bluuebunny/crossref_metadata_2025_split huggingface dataset:
ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data
Authors: Vadnais David , Middleton Michael , Oluwadare Oluwatosin 
Published: September 2022

AbstractBackgroundThe three-dimensional (3D) structure of chromatin has a massive effect on its function. Because of this, it is desirable to have an understanding of the 3D structural organization of chromatin. To gain greater insight into the spatial organization of chromosomes and genomes and the functions they perform, chromosome conformation capture (3C) techniques, particularly Hi-C, have been developed. The Hi-C technology is widely used and well-known because of its ability to profile interactions for all read pairs in an entire genome. The advent of Hi-C has greatly expanded our understanding of the 3D genome, genome folding, gene regulation and has enabled the development of many 3D chromosome structure reconstruction methods.ResultsHere, we propose a novel approach for 3D chromosome and genome structure reconstruction from Hi-C data using Particle Swarm Optimization (PSO) approach called ParticleChromo3D. This algorithm begins with a grouping of candidate solution locations for each chromosome bin, according to the particle swarm algorithm, and then iterates its position towards a global best candidate solution. While moving towards the optimal global solution, each candidate solution or particle uses its own local best information and a randomizer to choose its path. Using several metrics to validate our results, we show that ParticleChromo3D produces a robust and rigorous representation of the 3D structure for input Hi-C data. We evaluated our algorithm on simulated and real Hi-C data in this work. Our results show that ParticleChromo3D is more accurate than most of the existing algorithms for 3D structure reconstruction.ConclusionsOur results also show that constructed ParticleChromo3D structures are very consistent, hence indicating that it will always arrive at the global solution at every iteration. The source code for ParticleChromo3D, the simulated and real Hi-C datasets, and the models generated for these datasets are available here:https://github.com/OluwadareLab/ParticleChromo3D
A multi-point constraint unfitted finite element method
Authors: Freeman Brubeck Lee 
Published: September 2022

AbstractIn this work a multi-point constraint unfitted finite element method for the solution of the Poisson equation is presented. Key features of the approach are the strong enforcement of essential boundary, and interface conditions. This, along with the stability of the method, is achieved through the use of multi-point constraints that are applied to the so-called ghost nodes that lie outside of the physical domain. Another key benefit of the approach lies in the fact that, as the degrees of freedom associated with ghost nodes are constrained, they can be removed from the system of equations. This enables the method to capture both strong and weak discontinuities with no additional degrees of freedom. In addition, the method does not require penalty parameters and can capture discontinuities using only the standard finite element basis functions. Finally, numerical results show that the method converges optimally with mesh refinement and remains well conditioned.
Malaria research in the Central African Republic from 1987 to 2020: an overview
Authors: Nzoumbou-Boko Romaric , Velut Guillaume , Imboumy-Limoukou Romeo-Karl , Manirakiza Alexandre , Lekana-Douki Jean-Bernard 
Published: September 2022

Abstract
Background
The national malaria control policy in the Central African Republic (CAR) promotes basic, clinical, and operational research on malaria in collaboration with national and international research institutions. Preparatory work for the elaboration of National Strategic Plans for the implementation of the national malaria control policy includes developing the research component, thus requiring an overview of national malaria research. Here, this survey aims to provide an inventory of malaria research as a baseline for guiding researchers and health authorities in choosing the future avenues of research.

Methods
Data sources and search strategy were defined to query the online Medline/PubMed database using the “medical subject headings” tool. Eligibility and study inclusion criteria were applied to the selected articles, which were classified based on year, research institute affiliations, and research topic.

Results
A total of 118 articles were retrieved and 51 articles were ultimately chosen for the bibliometric analysis. The number of publications on malaria has increased over time from 1987 to 2020. These articles were published in 32 different journals, the most represented being the Malaria Journal (13.73%) and the American Journal of Tropical Medicine and Hygiene (11.76%). The leading research topics were drug evaluation (52.94%), expatriate patients (23.54%), malaria in children (17.65%), morbidity (13.7%), and malaria during pregnancy (11.76%). The publications’ authors were mainly affiliated with the Institut Pasteur of Bangui (41%), the French Military Medical Service (15.5%), and the University of Bangui (11.7%). Collaborations were mostly established with France, the UK, and the USA; some collaborations involved Switzerland, Austria, Pakistan, Japan, Sri Lanka, Benin, Cameroun, Ivory Coast, and Madagascar. The main sources of research funding were French agencies (28.6%) and international agencies (18.3%). Most studies included were not representative of the whole country. The CAR has the capacity to carry out research on malaria and to ensure the necessary collaborations.

