bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields
Authors: Steyaert Aranka , Audenaert Pieter , Fostier Jan 
Published: September 2020

AbstractBackgroundDe Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence. However, sequencing errors and repeated subsequences render the identification of the true underlying sequence difficult. A key step in this process is the inference of the multiplicities of nodes and arcs in the graph. These multiplicities correspond to the number of times eachk-mer (resp.k+1-mer) implied by a node (resp. arc) is present in the genomic sequence. Determining multiplicities thus reveals the repeat structure and presence of sequencing errors. Multiplicities of nodes/arcs in the de Bruijn graph are reflected in their coverage, however, coverage variability and coverage biases render their determination ambiguous. Current methods to determine node/arc multiplicities base their decisions solely on the information in nodes and arcs individually, under-utilising the information present in the sequencing data.ResultsTo improve the accuracy with which node and arc multiplicities in a de Bruijn graph are inferred, we developed a conditional random field (CRF) model to efficiently combine the coverage information within each node/arc individually with the information of surrounding nodes and arcs. Multiplicities are thus collectively assigned in a more consistent manner.ConclusionsWe demonstrate that the CRF model yields significant improvements in accuracy and a more robust expectation-maximisation parameter estimation. Truek-mers can be distinguished from erroneousk-mers with a higher F1score than existing methods. A C++11 implementation is available athttps://github.com/biointec/detoxunder the GNU AGPL v3.0 license.
Recruitment of adolescents with suicidal ideation in the emergency department: lessons from a randomized controlled pilot trial of a youth suicide prevention intervention
Authors: Tracey Matthew , Finkelstein Yaron , Schachter Reva , Cleverley Kristin , Monga Suneeta , Barwick Melanie , Szatmari Peter , Moretti Myla E. , Willan Andrew , Henderson Joanna , Korczak Daphne J. 
Published: September 2020

AbstractBackgroundEmergency Departments (EDs) are a first point-of-contact for many youth with mental health and suicidality concerns and can serve as an effective recruitment source for randomized controlled trials (RCTs) of mental health interventions. However, recruitment in acute care settings is impeded by several challenges. This pilot RCT of a youth suicide prevention intervention recruited adolescents aged 12 to 17 years presenting to a pediatric hospital ED with suicide related behaviors.MethodsRecruitment barriers were identified during the initial study recruitment period and included: the time of day of ED presentations, challenges inherent to study presentation, engagement and participation during an acute presentation, challenges approaching and enrolling acutely suicidal patients and families, ED environmental factors, and youth and parental concerns regarding the study. We calculated the average recruitment productivity for published trials of adolescent suicide prevention strategies which included the ED as a recruitment site in order to compare our recruitment productivity.ResultsIn response to identified barriers, an enhanced ED-centered recruitment strategy was developed to address low recruitment rate, specifically (i) engaging a wider network of ED and outpatient psychiatry staff (ii) dissemination of study pamphlets across multiple areas of the ED and relevant outpatient clinics. Following implementation of the enhanced recruitment strategy, the pre-post recruitment productivity, a ratio of patients screened to patients randomized, was computed. A total of 120 patients were approached for participation, 89 (74.2%) were screened and 45 (37.5%) were consented for the study from March 2018 to April 2019. The screening to randomization ratio for the study period prior to the introduction of the enhanced recruitment strategies was 3:1, which decreased to 1.8:1 following the implementation of enhanced recruitment strategies. The ratio for the total recruitment period was 2.1:1. This was lower than the average ratio of 3.2:1 for published trials.ConclusionsEDs are feasible sites for participant recruitment in RCTs examining new interventions for acute mental health problems, including suicidality. Engaging multi-disciplinary ED staff to support recruitment for such studies, proactively addressing anticipated concerns, and creating a robust recruitment pathway that includes approach at outpatient appointments can optimize recruitment.Trial registrationClinicalTrials.gov:NCT03488602, retrospectively registered April 4, 2018.
Lutetium-177-PSMA-I&T as metastases directed therapy in oligometastatic hormone sensitive prostate cancer, a randomized controlled trial
Authors: Privé Bastiaan M. , Janssen Marcel J. R. , van Oort Inge M. , Muselaers Constantijn H. J. , Jonker Marianne A. , de Groot Michel , Mehra Niven , Verzijlbergen J. Fred , Scheenen Tom W. J. , Zámecnik Patrik , Barentsz Jelle O. , Gotthardt Martin , Noordzij Walter , Vogel Wouter V. , Bergman Andries M. , van der Poel Henk G. , Vis André N. , Oprea-Lager Daniela E. , Gerritsen Winald R. , Witjes J. Alfred , Nagarajah James 
Published: September 2020

