bluuebunny/crossref_metadata_2025 huggingface dataset:
The tracking of internal and external training loads with next-day player-reported fatigue at different times of the season in elite soccer players
Authors: Draper Garrison , Wright Matthew , Chesterton Paul , Atkinson Greg
Published: January 2021

The aim was to assess factor structure of player-reported fatigue and quantify within-subjects association between changes in training load measures and next day player-reported fatigue at different time points of an elite football season. Using longitudinal research design, twenty-four professional footballers, mean (SD) age of 25.7 (3.4) years, were monitored during their competitive season, including pre-season. Player-reported fatigue data and session ratings of perceived exertion (session-RPE) were collected via a mobile application. Player’s Heart rate (HR) and global positioning system (GPS) data were collected daily for each player in field sessions. Principal component analysis (PCA) indicated three components with Eigenvalues above 1.0; “soreness”, “mood, and “hydration”. Within-player correlations between training load values and next day player-reported fatigue values were trivial to moderate (r ≈ −0.42 to −0.04). In-season we observed large correlations between Total Distance (TD) and PlayerLoad with Soreness (r = −0.55, 95% CI: −0.62 to −0.46; r = −.054, 95% CI: −0.62 to −0.46), but during pre-season, correlations were small (r = −0.15, 95% CI: −0.28 to −0.01; r = −0.13, 95% CI: −0.26 to 0.01). The HR TRIMP, TD and session-RPE measures each showed trivial to moderate correlations (r ≈ −0.41 to −0.08) with next day “mood”. Our in-house player-reported fatigue questionnaire was sensitive to the multi-dimensional nature of fatigue, identifying physiological (soreness), psychological (mood and stress) and nutritional (hydration and nutrition) components. We found the in-season correlations with training load to be greater than previously reported in the literature, specifically with next day player-reported “soreness”. Nevertheless, the correlations between the items of our scale and pre-season training load were small.
Use of Artificial Intelligence to understand adults’ thoughts and behaviours relating to COVID-19
Authors: Flint SW , Piotrkowicz A , Watts K
Published: January 2021

Aims:

The outbreak of severe acute respiratory syndrome coronavirus 2 (COVID-19) is a global pandemic that has had substantial impact across societies. An attempt to reduce infection and spread of the disease, for most nations, has led to a lockdown period, where people’s movement has been restricted resulting in a consequential impact on employment, lifestyle behaviours and wellbeing. As such, this study aimed to explore adults’ thoughts and behaviours in response to the outbreak and resulting lockdown measures.

Methods:

Using an online survey, 1126 adults responded to invitations to participate in the study. Participants, all aged 18 years or older, were recruited using social media, email distribution lists, website advertisement and word of mouth. Sentiment and personality features extracted from free-text responses using Artificial Intelligence methods were used to cluster participants.

Results:

Findings demonstrated that there was varied knowledge of the symptoms of COVID-19 and high concern about infection, severe illness and death, spread to others, the impact on the health service and on the economy. Higher concerns about infection, illness and death were reported by people identified at high risk of severe illness from COVID-19. Behavioural clusters, identified using Artificial Intelligence methods, differed significantly in sentiment and personality traits, as well as concerns about COVID-19, actions, lifestyle behaviours and wellbeing during the COVID-19 lockdown.

Conclusions:

This time-sensitive study provides important insights into adults’ perceptions and behaviours in response to the COVID-19 pandemic and associated lockdown. The use of Artificial Intelligence has identified that there are two behavioural clusters that can predict people’s responses during the COVID-19 pandemic, which goes beyond simple demographic groupings. Considering these insights may improve the effectiveness of communication, actions to reduce the direct and indirect impact of the COVID-19 pandemic and to support community recovery.
Clinical outcomes and structural integrity rate of arthroscopic augmented rotator cuff repairs using extracellular porcine matrix patch
Authors: Consigliere Paolo , Bernasconi Alessio , Dimock Richard , Narvani A Ali
Published: January 2021

Background

Structural failure rate in rotator cuff repairs is still high. The purpose of the study is to assess the structural integrity of a series of augmented rotator cuff repairs with porcine matrix patch and report the functional outcomes.

Methods

Between 2014 and 2017, 44 consecutive patients underwent arthroscopic double-row repair of medium to massive rotator cuff tears with extracellular porcine dermal matrix augmentation. At one-year follow-up, magnetic resonance imaging scan was performed to assess the integrity of the repair. Oxford Shoulder Score (OSS), Constant Score (CS) and Visual Analogue Scale pain score, together with range of motion were used to assess patients.

Results

Patients mean age was 68 (53–82); mean follow-up was 17.2 (12–24) months. On magnetic resonance imaging scans, seven rotator cuff repair failures (15.9%) were observed: tear size was an independent predictor of re-rupture at one-year follow-up. Clinical scores showed a statistically significant improvement at three months and until final follow-up ( p< 0.001). No complications occurred.

