bluuebunny/crossref_metadata_2025 huggingface dataset:
Flood Vulnerability Mapping Using Geographic Information System (GIS) in Gajah Wong Sub Watershed, Yogyakarta County Province
Authors: Ardiansyah A. , Sumunar Dyah Respati Suryo
Published: April 2020

Gajah Wong Sub Watersheds frequently hit by floods which are potentially damaging. Therefore, a study on a flood vulnerability of the area is deemed necessary. This study aims to map floods vulnerability, to know the level and its spread in Gajah Wong Sub Watershed of Yogyakarta County Province by using Geographic Information System (GIS). The methods implemented in this study was weighing and scoring analysis and overlay of parameter attributes data of flood vulnerability framer, consisting of land use, slope of mountain, rainfall, soil type, geology, height of location and river buffer. Each parameter of flood vulnerability framer is classified based on the magnitude of effect towards flood vulnerability. The results of this study indicate that there were three levels of flood vulnerability in  Gajah Wong Sub Watershed, i.e. low flood vulnerability of 338.34 Ha (6.86%), medium flood vulnerability level of 4,595.62 Ha (93.13%) and high flood vulnerability level of  0.76 Ha (0.02%). Low flood vulnerability level is ditributed randomly to all areas of  Gajah Wong Sub Watershed cover of Ngaglik Sub-district, Depok Sub-district, small part of  Pleret Sub-district and was predominantly in  Banguntapan Sub-district, an area with rainfall. Medium flood vulnerability areas dominated Gajah Wong Watershed. Meanwhile, high flood vulnerability level occupied small portion of the area and spread in the southern part of Pleret Sub-district which was taken as the area of River Buffer analysis.

Keywords: GIS; Gajah Wong; Sub Watershed; Yogyakarta.

 

Copyright (c) 2020 Geosfera Indonesia Journal and Department of Geography Education, University of Jember

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Application of Information and Communication Technology (ICT) in Dissemination of Information in Selected Special Libraries in Ilorin Metropolis, Kwara State, Nigeria
Authors: Akanbi Mohammed Lawal , Ogunleye Dorcas Odunayo , Sulaiman Kabir Alabi
Published: April 2020

Background of the study: This study examined the Application of ICT in Dissemination of Information in Selected Special Libraries in Ilorin Metropolis, Kwara State, Nigeria. Three Special libraries from the metropolis of the state comprised the sample population of the study; Central Bank of Nigeria Library, Michael Imoudu Institute of Labor Studies Library and Ghalib Chamber Library.Purpose: The study employed a survey research design using the Enumeration sampling technique. A questionnaire was used to obtain data from the respondents. The population of the study consisted of twenty-one (21) respondents which comprised of library professionals and library assistants.  The usage of Email to render CAS is not a norm in these special libraries.Method: Data collected from the field were analyzed using descriptive method of analysis.Findings: Apart from CAS, it was found that selective dissemination of information (SDI) is not done with the aid of technological tools in these Libraries and these libraries rarely make use of OPAC to provide easy access to their resources, efficiency and effectiveness of ICT in the dissemination of information were not realized because of the low usage of ICT to drive operations in the library. The study recommended that there should be a standard alternative source of power for proper Usage of ICT facilities and management of special libraries should help their users in subscribed for a database that would assist them in having access to robust information.Conclusion: The study concluded that ICT facilities are put in place in the selected special libraries are not adequate and are as well not fully utilized. It was gathered that the usage of ICT facilities to render services like current awareness services (CAS) is not up to expectation.
Integrating Information System Success Model (ISSM) And Technology Acceptance Model (TAM): Proposing Students’ Satisfaction with University Web Portal Model
Authors: Adeyemi Ismail Olatunji , Issa Abdulwahab Olanrewaju
Published: April 2020

