bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiome function predicts amphibian chytridiomycosis disease dynamics
Authors: Bates Kieran A. , Sommer Ulf , Hopkins Kevin P. , Shelton Jennifer M. G. , Wierzbicki Claudia , Sergeant Christopher , Tapley Benjamin , Michaels Christopher J. , Schmeller Dirk S. , Loyau Adeline , Bosch Jaime , Viant Mark R. , Harrison Xavier A. , Garner Trenton W. J. , Fisher Matthew C. 
Published: March 2022

Abstract
Background
The fungal pathogen
Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the clinical outcome of Bd infections, yet its overall functional importance is poorly understood.

Methods
Microbiome taxonomic and functional profiles were assessed using high-throughput bacterial 16S rRNA and fungal ITS2 gene sequencing, bacterial shotgun metagenomics and skin mucosal metabolomics. We sampled 56 wild midwife toads (Alytes obstetricans) from montane populations exhibiting Bd epizootic or enzootic disease dynamics. In addition, to assess whether disease-specific microbiome profiles were linked to microbe-mediated protection or Bd-induced perturbation, we performed a laboratory Bd challenge experiment whereby 40 young adult A. obstetricans were exposed to Bd or a control sham infection. We measured temporal changes in the microbiome as well as functional profiles of Bd-exposed and control animals at peak infection.

Results
Microbiome community structure and function differed in wild populations based on infection history and in experimental control versus Bd-exposed animals. Bd exposure in the laboratory resulted in dynamic changes in microbiome community structure and functional differences, with infection clearance in all but one infected animal. Sphingobacterium, Stenotrophomonas and an unclassified Commamonadaceae were associated with wild epizootic dynamics and also had reduced abundance in laboratory Bd-exposed animals that cleared infection, indicating a negative association with Bd resistance. This was further supported by microbe-metabolite integration which identified functionally relevant taxa driving disease outcome, of which Sphingobacterium and Bd were most influential in wild epizootic dynamics. The strong correlation between microbial taxonomic community composition and skin metabolome in the laboratory and field is inconsistent with microbial functional redundancy, indicating that differences in microbial taxonomy drive functional variation. Shotgun metagenomic analyses support these findings, with similar disease-associated patterns in beta diversity. Analysis of differentially abundant bacterial genes and pathways indicated that bacterial environmental sensing and Bd resource competition are likely to be important in driving infection outcomes.

Conclusions
Bd infection drives altered microbiome taxonomic and functional profiles across laboratory and field environments. Our application of multi-omics analyses in experimental and field settings robustly predicts Bd disease dynamics and identifies novel candidate biomarkers of infection.
MetaDecoder: a novel method for clustering metagenomic contigs
Authors: Liu Cong-Cong , Dong Shan-Shan , Chen Jia-Bin , Wang Chen , Ning Pan , Guo Yan , Yang Tie-Lin 
Published: March 2022

Abstract
Background
Clustering the metagenomic contigs into potential genomes is a key step to investigate the functional roles of microbial populations. Existing algorithms have achieved considerable success with simulated or real sequencing datasets. However, accurately classifying contigs from complex metagenomes is still a challenge.

Results
We introduced a novel clustering algorithm, MetaDecoder, which can classify metagenomic contigs based on the frequencies of k-mers and coverages. MetaDecoder was built as a two-layer model with the first layer being a GPU-based modified Dirichlet process Gaussian mixture model (DPGMM), which controls the weight of each DPGMM cluster to avoid over-segmentation by dynamically dissolving contigs in small clusters and reassigning them to the remaining clusters. The second layer comprises a semi-supervised k-mer frequency probabilistic model and a modified Gaussian mixture model for modeling the coverage based on single copy marker genes. Benchmarks on simulated and real-world datasets demonstrated that MetaDecoder can be served as a promising approach for effectively clustering metagenomic contigs.