Conclusion
Malaria research activities in the CAR seem to reflect the priorities of national policy. One remaining challenge is to develop a more representative approach to better characterize malaria cases across the country. Finally, future research and control measures need to integrate the effect of COVID-19.
Impact of COVID-19 pandemic on physical and mental health status and care of adults with epilepsy in Germany
Authors: Körbel Kimberly , Rosenow Felix , Maltseva Margarita , Müller Heiko , Schulz Juliane , Tsalouchidou Panagiota-Eleni , Langenbruch Lisa , Kovac Stjepana , Menzler Katja , Hamacher Mario , von Podewils Felix , Willems Laurent M. , Mann Catrin , Strzelczyk Adam 
Published: September 2022

Abstract
Background
To mitigate the potential consequences of the coronavirus disease 2019 (COVID-19) pandemic on public life, the German Federal Government and Ministry of Health enacted a strict lockdown protocol on March 16, 2020. This study aimed to evaluate the impact of the COVID-19 pandemic on physical and mental health status and the supply of medical care and medications for people with epilepsy (PWE) in Germany.

Methods
The Epi2020 study was a large, multicenter study focused on different healthcare aspects of adults with epilepsy. In addition to clinical and demographic characteristics, patients were asked to answer a questionnaire on the impact of the first wave of the COVID-19 pandemic between March and May 2020. Furthermore, the population-based number of epilepsy-related admissions in Hessen was evaluated for the January-June periods of 2017–2020 to detect pandemic-related changes.

Results
During the first wave of the pandemic, 41.6% of PWE reported a negative impact on their mental health, while only a minority reported worsening of their seizure situation. Mental and physical health were significantly more negatively affected in women than men with epilepsy and in PWE without regular employment. Moreover, difficulties in ensuring the supply of sanitary products (25.8%) and antiseizure medications (ASMs; 19.9%) affected PWE during the first lockdown; no significant difference regarding these impacts between men and women or between people with and without employment was observed. The number of epilepsy-related admissions decreased significantly during the first wave.

Conclusions
This analysis provides an overview of the general and medical care of epilepsy patients during the COVID-19 pandemic. PWE in our cohort frequently reported psychosocial distress during the first wave of the pandemic, with significant adverse effects on mental and physical health. Women and people without permanent jobs especially reported distress due to the pandemic. The COVID‐19 pandemic has added to the mental health burden and barriers to accessing medication and medical services, as self-reported by patients and verified in population-based data on hospital admissions.

Trial registration

German Clinical Trials Register (DRKS), DRKS00022024. Registered October 2, 2020, http://www.drks.de/DRKS00022024
BRAF and NRAS Mutation Status and Response to Checkpoint Inhibition in Advanced Melanoma
Authors: van Not Olivier J. , Blokx Willeke A.M. , van den Eertwegh Alfons J.M. , de Meza Melissa M. , Haanen John B. , Blank Christian U. , Aarts Maureen J.B. , van den Berkmortel Franchette W.P.J. , de Groot Jan Willem B. , Hospers Geke A.P. , Kapiteijn Ellen , Piersma Djura , van Rijn Rozemarijn S. , Stevense-den Boer Marion , van der Veldt Astrid A.M. , Boers-Sonderen Marye J. , Jansen Anne M.L. , Wouters Michel W.J.M. , Suijkerbuijk Karijn P.M. 
Published: September 2022