Background of the study: The web portal is a tool that has been adopted by universities to manage data and information of students and faculty. The portal is an information system as it is driven by information.Purpose: The study proposes a model of students’ satisfaction with Web portal for the integration of Information System Success Model ISSM and Davis’ Technology Acceptance Model (TAM).Method: The methodology adopted for this study is the critical review of literature that borders on the constructs and/or variables embedded in ISSM and TAM.Findings: The study theorizes that information quality, service quality and system quality and perceived usefulness individually determine students’ satisfaction of a Web portal. The study also predicts that all of these variables compositely determine the students’ satisfaction of university Web.Conclusion: The study established that the “mandatory use” of Web portal does not primarily translate to students’ satisfaction with the portal. This is because whether users are satisfied or not, the onus is still on them to come back to use the portal.
Gaok's Oral Tradition Document Management as a Manifestation Of Cultural Preservation in The Library
Authors: Septa Septa , Heriyanto Heriyanto
Published: April 2020

Background of the study: This research identifies ways of the document management of local oral traditions in Majalengka.Purpose: It aims to uncover how the library has managed the local oral document which intended to preserve the Gaok local content.Method: A qualitative method was implemented by using semi-structured interviews as a data collection technique. The collected data were then analyzed by using Thematic Analysis, which generates three themes related to the research questions. The themes are Motivation, Document Management, and Dissemination Planning. Findings: Motivation describes the background of the initiative by managing the Gaok Oral Documents. While the second theme, Document Management, portrays the effort taken by the library in managing the documents, that include retrieving information about Gaok, writing its resume, and disseminate the information. Finally, the third theme,  Dissemination Plan, describing the library strategic plans on disseminating and implementing their strategy of the Gaok Documents locally and nationally. The library believes that by managing the Gaok Oral Documents effectively, this local tradition will keep alive and known and hopefully preserved by the future generations.Conclusion: This study reflects how a library plays an important role in managing and preserving local culture.
Microbiome-aware Ecotoxicology: Relevance, Pitfalls and Challenges
Authors: Duperron Sébastien , Halary Sébastien , Gallet Alison , Marie Benjamin
Published: April 2020

The diversity and significance of host-associated microbial communities has emerged over the last 15 years to the point when some may now assume that “Nothing in Biology makes sense except in the light of the microbiome”. The advent of high-throughput ‘omics’ techniques has revealed the multiple roles and interactions occurring among hosts, their microbial partners and their environment, and has radically changed our views of biology, evolution and individuality. Sit at the interface between a host and its environment, the microbiome is a dynamic interface that responds to both host and environmental factors, for better or worse. For this reason, the microbiome now appears as a relevant, yet understudied compartment for ecotoxicology research. Various examples show that the microbiome reacts to and interacts with contaminants, with consequences for hosts and the ecosystem, and great advances can be expected from studies in which microbiome research meets toxicology. Yet, for the encounter to be scientifically productive, caution is needed in study design, inferences and extrapolations. In this paper, we emphasize the relevance and challenges of microbiome research in environmental toxicology through documented examples, and draw readers attention to pitfalls that should not be overlooked when producing and analyzing their data. We advocate for the development of a “microbiome-aware ecotoxicology”.
Adsorptive Removal of Congo red dye from wastewater using Fenugreek Powder
Authors: bhadauria Neha , Suresh Arjun
Published: April 2020

The present study analyzed the efficiency of a naturally derived fenugreek powder for removal of Congo red dye from the aqueous solution. The flocculation Studies on Congo Red (CR) a hazardous, textile dye onto Fenugreek Powder and its adsorption was analyzed. Fenugreek Powder is Eco-friendly, biodegradable and locally available in the market. The dye adsorption process was performed in different batches at varying pH, dye concentration, adsorbent concentration and contact time to get the best results. The result showed that the maximum removal of dye was 42.4% with 10mg/l of Fenugreek powder at pH 4.
Identification of Distinct Heterogenic Subtypes and Molecular Signatures Associated With African Ancestry in Triple Negative Breast Cancer Using Quantified Genetic Ancestry Models in Admixed Race Populations
Authors: Davis Melissa , Martini Rachel , Newman Lisa , Elemento Olivier , White Jason , Verma Akanksha , Datta Indrani , Adrianto Indra , Gardner Kevin , Kim Hyung-Gyoon , Dean-Colomb Windy , Eldin Eltoum Isam , R Frost Andra , Grizzle William E. , Sboner Andrea , Manne Upender , Yates Clayton
Published: April 2020

