bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community
Authors: Gong Ga , Zhou Saisai , Luo Runbo , Gesang Zhuoma , Suolang Sizhu 
Published: October 2020

AbstractBackgroundYaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity of the major microorganisms and putative carbohydrate-metabolizing enzymes for the degradation of complex lignocellulosic biomass in its gut ecosystem.ResultsHere, this study aimed to decode biomass-degrading genes and genomes in the yak fecal microbiota using deep metagenome sequencing. A comprehensive catalog comprising 4.5 million microbial genes from the yak feces were established based on metagenomic assemblies from 92 Gb sequencing data. We identified a full spectrum of genes encoding carbohydrate-active enzymes, three-quarters of which were assigned to highly diversified enzyme families involved in the breakdown of complex dietary carbohydrates, including 120 families of glycoside hydrolases, 25 families of polysaccharide lyases, and 15 families of carbohydrate esterases. Inference of taxonomic assignments to the carbohydrate-degrading genes revealed the major microbial contributors wereBacteroidaceae,Ruminococcaceae,Rikenellaceae,Clostridiaceae, andPrevotellaceae. Furthermore, 68 prokaryotic genomes were reconstructed and the genes encoding glycoside hydrolases involved in plant-derived polysaccharide degradation were identified in these uncultured genomes, many of which were novel species with lignocellulolytic capability.ConclusionsOur findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications.
Serum miRNA125a-5p, miR-125b-5p, and miR-433-5p as biomarkers to differentiate between posterior circulation stroke and peripheral vertigo
Authors: Kijpaisalratana Naruchorn , Nimsamer Pattaraporn , Khamwut Ariya , Payungporn Sunchai , Pisitkun Trairak , Chutinet Aurauma , Utoomprurkporn Nattawan , Kerr Stephen J. , Vongvasinkul Pakkawan , Suwanwela Nijasri C. 
Published: October 2020

Abstract
Background
Acute vertigo is a common presentation of inner ear disease. However, it can also be caused by more serious conditions, especially posterior circulation stroke. Differentiating between these two conditions by clinical presentations and imaging studies during the acute phase can be challenging. This study aimed to identify serum microRNA (miRNA) candidates that could differentiate between posterior circulation stroke and peripheral vertigo, among patients presenting with acute vertigo.

Methods
Serum levels of six miRNAs including miR-125a-5p, miR-125b-5p, miR-143-3p, miR-342-3p, miR-376a-3p, and miR-433-5p were evaluated. Using quantitative reverse-transcription polymerase chain reaction (RT-qPCR), the serum miRNAs were assessed in the acute phase and at a 90 day follow-up visit.

Results
A total of 58 patients with posterior circulation stroke (n = 23) and peripheral vertigo (n = 35) were included in the study. Serum miR-125a-5p (P = 0.001), miR-125b-5p (P <  0.001), miR-143-3p (P = 0.014) and miR-433-5p (P = 0.0056) were present at significantly higher levels in the acute phase, in the patients with posterior circulation infarction. Based on the area under the receiver operating characteristic curve (AUROC) only miR-125a-5p (0.75), miR-125b-5p(0.77), and miR-433-5p (0.71) had an acceptable discriminative ability to differentiate between the central and peripheral vertigo. A combination of miRNAs revealed no significant improvement of AUROC when compared to single miRNAs.

Conclusion
This study demonstrated the potential of serum miR-125a-5p, miR-125b-5p, and miR-433-5p as biomarkers to assist in the diagnosis of posterior circulation infarction among patients presenting with acute vertigo.
Traumatic index extensor tendon attenuation mimicking closed tendon rupture: two case reports
Authors: Miyashima Yusuke , Uemura Takuya , Yokoi Takuya , Hama Shunpei , Okada Mitsuhiro , Konishi Sadahiko , Nakamura Hiroaki 
Published: October 2020

Abstract
Background
While some traumatic closed index extensor tendon ruptures at the musclotendinous junction have been previously reported, closed index extensor tendon pseudorupture due to intertendinous attenuation is exceedingly rare with only one case report of a gymnastics-related sports injury in the English literature. Herein, we report two non-sports injury related cases of traumatic index extensor tendon attenuation mimicking closed tendon rupture, including the pathological findings and intraoperative video of the attenuated extensor indicis proprius tendon.