Abstract
Background
In recent years, there is increasing evidence showing a beneficial outcome (e.g. progression free survival; PFS) after metastases-directed therapy (MDT) with external beam radiotherapy (EBRT) or targeted surgery for oligometastatic hormone sensitive prostate cancer (oHSPC). However, many patients do not qualify for these treatments due to prior interventions or tumor location. Such oligometastatic patients could benefit from radioligand therapy (RLT) with 177Lu-PSMA; a novel tumor targeting therapy for end-stage metastatic castration-resistant prostate cancer (mCRPC). Especially because RLT could be more effective in low volume disease, such as the oligometastatic status, due to high uptake of radioligands in smaller lesions. To test the hypothesis that 177Lu-PSMA is an effective treatment in oHSPC to prolong PFS and postpone the need for androgen deprivation therapy (ADT), we initiated a multicenter randomized clinical trial. This is globally, the first prospective study using 177Lu-PSMA-I&T in a randomized multicenter setting.

Methods & design
This study compares 177Lu-PSMA-I&T MDT to the current standard of care (SOC); deferred ADT. Fifty-eight patients with oHSPC (≤5 metastases on PSMA PET) and high PSMA uptake (SUVmax > 15, partial volume corrected) on 18F-PSMA PET after prior surgery and/or EBRT and a PSA doubling time of < 6 months, will be randomized in a 1:1 ratio. The patients randomized to the interventional arm will be eligible for two cycles of 7.4GBq 177Lu-PSMA-I&T at a 6-week interval. After both cycles, patients are monitored every 3 weeks (including adverse events, QoL- and xerostomia questionnaires and laboratory testing) at the outpatient clinic. Twenty-four weeks after cycle two an end of study evaluation is planned together with another 18F-PSMA PET and (whole body) MRI. Patients in the SOC arm are eligible to receive 177Lu-PSMA-I&T after meeting the primary study objective, which is the fraction of patients who show disease progression during the study follow up. A second primary objective is the time to disease progression. Disease progression is defined as a 100% increase in PSA from baseline or clinical progression.

Discussion
This is the first prospective randomized clinical study assessing the therapeutic efficacy and toxicity of 177Lu-PSMA-I&T for patients with oHSPC.

Trial registration
Clinicaltrials.gov identifier: NCT04443062.
COVID-19 related reduction in pediatric emergency healthcare utilization – a concerning trend
Authors: Dopfer Christian , Wetzke Martin , Zychlinsky Scharff Anna , Mueller Frank , Dressler Frank , Baumann Ulrich , Sasse Michael , Hansen Gesine , Jablonka Alexandra , Happle Christine 
Published: September 2020

Abstract
Background
The COVID-19 pandemic has disrupted healthcare systems worldwide. In addition to the direct impact of the virus on patient morbidity and mortality, the effect of lockdown strategies on health and healthcare utilization have become apparent. Little is known on the effect of the pandemic on pediatric and adolescent medicine. We examined the impact of the pandemic on pediatric emergency healthcare utilization.

Methods
We conducted a monocentric, retrospective analysis of n = 5,424 pediatric emergency department visits between January 1st and April 19th of 2019 and 2020, and compared healthcare utilization during the pandemic in 2020 to the same period in 2019.

