformatics methods to conduct pan-cancer analysis, including differential expression, clinical evaluation, tumor microenvironment (TME) and immune-related analysis, GSEA, functional association analysis, DNA mutation and methylation level, and microsatellite instability (MSI) and tumor mutation burden (TMB). Our results showed that the expression of CCR7 showed significant differentiation between tumor tissues and normal tissues. CCR7 had the potential to be a biomarker in the diagnosis and prognosis of patients. Moreover, the CCR7 expression was closely associated with immune cell infiltration, immune-related genes, TMB, MSI, and DNA mutation. Through GSEA, it was revealed that CCR7 had a strong correlation with multiple immunological functions. Overall, we testified that CCR7 could be a novel tool for the diagnosis and prognosis of cancer patients. Moreover, the correlation between CCR7 and TME and immunological processes elucidated the value of CCR7 as a target in cancer immunotherapy.
Training certified detectives to track down the intrinsic shortcuts in COVID-19 chest x-ray data sets
Authors: Zhang Ran , Griner Dalton , Garrett John W. , Qi Zhihua , Chen Guang-Hong 
Published: April 2023

Abstract
Deep learning faces a significant challenge wherein the trained models often underperform when used with external test data sets. This issue has been attributed to spurious correlations between irrelevant features in the input data and corresponding labels. This study uses the classification of COVID-19 from chest x-ray radiographs as an example to demonstrate that the image contrast and sharpness, which are characteristics of a chest radiograph dependent on data acquisition systems and imaging parameters, can be intrinsic shortcuts that impair the model’s generalizability. The study proposes training certified shortcut detective models that meet a set of qualification criteria which can then identify these intrinsic shortcuts in a curated data set.
Data Detection in Distributed Environment Based on Voice Interaction and English Network Teaching Management
Authors: Yanfei Shi 
Published: April 2023

Abstract
In recent years, due to the continuous progress of the intelligent society, information data has shown explosive growth in various industries such as transportation, healthcare, finance, education, and so on. Such a large amount of data has led to an increase in the difficulty of knowledge discovery. Due to the increasing amount of data in databases, it is difficult for these algorithms to ensure their recognition ability. Based on this, some scholars proposed a distributed environment data detection algorithm, and conducted research and analysis on online English teaching on this basis. Due to the rapid development of the Internet and information technology, traditional face-to-face classroom teaching has gradually been unable to meet today's diverse and personalized learning needs due to problems such as a single model and low interaction between teachers and students. The English online teaching management system fully utilizes the characteristics of the rapid transmission and multiple display methods of Internet information, and provides online teaching of traditional classroom teaching content through multimedia networks, fully meeting the personalized needs of students and enabling them to learn quickly. This article applies it to the management of English online teaching systems, increasing the effectiveness of English online teaching.
Rare presentation of BRASH syndrome with hypoglycemia and altered mental status
Authors: Sedlák Marián , Brúsiková Kamila , Sobolová Vladimíra , Králik Michal 
Published: April 2023

Abstract
Background BRASH syndrome (bradycardia, renal failure, atrioventricular nodal blockade, shock, and hyperkalemia) is a rare clinical condition with potentially severe outcomes. Patients with BRASH syndrome can present with diverse signs and symptoms and are usually in critical condition, but if recognized early, the syndrome is treatable and may have a favorable prognosis.Case presentation: This case study presents a 74-year-old patient with a history of multiple chronic conditions who was brought to the emergency department with a suspected stroke, altered mental status, and bradycardia. A head computed tomography scan did not confirm stroke, but laboratory results showed hyperkalemia, acidosis, and renal failure with concomitant progressive hypoglycemia. The patient was diagnosed with a BRASH syndrome characterized by a vicious cycle of atrioventricular nodal blockade induced by the potentiated effect of beta-blockers or calcium channel blockers, in combination with progressive hypoglycemia due to the suspected accumulation of anti-diabetic medications, which influenced the presentation and initial triage in the emergency department. She was admitted to the intensive care unit for further management, where she continued to improve and was ultimately discharged in a relatively stable condition.Conclusion This case study highlights the importance of considering rare and atypical presentations of medical conditions, particularly in elderly patients who may have multiple comorbidities. Early recognition and prompt management of such cases are crucial for improving patient outcomes.
Perceptions and drivers of healthcare provider and drug dispenser practices for the case management of malaria in pregnancy in the context of multiple first-line therapies in western Kenya: a qualitative study
Authors: Osoro Caroline Bonareri , Dellicour Stephanie , Ochodo Eleanor , Young Taryn , Kuile Feiko O. ter , Gutman Julie R. , Hill Jenny 
Published: April 2023

