bluuebunny/crossref_metadata_2025_split huggingface dataset:
Home-based pulmonary rehabilitation in people with bronchiectasis: a randomised controlled trial
Authors: José Anderson , Holland Anne E. , Selman Jessyca P.R. , de Camargo Cristiane Oliveira , Fonseca Diogo Simões , Athanazio Rodrigo A. , Rached Samia Z. , Cukier Alberto , Stelmach Rafael , Dal Corso Simone 
Published: April 2021

AimTo investigate the short- and long-term effects of home-based pulmonary rehabilitation (HBPR) on functional capacity, quality of life, peripheral muscle strength, dyspnoea and daily physical activity in people with bronchiectasis.MethodsRandomised controlled trial with 63 participants with bronchiectasis. The HBPR group performed three sessions per week for 8 weeks (aerobic exercise: step training for 20 min; resistance training: exercises for quadriceps, hamstrings, deltoids and biceps brachii using elastic bands). The control group received a recommendation to walk at moderate intensity, three times per week. A weekly phone call was conducted for all participants, and the HBPR group received a home visit every 15 days. The primary outcome was distance in the incremental shuttle walk test (ISWT). Secondary outcomes were time in the endurance shuttle walk test (ESWT), number of steps in the incremental step test, quality of life, quadriceps muscle strength and daily physical activity. Measures were taken before and after intervention and 6 months later.ResultsAfter the intervention, the HBPR group had increased ISWT distance compared with the control group with between-group difference 87.9 m (95% CI 32.4–143.5 m). In addition, between-group differences were found in the ESWT, incremental step test, quality of life and quadriceps muscle strength, favouring the HBPR group. After 6 months, no differences were observed between the groups.ConclusionHBPR is an effective alternative offering of pulmonary rehabilitation for people with bronchiectasis. However, the programme was not effective in maintaining the benefits after 6 months of follow-up.
Delivered dose with jet and mesh nebulisers during spontaneous breathing, noninvasive ventilation and mechanical ventilation using adult lung models
Authors: Ari Arzu , Fink James B. 
Published: April 2021

What is the delivered dose with jet and mesh nebulisers during spontaneous breathing (SB), noninvasive ventilation (NIV), and mechanical ventilation (MV) using an adult lung model with exhaled humidity (EH)?The delivery of salbutamol sulfate (2.5 mg per 3 mL) with jet (Mistymax10) and mesh nebulisers (Aerogen Solo) was compared during SB, NIV, and MV using breathing parameters (tidal volume 450 mL, respiratory rate 20 breaths per min, inspiratory:expiratory ratio 1:3) with three lung models simulating exhaled humidity. A manikin was attached to a sinusoidal pumpviaa filter at the bronchi to simulate an adult with SB. A ventilator (V60) was attachedviaa facemask to a manikin with a filter at the bronchi connected to a test lung to simulate an adult receiving NIV. A ventilator-dependent adult was simulated through a ventilator (Servo-i) operated with a heated humidifier (Fisher & Paykel) attached to an endotracheal tube (ETT) with a heated-wire circuit. The ETT was inserted into a filter (Respirgard II). A heated humidifier was placed between the filter and test lung to simulate exhaled humidity (35±2°C, 100% relative humidity). Nebulisers were placed at the Y-piece of the inspiratory limb during MV and positioned between the facemask and the leak-port during NIV. A mouthpiece was used during SB. The delivered dose was collected in an absolute filter that was attached to the bronchi of the mannequin during each aerosol treatment and measured with spectrophotometry.Drug delivery during MV was significantly greater than during NIV and SB with a mesh nebuliser (p=0.0001) but not with a jet nebuliser (p=0.384). Delivery efficiency of the mesh nebuliser was greater than the jet nebuliser during MV (p=0.0001), NIV (p=0.0001), and SB (p=0.0001).Aerosol deposition obtained with a mesh nebuliser was greater and differed between MV, NIV, and SB, while deposition was low with a jet nebuliser and similar between the modes of ventilation tested.
Endobronchial autologous bone marrow–mesenchymal stromal cells in idiopathic pulmonary fibrosis: a phase I trial
Authors: Campo Arantza , González-Ruiz José María , Andreu Enrique , Alcaide Ana B. , Ocón María M. , De-Torres Juan , Pueyo Jesús , Cordovilla Rosa , Villaron Eva , Sanchez-Guijo Fermín , Barrueco Miguel , Nuñez-Córdoba Jorge , Prósper Felipe , Zulueta Javier J. 
Published: April 2021