Results
In the four weeks after lockdown in Germany began, we observed a massive drop of 63.8% in pediatric emergency healthcare utilization (mean daily visits 26.8 ± SEM 1.5 in 2019 vs. 9.7 ± SEM 1 in 2020, p < 0.005). This drop in cases occurred for both communicable and non-communicable diseases. A larger proportion of patients under one year old (daily mean of 16.6% ±SEM 1.4 in 2019 vs. 23.1% ±SEM 1.7 in 2020, p < 0.01) and of cases requiring hospitalisation (mean of 13.9% ±SEM 1.6 in 2019 vs. 26.6% ±SEM 3.3 in 2020, p < 0.001) occurred during the pandemic. During the analysed time periods, few intensive care admissions and no fatalities occurred.

Conclusions
Our data illustrate a significant decrease in pediatric emergency department visits during the COVID-19 pandemic. Public outreach is needed to encourage parents and guardians to seek medical attention for pediatric emergencies in spite of the pandemic.
What we know and don’t know about the immunization program of Ethiopia: a scoping review of the literature
Authors: Tilahun Binyam , Mekonnen Zeleke , Sharkey Alyssa , Shahabuddin Asm , Feletto Marta , Zelalem Meseret , Sheikh Kabir 
Published: September 2020

Abstract
Background
There has been significant recent prioritization and investment in the immunization program in Ethiopia. However, coverage rates have stagnated and remained low for many years, suggesting the presence of systemic barriers to implementation. Hence, there is a need to consolidate the existing knowledge, in order to address them and consequently improve program effectiveness.

Methods
A thorough literature review and Delphi method were used. In this review, we searched Pubmed/Medline, WHO library, Science direct, Cochrane library, Google scholar and Google using different combinations of search strategies. Studies that applied any study design, data collection and analysis methods related to immunization program were included. In the Delphi method, a panel of 28 national and international experts were participated to identify current evidence gaps and set research priorities under the immunization program.

Results
In this review, a total of 55 studies and national documents were included. The review showed that the vaccination coverage ranged from 20.6% in Afar to 91.7% in Amhara region with large inequities related to socio-economic, health service access and knowledge about vaccination across different settings. Only one study reported evidence on timeliness of immunization as 60%. The review revealed that 80% of health facilities provide immunization service nationally while service availability was only 2% in private health facilities. This review indicated that poor vaccine storage, vaccine shortage, service interruptions, poor defaulter tracing, low community engagement and poor documentation were the main barriers for the Expanded Program on Immunization with variations across different regions. Through expert panel of discussion using Delphi method, 10 priority research areas were identified across different domains of the immunization program at national level.

Conclusion
We found out that there is substantial knowledge on vaccination coverage, however, there is little evidence on timeliness of vaccination. The existing barriers that affect full immunization coverage also varied from context to context which indicates there is a need to design and implement evidence based locally tailored interventions. This review also indicated evidence gaps with more focus on health system related implementation barriers at lower level and identified further research priorities in the immunization program of Ethiopia.
Which interventions increase hearing protection behaviors during noisy recreational activities? A systematic review
Authors: Loughran Michael T. , Lyons Stephanie , Plack Christopher J. , Armitage Christopher J. 
Published: September 2020

Abstract
Background
Hearing loss and tinnitus are global concerns that can be reduced through hearing protection behaviors (e.g., earplug use). Little is known about the effectiveness of interventions to increase hearing protection use in recreational domains. For the first time we review systematically the effectiveness of such interventions.

Methods
Systematic searches of nine databases, as well as grey literature and hand-searching, were conducted. Any study design was included if it assessed quantitatively a purposeful attempt to increase hearing protection in recreational settings. Studies were excluded if they assessed noise exposure from occupational sources and headphones/earphones, as these have been reviewed elsewhere. PROSPERO protocol: CRD42018098573.

