bluuebunny/crossref_metadata_2025 huggingface dataset:
Legal medicine implications in fibrinolytic therapy of acute ischemic stroke
Authors: Sabau Monica , Bungau Simona , Buhas Camelia Liana , Carp Gheorghe , Daina Lucia-Georgeta , Judea-Pusta Claudia Teodora , Buhas Bogdan Adrian , Jurca Claudia Maria , Daina Cristian Marius , Tit Delia Mirela
Published: October 2019

Background

Before the advent of fibrinolytic therapy as a gold standard method of care for cases of acute ischemic stroke in Romania, issues regarding legal medicine aspects involved in this area of medical expertise were already presented and, in the majority of cases, the doctors seem to be unprepared for these situations.

Main text

The present research illustrates some of the cases in which these aspects were involved, that adressed a clinical center having 6 years of professional experience in the application of fibrinolytic treatment for stroke. The following cases report either situations in which the afore mentioned therapy was not rightfully administrated or legal aspects regarding the obtainment of informed consent.

Conclusion

Obtaining informed consent is a mandatory procedure, which takes time, to the detriment of application of fibrinolytic treatment.
(−)-Epigallocatechin-3-gallate derivatives combined with cisplatin exhibit synergistic inhibitory effects on non-small-cell lung cancer cells
Authors: Wang Jing , Sun Peiyuan , Wang Qi , Zhang Pan , Wang Yuna , Zi Chengting , Wang Xuanjun , Sheng Jun
Published: October 2019

Background

Non-small-cell lung cancer (NSCLC) is the leading cause of cancer-related death worldwide. The inhibition of epidermal growth factor receptor (EGFR) signaling by tyrosine kinase inhibitors or monoclonal antibodies plays a key role in NSCLC treatment. Unfortunately, these treatment strategies are limited by eventual resistance and cell lines with differential EGFR status. Therefore, new therapeutic strategies for NSCLC are urgently required.

Methods

To improve the stability and absorption of (−)-epigallocatechin-3-gallate (EGCG), we synthesized a series of EGCG derivatives. The antitumor activities of EGCG derivatives with or without cisplatin were investigated in vitro and vivo. Cell proliferation, cell cycle distribution and apoptosis were measured in NSCLC cell lines and in vivo in a NCI-H441 xenograft model.

Results

We found that the EGCG derivatives inhibited cell viability and colony formation, caused cell cycle redistribution, and induced apoptosis. More importantly, the combination of the EGCG derivative and cisplatin led to increased growth inhibition, caused cell cycle redistribution, and enhanced the apoptosis rate compared to either compound alone. Consistent with the experiments in vitro, EGCG derivatives plus cisplatin significantly reduced tumor growth.

Conclusions

The combination treatment was found to inhibit the EGFR signaling pathway and decrease the expression of p-EGFR, p-AKT, and p-ERK in vitro and vivo. Our results suggest that compound 3 is a novel potential compound for NSCLC patients.
Conventional versus hypofractionated postmastectomy radiotherapy: a report on long-term outcomes and late toxicity
Authors: Chitapanarux Imjai , Klunklin Pitchayaponne , Pinitpatcharalert Attapol , Sripan Patumrat , Tharavichitkul Ekkasit , Nobnop Wannapha , Onchan Wimrak , Chakrabandhu Somvilai , Jia-Mahasap Bongkot , Euathrongchit Juntima , Wannasopha Yutthaphan , Srisuwan Tanop
Published: October 2019

Objective

We evaluated the long-term outcomes and late toxicity of conventional fractionated (CF) and hypofractionated (HF) postmastectomy radiotherapy (PMRT) in terms of locoregional recurrence-free survival (LRRFS), disease-free survival (DFS), overall survival (OS), and late toxicity.

Methods

A cohort of 1640 of breast cancer patients receiving PMRT between January 2004 and December 2014 were enrolled. Nine hundred eighty patients were treated with HF-PMRT: 2.65 Gy/fraction to a total of 42.4–53 Gy and 660 patients were treated with CF-PMRT: 2 Gy/fraction to a total of 50–60 Gy.

Results

The median follow-up time was 71.8 months (range 41.5–115.9 months). No significant difference was found in the rates of 5-year LRRFS, DFS, and OS of HF-PMRT vs CF-PMRT; 96% vs. 94% (p = 0.373), 70% vs. 72% (p = 0.849), and 73% vs. 74% (p = 0.463), respectively. We identified a cohort of 937 eligible breast cancer patients who could receive late toxicities assessment. With a median follow-up time of this patient cohort of 106.3 months (range 76–134 months), there was a significant higher incidence of grade 2 or more late skin (4% vs 1%) and subcutaneous (7% vs 2%) toxicity in patients treated with HF-PMRT vs CF-PMRT. Patients who received additional radiation boost were significantly higher in the HF-PMRT group. Grade 2 or more late RTOG/EORTC lung toxicity was significant lesser in HF-PMRT vs CF-PMRT (9% vs 16%). Grade 1 brachial plexopathy was also significant lesser in HF-PMRT vs CF-PMRT (2% vs 8%). Heart toxicity and lymphedema were similar in both groups.

