bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pediatric Syncope: A Systematic Review
Authors: Zavala Rennette , Metais Benjamin , Tuckfield Lynnia , DelVecchio Michael , Aronoff Stephen 
Published: June 2020

Objectives
The aims of the study were to perform the first systematic review of pediatric syncope etiologies and to determine the most common diagnoses with credible intervals (CredIs).

Methods
Review was performed within Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines and used Embase, Scopus, PubMed, and the Cochrane Controlled Trial databases. The following inclusion criteria for the articles were used: minimum of 10 patients, standard definition of syncope used, subjects who were 21 years or younger, and subjects who were either a consecutive retrospective group or a prospective group. No restrictions were made regarding language of the studies, but an English abstract was required. The following information was collected: purpose of the study, definition of syncope, number of patients, patient age range, inclusion/exclusion criteria, and etiologies of syncope.

Results
Of the 500 articles initially identified, 11 studies met the inclusion criteria and were the basis for this review. Three thousand seven hundred patients were included, ranging in age from 3 months to 21 years. The most common etiologies identified were vasovagal (52.2%; 95% CredI, 50.6–53.9), postural orthostatic tachycardia syndrome (13.1%; 95% CredI, 12.1–14.2), and cardiac causes (4.0%; 95% CredI, 3.39–4.65). A total of 18.3% (95% CredI, 17.0–19.5) of patients were found to have syncope of unknown cause.

Conclusions
Syncope is a common pediatric complaint. Most cases seen are a result of benign causes, with only a small percentage because of serious medical conditions. In addition, most syncopal episodes in the pediatric population are diagnosed clinically or with minimally invasive testing, emphasizing the importance of a detailed history and physical examination.
Advances in Treatment of Follicular Lymphoma
Authors: Luminari Stefano , Trotman Judith , Federico Massimo 
Published: June 2020

Abstract
Follicular lymphoma (FL) is a heterogeneous disease with varying prognosis owing to differences in clinical, laboratory, and disease parameters. Although generally considered incurable, prognosis for early and advanced stage disease has improved because of therapeutic advances, several of which have resulted from elucidation of the biologic and molecular basis of the disease. The choice of treatment for FL is highly dependent on patient and disease characteristics. Several tools are available for risk stratification, although limitations in their routine clinical use exist. For limited disease, treatment options include radiotherapy, rituximab monotherapy or combination regimens, and surveillance. Treatment of advanced disease is often determined by tumor burden, with surveillance or rituximab considered for low tumor burden and chemoimmunotherapy for high tumor burden disease. Treatment for relapsed or refractory disease is influenced by initial first-line therapy and the duration and quality of the response. At present, there is no consensus for treatment of patients with early or multiply-relapsed disease; however, numerous agents, combination regimens, and transplant options have demonstrated efficacy. While the number of therapies available to treat FL has increased together with an improved understanding of the underlying biologic basis of disease, the best approach to select the most appropriate treatment strategy for an individual patient at a particular time continues to be elucidated. This chapter considers prognostic factors and the evolving treatment landscape of FL, including recent and emerging therapies, as well as remaining unmet needs.
Molecular Diagnostics of Non-Hodgkin Lymphoma
Authors: Solomon James P. , Arcila Maria E. 
Published: June 2020

Abstract
Non-Hodgkin lymphoma encompasses a diverse group of B-cell and T-cell neoplasms. Current classification is based on clinical information, histologic assessment, immunophenotypic characteristics, and molecular alterations. A wide range of genetic alterations, including large chromosomal structural rearrangements, aneuploidies, point mutations, and copy number alterations, have been reported across all types of lymphomas. Many of these are now incorporated into the World Health Organization–defined criteria for the diagnostic evaluation of patients with lymphoid proliferations and, therefore, their accurate identification is paramount for diagnosis, subclassification, and selection of treatment. In addition to their value in the diagnostic setting, many alterations that are not routinely evaluated in standard clinical practice may still define specific disease entities as they have important implications in risk stratification, as well as roles in emerging alternate therapies and disease monitoring. Because of the complexity and range of alterations, their accurate and sensitive assessment requires a careful selection of technology. Here, we discuss the most commonly used molecular techniques in current clinical practice and highlight some of the benefits and pitfalls based on the type of alteration.
Intersecting Pandemics: Impact of SARS-CoV-2 (COVID-19) Protective Behaviors on People Living With HIV, Atlanta, Georgia
Authors: Kalichman Seth C. , Eaton Lisa A. , Berman Marcie , Kalichman Moira O. , Katner Harold , Sam Soya S. , Caliendo Angela M. 
Published: June 2020

Background:
COVID-19 and its social responses threaten the health of people living with HIV. We conducted a rapid-response interview to assess COVID-19 protective behaviors of people living with HIV and the impact of their responses on HIV-related health care.