Results
Eight studies were retrieved following the screening of 1908 articles. Two pretest-posttest studies detected a small to medium effect (d ≥ 0·3 ≤ 0·5), one a small effect (d ~ =0·2) and two no real effect. Three posttest experimental studies detected small to medium effects (d ≥ 0·3 ≤ 0·5). Studies were rated as “poor quality” and 17 out of a possible 93 behavior change techniques were coded, with the majority targeting the intervention function ‘education’.

Conclusions
Hearing loss and tinnitus due to recreational noise exposure are major public health concerns yet very few studies have examined preventive interventions. The present systematic review sets the agenda for the future development and testing of evidence-based interventions designed to prevent future hearing loss and tinnitus caused by noise in recreational settings, by recommending systematic approaches to intervention design, and implementation of intervention functions beyond education, such as incentivization, enablement and modeling.
Psychological correlates of COVID-19 pandemic in the Austrian population
Authors: Traunmüller Claudia , Stefitz Rene , Gaisbachgrabner Kerstin , Schwerdtfeger Andreas 
Published: September 2020

Abstract
Background
COVID-19 poses the greatest challenge for the entire world since the Second World War. Governments are forced to define strict measures to avoid the spreading of the virus, which may further impose psychological burden for the majority of the population. The aim of this study was to evaluate the psychological distress in Austria during the initial stage of the COVID-19 outbreak.

Methods
From 25 March to 3 April 2020, an anonymous online survey was conducted. Target group included all members of the Austrian population older than 16 years. The survey addressed the following areas (1) and sociodemographic data, (2) physical and mental health; (3) knowledge and concerns about COVID-19; (4) contact with infected people; (5) prevention efforts; (6) need for further information. The Impact of Event Scale-Revised (IES-R) and the Depression, Anxiety and Stress Scale (DASS-21) were used to assess mental health. Analyses were based on 4126 individuals (74% female, age: M = 38.68, SD = 13.36).

Results
43.3% rated the psychological impact as moderate (5.6%) or severe (37.7%). 26.5% reported moderate (13.3%) to severe (13.2%) depression; 20.3% moderate (8.9%) to severe (11.4%) anxiety and 21.2% reported to suffer from moderate (10.5%) or severe stress (10.7%). Being female, higher age, lower levels of education, concern about family members, internet as main source of information, student or pupil status, poor self-rated health, and downplaying the seriousness of the problem were significantly associated with higher psychological burden. Protective factors were the possibility to work in home office, frequent (indirect) contact with family or friends, the availability of virus-specific information, confidence in the diagnosis capability, and physical activity during the crisis.

Conclusion
This study is among the first in Europe on the psychological correlates of the COVID-19 pandemic. 37.7% of the Austrian study population reported a severe psychological impact on the event and 1 in 10 is considered to suffer from severe depression, anxiety or stress. The present findings inform about the identification of protective factors, psychologically vulnerable groups and may guide the development of psychological interventions.
Social diversity and access to healthcare in Europe: how does European Union’s legislation prevent from discrimination in healthcare?
Authors: Orzechowski Marcin , Nowak Marianne , Bielińska Katarzyna , Chowaniec Anna , Doričić Robert , Ramšak Mojca , Łuków Paweł , Muzur Amir , Zupanič-Slavec Zvonka , Steger Florian 
Published: September 2020

