bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of Nanopore sequencing as a pragmatic workflow for copy number variant confirmation in the clinic
Authors: Greer Stephanie U. , Botello Jacquelin , Hongo Donna , Levy Brynn , Shah Premal , Rabinowitz Matthew , Miller Danny E. , Im Kate , Kumar Akash 
Published: June 2023

Abstract
Background
Diagnosis of rare genetic diseases can be a long, expensive and complex process, involving an array of tests in the hope of obtaining an actionable result. Long-read sequencing platforms offer the opportunity to make definitive molecular diagnoses using a single assay capable of detecting variants, characterizing methylation patterns, resolving complex rearrangements, and assigning findings to long-range haplotypes. Here, we demonstrate the clinical utility of Nanopore long-read sequencing by validating a confirmatory test for copy number variants (CNVs) in neurodevelopmental disorders and illustrate the broader applications of this platform to assess genomic features with significant clinical implications.

Methods
We used adaptive sampling on the Oxford Nanopore platform to sequence 25 genomic DNA samples and 5 blood samples collected from patients with known or false-positive copy number changes originally detected using short-read sequencing. Across the 30 samples (a total of 50 with replicates), we assayed 35 known unique CNVs (a total of 55 with replicates) and one false-positive CNV, ranging in size from 40 kb to 155 Mb, and assessed the presence or absence of suspected CNVs using normalized read depth.

Results
Across 50 samples (including replicates) sequenced on individual MinION flow cells, we achieved an average on-target mean depth of 9.5X and an average on-target read length of 4805 bp. Using a custom read depth-based analysis, we successfully confirmed the presence of all 55 known CNVs (including replicates) and the absence of one false-positive CNV. Using the same CNV-targeted data, we compared genotypes of single nucleotide variant loci to verify that no sample mix-ups occurred between assays. For one case, we also used methylation detection and phasing to investigate the parental origin of a 15q11.2-q13 duplication with implications for clinical prognosis.

Conclusions
We present an assay that efficiently targets genomic regions to confirm clinically relevant CNVs with a concordance rate of 100%. Furthermore, we demonstrate how integration of genotype, methylation, and phasing data from the Nanopore sequencing platform can potentially simplify and shorten the diagnostic odyssey.
Cultural considerations and beliefs surrounding preterm birth in Kenya and South Africa
Authors: Milford Cecilia , Smith Emma , Ngure Kenneth , Thuo Nicholas B. , Newmann Sara , Lazarus Nalinie , Beksinska Mags , Mugo Nelly , Rand Larry 
Published: June 2023

Abstract
Background
Preterm birth (PTB) is a global health epidemic, sub-Saharan Africa is severely impacted due to its limited healthcare resources. Pregnancy knowledge, cultural beliefs and practices play a role in the identification of risk and management of PTB. This study explored knowledge, understandings, cultural beliefs and attitudes to pregnancy and PTB, as well as cultural considerations for the introduction of an intravaginal device which could be used to identify PTB risk.

Methods
Qualitative research was conducted in South Africa and Kenya. In-depth interviews were conducted using semi-structured guides with women with a history of PTB (n = 10), healthcare providers (n = 16) and health systems experts (n = 10); and 26 focus group discussions with pregnant women seeking antenatal care (n = 132) and community male partners/fathers (n = 54). Interviews/discussions were transcribed, translated, and analysed thematically.

Results
Pregnancy knowledge, especially for first time pregnancies was poor, with many reporting late entry to antenatal care. Knowledge about PTB was understood in terms of gestational age, weight or small size of baby, with concerns about long term health and stigma. Various risk factors for PTB were described, including those related to traditions and beliefs of witchcraft/curses. Cultural practices, such as the use of traditional medicines and pica, and religion and its impact on health seeking behaviour were also viewed as risk factors. Although insertion of intravaginal devices was not widely acceptable in traditional communities, especially during pregnancy, it was felt that the use of one to detect risk of PTB would be accepted if proven effective in reducing PTB risk.