Conclusion

Observed structural failure rate of 15.9% is lower than those reported in the literature for standard rotator cuff repair of medium to massive tears in similar cohorts to ours. Extracellular matrix augmentation for rotator cuff repair was shown to be a safe and reliable support to the repairs and patients recovered good shoulder function. Level of Evidence: Level IV.
How to Best Protect People With Diabetes From the Impact of SARS-CoV-2: Report of the International COVID-19 and Diabetes Summit
Authors: Zhang Jennifer Y. , Shang Trisha , Ahn David , Chen Kong , Coté Gerard , Espinoza Juan , Mendez Carlos E. , Spanakis Elias K. , Thompson Bithika , Wallia Amisha , Wisk Lauren E. , Kerr David , Klonoff David C.
Published: January 2021

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has rapidly involved the entire world and exposed the pressing need for collaboration between public health and other stakeholders from the clinical, scientific, regulatory, pharmaceutical, and medical device and technology communities. To discuss how to best protect people with diabetes from serious outcomes from COVID-19, Diabetes Technology Society, in collaboration with Sansum Diabetes Research Institute, hosted the “International COVID-19 and Diabetes Virtual Summit” on August 26-27, 2020. This unique, unprecedented real-time conference brought together physicians, scientists, government officials, regulatory experts, industry representatives, and people with diabetes from six continents to review and analyze relationships between COVID-19 and diabetes. Over 800 attendees logged in. The summit consisted of five sessions: (I) Keynotes, (II) Preparedness, (III) Response, (IV) Recovery, and (V) Surveillance; eight parts: (A) Background, (B) Resilience, (C) Outpatient Care, (D) Inpatient Care, (E) Resources, (F) High-Risk Groups, (G) Regulation, and (H) The Future; and 24 sections: (1) Historic Pandemics and Impact on Society, (2) Pathophysiology/Risk Factors for COVID-19, (3) Social Determinants of COVID-19, (4) Preparing for the Future, (5) Medications and Vaccines, (6) Psychology of Patients and Caregivers, (7) Outpatient Treatment of Diabetes Mellitus and Non-Pharmacologic Intervention, (8) Technology and Telehealth for Diabetes Outpatients, (9) Technology for Inpatients, (10) Management of Diabetes Inpatients with COVID-19, (11) Ethics, (12) Accuracy of Diagnostic Tests, (13) Children, (14) Pregnancy, (15) Economics of Care for COVID-19, (16) Role of Industry, (17) Protection of Healthcare Workers, (18) People with Diabetes, (19) International Responses to COVID-19, (20) Government Policy, (21) Regulation of Tests and Treatments, (22) Digital Health Technology, (23) Big Data Statistics, and 24) Patient Surveillance and Privacy. The two keynote speeches were entitled (1) COVID-19 and Diabetes—Meeting the Challenge and (2) Knowledge Gaps and Research Opportunities for Diabetes and COVID-19. While there was an emphasis on diabetes and its interactions with COVID-19, the panelists also discussed the COVID-19 pandemic in general. The meeting generated many novel ideas for collaboration between experts in medicine, science, government, and industry to develop new technologies and disease treatment paradigms to fight this global pandemic.
Developing a Child and Adolescent Chorister Engagement Survey: Probing Perceptions of Early Collective Experiences and Outcomes
Authors: Zhukov Katie , Barrett Margaret S. , Welch Graham F.
Published: January 2021

This article describes the design and implementation of a survey instrument specifically developed for 6–17-year-old Australian choral singers to access and measure participants’ perceptions of their self-esteem, self-efficacy, musical identity and social engagement as outcomes of participation in a high-quality choral ensemble. After reviewing existing music surveys and identifying their strengths, complementarities, differences and potential weaknesses, we adapted established surveys from psychology and social science literature to the choral music setting. An initial draft survey was trialled with higher education choristers and refined prior to implementation in six young choirs that were noted for their high-quality performance. Data from 202 surveys were analysed using confirmatory factor analysis and this resulted in a four-factor model. The validated survey was implemented twice over a six-month period with 61 choristers drawn from three choirs. Results showed that social and psychological benefits of choir participation were evidenced, maintained and even improved over time. Findings support the suitability and psychometric soundness of this new survey instrument, and demonstrate the usefulness of adapting psychological/social survey instruments to music research.
Jejunal Dieulafoy’s Lesion: A Systematic Review of Evaluation, Diagnosis, and Management
Authors: Malik Adnan , Inayat Faisal , Goraya Muhammad Hassan Naeem , Almas Talal , Ishtiaq Rizwan , Malik Sohira , Tarar Zahid Ijaz
Published: January 2021