AbstractBackgroundSocial diversity can affect healthcare outcomes in situations when access to healthcare is limited for specific groups. Although the principle of equality is one of the central topics on the agenda of the European Union (EU), its scope in the field of healthcare, however, is relatively unexplored. The aim of this study is to identify and systematically analyze primary and secondary legislation of the EU Institutions that concern the issue of access to healthcare for various minority groups. In our research, we have concentrated on three features of diversity: a) gender identity and sexual orientation, b) race and ethnicity, and c) religion or belief.Method and materialsFor the purpose of this analysis, we conducted a search of database Eur-Lex, the official website of European Union law and other public documents of the European Union, based on specific keywords accompanied by review of secondary literature. Relevant documents were examined with regard to the research topic. Our search covered documents that were in force between 13 December 2007 and 31 July 2019.ResultsGenerally, the EU legal system prohibits discrimination on grounds of religion or belief, racial or ethnic origin, sex, and sexual orientation. However, with regard to the issue of non-discrimination in access to healthcare EU secondary law provides protection against discrimination only on the grounds of racial or ethnic origin and sex. The issue of discrimination in healthcare on the grounds of religion or belief, gender identity and sexual orientation is not specifically addressed under EU secondary law.DiscussionThe absence of regulations regarding non-discrimination in the EU secondary law in the area of healthcare may result from the division of competences between the European Union and the Member States. Reluctance of the Member States to adopt comprehensive antidiscrimination regulations leads to a situation, in which protection in access to healthcare primarily depends on national regulations.ConclusionsOur study shows that EU antidiscriminatory law with regard to access to healthcare is fragmentary. Prohibition of discrimination of the level of European binding law does not fully encompass all aspects of social diversity.
Intrapulmonary mature cystic teratoma of the lung: case report of a rare entity
Authors: Mardani Parviz , Naseri Reyhaneh , Amirian Armin , Shahriarirad Reza , Anbardar Mohammad Hossein , Fouladi Damoun , Ranjbar Keivan 
Published: September 2020

Abstract
Background
Intrapulmonary teratoma (IPT) is a rare type of extra gonadal teratoma which often presents with non-specific symptoms and can be misdiagnosed as other diseases. Here we report a patient with IPT which was initially misdiagnosed as lung hydatid cyst versus abscess.

Case presentation
We report an intrapulmonary teratoma in a 27-year-old female presenting with persistent chest pain and dyspnea since a few years prior to her admission with associated symptoms of cough and fever. Chest x-ray only showed left side massive pleural effusion and computed tomography scan of the lungs was suggestive of hydatid cyst or a lung abscess. She underwent lobectomy and postoperative histopathological study revealed IPT as the final diagnosis.

Conclusion
Due to the non-specific symptoms and rarity, IPT can be easily misdiagnosed at first. It is essential that physicians take into account the possibility of IPT when approaching a new case of lung mass.
Women’s views about physical activity as a treatment for vasomotor menopausal symptoms: a qualitative study
Authors: Thomas Adèle , Daley Amanda J. 
Published: September 2020

Abstract
Background
Women commonly seek medical advice about menopausal symptoms. Although menopausal hormone therapy is the most effective treatment, many women prefer non-pharmacological treatments, such as physical activity. The effectiveness of physical activity has been inconclusive when assessed by randomised controlled trials, and it remains unclear how women feel about it as a possible treatment approach. The aim of the study was to explore symptomatic menopausal women’s views and experiences of physical activity as a treatment for vasomotor and other menopausal symptoms.

Methods
An in-depth qualitative study was embedded within a randomised controlled trial that assessed the effectiveness of physical activity as a treatment for vasomotor menopausal symptoms in previously inactive vasomotor symptomatic women. Participants were randomised to one of two physical activity interventions or a usual care group. Both physical activity interventions involved two one-to-one consultations, plus either supporting materials or access to physical activity support groups, over 6 months. Semi-structured interviews were conducted with 17 purposively selected participants from all three trial groups after they had completed trial follow-up. Interviews were audio recorded, transcribed verbatim, and analysed by constant comparison.

Results
All participants talked positively about physical activity as a treatment for their menopausal symptoms, with most reporting participation had improved their hot flushes and night sweats. They reported that they had experienced improved sleep, physical health and psychological well-being. Those who received the physical activity plus social-support intervention reported their ability to cope with their menopausal symptoms had improved. Many participants commented that they would prefer doctors to discuss physical activity as a possible treatment for their hot flushes and night sweats, before offering medication.

Conclusions
Based on the views and experiences of the women who participated in this study, healthcare professionals should continue discussing physical activity as a potential first treatment option with menopausal women. Furthermore, healthcare professionals should ensure they prepare, support, and encourage these women both physically and emotionally.

Trial registration
ISRCTN ISRCTN06495625 Registered 10/11/2010