bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing consistency of calculating homologous recombination deficiency (HRD) score using different segmentation method.
Authors: Chao Xiaopei , Li Lei , Kai Zhentian , Zhang Shuilong , Huang Lisha , He Hongsheng 
Published: August 2023

89 Background: A number of similar tests were developed since FDA approval of using niraparib in HRD positive (HRD score >=42) patients. However, various factors can substantially influence HRD score estimation. We hereby evaluated the concordancy of bioinformatics pipelines, especially different copy number variation (CNV) algorithms, in inferring HRD scores. Methods: A total of 195 ovarian cancer patients enrolled from April 2021 to Dec 2022 were used for retrospective analysis in this study. Both tumor tissue and blood samples were sequenced with Topgen HRD panel, which covered ~35,000 single nucleotide polymorphisms (SNPs). Sequence data were trimmed and aligned to hg19 reference genome. Two commonly used CNV pipeline (i.e. Sequenza, and PureCN which have tumor-normal mode and tumor-only mode) were adopted to generate allele specific copy number (ASCN) profile. HRD scores were then inferred from ASCN profile using R package scarHRD. Pearson correlation was used for evaluating correlation between HRD scores generated with different algorithms. Paired T-test and Wilcoxon signed-rank test was used in comparing differences in HRD scores and segment counts from different algorithms. Percentage agreement was evaluated based on cutoff of HRD score >=42. Results: HRD scores produced from Sequenza and PureCN (tumor-normal mode) showed significant correlation (R = 0.83, P value < 0.001). Sequenza tended to over-segment than PureCN (median segment counts: 139 vs 82, P value < 0.001) and have higher HRD scores (mean HRD scores: 55.0 vs 23.5, P value < 0.001). Using Sequenza, HRD-positivity was observed in 70.0% of the total population, whereas PureCN classified only 39.0% as HRD-positive. HRD scores inferred from two modes of PureCN showed improved correlation (R = 0.89, P value < 0.001). Tumor-only mode generated higher mean HRD score than tumor-normal mode (42.7 vs 36.0, p-value < 0.001). Prevalence of HRD-positivity was 47.7% using tumor-only mode. Using tumor-normal mode as the reference test, the percentages of agreement were shown in the Table. Conclusions: Comparison of different CNV algorithms demonstrated significant variances in HRD scores estimation. Despite good correlation between different pipelines was observed on HRD scores, the estimated prevalence of HRD-positive patients varied significantly from 39% to 70%. Our results urge the necessity of harmonisation on bioinformatics pipeline during HRD score calculation. [Table: see text]
Physician Perceptions of and Barriers to Pediatric Palliative Care for Children With Cancer in Brazil
Authors: McNeil Michael J. , Godfrey Alyssa , Loggetto Patricia , de Oliveira Junior André , Job Godwin , Boldrini Erica , Regina Costa Murra Glaucia , Antunes Geronutti Ayub Dileiny , Francisco Oliveira de Lima Allan , Esmeraldo Andrade de Almeida Aline , Lopes Garcia Julia , Beatriz Costa Neves do Amaral Anna , Cristina Cunha Ferreira e Fonseca Iêda , Friedrich Paola , Metzger Monika L. , Devidas Meenakshi , Agulnik Asya , Baker Justin N. ,   on behalf of the ADAPT Brazil Team
Published: August 2023

PURPOSE Early integration of pediatric palliative care (PPC) for children with cancer is critical to improving the quality of life of both the patient and family. Understanding physician perceptions of palliative care and perceived barriers to early integration is necessary to develop PPC in Brazil. METHODS The Assessing Doctors' Attitudes on Palliative Treatment survey was modified for use in Brazil. The survey was open from January 2022 to June 2022 and distributed to physicians of all specialties from participating institutions who treat children with cancer. Statistical analysis was complemented by qualitative analysis of open-ended responses. RESULTS A total of 272 respondents participated. Most respondents reported access to PPC experts for consultation (77.2%) and 34.5% indicated previous palliative care training. Physician knowledge of PPC was generally aligned with WHO guidance (median alignment, 93.0%; range, 80.5%-98.2%). However, about half (53.3%) felt comfortable addressing physical needs of patients receiving PPC, 35.3% addressing emotional needs, 25.8% addressing spiritual needs, and 33.5% addressing grief and bereavement needs. Most respondents (65.4%) felt palliative care should be involved from diagnosis, but only 10.3% stated that this occurred in their setting. The most important barriers identified were physician discomfort (89.0%), limited physician knowledge (88.6%), and lack of home-based services (83.8%). CONCLUSION Despite a strong understanding of the role of palliative care, physicians in Brazil reported low confidence delivering PPC to children with cancer. Additionally, physicians generally believed that PPC should be integrated earlier in the disease trajectory of children with cancer. This work will direct educational and capacity building initiatives to ensure greater access to high-quality PPC for children with cancer in Brazil to address patient and family suffering.
Nodal Metastases Associated With Fusion Oncogenes Are Age Dependent in Young Adult Patients With Thyroid Cancer
Authors: Li Haorong , Han Rulai , Meng Lingyang , Sun Yingkai , Zhao Ming , Zhou Wei , Xie Jing , Yu Danyan , Shen Liyun , Zhou Yulin , Wang Shu , Yan Jiqi , Wang Weiqing , Ye Lei 
Published: August 2023