Conclusions

HF-PMRT is feasible to deliver with comparable long-term efficacy to CF-PMRT. HF-PMRT had higher grade 2 or more skin and subcutaneous toxicity but less lung and brachial plexus toxicity.
Soluble egg antigen of Schistosoma japonicum induces pyroptosis in hepatic stellate cells by modulating ROS production
Authors: Kong De-Long , Kong Fan-Yun , Liu Xiang-Ye , Yan Chao , Cui Jie , Tang Ren-Xian , Zheng Kui-Yang
Published: October 2019

Background

Inflammation-induced dysfunction of hepatic stellate cells (HSCs) is involved in schistosomiasis-associated liver fibrosis, and soluble egg antigen (SEA) is a crucial pathogen-associated molecular pattern associated with liver injury in schistosomiasis. In addition, numerous studies have shown that caspase-1-mediated pyroptosis participates in the development of multiple inflammation-related diseases. However, whether pyroptotic cell death of HSCs is involved in SEA-mediated liver damage is not well understood.

Methods

Primary cultured HSCs and Schistosoma japonicum-infected mouse liver tissue were analysed for histological changes and caspase-1 activation, and the role of pyroptosis in the mechanisms underlying SEA-induced HSC death was investigated. Accumulation of reactive oxygen species (ROS) in infected livers and SEA-stimulated HSCs was measured by flow cytometry and immunofluorescence.

Results

Caspase-1 activity was elevated in both liver tissues and HSCs of S. japonicum-infected mice. Furthermore, SEA stimulation increased the proportion of pyroptotic HSCs, as shown by lactate dehydrogenase (LDH) release assays and by flow cytometric analysis of propidium iodide (PI) and caspase-1 double staining in cells. In addition, ROS generation was elevated in infected liver tissues and SEA-stimulated HSCs, and ROS inhibition downregulated SEA-induced caspase-1 activation and pyroptosis in HSCs.

Conclusions

Our present study demonstrates that pyroptotic cell death in HSCs induced by SEA via ROS-mediated caspase-1 activation may serve as a significant mechanism to initiate the inflammatory response and thereby exacerbate liver injury during S. japonicum infection.
Correction to: Aedes vittatus in Spain: current distribution, barcoding characterization and potential role as vectors of human diseases
Authors: Díez-Fernández Alazne , Martínez-de la Puente Josué , Ruiz Santiago , Gutiérrez-López Rafael , Soriguer Ramón , Figuerola Jordi
Published: October 2019

Unfortunately, the original version of this article [1] contained an error. In the distribution map in Fig. 3, the presence of the mosquito Aedes vittatus was incorrectly indicated for Libya and Egypt.
Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People’s Democratic Republic
Authors: Motoki Maysa Tiemi , Fonseca Dina Madera , Miot Elliott Frederic , Demari-Silva Bruna , Thammavong Phoutmany , Chonephetsarath Somsanith , Phommavanh Nothasine , Hertz Jeffrey Conrad , Kittayapong Pattamaporn , Brey Paul Trevor , Marcombe Sebastien
Published: October 2019

Background

The Asian tiger mosquito,Aedes(Stegomyia)albopictus(Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure ofAe. albopictusin Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability ofAe. albopictusacross a north-south transect in Lao PDR.

Methods

We used variability in a 1337-bp fragment of the mitochondrial cytochromecoxidase subunit 1 gene (cox1), to assess the population structure ofAe. albopictusin Lao PDR. For context, we also examined variability at the same genetic locus in samples ofAe. albopictusfrom Thailand, China, Taiwan, Japan, Singapore, Italy and the USA.

Results

We observed very high levels of genetic polymorphism with 46 novel haplotypes inAe. albopictusfrom 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in LaotianAe. albopictusand mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions.

Conclusions

Aedes albopictusin Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.
Effect of chemical amendments on reduction of bioavailable heavy metals and ecotoxicity in soil
Authors: Yoon Dong-Hyun , Choi Won Seok , Hong Young Kyu , Lee Young Bok , Kim Sung Chul
Published: October 2019

Heavy metal pollution in soil has been concerned because of toxicity in ecosystem and adverse effect on human health. Main objective of this study was to examine reduction of bioavailable heavy metals and consequently, decrease of ecotoxicity to biota when chemical amendments were applied in soil. Three chemical amendments, acid mine drainage sludge (AMDS), lime stone (LS), and steel slag (SS) were applied with varied application ratio (1, 3, 5%) in heavy metal polluted soil and bioavailable fraction of heavy metal was monitored. In addition, ecotoxicity test using earthworm (Eisenia fetida) was conducted for 28 days examining mortality, weight increase, and bioaccumulation of heavy metal in the earthworm. Result showed that AMDS was the most efficient amendment for reducing bioavailable heavy metals in soil while SS showed the least efficiency. Reduction ratio of bioavailable-As, Cd, and Pb was ranged 39.0–92.0% depending on application ratio and heavy metal species for AMDS application. However, only bioavailable-Pb was reduced at the range between 39.1% and 56.5% when SS was applied in soil. In contrast, the lowest concentration of As, Cd, and Pb and ecotoxicity effect in the earthworm was observed in SS treatment indicating that exposure route of heavy metals or particle size of amendments might effect on uptake of heavy metals to the earthworm. Overall, ecotoxicity test in combination with chemical concentration monitoring is a useful tool for evaluating remediation efficiency of heavy metal polluted soil.
Effect of the Incretin Hormones on the Endocrine Pancreas in End-Stage Renal Disease
Authors: Jørgensen Morten B , Idorn Thomas , Rydahl Casper , Hansen Henrik P , Bressendorff Iain , Brandi Lisbet , Wewer Albrechtsen Nicolai J , van Hall Gerrit , Hartmann Bolette , Holst Jens J , Knop Filip K , Hornum Mads , Feldt-Rasmussen Bo
Published: October 2019

Context

The insulin-stimulating and glucagon-regulating effects of the 2 incretin hormones, glucagon-like peptide 1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP), contribute to maintain normal glucose homeostasis. Impaired glucose tolerance occurs with high prevalence among patients with end-stage renal disease (ESRD).

