bluuebunny/crossref_metadata_2025_split huggingface dataset:
SMCHD1 genetic variants in type 2 FacioScapuloHumeral dystrophy and challenges in predicting pathogenicity and disease penetrance.
Authors: Magdinier Frederique , Gerard Laurene , Delourme Megane , Ganne Benjamin , Perrin Pierre , Chaix Charlène , Trani Jean Philippe , Eudes Nathalie , Laberthonniere Camille , Tardy Charlotte , Bertaux Karine , Missirian Chantal , Bassez Guillaume , BEHIN Anthony , Cintas Pascal , Cluse Florent , Cruz Elisa de la , Delmont Emilien , Evangelista Teresinha , FRADIN Mélanie , Hadouri Nawale , Kouton Ludivine , LAFORET Pascal , Lefeuvre Claire , Magot Armelle , Manel Véronique , Nectoux Juliette , Pegat Antoine , Sol� Guilhem , Spinazzi Marco , STOJKOVIC Tanya , Svahn Juliette , Tard Celine , Thauvin Christel , Camille Verebi , Campana-Salort Emmanuelle , Attarian Shahram , Nguyen Karine , Badache Ali , Bernard Rafaelle 
Published: February 2024

Abstract

The molecular diagnosis of type 1 FacioScapuloHumeral Dystrophy (FSHD1) relies on the detection of a shortened D4Z4 array at the 4q35 locus while until recently, the diagnosis of FSHD2 relied on the absence of a shortened D4Z4 allele in clinically affected patients. The vast majority of FSHD2 patients carry a heterozygous variant in the SMCHD1 gene. In addition, a decreased in D4Z4 DNA methylation is consistently associated with FSHD1 and FSHD2. In molecular genetic diagnostics, predicting the pathogenicity of SMCHD1 variants remains challenging, as many are classified as variants of unknown significance or likely pathogenic. To refine the diagnosis of FSHD2, define 4q-associated molecular features and validate the pathogenicity of SMCHD1 variants, we explored a cohort of 54 FSHD2 patients carrying a variant in SMCHD1 or hemizygosity of the 18p32 locus encompassing the gene. Genetic and epigenetic analyses together with a clinical description of patients were combined to confirm the pathogenicity of new SMCHD1 variants and previously reported ones initially classified as likely pathogenic. We defined a threshold of 40% of methylation at the D4Z4 DR1 site as associated with SMCHD1 pathogenic variants. We also showed that the number of D4Z4 units on the shortest 4qA allele ranges from 11 up to 35 units in patients clinically affected with FSHD2. Using prediction tools, our study further highlighted the difficulty in interpretating the impact of pathogenic variants on the severity of the disease. Our study further emphasizes the complex relationship between D4Z4 methylation, SMCHD1 variants, and disease penetrance in FSHD.
Metagenomic Analysis of Bronchoalveolar Lavage Fluid Enables Differential Diagnosis Between Lung Cancer and Pulmonary Infections
Authors: Chen Yu , Han Dongsheng , Yu Fei , Yang Bin , Shen Yifei , Zhang Dan , Liu Huifang , Bin Lou , Lou Bin , Wang Jingchao , Murugesan Kanagavel , Tang Hui , Zhou Hua , Xie Mengxiao , Yuan Lingjun , Zhou Jieting , Zheng Shufa 
Published: February 2024

Abstract

Recent advances in unbiased metagenomic next-generation sequencing (mNGS) have enabled the simultaneous examination of both microbial and host genetic material in a single test. This study harnesses cost-effective bronchoalveolar lavage fluid (BALF) mNGS data from patients with lung cancer (n=123) and pulmonary infections (n=279). We developed a machine learning-based diagnostic approach to differentiate between these two conditions, which are often misdiagnosed in clinical settings. To ensure independence between model construction and validation, we divided the cohorts based on the collection dates of the samples. The training cohort (lung cancer, n=87; pulmonary infection, n=197) revealed distinct differences in DNA/RNA microbial composition, bacteriophage abundances, and host responses, including gene expression, transposable element levels, immune cell composition, and tumor fraction determined by copy number variation (CNV). These features, blinded to the validation cohort, were integrated into a host/microbe metagenomics-driven machine learning model (Model VI). The model demonstrated an Area Under the Curve (AUC) of 0.87 (95% CI = 0.857-0.883) in the training cohort and 0.831 (95% CI = 0.819-0.843) in the validation cohort for differentiating between patients with lung cancer and pulmonary infections. Applying a composite predictive model based on a rule-in and rule-out strategy significantly increased accuracy in distinguishing lung cancer from tuberculosis (ACC=0.913), fungal infection (ACC=0.955), and bacterial infection (ACC=0.836). These results underscore the potential of mNGS-based analysis as a valuable, cost-effective tool for the early differentiation of lung cancer from pulmonary infections, offering a comprehensive testing solution in a clinical context.
Laparoscopic Surgical Techniques and Outcomes for Surgically Managed Ectopic Pregnancies. A 10-Year Synopsis at a tertiary referral center in Nairobi, Kenya
Authors: Mutiso Steve Kyende 
Published: February 2024