Case presentation
A 28-year-old man and a 30-year-old man caught their hands in a high-speed drill and lathe, respectively, which caused a sudden forced flexion of their wrists. They could not actively extend the metacarpophalangeal joints of their index fingers. Intraoperatively, although the extensor indicis proprius and index extensor digitorum communes tendons were in continuity without ruptures, both tendons were attenuated and stretched. The attenuated index extensor tendons were reconstructed either with shortening by plication or step-cut when the tendon damage was less severe or, in severely attenuated tendons, with tendon grafting (ipsilateral palmaris longus) or tendon transfer. Six months after the operation, the active extension of the index metacarpophalangeal joints had recovered well.

Conclusions
Two cases of traumatic index extensor tendon attenuation were treated successfully by shortening the attenuated tendon in combination with tendon graft or transfer. We recommend WALANT (wide-awake local anesthesia and no tourniquet) in the reconstruction surgery of index extensor tendon attenuation to determine the appropriate amount of tendon shortening or optimal tension for tendon grafting or transfer. Intraoperative voluntary finger movement is essential, as it is otherwise difficult to judge the stretch length of intratendinous elongation and extent of traumatic intramuscular damage affecting tendon excursion.
A cluster randomized controlled trial on a multifaceted implementation strategy to promote integrated palliative care in COPD: study protocol of the COMPASSION study
Authors: Broese Johanna M. C. , van der Kleij Rianne M. J. J. , Kerstjens Huib A. M. , Verschuur Els M. L. , Engels Yvonne , Chavannes Niels H. 
Published: October 2020

AbstractBackgroundDespite the urgent need for palliative care for patients with advanced chronic obstructive pulmonary disease (COPD), it is not yet daily practice. Important factors influencing the provision of palliative care are adequate communication skills, knowing when to start palliative care and continuity of care. In the COMPASSION study, we address these factors by implementing an integrated palliative care approach for patients with COPD and their informal caregivers.MethodsAn integrated palliative care intervention was developed based on existing guidelines, a literature review, and input from patient and professional organizations. To facilitate uptake of the intervention, a multifaceted implementation strategy was developed, comprising a toolbox, (communication) training, collaboration support, action planning and monitoring. Using a hybrid effectiveness-implementation type 2 design, this study aims to simultaneously evaluate the implementation process and effects on patient, informal caregiver and professional outcomes. In a cluster randomized controlled trial, eight hospital regions will be randomized to receive the integrated palliative care approach or to provide care as usual. Eligible patients are identified during hospitalization for an exacerbation using the Propal-COPD tool. The primary outcome is quality of life (FACIT-Pal) at 6 months. Secondary outcome measures include spiritual well-being, anxiety and depression, unplanned healthcare use, informal caregiver burden and healthcare professional’s self-efficacy to provide palliative care. The implementation process will be investigated by a comprehensive mixed-methods evaluation assessing the following implementation constructs: context, reach, dose delivered, dose received, fidelity, implementation level, recruitment, maintenance and acceptability. Furthermore, determinants to implementation will be investigated using the Consolidated Framework for Implementation Research.DiscussionThe COMPASSION study will broaden knowledge on the effectiveness and process of palliative care integration into COPD-care. Furthermore, it will improve our understanding of which strategies may optimize the implementation of integrated palliative care.Trial registrationNetherlands Trial Register (NTR):NL7644. Registration date: April 7, 2019.
Variation in surgical demand and time to hip fracture repair: a Canadian database study
Authors: Sheehan Katie J. , Sobolev Boris , Guy Pierre , Kim Jason D. , Kuramoto Lisa , Beaupre Lauren , Levy Adrian R. , Morin Suzanne N. , Sutherland Jason M. , Harvey Edward J. ,   for the Canadian Collaborative Study on Hip Fractures, Beaupre Lauren , Bohm Eric , Dunbar Michael , Griesdale Donald , Guy Pierre , Harvey Edward , Hellsten Erik , Jaglal Susan , Kreder Hans , Kuramoto Lisa , Levy Adrian , Morin Suzanne N. , Sheehan Katie J. , Sobolev Boris , Sutherland Jason M. , Waddell James 
Published: October 2020

Abstract
Background
Competing demands for operative resources may affect time to hip fracture surgery. We sought to determine the time to hip fracture surgery by variation in demand in Canadian hospitals.

