bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining online and offline peer support groups in community mental health care settings: a qualitative study of service users’ experiences
Authors: Strand Monica , Eng Lillian Sofie , Gammon Deede 
Published: May 2020

AbstractBackgroundPeer support for people with long-term mental health problems is central to recovery-oriented approaches in mental health care. Peer support has traditionally been conducted offline in face-to-face groups, while online groups on the Internet have increased rapidly. Offline and online peer support groups are shown to have differing strengths and weaknesses. However, little is known about how combining the two formats might be experienced by service users, which this paper aims to illuminate.MethodsIn this exploratory and descriptive study, a recovery-oriented Internet-based portal called ReConnect was used by service users in two mental health communities in Norway for 6–12 months. The portal included an online peer support group which also facilitated participation in local offline peer support groups. Both group formats were moderated by an employed service user consultant. Qualitative data about service users’ experiences were collected through focus groups and individual interviews and inductively analyzed thematically.ResultsA total of 14 female service users 22–67 years of age with various diagnoses participated in three focus groups and 10 individual interviews. Two main themes were identified: (1) balancing anonymity and openness, and (2) enabling connectedness. These themes are further illustrated with the subthemes: (i) dilemmas of anonymity and confidentiality, (ii) towards self-disclosure and openness, (iii) new friendships, and (iv) networks in the local community. Three of the subthemes mainly describe benefits, while challenges were more implicit and cut across the subthemes. Identified challenges were related to transitions from anonymity online to revealing one’s identity offline, confidentiality, and barriers related to participation in offline peer support groups.ConclusionsThis study suggests that online and offline peer support groups complement each other, and that combining them is mainly described as beneficial by service users. Identified benefits appeared to arise from service users’ options of one format or the other, or that they could combine formats in ways that suited their individual values and comfort zones. Moderation by a trained service user consultant appeared essential for both formats and can be used systematically to address identified challenges. Combining online and offline peer support groups is a promising concept for facilitating recovery-oriented care and warrants continued research.
Developmental regulation of canonical and small ORF translation from mRNAs
Authors: Patraquim Pedro , Mumtaz Muhammad Ali Shahzad , Pueyo José Ignacio , Aspden Julie Louise , Couso Juan-Pablo 
Published: May 2020

Abstract
Background
Ribosomal profiling has revealed the translation of thousands of sequences outside annotated protein-coding genes, including small open reading frames of less than 100 codons, and the translational regulation of many genes. Here we present an improved version of Poly-Ribo-Seq and apply it to Drosophila melanogaster embryos to extend the catalog of in vivo translated small ORFs, and to reveal the translational regulation of both small and canonical ORFs from mRNAs across embryogenesis.

Results
We obtain highly correlated samples across five embryonic stages, with nearly 500 million putative ribosomal footprints mapped to mRNAs, and compare them to existing Ribo-Seq and proteomic data. Our analysis reveals, for the first time in Drosophila, footprints mapping to codons in a phased pattern, the hallmark of productive translation. We propose a simple binomial probability metric to ascertain translation probability. Our results also reveal reproducible ribosomal binding apparently not resulting in productive translation. This non-productive ribosomal binding seems to be especially prevalent amongst upstream short ORFs located in the 5′ mRNA leaders, and amongst canonical ORFs during the activation of the zygotic translatome at the maternal-to zygotic transition.

Conclusions
We suggest that this non-productive ribosomal binding might be due to cis-regulatory ribosomal binding and to defective ribosomal scanning of ORFs outside periods of productive translation. Our results are compatible with the main function of upstream short ORFs being to buffer the translation of canonical canonical ORFs; and show that, in general, small ORFs in mRNAs display markers compatible with an evolutionary transitory state towards full coding function.
Cognitive behavioural therapy for insomnia in patients with rheumatoid arthritis: protocol for the randomised, single-blinded, parallel-group Sleep-RA trial
Authors: Latocha K. M. , Løppenthin K. B. , Østergaard M. , Jennum P. J. , Christensen R. , Hetland M. , Røgind H. , Lundbak T. , Midtgaard J. , Esbensen B. A. 
Published: May 2020