Jejunal Dieulafoy’s lesion is an exceedingly rare but important cause of gastrointestinal bleeding. It frequently presents as a diagnostic and therapeutic conundrum due to the rare occurrence, intermittent bleeding symptoms often requiring prompt clinical action, variability in the detection and treatment methods, and the risk of rebleeding. We performed a systematic literature search of MEDLINE, Cochrane, Embase, and Scopus databases regarding jejunal Dieulafoy’s lesio from inception till June 2020. A total of 136 cases were retrieved from 76 articles. The mean age was 55 ± 24 years, with 55% of cases reported in males. Patients commonly presented with melena (33%), obscure-overt gastrointestinal bleeding (29%), and hemodynamic compromise (20%). Hypertension (26%), prior gastrointestinal surgery (14%), and valvular heart disease (13%) were the major underlying disorders. Conventional endoscopy often failed but single- and double-balloon enteroscopy identified the lesion in 96% and 98% of patients, respectively. There was no consensus on the treatment. Endoscopic therapy was instituted in 64% of patients. Combination therapy (34%) with two or more endoscopic modalities, was the preferred approach. With regard to endoscopic monotherapy, hemoclipping (19%) and argon plasma coagulation (4%) were frequently employed procedures. Furthermore, direct surgical intervention in 32% and angiographic embolization was performed in 4% of patients. The rebleeding rate was 13.4%, with a mean follow-up duration of 17.6 ± 21.98 months. The overall mortality rate was 4.4%. Jejunal Dieulafoy’s lesion is still difficult to diagnose and manage. Although the standard diagnostic and therapeutic modalities remain to be determined, device-assisted enteroscopy might yield promising outcomes.
Research Trends on the Rotator Cuff Tendon: A Bibliometric Analysis of the Past 2 Decades
Authors: Lei Lei , Zhang Chi , Sun Fu-Hua , Xie Yujie , Liang Bin , Wang Li , Pang Guoyin , Chen Ruyan , Jiang Wei , Ou Xia , Miyamoto Akira , Wang Jianxiong
Published: January 2021

Background:

Clinical research on the rotator cuff tendon is increasing, and new approaches are being applied to rotator cuff disease. Considering the integration of research resources and research trends, it is necessary to conduct an analysis of recent research on the topic.

Purpose:

To identity the research trends, influential journals, key researchers, and core countries of rotator cuff tendon research between 2000 and 2019.

Study Design:

Cross-sectional study.

Methods:

All the literature related to rotator cuff tendon research was retrieved from the Web of Science Core Collection on January 7, 2020. Qualitative and quantitative analyses were processed based on Web of Science and CiteSpace.

Results:

A total of 4131 studies, which included 3830 articles and 301 reviews, were obtained. There was an upward trend of studies on the topic, with small fluctuations in the past 2 decades. The United States had the most studies, and the number of studies from other countries increased over the study period. Most of the funding sources came from the United States. Articles in the Journal of Shoulder and Elbow Surgery had the most citations for rotator cuff research. Frontier topics, such as arthroscopic repair, mesenchymal stem cell, and “platelet-rich plasma, were identified. The number of citations in 2018 ( r = 0.280; P = .005) and 2019 ( r = 0.307; P = .002) had a weak positive correlation with publication date, indicating that the more recently published articles had a higher number of citations.

Conclusion:

Valuable information on rotator cuff research based on bibliometric analysis was identified. Arthroscopic repair, mesenchymal stem cell, and platelet-rich plasma might be the research frontiers in this field, and researchers should focus on these topics in future studies.
An in situ, micro-scale investigation of inorganically and organically driven rare-earth remobilisation during weathering
Authors: Kalintsev Alexander , Brugger Joël , Etschmann Barbara , Ram Rahul
Published: January 2021

At present, a significant portion of rare-earth elements (REEs) are sourced from weathering profiles. The mineralogy of the protolith plays an important role in controlling the fate of REEs during weathering, as accessory minerals contain the bulk the REE budget in most rocks, and different minerals vary in their susceptibilities to weathering processes. REE supergene deposits (‘adsorption clay deposits’) are associated with deep weathering in tropical environments, which often precludes characterisation of the incipient steps in REE liberation from their host minerals in the protolith. Here we have targeted a weathered REE-enriched lithology from a sub-arid environment undergoing relatively rapid uplift, namely the Yerila Gneiss from the Northern Flinders Ranges, Australia, where regolith was shallow or absent and parent rock material had yet to completely break down. Results from X-ray fluorescence mapping, scanning electron microscopy (SEM), SEM-focussed ion beam milling (FIB-SEM), inductively-coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS highlight the migration pathways of REEs and associated U and Th from allanite-(Ce) grains that are the main REE host within Yerila Gneiss material. Migration of light REEs and Th away from the allanite-(Ce) grains via radial cracks resulting from allanite-(Ce) metamictisation was interpreted to result from weathering, as Ce is partially present in its tetravalent oxidation state and Th mobility is most easily explained by the involvement of organic ligands. FIB-SEM provides further evidence for the importance of biogenic processes in REE+U/Th mobility and fractionation in uranothorite-associated spheroidal structures associated with the weathering of allanite-(Ce). Organic carbon was also found in association with a xenotime-(Y) grain; in this case, REE liberation is most likely a by-product of biogenic phosphate utilisation. These results highlight that local controls (at mineral interfaces) mediated by biota and/or biogenic organic matter can control the initiation of REE (+Th,U) mobilisation during weathering.
How I treat warm autoimmune hemolytic anemia
Authors: Barcellini Wilma , Fattizzo Bruno
Published: January 2021