Abstract

Background:
Ectopic Pregnancies(EP) are a pregnancy related complication that can have significant morbidity. Due to this fact and the fact that most present after rupture, surgical management forms the cornerstone of management of most EP. We set out to conduct an audit ,for a 10-year period, on laparoscopically managed EP at a tertiary referral center with focus on surgical techniques used, outcomes and correlations of complications to outcomes.
Methods:
This study was designed as a Retrospective Clinical Audit based at the Aga Khan University Hospital (AKUH). Study population was all women admitted to AKUH with a diagnosis of ectopic pregnancy that was surgically managed between the period of January 1st 2011 to December 31st 2020. Analysis of data was done against a pre-set checklist. Descriptive statistics for continuous variables was calculated and tabulated in graphs and tables. SPSS version 22 was used for analysis of data.
Results:
A total of 324 patients were recruited in the analysis of surgical treatment of EP. 86.1% had a total salpingectomy done; 5.2% had a partial salpingectomy done; 2.2% had a salpingostomy done; 4% had a fimbrial milking done; 1.9% had resection of the EP and 0.6% had and oophorectomy done. 64.8% of the surgeries used bipolar and scissors; 21.2% used endoloop while 5.6%(n = 18) used a combination of instruments. Most (92.4%; n = 302) of the patient did not require conversion to an open procedure. The rate of conversion decreased with advancing years. Almost all the surgeries were less than 2 hours (91.7%,n = 297) with only 1(0.3%) going past 3 hours. Most of the surgeries did not have complications (96.3%, n = 334). Duration of stay after surgery varied from 1–13 days. Most of the patients stayed for 2 days (90.8%, n = 296); 5.8%(n = 19) had a stay of 3 days and 3.4%(n = 11) had a stay of more than 4 days. Only 50 (15.2% of 347) patients in the present study had a documented subsequent pregnancy. 42 patients had an intrauterine pregnancy: 84%,n = 42 and 16%,n = 8 had a repeat ectopic pregnancy.
Conclusion:
In conclusion, the present study shows that total salpingectomy is the most common surgical treatment option for patients with EP with bipolar and scissors technique being used frequently. Low conversion to open surgery rates are observed with a decline being seen as the centers’ experience grows over the years. Surgery duration and hospital stay are within the expected norms for laparoscopically managed EP when compared to more experienced centers. Moreover, the low complication rate in the present study can be attributed to the advancing experience with EP over the years coupled with the low conversion rate to open surgery hence accrued benefits from a laparoscopic approach. Lastly, most of the patients with a recurred EP had had total salpingectomy pointing towards an inherent tubal disorder causing the recurrence.
Feasibility Study of an Embodied and Embedded Mindfulness- and Compassion-Based Intervention for Non-Suicidal Self-Injury Disorder
Authors: Schmelefske Emma , Per Megan , Anand Leena , Khoury Bassam , Heath Nancy 
Published: February 2024

Abstract
Background
Non-suicidal self-injury (NSSI) is associated with suicide risk, as well as a number of psychological disorders. This, coupled with its high prevalence rate, make it imperative that effective treatments for those who engage in NSSI are investigated and made available to the public. Despite this, few interventions specifically targeting NSSI have been researched. In fact, to date, there are no evidence-based treatments for NSSI. This study aimed to address this gap in the existing research by investigating the effectiveness, feasibility, and acceptability of an embodied and embedded mindfulness and compassion treatment (EEMCT) for individuals who engage in self-injury.
Methods
Six participants attended eight weekly two-hour group therapy sessions. Outcomes measured included urges to self-injure, as well as mental health symptoms commonly associated with NSSI (i.e., depression, anxiety, difficulty with emotion regulation, perceived stress). Outcomes were measured at pre-intervention, post-intervention, and six months follow-up.
Results
Anxiety decreased significantly from pre-intervention to post-intervention and from pre-intervention to follow-up. Depressive symptoms also significantly decreased from pre-intervention to follow-up, as did emotion regulation. Perceived stress did not show significant change across time points, nor did urges to self-injure. Participants gave feedback about the intervention in semi-structured interviews. They noted benefits of the intervention (e.g., learning self-kindness and awareness of thoughts and feelings), as well as several ways in which the intervention could be improved (e.g., more take-home practice material, shorter meditations). Conclusions
Is palliative care a utopia for older patients with organ failure, dementia or frailty? A qualitative study through the prism of emergency department admission
Authors: Bourmorck Delphine , Pétré Benoit , de Saint-Hubert Marie , De Brauwer Isabelle 
Published: February 2024