Triple negative breast cancers (TNBCs) are molecularly heterogeneous, and the link between their aggressiveness with African ancestry is not established. We investigated primary TNBCs for gene expression among self-reported race (SRR) groups of African American (AA, n=42) and European American (EA, n=33) women. Using The Cancer Genome Atlas (TCGA) approaches, we analyzed RNA sequencing data to measure changes in genome-wide expression and used logistic regressions to identify ancestry-associated gene expression signatures. To determine global ancestry, GATK best practices were followed for variant calling, and used the 1000 Genomes Project as reference data. We identified >150 African ancestry-associated genes and found that, compared to SRR, quantitative genetic analysis was a more robust method to identify racial/ethnic-specific genes that were differentially expressed. A subset of African ancestry-specific genes that were upregulated in TNBCs of our AA patients were validated in TCGA data. In AA patients, there was a higher incidence of basal-like 2 tumors and altered TP53, NFB1, and AKT pathways. The distinct distribution of TNBC subtypes and altered oncologic pathways show that the ethnic variations in TNBCs are driven by shared genetic ancestry. Thus, to appreciate the molecular diversity of TNBCs, tumors from patients of various ancestral origins should be evaluated.
Prevalence of COVID-19: A Look behind the Scenes from the UAE and India
Authors: Haj Bloukh Samir , Shaikh Annis , Pathan Habib M. , Edis Zehra
Published: April 2020

Mankind faces a coronavirus pandemic originating from a seafood market in Wuhan, China since December 2019. The pathogen was named novel coronavirus (n-CoV) and bats are the identified key reservoir. The coronavirus disease 2019 (COVID-19) quickly spread over China across the globe, turned into a pandemic with exponentially increasing numbers of cases and significant mortality rate. China reacted with lockdowns and strict control measurements to prevent spreading the virus. The treatment of severe cases was hampered by lack of specific vaccines. Vaccine-development and production is a painstaking process and can only be enforced by international cooperation. Different supportive treatment options surfaced due to combinations of antiviral agents with antibiotic drugs. Elderly, male, immune-suppressed patients with co-morbidities showed a high mortality rate. Health literacy, strong immune system, adequate serum 25-hydroxyvitamin D (25(OH)D) concentrations and healthy life style choices can support fast recovery. Antibiotic resistance needs to be addressed by development of new generation antimicrobials against nosocomial infections in preparation for future outbreaks. Plant-biosynthesis of nanomaterials and antiseptics may help in prevention and recovery rate. Prevalence of COVID-19 maybe inversely related to BCG vaccination, endemicity of malaria, humidy and temperature but directly with latitude. Recommendations to prevent the spread of COVID-19 should be followed strictly.
The Eukaryotic Last Common Ancestor Was Bifunctional for Hopanoid and Sterol Production
Authors: Francis Warren
Published: April 2020

Steroid and hopanoid biomarkers can be found in ancient rocks and, in principle, can give a glimpse of what life was present at that time. Sterols and hopanoids are produced by two related enzymes, though the evolutionary history of this protein family is complicated by losses and horizontal gene transfers, and appears to be widely misinterpretted. Here, I have added sequences from additional key species, and re-analysis of the phylogeny of SHC and OSC indicates a single origin of both enzymes among eukaryotes. This pattern is best explained by vertical inheritance of both enzymes from a bacterial ancestor, followed by widespread loss of SHC, and two subsequent HGT events to ferns and ascomycetes. Thus, the last common ancestor of eukaryotes would have been bifunctional for both sterol and hopanoid production. Later enzymatic innovations allowed diversification of sterols in eukaryotes. Contrary to previous interpretations, the LCA of eukaryotes potentially would have been able to produce hopanoids as a substitute for sterols in anaerobic conditions. Without invoking any other metabolic demand, the LCA of eukaryotes could have been a facultative aerobe, living in unstable conditions with respect to oxygen level.
COVID-19 and the Digital Transformation of Education: What We Are Learning in South Africa
Authors: Mhlanga David , Moloi Tankiso
Published: April 2020