Conclusions
In conclusion, we developed the GPU-based MetaDecoder for effectively clustering metagenomic contigs and reconstructing microbial communities from microbial data. Applying MetaDecoder on both simulated and real-world datasets demonstrated that it could generate more complete clusters with lower contamination. Using MetaDecoder, we identified novel high-quality genomes and expanded the existing catalog of bacterial genomes.
Interplay of disability, caregiver impact, and out-of-pocket expenditures in Duchenne muscular dystrophy: a cohort study
Authors: Schwartz Carolyn E. , Stark Roland B. , Borowiec Katrina , Audhya Ivana F. , Gooch Katherine L. 
Published: March 2022

AbstractBackgroundProviding caregiving support to people with Duchenne muscular dystrophy (DMD) is challenging, beginning in early childhood, and continuing through the progression of multidimensional disability. This study addressed the interplay between caregiver impact, out-of-pocket expenditures, and DMD disability. To examine these interconnections, we investigated the association between caregiver impact domains and out-of-pocket expenditures; and the presence of clusters in caregivers on the basis of DMD-related disability domains in the patients for whom they provided caregiving support.MethodsThis web-based study recruited 566 DMD caregivers (140 males, 426 females; mean age 41.6 years, SD 8.8, range 21–72), examining caregiver impact using the DMD Caregiver Impact Measure, PROMIS-derived parent-proxy (PPP) measures of their child’s disability, and items tapping out-of-pocket expenditures related to home and vehicle accommodations and assistive devices. T-tests compared caregiver impact scores by out-of-pocket expenditures incurred. Latent Profile Analyses (LPA) were conducted to generate impact profiles related to child’s disability as reported by caregiver proxies.ResultsHigher out-of-pocket expenditures were generally associated with worse impact on the subscales, but several expenditures (e.g., kitchen, bathroom, scooter) were associated with lower impact. LPA indicated that the four-group solution provided the best relative fit and yielded good profile separation (entropy = 0.91). Caregivers with lowest impact reported the highest mobility, cognitive, and upper extremity functioning of their DMD care recipients, whereas the highest caregiver impact was driven by their care recipient’s negative affect and fatigue. The upper-middle impact group showed great variability in proxy-disability domains, whereas the lower-middle group had similar levels of disability across domains. Profiles were represented across all child ages.ConclusionOut-of-pocket expenditures were often associated with worse caregiver impact, but some associated with milder impact (i.e., bathroom or kitchen modification, investing in a ceiling lift or medical scooter). While their son’s level of disability and age were related to impact on the DMD caregiver, the domains giving rise to highest caregiver impact were not the most visible aspects of disability, such as mobility, but rather negative affect and fatigue. Other contextual attributes are likely implicated, and will be addressed in the companion paper.
Preoperative hematological inflammatory markers associated with grade and survival in Meningiomas
Authors: de Oliveira Silva Camila Batista , Araújo Bruna , Ongaratti Bárbara Roberta , dos Santos Tainá Mafalda , Rech Carolina Garcia Soares Leães , Coutinho Lígia Barbosa , Ferreira Nelson Pires , da Costa Oliveira Miriam , Pereira-Lima Julia Fernanda Semmelmann 
Published: March 2022

AbstractMeningiomas represent the most frequently diagnosed intracranial tumors. Inflammatory cells present in the tumor can modulate both antitumor and protumor functions, and modify the therapeutic response. Hematological inflammatory parameters have provided prognostic information useful in the treatment and clinical evaluation of several tumors. The aim of this study was to evaluate preoperative hematological markers of patients with meningiomas and to relate them to clinical variables and recurrence-regrowth free survival. Eighty-nine patients without corticosteroid therapy were included. Blood test results and tumor characteristics were collected from medical records. Associations between clinical characteristics and the recurrence-regrowth free survival (RFS) were evaluated using Cox proportional hazard analysis and Kaplan-Meier curves. The receiver operating characteristic (ROC) curves were constructed. Of the 89 cases, 73 (82%) were grade I and 16 (18%) grade II. The mean age was 53 ± 13.9 years, with higher frequency in women. Anemia was observed in 23.6% and neutrophilia in 42% of the patients. In univariate analysis, anemia (p = 0.04), neutrophilia (p = 0.02) and neutrophil/lymphocyt ratio (NLR) (p = 0.02) were associated with an increased risk of recurrence-regrowth and shorter RFS. In multivariate analysis, anemia and NLR > 4.1 represented a higher risk of recurrence-regrowth (p = 0.003). The ROC curve analysis showed that only the lymphocyte/monocyte (L/M) > 2.5 was able to predict the tumor grade. The preoperative presence of anemia, neutrophilia, NLR > 4.1 and L/M > 2.5 were associated with a worse prognosis in meningiomas. The use of preoperative hematological inflammatory parameters as prognostic factors can be promissing for evaluation and follow-up of meningiomas.
Expanding the field: using digital to diversify learning in outdoor science
Authors: Stagg Bethan C. , Dillon Justin , Maddison Janine 
Published: March 2022