Objective

To evaluate the effect of the incretin hormones on endocrine pancreatic function in patients with ESRD.

Design and Setting

Twelve ESRD patients on chronic hemodialysis and 12 matched healthy controls, all with normal oral glucose tolerance test, were included. On 3 separate days, a 2-hour euglycemic clamp followed by a 2-hour hyperglycemic clamp (3 mM above fasting level) was performed with concomitant infusion of GLP-1 (1 pmol/kg/min), GIP (2 pmol/kg/min), or saline administered in a randomized, double-blinded fashion. A 30% lower infusion rate was used in the ESRD group to obtain comparable incretin hormone plasma levels.

Results

During clamps, comparable plasma glucose and intact incretin hormone concentrations were achieved. The effect of GLP-1 to increase insulin concentrations relative to placebo levels tended to be lower during euglycemia in ESRD and was significantly reduced during hyperglycemia (50 [8–72]%, P = 0.03). Similarly, the effect of GIP relative to placebo levels tended to be lower during euglycemia in ESRD and was significantly reduced during hyperglycemia (34 [13–50]%, P = 0.005). Glucagon was suppressed in both groups, with controls reaching lower concentrations than ESRD patients.

Conclusions

The effect of incretin hormones to increase insulin release is reduced in ESRD, which, together with elevated glucagon levels, could contribute to the high prevalence of impaired glucose tolerance among ESRD patients.
An Anesthesia Attempt to Be Green: How Do You Waste Your Carbon Dioxide Absorbers?
Authors: Burbridge Mark A. , Chua Pandora , Jaffe Richard A. , Pearl Ronald G. , Brock-Utne John G.
Published: October 2019

Operating room waste is categorized as noncontaminated solid waste (SW) and regulated medical waste (RMW). RMW is treated by autoclaving at an increased economic and environmental cost. We evaluated these costs with a focus on the disposable carbon dioxide (CO2) absorbers. At our institution, exhausted CO2 absorbers were discarded as RMW. We collaborated with product representatives, anesthesia and perioperative staff, and waste management personnel to identify opportunities and barriers for recycling and waste reduction. Ultimately, we agreed to discard CO2 absorbers as SW instead of RMW, a strategy that is practical, less expensive, and more environmentally appropriate.
From New Institutional Economics of the Commons to the Common as a Mode of Production
Authors: Giuliani Alfonso , Vercellone Carlo
Published: October 2019

The vitality of the new field of study on the commons crosses the entire field of social sciences, and it is analyzed from very different perspectives. On the one side, the Ostromian new Institutional economics uses the term commons as plural and seeks to give an account of the variety of the institutional forms of economic regulation. On the other, some new approaches interpret commons as an element of subversion of capitalism. These authors insist on the use of the concept as singular and they interpret it as a general principle of reorganization of economy and society. This article aims at analyzing the meanings of common and commons at stake in this debate. After a critical assessment of Elinor Ostrom’s contribution, the analysis will focus on the presentation of the theories of common as singular, distinguishing two currents of thought: the political conception of Dardot and Laval and the neo-workerist thesis of common as mode of production.
Making the Multiple:
Authors: Spanò Michele
Published: October 2019

The essay argues for the compatibility between private law and the commons. In order to do so, it proposes an archeology of modern private law, which traces both the emergence of what will be called “modern topology” and the historical transformation of civil law into what we still know as private law. Private law is considered to be a product of modern legal theory which is radically tied with public law. The two are meant to have the very same logical form—individuality—which was the premise for the social relation of capital to be established. The pivot of this legal maneuver—which ended up with the exclusion of the commons from the realm of both private and public law—was the theory of subjective rights. To dismantle this construction, the essay proposes a critique of subjective rights as well as a trans-subjective approach to private law.
Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data
Authors: Diaz-Mejia J. Javier , Meng Elaine C. , Pico Alexander R. , MacParland Sonya A. , Ketela Troy , Pugh Trevor J. , Bader Gary D. , Morris John H.
Published: October 2019

Background: Identification of cell type subpopulations from complex cell mixtures using single-cell RNA-sequencing (scRNA-seq) data includes automated steps from normalization to cell clustering. However, assigning cell type labels to cell clusters is often conducted manually, resulting in limited documentation, low reproducibility and uncontrolled vocabularies. This is partially due to the scarcity of reference cell type signatures and because some methods support limited cell type signatures.

Methods: In this study, we benchmarked five methods representing first-generation enrichment analysis (ORA), second-generation approaches (GSEA and GSVA), machine learning tools (CIBERSORT) and network-based neighbor voting (METANEIGHBOR), for the task of assigning cell type labels to cell clusters from scRNA-seq data. We used five scRNA-seq datasets: human liver, 11 Tabula Muris mouse tissues, two human peripheral blood mononuclear cell datasets, and mouse retinal neurons, for which reference cell type signatures were available. The datasets span Drop-seq, 10X Chromium and Seq-Well technologies and range in size from ~3,700 to ~68,000 cells.