Abstract
Background
Nearly three out of four older people will use the emergency department (ED) during their last year of life. However, most of them do not benefit from palliative care. Providing palliative care is a real challenge for ED clinicians who are trained in acute, life-saving medicine. Our aim is to understand the ED’s role in providing palliative care for this population.
Methods
We designed a qualitative study based on 1) interviews – conducted with older patients (≥75 years) with a palliative profile and their informal caregivers – and 2) focus groups – conducted with ED and primary care nurses and physicians. Palliative profiles were defined by the Supportive and Palliative Indicators tool (SPICT). Qualitative data was collected in French-speaking Belgium between July 2021 and July 2022. We used a constant inductive and comparative analysis.
Results
Five older patients with a palliative profile, four informal caregivers, 55 primary and ED caregivers participated in this study. A priori, the participants did not perceive any role for the ED in palliative care. In fact, there is a widespread discomfortwith caring for older patients and providing palliative care. This is explained by multiple areas of tensions. Palliative care is an approach fraught with pitfalls, i.e.: knowledge and know-how gaps, their implementation depends on patients’(co)morbidity profile and professional values, experiences and type of practice. In ED, there are constant tensions between emergency and palliative care requirements, i.e.: performance, clockwork and needs for standardised procedures versus relational care, time and diversity of palliative care projects. However, even though the ED’s role in palliative care is not recognised at first sight, we highlighted four roles assumed by ED caregivers: 1) Investigator, 2) Objectifier, 3) Palliative care provider, and 4) Decision-maker on the intensity of care. Their main perspective is that ED caregivers could be the identifiers of early palliative profile.
Conclusions
Even if there are still major obstacles to implementing palliative care for older patients upon admission to the emergency department, ED caregivers already assume certain roles, although they do not recognise them as such. In the future, ED caregivers might also endorse the role of early identifier.
Unraveling the atomic structure evolution of titanium nitride upon oxidation
Authors: Li Qianqian , Hao Ronghui , Miao Wenkang , Xu Wanyin , Lin Yicheng , Xiao Qiling , Wang Zihan , Wang Peng , Wang Tianzhong , Nie Anmin , Wu Jinsong , Wang Hongtao 
Published: February 2024

Abstract
Oxidation-induced structural failure is a major issue in high-strength non-oxide ceramics, yet the atomic-level structural changes underlying phase transformation have remained elusive. Here, we present a study that employs state-of-the-art aberration-corrected environmental transmission electron microscopy to unravel the atomic-scale structural evolution of titanium nitride during dynamic oxidation. Our findings reveal two distinct reaction pathways, each characterized by the migration of titanium atoms through the formation of chains of titanium vacancies and staggered titanium vacancies. We demonstrate that these pathways are significantly influenced by both crystal orientation and surface curvature. Our rigorous First-principles calculations elucidate the underlying mechanism, revealing that titanium atoms have the highest kinetics for moving out along the {200} family, while their movement is modulated by surface strain involved in curvature changes. This insight is further substantiated by macroscopic oxidation experiments, affirming that the precision control of material orientation indeed enhances antioxidative performance. Our research holds immense scientific and technological significance, advancing our understanding of materials' antioxidation performance and ultimately bolstering durability and extending lifespan.
Clinical, genomic, and neurophysiological correlates of lifetime suicide attempts among individuals with alcohol dependence
Authors: Barr Peter , Neale Zoe , Chatzinakos Chris , Schulman Jessica , Mullins Niamh , Zhang Jian , Chorlian David , Kamarajan Chella , Kinreich Sivan , Pandey Ashwini , Pandey Gayathri , de Viteri Stacey Saenz , Acion Laura , Bauer Lance , Bucholz Kathleen , Chan Grace , Dick Danielle , Edenberg Howard , Foroud Tatiana , Goate Alison , Hesselbrock Victor , Johnson Emma , Kramer John , Lai Dongbing , Plawecki Martin , Salvatore Jessica , Wetherill Leah , Agrawal Arpana , Porjesz Bernice , Meyers Jacquelyn 
Published: February 2024

