bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter
Authors: De Rituparna , Mukhopadhyay Asish Kumar , Dutta Shanta 
Published: July 2020

Abstract
Background
Metagenomic analysis of the gut microbiome and resistome is instrumental for understanding the dynamics of diarrheal pathogenesis and antimicrobial resistance transmission (AMR). Metagenomic sequencing of 20 diarrheal fecal samples from Kolkata was conducted to understand the core and variable gut microbiota. Five of these samples were used for resistome analysis. The pilot study was conducted to determine a microbiota signature and the source of antimicrobial resistance genes (ARGs) in the diarrheal gut.

Results
16S rRNA amplicon sequencing was performed using Illumina MiSeq platform and analysed using the MGnify pipeline. The Genome Taxonomy Database (GTDB-Tk) was used for bacterial taxonomic identification. Diarrheal etiology was determined by culture method. Phylum Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were consistently present in 20 samples. Firmicutes was the most abundant phylum in 11 samples. The Bacteroidetes/Firmicutes ratio was less than 1 in 18 samples. 584 genera were observed. 18 of these were present in all the 20 samples. Proteobacteria was the dominant phylum in 6 samples associated with Vibrio cholerae infection. Conservation of operational taxonomic units (OTUs) among all the samples indicated the existence of a core microbiome. Asymptomatic carriage of pathogens like Vibrio cholerae and Helicobacter pylori was found. Signature of Candidate phyla or “microbial dark matter” occurred. Significant correlation of relative abundance of bacterial families of commensals and pathogens were found. Whole-genome sequencing (WGS) on Illumina MiSeq system and assembly of raw reads using metaSPAdes v3.9.1 was performed to study the resistome of 5 samples. ABRicate was used to assign ARG function. 491 resistance determinants were identified. In 80% of the samples tetracycline resistance was the most abundant resistance determinant. High abundance of ARGs against β-lactams, aminoglycosides, quinolones and macrolides was found. Eschericia sp. was the major contributor of ARGs.

Conclusions
This is the first comparative study of the gut microbiome associated with different diarrheal pathogens. It presents the first catalogue of different bacterial taxa representing the core and variable microbiome in acute diarrheal patients. The study helped to define a trend in the gut microbiota signature associated with diarrhea and revealed which ARGs are abundantly present and the metagenome-assembled genomes (MAGs) contributing to AMR.
Small lymphocytic lymphoma in true trilineage hematopoietic tissue within heterotopic ossification in an enucleated blind painful eye: a case report
Authors: Borgia Alfredo , Manara Sofia , Balzarotti Monica , Vinciguerra Paolo , Di Maria Alessandra 
Published: July 2020

Abstract
Background
The finding of hematological malignancies within bone marrow in heterotopic ossification has been reported only a handful of times previously in the literature. We described a case of true trilineage hematopoiesis in an excised area of heterotopic ossification from an enucleated blind painful eye.

Case presentation
A 70-year-old Caucasian man, positive for asymptomatic lymphoplasmacytic lymphoma, presented with a blind painful right eye in our ophthalmology department to evaluate enucleation bulbi. After enucleation, a histopathologic examination revealed the presence of intertrabecular infiltration in the metaplastic bone marrow of non-Hodgkin B lymphoma, with small lymphocytes, with similar characteristics to the already known disease.

Conclusion
This uncommon case reveals the possibility of the localization of malignant cells within bone metaplasia of intraocular ossification in an enucleated blind painful eye. From a practical point of view, a careful systematic histopathological examination of all resected tissues in patients with a history of malignant neoplastic pathology is necessary to confirm the diagnosis and exclude occult malignancies.
Phylogenetic analysis of Anguilla marmorata population in Thua Thien Hue, Vietnam based on the cytochrome C oxidase I (COI) gene fragments
Authors: Huyen Kieu Thi , Linh Nguyen Quang 
Published: July 2020