PURPOSE Little is known about the effect of specific gene mutations on efficacy of immune checkpoint inhibitors in patients with advanced melanoma. MATERIALS AND METHODS All patients with advanced melanoma treated with first-line anti–PD-1 or ipilimumab-nivolumab between 2012 and 2021 in the nationwide Dutch Melanoma Treatment Registry were included in this cohort study. Objective response rate, progression-free survival (PFS), and overall survival (OS) were analyzed according to BRAF and NRAS status. A multivariable Cox model was used to analyze prognostic factors associated with PFS and OS. RESULTS In total, 1764 patients received anti–PD-1 and 759 received ipilimumab-nivolumab. No significant differences in PFS were found in the anti–PD-1 cohort. In the ipilimumab-nivolumab cohort, median PFS was significantly higher for BRAF-mutant melanoma (9.9 months; 95% CI, 6.8 to 17.2) compared with NRAS-mutant (4.8 months; 95% CI, 3.0 to 7.5) and double wild-type (5.3 months; 95% CI, 3.6 to 7.1). In multivariable analysis, BRAF-mutant melanoma was significantly associated with a lower risk of progression or death in the ipilimumab-nivolumab cohort. Median OS was significantly higher for BRAF-mutant melanoma compared with NRAS-mutant and double wild-type melanoma for both immune checkpoint inhibitor regimens. CONCLUSION Ipilimumab-nivolumab–treated patients with BRAF-mutant melanoma display improved PFS and OS compared with patients with NRAS-mutant and double wild-type melanoma. BRAF mutation status is a factor to consider while choosing between mono and dual checkpoint inhibition in advanced melanoma.
Sex Differences in the Molecular Programs of Pancreatic Cells Contribute to the Differential Risks of Type 2 Diabetes
Authors: Yong Hyo Jeong , Toledo Maria Pilar , Nowakowski Richard S , Wang Yue J 
Published: September 2022

Abstract
Epidemiology studies demonstrate that women are at a significantly lower risk of developing type 2 diabetes (T2D) compared to men. However, the molecular basis of this risk difference is not well understood. In this study, we examined the sex differences in the genetic programs of pancreatic endocrine cells. We combined pancreas perifusion data and single-cell genomic data from our laboratory and from publicly available data sets to investigate multiple axes of the sex differences in the human pancreas at the single-cell type and single-cell level. We systematically compared female and male islet secretion function, gene expression program, and regulatory principles of pancreatic endocrine cells. The perifusion data indicate that female endocrine cells have a higher secretion capacity than male endocrine cells. Single-cell RNA-sequencing analysis suggests that endocrine cells in male controls have molecular signatures that resemble T2D. In addition, we identified genomic elements associated with genome-wide association study T2D loci to have differential accessibility between female and male delta cells. These genomic elements may play a sex-specific causal role in the pathogenesis of T2D. We provide molecular mechanisms that explain the differential risk of T2D between women and men. Knowledge gained from our study will accelerate the development of diagnostics and therapeutics in sex-aware precision medicine for diabetes.
Predictors of Subsequent Intervention After Middle Meningeal Artery Embolization for Treatment of Subdural Hematoma: A Nationwide Analysis
Authors: Fuentes Angelica M. , Khalid Syed I. , Mehta Ankit I. 
Published: September 2022

BACKGROUND:Middle meningeal artery (MMA) embolization has recently emerged as an effective technique to treat subdural hematomas (SDHs). Studies to date have been limited, largely, to single-center studies with limited follow-up and have not assessed subsequent surgical interventions and factors associated with these interventions.OBJECTIVE:To evaluate rates of retreatment for SDH after MMA embolization and patient-specific factors that may be important predictors for these interventions.METHODS:Using an all-payer claims database, Mariner, patients who underwent MMA embolization between January 2010 and October 2020 after the diagnosis of SDH were identified. Rates of post-MMA embolization surgical interventions, including craniotomy and burr hole drainage, were accessed within 5 years following. Patient-specific contributors to the rates of these interventions were studied using Gaussian logistic regression models.RESULTS:A total of 322 patients were included. Of this cohort, 55 (17.1%) required subsequent intervention within 5 years, with 36 (11.2%) receiving burr hole evacuation and 19 (5.9%) receiving craniotomy. Factor Xa inhibitor use was independently associated with subsequent interventions after MMA embolization procedures (odds ratio: 1.20 [95% CI: 1.02-1.40]). Of the other patient factors evaluated, including age, sex, comorbidity status, and use of vitamin K antagonists, antiplatelets, and factor Xa inhibitors, none were found to be significantly associated with future interventions.CONCLUSION:Although previous literature has shown MMA embolization to be safe and successful in preventing recurrent SDH, patients undergoing this procedure still carry a risk of future interventions. Patients taking factor Xa inhibitors are at especially high risk of subsequent intervention after MMA embolization.
DRIVER’S TRIP TICKET IN A DIGITAL MODEL OF AN EFFICIENT MOTOR TRANSPORT COMPANY
Authors: Kurganov Valery M. , Dorofeev Aleksey N. , Gryaznov Mikhail V. , Filippova Nadezhda A. 
Published: September 2022

