bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clozapine reduces infiltration into the CNS by targeting migration in experimental autoimmune encephalomyelitis
Authors: Robichon Katharina , Patel Vimal , Connor Bronwen , La Flamme Anne Camille 
Published: February 2020

AbstractBackgroundAtypical antipsychotic agents, such as clozapine, are used to treat schizophrenia and other psychiatric disorders by a mechanism that is believed to involve modulating the immune system. Multiple sclerosis is an immune-mediated neurological disease, and recently, clozapine was shown to reduce disease severity in an animal model of MS, experimental autoimmune encephalomyelitis (EAE). However, the mode of action by which clozapine reduces disease in this model is poorly understood.MethodsBecause the mode of action by which clozapine reduces neuroinflammation is poorly understood, we used the EAE model to elucidate the in vivo and in vitro effects of clozapine.ResultsIn this study, we report that clozapine treatment reduced the infiltration of peripheral immune cells into the central nervous system (CNS) and that this correlated with reduced expression of the chemokines CCL2 and CCL5 transcripts in the brain and spinal cord. We assessed to what extent immune cell populations were affected by clozapine treatment and we found that clozapine targets the expression of chemokines by macrophages and primary microglia. Furthermore, in addition to decreasing CNS infiltration by reducing chemokine expression, we found that clozapine directly inhibits chemokine-induced migration of immune cells. This direct target on the immune cells was not mediated by a change in receptor expression on the immune cell surface but by decreasing downstream signaling via these receptors leading to a reduced migration.ConclusionsTaken together, our study indicates that clozapine protects against EAE by two different mechanisms; first, by reducing the chemoattractant proteins in the CNS; and second, by direct targeting the migration potential of peripheral immune cells.
Emergency general surgeons: the special forces of general surgery (the “navy seals paradigm”)
Authors: Catena Fausto , Biffl Walter , De Simone Belinda , Sartelli Massimo , Di Saverio Salomone , Kluger Yoram , Moore Ernest E. , Ansaloni Luca , Coccolini Federico 
Published: February 2020

AbstractEmergency surgeons have a crucial role in bridging the gap of skills resulting from the well-known general surgery fragmentation. The multi-specialist general surgery approach is still necessary to define proper diagnosis and therapy priorities in an emergency. Governments have to find effective organizational solutions to maintain emergency general surgery standards of care and to improve them further.
Thoracoscopic surgery approach to mediastinal mature teratomas: a single-center experience
Authors: Pham Lu Huu , Trinh Diep Ke , Nguyen Anh Viet , Nguyen Lanh Sy , Le Dung Thanh , Nguyen Dinh-Hoa , Doan Hung Quoc , Nguyen Uoc Huu 
Published: February 2020

Abstract
Background
Mediastinal mature teratomas are rare tumors with diverse surgical approaches. The aim of this study is to review our experience of thoracoscopic surgery management in patients with teratomas.

Methods
We retrospectively reviewed 28 consecutive patients with mediastinal mature teratomas who underwent thoracoscopic surgery at Viet Duc University Hospital from January 2008 to August2018. Patients were divided into 2 groups with 2 types of thoracoscopic surgery, closed thoracoscopic surgery (CTS) group and video-assisted thoracoscopic surgery (VATS) group. The selection of sugical approach was based on sizes, locations and characteristics of tumors. Post-operative outcomes were assessed and compared between these 2 groups.

Results
There were 14 female and 14 male patients with a median age of 41.2 ± 13.8 years. A total of 22 teratomas were located on the right side of the chest cavity and 6 on the left side. We performed CTS in 21 patients (75%) and VATS in 7 patients (25%) for tumor resection. There were 3 cases (10.7%) required conversion to minithoracotomy (5 cm in incision length). Skin appendages accounted for the highest rate (96.4%) in pathology. There was no record of mortality or tumor recurrence detected by computerized tomography.