Methods
We obtained discharge abstracts of 151,952 patients aged 65 years or older who underwent surgery for a hip fracture between January, 2004 and December, 2012 in nine Canadian provinces. We compared median time to surgery (in days) when demand could be met within a two-day benchmark and when demand required more days, i.e. clearance time, to provide surgery, overall and stratified by presence of medical reasons for delay.

Results
For persons admitted when demand corresponded to a 2-day clearance time, 68% of patients underwent surgery within the 2-day benchmark. When demand corresponded to a clearance time of one week, 51% of patients underwent surgery within 2 days. Compared to demand that could be served within the two-day benchmark, adjusted median time to surgery was 5.1% (95% confidence interval [CI] 4.1–6.1), 12.2% (95% CI 10.3–14.2), and 22.0% (95% CI 17.7–26.2) longer, when demand required 4, 6, and 7 or more days to clear the backlog, respectively. After adjustment, delays in median time to surgery were similar for those with and without medical reasons for delay.

Conclusion
Increases in demand for operative resources were associated with dose-response increases in the time needed for half of hip fracture patients to undergo surgery. Such delays may be mitigated through better anticipation of day-to-day supply and demand and increased response capability.
Development of genetic tools for the thermophilic filamentous fungus Thermoascus aurantiacus
Authors: Gabriel Raphael , Prinz Julia , Jecmenica Marina , Romero-Vazquez Carlos , Chou Pallas , Harth Simon , Floerl Lena , Curran Laure , Oostlander Anne , Matz Linda , Fritsche Susanne , Gorman Jennifer , Schuerg Timo , Fleißner André , Singer Steven W. 
Published: October 2020

Abstract
Background
Fungal enzymes are vital for industrial biotechnology, including the conversion of plant biomass to biofuels and bio-based chemicals. In recent years, there is increasing interest in using enzymes from thermophilic fungi, which often have higher reaction rates and thermal tolerance compared to currently used fungal enzymes. The thermophilic filamentous fungus Thermoascus aurantiacus produces large amounts of highly thermostable plant cell wall-degrading enzymes. However, no genetic tools have yet been developed for this fungus, which prevents strain engineering efforts. The goal of this study was to develop strain engineering tools such as a transformation system, a CRISPR/Cas9 gene editing system and a sexual crossing protocol to improve the enzyme production.

Results
Here, we report Agrobacterium tumefaciens-mediated transformation (ATMT) of T. aurantiacus using the hph marker gene, conferring resistance to hygromycin B. The newly developed transformation protocol was optimized and used to integrate an expression cassette of the transcriptional xylanase regulator xlnR, which led to up to 500% increased xylanase activity. Furthermore, a CRISPR/Cas9 gene editing system was established in this fungus, and two different gRNAs were tested to delete the pyrG orthologue with 10% and 35% deletion efficiency, respectively. Lastly, a sexual crossing protocol was established using a hygromycin B- and a 5-fluoroorotic acid-resistant parent strain. Crossing and isolation of progeny on selective media were completed in a week.

Conclusion
The genetic tools developed for T. aurantiacus can now be used individually or in combination to further improve thermostable enzyme production by this fungus.
Engineering endogenous ABC transporter with improving ATP supply and membrane flexibility enhances the secretion of β-carotene in Saccharomyces cerevisiae
Authors: Bu Xiao , Lin Jing-Yuan , Cheng Jing , Yang Dong , Duan Chang-Qing , Koffas Mattheos , Yan Guo-Liang 
Published: October 2020

Abstract
Background
Product toxicity is one of the bottlenecks for microbial production of biofuels, and transporter-mediated biofuel secretion offers a promising strategy to solve this problem. As a robust microbial host for industrial-scale production of biofuels, Saccharomyces cerevisiae contains a powerful transport system to export a wide range of toxic compounds to sustain survival. The aim of this study is to improve the secretion and production of the hydrophobic product (β-carotene) by harnessing endogenous ABC transporters combined with physiological engineering in S. cerevisiae.

