bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive and realistic simulation of tumour genomic sequencing data
Authors: O’Sullivan Brian , Seoighe Cathal 
Published: September 2023

Abstract
Accurate identification of somatic mutations and allele frequencies in cancer has critical research and clinical applications. Several computational tools have been developed for this purpose but, in the absence of comprehensive ‘ground truth’ data, assessing the accuracy of these methods is challenging. We created a computational framework to simulate tumour and matched normal sequencing data for which the source of all loci that contain non-reference bases is known, based on a phased, personalized genome. Unlike existing methods, we account for sampling errors inherent in the sequencing process. Using this framework, we assess accuracy and biases in inferred mutations and their frequencies in an established somatic mutation calling pipeline. We demonstrate bias in existing methods of mutant allele frequency estimation and show, for the first time, the observed mutation frequency spectrum corresponding to a theoretical model of tumour evolution. We highlight the impact of quality filters on detection sensitivity of clinically actionable variants and provide definitive assessment of false positive and false negative mutation calls. Our simulation framework provides an improved means to assess the accuracy of somatic mutation calling pipelines and a detailed picture of the effects of technical parameters and experimental factors on somatic mutation calling in cancer samples.
Most protein domains exist as variants with distinct functions across cells, tissues and diseases
Authors: Vitting-Seerup Kristoffer 
Published: September 2023

AbstractProtein domains are the active subunits that provide proteins with specific functions through precise three-dimensional structures. Such domains facilitate most protein functions, including molecular interactions and signal transduction. Currently, these protein domains are described and analyzed as invariable molecular building blocks with fixed functions. Here, I show that most human protein domains exist as multiple distinct variants termed ‘domain isotypes’. Domain isotypes are used in a cell, tissue and disease-specific manner and have surprisingly different 3D structures. Accordingly, domain isotypes, compared to each other, modulate or abolish the functionality of protein domains. These results challenge the current view of protein domains as invariable building blocks and have significant implications for both wet- and dry-lab workflows. The extensive use of protein domain isotypes within protein isoforms adds to the literature indicating we need to transition to an isoform-centric research paradigm.
Racism hurts, can antiracism heal?: Positive mental health correlates of antiracist engagement
Authors: Brannon Tiffany N 
Published: September 2023

Abstract
Racism can hurt by negatively impacting mental health. For instance, large-scale events tied to racism like the May 2020 police-involved murder of George Floyd have been linked to poor mental health indicators (e.g. depression and anxiety). Notably, racism can spark antiracist engagement—support for addressing systemic racism. For example, Floyd's murder sparked unprecedented antiracist engagement, including heightened Black Lives Matter (BLM) support and protest participation. The present research explored the potential that antiracist engagement can heal: be positively associated with well-being. First, study 1 found that state-level BLM engagement (i.e. protest numbers, antiracism information-seeking on Google/YouTube) during an 8-week period following Floyd's death was associated with positive mental health indicators (i.e. lower depression and anxiety, higher self-rated health). It found these effects among racial/ethnic minorities (e.g. Black/African Americans, Hispanics, N = 161,359) and Whites (N = 516,002). Then, study 2 examined social media data (i.e. tweets) and emotional well-being. It used a measure of happiness indexed across 144,649,285,571 tweets from 2019 through 2021. It found a positive correlation between the volume of tweets with antiracist engagement content (e.g. referenced efforts to address systemic racism) and the happiness measure. Finally, study 3 examined antiracism protest data/information-seeking and a sample of BLM tweets (N = 100,321) posted between April and July 2020. Conceptually replicating studies 1–2, study 3 found that antiracist engagement was associated with greater positive emotion/sentiment (e.g. happiness) relative to negative emotion/sentiment (e.g. anxiety). Relevant to theory and policy, the observed results suggest that antiracist engagement can be associated with benefits for well-being across racial/ethnic groups.
The unique 3D arrangement of macrophage galactose lectin enables Escherichia coli lipopolysaccharide recognition through two distinct interfaces
Authors: Abbas Massilia , Maalej Meriem , Nieto-Fabregat Ferran , Thépaut Michel , Kleman Jean-Philippe , Ayala Isabel , Molinaro Antonio , Simorre Jean-Pierre , Marchetti Roberta , Fieschi Franck , Laguri Cedric 
Published: September 2023