Method:
Men and women living with HIV (N = 162) aged 20–37 years participating in a longitudinal study of HIV treatment and care completed routine study measures and an assessment of COVID-19–related experiences.

Results:
At baseline, most participants demonstrated HIV viremia, markers indicative of renal disorders, and biologically confirmed substance use. At follow-up, in the first month of responding to COVID-19, engaging in more social distancing behaviors was related to difficulty accessing food and medications and increased cancelation of health care appointments, both by self and providers. We observed antiretroviral therapy adherence had improved during the initial month of COVID-19 response.

Conclusions:
Factors that may pose added risk for COVID-19 severity were prevalent among people living with HIV, and those with greater risk factors did not practice more COVID-19 protective behaviors. Social distancing and other practices intended to mitigate the spread of COVID-19 interfered with HIV care, and impeded access to food and medications, although an immediate adverse impact on medication adherence was not evident. These results suggest social responses to COVID-19 adversely impacted the health care of people living with HIV, supporting continued monitoring to determine the long-term effects of co-occurring HIV and COVID-19 pandemics.
Role of Serum MRP8/14 in Predicting Response to Methotrexate in Children With Juvenile Idiopathic Arthritis
Authors: Bagri Narendra Kumar , Karmakar Subhradip , Haldar Partha , Lodha Rakesh , Kabra S. K. 
Published: June 2020

Objective
Nearly 40% of children with juvenile idiopathic arthritis (JIA) might not respond to first-line disease-modifying antirheumatic drugs (DMARDs) including methotrexate (MTX). Hence, there is a need for a biomarker that can predict MTX response and help in tailoring initial therapy. Our objective was to study the role of serum myeloid-related protein (MRP) 8/14, and other inflammatory cytokines, as predictors of response to MTX among children with JIA.

Methods
We did a longitudinal follow-up study among children diagnosed with JIA at our institute. All MTX-naive children with JIA requiring DMARDs were eligible for this study; those who either took corticosteroids or DMARDs for more than 6 weeks at time of presentation were excluded. The demographic and clinical information was collected using a pretested semistructured questionnaire, and selected biomarkers were collected at baseline and again at 3 months. Response at 3 months was assessed using the American College of Rheumatology (ACR) criteria; responders were children who achieved ACR50, whereas those failing to achieve ACR30 were classified as nonresponders. Multivariate binary logistic regression was done to assess determinants of being a responder.

Results
We enrolled 69 children (36 boys) with JIA, of which 48 (69.5%) were responders. The baseline value of serum MRP8/14 was significantly higher in responders (median, 144.34 [interquartile range, 88.54–188.34] ng/mL) compared with the nonresponders (median, 95.34 [interquartile range, 76.54–130.28] ng/mL), p = 0.047. Being a responder was significantly associated with baseline serum MRP8/14 with adjusted odds ratio of 1.01 (95% confidence interval, 1.00–1.02).

Conclusions
The baseline levels of MRP8/14 were significantly raised in children meeting ACR50 at follow-up and suggest a prognostic value in predicting response to MTX.
Prevalence of Osteopenia in Drug-Naive Patients With Antineutrophil Cytoplasmic Antibody–Associated Vasculitis
Authors: Yoo Byung-Woo , Jung Seung Min , Song Jason Jungsik , Park Yong-Beom , Lee Sang-Won 
Published: June 2020

Objectives
To examine the bone mineral density and prevalence of osteoporosis and osteopenia in glucocorticoid- and immunosuppressive drug–naive patients younger than 55 years with antineutrophil cytoplasmic antibody–associated vasculitis (AAV).