RationaleIdiopathic pulmonary fibrosis (IPF) has a dismal prognosis. Mesenchymal stromal cells (MSCs) have shown benefit in other inflammatory diseases.ObjectivesTo evaluate the safety and feasibility of endobronchial administration of bone marrow autologous MSCs (BM-MSC) in patients with mild-to-moderate IPF.MethodsA phase I multicentre clinical trial (ClinicalTrials.govNCT01919827) with a single endobronchial administration of autologous adult BM-MSCs in patients diagnosed with mild-to-moderate IPF. In a first escalating-dose phase, three patients were included sequentially in three dose cohorts (10×106, 50×106and 100×106cells). In a second phase, nine patients received the highest tolerated dose. Follow-up with pulmonary function testing, 6-min walk test and St George's Respiratory Questionnaire was done at 1, 2, 3, 6 and 12 months, and with computed tomography at 3, 6 and 12 months.Results21 bone marrow samples were obtained from 17 patients. Three patients were excluded from treatment due to chromosome aberrations detected in MSCs after culture, and one patient died before treatment. Finally, 13 patients received the BM-MSC infusion. No treatment-related severe adverse events were observed during follow-up. Compared to baseline, the mean forced vital capacity showed an initial decline of 8.1% at 3 months. The number of patients without functional progression was six (46%) at 3 months and three (23%) at 12 months.ConclusionsThe endobronchial infusion of BM-MSCs did not cause immediate serious adverse events in IPF patients, but a relevant proportion of patients suffered clinical and/or functional progression. Genomic instability of BM-MSCs during culture found in three patients may be troublesome for the use of autologous MSCs in IPF patients.
GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments
Authors: Bae Jeongmin , Jeon Hajin , Kim Min-Soo 
Published: April 2021

AbstractBackgroundDesign of valid high-quality primers is essential for qPCR experiments. MRPrimer is a powerful pipeline based on MapReduce that combines both primer design for target sequences and homology tests on off-target sequences. It takes an entire sequence DB as input and returns all feasible and valid primer pairs existing in the DB. Due to the effectiveness of primers designed by MRPrimer in qPCR analysis, it has been widely used for developing many online design tools and building primer databases. However, the computational speed of MRPrimer is too slow to deal with the sizes of sequence DBs growing exponentially and thus must be improved.ResultsWe develop a fast GPU-based pipeline for primer design (GPrimer) that takes the same input and returns the same output with MRPrimer. MRPrimer consists of a total of seven MapReduce steps, among which two steps are very time-consuming. GPrimer significantly improves the speed of those two steps by exploiting the computational power of GPUs. In particular, it designs data structures for coalesced memory access in GPU and workload balancing among GPU threads and copies the data structures between main memory and GPU memory in a streaming fashion. For human RefSeq DB, GPrimer achieves a speedup of 57 times for the entire steps and a speedup of 557 times for the most time-consuming step using a single machine of 4 GPUs, compared with MRPrimer running on a cluster of six machines.ConclusionsWe propose a GPU-based pipeline for primer design that takes an entire sequence DB as input and returns all feasible and valid primer pairs existing in the DB at once without an additional step using BLAST-like tools. The software is available athttps://github.com/qhtjrmin/GPrimer.git.
Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars
Authors: Dyrka Witold , Gąsior-Głogowska Marlena , Szefczyk Monika , Szulc Natalia 
Published: April 2021

Abstract
Background
Amyloid signaling motifs are a class of protein motifs which share basic structural and functional features despite the lack of clear sequence homology. They are hard to detect in large sequence databases either with the alignment-based profile methods (due to short length and diversity) or with generic amyloid- and prion-finding tools (due to insufficient discriminative power). We propose to address the challenge with a machine learning grammatical model capable of generalizing over diverse collections of unaligned yet related motifs.

