bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spontaneous Cervical Artery Dissection in Vascular Ehlers-Danlos Syndrome
Authors: Adham Salma , Billon Clarisse , Legrand Anne , Domigo Valérie , Denarié Nicolas , Charpentier Etienne , Jeunemaitre Xavier , Frank Michael 
Published: March 2021

Background and Purpose:

Vascular Ehlers-Danlos syndrome is a rare inherited connective tissue disorder because of pathogenic variants in the
COL3A1
gene. Arterial complications can affect all anatomic areas and about 25% involve supra-aortic trunks (SATs) but no systematic assessment of cervical artery lesions has been made. The primary objective was to determine an accurate prevalence of spontaneous SAT lesions in a large series of patients with vascular Ehlers-Danlos syndrome at diagnosis and during follow-up. Secondary objectives were to study their neurological consequences (transient ischemic attack or stroke) and the possible relationships with sex, genotype, ascertainment status.

Methods:
A retrospective review of a monocentric cohort of patients with molecularly proven vascular Ehlers-Danlos syndrome followed in a tertiary referral center from 2000 to 2017.

Results:

One hundred forty-four patients were analyzed, 56.9% (n=82) had SAT lesions: 64.6% females, 74.4% index-case patients. Most lesions were identified in early arterial assessment (48% at first work-up, mean age of 35.7±13.0 years). Cumulative incidence of a first identification of a SAT lesion was 41.7% at 40 years old. On the complete period of survey, 183 SAT lesions (with 132 dissections and 33 aneurysms) were identified, mainly in internal carotid arteries (56.3%) and vertebral arteries (28.9%), more rarely in patients with
COL3A1
null mutations (
P
=0.008). Transient ischemic attack or stroke were reported in n=16 (19.5%) of the 82 patients with SAT lesions without relation with age, sex, treatment, or hypertension.

Conclusions:
Cervical artery lesions are frequent and mostly asymptomatic in patients with vascular Ehlers-Danlos syndrome. Local dissections and aneurysms are the most frequent type of lesions, but transient ischemic attack or stroke seem rare.
Reforecasting Two Heavy-Precipitation Events with Three Convection-Permitting Ensembles
Authors: Capecchi Valerio 
Published: March 2021

AbstractWe investigate the potential added value of running three limited-area ensemble systems (with the WRF, Meso-NH, and MOLOCH models and a grid spacing of approximately 2.5 km) for two heavy-precipitation events in Italy. Such high-resolution ensembles include an explicit treatment of convective processes and dynamically downscale the ECMWF global ensemble predictions, which have a grid spacing of approximately 18 km. The predictions are verified against rain gauge data, and their accuracy is evaluated over that of the driving coarser-resolution ensemble system. Furthermore, we compare the simulation speed (defined as the ratio of simulation length to wall-clock time) of the three limited-area models to estimate the computational effort for operational convection-permitting ensemble forecasting. We also study how the simulation wall-clock time scales with increasing numbers of computing elements (from 36 to 1152 cores). Objective verification methods generally show that convection-permitting forecasts outperform global forecasts for both events, although precipitation peaks remain largely underestimated for one of the two events. Comparing simulation speeds, the MOLOCH model is the fastest and the Meso-NH is the slowest one. The WRF Model attains efficient scalability, whereas it is limited for the Meso-NH and MOLOCH models when using more than 288 cores. We finally demonstrate how the model simulation speed has the largest impact on a joint evaluation with the model performance because the accuracy of the three limited-area ensembles, amplifying the forecasting capability of the global predictions, does not differ substantially.
From the Margins of the Spice Garden Economy: Agroforestry and Gendered Practices in the Western Ghats, Karnataka
Authors: Rao Manisha 
Published: March 2021