Methods
This was a cross-sectional study. We reviewed the medical records of 35 AAV patients and 35 age-, sex-, and body mass index (BMI)–matched control subjects. We collected clinical data such as AAV-related variables and conventional risk factors for osteoporosis and assessed bone mineral density and the prevalence of osteoporosis and osteopenia in both groups. Categorical and continuous variables were compared between the 2 groups using the χ2 or Fisher exact test and Mann-Whitney U test, respectively. Multivariate logistic regression analysis was used to calculate the odds ratio (OR).

Results
There were no statistically significant differences between the demographical data of AAV patients and control subjects. Patients with AAV showed significantly higher frequencies of conventional risk factors for osteoporosis than the control subjects, except for hyperthyroidism. Osteopenia was found more commonly in AAV patients than in control subjects (57.1% vs. 31.4%, p = 0.030). In the univariate logistic regression analysis, BMI (OR, 0.813) and AAV (OR, 2.620) were associated with osteopenia in all participants. In the multivariate analysis, both BMI and AAV were associated with osteopenia, but this was not statistically significant. In contrast, when analyzing AAV patients only, neither conventional risk factors nor AAV-related variables were associated with the prevalence of osteopenia.

Conclusions
Antineutrophil cytoplasmic antibody–associated vasculitis and BMI were both associated with osteopenia.
Circulating Exosomes From Lipopolysaccharide-Induced Ards Mice Trigger Endoplasmic Reticulum Stress in Lung Tissue
Authors: Tang Xumao , Yu Qian , Wen Xiaoting , Qi Di , Peng Jiao , He Jing , Deng Wang , Zhu Tao , Zhao Yan , Wang Daoxin 
Published: June 2020

ABSTRACT

Background:
Acute respiratory distress syndrome (ARDS) is a critical clinical syndrome with high mortality rate, and few effective therapies have been found in the past 50 years, indicating that the pathogenesis of ARDS remains unclear. Exosomes, a novel cross-communication mechanism, are involved in critical diseases. However, the role of circulating exosomes in the development of ARDS remains poorly understood.

Methods:
In the present study, naive mice were treated with circulating exosomes from lipopolysaccharide (LPS)-induced ARDS mice or exosome-depleted serum. Histological lung damage, bronchoalveolar lavage fluid (BALF), and endoplasmic reticulum (ER) stress were measured.

Results:
Increased tumor necrosis factor (TNF)-α, interleukin (IL)-6, total cell counts, polymorphonuclear (PMN) leukocyte proportions and myeloperoxidase (MPO) activity in BALF, and increased wet/dry weight ratios and protein concentrations in BALF were found in mice after exosome injection but not in mice treated with exosome-depleted serum. Furthermore, western blot analysis showed that circulating exosomes from ARDS mice upregulated glucose-regulated protein 78 (GRP78) and C/EBP homologous protein (CHOP) expression and downregulated β-Catenin and VE-cadherin expression in lung tissues.

Conclusions:
Collectively, these data demonstrate that circulating exosomes from LPS-induced ARDS mice trigger ER stress in lung tissue, facilitating the development of ARDS, at least partly by promoting endothelial dysfunction.
Molecular phylogeny and historical biogeography of andrenine bees (Hymenoptera: Andrenidae)
Authors: Pisanty Gideon , Richter Robin , Martin Teresa , Dettman Jeremy , Cardinal Sophie 
Published: June 2020