AbstractThis is an empirical study of teacher experiences with school learners (7–18 years) engaging in cross-curricular environmental science during the COVID-19 pandemic. The study focuses on #FieldworkLive, a programme of live-streamed outdoor science lessons produced by the Field Studies Council and Encounter Edu during the UK lockdown (April – May 2020). The experiences of approximately 377,000 teachers and students from 32 countries were captured using an online survey and direct staff consultation. This delivery method allowed us to reach untapped audiences and to provide learners with a virtual fieldwork experience during the constraints of lockdown. Teachers were highly positive about the technology-enhanced learning which provided them with novel perspectives and approaches for the classroom. We propose a model for the affordances provided by this delivery approach based on the Technological Pedagogical Content Knowledge framework. The Field Studies Council has developed a flexible package of multimedia resources for secondary schools as a route to enriching outdoor experience and learning despite the constraints imposed by the pandemic.
The significance of fibroblast growth factor-2 and kidney injury molecule-1 as biomarker of interstitial renal fibrosis in glomerulonephritis
Authors: Shaker Amr M. , Rakha Nahal K. , El-Shehaby Amal M. R. , Ramzy Tarek , Hamza Wael M. , Elkhatib Mohamed M. 
Published: March 2022

Abstract
Background
Renal tubulointerstitial fibrosis is a structural marker and prominent pathological characteristic of chronic progressive kidney disease, fibroblast growth factor-2 (FGF2) is a key fibrogenic cytokine that is likely to be involved in the pathogenesis of renal fibrosis, kidney injury molecule-1 (KIM-1) is one of the most promising, early biomarkers of renal disease, either acute or chronic, due to its translatability between preclinical and clinical trials. It is believed that this molecule participates in the process of both kidney injury and healing.

Methods
We prospectively enrolled a cohort study of eighty adult patients who had glomerular diseases (with glomerular filtration rate (GFR) > 30 ml/min/m2); serum level of FGF-2 and KIM-1 was measured at the same time of renal biopsy and was correlated with the degree of interstitial renal fibrosis.

Results
We found a significant positive correlation between FGF-2 and KIM-1 and the degree of interstitial renal fibrosis, albumin, and creatinine (P≤ 0.001), and a negative significant correlation with GFR and proteinuria. there is a positive significant correlation between serum KIM-1 and FGF-2 and hypertension with a significant P value (<0.001) that serum KIM-1 has sensitivity 90% and specificity of 95% and serum FGF-2 has sensitivity 95% and specificity 95% for detection of interstitial renal fibrosis.

Conclusions
Serum FGF-2 and KIM-1 seem to be a non-invasive novel biomarker of interstitial renal fibrosis in glomerulonephritis patients. It may become a useful biomarker without the need for the invasive maneuver of the renal biopsy. FGF-2 and KIM-1 are expected to be therapeutic targets for kidney injury.
The role of CGIAR Germplasm Health Units in averting endemic crop diseases: the example of rice blast in Bangladesh
Authors: Enriquez Yuji , Smale Melinda , Jamora Nelissa , Hossain Mohammod , Kumar Lava 
Published: March 2022

Abstract
Background
One of the less known benefits of the CGIAR is the facilitation of international agricultural research for crop improvement by providing a continuous supply of breeding materials for the development of disease resistant varieties. The Germplasm Health Units (GHUs) of the CGIAR are phytosanitary mechanisms put in place to help ensure safe (from pests and diseases) and efficient international transfer of germplasm among genebanks and breeding programs around the world. To date, there is no systematic documentation of the pathways and extent to which GHUs contribute to economic impact in recipient countries.