Abstract
Background Emergence of Plasmodium falciparum resistance to artemether-lumefantrine in Africa prompted the pilot introduction of multiple first-line therapies (MFT) against malaria in Kenya, potentially exposing women-of-childbearing-age (WOCBAs) to antimalarials with unknown safety profiles in the first trimester. We undertook a qualitative study to explore knowledge and perceptions among healthcare providers providing malaria treatment to WOCBAs and pregnant women.Methods In-depth interviews were conducted with purposively selected public and private health facility (HF) and drug outlet (DO) providers within and outside the pilot-MFT area. County health managers were interviewed about their knowledge of the national treatment guidelines. Transcripts were coded by content analysis using the WHO health system building blocks (leadership/governance, financing, health workforce, health information systems, access to medicines, and service delivery).Results Thirty providers (HF:21, DO:9) and three health managers were interviewed. Eighteen providers were from HFs in the pilot-MFT area; the remaining three and all nine DOs were outside the pilot-MFT area. The analysis revealed that providers had not been trained in malaria case management in the previous twelve months. DO providers were unfamiliar with national treatment guidelines in pregnancy and reported having no pregnancy tests. Health managers were unable to supervise DOs due to resource limitations. Providers from HFs and DOs noted poor sensitivity of malaria rapid diagnostic tests (RDTs) and hesitancy among patients who associated malaria-RDTs with HIV testing. Almost all providers reported antimalarial stock-outs, with quinine most affected. Patient preference was a major factor in prescribing antimalarials. Providers in HFs and DOs reported preferentially using artemether-lumefantrine in the first trimester due to the side effects and unavailability of quinine.Conclusion Knowledge of malaria case management in drug outlets and health facilities remains poor. Improved regulation of DO providers is warranted. Optimising treatment of malaria in pregnancy requires training, availability of malaria commodities, and pregnancy tests.
Integrating Climate Consequences from Flood Risk into Future Population Projections
Authors: Shu Evelyn , Porter Jeremy , Hauer Mathew , Olascoaga Sebastian Sandoval , Gourevitch Jesse , Wilson Bradley , Pope Mariah , Melecio-Vazquez David , Kearns Edward 
Published: April 2023

Abstract
Population exposure to flood risk has been linked to property value decreases, negative health/well-being consequences, and both short and long term population displacement resulting in shifts in population size and composition. To date, research in this area has examined this issue on a case-by-case basis, or at a level that generally hides the observed patterns associated with population shifts within housing markets. Using historic flood exposure and current flood risk data, we identify relationships between exposure to flood risk and population change. Using those observed relationships, in conjunction with future climate adjusted population projections, we forecast future population levels and changes to the underlying population in 2055. We find that declines in population size are associated with exposure to flood risk, particularly in areas with high climate vulnerability. Specifically, several high risk locations have already begun to see population responses to flood exposure and are forecast to have uneven growth directly related to future risk. These locations include some of the most populated areas in the US, including the states of Florida, Texas and California. We also find that population growth rates in communities that are exposed to high frequency flooding (5 and 20 year return period risk) are 2-7% lower than baseline. This finding is exacerbated in areas at disproportionate risk of the most frequent flooding where growth is expected to reverse and decline over the next 30 years.
Effects of extracorporeal circulation with different time on platelet count after cardiac surgery: A retrospective study based on medical records
Authors: Wang Na , Li Jiabei , Zeng Sisi , Wan Jixiang , Li Xuechao , Wang Fangjun 
Published: April 2023