The study sought to gauge the impact of COVID-19 pandemic in unleashing digital transformation in the education sector in South Africa. In order to gauge the impact, the study tracked the rate at which the 4IR tools were used by various institutions during the COVID-19 lockdown. Data were obtained from secondary sources, mainly newspaper articles, magazines and peer-reviewed journals. The findings are that, in South Africa, during the lockdown, a variety of 4IR tools were unleashed from primary education to higher and tertiary education where educational activities switched to remote learning (online learning). These observations point to the fact that South Africa generally has, some pockets of excellence to drive the education sector into the 4IR, which has the potential to increase access. Access to education, particularly at a higher education level, has always been a challenge due to a limited number of spaces available. Much as this pandemic has brought with it massive human suffering across the globe, there is an opportunity to assess successes and failures of deployed technologies, costs associated with them, and scaling these technologies to improve access.
Modelling and Simulation of the Hydrodynamics and Mixing Profiles in the Human Proximal Colon Using Discrete Multiphysics
Authors: Schütt Michael , Stamatopoulos Konstantinos , Simmons Mark , Batchelor Hannah , Alexiadis Alessio
Published: April 2020

The proximal part of the colon offers opportunities to prolong the absorption window following oral administration of a drug. In this work, we used computer simulations to understand how the hydrodynamics in the proximal colon might affect the release from dosage forms designed to target the colon. For this purpose, we developed and compared three different models: a completely-filled colon, a partially-filled colon and a partially-filled colon with a gaseous phase present (gas-liquid model).The highest velocities of the liquid were found in the completely-filled model, which also shows the best mixing profile, defined by the distribution of tracking particles over time. No significant differences with regard to the mixing and velocity profiles were found between the partially-filled model and the gas-liquid model. The fastest transit time of an undissolved tablet was found in the completely-filled model. The velocities of the liquid in the gas-liquid model are slightly higher along the colon than in the partially-filled model. The filling level has an impact on the exsisting shear forces and shear rates, which are decisive factors in the development of new drugs and formulations.
Is COVID-19 an Endothelial Disease? Clinical and Basic Evidence
Authors: Sardu Celestino , Gambardella Jessica , Morelli Marco Bruno , Wang Xujun , Marfella Raffaele , Santulli Gaetano
Published: April 2020

The symptoms most commonly reported by patients affected by coronavirus disease 2019 (COVID-19) include cough, fever, and shortness of breath. However, other major events usually observed in COVID-19 patients (e.g. high blood pressure, thrombosis, pulmonary embolism) seem to suggest that the virus is targeting the endothelium, one of the largest organs in the human body. Herein, we report both clinical and preclinical evidence supporting the hypothesis that the endothelium is a key target organ of COVID-19.
Effect of moisture and temperature on the extrudate properties of milkfish (Chanos chanos) feed
Authors: Ali S. Syed Raffic , Ambasankar K. , Balachandran S. , Ramachandran K.
Published: April 2020

The present study evaluated the effect of varying levels of moisture and temperature on the extrudate properties of the milkfish (Chanos chanos) feed containing 31.49% protein and 4.71% lipid. Two trials were conducted in a pilot scale twin screw extruder using 3 mm die. In the first trial, the effect of temperature on extrudate properties was studied at five different temperatures viz., 80-90, 90-100, 100-110, 110-120 and 120-130°C. The results revealed that the temperature levels of 100-110, 110-120 and 120-130°C resulted in significantly (p<0.05) lower bulk density (BD) of the extrudate than at 80-90 and 90-100°C. Significantly (p<0.05) lower water solubility index (WSI) was recorded at 100-110°C, while further increase in temperature failed to show further reduction in water solubility. The pellet durability index (PDI) and expansion ratio (ER) showed a non-significant difference among the extrudates at 100-110, 110-120 and 120-130°C. In the second trial, the effect of additional moisture on the extrudate was evaluated by including water at 20, 25, 30 and 35% and the results revealed that 30% moisture addition resulted in significantly (p<0.05) lower BD, WSI and PDI of the extrudate than the other levels. The highest moisture level of 35% led to difficulty in operation while the lower levels from 25% failed to produce floating pellets. Results of this study infers that 30% moisture addition and a temperature of 100-110°C is optimalfor production of water stable floating milk fish feeds.
In vivo assessment of oxidative stress in heart cells of Cirrhinus mrigala (Hamilton, 1822) challenged with sublethal doses of Aeromonas hydrophila
Authors: Ray Sriparna Datta , Homechaudhuri Sumit
Published: April 2020