The present coronavirus pandemic has created havoc in lives and livelihoods of people across the world. In just a few months, the world as we knew it has irretrievably changed. If one were to trace the roots of the crisis, it would lead one to the shift from sustainable farming systems to market-based systems that have increased agricultural productivity but have led to the breakdown of humanity’s relationship with nature. In the Malnad (up-ghat) region of the Uttara Kannada district of Karnataka, known for its diversified spice garden agroforestry practices, a similar change can be observed. Over the last decade, there has been an increasing conversion of paddy land and forest encroachments for cultivation of areca, leading to a change in the biodiversity of the region. The changes in the land use patterns and the destruction of the environment caused by infrastructure projects are among some of the important reasons that have resulted in increasing drought-like situations in an area known to be the wettest region of the Western Ghats and resulting in epidemics endemic to the region. However, in the shadow of the areca-spice garden economy of this region, there is a lesser known but growing economy—the home garden agroforestry. The gendered practices of the home gardens, run mainly by the women of the community, provide the vital everyday inputs for the household. Though high in terms of use value, the home gardens are low in terms of exchange value. It is in the context of mapping the cultural and developmental contours of this region that one tries to understand the gendered practices of the local communities that are a beacon of hope in times of a pandemic. In this article, one attempts to examine the marginal though crucial initiatives of women of this district to preserve the biodiversity of the region and provide for food in the kitchens. Finally, it attempts to connect the dots between gender, environment and development and argues for the adoption of a critical feminist political ecology perspective to analyse the gendered agroforestry practices.
Quantifying the Influence of Individual, Community, and Health System Factors on Quality of Life Among Inner-City African Americans With Type 2 Diabetes
Authors: Campbell Jennifer A. , Yan Alice , Walker Renee E. , Weinhardt Lance , Wang Yang , Walker Rebekah J. , Egede Leonard E. 
Published: March 2021

Purpose The purpose of this study is to examine the association of individual, community, and health system factors on quality of life among inner-city African Americans with type 2 diabetes. Methods Primary data from a cross-sectional study with a community sample of 241 inner-city African Americans with type 2 diabetes were analyzed. Paper-based surveys were administered in which the SF-12 was used to capture the physical component (PCS) and mental component (MCS) of quality of life. Four regression approaches (sequential, stepwise with backward and forward selection, and all possible subsets regression) were used to examine the influence of individual, community, and health system factors on PCS and MCS after adjusting for relevant covariates using a conceptual framework. Results In fully adjusted models, having less than a high school education and having major depression were associated with lower quality-of-life scores for MCS across all 4 regression approaches. Being employed was positively associated with better quality-of-life scores for PCS across all 4 regression approaches. PCS was higher across all 4 regression approaches for those reporting a history of trauma. At the health systems level, usual source of care was associated with better PCS across 3 regression approaches. Conclusions These results highlight key factors that influence quality of life among inner-city African Americans with type 2 diabetes that could be targets for interventions in this population. However, additional research is needed to understand existing pathways that may be driving many of these relationships.
The Statistical Fragility of Platelet-Rich Plasma in Rotator Cuff Surgery: A Systematic Review and Meta-analysis
Authors: Parisien Robert L. , Ehlers Cooper , Cusano Antonio , Tornetta Paul , Li Xinning , Wang Dean 
Published: March 2021