Results
Substrate inducibility is a prominent characteristic of most endogenous transporters. Through comparative proteomic analysis and transcriptional confirmation, we identified five potential ABC transporters (Pdr5p, Pdr10p, Snq2p, Yor1p, and Yol075cp) for β-carotene efflux. The accumulation of β-carotene also affects cell physiology in various aspects, including energy metabolism, mitochondrial translation, lipid metabolism, ergosterol biosynthetic process, and cell wall synthesis. Here, we adopted an inducible GAL promoter to overexpress candidate transporters and enhanced the secretion and intracellular production of β-carotene, in which Snq2p showed the best performance (a 4.04-fold and a 1.33-fold increase compared with its parental strain YBX-01, respectively). To further promote efflux capacity, two strategies of increasing ATP supply and improving membrane fluidity were following adopted. A 5.80-fold increase of β-carotene secretion and a 1.71-fold increase of the intracellular β-carotene production were consequently achieved in the engineered strain YBX-20 compared with the parental strain YBX-01.

Conclusions
Overall, our results showcase that engineering endogenous plasma membrane ABC transporters is a promising approach for hydrophobic product efflux in S. cerevisiae. We also highlight the importance of improving cell physiology to enhance the efficiency of ABC transporters, especially energy status and cell membrane properties.
An adolescent girl with premature ovarian failure, Graves’ disease, and chronic urticaria: a case report
Authors: Lin Danhong , Quan Huibiao , Chen Kaining , Lin Lu , Lin Leweihua , Ji Qun 
Published: October 2020

Abstract
Background
Premature ovarian failure is characterized by amenorrhea, hypoestrogenism, and hypergonadotropinism, and occurs in women under 40 years of age. The prevalence of premature ovarian failure in women younger than 20 years of age is only 0.01%. Immune disorders are one of the causes of premature ovarian failure. Graves’ disease and chronic urticaria are also associated with immune disorders.

Case presentation
We report a case of a 15-year-old Han Chinese girl with premature ovarian failure complicated by Graves’ disease and chronic urticaria. She experienced menarche at 13 years of age and presented with amenorrhea after 7 months of irregular menstruation. Laboratory examinations indicated hypoestrogenism and hypergonadotropinism. Ultrasound imaging revealed that her uterus and ovaries were small in size. Gene and antibody tests related to premature ovarian failure returned negative results. Both thyroid peroxidase autoantibody and thyrotropin receptor antibody were positive.
After reviewing the literature on the relationship between these three diseases and immune disorders, our patient was diagnosed as having atypical autoimmune polyglandular syndrome. After taking small doses of estrogen for 6 months, the size of her uterus increased, and her psychological anxiety was relieved.

Conclusions
We report a case of an unusual association of premature ovarian failure, Graves’ disease, and chronic urticaria. This case presents an atypical combination of adolescent autoimmune polyglandular syndrome, which is worthy of the attention of clinicians and presents an important lesson for them. Our case highlights that premature ovarian failure in adolescents requires long-term follow-up and medical treatment as well as psychological counselling.
Negative pressure wound therapy in patients with wounds healing by secondary intention: a systematic review and meta-analysis of randomised controlled trials
Authors: Zens Yvonne , Barth Michael , Bucher Heiner C. , Dreck Katrin , Felsch Moritz , Groß Wolfram , Jaschinski Thomas , Kölsch Heike , Kromp Mandy , Overesch Inga , Sauerland Stefan , Gregor Sven 
Published: October 2020

Abstract
Background
Negative pressure wound therapy (NPWT) is a widely used method of wound treatment. We performed a systematic review of randomised controlled trials (RCTs) comparing the patient-relevant benefits and harms of NPWT with standard wound therapy (SWT) in patients with wounds healing by secondary intention.