Abstract

Context
Fusion oncogenes, especially those involving RET or NTRK, are known drivers of papillary thyroid cancer (PTC). They are prevalent in pediatric patients and correlate with aggressive tumor behavior.

Objective
We explored the age dependence of fusion oncogenes and aggressive tumor behavior in young adult PTC patients.

Experimental Design
We examined 150 tumors from 142 PTC patients aged between 17∼35 years old with established tumor-node-metastasis stages. Oncogenic drivers and the thyroid differentiation score (TDS) were determined by DNA and RNA sequencing of a target panel. Transcriptome analysis was performed in PTCs with RET fusions.

Results
Among 150 PTCs, we detected BRAF V600E (n = 105), RET fusions (n = 15), NTRK3 fusions (n = 8), and BRAF fusions (n = 4). We found that fusion oncogenes were associated with nodal metastasis when age was tiered into 3 groups: &lt;25 years, 25∼29 years, and 30∼35 years. Patients under 25 years old showed a marginal increase in tumor stage compared to those over 25 years (75.00% vs 21.74%, P = .0646). Risk of lateral lymph node metastasis increased with younger age (75.00% vs 27.27% vs 8.33%, P = .0369). As with advanced tumor and node stage, patients harboring fusion oncogenes and aged under 25 years showed the lowest TDS; genes associated with immunoglobulin production and production of molecular mediators of the immune response were significantly upregulated.

Conclusions
Adult PTC patients under 25 years with fusion oncogenes showed a tendency toward advanced tumor stage and lower thyroid differentiation. Integrating onset age together with oncogenic alterations is worthwhile when managing adult PTC patients.
Actin cytoskeletal dynamics do not impose an energy drain on growth cone bioenergetics
Authors: Holland Sabrina M. , Gallo Gianluca 
Published: August 2023

ABSTRACTThe regulation of the intracellular level of ATP is a fundamental aspect of bioenergetics. Actin cytoskeletal dynamics have been reported to be an energetic drain in developing neurons and platelets. We addressed the role of actin dynamics in primary embryonic chicken neurons using luciferase assays, and by measurement of the ATP/ADP ratio using the ratiometric reporter PercevalHR and the ATP level using the ratiometric reporter mRuby-iATPSnFR. None of the methods revealed an effect of suppressing actin dynamics on the decline in the neuronal ATP level or the ATP/ADP ratio following shutdown of ATP production. Similarly, we find that treatments that elevate or suppress actin dynamics do not alter the ATP/ADP ratio in growth cones, the subcellular domain with the highest actin dynamics in developing neurons. Collectively, the data indicate that actin cytoskeletal dynamics are not a significant energy drain in developing neurons and that the ATP/ADP ratio is maintained when energy utilization varies. Discrepancies between prior work and the current data are discussed with emphasis on methodology and interpretation of the data.
On New Forms of Diatomaceæ from Dredgings off the Arran Islands, County Galway
Authors: O’meara Eugene 
Published: August 2023

ABSTRACT
The forms from the Arran material referred to in this my third paper on the subject have already, from time to time, been exhibited at the meetings of the Dublin Microscopical Club, so that nothing remains to be done respecting them except to add the minute details of description.
Fine Control of TiO2- and Pt/TiO2-Catalyzed Sequential Photoreduction and Reductive N-Alkylation of Nitroarenes by Connecting Different Types of Microflow Reactors
Authors: Yamashita Toshiaki , Tomiyama Mitsuteru , Noguchi Daisuke , Okabe Yuji 
Published: August 2023