Background: The practice of evidence-based medicine relies on objective data to guide clinical decision-making with specific statistical thresholds conveying study significance. Purpose: To determine the utility of applying the fragility index (FI) and the fragility quotient (FQ) analysis to randomized controlled trials (RCTs) evaluating the utilization of platelet-rich plasma (PRP) in rotator cuff repairs (RCRs). Study Design: Systematic review and meta-analysis. Methods: RCTs pertaining to the utilization of PRP in surgical RCRs published in 13 peer-reviewed journals from 2000 to 2020 were evaluated. The FI was determined by manipulating each reported outcome event until a reversal of significance was appreciated. The associated FQ was determined by dividing the FI by the sample size. Results: Of the 9746 studies screened, 19 RCTs were ultimately included for analysis. The overall FI incorporating all 19 RCTs was only 4, suggesting that the reversal of only 4 events is required to change study significance. The associated FQ was determined as 0.092. Of the 43 outcome events reporting lost to follow-up data, 13 (30.2%) represented lost to follow-up >4. Conclusion: Our analysis suggests that RCTs evaluating PRP for surgical RCRs may lack statistical stability with only a few outcome events required to alter trial significance. Therefore, we recommend the reporting of an FI and an FQ in conjunction with P value analysis to carefully interpret the integrity of statistical stability in future comparative trials. Clinical Relevance: Clinical decisions are often informed by statistically significant results. Thus, a true understanding of the robustness of the statistical findings informing clinical decision-making is of critical importance.
Gold particle geomicrobiology: Using viable bacteria as a model for understanding microbe–mineral interactions
Authors: Sanyal Santonu Kumar , Shuster Jeremiah 
Published: March 2021

AbstractThe biogeochemical cycling of gold has been proposed from studies focusing on gold particle morphology, surface textures and associated bacteria living on the surface of gold particles. Additionally, it has been suggested that metabolically active bacteria on particles catalyse gold dissolution and gold re-precipitation processes, i.e. fluid–bacterial–mineral interaction within microenvironments surrounding particles. Therefore, the isolation and characterisation of viable bacteria from gold particles can be used as a model to improve the understanding of bacterial–gold interactions. In this study, classical microbiology methods were used to isolate a gold-tolerant bacterium (Acinetobactersp. SK-43) directly from gold particles. The genome of this isolate contained diverse (laterally acquired) heavy-metal resistance genes and stress tolerance genes, suggesting that gene expression would confer resistance to a wide range of potentially toxic metals that could occur in the surrounding microenvironment. The presence of these genes, along with genes for nutrient cycling under nutrient-limited conditions highlights the genomic capacity of howAcinetobactersp. SK-43 could survive on gold particles and remain viable. Laboratory experiments demonstrated that this isolate could grow in the presence of soluble gold up to 20 μM (AuCl3) and that >50% of soluble gold was reduced upon exposure. Collectively, these results suggest thatAcinetobactersp. SK-43 (and presumably similar bacteria) could survive the cytotoxic effects of soluble Au from particles undergoing dissolution. This study provides comprehensive insight on the possible bacterial contributions to gold biogeochemical cycling in natural environments.
Platelet-targeted hyperfunctional FIX gene therapy for hemophilia B mice even with preexisting anti-FIX immunity
Authors: Schroeder Jocelyn A. , Chen Juan , Chen Yingyu , Cai Yuanhua , Yu Hongyin , Mattson Jeremy G. , Monahan Paul E. , Shi Qizhen 
Published: March 2021

Abstract
Gene therapy may lead to a cure for hemophilia B (HB) if it is successful. Data from clinical trials using adeno-associated virus (AAV)–mediated liver-targeted FIX gene therapy are very encouraging. However, this protocol can be applied only to adults who do not have liver disease or anti-AAV antibodies, which occur in 30% to 50% of individuals. Thus, developing a protocol that can be applied to all HB patients is desired. Our previous studies have demonstrated that lentivirus-mediated platelet-specific FIX (2bF9) gene therapy can rescue bleeding diathesis and induce immune tolerance in FIXnull mice, but FIX expression was only ∼2% to 3% in whole blood. To improve the efficacy, we used a codon-optimized hyperfunctional FIX-Padua (2bCoF9R338L) to replace the 2bF9 cassette, resulting in 70% to 122% (35.08-60.77 mU/108 platelets) activity levels in 2bCoF9R338L-transduced FIXnull mice. Importantly, sustained hyperfunctional platelet-FIX expression was achieved in all 2bCoF9R338L-transduced highly immunized recipients with activity levels of 18.00 ± 9.11 and 9.36 ± 12.23 mU/108 platelets in the groups treated with 11 Gy and 6.6 Gy, respectively. The anti-FIX antibody titers declined with time, and immune tolerance was established after 2bCoF9R338L gene therapy. We found that incorporating the proteasome inhibitor bortezomib into preconditioning can help eliminate anti-FIX antibodies. The bleeding phenotype in 2bCoF9R338L-transduced recipients was completely rescued in a tail bleeding test and a needle-induced knee joint injury model once inhibitors dropped to undetectable. The hemostatic efficacy in 2bCoF9R338L-transduced recipients was further confirmed by ROTEM and thrombin generation assay (TGA). Together, our studies suggest that 2bCoF9R338L gene therapy can be a promising protocol for all HB patients, including patients with inhibitors.
barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection
Authors: Bernhards Casey B. , Lux Matthew W. , Katoski Sarah E. , Goralski Tyler D. P. , Liem Alvin T. , Gibbons Henry S. 
Published: March 2021