Results
First, we introduce and test improvements to our probabilistic context-free grammar framework for protein sequences that allow for inferring more sophisticated models achieving high sensitivity at low false positive rates. Then, we infer universal grammars for a collection of recently identified bacterial amyloid signaling motifs and demonstrate that the method is capable of generalizing by successfully searching for related motifs in fungi. The results are compared to available alternative methods. Finally, we conduct spectroscopy and staining analyses of selected peptides to verify their structural and functional relationship.

Conclusions
While the profile HMMs remain the method of choice for modeling homologous sets of sequences, PCFGs seem more suitable for building meta-family descriptors and extrapolating beyond the seed sample.
Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications
Authors: Yang Chao , Li Xuejuan , Wang Qingxiong , Yuan Hao , Huang Yuan , Xiao Hong 
Published: April 2021

Abstract
Background
The relict gull (Larus relictus), was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of its evolution and its conservation.

Results
In this study, based on the Illumina and PacBio sequencing platforms, we successfully assembled the genome of L. relictus, one of the few known reference genomes in genus Larus. The size of the final assembled genome was 1.21 Gb, with a contig N50 of 8.11 Mb. A total of 18,454 genes were predicted from the assembly results, with 16,967 (91.94%) of these genes annotated. The genome contained 92.52 Mb of repeat sequence, accounting for 7.63% of the assembly. A phylogenetic tree was constructed using 4902 single-copy orthologous genes, which showed L. relictus had closest relative of L. smithsonianus, with divergence time of 14.7 Mya estimated between of them. PSMC analyses indicated that L. relictus had been undergoing a long-term population decline during 0.01-0.1 Mya with a small effective population size fom 8800 to 2200 individuals.

Conclusions
This genome will be a valuable genomic resource for a range of genomic and conservation studies of L. relictus and will help to establish a foundation for further studies investigating whether the breeding population is a complex population. As the species is threatened by habitat loss and fragmentation, actions to protect L. relictus are suggested to alleviate the fragmentation of breeding populations.
Prophylactic temporary abdominal aortic balloon occlusion for patients with pernicious placenta previa: a retrospective study
Authors: Huo Fei , Liang Hansheng , Feng Yi 
Published: April 2021

Abstract
Background
Pernicious placenta previa (PPP) can increase the risk of perioperative complications. During caesarean section in patients with adherent placenta, intraoperative blood loss, hysterectomy rate and transfusion could be reduced by interventional methods. Our study aimed to investigate the influence of maternal hemodynamics control and neonatal outcomes of prophylactic temporary abdominal aortic balloon (PTAAB) occlusion for patients with pernicious placenta previa.

Methods
This was a retrospective study using data from the Peking University People’s Hospital from January 2014 through January 2020. Clinical records of pregnant women undergoing cesarean section were collected. Patients were divided into two groups: treatment with PTAAB placement (group A) and no balloon placement (group B). Group A was further broken down into two groups: prophylactic placement (Group C) and balloon occlusion (group D).

Results
Clinical records of 33 cases from 5205 pregnant women underwent cesarean section were collected. The number of groups A, B, C, and D were 17, 16, 5 and 12.We found that a significant difference in the post-operative uterine artery embolism rates between group A and group B (0% vs.31.3%, p = 0.018). There was a significant difference in the Apgar scores at first minute between group A and group B (8.94 ± 1.43 vs 9.81 ± 0.75,p = 0.037),and the same significant difference between two groups in the pre-operative central placenta previa (29.4% vs. 0%,p = 0.044), complete placenta previa (58.8% vs 18.8%, p = 0.032),placenta implantation (76.5% vs 31.3%, p = 0.015). We could also observe the significant difference in the amount of blood cell (2.80 ± 2.68vs.10.66 ± 11.97, p = 0.038) and blood plasma transfusion (280.00 ± 268.32 vs. 1033.33 ± 1098.20, p = 0.044) between group C and group D. The significant differences in the preoperative vaginal bleeding conditions (0% vs 75%, p = 0.009), the intraoperative application rates of vasopressors (0% vs. 58.3%, p = 0.044) and the postoperative ICU (intensive care unit) admission rates (0% vs. 58.3%, p = 0.044) were also kept.