Methods
We conducted interviews with key experts and reviewed secondary literature and data to trace the pathways through which the GHU of the International Rice Research Institute (IRRI) contributes to the impact of breeding for rice blast. We applied an ex ante economic surplus framework to the case of rice blast in Bangladesh, considering productivity maintenance and time saving factors from GHU facilitation. Data were drawn from a national panel dataset of farm households (from 2013 to 2016 with about 4490 households) and field surveys of blast incidence and severity (from 2011 to 2012 in 10 agroecological zones). We augmented our model with Monte Carlo sampling to simulate distributions of parameters.

Results
Our model predicts that, in the most probable scenario (modal values), the IRRI GHU contributed about US$ 5.9 million of the total US$ 295 million net benefits over a 20-year time frame of continuous blast resistance breeding and deployment. In the most optimistic conditions (maximum), the IRRI GHU contributed as much as US$ 62 million of the US$ 1.46 billion benefits. The modal benefit–cost ratio of the GHU in this breeding program alone was estimated at 112. The results are sensitive to the rate of yield savings, which is contingent on yield levels, timing of deployment, effectiveness of resistance, and lifespan of resistance to blast.

Conclusions
The study reinforces the important, and often overlooked, role of the GHUs in the international agricultural research that aims to enhance genetic gains in crops through efficient and timely access to clean and healthy germplasm.
Genomic structural variation in tomato and its role in plant immunity
Authors: Jobson Emma , Roberts Robyn 
Published: March 2022

AbstractIt is well known that large genomic variations can greatly impact the phenotype of an organism. Structural Variants (SVs) encompass any genomic variation larger than 30 base pairs, and include changes caused by deletions, inversions, duplications, transversions, and other genome modifications. Due to their size and complex nature, until recently, it has been difficult to truly capture these variations. Recent advances in sequencing technology and computational analyses now permit more extensive studies of SVs in plant genomes. In tomato, advances in sequencing technology have allowed researchers to sequence hundreds of genomes from tomatoes, and tomato relatives. These studies have identified SVs related to fruit size and flavor, as well as plant disease response, resistance/susceptibility, and the ability of plants to detect pathogens (immunity). In this review, we discuss the implications for genomic structural variation in plants with a focus on its role in tomato immunity. We also discuss how advances in sequencing technology have led to new discoveries of SVs in more complex genomes, the current evidence for the role of SVs in biotic and abiotic stress responses, and the outlook for genetic modification of SVs to advance plant breeding objectives.
Study on surface modification and fabrication of surface composites of magnesium alloys by friction stir processing: a review
Authors: Manroo Suhail Ahmed , Khan Noor Zaman , Ahmad Babar 
Published: March 2022

AbstractMagnesium alloys and their composites are fast replacing aluminum alloys and other materials in the aerospace and automotive industries. Significant progress has been made in the fabrication of these composites to make them materials of choice for these industries. The choice of the fabrication process is crucial to realize the composites with properties that can compete with the materials currently in vogue. Conventional methods of fabrication of magnesium alloys and their composites are seriously limited as they lead to defects such as porosity and particle clustering. Friction stir processing (FSP) is turning out to be a promising fabrication technique to surmount these challenges. The process being a solid state technique is highly amenable to production of surface modified composites with very attractive mechanical and tribological properties. The main factor making FSP attractive is the relative ease of modification of the surface layers and the incorporation of reinforcement particles. The underlying plastic deformation in FSP ensures that the reinforcement particles are incorporated and distributed uniformly throughout the matrix. This paper attempts to review the current status of FSP as a technique of enabling the surface modification and fabrication of surface composites of magnesium alloys. The objective is to summarize the progress made towards the realization of surface-modified magnesium alloys, primarily in two systems, namely, Mg-AZ system and Mg/rare earth system. The operating conditions (and process parameters) and their subsequent effect on mechanical and tribological properties of the fabricated composites are summarized through the consideration of fabrication of three representative systems, viz., Mg-metal oxide (Mg-MO), Mg-metal carbide (Mg-MC), and Mg-carbon nano tube (Mg-CNT) systems.
Copy number variants in the context of evolving psychogenomic understanding
Authors: Roberts Kris 
Published: March 2022