Abstract
Lipopolysaccharides are a hallmark of gram-negative bacteria, and their presence at the cell surface is key for bacterial integrity. As surface-exposed components, they are recognized by immunity C-type lectin receptors present on antigen-presenting cells. Human macrophage galactose lectin binds Escherichia coli surface that presents a specific glycan motif. Nevertheless, this high-affinity interaction occurs regardless of the integrity of its canonical calcium-dependent glycan-binding site. NMR of macrophage galactose-type lectin (MGL) carbohydrate recognition domain and complete extracellular domain revealed a glycan-binding site opposite to the canonical site. A model of trimeric macrophage galactose lectin was determined based on a combination of small-angle X-ray scattering and AlphaFold. A disulfide bond positions the carbohydrate recognition domain perpendicular to the coiled-coil domain. This unique configuration for a C-type lectin orients the six glycan sites of MGL in an ideal position to bind lipopolysaccharides at the bacterial surface with high avidity.
Representing the special linear group with block unitriangular matrices
Authors: Urschel John 
Published: September 2023

Abstract
We prove that every element of the special linear group can be represented as the product of at most six block unitriangular matrices, and that there exist matrices for which six products are necessary, independent of indexing. We present an analogous result for the general linear group. These results serve as general statements regarding the representational power of alternating linear updates. The factorizations and lower bounds of this work immediately imply tight estimates on the expressive power of linear affine coupling blocks in machine learning.
Macroprudential Policy, Mortgage Cycles, and Distributional Effects: Evidence from the United Kingdom
Authors: Peydró José-Luis , Rodriguez-Tous Francesc , Tripathy Jagdish , Uluc Arzu 
Published: September 2023

Abstract
We analyze the distributional effects of macroprudential policy on mortgage cycles by exploiting the U.K. mortgage register and a 2014 15% limit imposed on lenders’ high loan-to-income (LTI) mortgages. Constrained lenders issue fewer and more expensive high-LTI mortgages, with stronger effects on low-income borrowers. Unconstrained lenders strongly substitute high-LTI loans in local areas with higher constrained lender presence, but not high-LTI loans to low-income borrowers—consistent with adverse selection problems—implying lower overall credit to low-income borrowers. Consistently, policy-affected areas experience lower house price growth postregulation and, following the Brexit referendum (negative aggregate shock), better house price growth and lower mortgage defaults for low-income borrowers.
Reproductive health in female patients with systemic sclerosis: a cross-sectional study
Authors: Dai Liyi , Xu Dan , Li Xinyi , Huang Sicheng , Duan Xiangyue , Zheng Ai , Yang Jing , Zhao Jie , Zeng Lin , Mu Rong 
Published: September 2023

Abstract

Objectives
To explore the status of reproductive health and related factors in female patients with systemic sclerosis (SSc).

Methods
A cross-sectional study was conducted among female patients from the Chinese Organization for Scleroderma through a questionnaire. Data on the status of reproductive health including fertility condition and menstrual status were obtained. The clinical and laboratory data of SSc were collected. For patients with pregnancies after disease onset, each pregnancy was matched with a healthy control. Associations between clinical characteristics and the status of reproductive health were analysed.

Results
A total of 342 female patients with SSc were included, and 31.8% (108/342, 95% CI 26.9%–36.7%) of them presented problems with reproductive health. Compared with the national data, the menopausal age of patients with disease onset before menopause was earlier (45.2 ± 6.1 vs 48.2 ± 4.4, P &lt; 0.001). Age of disease onset (P = 0.018) and digital ulcer (P = 0.020) had statistically significant effects on menopausal age. Although the infertility rate of patients was not increased, the rate of spontaneous abortions was higher compared with the national data (9/74, 12.2% vs 4.3%, P &lt; 0.001). Compared with the healthy control group, the rate of premature infants (12/55, 21.8% vs 7/110, 6.4%, P = 0.003), low birth weight infants (15/55, 27.3% vs 6/110, 5.5%, P &lt; 0.001), and cesarean section (27/55, 49.1% vs 21/110, 19.1%, P &lt; 0.001) increased significantly.