AbstractThe giant mottled eel is a species with high commercial value so overfishing, river management, and water pollution have negatively affected its movement and population numbers.Anguilla marmorata(eel) was listed in the Vietnam Red Data Book 2007 with a description of Vulnerability. This study used a barcode technique to analyze molecular characteristics and build genetic plants based on the cytochrome c oxidase I gene segment isolated from the mitochondrial genome of 48 individuals ofA. marmoratacollected in five different ecological regions of Thua Thien Hue, Vietnam. The isolated the cytochrome c oxidase I sequence has a length of 843 nucleotides, four base nucleotides of 30.03% Thymine, 25.15% Cytosine, 27.49% Adenine, and 17.43% Guanine. The percentage of Guanine + Cytosine content (42.58%) is acceptable, lower than the Adenine + Thymine content. The replacement capacity of Adenine and Guanine is 22.45% highest, the ratio between Thymine and Guanine; Cytosine and Guanine are the lowest at 2.72%. The establishment of genetically modified plants has shown the high genetic similarity of individuals in eel populations in Thua Thien Hue. The population ofAnguilla marmorataeels in Thua Thien Hue, Vietnam is divided into two separate groups that are guided by the migration process and specific ecological. This is particularly important in building strategies to conserve and develop the gene for eel in Vietnam and Thua Thien Hue.
Metformin sensitizes therapeutic agents and improves outcome in pre-clinical and clinical diffuse large B-cell lymphoma
Authors: Singh Anil R. , Gu Juan J. , Zhang Qunling , Torka Pallawi , Sundaram Suchitra , Mavis Cory , Hernandez-Ilizaliturri Francisco J. 
Published: July 2020

AbstractBackgroundThe treatment of diffuse large B-cell lymphoma (DLBCL) is limited by the development of resistance to therapy, and there is a need to develop novel therapeutic strategies for relapsed and refractory aggressive lymphoma. Metformin is an oral agent for type 2 diabetes that has been shown to decrease cancer risk and lower mortality in other types of cancer.MethodsWe performed a retrospective analysis of the RPCCC database looking at patients with DLBCL treated with front-line chemotherapy. We also performed pre-clinical studies looking at the effect of metformin on cell viability, cell number, Ki67, ATP production, apoptosis, ROS production, mitochondrial membrane potential, cell cycle, effect with chemotherapeutic agents, and rituximab. Finally, we studied mouse models to see the anti-tumor effect of metformin.ResultsAmong diabetic patients, metformin use was associated with improved progression-free survival (PFS) and overall survival (OS) compared to diabetic patients not on metformin. Our pre-clinical studies showed metformin is itself capable of anti-tumor effects and causes cell cycle arrest in the G1 phase. Metformin induces apoptosis, ROS production, and increased mitochondrial membrane permeability. Metformin exhibited additive/synergistic effects when combined with traditional chemotherapy or rituximab in vitro. In vivo, metformin in combination with rituximab showed improved survival compared with rituximab monotherapy.ConclusionsOur retrospective analysis showed that metformin with front-line chemotherapy in diabetic patients resulted in improved PFS and OS. Our pre-clinical studies demonstrate metformin has potential to re-sensitize resistant lymphoma to the chemo-immunotherapy and allow us to develop a hypothesis as to its activity in DLBCL.
Disruption of hypoxia-inducible fatty acid binding protein 7 induces beige fat-like differentiation and thermogenesis in breast cancer cells
Authors: Kawashima Masahiro , Bensaad Karim , Zois Christos E. , Barberis Alessandro , Bridges Esther , Wigfield Simon , Lagerholm Christoffer , Dmitriev Ruslan I. , Tokiwa Mariko , Toi Masakazu , Papkovsky Dmitri B. , Buffa Francesca M. , Harris Adrian L. 
Published: July 2020

Abstract
Background
Humans produce heat through non-shivering thermogenesis, a metabolic process that occurs in inducible beige adipocytes expressing uncoupling protein 1 (UCP1). UCP1 dissipates the proton gradient of the mitochondrial inner membrane and converts that energy into heat. It is unclear whether cancer cells can exhibit autonomous thermogenesis. Previously, we found that the knockdown of hypoxia-inducible fatty acid binding protein 7 (FABP7) increased reactive oxygen species (ROS) in breast cancer cells. ROS are known to induce beige adipocyte differentiation.