Conclusions
PTAAB occlusion could be useful in reducing the rate of post-operative uterine artery embolism and the amount of transfusion, and be useful in coping with patients with preoperative vaginal bleeding conditions, so as to reduce the rate of intraoperative applications of vasopressors and the postoperative ICU (intensive care unit) admission. In PPP patients with placenta implantation, central placenta previa and complete placenta previa, we advocate the utilization of prophylactic temporary abdominal aortic balloon placement.
Causes of hospitalisation among a cohort of people with HIV from a London centre followed from 2011 to 2018
Authors: Rein Sophia M. , Lampe Fiona C. , Chaloner Clinton , Stafford Adam , Rodger Alison J. , Johnson Margaret A. , McDonnell Jeffrey , Burns Fiona , Madge Sara , Miners Alec , Sherr Lorraine , Collins Simon , Speakman Andrew , Phillips Andrew N. , Smith Colette J. 
Published: April 2021

Abstract
Background
We describe the spectrum of ICD-10 classified causes for hospitalisations occurring between 2011 and 2018 in a cohort of people living with HIV (PLHIV).

Methods
This sub-study includes 798 PLHIV participating in the Antiretroviral, Sexual Transmission Risk and Attitudes (ASTRA) questionnaire study who were recruited from a large London centre. A medical record review identified the occurrence and causes of hospitalisation from the date of questionnaire completion (February–December 2011) until 1 June 2018. Up to five causes were classified by an HIV clinician using the ICD-10 system.

Results
There were 274 hospitalisations in 153 people (rate = 5.8/100 person-years; 95% CI: 5.1, 6.5). Causes were wide-ranging; the most common were circulatory (16.8%), digestive (13.1%), respiratory (11.7%), infectious diseases (11.0%), injury/poisoning (10.6%), genitourinary diseases (9.9%) and neoplasms (9.1%). A tenth (27/274) of hospitalisations were related to at least one AIDS-defining illness. Median duration of hospitalisation was 5 days (IQR 2–9). At the time of hospitalisation, median CD4 count was high (510 cells/μl; IQR: 315–739), while median CD4 nadir was relatively low (113 cells/μl; IQR: 40–239). At admission, half of individuals (51%) had a previous AIDS-defining illness and 21% had viral load > 50 copies/ml. Individuals admitted for infectious diseases were particularly likely to have unfavourable HIV-related clinical characteristics (low CD4, viral non-suppression, not on antiretroviral therapy (ART), previous AIDS).

Conclusions
In the modern combination antiretroviral therapy era, the spectrum of causes of hospitalisation in PLHIV in the UK is wide-ranging, highlighting the importance of holistic care for PLHIV, including prevention, early detection and treatment of comorbidities.
Social support and depressive symptoms among physicians in tertiary hospitals in China: a cross-sectional study
Authors: Fu Chang , Wang Guowen , Shi Xiuxin , Cao Fenglin 
Published: April 2021

Abstract
Background
Social support is an important factor for individual’s mental health. However, the association between social support and depressive symptoms among physicians in China’ tertiary hospitals has not been explored. This study aimed to investigate its association among physicians stratifying by sex.

Methods
Six hundred fifty-six physicians were enrolled from 12 tertiary hospitals of Shandong Province, China. Depressive symptoms were assessed using the 10-item Center for Epidemiologic Studies Depression Scale. Social support was evaluated using the Social Support Rating Scale. Multiple linear regression analysis was used to examine the relationship between social support and depressive symptoms among physicians.

Results
The prevalence of depressive symptoms was 42.3% and the average social support score was 38.82 ± 7.53 among physicians. Lower subjective social support scores (male: β = − 0.317, p < 0.001; female: β = − 0.241, p < 0.001) and lower objective social support scores (male: β = − 0.218, p = 0.038; female: β = − 0.277, p = 0.035) were associated with high depressive symptoms among physicians. Lower support utilization scores (β = − 0.472, p < 0.001) were associated with high depressive symptoms among male physicians.