Abstract
Background
Tracking dispersal of microbial populations in the environment requires specific detection methods that discriminate between the target strain and all potential natural and artificial interferents, including previously utilized tester strains. Recent work has shown that genomic insertion of short identification tags, called “barcodes” here, allows detection of chromosomally tagged strains by real-time PCR. Manual design of these barcodes is feasible for small sets, but expansion of the technique to larger pools of distinct and well-functioning assays would be significantly aided by software-guided design.

Results
Here we introduce barCoder, a bioinformatics tool that facilitates the process of creating sets of uniquely identifiable barcoded strains. barCoder utilizes the genomic sequence of the target strain and a set of user-specified PCR parameters to generate a list of suggested barcode “modules” that consist of binding sites for primers and probes, and appropriate spacer sequences. Each module is designed to yield optimal PCR amplification and unique identification. Optimal amplification includes metrics such as ideal melting temperature and G+C content, appropriate spacing, and minimal stem-loop formation; unique identification includes low BLAST hits against the target organism, previously generated barcode modules, and databases (such as NCBI). We tested the ability of our algorithm to suggest appropriate barcodes by generating 12 modules for Bacillus thuringiensis serovar kurstaki—a simulant for the potential biowarfare agent Bacillus anthracis—and three each for other potential target organisms with variable G+C content. Real-time PCR detection assays directed at barcodes were specific and yielded minimal cross-reactivity with a panel of near-neighbor and potential contaminant materials.

Conclusions
The barCoder algorithm facilitates the generation of synthetically barcoded biological simulants by (a) eliminating the task of creating modules by hand, (b) minimizing optimization of PCR assays, and (c) reducing effort wasted on non-unique barcode modules.
Extensive non-redundancy in a recently duplicated developmental gene family
Authors: Baker E. A. , Gilbert S. P. R. , Shimeld S. M. , Woollard A. 
Published: March 2021

AbstractBackgroundIt has been proposed that recently duplicated genes are more likely to be redundant with one another compared to ancient paralogues. The evolutionary logic underpinning this idea is simple, as the assumption is that recently derived paralogous genes are more similar in sequence compared to members of ancient gene families. We set out to test this idea by using molecular phylogenetics and exploiting the genetic tractability of the model nematode,Caenorhabditis elegans,in studying the nematode-specific family of Hedgehog-related genes, the Warthogs. Hedgehog is one of a handful of signal transduction pathways that underpins the development of bilaterian animals. While having lost abona fideHedgehog gene, most nematodes have evolved an expanded repertoire of Hedgehog-related genes, ten of which reside within the Warthog family.ResultsWe have characterised their evolutionary origin and their roles inC. elegansand found that these genes have adopted new functions in aspects of post-embryonic development, including left–right asymmetry and cell fate determination, akin to the functions of their vertebrate counterparts. Analysis of various double and triple mutants of the Warthog family reveals that more recently derived paralogues are not redundant with one another, while a pair of divergent Warthogs do display redundancy with respect to their function in cuticle biosynthesis.ConclusionsWe have shown that newer members of taxon-restricted gene families are not always functionally redundant despite their recent inception, whereas much older paralogues can be, which is considered paradoxical according to the current framework in gene evolution.
Stressors, coping, and resources needed during the COVID-19 pandemic in a sample of perinatal women
Authors: Barbosa-Leiker Celestina , Smith Crystal Lederhos , Crespi Erica J. , Brooks Olivia , Burduli Ekaterina , Ranjo Samantha , Carty Cara L. , Hebert Luciana E. , Waters Sara F. , Gartstein Maria A. 
Published: March 2021