Warm autoimmune hemolytic anemia (wAIHA) is caused by increased erythrocyte destruction by immunoglobulin G (IgG) autoantibodies, with or without complement activation. Antibody-dependent cell-mediated cytotoxicity by macrophages/activated lymphocytes occurs in the lymphoid organs and spleen (extravascular hemolysis). The ability of the bone marrow (BM) to compensate determines clinical severity. The different pathogenic mechanisms, their complex interplay, and changes over time may explain wAIHA’s great clinical heterogeneity and unpredictable course. The disease may be primary, drug induced, or associated with lymphoproliferative neoplasms, autoimmune and infectious diseases, immunodeficiencies, solid tumors, or transplants. Therapeutic interventions include steroids, splenectomy, immunosuppressants, and rituximab; the latter is increasingly used in steroid-refractory cases based on evidence from the literature and a few prospective trials. We present 5 patient case studies highlighting important issues: (1) the diagnosis and proper use of steroid therapy, (2) the concerns about the choice between rituximab and splenectomy in second-line treatment, (3) the need of periodical re-evaluation of the disease to assess the possible evolution of relapsed/refractory cases in myelodysplastic and BM failure syndromes, and (4) the difficulties in managing cases of severe/acute disease that are at high risk of relapse. Incorporating novel targeted therapies into clinical practice will be an exciting challenge in the future.
How I treat cold agglutinin disease
Authors: Berentsen Sigbjørn
Published: January 2021

The last decades have seen great progress in the treatment of cold agglutinin disease (CAD). Comparative trials are lacking, and recommendations must be based mainly on nonrandomized trials and will be influenced by personal experience. Herein, current treatment options are reviewed and linked to 3 cases, each addressing specific aspects of therapy. Two major steps in CAD pathogenesis are identified, clonal B-cell lymphoproliferation and complement-mediated hemolysis, each of which constitutes a target of therapy. Although drug treatment is not always indicated, patients with symptomatic anemia or other bothersome symptoms should be treated. The importance of avoiding ineffective therapies is underscored. Corticosteroids should not be used to treat CAD. Studies on safety and efficacy of relevant drugs and combinations are briefly described. The author recommends that B cell–directed approaches remain the first choice in most patients requiring treatment. The 4-cycle bendamustine plus rituximab combination is highly efficacious and sufficiently safe and induces durable responses in most patients, but the time to response can be many months. Rituximab monotherapy should be preferred in frail patients. The complement C1s inhibitor sutimlimab is an emerging option in the second line and may also find its place in the first line in specific situations.
How I treat microangiopathic hemolytic anemia in patients with cancer
Authors: Thomas M. R. , Scully M.
Published: January 2021

Microangiopathic hemolytic anemia (MAHA) with thrombocytopenia, suggests a thrombotic microangiopathy (TMA), linked with thrombus formation affecting small or larger vessels. In cancer patients, it may be directly related to the underlying malignancy (initial presentation or progressive disease), to its treatment, or a separate incidental diagnosis. It is vital to differentiate incidental thrombotic thrombocytopenia purpura or atypical hemolytic uremic syndrome in cancer patients presenting with a TMA, as they have different treatment strategies, and prompt initiation of treatment impacts outcome. In the oncology patient, widespread microvascular metastases or extensive bone marrow involvement can cause MAHA and thrombocytopenia. A disseminated intravascular coagulation (DIC) picture may be precipitated by sepsis or driven by the cancer itself. Cancer therapies may cause a TMA, either dose-dependent toxicity, or an idiosyncratic immune-mediated reaction due to drug-dependent antibodies. Many causes of TMA seen in the oncology patient do not respond to plasma exchange and, where feasible, treatment of the underlying malignancy is important in controlling both cancer-TMA or DIC driven disease. Drug-induced TMA should be considered and any putative causal agent stopped. We will discuss the differential diagnosis and treatment of MAHA in patients with cancer using clinical cases to highlight management principles.
Hematologic disorder–associated Cxcr4 gain-of-function mutation leads to uncontrolled extrafollicular immune response
Authors: Alouche Nagham , Bonaud Amélie , Rondeau Vincent , Hussein-Agha Rim , Nguyen Julie , Bisio Valeria , Khamyath Mélanie , Crickx Etienne , Setterblad Niclas , Dulphy Nicolas , Mahevas Matthieu , McDermott David H. , Murphy Philip M. , Balabanian Karl , Espéli Marion
Published: January 2021

The extrafollicular immune response is essential to generate a rapid but transient wave of protective antibodies during infection. Despite its importance, the molecular mechanisms controlling this first response are poorly understood. Here, we demonstrate that enhanced Cxcr4 signaling caused by defective receptor desensitization leads to exacerbated extrafollicular B-cell response. Using a mouse model bearing a gain-of-function mutation of Cxcr4 described in 2 human hematologic disorders, warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome and Waldenström macroglobulinemia, we demonstrated that mutant B cells exhibited enhanced mechanistic target of rapamycin signaling, cycled more, and differentiated more potently into plasma cells than wild-type B cells after Toll-like receptor (TLR) stimulation. Moreover, Cxcr4 gain of function promoted enhanced homing and persistence of immature plasma cells in the bone marrow, a phenomenon recapitulated in WHIM syndrome patient samples. This translated in increased and more sustained production of antibodies after T-independent immunization in Cxcr4 mutant mice. Thus, our results establish that fine-tuning of Cxcr4 signaling is essential to limit the strength and length of the extrafollicular immune response.
Framework for the evaluation of new tests for tuberculosis infection
Authors: Hamada Yohhei , den Boon Saskia , Cirillo Daniela Maria , Penn-Nicholson Adam , Ruhwald Morten , Menzies Dick , Oxlade Olivia , Falzon Dennis , Kanchar Avinash , Korobitsyn Alexei , Zignol Matteo , Matteelli Alberto , Kasaeva Tereza
Published: January 2021