Methods
We investigated the association of tumor hypoxia, FABP7, and UCP1 across breast cancer patients using METABRIC and TCGA data sets. Furthermore, using a breast cancer cell line, HCC1806, we tested the effect of FABP7 knockdown on cellular physiology including thermogenesis.

Results
We found a strong mutual exclusivity of FABP7 and UCP1 expression both in METABRIC and in TCGA, indicating major metabolic phenotypic differences. FABP7 was preferentially distributed in poorly differentiated-, estrogen receptor (ER) negative tumors. In contrast, UCP1 was highly expressed in normal ducts and well-differentiated-, ER positive-, less hypoxic tumors. In the cell line-based experiments, UCP1 and its transcriptional regulators were upregulated upon FABP7 knockdown. UCP1 was induced in about 20% of cancer cells, and the effect was increased further in hypoxia. UCP1 depolarized mitochondrial membranes at the site of expression. UCP1 induction was associated with the increase in proton leak, glycolysis, and maximal respiration, mimicking the typical energy profile of beige adipocytes. Most importantly, UCP1 induction elevated cancer cell temperature associated with increased vulnerability to hypoxia and γ-irradiation.

Conclusions
We demonstrated that breast cancer cells can undergo thermogenesis through UCP1 induction. Disrupting FABP7-mediated fatty acid metabolism can unlock UCP1-mediated thermogenesis, potentially making it possible to develop therapies to target thermogenesis. Further study would be warranted to investigate the effect of rise in temperature of cancer cells on patients’ outcomes and the relationship to other metabolic pathways.
The deterioration process of limestone in the Anahita Temple of Kangavar (West Iran)
Authors: Barnoos Vahid , Oudbashi Omid , Shekofteh Atefeh 
Published: July 2020

Abstract
The well-known archaeological site of Anahita Temple at Kangavar is one of the most important Iranian stone monuments. It has been dated by various authors in an interval extended from Achaemenid to Sasanian Persian Empires (sixth century BCE to seventh century AD). Significant weathering has been occurred in various stone blocks used in the construction of this monument. The aim of this research is to study the deterioration process of the stone blocks used in the Temple. It includes chemical and mineralogical analysis of stones, characterization of deterioration patterns and processes, and identification of factors influenced the process. Results have been obtained by on-site and laboratory studies, including optical microscopy, petrography, X-ray fluorescence, X-ray diffraction and scanning electron microscopy coupled with energy dispersive X-ray spectroscopy methods. They showed that low-porosity limestone and dolomitic limestone have been used in the construction of the Temple, which have a compact micritic structure with variable size calcite veins (sparite) and clay veins. According to the on-site and laboratory studies, the deterioration patterns are partially similar in majority of the stone blocks and include different types of detachments as well as biological colonisations. The multianalytical results proved that the deterioration process is mainly of physical weathering type, due to structural and chemical characteristics of the limestone as well as climate factors, temperature fluctuations in particular. It turned out that limestone characteristics (including presence of clay veins as well as heterogeneity of calcitic matrix (micrite and sparite)) can affect the behaviour of stone blocks against climate factors; helping us to find reasons behind physical weathering of limestone in the cultural/historical sites and monuments.
Fast and simple selenium speciation by solid phase extraction and laser-induced breakdown spectroscopy
Authors: Lee Seon Hwa , Kwon Seul-Woo , Lee Yonghoon , Nam Sang-Ho 
Published: July 2020

AbstractThe chemical properties including toxicity of selenium depend on the concentration and chemical structure present in the natural environment. Inorganic selenium is more toxic than organic selenium; thus, the accurate determination of inorganic selenium in various sample has been needed. HG-AAS, HPLC-ICP-MS, and GC-MS are the current methods for the determination of inorganic selenium. However, these methods have the disadvantage of expensive equipment, complicated sample preparation, and long analysis time. LIBS coupled with ion exchange membrane was used for the determination of inorganic selenium. The detection limit of inorganic selenium by the analytical method was 11.21 mg/kg, and the recoveries of 50 and 100 mg/kg Se(VI) were 98.5 % and 101.80 %, respectively. The speciation method is cost-effective, simple, and not labor intensive for the quantitation of inorganic selenium.
Speaking up: a model of self-advocacy for STEM undergraduates with ADHD and/or specific learning disabilities
Authors: Pfeifer Mariel A. , Reiter Eve Melanie , Hendrickson McKenna , Stanton Julie Dangremond 
Published: July 2020