Conclusion
A thoracoscopic surgery for a mediastinal mature teratoma was a feasible choice. Challenging factors such as large tumors, intraoperative bleeding and strong tumor cell adhesion were considered handling by conversion to mini-thoracotomy that could ensure safety procedures and complete removal of tumors. Extraction of tumor contents might be performed for patients with large mature cystic teratomas to facilitate thoracoscopic surgery.
Genotyping structural variants in pangenome graphs using the vg toolkit
Authors: Hickey Glenn , Heller David , Monlong Jean , Sibbesen Jonas A. , Sirén Jouni , Eizenga Jordan , Dawson Eric T. , Garrison Erik , Novak Adam M. , Paten Benedict 
Published: February 2020

AbstractStructural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against state-of-the-art SV genotypers using three sequence-resolved SV catalogs generated by recent long-read sequencing studies. In addition, we use assemblies from 12 yeast strains to show that graphs constructed directly from aligned de novo assemblies improve genotyping compared to graphs built from intermediate SV catalogs in the VCF format.
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
Authors: Holland Christian H. , Tanevski Jovan , Perales-Patón Javier , Gleixner Jan , Kumar Manu P. , Mereu Elisabetta , Joughin Brian A. , Stegle Oliver , Lauffenburger Douglas A. , Heyn Holger , Szalai Bence , Saez-Rodriguez Julio 
Published: February 2020

AbstractBackgroundMany functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way.ResultsTo address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. We also provide the benchmark data for further use by the community.ConclusionsOur analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used.
Evaluating a couple-based intervention addressing sexual concerns for breast cancer survivors: study protocol for a randomized controlled trial
Authors: Reese Jennifer Barsky , Zimmaro Lauren A. , Lepore Stephen J. , Sorice Kristen A. , Handorf Elizabeth , Daly Mary B. , Schover Leslie R. , Kashy Deborah , Westbrook Kelly , Porter Laura S. 
Published: February 2020

Abstract
Background
Sexual concerns are distressing for breast cancer survivors and interfere with their intimate relationships. This study evaluates the efficacy of a four-session couple-based intervention delivered via telephone, called Intimacy Enhancement (IE). The IE intervention is grounded in social cognitive theory and integrates evidence-based techniques from cognitive behavioral couple therapy and sex therapy to address survivors’ sexual concerns and enhance their and their partners’ sexual, relationship, and psychological outcomes.

Methods
This trial is designed to evaluate the efficacy of the IE intervention in improving survivors’ sexual function, the primary study outcome. Secondary outcomes include survivors’ sexual distress, partners’ sexual function, and survivors’ and partners’ relationship intimacy and quality as well as psychological distress (depressive symptoms and anxiety symptoms). Additional aims are to examine whether treatment effects on patient sexual function are mediated by sexual communication and self-efficacy for coping with sexual concerns and to explore whether survivor age and race/ethnicity moderate intervention effects on survivors’ sexual function. Eligible adult female breast cancer survivors reporting sexual concerns and their intimate partners are recruited from two academic sites in the USA and are randomized to either the IE intervention or to a control condition of equal length offering education and support around breast cancer-related health topics (Living Healthy Together). The target sample size is 120 couples. Self-report outcome measures are administered to participants in both conditions at baseline (T1), post-treatment (T2), 3 months post-treatment (T3), and 6 months post-treatment (T4).

Discussion
Evidence-based interventions are needed to address sexual concerns for breast cancer survivors and to enhance their and their intimate partners’ sexual, relationship, and psychological well-being. This randomized controlled trial will allow us to examine the efficacy of a novel couple-based intervention delivered via telephone for breast cancer survivors experiencing sexual concerns and their intimate partners, in comparison with an attention control. Findings of this study could influence clinical care for women with breast cancer and inform theory guiding cancer-related sexual rehabilitation.

Trial registration
ClinicalTrials.gov, NCT03930797. Registered on 24 April 2019.
Onchocerca jakutensis ocular infection in Poland: a new vector-borne human health risk?
Authors: Wesołowska Maria , Zając-Pytrus Hanna , Masny Aleksander , Pytrus Wiktoria , Knysz Brygida , Golab Elzbieta , Sałamatin Rusłan 
Published: February 2020

Abstract
Background
Zoonotic onchocerciasis is a vector-borne disease, which involves many animal species, including large ungulates, boars, dogs, and sporadically, humans. So far, 39 cases of zoonotic onchocerciasis have been reported worldwide, 30 of which have been found in the last 20 years. Onchocerca nematodes are transmitted to humans by blood-sucking vectors during a blood meal. The following species have been responsible for zoonotic infections: Onchocerca cervicalis, O. dewittei japonica, O. gutturosa, O. jakutensis and O. lupi. In humans, the worms have usually been found in the subcutaneous tissues where they form subcutaneous nodules, induce inflammation of musculature, or penetrate the eye. Thirteen ocular zoonotic onchocerciasis cases have been reported so far. In the eye, nematodes were localized in the subconjunctival space, anterior chamber and within the vitreous body.

