bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces
Authors: Cuscó Anna , Pérez Daniel , Viñes Joaquim , Fàbregas Norma , Francino Olga 
Published: May 2021

AbstractBackgroundLong-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the mobile genetic elements, which are usually missed with short-reads. We applied long-read metagenomics with Nanopore sequencing to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample.ResultsWe used nanopore long-read metagenomics and frameshift aware correction on a canine fecal sample and retrieved eight single-contig HQ MAGs, which were > 90% complete with < 5% contamination, and contained most ribosomal genes and tRNAs. At the technical level, we demonstrated that a high-molecular-weight DNA extraction improved the metagenomics assembly contiguity, the recovery of the rRNA operons, and the retrieval of longer and circular contigs that are potential HQ MAGs. These HQ MAGs corresponded toSuccinivibrio,Sutterella,Prevotellamassilia,Phascolarctobacterium,Catenibacterium, Blautia, andEnterococcusgenera. Linking our results to previous gastrointestinal microbiome reports (metagenome or 16S rRNA-based), we found that some bacterial species on the gastrointestinal tract seem to be more canid-specific –Succinivibrio,Prevotellamassilia,Phascolarctobacterium,Blautia_Asp900541345–, whereas others are more broadly distributed among animal and human microbiomes –Sutterella,Catenibacterium,Enterococcus,andBlautia sp003287895.SutterellaHQ MAG is potentially the first reported genome assembly forSutterella stercoricanis, as assigned by 16S rRNA gene similarity. Moreover, we show that long reads are essential to detect mobilome functions, usually missed in short-read MAGs.ConclusionsWe recovered eight single-contig HQ MAGs from canine feces of a healthy dog with nanopore long-reads. We also retrieved relevant biological insights from these specific bacterial species previously missed in public databases, such as complete ribosomal operons and mobilome functions. The high-molecular-weight DNA extraction improved the assembly’s contiguity, whereas the high-accuracy basecalling, the raw read error correction, the assembly polishing, and the frameshift correction reduced the insertion and deletion errors. Both experimental and analytical steps ensured the retrieval of complete bacterial genomes.
Whole-genome resequencing using next-generation and Nanopore sequencing for molecular characterization of T-DNA integration in transgenic poplar 741
Authors: Chen Xinghao , Dong Yan , Huang Yali , Fan Jianmin , Yang Minsheng , Zhang Jun 
Published: May 2021

Abstract
Background
The molecular characterization information of T-DNA integration is not only required by public risk assessors and regulators, but is also closely related to the expression of exogenous and endogenous genes. At present, with the development of sequencing technology, whole-genome resequencing has become an attractive approach to identify unknown genetically modified events and characterise T-DNA integration events.

Results
In this study, we performed genome resequencing of Pb29, a transgenic high-resistance poplar 741 line that has been commercialized, using next-generation and Nanopore sequencing. The results revealed that there are two T-DNA insertion sites, located at 9,283,905–9,283,937 bp on chromosome 3 (Chr03) and 10,868,777–10,868,803 bp on Chr10. The accuracy of the T-DNA insertion locations and directions was verified using polymerase chain reaction amplification. Through sequence alignment, different degrees of base deletions were detected on the T-DNA left and right border sequences, and in the flanking sequences of the insertion sites. An unknown fragment was inserted between the Chr03 insertion site and the right flanking sequence, but the Pb29 genome did not undergo chromosomal rearrangement. It is worth noting that we did not detect the API gene in the Pb29 genome, indicating that Pb29 is a transgenic line containing only the BtCry1AC gene. On Chr03, the insertion of T-DNA disrupted a gene encoding TAF12 protein, but the transcriptional abundance of this gene did not change significantly in the leaves of Pb29. Additionally, except for the gene located closest to the T-DNA integration site, the expression levels of four other neighboring genes did not change significantly in the leaves of Pb29.