Abstract
Background
More than half of patients with rheumatoid arthritis complain of insomnia, which is predominantly treated with hypnotic drugs. However, cognitive behavioural therapy for insomnia is recommended as the first-line treatment in international guidelines on sleep. Patients with rheumatoid arthritis suffer from debilitating symptoms, such as fatigue and pain, which can also be linked to sleep disturbance. It remains to be determined whether cognitive behavioural therapy for insomnia can be effective in patients with rheumatoid arthritis. The aim of the Sleep-RA trial is to investigate the efficacy of cognitive behavioural therapy for insomnia on sleep and disease-related symptoms in patients with rheumatoid arthritis. The primary objective is to compare the effect of cognitive behavioural therapy for insomnia relative to usual care on changes in sleep efficiency from baseline to week 7 in patients with rheumatoid arthritis. The key secondary objectives are to compare the effect of cognitive behavioural therapy for insomnia relative to usual care on changes in sleep onset latency, wake after sleep onset, total sleep time, insomnia, sleep quality, fatigue, impact of rheumatoid arthritis and depressive symptoms from baseline to week 26 in patients with rheumatoid arthritis.

Methods
The Sleep-RA trial is a randomised controlled trial with a two-group parallel design. Sixty patients with rheumatoid arthritis, insomnia and low-to-moderate disease activity will be allocated 1:1 to treatment with cognitive behavioural therapy for insomnia or usual care. Patients in the intervention group will receive nurse-led, group-based cognitive behavioural therapy for insomnia once a week for 6 weeks. Outcome assessments will be carried out at baseline, after treatment (week 7) and at follow-up (week 26).

Discussion
Data on treatment of insomnia in patients with rheumatoid arthritis are sparse. The Sleep-RA trial is the first randomised controlled trial to investigate the efficacy of cognitive behavioural therapy for insomnia in patients with rheumatoid arthritis. Because symptoms of rheumatoid arthritis and insomnia have many similarities, we also find it relevant to investigate the secondary effects of cognitive behavioural therapy for insomnia on fatigue, impact of rheumatoid arthritis, depressive symptoms, pain, functional status, health-related quality of life and disease activity.
If we find cognitive behavioural therapy for insomnia to be effective in patients with rheumatoid arthritis this will add weight to the argument that evidence-based non-pharmacological treatment for insomnia in rheumatological outpatient clinics is eligible in accordance with the existing international guidelines on sleep.

Trial registration
ClinicalTrials.gov: NCT03766100. Registered on 30 November 2018.
Resistance training combined with blood flow restriction in cirrhosis: study protocol for a randomized controlled trial
Authors: Nóbrega Sanmy Rocha , Chachá Silvana Gama Florencio , Libardi Cleiton Augusto 
Published: May 2020

Abstract
Background
Patients affected by hepatic cirrhosis show reductions in muscle mass and function, with poor quality of life and functional performance. As such, resistance training with blood flow restriction (BFR-RT) could be a useful therapeutic tool for health promotion. Thus, we aim to verify the effects of this intervention on muscle strength, muscle mass, fiber Pennation angle, fascicle length, functional performance, quality of life, and fall risk scores in this population.

Methods
Thirty participants will be randomly distributed between 1) BFR-RT and 2) control (CTRL). Assessments will occur at three time points: before the training intervention (0 W), after 12 weeks (12 W), and at follow-up (24 W). The following variables will be assessed: Child-Pugh classification; MELD score; SF-36 questionnaire; fatigue severity index; 6-min walk test; timed-up and go; 30-s sitting and rising test; dietary record; one-repetition maximum (1-RM) strength test (knee extension exercise); and vastus lateralis’ cross-sectional area, Pennation angle, and fascicle length. The BFR-RT group will undergo 12 weeks of knee extension exercise (1 × 30 repetitions and 3 × 15 repetitions at 20% 1-RM and 50% of total blood flow occlusion pressure), with two sessions per week. Data normality will be assessed using the Shapiro-Wilk test. In case of normal distribution, a one-way repeated measures analysis of variance will be implemented to test for differences in baseline values. A mixed model then will be applied for each dependent variable. In case of non-normal data distribution, a Kruskal–Wallis test will be implemented to test for differences in baseline values. Next, the Friedman test will be used to analyze repeated measures. Within- and between-group effect sizes will be calculated using Cohen’s d for each outcome. Finally, the minimal clinically important difference will be analyzed with distribution-based methods.