Results: Our results show that, in general, all five methods perform well in the task as evaluated by receiver operating characteristic curve analysis (average area under the curve (AUC) = 0.91, sd = 0.06), whereas precision-recall analyses show a wide variation depending on the method and dataset (average AUC = 0.53, sd = 0.24). We observed an influence of the number of genes in cell type signatures on performance, with smaller signatures leading more frequently to incorrect results.

Conclusions: GSVA was the overall top performer and was more robust in cell type signature subsampling simulations, although different methods performed well using different datasets. METANEIGHBOR and GSVA were the fastest methods. CIBERSORT and METANEIGHBOR were more influenced than the other methods by analyses including only expected cell types. We provide an extensible framework that can be used to evaluate other methods and datasets at https://github.com/jdime/scRNAseq_cell_cluster_labeling.
Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures
Authors: Bhuva Dharmesh D. , Foroutan Momeneh , Xie Yi , Lyu Ruqian , Cursons Joseph , Davis Melissa J.
Published: October 2019

Advances in RNA sequencing (RNA-seq) technologies that measure the transcriptome of biological samples have revolutionised our ability to understand transcriptional regulatory programs that underpin diseases such as cancer. We recently published singscore - a single sample, rank-based gene set scoring method which quantifies how concordant the transcriptional profile of individual samples are relative to specific gene sets of interest. Here we demonstrate the application of singscore to investigate transcriptional profiles associated with specific mutations or genetic lesions in acute myeloid leukemia. Using matched genomic and transcriptomic data available through the TCGA we show that scoring of appropriate signatures can distinguish samples with corresponding mutations, reflecting the ability of these mutations to drive aberrant transcriptional programs involved in leukemogenesis. We believe the singscore method is particularly useful for studying heterogeneity within a specific subsets of cancers, and as demonstrated, we show the ability of singscore to identify where alternative mutations appear to drive similar transcriptional programs.
Pragmatic Home-Based Exercise after Total Hip Arthroplasty - Silkeborg: Protocol for a prospective cohort study (PHETHAS-1)
Authors: Mikkelsen Lone Ramer , Madsen Merete Nørgaard , Rathleff Michael Skovdal , Thorborg Kristian , Rossen Camilla Blach , Kallemose Thomas , Bandholm Thomas
Published: October 2019

Introduction: Rehabilitation exercises are offered to patients after total hip arthroplasty (THA); however, the effectiveness and optimal type and dose of exercise remains unknown. The primary objective of this trial is to indicate the preliminary efficacy of home-based rehabilitation using elastic band exercise on performance-based function after THA, based on the relationship between the performed exercise dose and the change in performance-based function (gait speed) from 3 (start of intervention) to 10 weeks (end of intervention) after surgery. The secondary objective is to investigate if a dose-response relationship exists between the performed exercise dose and changes in: hip-related disability, lower-extremity functional performance, and hip muscle strength

Methods: In this prospective cohort study, patients scheduled for THA will be consecutively included until 88 have completed the intervention period from 3 to 10 weeks postoperatively. Participants perform the standard rehabilitation program with elastic band exercises. Exercise dose (exposure) will be objectively quantified using a sensor attached to the elastic band. The primary outcome is gait speed measured by the 40-m fast-paced walk test. Secondary outcomes include: patient reported hip disability (Hip disability and Osteoarthritis Outcome Score (HOOS)), hip muscle strength (hand-held dynamometry) and lower extremity function (30-s chair stand test).

Discussion: This trial will add knowledge concerning the relationship between performed exercise dose and post-operative outcomes after THA. The protocol paper describes the study design and methods in detail, including the statistical analysis plan.

Trial registration: Pre-registered on March 27, 2017 at ClinicalTrails.gov (ID: NCT03109821).
Fertility transition in selected sub-Saharan African countries: the role of family planning programs
Authors: Otieno Vincent , Agwanda Alfred , Khasakhala Anne
Published: October 2019

Background: Change in fertility rate across societies is a complex process that involves changes in the demand for children, the diffusion of new attitudes about family planning and greater accessibility to contraception provided by family planning programs. Among the neo-Malthusian adherents, it is believed that rapid population growth strain countries’ capacity and performance. Fertility has, however, decelerated in most countries in the recent past. Scholars have concentrated on wide range of factors associated with fertility majorly at the national scale. However, considerably less attention has been paid to the fertility preference - a pathway through which various variables act on fertility. The Sub-Saharan African countries’ disparities amid almost similarities in policies is a cause of concern to demographers.

Methods: Using Bongaarts reformulation of Easterlin and Crimmins conceptual scheme of 1985 on Demographic and Health Survey Data (DHS) data collected overtime across countries, the understanding of the current transition in general would help to reassess and provide explanations to the observed latest fertility dynamics at play. This study therefore is an attempt to explain the current fertility transition through women’s fertility preference.

Results: Results reveal that indeed fertility transition is diverse across countries though generally on a decline course in most of the sub-Saharan countries. The huge disparities in fertility preferences among women of reproductive age and its non-significant change in the implementation indices overtime points at the levels of unmet need to contraception underneath as well as the proportion of demand to family planning commodities satisfied by programs in a bid to allow women implement their fertility desires.