The scale-up of tuberculosis (TB) preventive treatment (TPT) must be accelerated to achieve the targets set by the United Nations High-level Meeting on TB and the End TB Strategy. The scale-up of effective TPT is hampered by concerns about operational challenges to implement the existing tests for TB infection. New simpler tests could facilitate the scale-up of testing for TB infection. We present a framework for evaluation of new immunodiagnostic tests for the detection of TB infection, with an aim to facilitate their standardised evaluation and accelerate adoption into global and national policies and subsequent scale-up. The framework describes the principles to be considered when evaluating new tests for TB infection and provides guidance to manufacturers, researchers, regulators and other users on study designs, populations, reference standards, sample size calculation and data analysis and it is also aligned with the Global Strategy for TB Research and Innovation adopted by the World Health Assembly in 2020. In addition, we briefly describe technical issues that should be considered when evaluating new tests, including the safety for skin tests, costs incurred by patients and the health system, and operational characteristics.
Self-inflicted gunshot injury to the external genitalia: a case report and review of literature
Authors: Obi Anselm Okwudili , Ulebe Augustine Obasi , Nnadozie Ugochukwu Uzodinmma , Maduba Charles Chidiebele , Okorie Chukwudi Ogonnaya , Anikwe Obinna Nnabuife
Published: January 2021

Background

Gunshot wounds of the external genitalia are rare. Rarer still are civilian self-inflicted gunshot wounds of the external genitalia. The protocol for the management of gunshot wounds of the penis especially with respect to urethral injuries is not fully established.

Case presentation

We present a 27-year-old male undergraduate student, who accidentally shot himself in the penis. He sustained American Association for the Surgery of Trauma (AAST) grades IV to V injuries to the penis, scrotum and left testes. He was managed in a multistage, multi-disciplinary fashion including staged buccal mucosal graft repair of 4 cm proximal penile urethral defect with satisfactory cosmetic and functional outcome.

Conclusions

Excellent functional and cosmetic results may be obtained after severe penetrating trauma to the external genitalia even in low resource centres in the hands of non-reconstructive urologists. Buccal mucosal graft is a viable option for two stage reconstruction of the urethra.
MHC class I evolution; from Northern pike to salmonids
Authors: Grimholt U. , Lukacs M.
Published: January 2021

Background

Salmonids are of major importance both as farmed and wild animals. With the changing environment comes changes in pathogenic pressures so understanding the immune system of all salmonid species is of essence. Major histocompatibility complex (MHC) genes are key players in the adaptive immune system signalling infection to responding T-cells populations. Classical MHC class I (MHCI) genes, defined by high polymorphism, broad expression patterns and peptide binding ability, have a key role in inducing immunity. In salmonids, the fourth whole genome duplication that occurred 94 million years ago has provided salmonids with duplicate MHCI regions, while Northern Pike, a basal sister clade to salmonids, represent a species which has not experienced this whole genome duplication.

Results

Comparing the gene organization and evolution of MHC class I gene sequences in Northern pike versus salmonids displays a complex picture of how many of these genes evolved. Regional salmonid Ia and Ib Z lineage gene duplicates are not orthologs to the Northern pike Z lineage sequences. Instead, salmonids have experienced unique gene duplications in both duplicate regions as well as in the Salmo and Oncorhynchus branch. Species-specific gene duplications are even more pronounced for some L lineage genes.

Conclusions

Although both Northern pike as well as salmonids have expanded their U and Z lineage genes, these gene duplications occurred separately in pike and in salmonids. However, the similarity between these duplications suggest the transposable machinery was present in a common ancestor. The salmonid MHCIa and MHCIb regions were formed during the 94 MYA since the split from pike and before the Oncorhynchus and Salmo branch separated. As seen in tetrapods, the non-classical U lineage genes are diversified duplicates of their classical counterpart. One MHCI lineage, the L lineage, experienced massive species-specific gene duplications after Oncorhynchus and Salmo split approximately 25 MYA. Based on what we currently know about L lineage genes, this large variation in number of L lineage genes also signals a large functional diversity in salmonids.
Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing
Authors: Kellman Benjamin P. , Baghdassarian Hratch M. , Pramparo Tiziano , Shamie Isaac , Gazestani Vahid , Begzati Arjana , Li Shangzhong , Nalabolu Srinivasa , Murray Sarah , Lopez Linda , Pierce Karen , Courchesne Eric , Lewis Nathan E.
Published: January 2021

Background

Both RNA-Seq and sample freeze-thaw are ubiquitous. However, knowledge about the impact of freeze-thaw on downstream analyses is limited. The lack of common quality metrics that are sufficiently sensitive to freeze-thaw and RNA degradation, e.g. the RNA Integrity Score, makes such assessments challenging.