Conclusions
Various culturally-informed beliefs exist which explain understandings of and attitudes toward pregnancy, pregnancy risk, and PTB. An inclusive exploratory process is critical to facilitate an understanding of the beliefs and traditions which could impact the introduction and design of a product to detect the risk of PTB.
Increased prevalence of depression and anxiety among adults initiating antiretroviral therapy during the COVID-19 pandemic in Shinyanga region, Tanzania
Authors: Winters Solis , Sabasaba Amon , Fahey Carolyn A. , Packel Laura , Katabaro Emmanuel , Ndungile Yudas , Njau Prosper F. , McCoy Sandra I. 
Published: June 2023

Abstract
Background
Concerns about the interconnected relationship between HIV and mental health were heightened during the COVID-19 pandemic. This study assessed whether there were temporal changes in the mental health status of people living with HIV presenting for care in Shinyanga region, Tanzania. Specifically, we compared the prevalence of depression and anxiety before and during COVID-19, with the goal of describing the changing needs, if any, to person-centered HIV services.

Methods
We analyzed baseline data from two randomized controlled trials of adults initiating ART in Shinyanga region, Tanzania between April-December 2018 (pre-COVID-19 period, n = 530) and May 2021-March 2022 (COVID-19 period, n = 542), respectively. We compared three mental health indicators that were similarly measured in both surveys: loss of interest in things, hopelessness about the future, and uncontrolled worrying. We also examined depression and anxiety which were measured using the Hopkins Symptom Checklist-25 in the pre-COVID-19 period and the Patient Health Questionnaire-4 in the COVID-19 period, respectively, and classified as binary indicators per each scale’s threshold. We estimated prevalence differences (PD) in adverse mental health status before and during the COVID-19 pandemic, using stabilized inverse probability of treatment weighting to adjust for underlying differences in the two study populations.

Results
We found significant temporal increases in the prevalence of feeling ‘a lot’ and ‘extreme’ loss of interest in things [‘a lot’ PD: 38, CI 34,41; ‘extreme’ PD: 9, CI 8,12)], hopelessness about the future [‘ a lot’ PD: 46, CI 43,49; ‘extreme’ PD: 4, CI 3,6], and uncontrolled worrying [‘ a lot’ PD: 34, CI 31,37; ‘extreme’ PD: 2, CI 0,4] during the COVID-19 pandemic. We also found substantially higher prevalence of depression [PD: 38, CI 34,42] and anxiety [PD: 41, CI 37,45].

Conclusions
After applying a quasi-experimental weighting approach, the prevalence of depression and anxiety symptoms among those starting ART during COVID-19 was much higher than before the pandemic. Although depression and anxiety were measured using different, validated scales, the concurrent increases in similarly measured mental health indicators lends confidence to these findings and warrants further research to assess the possible influence of COVID-19 on mental health among adults living with HIV.
Trial Registration NCT03351556, registered November 24, 2017; NCT04201353, registered December 17, 2019.
Comparison of the clinical effects for different positions of the weight-bearing axis after high tibial osteotomy
Authors: Xu Han , Tu Huali , Zhao Tianzuo , Xu Daofei , Yu Qinglong , Liao Long , Tang Shitian , Shi Bo 
Published: June 2023

Abstract
Purpose
To analyze the clinical effects of different positions of the weight-bearing axis (WBA) after high tibial osteotomy (HTO).

Methods
The clinical data of 90 patients who underwent HTO in the Department of Orthopedics at our hospital from June 2018 to June 2021 were retrospectively analyzed. Patients were divided into groups A and B (n = 45 per group) according to different post-HTO WBA positions of the affected side. WBAs in both groups were at 50–60% and 62–66% of the tibial plateau, from inside to outside, respectively. American Hospital for Special Surgery Knee Score (HSS), visual analog scale (VAS) score, femorotibial angle (FTA), and medial proximal tibial angle (MPTA) were recorded and analyzed.