Methods
In a 39-year-old male patient, a writhing worm in the vitreous body of the left eye was detected and surgically removed. Laboratory identification of the worm was based on macroscopic and molecular identification, based on sequencing of the cytochrome c oxidase subunit 1 gene (cox1). Phylogenetic analysis of the first 250 nucleotide sequences showing the highest levels of similarity with the present isolate in a BLAST analysis was performed.

Results
Here, we report the first case worldwide of human ocular infection with O. jakutensis, a natural parasite of red deer. By exploiting a PCR assay, we detected the sequence almost identical to O. jakutensis (GenBank: KT001213.1; positions 1–650) with a single mismatch G/A at position 622. The sequence reported in this paper was deposited in the GenBank database under the accession number MK491767.

Conclusions
Our case together with the previous case reports indicate that zoonotic Onchocerca worms exhibit no tissue specificity and an eye infection has been described in over one third of human zoonotic onchocerciasis cases. In terms of the growing number of cases of zoonotic onchocerciasis in Europe, the USA and Japan, attention should be paid to the diagnosis of subcutaneous nodules and eye infestations.
Humoral immune response of pigs, Sus scrofa domesticus, upon repeated exposure to blood-feeding by Ornithodoros turicata Duges (Ixodida: Argasidae)
Authors: Kim Hee J. , Krishnavajhala Aparna , Armstrong Brittany A. , Pérez de León Adalberto A. , Filatov Serhii , Teel Pete D. , Lopez Job E. 
Published: February 2020

AbstractBackgroundOrnithodoros turicatais an important vector of both human and veterinary pathogens. One primary concern is the global spread of African swine fever virus and the risk of its re-emergence in the Americas through potential transmission byO.turicatato domestic pigs and feral swine. Moreover, in Texas, African warthogs were introduced into the state for hunting purposes and evidence exists that they are reproducing and have spread to three counties in the state. Consequently, it is imperative to develop strategies to evaluate exposure of feral pigs and African warthogs toO. turicata.ResultsWe report the development of an animal model to evaluate serological responses of pigs toO. turicatasalivary proteins after three exposures to tick feeding. Serological responses were assessed for ~ 120 days by enzyme-linked immunosorbent assay and immunoblotting using salivary gland extracts fromO. turicata.ConclusionsOur findings indicate that domestic pigs seroconverted toO. turicatasalivary antigens that is foundational toward the development of a diagnostic assay to improve soft tick surveillance efforts.
Innate lymphoid cells in inflammatory arthritis
Authors: Fang Weiting , Zhang Yuanyuan , Chen Zhu 
Published: February 2020

AbstractAberrant activation and dysregulation of immune system is a common feature of many forms of inflammatory arthritis. Since their identification as a distinctive population of leukocytes, innate lymphoid cells (ILCs) have been considered crucial in maintaining tissue homeostasis and bridges between innate and adaptive immune system. Altered ILCs’ subset distribution and function have been observed in a variety of autoimmune and chronic inflammatory diseases and suggest a subset-specific role of ILCs in the pathogenesis of immune-mediated inflammation. In this review, we focus on the current knowledge of ILC subset and their role in inflammatory arthritis, including rheumatoid arthritis (RA), ankylosing spondylitis (AS), psoriatic arthritis (PsA), enteropathic arthritis, and other seronegative spondyloarthritis. By better understanding the biology and function of ILC subset in different disease settings, new therapeutic interventions can be anticipated by modulating dysregulated ILC responses toward promoting resolution of inflammation.
The prevalence of musculoskeletal pain among above 50-year-old population referred to the Kermanshah-Iran health bus in 2016
Authors: Shamsi MohammadBagher , Safari Ameneh , Samadzadeh Soheila , Yoosefpour Nasrin 
Published: February 2020

Abstract
Objective
Musculoskeletal disorders are one of the most important causes of disability. The aim of this study was to evaluate the prevalence of musculoskeletal disorders among the above 50-year-old population who referred to the health bus in Kermanshah. A questionnaire was used to collect data regarding musculoskeletal disorders of 589 people who voluntarily referred to the health bus. Means (SD) and range were used in descriptive statistics.