Methods
We searched for RCTs in MEDLINE, Embase, the Cochrane Central Register of Controlled Trials, and study registries (last search: July 2018) and screened reference lists of relevant systematic reviews and health technology assessments. Manufacturers and investigators were asked to provide unpublished data. Eligible studies investigated at least one patient-relevant outcome (e.g. wound closure). We assessed publication bias and, if feasible, performed meta-analyses, grading the results into different categories (hint, indication or proof of a greater benefit or harm).

Results
We identified 48 eligible studies of generally low quality with evaluable data for 4315 patients and 30 eligible studies with missing data for at least 1386 patients. Due to potential publication bias (proportion of inaccessible data, 24%), we downgraded our conclusions. A meta-analysis of all wound healing data showed a significant effect in favour of NPWT (OR 1.56, 95% CI 1.15 to 2.13, p = 0.008). As further analyses of different definitions of wound closure did not contradict that analysis, we inferred an indication of a greater benefit of NPWT. A meta-analysis of hospital stay (in days) showed a significant difference in favour of NPWT (MD − 4.78, 95% CI − 7.79 to − 1.76, p = 0.005). As further analyses of different definitions of hospital stay/readmission did not contradict that analysis, we inferred an indication of a greater benefit of NPWT. There was neither proof (nor indication nor hint) of greater benefit or harm of NPWT for other patient-relevant outcomes such as mortality and adverse events.

Conclusions
In summary, low-quality data indicate a greater benefit of NPWT versus SWT for wound closure in patients with wounds healing by secondary intention. The length of hospital stay is also shortened. The data show no advantages or disadvantages of NPWT for other patient-relevant outcomes. Publication bias is an important problem in studies on NPWT, underlining that all clinical studies need to be fully reported.
Understanding surgical antimicrobial prescribing behaviour in the hospital setting: a systematic review and meta-ethnography protocol
Authors: Parker Hazel , Frost Julia , Britten Nicky , Robinson Sophie , Mattick Karen 
Published: October 2020

Abstract
Background
Surgical specialities use extensive amounts of antimicrobials, and misuse has been widely reported, making them a key target for antimicrobial stewardship initiatives. Interventions informed by, and tailored to, a clear understanding of the contextual barriers to appropriate antimicrobial use are more likely to successfully improve practice. However, this approach has been under utilised. Our aim is to synthesise qualitative studies on surgical antimicrobial prescribing behaviour (APB) in hospital settings to explain how and why contextual factors act and interact to influence APB amongst surgical teams. We will develop new theory to advance understanding and identify knowledge gaps to inform further research.

Methods
The meta-ethnography will follow the seven-phase method described by Noblit and Hare. We will conduct a comprehensive search using eight databases (AMED, CINAHL, EMBASE, MEDLINE, MEDLINE-in-process, Web of Science, Cochrane Library and PsycINFO) with no date restrictions; forwards and backwards citation searches; and contacting first authors of relevant papers. Studies will be dual screened and included if they use recognised qualitative methods and analysis; focus on contextual factors associated with surgical APB within hospital settings; are available in full in English; and are relevant to the research question. Any disagreements between reviewers will be resolved through discussion to reach consensus. Included studies will be read repeatedly to illuminate key concepts and the relationship between key concepts across studies. Then, key concepts will be sorted into conceptual categories or ‘piles’ which will be further abstracted to form a conceptual framework explaining surgical APB. During the synthesis, emerging interpretations will be discussed with stakeholders (including authors of included studies where possible; surgical and stewardship practitioners; and patient representatives) to ensure new knowledge is meaningful.

Discussion
This research has several strengths: (1) the protocol has been written with reference to established guidance maximising rigour and transparency; (2) the multi-disciplinary research team bring varied interpretative repertoires and relevant methodological skills; and (3) stakeholders will be involved to ensure that findings are relevant, and disseminated via suitable channels, to support improved patient care.

Systematic review registration
PROSPERO CRD42020184343