Conclusions: It is therefore plausible to conclude that the improvement of the availability and the uptake of quality birth control technologies is one of the most feasible means through which countries can fast track their fertility transitions.
Creating and sharing reproducible research code the workflowr way
Authors: Blischak John D. , Carbonetto Peter , Stephens Matthew
Published: October 2019

Making scientific analyses reproducible, well documented, and easily shareable is crucial to maximizing their impact and ensuring that others can build on them. However, accomplishing these goals is not easy, requiring careful attention to organization, workflow, and familiarity with tools that are not a regular part of every scientist's toolbox. We have developed an R package,workflowr, to help all scientists, regardless of background, overcome these challenges.Workflowraims to instill a particular "workflow" — a sequence of steps to be repeated and integrated into research practice — that helps make projects more reproducible and accessible.This workflow integrates four key elements: (1) version control (viaGit); (2) literate programming (via R Markdown); (3) automatic checks and safeguards that improve code reproducibility; and (4) sharing code and results via a browsable website. These features exploit powerful existing tools, whose mastery would take considerable study. However, theworkflowrinterface is simple enough that novice users can quickly enjoy its many benefits. By simply following theworkflowr "workflow", R users can create projects whose results, figures, and development history are easily accessible on a static website — thereby conveniently shareable with collaborators by sending them a URL — and accompanied by source code and reproducibility safeguards. TheworkflowrR package is open source and available on CRAN, with full documentation and source code available athttps://github.com/jdblischak/workflowr.
Potential for diagnosis of infectious disease from the 100,000 Genomes Project Metagenomic Dataset: Recommendations for reporting results
Authors: Magiorkinis Gkikas , Matthews Philippa C. , Wallace Susan E. , Jeffery Katie , Dunbar Kevin , Tedder Richard , Mbisa Jean L. , Hannigan Bernadette , Vayena Effy , Simmonds Peter , Brewer Daniel S. , Gihawi Abraham , Rallapalli Ghanasyam , Lahnstein Lea , Fowler Tom , Patch Christine , Maleady-Crowe Fiona , Lucassen Anneke , Cooper Colin
Published: October 2019

The identification of microbiological infection is usually a diagnostic investigation, a complex process that is firstly initiated by clinical suspicion. With the emergence of high-throughput sequencing (HTS) technologies, metagenomic analysis has unveiled the power to identify microbial DNA/RNA from a diverse range of clinical samples (1). Metagenomic analysis of whole human genomes at the clinical/research interface bypasses the steps of clinical scrutiny and targeted testing and has the potential to generate unexpected findings relating to infectious and sometimes transmissible disease. There is no doubt that microbial findings that may have a significant impact on a patient’s treatment and their close contacts should be reported to those with clinical responsibility for the sample-donating patient. There are no clear recommendations on how such findings that are incidental, or outside the original investigation, should be handled. Here we aim to provide an informed protocol for the management of incidental microbial findings as part of the 100,000 Genomes Project which may have broader application in this emerging field. As with any other clinical information, we aim to prioritise the reporting of data that are most likely to be of benefit to the patient and their close contacts. We also set out to minimize risks, costs and potential anxiety associated with the reporting of results that are unlikely to be of clinical significance. Our recommendations aim to support the practice of microbial metagenomics by providing a simplified pathway that can be applied to reporting the identification of potential pathogens from metagenomic datasets. Given that the ambition for UK sequenced human genomes over the next 5 years has been set to reach 5 million and the field of metagenomics is rapidly evolving, the guidance will be regularly reviewed and will likely adapt over time as experience develops.
Evaluation of protective role of selenium on mercury toxicity by superoxide dismutase, catalase and malondialdehyde parameters in Oreochromis niloticus (Linnaeus, 1758)
Authors: Fırat Özgür , Kaya Özlem
Published: October 2019

In this research, to determine toxicity of mercury (Hg) and whether selenium (Se) has any role in protection of this toxicity, it was investigated the alterations in oxidative stress parameters in tissues of Oreochromis niloticus. For this purpose, fish were exposed to 0.01 and 0.05 ppm Hg and 0.01 ppm Hg+0.01 ppm Se and 0.05 ppm Hg+0.05 ppm Se for 4 and 21 days and activities of superoxide dismutase (SOD) and catalase (CAT) and levels of malondialdehyde (MDA) in gill and liver were determined. It was observed significant changes in all analyzed parameters due to tissue, medium concentration and exposure period in the exposure of mercury alone and Hg+Se mixtures. In Hg alone, and in combination with Se especially in their higher medium concentrations, activities of SOD and CAT in the gill and liver significantly increased at 4 days (P˂0.05), while they significantly decreased at 21 days (P˂0.05). In the exposure of Hg and Hg+Se and in the both tissues, it not determined significant alteration in the MDA levels at 4 days (P˃0.05), while they elevated in their higher concentrations at 21 days (P˂0.05). In conclusion, it was determined the increases or decreases in activities of SOD and CAT and levels of MDA in O. niloticus were higher in the Hg alone than Hg+Se mixtures and selenium has a protective effect on oxidative toxicity of mercury.
Wild fish diversity around the sea-cage fish farms in the Aegean Sea
Authors: Akyol Okan , Ceyhan Tevfik , Düzbastılar F. Ozan , Özgül Aytaç , Şen Halil
Published: October 2019