Results

Here we quantify the impact of repeated freeze-thaw cycles on the reliability of RNA-Seq by examining poly(A)-enriched and ribosomal RNA depleted RNA-seq from frozen leukocytes drawn from a toddler Autism cohort. To do so, we estimate the relative noise, or percentage of random counts, separating technical replicates. Using this approach we measured noise associated with RIN and freeze-thaw cycles. As expected, RIN does not fully capture sample degradation due to freeze-thaw. We further examined differential expression results and found that three freeze-thaws should extinguish the differential expression reproducibility of similar experiments. Freeze-thaw also resulted in a 3′ shift in the read coverage distribution along the gene body of poly(A)-enriched samples compared to ribosomal RNA depleted samples, suggesting that library preparation may exacerbate freeze-thaw-induced sample degradation.

Conclusion

The use of poly(A)-enrichment for RNA sequencing is pervasive in library preparation of frozen tissue, and thus, it is important during experimental design and data analysis to consider the impact of repeated freeze-thaw cycles on reproducibility.

Graphical abstract
Neutrophil extracellular traps are present in the airways of ENaC-overexpressing mice with cystic fibrosis-like lung disease
Authors: Tucker Samantha L. , Sarr Demba , Rada Balázs
Published: January 2021

Background

Neutrophils are key components of the exacerbated inflammation and tissue damage in cystic fibrosis (CF) airways. Neutrophil extracellular traps (NETs) trap and kill extracellular pathogens. While NETs are abundant in the airways of CF patients and have been hypothesized to contribute to lung damage in CF, the in vivo role of NETs remains controversial, partially due to lack of appropriate animal models. The goal of this study was to detect NETs and to further characterize neutrophil-mediated inflammation in the airways of mice overexpressing the epithelial sodium channel (βENaC-Tg mice on C57BL/6 background) in their lung with CF-like airway disease, in the absence of any apparent bacterial infections.

Methods

Histology scoring of lung tissues, flow cytometry, multiplex ELISA, immunohistochemistry and immunofluorescence were used to characterize NETs and the airway environment in uninfected, βENaC-Tg mice at 6 and 8 weeks of age, the most chronic time points so far studied in this model.

Results

Excessive neutrophilic infiltration characterized the lungs of uninfected, βENaC-Tg mice at 6 and 8 weeks of age. The bronchoalveolar lavage fluid (BALF) of βENaC-Tg mice contains increased levels of CF-associated cytokines and chemokines: KC, MIP-1α/β, MCP-1, G-CSF, IL-5, and IL-6. The BALF of βENaC-Tg mice contain MPO-DNA complexes, indicative of the presence of NETs. Immunofluorescence and flow cytometry of BALF neutrophils and lung tissues demonstrated increased histone citrullination, a NET-specific marker, in βENaC-Tg mice.

Conclusions

NETs are detected in the airways of βENaC-Tg mice, in the absence of bacterial infections. These data demonstrate the usefulness of the βENaC-Tg mouse to serve as a model for studying the role of NETs in chronic CF airway inflammation.
Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance
Authors: Wang Xingyi , Liu Hui , Siddique Kadambot H. M. , Yan Guijun
Published: January 2021

Background

Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL)QPhs.ccsu-3A.1for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated.

Results

Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlieQPhs.ccsu-3A.1responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines.

Conclusions

The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.
Non-targeted and targeted metabolomics profiling of tea plants (Camellia sinensis) in response to its intercropping with Chinese chestnut
Authors: Wu Tian , Zou Rui , Pu Dian , Lan Zengquan , Zhao Bingyu
Published: January 2021

Background

Intercropping is often used in the tea producing areas where land resources are not so abundant, and the produced green tea is tasted more delicious through a tea-Chinese chestnut intercropping system according to the experience of indigenous farmers. The length and weight of tea leaf increase under this intercropping system and their root systems are stratified vertically and coordinate symbiosis. However, the delicacy mechanism under the intercropping is not fully understood.

Results

Green tea from the Chinese chestnut–tea intercropping system established in the 1980s ranked highest compared with a pure tea plantation from the same region. Based on the non-targeted metabolomics, 100 differential metabolites were upregulated in the tea leaves from intercropping system relative to monoculture system. Twenty-one amino acids were upregulated and three downregulated in response to the intercropping based on the targeted metabolomics; half of the upregulated amino acids had positive effects on the tea taste. Levels of allantoic acid, sugars, sugar alcohols, and oleic acid were higher and less bitter flavonoids in the intercropping system than those in monoculture system. The upregulated metabolites could promote the quality of tea and its health-beneficial health effects. Flavone and flavonol biosynthesis and phenylalanine metabolism showed the greatest difference. Numerous pathways associated with amino acid metabolism altered, suggesting that the intercropping of Chinese chestnut–tea could greatly influence amino acid metabolism in tea plants.