Results
The most prevalence of musculoskeletal complaints was related to the knee (338, 57.4%). After that, the low back pain had the most frequency (319, 54.3%). The lowest prevalence of musculoskeletal complaints was related to the thighs with a frequency of 95 (16.1%). The highest rate of musculoskeletal complaints over the past week in both genders with a frequency of 251 (59.3%) among women and 68 (41%) among men was related to the low back region The highest rate of musculoskeletal complaints over the past year was also related to the low back region, with a frequency of 220 (41%) among women and 61 (36.7%) among men. Concerning the physical health of the elderly, special attention is required for the knee joint and the low back region.
Visualization of very large high-dimensional data sets as minimum spanning trees
Authors: Probst Daniel , Reymond Jean-Louis 
Published: February 2020

AbstractThe chemical sciences are producing an unprecedented amount of large, high-dimensional data sets containing chemical structures and associated properties. However, there are currently no algorithms to visualize such data while preserving both global and local features with a sufficient level of detail to allow for human inspection and interpretation. Here, we propose a solution to this problem with a new data visualization method, TMAP, capable of representing data sets of up to millions of data points and arbitrary high dimensionality as a two-dimensional tree (http://tmap.gdb.tools). Visualizations based on TMAP are better suited than t-SNE or UMAP for the exploration and interpretation of large data sets due to their tree-like nature, increased local and global neighborhood and structure preservation, and the transparency of the methods the algorithm is based on. We apply TMAP to the most used chemistry data sets including databases of molecules such as ChEMBL, FDB17, the Natural Products Atlas, DSSTox, as well as to the MoleculeNet benchmark collection of data sets. We also show its broad applicability with further examples from biology, particle physics, and literature.
The effectiveness of solar disinfection water treatment method for reducing childhood diarrhea: a systematic review and meta-analysis protocol
Authors: Soboksa Negasa Eshete , Gari Sirak Robele , Hailu Abebe Beyene , Donacho Dereje Oljira , Alemu Bezatu Mengistie 
Published: February 2020

Abstract
Background
Several studies employing the effectiveness of solar disinfection water treatment method for reducing diarrhea have reported heterogeneous outcomes, necessitating a systematic review to provide an exhaustive summary of current evidence. Thus, the objective of this review is to pool out the available evidence on the effectiveness of solar disinfection water treatment method for reducing childhood diarrhea.

Methods
Searches will be conducted in PubMed/Medline, Scopus, Google Scholar, Cochrane Library databases, and reference of other studies published through in December 2019. Studies that compare the diarrhea incidence among the intervention group who were exposed to solar disinfection water treatment and the control group who were not exposed to such water treatment were included. The primary outcome of the study is the change in observed diarrhea incidence risk from baseline to post-intervention. Randomized controlled trial study designs will be included. Selected studies will be critically appraised by two independent reviewers. Extracted data will include details about the interventions, populations, study methods, and outcomes of significance to the review question and objectives. Effect sizes will be expressed as risk ratio, and their 95% confidence intervals will be calculated for analysis.

Discussion
This review and meta-analysis will systematically explore and integrate the evidence available on the effectiveness of solar disinfection water treatment method for reducing diarrhea. In this review, information about the potential impact of solar disinfection water treatment to inactivate pathogenic microbes for reducing diarrhea will be gathered and summarized. The findings from this study will provide directions for future research and public health professionals with an understanding of the importance of solar disinfection water treatment and point to directions for applicability of the interventions in the community.
Certain new dynamic nonlinear inequalities in two independent variables and applications
Authors: El-Deeb A. A. , Khan Zareen A. 
Published: February 2020

AbstractSeveral inequalities were proved in 2018 by Boudeliou, in 2015 by Abdeldain and El-Deeb and in 1998 by Pachpatte. It is our aim in this paper to generalize these inequalities to time scales. Beside that, we also apply our inequalities to discrete and continuous calculus to obtain some new inequalities as special cases. Furthermore, we study the boundedness of some problems by applying our results.
Bespoke career up-skilling: the case of Mellon Skills Accelerator
Authors: Tsimas Konstantin 
Published: February 2020

AbstractIn the absence of a sufficient number of state-run institutional interventions, any action stemming from autonomous, voluntary private sector initiatives providing counseling and up-skilling to unemployed women is de facto important, especially when referring to confirmed successful and recurring efforts. This contribution provides a detailed discussion and analysis of the methodological approach and extraordinary results of the “Mellon Skills Accelerator” initiative, designed and delivered by knowl Social Enterprise to increase employability. It provides a preliminary evaluation of the initiative’s impact and suitability to be adopted as a standard course of action, across the Greek nation and possibly across Europe and beyond. The author has had first-hand experience of Mellon Skills Accelerator working as a volunteer counsel and coach with the organization.