Structures, floating on the surface of the ocean attract both juvenile and adult fishes in great numbers and diversity. Natural and artificial Fish Aggregation Devices (FADs) in open seas are widely recognised for their capacity to attract pelagic fishes. It can be assumed that floating sea-cages act as a kind of FAD. Even, fish aggregations beneath the sea-cages increase much more by the influence of feeding. In this study, aggregations of wild fish were counted around six sea-cage fish farms in both northern and southern Aegean Sea. Each fish farm cultivated Sparus aurata and Dicentrarchus labrax and the farms deployed between 720 m and 3 km far from the coast. Between July 2015 and July 2017, assemblages of wild fish were counted bimonthly on two separate days at each of these farms. The Rapid Visual Counts (RVC) in five minutes with SCUBA and covering 11250 m3 were performed for six times within each farm. A total of 40 species, belonging to 22 families were recorded at fish farms, with 3 families, Sparidae (7 species), Carangidae (6 species) and Mugilidae (4 species) being particularly abundant. The results of the study and other studies conducted in other parts of the Mediterranean were merged; it was found that a total of 99 fish species were listed around sea-cage fish farms in the Mediterranean Sea.
Рост и развитие Ferula tadshikorum Pimenov в условиях интродукции
Authors: Khamraeva D.T. , Khojimatov O.K. , Uralov A.I.
Published: October 2019

Впервые в условиях интродукции выявлены оптимальные сроки посадки лекарственного и эндемичного растения Средней Азии Ferula tadshikorum из семейства Apiaceae Lindl. Результаты проведенного эксперимента подтвердили, что как у большинства интродуцированных растений, у Ferula tadshikorum наблюдается ускорение темпов развития. Принимая во внимание длительность естественного возраста Ferula tadshikorum, укорачивание его жизненного цикла при культивировании имеет положительный экономический эффект для быстрого получения сырья из подземных органов.
Gut Microbiota Functional Biomolecules With Immune-Lipid Metabolism for a Prognostic Compound Score in Epstein-Barr Virus-Associated Gastric Adenocarcinoma: A Pilot Study
Authors: Wang Fang , Wu Jingyi , Wang Yan , Jin Yufen , Jiang Xin , Qiu Zhichao , Qin Yan , Liu Yankui , Qi Xiaowei , Ge Xiaosong , Mao Yong , Cheng Yang , Hua Dong
Published: October 2019

OBJECTIVE:

Increasing evidence has indicated an association between gut microbiota in gastrointestinal cancer and clinical outcome. Herein, we aim to develop a prognosis-prediction tool based on an immune-lipid metabolism signature, tumor cell-associated immune microenvironment, and lipid metabolism proteins inferred from the function of gut microbiota.

METHODS:

16S gene ribosomal RNA sequencing was performed on 10 fecal samples obtained after tumor resection but before chemotherapy (EBVaGC = 4 and EBVnGC = 6). Least absolute shrinkage and selection operator (LASSO) Cox regression was applied to screening for highly accurate marker proteins. A compound score based on the fraction of screened markers was then constructed using a LASSO logistic regression model.

RESULTS:

The Tax4Fun analysis based on Kyoto Encyclopedia of Genes and Genomes data indicated differentially expressed tumor pathway between EBVnGC and EBVaGC. Using the LASSO logistic model, a compound score was established consisting of 14 types of immune microenvironment and lipid metabolism proteins. In the training set (378 patients), significant differences were found between high- and low-compound score groups in overall survival across and within subpopulations with an identical EBV. Multivariable analysis revealed that the compound score was an independent prognostic factor (hazard ratio, 2.26; 95% confidence interval = 2.28–3.36). The prognostic value ;of the compound score was also confirmed in the validation (162 patients) and entire (540 patients) sets.

DISCUSSION:

The proposed compound score is a promising signature for estimating overall survival in patients with gastric cancer having EBVaGCs or EBVnGCs.
Socialist Internationalism Against the European Union
Authors: Davidson Neil
Published: October 2019

Costas Lapavitsas's The Left Case Against the EU (Polity, 2019) is recognized as the leading work advocating Lexit, the left-wing case for Brexit, and for nations leaving the European Union more generally. In light of current Conservative British Prime Minister Boris Johnson's commitment to exit the European Union by October 31, even if it means a no-deal Brexit, the role of the left takes on growing importance. Moreover, this raises issues of the European Union generally, including the dominance of neoliberalism within it and the question of German hegemony. Here, Neil Davidson offers an assessment of Lapavitsas's book.
A New Revolutionary Subject
Authors: Harnecker Marta
Published: October 2019

Monthly Review and Monthly Review Press author, world socialist activist, and theorist of revolution, Marta Harnecker, died on June 15, 2019, at age 82. In her memory, we republish an exchange between her and Greek journalist Tassos Tsakiroglou, conducted in advance of the 2017 conference on 150 Years of Marx's Capital: Reflections for the Twenty-First Century.
Semi-Supervised learning with Collaborative Bagged Multi-label K-Nearest-Neighbors
Authors: Settouti Nesma , Douibi Khalida , Bechar Mohammed El Amine , Daho Mostafa El Habib , Saidi Meryem
Published: October 2019