Abstract
Eleven microflow reactors (MCRs) with different microchannel structures and catalytic activities were easily fabricated using glass plates with TiO2 and Pt/TiO2 thin films prepared by a sputtering method. Connecting different types of MCRs enabled the sequential photoreduction and reductive N-alkylation of p-nitrotoluene, affording the corresponding amine, imine, N-alkyl amine, and N,N-dialkyl amine in 89%, 90%, 83%, and 78% yields, respectively. The selective photoreduction of nitroarenes and hydrogenation of the styrene analogs were investigated using the MCRs.
Diagnostic strategies for muscular dystrophies: a cross-sectional study
Authors: Hanna Rodriguez Franklin , Estrada-Alvarez Jorge Mario , Guillermo Murillo Juan , Porras-Hurtado Gloria Liliana 
Published: August 2023

Background: Muscular dystrophies are a wide heterogeneity group of neuromuscular diseases that very often constitutes a challenge for clinicians to perform an adequate diagnosis. Many patients remain underdiagnosed o misdiagnosed consequently affecting their prognosis and quality of life. Therefore, we aimed to establish clinical and molecular characteristics of patients with increased CPK levels and muscular dystrophies in our region to facilitate diagnosis and follow-up on patients with suspected muscular dystrophies. Methods: A cross-sectional study was made using a retrospective search of patients attended in Comfamiliar Risaralda between 2010 and 2021. The study included patients from both genders and all ages who presented with a diagnosis of polymyositis, myoclonus, myopathy, and muscular dystrophy between 2010 and 2022 in Comfamiliar Risaralda. Patients with CPK levels lower than 500 U/L were excluded. Results: A database analysis was carried out from 2010 to 2022 of 5219 patients treated in a fourth-level care institution in the Eje Cafetero region, finding 221 patients filtered by a diagnosis of myopathy, myoclonus, polymyositis, and dystrophy. We found a combined prevalence of all muscular dystrophies of 4.2 per 100.000 habitants, Duchenne muscular dystrophy of 0.6 per 100.000 habitants, limb-girdle muscular dystrophy of 0.6 per 100.000 habitants, facioscapulohumeral dystrophy of 0.5 per 100.000 habitants, Bethem dystrophy, type 2 Emery Dreifuss muscular dystrophy and merosin-deficient muscular dystrophy of 0.1 per 100.000 habitants. A diagnostic sequence was elaborated from clinical and paraclinical features found in our patients. Conclusions: Although muscular dystrophies consist of a heterogeneous group of neuromuscular diseases, there are still clinical and paraclinical features that can help physicians to detect any particular case and perform a good approach and follow-up. Our diagnostic sequence will facilitate physicians to determine any particular muscular dystrophy.
Nonlinear processes and laser damage induced by a temporally modulated nanosecond UV laser beam. Part II: Kerr self-focusing
Authors: Bouyer Charles , Nuter Rachel , Cormier Martin , Gleyze Jean-François , Grosjean Sylvain , Roquin Nadja , Natoli Jean-Yves , Lamaignère Laurent 
Published: August 2023

In this paper, we study the impact of Kerr self-focusing on laser-induced damage of fused silica with temporal modulation. In our experiments, temporal modulations are generated with high bandwidth amplitude modulators between 2 and 10 GHz. Measurement of the spatial profile after propagation is made possible due to a dedicated imaging setup. First results without temporal modulation experimentally and numerically show that the nonlinear gain increases exponentially with intensity. Complementary experiments with temporal modulation at different frequencies show an increase in the nonlinear gain. Eventually, we show that laser-induced damage is enhanced with amplitude modulation, with a dependence on the frequency of the amplitude modulation. Optimization of phase modulation allowed us to mitigate backwards stimulated Brillouin scattering and to focus on the sole impact of Kerr self-focusing on laser-induced damage.
Epilepsy and nodding syndrome in association with an Onchocerca volvulus infection drive distinct immune profile patterns
Authors: Arndts Kathrin , Kegele Josua , Massarani Alain S. , Ritter Manuel , Wagner Thomas , Pfarr Kenneth , Lämmer Christine , Dörmann Peter , Peisker Helga , Menche Dirk , Al-Bahra Mazen , Prazeres da Costa Clarissa , Schmutzhard Erich , Matuja William , Hoerauf Achim , Layland-Heni Laura E. , Winkler Andrea S. 
Published: August 2023