Conclusions

These results enhance our understanding of the metabolic mechanisms by which tea quality is improved in the Chinese chestnut–tea intercropping system and demonstrate that there is great potential to improve tea quality at the metabolomic level by adopting such an intercropping system.
Expression of a bacterial 3-dehydroshikimate dehydratase (QsuB) reduces lignin and improves biomass saccharification efficiency in switchgrass (Panicum virgatum L.)
Authors: Hao Zhangying , Yogiswara Sasha , Wei Tong , Benites Veronica Teixeira , Sinha Anagh , Wang George , Baidoo Edward E. K. , Ronald Pamela C. , Scheller Henrik V. , Loqué Dominique , Eudes Aymerick
Published: January 2021

Background

Lignin deposited in plant cell walls negatively affects biomass conversion into advanced bioproducts. There is therefore a strong interest in developing bioenergy crops with reduced lignin content or altered lignin structures. Another desired trait for bioenergy crops is the ability to accumulate novel bioproducts, which would enhance the development of economically sustainable biorefineries. As previously demonstrated in the model plant Arabidopsis, expression of a 3-dehydroshikimate dehydratase in plants offers the potential for decreasing lignin content and overproducing a value-added metabolic coproduct (i.e., protocatechuate) suitable for biological upgrading.

Results

The 3-dehydroshikimate dehydratase QsuB from Corynebacterium glutamicum was expressed in the bioenergy crop switchgrass (Panicum virgatum L.) using the stem-specific promoter of an O-methyltransferase gene (pShOMT) from sugarcane. The activity of pShOMT was validated in switchgrass after observation in-situ of beta-glucuronidase (GUS) activity in stem nodes of plants carrying a pShOMT::GUS fusion construct. Under controlled growth conditions, engineered switchgrass lines containing a pShOMT::QsuB construct showed reductions of lignin content, improvements of biomass saccharification efficiency, and accumulated higher amount of protocatechuate compared to control plants. Attempts to generate transgenic switchgrass lines carrying the QsuB gene under the control of the constitutive promoter pZmUbi-1 were unsuccessful, suggesting possible toxicity issues associated with ectopic QsuB expression during the plant regeneration process.

Conclusion

This study validates the transfer of the QsuB engineering approach from a model plant to switchgrass. We have demonstrated altered expression of two important traits: lignin content and accumulation of a co-product. We found that the choice of promoter to drive QsuB expression should be carefully considered when deploying this strategy to other bioenergy crops. Field-testing of engineered QsuB switchgrass are in progress to assess the performance of the introduced traits and agronomic performances of the transgenic plants.
Incidence and risk factors of micronutrient deficiency in patients with IBD and intestinal Behçet’s disease: folate, vitamin B12, 25-OH-vitamin D, and ferritin
Authors: Park Yong Eun , Park Soo Jung , Park Jae Jun , Cheon Jae Hee , Kim TaeIl , Kim Won Ho
Published: January 2021

Background

Patients with inflammatory bowel disease (IBD) and intestinal Behçet’s disease (BD) are vulnerable to micronutrient deficiencies due to diarrhea-related gastrointestinal loss and poor dietary intake caused by disease-related anorexia. However, few studies have investigated the incidence and risk factors for micronutrient deficiency.

Methods

We retrospectively analyzed 205 patients with IBD who underwent micronutrient examination, including folate, vitamin B12, 25-OH-vitamin D, and/or ferritin level quantification, with follow-up blood tests conducted 6 months later.

Results

Eighty patients (39.0%), who were deficient in any of the four micronutrients, were classified as the deficiency group, and the remaining 125 (61.0%) were classified as the non-deficient group. Compared to those in the non-deficiency group, patients in the deficiency group were much younger, had more Crohn's disease (CD) patients, more patients with a history of bowel operation, and significantly less 5-amino salicylic acid usage. Multivariate analysis revealed that CD and bowel operation were significant independent factors associated with micronutrient deficiency.

Conclusions

The incidence of micronutrient deficiency was high (39.0%). Factors including CD, bowel operation, and younger ages were found to be associated with higher risks of deficiency. Therefore, patients with IBD, especially young patients with CD who have undergone bowel resection surgery, need more attention paid to micronutrition.
‘The newest vital sign among pregnant women attending women wellness and research Centre in Qatar: a cross-sectional study’
Authors: Naja Sarah , Elyamani Rowaida , Al Ibrahim Abdullah , Al Kubaisi Noora , Itani Rayan , AbdulRouf Palli
Published: January 2021

Background

Health literacy is a vital strategy to consider when designing health-promoting programs, and health literacy is a priority in Qatar’s national health agenda. In the context of pregnancy, inadequate health literacy has been linked to several adverse outcomes among pregnant women such as unplanned conception, smoking, and lack of multi-vitamin intake. Given the paucity of data, this study aimed to assess the level of health literacy and its determinants among pregnant women in the State of Qatar.

Methods

An analytical cross-sectional design was utilized. First, we piloted the measurement tools on 10% of the calculated sample size. Accordingly, the items of the measurement tools were revised. Next, we utilized a structured questionnaire to interview the participants about their socio-demographic characteristics, pregnancy-related factors, and the Newest Vital Sign Tool. A chi-square test was employed to investigate the association level among variables, with significance set to P < 0.05. A logistic regression model was used to identify the factors associated with a low literacy level.

Results

We found that almost four in 10 pregnant women (n = 138,45.4%) had inadequate health literacy. Furthermore, the insufficient level of health literacy was significantly associated with low educational background, decreased household income, and primigravida. However, uncontrolled glycaemia was the only significant predictor of inadequate health literacy through logistic regression. The scale was found to be reliable, with a calculated Cronbach’s alpha of 0.8.