Conclusions
Chinese physicians had a higher prevalence of depressive symptoms and lower social support than the Chinese general population. Objective and subjective social support were inversely associated with depressive symptoms among male and female physicians while support utilization was inversely associated with depressive symptoms among male rather than female physicians. It is critical to improve physicians’ mental health through strengthening social support in China.
Effectiveness of personal protective health behaviour against COVID-19
Authors: Lio Chon Fu , Cheong Hou Hon , Lei Chin Ion , Lo Iek Long , Yao Lan , Lam Chong , Leong Iek Hou 
Published: April 2021

Abstract
Background
Novel coronavirus disease 2019 (COVID-19) has become a pandemic, and over 80 million cases and over 1.8 million deaths were reported in 2020. This highly contagious virus is spread primarily via respiratory droplets from face-to-face contact and contaminated surfaces as well as potential aerosol spread. Over half of transmissions occur from presymptomatic and asymptomatic carriers. Although several vaccines are currently available for emergency use, there are uncertainties regarding the duration of protection and the efficacy of preventing asymptomatic spread. Thus, personal protective health behaviour and measures against COVID-19 are still widely recommended after immunization. This study aimed to clarify the efficacy of these measures, and the results may provide valuable guidance to policymakers to educate the general public about how to reduce the individual-level risk of COVID-19 infection.

Methods
This case-control study enrolled 24 laboratory-confirmed COVID-19 patients from Centro Hospitalar Conde de São Januário (C.H.C.S.J.), which was the only hospital designated to manage COVID-19 patients in Macao SAR, China, and 1113 control participants who completed a 14-day mandatory quarantine in 12 designated hotels due to returning from high-risk countries between 17 March and 15 April 2020. A questionnaire was developed to extract demographic information, contact history, and personal health behaviour.

Results
Participants primarily came from the United Kingdom (33.2%), followed by the United States (10.5%) and Portugal (10.2%). Independent factors for COVID-19 infection were having physical contact with confirmed/suspected COVID-19 patients (adjusted OR, 12.108 [95% CI, 3.380–43.376], P < 0.005), participating in high-risk gathering activities (adjusted OR, 1.129 [95% CI, 1.048–1.216], P < 0.005), handwashing after outdoor activity (adjusted OR, 0.021 [95% CI, 0.003–0.134], P < 0.005), handwashing before touching the mouth and nose area (adjusted OR, 0.303 [95% CI, 0.114–0.808], P < 0.05), and wearing a mask whenever outdoors (adjusted OR, 0.307 [95% CI, 0.109–0.867], P < 0.05). The daily count of handwashing remained similar between groups. Only 31.6% of participants had a sufficient 20-s handwashing duration.

Conclusions
Participating in high-risk gatherings, wearing a mask whenever outdoors, and practising hand hygiene at key times should be advocated to the public to mitigate COVID-19 infection.
Does lock-down of Wuhan effectively restrict early geographic spread of novel coronavirus epidemic during chunyun in China? A spatial model study
Authors: Hu Yi , Kong Lingcai , Yao Tong , Chen Xinda , Du Wei 
Published: April 2021

Abstract
Background
Prior to Wuhan lock-down in 2020, chunyun, the largest population mobility on this planet, had begun. We quantified impact of Wuhan lock-down on COVID-19 spread during chunyun across the nation.

Methods
During the period of January 1 to February 9, 2020, a total of 40,278 confirmed COVID-19 cases from 319 municipalities in mainland China were considered in this study. The cross-coupled meta-population methods were employed using between-city Baidu migration index. We modelled four scenarios of geographic spread of COVID-19 including the presence of both chunyun and lock-down (baseline); lock-down without chunyun (scenario 1); chunyun without lock-down (scenario 2); and the absence of both chunyun and lock-down (scenario 3).

Results
Compared with the baseline, scenario 1 resulted in 3.84% less cases by February 9 while scenario 2 and 3 resulted in 20.22 and 32.46% more cases by February 9. The geographic distribution of cases revealed that chunyun facilitated the COVID-19 spread in the majority but not all cities, and the effectiveness of Wuhan lock-down was offset by chunyun. Impacts of Wuhan lock-down during chunyun on the COVID-19 spread demonstrated heterogenetic geographic patterns.

Conclusion
Our results strongly supported the travel restriction as one of the effective responses and highlighted the importance of developing area-specific rather than universal countermeasures.