Previous studies have described the association of onchocerciasis (caused by Onchocerca volvulus) with epilepsy, including nodding syndrome, although a clear etiological link is still missing. Cases are found in different African countries (Tanzania, South Sudan, Uganda, Democratic Republic of the Congo, Central African Republic and Cameroon). In our study we investigated immunological parameters (cytokine, chemokine, immunoglobulin levels) in individuals from the Mahenge area, Tanzania, presenting with either epilepsy or nodding syndrome with or without O. volvulus infection and compared them to O. volvulus negative individuals from the same endemic area lacking neurological disorders. Additionally, cell differentiation was performed using blood smears and systemic levels of neurodegeneration markers, leiomodin-1 and N-acetyltyramine-O, β-glucuronide (NATOG) were determined. Our findings revealed that cytokines, most chemokines and neurodegeneration markers were comparable between both groups presenting with epilepsy or nodding syndrome. However, we observed elevated eosinophil percentages within the O. volvulus positive epilepsy/nodding syndrome patients accompanied with increased eosinophilic cationic protein (ECP) and antigen-specific IgG levels in comparison to those without an O. volvulus infection. Furthermore, highest levels of NATOG were found in O. volvulus positive nodding syndrome patients. These findings highlight that the detection of distinct biomarkers might be useful for a differential diagnosis of epilepsy and nodding syndrome in O. volvulus endemic areas.
Trial-registration: NCT03653975.
Reproductive Coercion by Intimate Partners: Prevalence and Correlates in Canadian Individuals with the Capacity to be Pregnant
Authors: Lévesque Sylvie , Rousseau Catherine , Jean-Thorn Arianne , Lapierre Simon , Fernet Mylène , Cousineau Marie-Marthe 
Published: August 2023

Objectives
Despite the large body of research on violence against women, violence that specifically targets women’s reproductive autonomy and control over their reproductive health, called reproductive coercion (RC), is poorly documented in Canada. The purpose of this study is to determine the prevalence of RC behaviors in an adult Canadian community sample and to explore associated factors.

Study design
A self-report online questionnaire was administered from September 2020 to April 2021 in Quebec and Ontario, Canada. Participants were recruited via social media, sexual and reproductive health clinics, community-based anti-violence organizations, and the project’s partner organizations. The questionnaire contained validated RC questionnaire items and new items drawn from previous qualitative work. The sample comprised 427 participants, mostly self-identified as women (92%), aged 18 to 55 years (M = 29.01; SD = 6.64). Descriptive analyses and binary logistic regressions were conducted using SPSS 27.

Results
The results of this study show that 63.9% of participants reported at least one lifetime experience of RC. According to our data, contraceptive sabotage was the most common form (62.8%). Of the participants who had been pregnant, 9.8% reported control of pregnancy outcomes. Each RC category shows a different pattern of correlates. The findings also reveal that intimate partner violence (IPV) increases the likelihood of contraceptive sabotage. Moreover, the study suggests that low education level and IPV increase the risk for control of pregnancy outcomes.

Conclusion
These findings underscore the importance of RC in the lives of many Canadian individuals with the capacity to be pregnant, and they highlight certain factors that place individuals at greater risk for RC. This knowledge can inform the development of prevention efforts and clinical interventions.
The effect of adjuvant radiotherapy after breast-conserving surgery in elderly women with T1-2N0 estrogen receptor-negative breast cancer
Authors: Chen Can , Wang Runlu , Wang Bing , Wu Yue , Jiang Jingting 
Published: August 2023

Purpose
To evaluate whether adjuvant radiotherapy (RT) following breast-conserving surgery (BCS) results in better survival among women ≥ 70 years with T1-2N0 estrogen receptor (ER)-negative breast cancer.

Methods
In this retrospective cohort study, we included patients who met the inclusion criteria between 2010 and 2015 from the Surveillance, Epidemiology, and End Results (SEER) program. Univariate and Multivariate Cox proportional analysis were used to identify the risk factors for overall survival (OS) and breast cancer-specific survival (BCSS). Kaplan-Meier survival analysis was used to compare the prognosis of patients with or without adjuvant RT. Propensity score matching (PSM) was applied to perform a 1:1 matched case-control analysis.

Results
A total of 4201 women were included in this study, with a median follow-up time of 64 months (range: 0–107 months). Of these patients, 2811 (66.9%) received adjuvant RT, while 1390 (33.1%) did not. Patients who did not receive adjuvant RT were more likely to be aged ≥ 80 years old, have a single marital status, larger tumors, and HER2-positive status (p < 0.05). Multivariate Cox proportional analysis indicated that receiving adjuvant RT was an independent factor associated with better OS and BCSS before and after PSM (P < 0.001). The survival curves before and after PSM showed that patients achieved an improved OS and BCSS from adjuvant RT (P < 0.005). In the subgroup analysis, there was no survival benefit trend from adjuvant RT in patients who were ≥ 80 years, or those with T1mic+T1a, T1b tumors.