Results
All patients were followed up with for 12 months. HSS scores increased gradually and VAS scores decreased gradually in both groups preoperatively, and at 3 months, 6 months, and 1 year postoperatively (P < 0.05). Compared to group A, group B had better HHS scores at 6 months and 1 year postoperatively (P < 0.05). There was no significant between-group difference in VAS scores at all aforementioned timepoints (P > 0.05). Postoperative MPTA and FTA were 89.56° ± 2.18° and 177.11° ± 2.63° in group A, and 89.07° ± 1.98° and 177.07° ± 2.36° in group B, respectively, with no significant between-group difference (P > 0.05).

Conclusion
Patients with post-HTO WBA ranges of 50–60% and 62–66% achieved knee joint function improvement and pain relief. Half a year later, those with a WBA range of 62–66% had better knee joint function scores. However, a comparison of long-term effects warrants further investigation.
Managers as peer workers’ allies: A qualitative study of managers’ perceptions and actions to involve peer workers in Norwegian mental health and substance use services
Authors: Åkerblom Kristina Bakke , Mohn-Haugen Torbjørn , Agdal Rita , Ness Ottar 
Published: June 2023

AbstractBackgroundCitizens with experience and knowledge about what it is like to use mental health and substance use services are increasingly employed within similar services as peer workers. Peer workers are portrayed as achieving societal obligations and help ensure that the outputs from service provision are more effective. Even though peer workers have worked in mental health and substance use services for a while, few studies have focused on exploring managers’ experiences and perspectives about involving peer workers. This knowledge is needed because these managers can enable and hinder equitable involvement and collaboration with peer workers.MethodsA qualitative explorative study was chosen to explore the following research question:How do managers in Norwegian mental health and substance use services experience, relate to, and embrace peer workers as assets in these services?A researcher (Ph.D. student) and a coresearcher (peer worker) conducted four online focus groups with a strategic selection of 17 Norwegian mental health and substance use services managers who had some experience with the involvement of peer workers in their organizations.ResultsThe results identified using systematic text condensation are as follows: [1]Peer workers boost the ongoing shift toward increased service user involvement.[2]Peer workers are highly valued in the service transformation process.[3]Managers involve peer workers as partners in co-creation.The results show that managers connect with peer workers and facilitate their involvement in collaborative activities across the service cycle. Peer workers’ proximity to service users and bridging capacity is highlighted as the reasons for their involvement. Thus, peer workers are involved in co-defining challenges, co-designing potential solutions, co-delivering those service solutions, and, sometimes, co-assessing service solutions to rethink and improve services. As such, peer workers are considered partners in co-creation.ConclusionAs managers involve peer workers, they increasingly discover peer workers’ value, and because peer workers are involved, they increase their skills and capacity for collaboration. This research strengthens the knowledge base of the perceived value of peer workers’ roles, bringing in new perspectives from management about utilizing and evaluating peer worker roles.
Differences between problematic internet and smartphone use and their psychological risk factors in boys and girls: a network analysis
Authors: Rozgonjuk Dmitri , Blinka Lukas , Löchner Nana , Faltýnková Anna , Husarova Daniela , Montag Christian 
Published: June 2023

Abstract
Background
Problematic internet and smartphone use are significant health challenges for contemporary adolescents. However, their mutual relationship is unclear because studies investigating these phenomena are scarce. The present study aimed to investigate the psychological risks and protective factors associated with problematic internet and smartphone use.

Method
A representative sample of Slovak adolescents (N = 4070, Mage = 14.38, SDage = 0.77, 50.5% girls) from the Health Behavior in School-aged Children project was analyzed using network analysis separately for boys and girls.

Results
The results showed weak (for boys) and moderate (for girls) associations between problematic internet use and problematic smartphone use. Risk factors showed stronger associations with problematic internet use than problematic smartphone use, with the exception of fear of missing out, which was strongly associated with problematic smartphone use. The central nodes were externalizing problems for boys and internalizing problems, externalizing problems, and resilience for girls.