Conclusion
The impairment of reproductive health is common and in many quarters in patients with SSc. Further action should be taken to improve reproductive health in patients with SSc, especially in maternal care.
Can’t Just Send Our Children Out: Intensive Motherwork and Experiences of Black Motherhood
Authors: Brantley Mia 
Published: September 2023

AbstractRace and racism play an integral role in shaping mothering practices. Specifically, motherwork examines how Black mothers use strategies and practices to shield children from, as well as help them navigate through, experiences of racism. The necessity of these mothering practices may be fundamental in how motherhood is experienced for Black women. This study used qualitative in-depth semi-structured interviews with 35 predominantly middle-class Black mothers of children in adolescence and young/emerging adulthood. A grounded theoretical and Black feminist approach was taken to analyze data. Black mothers take on numerous laborious and exhaustive strategies to shield their children from racism through what I theorize as the concept of intensive motherwork. I define intensive motherwork as the exhaustive efforts and effects of Black mothers protecting and empowering their children and themselves in the face of anti-Black racism. Intensive motherwork can be seen in three broad themes: (1) protective mothering, (2) resistance mothering, and (3) encumbered mothering. This work expands current discourse on Black families by highlighting the overlap between the intensive nature of Black women’s mothering, the laborious practices that are deployed, and the role of race and racism on Black women’s mothering experience.
Testicular tissue response following a 90-day subchronic exposure to HTP aerosols and cigarette smoke in rats
Authors: Wang Hongjuan , Tian Yushan , Fu Yaning , Ma Shuhao , Xu Xiaoxiao , Wang Wenming , Lu Fengjun , Li Xianmei , Feng Pengxia , Han Shulei , Chen Huan , Hou Hongwei , Hu Qingyuan , Liu Chuan 
Published: September 2023

Abstract

Background
Researches have shown that chronic inhalation of cigarette smoke (CS) disrupts male reproductive system, but it is unclear about the mechanisms behind reproductive damages by tobacco toxicants in male rats. This study was designed to explore the effects of heated tobacco products (HTP) aerosols and CS exposure on the testicular health of rats.

Materials and Methods
Experiments were performed on male SD rats exposed to filtered air, HTP aerosols at 10 μg/L, 23 μg/L, and 50 μg/L nicotine-equivalent contents, and also CS at 23 μg/L nicotine-equivalent content for 90 days in five exposure groups (coded as sham, HTP_10, HTP_23, HTP_50 and Cig_23). The expression of serum testosterone, testicular tissue inflammatory cytokines (IL-1β, IL-6, IL-10, TNF-α), reactive oxygen species (ROS), superoxide dismutase (SOD) and malondialdehyde (MDA), NLRP3 inflammasome-related mRNAs and proteins (NLRP3, ASC, and Caspase-1), the degree of pyroptosis and histopathology were investigated.

Results
The results demonstrated that HTP_50 and Cig_23 caused varying degrees of oxidative damage to rat testis, resulting in a decrease of sperm quantity and serum testosterone contents, an increase in the deformity rate, expression levels of proinflammatory cytokines, and NLRP3 inflammasome-related mRNA, and an increase in the NLRP3, ASC, and Caspase-1-immunopositive cells, pyroptosis cell indices, and histopathological damage in the testes of rats. Responses from the HTP_10 and HTP_23 groups were less than those found in the above two exposure groups.

Conclusion
These findings indicate that HTP_50 and Cig_23 induced oxidative stress in rat testes, induced inflammation and pyroptosis through the ROS/NLRP3/Caspase-1 pathway, and destroyed the integrity of thetesticular tissue structure.
Clinical Characteristics of Gram-Negative Surgical Site Infections in Patients Treated With Mohs Micrographic Surgery: A Retrospective Analysis
Authors: Hicks Alexander , Mazumder Anika , Moody Rylee , Kumanan Krithika , Behshad Ramona 
Published: September 2023

BACKGROUND
Surgical site infections (SSIs) are the most common adverse events after Mohs micrographic surgery (MMS). However, there is a paucity of literature characterizing gram-negative (GN) SSIs after MMS.

OBJECTIVE
This study aimed to depict the clinical features and risk factors of GN infections after MMS.