Discussion
To our knowledge, this will be the first trial to investigate BFR-RT in patients with cirrhosis and evaluate the effects on neuromuscular parameters, functional performance, disease severity, and quality of life outcomes.

Trial registration
Brazilian Clinical Trials Registry (ReBec): RBR-395mfw. Registered on 25 August 2018.
Pre-concentration of microalga Euglena gracilis by alkalescent pH treatment and flocculation mechanism of Ca3(PO4)2, Mg3(PO4)2, and derivatives
Authors: Wu Mingcan , Li Jing , Qin Huan , Lei Anping , Zhu Hui , Hu Zhangli , Wang Jiangxin 
Published: May 2020

AbstractBackgroundMicroalgae are widely be used in carbon sequestration, food supplements, natural pigments, polyunsaturated fatty acids, biofuel applications, and wastewater treatment. However, the difficulties incurred in algae cell separation and harvesting, and the exorbitant cost required to overcome these challenges, are the primary limitations to large-scale industrial application of microalgae technology.ResultsHerein, we explore the potential of inducing flocculation by adjusting the pH for pre-concentratingEuglena gracilis. Our results demonstrate that flocculation can be induced by increasing the medium pH to 8.5; however, most of the algae cells were broken by increasing the pH > 10. Magnesium phosphate, calcium phosphate, and their derivatives precipitation jointly led to flocculation, although calcium phosphate and its derivatives precipitation had a greater effect.ConclusionsThis study demonstrates that pH treatment-induced flocculation is efficient and feasible for the pre-concentration ofE. gracilisunder a pilot-scale culture system. Moreover, it also maintained the microalgae cells’ integrity, chlorophyll production, and increased paramylon production. These findings provide a theoretical basis for reducing the cost of large-scaleE. gracilisharvesting; as well as provide a reference for harvesting other microalgae.
Identification of enzymatic genes with the potential to reduce biomass recalcitrance through lignin manipulation in Arabidopsis
Authors: Sakamoto Shingo , Kamimura Naofumi , Tokue Yosuke , Nakata Miyuki T. , Yamamoto Masanobu , Hu Shi , Masai Eiji , Mitsuda Nobutaka , Kajita Shinya 
Published: May 2020

Abstract
Background
During the chemical and biochemical decomposition of lignocellulosic biomasses, lignin is highly recalcitrant. Genetic transformation of plants to qualitatively and/or quantitatively modify lignin may reduce these recalcitrant properties. Efficient discovery of genes to achieve lignin manipulation is thus required.

Results
To screen for new genes to reduce lignin recalcitrance, we heterologously expressed 50 enzymatic genes under the control of a cinnamate 4-hydroxylase (C4H) gene promoter, derived from a hybrid aspen, which is preferentially active in tissues with lignified cell walls in Arabidopsis plants. These genes encode enzymes that act on metabolites in shikimate, general phenylpropanoid, flavonoid, or monolignol biosynthetic pathways. Among these genes, 30, 18, and 2 originated from plants, bacteria, and fungi, respectively. In our first screening step, 296 independent transgenic plants (T1 generation) harboring single or multiple transgenes were generated from pools of seven Agrobacterium strains used for conventional floral-dip transformation. Wiesner and Mäule staining patterns in the stems of the resultant plants revealed seven and nine plants with apparent abnormalities in the two respective staining analyses. According to genomic PCR and subsequent direct sequencing, each of these 16 plants possessed a gene encoding either coniferaldehyde dehydrogenase (calB), feruloyl-CoA 6′-hydroxylase (F6H1), hydroxycinnamoyl-CoA hydratase/lyase (couA), or ferulate 5-hydroxylase (F5H), with one transgenic plant carrying both calB and F6H1. The effects of these genes on lignin manipulation were confirmed in individually re-created T1 transgenic Arabidopsis plants. While no difference in lignin content was detected in the transgenic lines compared with the wild type, lignin monomeric composition was changed in the transgenic lines. The observed compositional change in the transgenic plants carrying calB, couA, and F5H led to improved sugar release from cell walls after alkaline pretreatment.