Conclusion
The study concluded that while problematic internet use and problematic smartphone use are somewhat related, they differ at the psychological level. In addition, the phenomena are rather different between boys and girls.
Examining the impact of a universal positive psychology program on mental health outcomes among Australian secondary students during the COVID-19 pandemic
Authors: Subotic-Kerry Mirjana , Braund Taylor A. , Gallen Dervla , Li Sophie H , Parker Belinda L. , Achilles Melinda R. , Chakouch Cassandra , Baker Simon , Werner-Seidler Aliza , O’Dea Bridianne 
Published: June 2023

Abstract
Background
This study aimed to examine the impact of a web-based positive psychology program delivered universally to secondary school students during school closures caused by the COVID-19 pandemic in New South Wales, Australia.

Methods
Using a quasi-experimental design conducted in 2020, 438 students aged 12–15 years (73% male) from 4 secondary schools were invited to complete the ‘Bite Back Mental Fitness Challenge’. This web-based program consisted of 7 self-directed modules that targeted 5 key domains of positive psychology. Self-reported symptoms of anxiety and depression and help-seeking intentions for mental health were assessed at baseline prior to school closures (February to March 2020) and at post-test after the return to school (July to August 2020). At post-test, students also reported on their perceived changes in mental health and help-seeking behavior for mental health during the pandemic. Completion of the program modules was recorded.

Results
A total of 445 students consented and 336 (75.5%) completed both assessments. On average, participants completed 2.31 modules (SD: 2.38, range: 0 to 7). There was no change in symptoms of anxiety and depression or help-seeking intentions between baseline and post-test, with no significant effects for gender and history of mental illness. Students who were symptomatic for anxiety and depression at baseline reported lower symptoms at post-test, but this change was not significant. Ninety-seven students (27.5%) reported that their mental health had worsened during the pandemic, and a significant increase in anxiety and depressive symptoms was found in this subsample at post-test. Only 7.7% of students reported a change in their help-seeking behavior, with increased mental health support sought from the Internet, parents, and friends.

Conclusions
The universal delivery of a web-based positive psychology program during school closures did not appear to be associated with improved mental health symptoms; however, completion of the modules was low. Different effects may emerge when selectively delivered to students with mild or greater symptoms. The findings also suggest that broader measures of mental health and wellbeing, including perceived change, are key to the mental health surveillance of students during periods of remote learning.
Improving the COI DNA barcoding library for Neotropical phlebotomine sand flies (Diptera: Psychodidae)
Authors: Posada-López Laura , Rodrigues Bruno Leite , Velez Ivan Dario , Uribe Sandra 
Published: June 2023

AbstractSand fly species are traditionally identified using morphological traits, though this method is hampered by the presence of cryptic species. DNA barcoding is a widely used tool in the case of insects of medical importance, where it is necessary to know quickly which species are present in a transmission area. Here, we assess the usefulness of mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding as a practical tool for species identification, correct assignment of isomorphic females, and to evaluate the detection of cryptic diversity that occurs in the same species. A fragment of the COI gene was used to generate 156 new barcode sequences for sand flies from different countries of the Neotropical region, mainly Colombia, which had been identified morphologically as 43 species. The sequencing of the COI gene allowed the detection of cryptic diversity within species and correctly associated isomorphic females with males identified by morphology. The maximum intraspecific genetic distances ranged from 0 to 8.32% and 0 to 8.92% using uncorrected p distances and the Kimura 2-parameter (K2P) model, respectively. The minimum interspecific distance (nearest neighbor) for each species ranged from 1.5 to 14.14% and 1.51 to 15.7% using p and K2P distances, respectively. Three species had more than 3% maximum intraspecific distance: Psychodopygus panamensis, Micropygomyia cayennensis cayennensis, and Pintomyia evansi. They also were split into at least two molecular operational taxonomic units (MOTUs) each, using different species delimitation algorithms. Regarding interspecific genetic distances, the species of the genera Nyssomyia and Trichophoromyia generated values lower than 3% (except Nyssomyia ylephiletor and Ny. trapidoi). However, the maximum intraspecific distances did not exceed these values, indicating the presence of a barcode gap despite their proximity. Also, nine sand fly species were DNA barcoded for the first time: Evandromyia georgii, Lutzomyia sherlocki, Ny. ylephiletor, Ny. yuilli pajoti, Psathyromyia punctigeniculata, Sciopemyia preclara, Trichopygomyia triramula, Trichophoromyia howardi, and Th. velezbernali. The COI DNA barcode analysis enabled the correct delimitation of several Neotropical sand fly species from South and Central America and raised questions about the presence of cryptic species for some taxa, which should be further assessed.
Graphical Abstract
The potential roles of gut microbiome in anal fistula
Authors: Cai Ping , Rong Hao , Zhu Qiaoqiao , Dai Xiaoyu , Zhao Jianpei 
Published: June 2023