Abstract
Background
Students with disabilities are underrepresented in undergraduate science, technology, engineering, and mathematics (STEM) courses. Students with disabilities who engage in self-advocacy earn higher GPAs and are more likely to graduate from college compared to students with disabilities who do not engage in self-advocacy. We utilized Test’s conceptual framework of self-advocacy, which breaks self-advocacy into four components: knowledge of self, knowledge of rights, communication, and leadership to investigate how students with invisible disabilities practice self-advocacy in undergraduate STEM courses. Through a partnership with a disability resource center (DRC), we recruited and interviewed 25 STEM majors who received accommodations for attention-deficit/hyperactivity disorder (ADHD) and/or a specific learning disorder (SLD). Data were collected using semi-structured interviews and analyzed using content analysis.

Results
We found evidence of all components of Test’s conceptual framework of self-advocacy and operationalize each based on our participants’ experiences. We identified novel components of self-advocacy for students with ADHD/SLD in undergraduate STEM courses, including knowledge of STEM learning contexts and knowledge of accommodations and the process to obtain them, as well as, a novel self-advocacy behavior, filling gaps. Filling gaps involved participants taking action to mitigate a perceived limitation in either their formal accommodations from the DRC or a perceived limitation in the instructional practices used in a STEM course. We also identified beliefs, such as view of disability and agency, which influenced the self-advocacy of our participants. We incorporated the emergent forms of self-advocacy into Test’s conceptual framework to propose a revised model of self-advocacy for students with ADHD/SLD in undergraduate STEM courses.

Conclusions
We developed a revised conceptual model of self-advocacy for students with ADHD/SLD in undergraduate STEM courses. This conceptual model provides a foundation for researchers who wish to study self-advocacy in undergraduate STEM courses for students with ADHD/SLD in the future. It also offers insights for STEM instructors and service providers about the self-advocacy experiences of students with ADHD/SLD in undergraduate STEM courses. We propose hypotheses for additional study based on our conceptual model of self-advocacy. Implications for research and teaching are discussed.
Approaching community priorities in youth sports injury prevention research
Authors: Kerr Zachary Y. , Gildner Paula , Nedimyer Aliza K. , Chandran Avinash , Kay Melissa C. , Byrd K. Hunter , Register-Mihalik Johna K. 
Published: July 2020

AbstractBackgroundResearch in youth sports is often complex. As interest in youth sports injury prevention grows, scientists should consider community priorities beyond a specific research study.Main textThis commentary discusses the authors’ personal experiences researching concussion prevention in middle school sports, as the overarching community faced multiple challenges. These challenges included a series of weather-related emergencies that resulted in a shift in the community’s priorities, multi-day school closures, and cancellations of sports activities and meetings. We discuss the importance of considering community priorities and providing support as scientists, colleagues, and members of the communities in which we conduct research.ConclusionScientists should consider the changing circumstances and dynamics surrounding community priorities in order to help drive their research-based decisions and ensure successful and respectful applications of research based on community values and priorities.
Between fragmentation and institutionalisation: the rise of migration studies as a research field
Authors: Levy Nathan , Pisarevskaya Asya , Scholten Peter 
Published: July 2020

AbstractIt is clear that the field of migration studies has grown significantly over the past decades. What is less known is how this growth has taken place. This article combines bibliometric metadata with expert interviews to analyse the institutionalisation of the field in terms of self-referentiality, internationalisation, and epistemic communities. Self-referentiality in migration studies has gradually increased as the field has grown, until recently. The field has internationalised in terms of international co-authorships but has done so unevenly. Finally, we find that epistemic communities in migration studies, based largely on disciplines, increasingly refer to one another and are increasingly interdisciplinary.
Best practice for the nuclear medicine technologist in CT-based attenuation correction and calcium score for nuclear cardiology
Authors: Camoni Luca , Santos Andrea , Attard Marieclaire , Mada Marius Ovidiu , Pietrzak Agata Karolina , Rac Sonja , Rep Sebastijan , Terwinghe Christelle , Fragoso Costa Pedro ,   on behalf of the Technologist Committee of the European Association of Nuclear Medicine (EANM)
Published: July 2020