AbstractThe mining bee subfamily Andreninae (Hymenoptera: Andrenidae) is a widely distributed and diverse group of ground-nesting solitary bees, including numerous species known as important pollinators. Most of the species diversity of Andreninae is concentrated in the mainly Holarctic genusAndrena, comprising ca. 1500 described species. The subfamily and especially the genus have remained relatively neglected by recent molecular phylogenetic studies, with current classifications relying largely on morphological characters. We sampled ultraconserved element (UCE) sequences from 235 taxa, including all andrenine genera and 98 out of 104 currently recognizedAndrenasubgenera. Using 419,858 aligned nucleotide sites from 1009 UCE loci, we present a comprehensive molecular phylogenetic analysis of the subfamily. Our analysis supports the recognition of seven distinct genera in the Andreninae:Alocandrena, Ancylandrena, Andrena, Cubiandrena, Euherbstia, Megandrena, andOrphana. Within the genusAndrena, present-day subgeneric concepts revealed high degrees of paraphyly and polyphyly, due to heavy morphological character homoplasy, necessitating a thorough, extensive revision of the higher classification of the genus. Our results also show that the MRCA ofAndrena+Cubiandrenadispersed from the New World to the Palaearctic probably during the Eocene– early Oligocene, followed by 10–14 Neogene dispersal events from the Palaearctic to the Nearctic and 1–6 Neogene dispersals back into the Palaearctic, all within the genusAndrena.HighlightsA phylogeny is presented for the bee subfamily Andreninae based on UCE sequencesThe Eastern Mediterranean subgenusCubiandrenais sister to all remainingAndrenaManyAndrenasubgenera exhibit paraphyly or polyphyly, requiring recircumscriptionAt least 11 Old World–New World exchange events have occurred withinAndrena
Pooling size sorted malaise trap fractions to maximise taxon recovery with metabarcoding
Authors: Elbrecht Vasco , Bourlat Sarah J. , Hörren Thomas , Lindner Angie , Mordente Adriana , Noll Niklas W. , Sorg Martin , Zizka Vera M.A. 
Published: June 2020

AbstractSmall and rare specimens can remain undetected when metabarcoding bulk samples with a high size heterogeneity of specimens. This is especially critical for malaise trap samples, where most of the biodiversity is often contributed by small specimens. How to size sort and in which proportions to pool these samples has not been widely explored. We set out to find a size sorting strategy that maximizes taxonomic recovery but remains highly scalable and time efficient.Three 3 malaise trap samples where size sorted into 4 size classes using dry sieving. Each fraction was homogenized and lysed. The corresponding lysates were pooled to simulate samples never sorted, pooled in equal proportions and in 4 different proportions favoring the small size fractions. DNA from the pooled fractions as well as the individual size classes were extracted and metabarcoded using the FwhF2 and Fol-degen-rev primer set. Additionally wet sieving strategies were explored.The small size fractions harbored the highest diversity, and were best represented when pooling in favor of small specimens. Not size sorting a sample leads to a 45-77% decrease in taxon recovery compared to size sorted samples. A size separation into only 2 fractions (below 4 mm and above) can already double taxon recovery compared to not sorting. However, increasing the sequencing depth 3-4 fold can also increase taxon recovery to comparable levels, but remains biased toward biomass rich taxa in the sample.We demonstrate that size fractionizing bulk malaise samples can increase taxon recovery. The most practical approach is wet sieving into two size fractions, and proportional pooling of the lysates in favor of the small size fraction (80-90% volume). However, in large projects with time constraints, increasing sequencing depth can also be an alternative solution.
Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV2
Authors: Mukherjee Moumita , Goswami Srikanta 
Published: June 2020

AbstractBackgroundThe world is going through the critical phase of COVID-19 pandemic, caused by human coronavirus, SARS-CoV2. Worldwide concerted effort to identify viral genomic changes across different sub-types has identified several strong changes in the coding region. However, there have not been many studies focusing on the variations in the 5’ and 3’ untranslated regions and their consequences. Considering the possible importance of these regions in host mediated regulation of viral RNA genome, we wanted to explore the phenomenon.MethodsTo have an idea of the global changes in 5’ and 3’-UTR sequences, we downloaded 8595 complete and high-coverage SARS-CoV2 genome sequence information from human host in FASTA format from Global Initiative on Sharing All Influenza Data (GISAID) from 15 different geographical regions. Next, we aligned them using Clustal Omega software and investigated the UTR variants. We also looked at the putative host RNA binding protein (RBP) and microRNA binding sites in these regions by ‘RBPmap’ and ‘RNA22 v2’ respectively. Expression status of selected RBPs and microRNAs were checked in lungs tissue.ResultsWe identified 28 unique variants in SARS-CoV2 UTR region based on a minimum variant percentage cut-off of 0.5. Along with 241C>T change the important 5’-UTR change identified was 187A>G, while 29734G>C, 29742G>A/T and 29774C>T were the most familiar variants of 3’UTR among most of the continents. Furthermore, we found that despite of the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs.ConclusionOur results, shows for the first time in SARS-Cov2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. The knowledge might be helpful in developing anti-viral compounds in future.
Activity-specificity trade-off gives PI5P4Kβ a nucleotide preference to function as a GTP-sensing kinase
Authors: Takeuchi Koh , Ikeda Yoshiki , Senda Miki , Harada Ayaka , Okuwaki Koji , Fukuzawa Kaori , Nakagawa So , Yu Hongyang , Nagase Lisa , Imai Misaki , Sasaki Mika , Lo YuHua , Sasaki Atsuo T. , Senda Toshiya 
Published: June 2020