Conclusions
This study provides molecular characterization information of T-DNA integration in transgenic poplar 741 line Pb29, which contribute to safety supervision and further extensive commercial planting of transgenic poplar 741.
Using the geometric average hazard ratio in sample size calculation for time-to-event data with composite endpoints
Authors: Cortés Martínez Jordi , Geskus Ronald B. , Kim KyungMann , Melis Guadalupe Gómez 
Published: May 2021

Abstract
Background
Sample size calculation is a key point in the design of a randomized controlled trial. With time-to-event outcomes, it’s often based on the logrank test. We provide a sample size calculation method for a composite endpoint (CE) based on the geometric average hazard ratio (gAHR) in case the proportional hazards assumption can be assumed to hold for the components, but not for the CE.

Methods
The required number of events, sample size and power formulae are based on the non-centrality parameter of the logrank test under the alternative hypothesis which is a function of the gAHR. We use the web platform, CompARE, for the sample size computations. A simulation study evaluates the empirical power of the logrank test for the CE based on the sample size in terms of the gAHR. We consider different values of the component hazard ratios, the probabilities of observing the events in the control group and the degrees of association between the components. We illustrate the sample size computations using two published randomized controlled trials. Their primary CEs are, respectively, progression-free survival (time to progression of disease or death) and the composite of bacteriologically confirmed treatment failure or Staphylococcus aureus related death by 12 weeks.

Results
For a target power of 0.80, the simulation study provided mean (± SE) empirical powers equal to 0.799 (±0.004) and 0.798 (±0.004) in the exponential and non-exponential settings, respectively. The power was attained in more than 95% of the simulated scenarios and was always above 0.78, regardless of compliance with the proportional-hazard assumption.

Conclusions
The geometric average hazard ratio as an effect measure for a composite endpoint has a meaningful interpretation in the case of non-proportional hazards. Furthermore it is the natural effect measure when using the logrank test to compare the hazard rates of two groups and should be used instead of the standard hazard ratio.
Evaluation by simulation of clinical trial designs for evaluation of treatment during a viral haemorrhagic fever outbreak
Authors: Manchon Pauline , Belhadi Drifa , Mentré France , Laouénan Cédric 
Published: May 2021

Abstract
Background
Viral haemorrhagic fevers are characterized by irregular outbreaks with high mortality rate. Difficulties arise when implementing therapeutic trials in this context. The outbreak duration is hard to predict and can be short compared to delays of trial launch and number of subject needed (NSN) recruitment. Our objectives were to compare, using clinical trial simulation, different trial designs for experimental treatment evaluation in various outbreak scenarios.

Methods
Four type of designs were compared: fixed or group-sequential, each being single- or two-arm. The primary outcome was 14-day survival rate. For single-arm designs, results were compared to a pre-trial historical survival rate pH. Treatments efficacy was evaluated by one-sided tests of proportion (fixed designs) and Whitehead triangular tests (group-sequential designs) with type-I-error = 0.025. Both survival rates in the control arm pC and survival rate differences Δ (including 0) varied. Three specific cases were considered: “standard” (fixed pC, reaching NSN for fixed designs and maximum sample size NMax for group-sequential designs); “changing with time” (increased pC over time); “stopping of recruitment” (epidemic ends). We calculated the proportion of simulated trials showing treatment efficacy, with K = 93,639 simulated trials to get a type-I-error PI95% of [0.024;0.026].

Results
Under H0 (Δ = 0), for the “standard” case, the type-I-error was maintained regardless of trial designs. For “changing with time” case, when pC > pH, type-I-error was inflated, and when pC < pH it decreased. Wrong conclusions were more often observed for single-arm designs due to an increase of Δ over time. Under H1 (Δ = + 0.2), for the “standard” case, the power was similar between single- and two-arm designs when pC = pH. For “stopping of recruitment” case, single-arm performed better than two-arm designs, and fixed designs reported higher power than group-sequential designs. A web R-Shiny application was developed.

Conclusions
At an outbreak beginning, group-sequential two-arm trials should be preferred, as the infected cases number increases allowing to conduct a strong randomized control trial. Group-sequential designs allow early termination of trials in cases of harmful experimental treatment. After the epidemic peak, fixed single-arm design should be preferred, as the cases number decreases but this assumes a high level of confidence on the pre-trial historical survival rate.
Tai Chi exercise improves age‐associated decline in cerebrovascular function: a cross‐sectional study
Authors: Li Lili , Wang Jingjing , Guo Shaoying , Xing Yangqi , Ke Xiongwen , Chen Yinghao , He Yuan , Wang Shun , Wang Jiayu , Cui Xinwu , Wang Zhihua , Tang Lixu 
Published: May 2021

Abstract
Background
Tai Chi exercise has been reported to enhance physical and mental health in the older adults; however, the mechanism remains elusive.