AbstractThe use of hybrid systems is increasingly growing in Europe and this is progressively important for the final result of diagnostic tests. As an integral part of the hybrid imaging system, computed tomography (CT) plays a crucial role in myocardial perfusion imaging diagnostics. Throughout Europe, a variety of equipment is available and also different university curricula of the nuclear medicine technologist are observed. Hence, the Technologist Committee of the European Association of Nuclear Medicine proposes to identify, through a bibliographic review, the recommendations for best practice in computed tomography applied to attenuation correction and calcium score in myocardial perfusion imaging, which courses in the set of knowledge, skills, and competencies for nuclear medicine technologists. This document aims at providing recommendations for CT acquisition protocols and CT image optimization in nuclear cardiology.
Study protocol of a pilot study on sirolimus-coated balloon angioplasty in salvaging clotted arteriovenous graft
Authors: Tan Ru Yu , Tan Chee Wooi , Pang Suh Chien , Foo Marjorie Wai Yin , Tang Tjun Yip , Gogna Apoorva , Chong Tze Tec , Tan Chieh Suai 
Published: July 2020

Abstract
Background
In arteriovenous graft (AVG) for haemodialysis, the primary cause of failure is venous stenosis of the graft-vein junction from neointimal hyperplasia (NIH), resulting in thrombosis. While interventions to salvage clotted AVG are known to have high clinical success rates, long-term patency rates have been suboptimal. Drug-coated balloon (DCB) has been used to treat stenosed arteriovenous access in recent years with encouraging results but data on its effect in clotted AVG is unavailable.

Methods
This is an investigator-initiated, single-center, single-arm prospective pilot study to determine the safety and outcome of the sirolimus-coated balloon (SCB) in the salvage of thrombosed AVG. Twenty patients who undergo successful percutaneous thrombectomy will receive treatment with SCB at the graft vein junction. The patients will be followed-up for 6-months. The primary endpoint is the patency rates at 3-month while the secondary endpoints are the patency rates and the number of interventions needed to maintain patency at 6-month.

Discussion
Unremitting efforts have been made to prolong the patency of AV accesses over the years. DCB angioplasty combines mechanical and biological treatment for vascular stenosis. Sirolimus, being a cystostatic anti-proliferative agent, has been successfully used in coronary artery interventions. As the primary pathology of vascular stenosis in the dialysis circuit is neointimal hyperplasia, the use of sirolimus in balloon angioplasty may be effective. With this prospective study, we evaluate the efficacy and safety of SCB in patients with clotted AVG.

Trial registration
ClinicalTrials.gov Identifier: NCT03666208 on 11 September 2018.
Anthropometric and metabolic pattern in obese Egyptian children: its association with C-reactive protein
Authors: Mohamed Nageh S. , Maher Sheren Esam , Abozaid Samah M. M. , Moenes Hend M. 
Published: July 2020

AbstractBackgroundObesity is the most common chronic metabolic disease in children. The global prevalence of obesity has doubled from 1990 to 2015. Worryingly, the increase is more in children than adults. It has reached epidemic ranges and is a significant global problem. High-sensitivity C-reactive protein (hs-CRP) is a parameter that is used to assess inflammation and risk factor for cardiovascular events. Some reports describe an association between hs-CRP and obesity. The objective of the study is to evaluate anthropometric and metabolic parameters in obese Egyptian children and correlate them with hs-CRP level.ResultsFor anthropometric variables, they were significantly higher in obese group than normal weight except for height (Pvalue 0.001). A significant difference was reported for all lipid profile parameters between obese and normal-weight groups (Pvalue 0.001). Also, CRP showed a positive correlation with both BMI as well as total cholesterol, while no correlation was observed with other parameters of obesity (r: 0.41, 0.29 respectively).ConclusionElevated CRP may have a role in predicting altered lipid metabolism in obese children and this raises the possibility of cardiovascular diseases. Hence, preventive measures to control obesity is necessary.