SummaryMost kinases function with ATP. However, contrary to the prevailing dogma, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) utilizes GTP as a primary phosphate donor with a unique binding mode for GTP. Although PI5P4Kβ is evolved from a primordial ATP-utilizing enzyme, PI4P5K, how PI5P4Kβ evolutionarily acquired the GTP preference to function as a cellular GTP sensor remains unclear. In this study, we show that the short nucleotide base-recognition motif, TRNVF, is responsible for the GTP binding of PI5P4Kβ, and also confers onto PI5P4Kβ an unexpected specificity that extends to inosine triphosphate (ITP) and xanthosine triphosphate (XTP). A mutational study with GTP analogues suggests that the extended specificity is an obligatory consequence to the acquisition of GTP-dependent activity. However, as the cellular concentrations of ITP and XTP are typically negligible, PI5P4Kβ can still function as a GTP sensor, suggesting that the cellular physiological conditions leave room for the functional evolution of PI5P4Kβ.
SARS-CoV-2 nucleocapsid protein undergoes liquid-liquid phase separation stimulated by RNA and partitions into phases of human ribonucleoproteins
Authors: Perdikari Theodora Myrto , Murthy Anastasia C. , Ryan Veronica H. , Watters Scott , Naik Mandar T. , Fawzi Nicolas L. 
Published: June 2020

AbstractTightly packed complexes of nucleocapsid protein and genomic RNA form the core of viruses and may assemble within viral factories, dynamic compartments formed within the host cells. Here, we examine the possibility that the multivalent RNA-binding nucleocapsid protein (N) from the severe acute respiratory syndrome coronavirus (SARS-CoV-2) compacts RNA via protein-RNA liquid-liquid phase separation (LLPS) and that N interactions with host RNA-binding proteins are mediated by phase separation. To this end, we created a construct expressing recombinant N fused to a N-terminal maltose binding protein tag which helps keep the oligomeric N soluble for purification. Usingin vitrophase separation assays, we find that N is assembly-prone and phase separates avidly. Phase separation is modulated by addition of RNA and changes in pH and is disfavored at high concentrations of salt. Furthermore, N enters intoin vitrophase separated condensates of full-length human hnRNPs (TDP-43, FUS, and hnRNPA2) and their low complexity domains (LCs). However, N partitioning into the LC of FUS, but not TDP-43 or hnRNPA2, requires cleavage of the solubilizing MBP fusion. Hence, LLPS may be an essential mechanism used for SARS-CoV-2 and other RNA viral genome packing and host protein co-opting, functions necessary for viral replication and hence infectivity.
First and broad detection of three typical carbapenemase genes on the surfaces of commercially available spices worldwide and isolation of complete NDM-1 genes from black pepper, cumin, and clove
Authors: Mochizuki Minako , Maeda Sumio 
Published: June 2020

ABSTRACTThe spread of multidrug-resistant bacteria, particularly those producing carbapenemases, has become a major public health concern. The presence of carbapenemase genes has primarily been reported in clinical samples, whereas the presence of these genes in commercially available foods has insufficiently been studied despite its growing importance. The present study aimed to detect and characterize carbapenemase genes (blaNDM,blaIMP,blaKPC, andblaOXA-48-like) on the surfaces of commercially available spices using PCR to amplify conserved regions of these genes. It was revealed that DNAs of these genes are commonly present (13 genes/29 samples) on spices derived from at least 9 different countries. This is the first detection of any carbapenemase gene on eight spices (black pepper, cumin, clove, cardamom, mustard, caraway, parsley, and rosemary) among these. This is also the first detection of theblaIMPandblaNDMas well as the broad detection of theblaOXA-48-likeon spices. We also isolated complete, functionalblaNDM-1genes from three spices (black pepper, cumin, and clove) up to the present.