MATERIALS AND METHODS
A retrospective review was performed from all postoperative wound cultures after MMS from 2017 to 2021 at Saint Louis University Medical Center. Patient demographics, surgical details, and wound clinical characteristics at follow-up appointments were reviewed.

RESULTS
Six hundred and seventy-six wound cultures were eligible with 15.1% yielding GN infection. Gram-negative SSIs had significantly lower rates of severe erythema and purulence compared with gram-positive (GP) SSIs, and only had significantly more edema compared with culture-negative wounds (p < .05). Although not significant, there was a trend for GN SSIs to have higher rates of pain compared with culture-negative wounds (p = .075).

CONCLUSION
Gram-negative SSIs after MMS may present with more subtle clinical features, especially compared with typical GP infections. Having a low threshold for obtaining wound culture for edematous or painful postoperative wounds may aid in detecting potentially overlooked GN infections.
Patient Denial of Myocardial Infarction in the Prehospital Phase
Authors: Abed Mona A. , Khalil Amani A. , Moser Debra K. 
Published: September 2023

Background
Limited knowledge exists regarding patients' denial of myocardial infarction (MI) before hospitalization for an MI.

Objective
The aim of this study was to determine the prevalence and correlates of denial of MI in the prehospital phase of a confirmed MI.

Methods
This secondary analysis included 166 hospitalized patients (mean [SD] age, 54.1 [10.5] years) who developed MI outside a healthcare facility and had high congruence between their experienced and expected symptoms. Measurements included the Denial subscale of the Brief COPE Inventory, the modified Response to Symptoms Questionnaire, and a Likert scale measuring perceived risk for MI. Patients who arrived at a hospital at least 1 hour after the onset of their symptoms were considered to have prolonged prehospital delay.

Results
Despite their high symptom congruence, 77% of patients denied the possibility of having an MI before hospitalization. The lower denial group was characterized by cardiac history, whereas the higher denial group was distinguished by nonsmoking, a lower perceived risk of MI, less anxiety at symptom onset, and more concerns about seeking medical help. Compared with the lower denial group, patients in the higher denial group were more likely to underestimate the seriousness of their symptoms and delay seeking medical help. The higher denial group responded to symptoms in a more passive manner (eg, waiting), whereas the lower denial group showed a more problem-solving approach (eg, contacting emergency services).

Conclusions
Denial of MI is highly prevalent in the prehospital phase and is negatively linked with cognitive, emotional, and behavioral responses to MI symptoms.
Hypothermic oxygenated perfusion in liver transplantation: a meta-analysis of randomized controlled trials and matched studies
Authors: Tang Gang , Zhang Linyu , Xia Lingying , Zhang Jie , Wei Zhengqiang , Zhou Rongxing 
Published: September 2023

Background:
Hypothermic Oxygenated Machine Perfusion (HOPE) is a novel organ-preservation technology designed to optimize organ quality. However, the effects of HOPE on morbidity and mortality after liver transplantation remain unclear. This meta-analysis evaluated the potential benefits of HOPE in liver transplantation.

Materials and methods:
The Embase, Web of Science, PubMed, Cochrane Library, and Scopus databases were searched for articles published up to June 15, 2023 (updated on August 12, 2023). Mean differences (MD), risk ratios (RR), and 95% confidence intervals were calculated.

Results:
Eleven studies encompassing five randomized controlled trials and six matched studies were included, with a total of 1000 patients. HOPE did not reduce the incidence of major postoperative complications (RR 0.80), primary nonfunction (PNF) (RR 0.54), reperfusion syndrome (RR 0.92), hepatic artery thrombosis (RR 0.92), renal replacement therapy (RR 0.98), length of hospital stay (MD, −1.38 d), 1-year recipient death (RR 0.67), or intensive care unit stay (MD, 0.19 d) after liver transplantation. HOPE reduced the incidence of biliary complications (RR 0.74), non-anastomotic biliary strictures (NAS) (RR 0.34), early allograft dysfunction (EAD) (RR 0.54), and acute rejection (RR 0.54). In addition, HOPE improved the retransplantation (RR 0.42) and 1-year graft loss rates (RR 0.38).