Conclusions
Simple colorimetric characterization of stem lignin is useful for simultaneous screening of many genes with the potential to reduce lignin recalcitrance. In addition to F5H, the positive control, we identified three enzyme-coding genes that can function as genetic tools for lignin manipulation. Two of these genes (calB and couA) accelerate sugar release from transgenic lignocelluloses.
Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer
Authors: Kim Yoo-Ah , Wojtowicz Damian , Sarto Basso Rebecca , Sason Itay , Robinson Welles , Hochbaum Dorit S. , Leiserson Mark D. M. , Sharan Roded , Vadin Fabio , Przytycka Teresa M. 
Published: May 2020

Abstract
Background
Studies of cancer mutations have typically focused on identifying cancer driving mutations that confer growth advantage to cancer cells. However, cancer genomes accumulate a large number of passenger somatic mutations resulting from various endogenous and exogenous causes, including normal DNA damage and repair processes or cancer-related aberrations of DNA maintenance machinery as well as mutations triggered by carcinogenic exposures. Different mutagenic processes often produce characteristic mutational patterns called mutational signatures. Identifying mutagenic processes underlying mutational signatures shaping a cancer genome is an important step towards understanding tumorigenesis.

Methods
To investigate the genetic aberrations associated with mutational signatures, we took a network-based approach considering mutational signatures as cancer phenotypes. Specifically, our analysis aims to answer the following two complementary questions: (i) what are functional pathways whose gene expression activities correlate with the strengths of mutational signatures, and (ii) are there pathways whose genetic alterations might have led to specific mutational signatures? To identify mutated pathways, we adopted a recently developed optimization method based on integer linear programming.

Results
Analyzing a breast cancer dataset, we identified pathways associated with mutational signatures on both expression and mutation levels. Our analysis captured important differences in the etiology of the APOBEC-related signatures and the two clock-like signatures. In particular, it revealed that clustered and dispersed APOBEC mutations may be caused by different mutagenic processes. In addition, our analysis elucidated differences between two age-related signatures—one of the signatures is correlated with the expression of cell cycle genes while the other has no such correlation but shows patterns consistent with the exposure to environmental/external processes.

Conclusions
This work investigated, for the first time, a network-level association of mutational signatures and dysregulated pathways. The identified pathways and subnetworks provide novel insights into mutagenic processes that the cancer genomes might have undergone and important clues for developing personalized drug therapies.
Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale
Authors: Zlitni Soumaya , Bishara Alex , Moss Eli L. , Tkachenko Ekaterina , Kang Joyce B. , Culver Rebecca N. , Andermann Tessa M. , Weng Ziming , Wood Christina , Handy Christine , Ji Hanlee P. , Batzoglou Serafim , Bhatt Ami S. 
Published: May 2020

AbstractBackgroundPopulations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read cloud sequencing to provide more complete microbial genome drafts, enabling precise differentiation and tracking of strain-level dynamics across metagenomic samples. In this case study, we present a proof-of-concept using read cloud sequencing to describe bacterial strain diversity in the gut microbiome of one hematopoietic cell transplantation patient over a 2-month time course and highlight temporal strain variation of gut microbes during therapy. The treatment was accompanied by diet changes and administration of multiple immunosuppressants and antimicrobials.MethodsWe conducted short-read and read cloud metagenomic sequencing of DNA extracted from four longitudinal stool samples collected during the course of treatment of one hematopoietic cell transplantation (HCT) patient. After applying read cloud metagenomic assembly to discover strain-level sequence variants in these complex microbiome samples, we performed metatranscriptomic analysis to investigate differential expression of antibiotic resistance genes. Finally, we validated predictions from the genomic and metatranscriptomic findings through in vitro antibiotic susceptibility testing and whole genome sequencing of isolates derived from the patient stool samples.ResultsDuring the 56-day longitudinal time course that was studied, the patient’s microbiome was profoundly disrupted and eventually dominated byBacteroides caccae. Comparative analysis ofB. caccaegenomes obtained using read cloud sequencing together with metagenomic RNA sequencing allowed us to identify differences in substrain populations over time. Based on this, we predicted that particular mobile element integrations likely resulted in increased antibiotic resistance, which we further supported using in vitro antibiotic susceptibility testing.ConclusionsWe find read cloud assembly to be useful in identifying key structural genomic strain variants within a metagenomic sample. These strains have fluctuating relative abundance over relatively short time periods in human microbiomes. We also find specific structural genomic variations that are associated with increased antibiotic resistance over the course of clinical treatment.
Proteoglycan loss in the articular cartilage is associated with severity of joint inflammation in psoriatic arthritis—a compositional magnetic resonance imaging study
Authors: Abrar Daniel B. , Schleich Christoph , Nebelung Sven , Frenken Miriam , Ullrich Tim , Radke Karl Ludger , Antoch Gerald , Vordenbäumen Stefan , Brinks Ralph , Schneider Matthias , Ostendorf Benedikt , Sewerin Philipp 
Published: May 2020