Conclusions

Low health literacy is common among pregnant women in the State of Qatar. Thus, public health officials should focus on delivering tailored health literacy interventions to pregnant women in the country.
Gestational weight gain outside the 2009 Institute of Medicine recommendations: novel psychological and behavioural factors associated with inadequate or excess weight gain in a prospective cohort study
Authors: Feng Yu Yang , Yu Zhijie Michael , van Blyderveen Sherry , Schmidt Louis , Sword Wendy , Vanstone Meredith , Biringer Anne , McDonald Helen , Beyene Joseph , McDonald Sarah Diana
Published: January 2021

Background

Previous studies have noted traditional physical, demographic, and obstetrical predictors of inadequate or excess gestational weight gain, but the roles of psychological and behavioral factors are not well established. Few interventions targeting traditional factors of gestational weight gain have been successful, necessitating exploration of new domains. The objective of this study was to identify novel psychological and behavioral factors, along with physical, demographic, and obstetrical factors, associated with gestational weight gain that is discordant with the 2009 Institute of Medicine guidelines (inadequate or excess gain).

Methods

We recruited English-speaking women with a live singleton fetus at 8 to 20 weeks of gestation who received antenatal care from 12 obstetrical, family medicine, and midwifery clinics. A questionnaire was used to collect information related to demographic, physical, obstetrical, psychological, and behavioural factors anticipated to be related to weight gain. The association between these factors and total gestational weight gain, classified as inadequate, appropriate, and excess, was examined using stepwise multinomial logistic regression.

Results

Our study population comprised 970 women whose baseline data were obtained at a mean of 14.8 weeks of gestation ±3.4 weeks (standard deviation). Inadequate gestational weight gain was associated with obesity, planned gestational weight gain (below the guidelines or not reported), anxiety, and eating sensibly when with others but overeating when alone, while protective factors were frequent pregnancy-related food cravings and preferring an overweight or obese body size image. Excess gestational weight gain was associated with pre-pregnancy overweight or obese body mass index, planned gestational weight gain (above guidelines), frequent eating in front of a screen, and eating sensibly when with others but overeating when alone, while a protective factor was being underweight pre-pregnancy.

Conclusions

In addition to commonly studied predictors, this study identified psychological and behavioral factors associated with inadequate or excess gestational weight gain. Factors common to both inadequate and excessive gestational weight gain were also identified, emphasizing the multidimensional nature of the contributors to guideline-discordant weight gain.
Phaco-UCP; combined phacoemulsification and ultrasound ciliary plasty versus phacoemulsification alone for management of coexisting cataract and open angle glaucoma: a randomized clinical trial
Authors: Torky Magda A. , Alzafiri Yousef A. , Abdelhameed Ameera G. , Awad Eman A.
Published: January 2021

Background

Various surgical techniques have been described, to be combined with cataract surgery in glaucoma patients, aiming for an additional reduction of intraocular pressure (IOP), hence minimizing the burden of anti-glaucoma medication (AGM). Ultrasound ciliary plasty (UCP) is a recent microinvasive glaucoma surgery (MIGS) recommended for primary and refractory glaucoma. This study was conducted to evaluate the safety and efficacy of a new technique; combined phacoemulsification and ultrasound ciliary plasty (Phaco-UCP) as a primary surgical treatment for coexisting cataract and open angle glaucoma.

Methods

A randomized clinical trial, including 61 eyes of 61 patients with visually significant cataract and open angle glaucoma, randomized to either Phaco-UCP (study group; 31 eyes) or phacoemulsification alone (Phaco-alone) (control group; 30 eyes). Primary outcomes included reduction in IOP and/or the number of AGM. Secondary outcomes included visual acuity improvement and complications. Qualified Success was defined as an IOP reduction ≥ 20% from baseline value, with an IOP 6–21 mmHg, with no additional AGM or glaucoma surgery. Failure was defined as either < 20% IOP reduction, despite AGM use, the need of glaucoma surgeries or serious complications.

Results

At 18 months postoperatively, Phaco-UCP group had a median IOP reduction of 7 mmHg (Q1, Q3 = 3, 10) compared to 2 mmHg (Q1, Q3 = 2, 3) in Phaco-alone group (P < 0.001). Phaco-UCP group had significantly higher success rate at all time points reaching 67.7% at the last follow-up versus 16.7% only in Phaco-alone group (P< 0.001). The median number of AGM significantly decreased from [3 (Q1, Q3 = 2, 4), 3 (Q1, Q3 = 2,3)] respectively, (P =0.3)] at baseline to [1 (Q1,Q3 = 1, 2), 2 (Q1,Q3 = 2, 2)] respectively, (P < 0.001)] at 18 months postoperatively. No serious intraoperative or postoperative complications were encountered in either group.

Conclusion

Phaco-UCP is a simple, safe and effective procedure for management of coexisting cataract and open angle glaucoma.

Trial registration

ClinicalTrials.gov identifier, NCT04430647; retrospectively registered. June 12, 2020.