Study and assessment of applications of a driver’s trip ticket within the scope of a motor transport company’s digital transformation are of practical interest. One of the functions of a trip ticket is ensuring road traffic safety during transportation, as it document ally confirms that the vehicle is technically sound and the driver has passed a medic al examination. Moreover, the trip ticket also allows monitoring if the driver complies with the work and rest schedule. The trip ticket is a document confirming the reasonableness of the amount spent by the motor transport company.
Study of a digital system for a motor transport company management has demonstrated the errors or fraud of employees during trip tickets processing. A conceptual diagram of the Transportation Management System is presented, which provides the application of route optimization programs, the results of vehicles satellite monitoring, the formation of daily tasks, and the preparation of work reports. This is the basis we propose for improving business processes to increase the efficiency of transport activities.
Purpose: study of the role of trip tickets and their processing by a digital management system in increasing the efficiency of a motor transport company.
Methodology: Process Mining associated with keeping and processing trip tickets.
Results: Collected statistics allows improving business processes of the motor transport company to increase the efficiency of its activities.
Practical implications: Companies with any form of incorporation and in any economic sector operating motor vehicles.
Ramsay Hunt syndrome
Authors: Perszke Michał , Egierska Dominika 
Published: September 2022

Ramsay-Hunt syndrome (RHS) is a disease caused by reactivation of varicella-zoster virus in the geniculate ganglion. It may be one of the common reasons of the facial palsy. Symptoms of the RHS include vesicular rash on the auricle, external auditory canal, soft palate, pharynx, facial nerve paralysis, ear pain, tinnitus, vertigo and hearing loss. There may be other symptoms connected to cranial nerves (CN) V, VIII, IX or X, when they are involved. Men are more likely to develop lesions than women. Risk of developing Ramsay-Hunt syndrome increases with age. Authors searched Google Scholar and PubMed, using searchterms Ramsay-Hunt syndrome, varicella-zoster virus, VZV, facial palsy. We manually searched the references of selected articles for additional relevant articles. We selected articles relevant to a general medicine readership and prioritised systematic reviews, clinical practice guidelines and cases. The literature contains the latest reports on Ramsay-Hunt syndrome. Clinicians should not ignore patients’ symptoms and always pay attention to possibility of VZV infection and the development of RHS, as treatment should be started within 72 hours after the onset of the symptoms. Main treatment includes antiviral drugs and corticosteroids. The results are promising.
Malignant hyperthermia – state of knowledge
Authors: Perszke Michał , Egierska Dominika , Cieślak Kamil , Berliński Miłosz , Świenc Witold , Tokarczuk Oskar , Walendzik Anna 
Published: September 2022

Malignant hyperthermia (MH) is a relatively rare, but potentially lethal genetic disorder. That disease is characterized by hypermetabolic response of the skeletal muscles caused by exposure to triggering agents e.g. volatile anesthetics or depolarizing neuromuscular blockers.
The object of this article was to review and assess the most recent published works about the epidemiology, etiology, pathomechanism, therapy of the MH and the new advances in all these fields.
Authors scrutinized PubMed and Google Scholar using keywords: malignant hyperthermia, volatile anesthetics, ryanodine receptor mutation. In addition to this, the references of chosen articles were manually scoured for supplementary applicable articles. The literature was selected on the basis of a general medicine readership and prioritized clinical practice guidelines, systematic reviews and case reports.
The references include the latest reports on malignant hyperthermia, apart from works of historical importance.
Available treatment methods consist mainly of pharmacotherapy, symptomatic treatment and monitoring of vital parameters. Dantrolene is a first-choice drug in initial treatment of MH and is considered the only specific antidote.
In spite of the constant advances in the areas of medicine there is still much to be discovered about MH. Further studies are necessary, as the amount of credible evidence is not adequate.
Engagement of health workers and peer educators from the National Adolescent Health Programme-Rashtriya Kishor Swasthya Karyakram during the COVID-19 pandemic: Findings from a situational analysis
Authors: Arora Monika , Dringus Stefanie , Bahl Deepika , Rizvi Zoya , Maity Heeya , Lama Smritima , Mason-Jones Amanda J. , Kumar Deepak , Koul Prairna , Bassi Shalini 
Published: September 2022