Trial design
We recruited 289 older adults practicing Tai Chi for over 3 years, together with 277 age-matched older and 102 young adults as controls. 168 Tai Chi practitioners were successfully matched to 168 older controls aged 60–69 based on a propensity score for statistics.

Methods
Cerebrovascular function was evaluated by measuring the hemodynamics of the carotid artery. Spearman correlation was performed to validate the age-associated physiological parameters.

Results
Cerebrovascular function in older adults significantly degenerated compared with the young, and was substantially correlated with age. Compared with the older control group, Tai Chi practitioners showed significant improvements in CVHI (cerebral vascular hemodynamics indices) Score (P = 0.002), mean blood flow velocity (P = 0.014), maximal blood flow velocity (P = 0.04) and minimum blood flow velocity (P < 0.001), whereas the age-related increases in pulse wave velocity (P = 0.022), characteristic impedance (P = 0.021) and peripheral resistance (P = 0.044) were lowered.

Conclusions
These data demonstrate a rejuvenation role of Tai Chi in improving the age-related decline of the cerebrovascular function.

Trial registration
Chinese Clinical Trial Registry (ChiCTR1900025187)
Rotavirus gastroenteritis in Pakistan, 2018: updated disease burden
Authors: Basharat Nosheen , Sadiq Asma , Dawood Muhammad , Ali Shahid , Khan Alam , Ullah Rooh , Khan Hayat , Aziz Aamir , Ali Hamid , Shah Aamer Ali , Ali Ijaz , Khan Jadoon 
Published: May 2021

Abstract
Objective
Rotavirus A (RVA) is a significant cause of severe diarrheal illness and one of the common causes of death in children under the age of five. This study was aimed at detecting the prevalence of RVA in Pakistan after rotavirus vaccines were introduced. Fecal samples were obtained from 813 children from different hospitals in Rawalpindi and Islamabad, Pakistan, from January 2018 to December 2018. To obtain additional information from the parents / guardians of the children, a standard questionnaire was used.

Results
Using an enzyme-linked immunosorbent assay kit (ELISA), rotavirus antigen was detected and ELISA positive samples were subjected to reverse transcription PCR (RT-PCR). The findings showed 22% prevalence of RVA in children with acute gastroenteritis (AGE) via ELISA and 21% prevalence via RT-PCR in children with AGE. There was no statistically significant difference between gender, age and RVA infections. The winter, spring and fall/autumn seasons were statistically significant for RVA prevalence.

Conclusion
The present study will provide post vaccine prevalence data for the health policy makers. The implementation of rotavirus vaccines, along with adequate nutrition for babies, clean water supply and maternal hygienic activities during infant feeding, is recommended. Furthermore, continuous surveillance is mandatory in the whole country to calculate the disease burden caused by RVA.
Artificial pneumothorax improves radiofrequency ablation of pulmonary metastases of hepatocellular carcinoma close to mediastinum
Authors: Zuo Taiyang , Lin Wenli , Liu Fengyong , Xu Jinshun 
Published: May 2021

Abstract
Background
To investigate the feasibility, safety and efficacy of percutaneous radiofrequency ablation (RFA) of pulmonary metastases from hepatocellular carcinoma (HCC) contiguous with the mediastinum using the artificial pneumothorax technique.

Method
A total of 40 lesions in 32 patients with pulmonary metastases from HCC contiguous with the mediastinum accepted RFA treatment from August 2014 to May 2018 via the artificial pneumothorax technique. After ablation, clinical outcomes were followed up by contrast enhanced CT. Technical success, local tumor progression (LTP), intrapulmonary distant recurrence (IDR), and adverse events were evaluated. Overall survival (OS) and local tumor progression free survival (LTPFS) were recorded for each patient.