Over the last few years, Multi-label classification has received significant attention from researchers to solve many issues in many fields. The manual annotation of available datasets is time-consuming and need a huge effort from the expert, especially for Multi-label applications in which each example of learning is associated with many labels at once. To overcome the manual annotation drawback, and to take advantages from the large amounts of unlabeled data, many semi-supervised approaches were proposed in the literature to give more sophisticated and fast solutions to support the automatic labeling of the unlabeled data. In this paper, a Collaborative Bagged Multi-label K-Nearest-Neighbors (CobMLKNN) algorithm is proposed, that extend theco-Trainingparadigm by a Multi-label K-Nearest-Neighbors algorithm. Experiments on ten real-world Multi-label datasets show the effectiveness ofCobMLKNNalgorithm to improve the performance ofMLKNNto learn from a small number of labeled samples by exploiting unlabeled samples.
Augmenting Neural Machine Translation through Round-Trip Training Approach
Authors: Ahmadnia Benyamin , Dorr Bonnie J.
Published: October 2019

The quality of Neural Machine Translation (NMT), as a data-driven approach, massively depends on quantity, quality and relevance of the training dataset. Such approaches have achieved promising results for bilingually high-resource scenarios but are inadequate for low-resource conditions. Generally, the NMT systems learn from millions of words from bilingual training dataset. However, human labeling process is very costly and time consuming. In this paper, we describe a round-trip training approach to bilingual low-resource NMT that takes advantage of monolingual datasets to address training data bottleneck, thus augmenting translation quality. We conduct detailed experiments on English-Spanish as a high-resource language pair as well as Persian-Spanish as a low-resource language pair. Experimental results show that this competitive approach outperforms the baseline systems and improves translation quality.
Comparative study of the bioavailability of magnesium salts
Authors: Eremenko Natalia Nikolaevna , Shikh Eugenia Valerievna , Serebrova Svetlana Yurievna , Sizova Zhanna Mikhailovna
Published: October 2019

Background

High values of endogenous levels of magnesium (Mg) in the body and mechanisms of homeostasis regulation make it difficult to assess the bioavailability of these drugs. The aim of this study was to assess the Mg concentration in blood in volunteers and in erythrocytes in patients with hypomagnesemia.

Methods

The study included 20 healthy volunteers and 62 patients with chronic heart failure (CHF) I–III functional class (FC) NYHA classification. We studied the composition of Mgorotate and Mgorotate plus potassium (К)orotate. Blood sampling was carried out at 8 a.m. and within 10 h after administering the drugs. Measurement of Mg pharmacokinetic parameters: AUC (concentration of the active substance-time), and Cmax (maximum concentration) in volunteers and measurement of the concentration of Mg in erythrocytes of patients.

Results

The results indicated that both the AUC in volunteers and concentration of Mg in erythrocytes of patients are comparable, and the differences are not statistically significant.

Conclusions

The study showed that the standard method of calculating the AUC (total serum Mg) is insufficient for comparative evaluation of Mg absorption due to the high levels of its endogenous content and a small increase in concentration after taking the drugs. It is advisable to assess the concentration of Mg in the red blood cells of patients.
The Maximal Operator in Variable Spaces 𝐿 𝑝(·)(Ω, ρ) with Oscillating Weights
Authors: Kokilashvili Vakhtang , Samko Natasha , Samko Stefan
Published: October 2019

We study the boundedness of the maximal operator in the spaces 𝐿 𝑝(·)(Ω, ρ) over a bounded open set Ω in 𝑅𝑛 with the weight , where 𝑤𝑘 has the property that belongs to a certain Zygmund-type class. Weight functions 𝑤𝑘 may oscillate between two power functions with different exponents. It is assumed that the exponent 𝑝(𝑥) satisfies the Dini–Lipschitz condition. The final statement on the boundedness is given in terms of index numbers of functions 𝑤𝑘 (similar in a certain sense to the Boyd indices for the Young functions defining Orlicz spaces).
A Vector-Valued Sharp Maximal Inequality on Morrey Spaces with Non-Doubling Measures
Authors: Sawano Yoshihiro
Published: October 2019

We consider the vector-valued extension of the Fefferman–Stein–Strömberg sharp maximal inequality under growth condition. As an application we obtain a vector-valued extension of the boundedness of the commutator. Furthermore, we prove the boundedness of the commutator.
Performance of electrical stimulated anaerobic baffled reactor for removal of typical pollutants from low-strength municipal wastewater at low temperatures
Authors: Moradgholi Marziye , Massoudinejad Mohamadreza , Aghayani Ehsan , Yazdanbakhsh Ahmadreza
Published: October 2019

Background: Although anaerobic system has been successfully used for treating the strong industrial wastewater, its efficiency for low-strength wastewater as municipal wastewater is not satisfying. This study aimed to enhance the capability of an anaerobic baffled reactor (ABR) for treating municipal wastewater. Methods: A 7-L ABR with 5 compartments was operated for a 287-day period fed with primary effluent from a wastewater treatment plant at 17 to 19°C. The study was conducted in 2 phases. In the first phase, the performance of ABR and in the second phase, the performance of ESABR (ABR integrated with an electrochemical system) were investigated. Results: The results of ABR operation indicated that at hydraulic retention time (HRT) =24 hours, the average removal efficiency of biochemical oxygen demand (BOD), chemical oxygen demand (COD), total suspended solids (TSS), total Kjeldahl nitrogen (TKN), total phosphorous (TP), and log reduction value (LRV) of coliforms were obtained to be 71%, 75%, 79%, 23%, 30.3%, and 5.8 Log, respectively. In this phase, when the HRT was decreased from 24 to 18 hours and from 18 to 14 hours, the removal efficiency of all parameters by the ABR was decreased. After the shift of ABR operation to ESABR, at HRT=24 hours and current density of 0.78 mA/cm2 , the performance of the reactor was enhanced, so that the removal efficiency of BOD, COD, TSS, TKN, TP, and LRV of coliforms were achieved 16.8%, 15%, 4%, 10.7%, 49%, and 1 Log, which was greater than those obtained by ABR. Conclusion: According to the results, this technology (SEABR) is suitable for treating the low-strength municipal wastewater.
Ecological risk assessment of heavy metals from cement factory dust
Authors: Yadegarnia Naeini Firouzeh , Azimzadeh Hamidreza , Mosleh Arani Asghar , Sotoudeh Ahad , Kian Bahman
Published: October 2019