Background
To understand the impact of COVID-19 on implementation of the peer education programme of the National Adolescent Health Programme-Rashtriya Kishor Swasthya Karyakram (RKSK); repurposing of the RKSK health workers and Peer Educators (PEs) in COVID-19 response activities and effect on adolescents´ health and development issues.

Methods
Virtual in-depth interviews were conducted with stakeholders (n = 31) (aged 15 to 54 years) engaged in the implementation of the RKSK and peer education programme at state, district, block, and village levels in Madhya Pradesh and Maharashtra (India). These interviews were thematically coded and analysed to address the research objectives.

Results
Despite most peer education programme activities being stopped, delayed, or disrupted during the pandemic and subsequent lockdown, some communication networks previously established, helped facilitate public health communication regarding COVID-19 and RKSK, between health workers, PEs, and adolescents. There was repurposing of RKSK health workers and PEs’ role towards COVID-19 response-related activities. PEs, with support from health workers, were involved in disseminating COVID-19 information, maintaining migrant and quarantine records, conducting household surveys for recording COVID-19 active cases and providing essential items (grocery, sanitary napkins, etc.) to communities and adolescents.

Conclusion
PEs with support from community health workers are able to play a crucial role in meeting the needs of the communities during a pandemic. There is a need to further engage, involve and build the skills of PEs to support the health system. PEs can be encouraged by granting more visibility and incorporating their role more formally by paying them within the public health system in India.
Living with a left ventricular assist device: Capturing recipients experiences using group concept mapping software
Authors: Slade Anita L. , O’Hara Margaret E. , Quinn David , Marley Laura , Griffith Stephen , Calvert Melanie , Haque M. Sayeed , Lim Hoong Sern , Doherty Philippa , Lane Deirdre A. 
Published: September 2022

Background
Left ventricular assist device (LVAD) implantation significantly impacts on a recipient’s symptoms and quality of life. Capturing their experiences and post implant journey is an important part of clinical practice, research and device design evolution. Patient reported outcome measures (PROMs) are a useful tool for capturing that experience. However, patient reported outcome measures need to reflect recipients’ experiences. Discussions with a patient partner group found that none of the frequently used cardiology PROMs captured their unique experiences.

Aims
To capture the experiences and important issues for LVAD recipients. Develop a conceptual map of domains and items that should be reflected in patient reported outcomes.

Methods
Group concept mapping (GCM) web-based software was used to remotely capture and structure recipients’ experiences across a wide geographical area. GCM is a semi-quantitative mixed method consisting of 3 stages: item generation, item sorting and rating (importance, relevance and frequency). Patient partners were involved in all aspects of the study design and development.

Results
18 LVAD recipients consented to take part. 101 statements were generated and multi-dimensional scaling, and hierarchical cluster analysis identified 9 clusters. Cluster themes included: Activities, Partner/family support, Travel, Mental wellbeing, Equipment and clothing, Physical and cognitive limitations, LVAD Restrictions, LVAD Challenges and positive impact of the LVAD (LVAD Positives). LVAD Positives were scored highest across all the rating variables, e.g., frequency (2.85), relevance (2.44) and importance (2.21). Other domains rated high for importance included physical and cognitive limitations (2.19), LVAD restrictions (2.11), Partner/family support (2.02), and Equipment and clothing (2.01).

Conclusion
Online GCM software facilitated the inclusion of geographically dispersed recipients and provided useful insights into the experiences of LVAD recipients. The conceptual framework identifies important domains and items that should be prioritised and included in patient reported outcomes in future research, LVAD design evolution, and clinical practice.