AbstractAnal fistula is a common proctological disease, but the thorough mechanisms of the anal fistula formation are still unclear. An increasing number of studies have revealed the crucial role of gut microbiota in intestinal diseases. We used 16S rRNA gene sequencing to analyze the intestinal microbiome in order to determine whether there are differences in the microbiome between anal fistula patients and healthy individuals. The microbiome samples were extracted by repeatedly wiping the rectal wall with intestinal swab. Before this operation, the whole intestine of all participants was irrigated and the score of the Boston bowel preparation scale reached 9. The biodiversity of gut microbiome of rectum revealed significant difference between anal fistula patients and healthy individuals. 36 discriminative taxa were identified by LEfSe analysis between two groups. At the phylum level, Synergistetes was enriched in anal fistula patients, while Proteobacteria was higher in healthy individuals. We also found that at the genus level, Blautia, Faecalibacterium, Ruminococcus, Coprococcus, Bacteroides, Clostridium, Megamonas and Anaerotruncus were highly enriched in anal fistula patients, while the microbiome of healthy individuals was enriched with Peptoniphilus and Corynebacterium. Spearman correlations showed the extensive and close association among genera and species. Finally, a diagnostic prediction model was constructed by random forest classifier, and the area under curve (AUC) reached 0.990. This study gave an important hint for analyzing gut microbiome of rectum in anal fistula patient.Keypoints.We use the 16S rRNA gene sequencing to test the microbiome samples extracted from the intestinal swab. This is the first study to explore the gut microbiome of rectum using this workflow. We also found the distinct gut microbiome of rectum differences between anal fistula patients and healthy individuals.
A resource scheduling method for cloud data centers based on thermal management
Authors: Mao Li , Chen Rui , Cheng Huiwen , Lin Weiwei , Liu Bo , Wang James Z. 
Published: June 2023

AbstractWith the rapid growth of cloud computing services, the high energy consumption of cloud data centers has become a critical concern of the cloud computing society. While virtual machine (VM) consolidation is often used to reduce energy consumption, excessive VM consolidation may lead to local hot spots and increase the risk of equipment failure. One possible solution to this problem is to utilize thermal-aware scheduling, but existing approaches have trouble realizing the balance between SLA and energy consumption. This paper proposes a novel method to manage cloud data center resources based on thermal management (TM-VMC), which optimizes total energy consumption and proactively prevents hot spots from a global perspective. Its VM consolidation process includes four phases where the VMs scheduler uses an improved ant colony algorithm (UACO) to find appropriate target hosts for VMs based on server temperature and utilization status obtained in real-time. Experimental results show that the TM-VMC approach can proactively avoid data center hot spots and significantly reduce energy consumption while maintaining low Service Level Agreement (SLA) violation rates compared to existing mainstream VM consolidation algorithms with workloads from real-world data centers.