Results
The tumor size was 1.4 ± 0.6 cm in diameter. RFA procedures were all successfully performed without intra-ablative complications. Technical success was noted in 100% of the patients. Five cases of LTP and 8 cases of IDR occurred following the secondary RFA for treatment. Slight pain was reported in all patients. No major complications were observed. The 1, 2, and 3-year LTPFS rates were 90.6, 81.2, and 71.8%, and the 1, 2, and 3-year OS rates were 100, 100 and 87.5%, respectively.

Conclusion
Artificial pneumothorax adjuvant RFA is a feasible, safe, and efficient method for treatment of pulmonary metastases from HCC contiguous with the mediastinum.
Short‐term changes in and preoperative factors affecting vaulting after posterior chamber phakic Implantable Collamer Lens implantation
Authors: Zhu Qiu-Jian , Chen Wen-Jing , Zhu Wei-Jian , Xiao Hai-Xiang , Zhu Man-Hui , Ma Lie , Yuan You , Song E. 
Published: May 2021

Abstract
Background
To describe the very early vault changes in the first month after Implantable Collamer Lens (ICL) implantation and to evaluate the effect of preoperative biometric factors on vault.

Methods
Eighty-three eyes from eighty-three subjects with complete data who met follow-up requirements were recruited in this retrospective study between May 2019 and March 2020. We quantitatively assessed the postoperative vault at 2 h, 1 day, 1 week, and 1 month following implantation. Associations between the postoperative vault and age, ICL size, spherical equivalent (SE), axial length (AL), central corneal thickness (CCT), flat keratometry (K), steep K, mean K, anterior chamber depth (ACD), crystalline lens thickness (LT), white-to-white (WTW) diameter obtained by three devices, horizontal and vertical sulcus-to-sulcus (STS) diameter, bright and dark pupil sizes (BPS and DPS) and DPS-BPS were investigated using Spearman’s correlation analysis and stepwise multiple regression analysis.

Results
The mean vault values at 2 h, 1 day, 1 week, and 1 month after ICL implantation were 672.05 ± 30.72, 389.15 ± 28.33, 517.23 ± 30.76 and 530.12 ± 30.22 μm, respectively. Significant differences were found in the vault values at 2 h, 1 day and 1 week after the operation. The ICL size (β = 0.942; p < 0.001), followed by horizontal STS (β = -0.517; p < 0.001), crystalline LT (β = -0.376; p < 0.001) and vertical STS (β = -0.257; p = 0.017), significantly influenced the vault at 1 month after the operation. The multiple regression equation was expressed as follows: central vault (µm) = -1369.05 + 657.121 × ICL size- 287.408 × horizontal STS − 432.497 × crystalline LT − 137.33 × vertical STS (adjusted R2 = 0.643).

Conclusions
After ICL implantation, the vault decreased and then increased, but it did not return to the vault value 2 h after surgery. The ICL size, horizontal and vertical STS and crystalline LT are key factors for predicting postoperative vaulting.
Intraocular pressure changes after phacoemulsification in pseudoexfoliation versus healthy eyes
Authors: Ramezani Farshid , Nazarian Mohammad , Rezaei Leila 
Published: May 2021

Abstract
Background
Pseudoexfoliation (PXF) syndrome is the most common cause of secondary glaucoma worldwide. This systemic disorder causes further damage to the optic nerve and ultimately increases the need for surgical interventions. Therefore, intraocular pressure (IOP) control is very important in these patients. The aim of this study was to compare IOP changes after phacoemulsification in subjects with PXF syndrome compared to those without this syndrome.

Methods
61 patients were enrolled in this prospective clinical study. Subjects were assigned into two groups based on presence or absence of PXF syndrome. IOP and anterior chamber angle parameters including: angle opening distance (AOD) and trabecular-iris surface area (TISA) measured one day preoperatively and 3 months postoperatively. Intraoperative metrics factors including: infusion fluid usage (IFU), cumulative dissipated energy (CDE) and aspiration time (AT) were obtained from the phacoemulsification machine at the end of each surgery. IOP changes, anterior chamber angle parameters and intraoperative metrics factors were compared between groups.

Results
Mean IOP before surgery was significantly higher in the PXF group (14.70 mm Hg) compared to controls (12.87 mm Hg) (P-value < 0.01). Phacoemulsification decreased IOP in both, but to greater extent in the PXF group (p-value < 0.01). AOD and TISA also increased significantly following surgery in both groups. The results showed that postoperative IOP was negatively correlated with preoperative IOP in both groups (p-value < 0.01). Also, IOP after phacoemulsification was negatively correlated with IFU in the PXF group (p-value = 0.03).