Conclusions
The use of RT following BCS in older women with T1-2N0 ER-negative breast cancer is associated with improve OS and BCSS. However, the potential benefit may be relatively limited for patients ≥ 80 years, or those with T1mic+T1a, T1b tumors.
Knowledge, attitudes and practices towards COVID-19: Community survey in southern Ethiopia
Authors: Endriyas Misganu , Shibru Endashaw , Hussen Mamush , Melka Mintesinot , Lemango Fiseha , Kibru Seyife , Taye Degu , Tadele Alelign 
Published: August 2023

Background
Being well informed about the pandemic and how the virus spreads help to prevent and control the pandemic. Health authorities should monitor community practice to prevent the pandemic to identify gaps and minimize risks. This study was, therefore, designed to assess community knowledge, attitude and practices (KAP) related to COVID-19 prevention and its associated factors in urban settings.

Methods
Community based cross-sectional study was conducted in southern Ethiopia. Twelve towns with high population density and mobility and 1162 participants were included in the study using multi-stage sampling. Semi-structured questionnaire was used to collect data. Mask use was assessed by observation while social distancing and handwashing were assessed by interview. Good practice was defined as wearing face mask, keeping social distance and handwashing. Data was collected by health professionals who have BSc and above (in nursing and public health) and analyzed using SPSS version 25. Descriptive statistics and binary logistic regression at 95% confidence level were performed.

Results
From 1162 respondents, about three fifths, 714 (61.4%), were females and 829 (64.2%) were married. The mean knowledge score was 69.7 (SD±17.87) while mean score for attitude was 80.6 (SD±6.29). Only about one third, 380 (32.7%), had good practice. Occupation, age and overall knowledge about COVID-19 and its prevention were associated with good COVID-19 prevention measures.

Conclusion
Knowledge and attitude related to COVID-19 prevention and control were moderate while practice was low. The risk communication strategy should be strengthened using precautionary advocacy.
Feasibility of a pragmatic randomized adaptive clinical trial to evaluate a brief negotiational interview for harmful and hazardous alcohol use in Moshi, Tanzania
Authors: Staton Catherine A. , Friedman Kaitlyn , Phillips Ashley J. , Minnig Mary Catherine , Sakita Francis M. , Ngowi Kennedy M. , Suffoletto Brian , Hirshon Jon Mark , Swahn Monica , Mmbaga Blandina T. , Vissoci Joao Ricardo Nickenig 
Published: August 2023

IntroductionLow-resourced settings often lack personnel and infrastructure for alcohol use disorder treatment. We culturally adapted a Brief Negotiational Interview (BNI) for Emergency Department injury patients, the “Punguza Pombe Kwa Afya Yako (PPKAY)” (“Reduce Alcohol For Your Health”) in Tanzania. This study aimed to evaluate the feasibility of a pragmatic randomized adaptive controlled trial of the PPKAY intervention.Materials and methodsThis feasibility trial piloted a single-blind, parallel, adaptive, and multi-stage, block-randomized controlled trial, which will subsequently be used to determine the most effective intervention, with or without text message booster, to reduce alcohol use among injury patients. We reported our feasibility pilot study using theReach,Effectiveness,Adoption,Implementation,Maintenance(RE-AIM) framework, with recruitment and retention rates being our primary and secondary outcomes. We enrolled adult patients seeking care for an acute injury at the Kilimanjaro Christian Medical Center in Tanzania if they (1) exhibited an Alcohol Use Disorder Identification Test (AUDIT) ≥8, (2) disclosed alcohol use prior to injury, or (3) had a breathalyzer ≥0.0 on arrival.Interventionarms were usual care (UC), PPKAY, PPKAY with standard text booster, or a PPKAY with a personalized text booster.ResultsOverall, 181 patients were screened and 75 enrolled with 80% 6-week, 82.7% 3-month and 84% 6-month follow-up rates showing appropriateReachand retention.Adoptionmeasures showed an overwhelmingly positive patient acceptance with 100% of patients perceiving a positive impact on their behavior. TheImplementationand trial processes were performed with high rates of PPKAY fidelity (76%) and SMS delivery (74%). Intervention nurses believedMaintenanceand sustainability of this 30-minute, low-cost intervention and adaptive clinical trial were feasible.ConclusionsOur intervention and trial design are feasible and acceptable, have evidence of good fidelity, and did not show problematic deviations in protocol. Results suggest support for undertaking a full trial to evaluate the effectiveness of the PPKAY, a nurse-driven BNI in a low-income country.Trial registrationTrial registration numberNCT02828267.https://classic.clinicaltrials.gov/ct2/show/NCT02828267.