Conclusions:
Compared with static cold storage (SCS), HOPE can reduce the incidence of biliary complications, NAS, EAD, and acute rejection and retransplantation rate after liver transplantation and improve the 1-year graft loss rate. These findings suggest that HOPE, when compared to SCS, can contribute to minimizing complications and enhancing graft survival in liver transplantation. Further research is needed to investigate long-term outcomes and confirm the promising advantages of HOPE in liver transplantation settings.
Comparison of two different methods for lymphadenectomy along the left recurrent laryngeal nerve by minimally invasive esophagectomy in patients with esophageal squamous cell carcinoma--a prospective randomized trial
Authors: Wang Ying-Jian , He Xian-Dong , He Yi-Qiu , Bao Tao , Xie Xian-Feng , Li Kun-Kun , Guo Wei 
Published: September 2023

Background:
Lymph nodes along the left recurrent laryngeal nerve (LRLN) is thought to be highly involved in esophageal cancer. Given the unique anatomical positioning of the nerve, performing lymphadenectomy in this region requires advanced techniques within limited working space. Meanwhile, high incidence of morbidity and mortality is associated with lymphadenectomy. Although several methods have been applied to reduce the technical requirement and the incidence of postoperative complication, the optimal method remains controversial.

Methods:
This study was a single-center, prospective, randomized trial to investigate the utility of lymphadenectomy along the LRLN during the minimally invasive esophagectomy (MIE) in esophageal squamous cell carcinoma (ESCC) patients by comparing the surgical outcome, postoperative complication, survival rate and quality of life (QoL) between the retraction method (RM) and the suspension method (SM) in patients with esophageal cancer from June 2018 to November 2020. QoL was assessed according to questionnaire: EQ-5D-5L.

Results:
Of 94 patients were enrolled and randomized allocated to RM and SM group equally. Characteristics did not differ between groups. The duration of lymph node dissection along LRLN was significant longer in SM group (P<0.001). No difference was observed about postoperative complications. One of in-hospital death was occurred in each group (P>0.999). Patients in neither of groups exhibiting difference about 3-year disease free survival rate (P=0.180) and overall survival rate (P=0.430). No difference was observed in postoperative QoL between groups at different time points (all, P>0.05).

Conclusion:
Both methods of lymph node dissection along the LRLN during MIE in ESCC patients are technically feasible and safe. The RM appears more favorable in terms of reducing surgical duration compared to the SM.
Neutrophil membrane engineered Panax ginseng root derived exosomes loaded miRNA 182-5p targets NOX4/Drp-1/NLRP3 signal pathway to alleviate acute lung injury in sepsis: experimental studies
Authors: Ma Chunhua , Liu Kun , Wang Fei , Fei Xiaochun , Niu Chaochao , Li Tao , Liu Liangming 
Published: September 2023

Background:
The purpose of this study was to prepare neutrophil membrane engineered Panax ginseng root derived exosomes (N-exo) and investigate the effects of N-exo miRNA 182-5p (N-exo-miRNA 182-5p) on acute lung injury (ALI) in sepsis.

Methods:

Panax ginseng root derived exosomes were separated by differential centrifugation. Neutrophil membrane engineering was performed on exo to obtain N-exo. miRNA182-5p was transmitted into N-exo by electroporation technology to obtain N-exo-miRNA 182-5p. LPS was used to establish an in vivo and in vitro model of acute lung injury (ALI) in sepsis to evaluate the anti-inflammatory effect of N-exo-miRNA 182-5p.

Results:
The results of transmission electron microscope (TEM) showed that exo was a double-layer membrane structure like a saucer. Nanoparticle tracking analysis (NTA) particle size analysis showed that the average particle size of exo was 129.7 nm. Further, compared with exo, the level of miRNA182-5p was significantly increased in N-exo. The experimental results showed that N-exo-miRNA 182-5p significantly improved ALI via target regulation of NOX4/Drp-1/NLRP3 signal pathway in vivo and in vitro.

Conclusion:
In conclusion, this study prepared a novel engineered exosome (N-exo) and N-exo-miRNA 182-5p significantly improved ALI in sepsis via target regulation of NOX4/Drp-1/NLRP3 signal pathway, providing new ideas and methods for treatment of ALI in sepsis.