Abstract
Background
Our objective was to observe the effects of extracorporeal circulation (ECC) with different time on platelet count in patients undergoing cardiac surgery.
Methods
A total of 427 patients who underwent elective cardiac surgery under ECC in affiliated hospital of north Sichuan medical college from January 1, 2018 to July 31, 2021 were divided into three groups according to ECC time. Their data were collected from the Do care and electronic medical record information system. All authors confirm that all methods were performed in accordance with the relevant guidelines and regulations.
Results
At the end of operation, platelet count was significantly lower in group C than in group A (p< 0.05); on the first day after operation, platelet count was significantly higher in groups A and B than in group C (p< 0.05); compared with group A, platelet count on the second day and the fifth day after operation were significantly lower in groups B and C (p< 0.05). The mean platelet volume (MPV) was significantly reduced at the end of operation in each group (p< 0.05). The absolute monocyte count at the end of operation was significantly higher in group C than in groups A and B (p< 0.05). The volume of blood loss and plasma transfusion were significantly lower in group A than in groups B and C (p< 0.05).
Conclusion
Platelet count in patients undergoing cardiac surgery after ECC was reduced significantly, which was more serious with the extension of ECC time. The recovery level and speed of platelet count in patients with long ECC time were lower than those with short ECC time.
Asymmetric two-dimensional ferroelectric transistor with anti- ambipolar transport characteristics
Authors: Zhao Yilin , Chi Mengshuang , Liu Jitao , Zhai Junyi 
Published: April 2023

Abstract
Two-dimensional (2D) ferroelectric transistors hold unique properties and positions, especially talking about low-power memories, in-memory computing, and multifunctional logic devices. To achieve better functions, appropriate design of new device structures and material combinations is necessary. We present an asymmetric 2D heterostructure integrating MoTe2, h-BN, and CuInP2S6 as a ferroelectric transistor, which exhibits an unusual property of anti-ambipolar transport characteristic under both positive and negative drain biases. Our results demonstrate that the anti-ambipolar behavior can be modulated by external electric field, achieving a peak-to-valley ratio up to 103. We also provide a comprehensive explanation for the occurrence and modulation of the anti-ambipolar peak based on a model describing linked lateral-and-vertical charge behaviors. Our findings provide insights for designing and constructing anti-ambipolar transistors and other 2D devices with significant potential for future applications.
The Significance of Monocyte Infiltration in the Immune Microenvironment for the Prognosis and Treatment of Pancreatic Cancer
Authors: Yao Wenchao , Liu Xuxu , Liu Tianming , Zheng Yi , Meng Ziang , Hao Yifei , Han Jinzuo , Wang Qiang , Lv Zhenyi , Xue Dongbo , Li Zhituo , Zhang Yingmei 
Published: April 2023