Experiment was performed to study the effect of Aeromonas hydrophila MTCC 646 on the heart of Cirrhinus mrigala (Hamilton, 1822) . The in vivo innate immune response was also monitored in these fishes. Fishes were inoculated with 3 asymptomatic doses (2x105, 2x106 and 2x107 CFU ml-1) intraperitoneally (i.p.) @ 0.5 ml 100 g-1. Dose dependent pattern of change was observed in the immune biomarkers chosen for the study. Histopathology revealed endocarditis and cell death identified as apoptosis. The percentage contribution of late apoptotic cells was 0.36% after 7 days in fish heart exposed to the highest dose of bacteria which was reduced to 0.01% after 30 days. Oxidative stress and dosage were directly proportional. The oxidised dichloro fluorescein peak was about 4.05 fold more than the control samples, after 7 days with respect to the highest dose and immune responses helped to decrease the mean peak to 1.02 after 30 days, signifying recovery of phagocytic activity, which is a part of the reticulo-endothelial system. This work presents an insight into the immune response and the results analysed statistically show that there was significant difference between percent population of early apoptotic cells (p<0.05) collected after 7 days and 30 days duration with respect to all the three doses.
Goods and Services Tax (GST) reforms and implementation : An economic analysis in the marine fisheries sector of Kerala, South India
Authors: Salim Shyam S. , James Harsha Elizabeth , Meharoof Mohammed
Published: April 2020

Goods and services tax (GST), hailed as a historic tax reform, is a step taken by Government of India to improve transparency and accountability in the taxation system of our country. The fisheries sector is also expected to have a varied impact consequent to the introduction of these reforms. The present study assessed the level of awareness and perception of impact of GST and to estimate the additional cost per annum in marine capture fisheries sector of Kerala due to implementation of GST and also to highlight the possible positive effects of inclusion of diesel price under GST. The study was undertaken in the fish landing centers/harbours of Alappuzha and Ernakulam districts of Kerala, south India aimed at measuring the extent of uncertainty generated by introduction of GST. The study revealed that the implementation came as a complete bolt from the blue with majority of the fishers in disagreement with the process of implementation of GST without taking all stakeholders into confidence. Compared to value added tax (VAT), the GST and post-Guwahati Council GST rates are found to be high, affecting the fishing community at multidimensional levels. The results revealed that the marine capture fishing operations across all sectors in Kerala will be incurring an additional cost of `171.25 million per year due to GST introduction. However introducing GST on fuels will lead to a reduction of diesel price by 30-40% and 25-30% at 18 and 28% GST slabs respectively, which would reduce the ever increasing cost of fishing. The study also advocates that the implementation of GST in fuel prices should not add to overexploitation of the already dwindling fisheries resources.
Effects of temperature, salinity and dissolved oxygen on excystment of podocysts in the edible jellyfish Rhopilema esculentum Kishinouye, 1891
Authors: Fu Zhide , Xing Yixuan , Gu Zhifeng , Liu Chunsheng , Chen Siqing
Published: April 2020