Abstract
Background
Even though cartilage loss is a known feature of psoriatic arthritis (PsA), little is known about its role in the pathogenesis of PsA. Using delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC) as a non-invasive marker of the tissue’s proteoglycan content, such early (i.e., pre-morphological) changes have been associated with inflammation in rheumatoid arthritis (RA). Yet, this association has not been studied before in PsA.

Methods
The metacarpophalangeal (MCP), proximal interphalangeal (PIP), and distal interphalangeal (DIP) joints of 17 patients with active PsA were evaluated by high-resolution clinical standard morphological and dGEMRIC sequences using a 3T MRI scanner (Magnetom Skyra, Siemens) and a dedicated 16-channel hand coil. Images were analyzed by two independent raters for dGEMRIC indices, PsA MRI scores (PsAMRIS), and total cartilage thickness (TCT). Kendall tau correlation coefficients (τ) were calculated.

Results
We found significant negative correlations between dGEMRIC indices and total PsAMRIS (τ = − 0.5, p = 0.012), synovitis (τ = − 0.56, p = 0.006), flexor tenosynovitis (τ = − 0.4, p = 0.049), and periarticular inflammation (τ = − 0.72, p < 0.001). Significant positive correlations were found between TCT and dGEMRIC indices at all joint levels (τ = 0.43, p < 0.001). No significant correlations were determined between dGEMRIC indices and bone erosion, bone edema, or bone proliferation.

Conclusion
In PsA, proteoglycan loss as assessed by dGEMRIC is associated with periarticular inflammation, synovitis, and flexor tenosynovitis, but not with bone erosion or proliferation. Thereby, these findings contribute to in vivo concepts of the disease’s pathophysiology. Beyond morphology, advanced MRI techniques may be used to assess cartilage composition in PsA and to identify early changes in the cartilage as an imaging biomarker with potential application in detection, monitoring, and prediction of outcomes of PsA.

Trial registration
2014123117, December 2014.
Catalog of small repeating earthquakes for the Japanese Islands
Authors: Igarashi Toshihiro 
Published: May 2020

AbstractGroups of repeating earthquakes, which occur in approximately the same location and possess a similar focal mechanism, have been extracted in various tectonic environments worldwide. Their recurrence interval has been used to estimate the spatiotemporal evolution of aseismic slip along major tectonic boundaries. Furthermore, slight changes between the waveforms of repeating earthquakes have been analyzed to delineate temporal changes in the local seismic velocity structure. Here, we construct a long-term catalog of small repeating earthquakes in the central Japan since 1981 and throughout the Japanese Islands since 2001 (2001–2019) based on waveform similarity and relative source locations. Most of the long-duration sequences are located near the strongly coupled areas of the Philippine Sea and Pacific plates as they subduct from the Ryukyu–Nankai–Sagami and Kuril–Japan trenches, respectively. Many of the repeating sequences that occur in shallow crustal environments are short-lived. This repeating earthquake catalog allows us to estimate the slip history along each tectonic boundary. We believe that this and similar catalogs will be useful for future investigations of source processes, temporal slip and stress changes along faults, and local velocity structures, thereby providing new insights into earthquake generation mechanisms.