Abstract
Background A large number of studies have confirmed that immunotherapy of tumor immune microenvironment is one of the important treatment methods. In pancreatic cancer, monocytes play an important role in poor prognosis, but the mechanism and prognosis prediction methods are unclear.Methods CIBERSORT was used to identify cellular immune score and evaluate the effect of each immune cell on prognosis. The gene modules related to monocytes were obtained by weighted correlation network analysis through WGCNA package. Consensus clustering was used to screen out prognostic genes. The regression signature was generated by LASSO Cox analysis, and its reliability was verified by univariate and multivariate Cox analysis. The ssGSEA and TIDE algorithms were used to predict immune status and sensitivity to immune checkpoint blockade (ICBs) in tumor microenvironment. Finally, the expression levels of each gene in the signature were verified at tissue level and single cell level.Results High infiltration of monocytes suggests poor prognosis of pancreatic cancer. After WGCNA analysis and cluster typing, 262 genes were significantly differentially expressed and prognostic. The 6 gene (MET, ITGB6, CEP55, NUSAP1, MYEOV, LY6D) prognostic signature was established by LASSO Cox analysis. It was verified to be an independent prognostic factor for pancreatic cancer. The high-risk group had high infiltration of monocytes in the immune microenvironment and was more sensitive to ICBs. At the tissue level, all 6 genes were highly expressed in cancer tissues. At the single-cell level, MET and MYEOV were significantly higher in malignant cells and lower in monocytes.Conclusions High infiltration of monocytes affects the poor prognosis of pancreatic cancer, suggesting that the immune microenvironment has a certain research prospect for the treatment of pancreatic cancer. The monocyte-related genes signature can accurately assess the prognostic risk of pancreatic cancer.
Comparing Simple Interrupted vs. Continuous Fascial Closure Methods in Elective Midline Laparotomy, a randomized controlled trial
Authors: Alamdari Nasser Malekpour , Shams Faezeh , Hajimirzaie Seyed Hossein , Besharat Sara , Fathi Mohammad , Farsi Yeganeh , Abbasi Maryam 
Published: April 2023

Abstract
Background As a common complication of midline laparotomy, Incisional hernia (IH) imposes an additional cost on the healthcare system. The wound closure method has been considered one of the most critical risk factors for IH.Methods This randomized clinical trial was conducted on elective laparotomy patients between January 2018 and January 2019. All the patients were randomly allocated to two simple interrupted and continuous suture groups. All the surgeries were performed by a single surgeon and used PDS sutures. Demographic information and data on CBC, abdominal ultrasonography reports, and dehiscence or hernia were recorded in a pre-designed checklist. Patients were followed up for one year regarding surgery site pain and infection and the incidence of incisional hernia or fascia dehiscence.Results We analyzed 56 male and 34 female patients with a mean age of 49.53 ± 14.58 in two simple interrupted and continuous suture groups. After a one-year follow-up, 12 (26.6%) patients in simple interrupted and 9(20%) patients in the continuous suture group developed incisional hernia (p = 0.455). In addition, 5 (11.1%) patients in the simple and 3 (6.6%) patients in the continuous suture group had fascial dehiscence (p = 0.459). After the operation, 4(8.8%) patients in the simple and 3 (6.6%) patients in the continuous group developed wound infection (p = 0.694). In addition, there was no significant difference between the two groups on the pain scale following surgery (p = 0.262).Conclusions There are no significant differences between simple interrupted and continuous laparotomy incision closure methods regarding incisional hernia, fascial dehiscence, wound infections, and pain scale.
The meaning of the recovery process and its stages for people admitted to the mental health day hospital: a qualitative study
Authors: Ventosa-Ruiz Ana , Moreno-Poyato Antonio R. , Lluch-Canut Teresa , Feria-Raposo Isabel , Puig-Llobet Montserrat 
Published: April 2023

AbstractBackgroundThis study sought to explore the meaning of the recovery process and its stages from the perspective of people attending mental health day hospitals.MethodsA descriptive exploratory qualitative study was carried out. Semi-structured interviews were conducted with people admitted to a mental health day hospital. The data were analysed deductively by means of content analysis.ResultsThe participants described the recovery process as a process based on three pillars; the attitude towards recovery, hardship, and the effort required throughout the process. Regarding the stages of recovery, for the participants in the first stage of the process (Moratorium) the search for hope was the most important element. In the second stage (Awareness), the reestablishment of their identity, through the acceptance of the consequences derived from the mental health disorder, together with being able to feel full and fulfilled, were the most outstanding elements. In the third stage (Preparation), participants highlighted the search for meaning in life, facing their fears and the process with an open mind. Finally, the last two stages (Rebuilding and Growth) were related to taking responsibility and empowerment for recovery.ConclusionsThe results of this study provide insight into the perception of the recovery process and its stages in people admitted to mental health day hospitals. These findings may contribute to aligning the nurse-patient perspective, helping nurses to understand the key elements of patients according to their stage of recovery, and thus be able to subsequently individualise interventions.