SUMMARYThere are well-established links between recurring copy number variants (CNVs) (ubiquitous structural variations within chromosomes) and many psychiatric diagnoses. This article considers potential advances that enhanced understanding of CNVs might offer psychiatry – a scientifically rigorous footing for the discipline and personalised prescribing based on genetic data that would benefit patients from pre-diagnosis to treatment.
HealthTree Cure Hub: A Patient-Derived, Patient-Driven Clinical Cancer Information Platform Used to Overcome Hurdles and Accelerate Research in Multiple Myeloma
Authors: Sweeney Nathan W. , Ahlstrom Jennifer M. , Fonseca Rafael , Davies Faith E. , Thompson Michael A. 
Published: March 2022

PURPOSEThe study of rare diseases, such as multiple myeloma (MM), often experiences unique research hurdles that can delay or prevent lifesaving discoveries. HealthTree Cure Hub is a first-in-class software program designed to overcome these potential research hurdles.METHODSWe assessed whether HealthTree Cure Hub improved four commonly experienced research hurdles such as (1) small numbers of patient accrual to clinical trials and research studies, (2) shallow and isolated data sets, (3) high costs to answer research questions, and (4) lack of long-term follow-up patient data.RESULTSAs of June 2021, HealthTree Cure Hub, with its unique portal features, has attracted 9,225 patients with MM and diverse demographic backgrounds. While completing an online health profile, patients shared comprehensive data, as well as provided consent to contribute data from electronic medical records. Portal use answered research questions using patient-driven real-world data. This also cultivated relationships with patients and established communication channels that enabled continual patient contact to allow for long-term follow-up.CONCLUSIONThese results suggest that a patient-driven data capture tool such as HealthTree Cure Hub will help alleviate common research hurdles, which, in turn, will accelerate MM research, develop new hypotheses, and ultimately improve survival.
Clopidogrel Bolus is Inferior to Sustained Clopidogrel Pretreatment in Patients Undergoing Carotid Artery Stent Placement
Authors: Qureshi Adnan I. , Huang Wei , Lobanova Iryna , Ishfaq M. Fawad , French Brandi R. , Siddiq Farhan , Gomez Camilo R. 
Published: March 2022

BACKGROUND:
Clopidogrel bolus is an option used before carotid artery stent (CAS) placement when sustained clopidogrel pretreatment is not used.

OBJECTIVE:
To compare the effect of clopidogrel bolus (450 mg administered ≥4 hours) with sustained clopidogrel pretreatment (48 hours or greater) before CAS among patients recruited in the Carotid Revascularization Endarterectomy versus Stenting Trial.

METHODS:
We compared the rates of primary end point (either any stroke, myocardial infarction, or death during the periprocedural period or any ipsilateral stroke within 4 years) between patients who received clopidogrel bolus and those who received sustained clopidogrel pretreatment using Cox proportional hazards analysis after adjusting for age, sex, symptomatic status, and initial severity of stenosis (≥70% vs <70%) over 4 years.

RESULTS:
The rate of periprocedural stroke (7.3% vs 3.4%, P = .03) and primary end point (11.3% vs 5.9%, P = .02) was significantly higher among patients who received clopidogrel bolus. The risk of primary end point was significantly higher in patients who received clopidogrel bolus (hazards ratio 1.9, 95% CI 1.1–3.4, P = .02) after adjusting for potential confounders. The overall mean (±standard deviation) primary end point–free survival based on Kaplan–Meier analysis was 7.0 ± 0.2 years for patients who received clopidogrel bolus and 8.9 ± 0.1 years for those who received sustained clopidogrel pretreatment (log-rank test P = .011).

CONCLUSION:
Clopidogrel bolus was associated with higher rates of adverse outcomes compared with sustained clopidogrel pretreatment in patients who underwent CAS. Therefore, clopidogrel bolus may not be equivalent to sustained clopidogrel pretreatment.