Abstract
Research has identified clinical, genomic, and neurophysiological markers associated with suicide attempts (SA) among individuals with psychiatric illness. However, there is limited research among those with an alcohol use disorder (AUD), despite their disproportionately higher rates of SA. We examined lifetime SA in 4,068 individuals with DSM-IV alcohol dependence from the Collaborative Study on the Genetics of Alcoholism (23% lifetime suicide attempt; 53% female; 17% Admixed African American ancestries; mean age: 38). We 1) conducted a genome-wide association study (GWAS) of SA and performed downstream analyses to determine whether we could identify specific biological pathways of risk, and 2) explored risk in aggregate across other clinical conditions, polygenic scores (PGS) for comorbid psychiatric problems, and neurocognitive functioning between those with AD who have and have not reported a lifetime suicide attempt. The GWAS and downstream analyses did not produce any significant associations. Participants with an AUD who had attempted suicide had greater rates of trauma exposure, major depressive disorder, post-traumatic stress disorder, and other substance use disorders compared to those who had not attempted suicide. Polygenic scores for suicide attempt, depression, and PTSD were associated with reporting a suicide attempt (ORs = 1.22–1.44). Participants who reported a SA also had decreased right hemispheric frontal-parietal theta and decreased interhemispheric temporal-parietal alpha electroencephalogram resting-state coherences relative to those who did not, but differences were small. Overall, individuals with alcohol dependence who report SA appear to experience a variety of severe comorbidities and elevated polygenic risk for SA. Our results demonstrate the need to further investigate suicide attempts in the presence of substance use disorders.
A Prospective Study on Incomplete Radiofrequency Ablation in the Treatment of Colorectal Cancer Liver Metastasis
Authors: Lu Huilin , Dong Xiangjun , Xie Xuancheng , Xia Xiangwen , Tang Bufu , Fan Hongjie 
Published: February 2024

Abstract

Objectives
To identify the predictors of incomplete percutaneous radiofrequency ablation (RFA) of colorectal cancer liver metastases (CLMs) and evaluate the impact of incomplete RFA (iRFA) on the overall survival (OS) of patients and new intrahepatic metastases (NIHM).
Methods
We prospectively analyzed the data of patients with CLM who received percutaneous RFA. Dynamic contrast-enhanced computed tomography was used to assess ablation. All CLMs were divided into development and internal validation cohorts. We analyzed the predictive factors of iRFA in the development cohort and assessed the status of NIHM and OS of all patients through the Kaplan–Meier method.
Results
One hundred and sixty-four patients (mean age, 60.6 ± 11.3 years; 104 men) with 338 tumors were included in this study. Perivascular tumor location, tumor size ≥ 20 mm, and minimal ablative margin were independent predictors of iRFA. The area under the receiver operating characteristic curve was 0.884 and 0.857 for the development and internal validation cohorts, respectively. NIHM were more likely to occur in the iRFA group than in the complete RFA (cRFA) group (χ2 = 26.811, P < 0.001). The estimated median OS was 45 months, and the cumulative OS for 1, 3, and 5 years was 92.2%, 59.7%, and 41.2%, respectively. The OS of the iRFA group was 39 months shorter than that of the cRFA group (χ2 = 12.269, P < 0.001).
Conclusions
Non-perivascular tumor location, tumor size < 2 cm, and a sufficient minimum ablation margin are essential for cRFA. Incomplete RFAs are related to the occurrence of NIHM and a much shorter OS.
Ongoing transmission of trachoma in low prevalence districts in Mozambique: Results from four cross-sectional enhanced impact surveys, 2022
Authors: Sitoe Henis , Oswald William Edward , Zita Felizmina , Fall Mawo , Momade Tamimo , Adams Molly W , Flueckiger Rebecca M , McPherson Scott , Eyob Sabrina , Doan Thuy , Lietman Thomas M , Arnold Benjamin F , Wickens Karana , Gwyn Sarah , Martin Diana L , Kasubi Mabula , Boyd Sarah , Bakhtiari Ana , Jimenez Cristina , Solomon Anthony W , Harding-Esch Emma M , Ngondi Jeremiah M 
Published: February 2024