Conclusions
Patients with PXF syndrome exhibited a reduction in IOP and increase in anterior chamber angle parameters after phacoemulsification. We observed a greater IOP reduction in PXF subjects when it was compared to controls. Higher preoperative IOP and intraoperative IFU were associated with more IOP reduction in the PXF group.
Experiences and outcomes of group volunteer befriending with patients with severe mental illness: an exploratory mixed-methods study in Colombia
Authors: Botero-Rodríguez Felipe , Hernandez María Camila , Uribe-Restrepo José Miguel , Cabariqe Camilo , Fung Catherine , Priebe Stefan , Gómez-Restrepo Carlos 
Published: May 2021

Abstract
Background
Improving care for patients with severe mental illness in Latin America requires effective strategies that are low-cost. One such strategy is a volunteering scheme, referred to as befriending, which seeks to support the social integration of patients. Despite positive reports in other world regions, this intervention has not been studied in Latin America. Whilst befriending programmes commonly form patient-volunteer dyads, group arrangements may be an alternative with some benefits. Here, we aim to explore the feasibility, experiences and outcomes of a group volunteer befriending intervention for patients with severe mental illness in Colombia.

Methods
In this exploratory non-controlled study, 10 groups of five individuals were formed, each consisting of three individuals with schizophrenia or bipolar disorder and two volunteers from the community in Bogotá, Colombia. Each group was encouraged to participate together in social activities within their community over a 6-month period. Patients’ quality of life, objective social outcomes, symptom levels and internalised stigma were assessed before and after the intervention. Patients’ and volunteers’ experiences were explored in semi-structured interviews which were analysed using inductive content analysis.

Results
Outcomes were available for 23 patients. Whilst their objective social situation had significantly improved at the end of the intervention, other outcomes did not show statistically significant differences. The interviews with participants revealed positive experiences which fell into five categories: 1) stigma reduction; 2) personal growth; 3) formation of relationships; 4) continuity and sustainability of befriending; 5) acceptability and feasibility of befriending.

Conclusions
A volunteer befriending programme in small groups of two volunteers and three patients is feasible and associated with positive experiences of participants. Such programmes may also improve the objective social situation of patients. This low-cost intervention may be useful for patients with severe mental illnesses in Latin America.

Trial registration
ISRCTN72241383 (Date of Registration: 04/03/2019, retrospectively registered).
Person-centred interventions for problem gaming: a stepped care approach
Authors: Park Jennifer J. , Wilkinson-Meyers Laura , King Daniel L. , Rodda Simone N. 
Published: May 2021

Abstract
Background
Problem gaming is reported by approximately 1–3% of the population and is associated with decreased health and wellbeing. Research on optimal health responses to problem gaming remains limited. This study aimed to identify and describe the key components of a person-centred approach to interventions for problem gaming for individuals who voluntary seek assistance.

Methods
Online interviews were conducted with 20 adults (90% male; Mage = 23y) currently seeking help for problem gaming. The interview protocol was guided by a health care access framework which investigated participants’ experiences and needs related to accessing professional support. Transcripts were analysed in NVivo using qualitative content analysis to systematically classify participant data into the themes informed by this framework.

Results
Participants had mixed views on how the negative consequences of problem gaming could be best addressed. Some indicated problems could be addressed through self-help resources whereas others suggested in-person treatment with a health professional who had expertise in gaming. Participants described the essential components of an effective health service for problem gaming as including: valid and reliable screening tools; practitioners with specialist knowledge of gaming; and access to a multimodal system of intervention, including self-help, internet and in-person options that allow gamers to easily transition between types and intensity of support.

Conclusion
A comprehensive health care approach for interventions for problem gaming is in its infancy, with numerous service access and delivery issues still to be resolved. This study highlights the importance of involving individuals with gaming-related problems in developing solutions that are fit for purpose and address the spectrum of individual preferences and needs. These findings recommend a stepped healthcare system that adheres to evidence-based practice tailored to each individual and the implementation of standard assessment and routine outcome monitoring.