Background: The release of metals from industrial factories is one of the most important sources ofenvironmental pollution. The present study aimed to determine the concentration of heavy metals likecadmium (Cd), chromium (Cr), manganese (Mn), nickel (Ni), and lead (Pb) in dust around the cementfactory.Methods: A total of 22 dust samples were collected from areas around the cement factory in Isfahanprovince in spring and summer and transferred to laboratory for chemical digestion. Risk index (RI),integrated pollution index (IPI), mean of contamination degree (mCd), and contamination factor (Cfi)were calculated to determine the contamination status.Results: The concentration of heavy metals in the falling dust around the factory was expressed as Cd<Ni <Pb <Mn <Cr. Pearson correlation showed that there is only a significant negative relationshipbetween the concentration of Cd and the distance from the factory. By increasing the distance from thefactory, the concentration of Cd in dust decreased. The results of falling dust analysis showed that Crhas a high-risk potential in two seasons of spring and summer and Cd has a middle level of pollutionin spring.Conclusion: According to the results, the deposited dust of study area is considered as a polluted dustand it is at higher risk of pollution with Cd and Cr.
Comparison ability of algae and nanoparticles on nitrate and phosphate removal from aquaculture wastewater
Authors: Askari Hesni Majid , Hedayati Seyed Aliakbar , Qadermarzi Amir , Pouladi Mojtaba , Zangiabadi Somayeh , Naqshbandi Nabat
Published: October 2019

Background: Aquaculture wastewater contains high levels of phosphate and nitrate. The reuse of this water requires standards beyond the secondary standards to eliminate more organic pollutants from aquaculture effluents. In this research, the removal of these pollutants from wastewater using Chlorella vulgaris and Fe3 O4 nanoparticles in the reactor space was investigated. Methods: This study was conducted on fish farms effluent in the laboratory system. For this purpose, a 5-L semi-industrial reactor with a mixer blade, porous plate, and a compressor was designed. Chlorella vulgaris samples were collected from the natural environment and cultured in the laboratory environment. Also, Fe3 O4 nanoparticles were prepared from Iranian Nano Pishgaman Company to make the desired solution. During the experiment (3 weeks), samples were taken weekly (in one phase) from the effluent. Dissolved oxygen (DO), pH, nitrate (NO3 ), and phosphate (PO4 ) factors from the influent and effluent of the farms were measured. The statistical data were analyzed using SPSS version 21 and Excel 2013. Results: The amounts of nitrate and phosphate were decreased by about 80.76 and 80.55% in the biological reactor, whereas these amounts were 70.52 and 70.48% in the nanoparticle reactor, respectively. Also, there were significant differences in the amounts of NO3 and PO4 between the control treatment and weekly treatment (P<0.05). Conclusion: Based on the results, both reactors were able to reduce nitrate and phosphate from aquaculture wastewater, but the efficiency of the biological reactor was higher than that of the nanoparticle reactor.
Removal of Acid Orange 7 dye from aqueous solutions using polyaniline-modified rice bran: isotherms, kinetics, and thermodynamics
Authors: Bagheri Marzieh , Mardani Esmail
Published: October 2019

Background: Today, due to increasing usage of dyes in various industrials and their destructive effects on health and environment, it is necessary to remove them from industrial wastes. Although there are few studies on the use of rice bran modified with polyaniline (RB/PANI) for removal of different dyes, but the effect of this adsorbent on the removal of Acid Orange 7 (AO7) dye has not been evaluated yet. Therefore, this study was conducted to investigate the removal of AO7 dye by RB/PANI as an adsorbent. Methods: The adsorbent characteristics were determined using scanning electron microscopy (SEM) and Fourier transform infrared (FT-IR) spectroscopy. Also, the adsorbent surface area was measured by Brunauer–Emmett–Teller (BET) technique. The method of one-factor-at-a-time was used to optimize various factors including pH, temperature, and adsorbent dosage. Results: The optimal values for the factors affecting AO7 dye removal were calculated. It was revealed that the maximum dye removal was obtained at pH = 3, temperature = 25˚C, dye concentration = 30 mg/L, adsorbent dosage = 30 mg/L, and contact time= 60 minutes. The maximum removal percentage for RB/PANI was 97.13%. It was also revealed that Langmuir isotherm is the best fitted isotherm model. Conclusion: According to the results, the polyaniline-modified rice bran could be used as an excellent adsorbent for the removal of AO7 from aqueous solutions. The maximum dye removal efficiency for AO7 was obtained at pH = 3. Also, it was revealed that AO7 dye removal follows the pseudo-secondorder kinetic model and it is a spontaneous process.