Abstract

Mozambique is making progress towards elimination of trachoma as a public health problem, but in some districts trachomatous inflammation—follicular (TF) prevalence remains above the 5% elimination threshold despite years of various interventions, including antibiotic mass drug administration. To characterize transmission in four districts, we incorporated testing of ocular infection and serology into routine trachoma impact surveys (TIS) in August 2022. We examined residents aged ≥ 1 year for trachoma and collected information on household water, sanitation, and hygiene. Among children aged 1–9 years, we tested conjunctival swabs for Chlamydia trachomatis nucleic acid and dried blood spots for C. trachomatis antibodies. We modeled age-dependent seroprevalence to estimate seroconversion rate (SCR). We examined 4,841 children aged 1–9 years. TF prevalence ranged between 1.1–6.0% with three districts below the 5% threshold. PCR-confirmed infection prevalence ranged between 1.1–4.8%, and Pgp3 seroprevalence ranged between 8.8–24.3%. Pgp3 SCR was 1.9 per 100 children per year in the district with the lowest TF prevalence. Two other districts with TF < 5% had SCR of 5.0 and 4.7. The district with TF ≥ 5% had a SCR of 6.0. This enhanced TIS furthered understanding of transmission in these districts and provides information on additional indicators for monitoring trachoma programs.
Significance of microbial binding in the formation and stabilization of a Silurian carbonate forereef slope
Authors: Torres Alejandra Santiago , Grammer G. Michael , Eberli Gregor P. , Diaz Mara R. , Gregg Jay 
Published: February 2024

Abstract
The effect of microbial binding for the stabilization of steep carbonate slopes is well documented in Cenozoic examples but its significance and relationship with abiotic marine cements in Paleozoic reef systems and steep slopes is not yet fully understood. Here, samples from a Late Silurian (Ludlovian) reef complex are evaluated by using an integrated approach that involves petrographic and isotope analyses, cathodoluminescence microscopy, and environmental scanning electron microscopy. This study reveals the in situ production of mineral fabrics of microbial origins, including micrite, peloidal micrite with dendritic fabrics, meniscus and bridge-like cements. This study stresses the leading role of microbes in the early lithification stages that led to the stabilization of Silurian steep carbonate slopes. These findings are further supported by the occurrence of fossilized microbes and extracellular polymeric substance. The micritic cements are first step in the diagenetic paragenesis followed by abiotic fibrous and equant calcite cements whose stable isotope values are in concert with estimated values of calcite precipitated in equilibrium with Silurian seawater. Based on these findings, we develop a model for the sedimentology and diagenesis of Silurian (Niagaran) reefs in and around the Michigan Basin. Results from this project provide insights into the relationship between microbial binding and early abiotic marine cements in ancient reef systems.
Relationship Between Heated Tobacco Products and Placental Abruption: A Prospective Cohort Study Using Online Questionnaire
Authors: Ooba Hikaru , Maki Jota , Tabuchi Takahiro , Masuyama Hisashi 
Published: February 2024

Abstract
Background
Placental abruption (PA) is a critical obstetric complication, with maternal smoking recognized as a key risk factor. Despite the increased use of heated tobacco products (HTPs), the impact of HTPs remains unclear. This study investigated whether pregnant women using HTPs are at a higher risk of PA than non-users.
Methods
We analyzed data from "the Japan COVID-19 and Society Internet Survey," a prospective, self-reported online survey cohort. Questionnaires were randomly distributed between July 28, 2021, and August 30, 2021. Pregnant respondents in 2021 were invited to complete an additional survey from February 14, 2022, to February 28, 2022. We set the outcome as the absolute risk difference (aRD) and relative risk ratio (rRR) of PA incidence due to smoking HTPs in the first trimester of pregnancy. The sample size included 12 836 participants. We calculated outcomes using a generalized linear model (GLM) and inverse probability of treatment weighting (IPTW). We also performed a Bayesian approach and multiple-bias analysis for sensitivity analysis.
Results
We found the robust aRD of 0.07 (95% confidence interval (CI): 0.06, 0.09) and the rRR of 11.3 (95% CI: 7.5, 17.0). Multiple bias analyses showed that unmeasurable confounders would need to have at least an rRR = 14 relationship with both exposure and outcome to disprove the observed association. There has not been post hoc analysis or secondary use of data.
Conclusion
Early pregnancy use of HTPs is associated with an increased risk of PA.