Abstract
Background
Psychological stress and coping experienced during pregnancy can have important effects on maternal and infant health, which can also vary by race, ethnicity, and socioeconomic status. Therefore, we assessed stressors, coping behaviors, and resources needed in relation to the COVID-19 pandemic in a sample of 162 perinatal (125 pregnant and 37 postpartum) women in the United States.

Methods
A mixed-methods study captured quantitative responses regarding stressors and coping, along with qualitative responses to open-ended questions regarding stress and resources needed during the COVID-19 pandemic. Logistic and linear regression models were used to analyze differences between pregnant and postpartum participants, as well as differences across key demographic variables. Qualitative content analysis was used to analyze open-ended questions.

Results
During the COVID-pandemic, food scarcity and shelter-in-place restrictions made it difficult for pregnant women to find healthy foods. Participants also reported missing prenatal appointments, though many reported using telemedicine to obtain these services. Financial issues were prevalent in our sample and participants had difficulty obtaining childcare. After controlling for demographic variables, pregnant women were less likely to engage in healthy stress-coping behaviors than postpartum women. Lastly, we were able to detect signals of increased stressors induced by the COVID-19 pandemic, and less social support, in perinatal women of racial and ethnic minority, and lower-income status. Qualitative results support our survey findings as participants expressed concerns about their baby contracting COVID-19 while in the hospital, significant others missing the delivery or key obstetric appointments, and wanting support from friends, family, and birthing classes. Financial resources, COVID-19 information and research as it relates to maternal-infant health outcomes, access to safe healthcare, and access to baby supplies (formula, diapers, etc.) emerged as the primary resources needed by participants.

Conclusions
To better support perinatal women’s mental health during the COVID-19 pandemic, healthcare providers should engage in conversations regarding access to resources needed to care for newborns, refer patients to counseling services (which can be delivered online/via telephone) and virtual support groups, and consistently screen pregnant women for stressors.
Metabolic alterations in meningioma reflect the clinical course
Authors: Masalha Waseem , Daka Karam , Woerner Jakob , Pompe Nils , Weber Stefan , Delev Daniel , Krüger Marie T. , Schnell Oliver , Beck Jürgen , Heiland Dieter Henrik , Grauvogel Juergen 
Published: March 2021

Abstract
Background
Meningiomas are common brain tumours that are usually defined by benign clinical course. However, some meningiomas undergo a malignant transformation and recur within a short time period regardless of their World Health Organization (WHO) grade. The current study aimed to identify potential markers that can discriminate between benign and malignant meningioma courses.

Methods
We profiled the metabolites from 43 patients with low- and high-grade meningiomas. Tumour specimens were analyzed by nuclear magnetic resonance analysis; 270 metabolites were identified and clustered with the AutoPipe algorithm.

Results
We observed two distinct clusters marked by alterations in glycine/serine and choline/tryptophan metabolism. Glycine/serine cluster showed significantly lower WHO grades and proliferation rates. Also progression-free survival was significantly longer in the glycine/serine cluster.

Conclusion
Our findings suggest that alterations in glycine/serine metabolism are associated with lower proliferation and more recurrent tumours. Altered choline/tryptophan metabolism was associated with increases proliferation, and recurrence. Our results suggest that tumour malignancy can be reflected by metabolic alterations, which may support histological classifications to predict the clinical outcome of patients with meningiomas.