The scyphozoan jellyfish Rhopilema esculentum Kishinouye, 1891 is a species occurring in the traditional fishery in China. However, the yield of this species in fishery has rapidly declined since 1980s. The podocyst is an important phase during asexual reproduction in Scyphozoa and is considered to be potentially important to the population dynamics of jellyfish. In this study, we investigated the microstructure and effects of environmental factors on the excystment of podocysts. Podocysts of greater than 8 months of age exhibited no morphological differences compared to newly formed podocysts. Following excystment, a smooth-edged hole, probably created by enzymatic digestion was observed. Excystment sharply increased when the water temperature was higher than 18°C, suggesting that temperature ranging from approximately 13-18°C triggers the excystment of podocysts in R. esculentum. Stepwise temperature variation suggested that cooling was much more effective than warming in the induction of R. esculentum podocysts to excyst. The optimal salinity and dissolved oxygen (DO) conditions for excystment were observed to be 20‰ and 6 mg O2 l-1 respectively. Furthermore, excystment was suppressed by both stepwise increase and decrease in salinity or DO. Though R. esculentum podocysts could survive extreme environmental conditions such as hypoxia and low salinity, excystment rates were markedly reduced compared to those of other bloom jellyfish species when the DO and salinity levels were returned to normal.
Effect of seawater pH on selected blood biochemical parameters of juvenile turbot Scophthalmus maximus (Linnaeus, 1758)
Authors: Wang Shuangyao , Jiang Zhiqiang , Mousavi Seyed Ehsan
Published: April 2020

The effect of seawater pH on blood physiology in juvenile turbot Scophthalmus maximus (Linnaeus, 1758) reared in recirculating aquaculture systems (RAS) was examined. S. maximus (19.89±0.25 g) were exposed to six pH levels at 6.3±0.2, 6.8±0.2, 7.3±0.2, 7.8±0.2, 8.3±0.2 and 8.8±0.2. Haemoglobin content (HBC) at acidic conditions was higher compared to that under alkaline conditions. The frequency of total nuclear anomalies (FTNA) was high at pH levels below 7.3 or above 8.3. The relationship between FTNA and pH was well described using a quadratic equation. Alkaline phosphatase activity was significantly declined at pH above 8.3, while total superoxide dismutase activity (T-SOD) remained virtually unchanged among all treatments. This study demonstrated that HBC and FTNA can be used as reliable biomarkers to evaluate the effect of pH in aquatic ectotherms from physiological standpoints. Our findings suggest that environmental pH in RAS ranging from 6.8 to 7.8 is appropriate for juvenile turbot aquaculture.
Real-Time Estimation and Management of Hydrate Plugging Risk During Deepwater Gas Well Testing
Authors: Zhang Jianbo , Wang Zhiyuan , Duan Wenguang , Fu Weiqi , Sun Baojiang , Sun JinSheng , Tong Shikun
Published: April 2020

Hydrate formation and deposition are usually encountered during deepwater gas well testing, and if hydrates are not detected and managed in time, a plugging accident can easily occur. In this study, we demonstrate a method for estimating and managing the risk of hydrate plugging in real time during the testing process. The method includes the following steps: predicting the hydrate stability region, calculating the hydrate formation and deposition behaviors, analyzing the effect of the hydrate behaviors on variations in wellhead pressure, monitoring the variations in wellhead pressure and estimating the hydrate plugging risk in real time, and managing the risk in real time. An improved pressure-drop calculation model is established to calculate the pressure drop in annular flows with hydrate behaviors, and it considers the dynamic effect of hydrate behavior on fluid flow and surface roughness. The pressure drops calculated at different times agree well with experimental and field data. A case study is conducted to investigate the applicability of the proposed method, and results show that with the continued formation and deposition of hydrates, both the effective inner diameter of the tubing and the wellhead pressure decrease accordingly. When the wellhead pressure decreases to a critical safety value under a given gas production rate, a hydrate inhibitor must be injected into the tubing to reduce the severity of hydrate plugging. It is also necessary to conduct real-time monitoring of variations in wellhead pressure to guarantee that the risk of hydrate plugging is within a safe range. This method enables the real-time estimation and management of hydrate plugging during the testing process, and it can provide a basis for the safe and efficient testing of deepwater gas wells.
Smart Expandable Fiber Additive To Prevent Formation of Microannuli
Authors: Santos Livio , Dahi Taleghani Arash , Li Guoqiang
Published: April 2020

One of the critical issues that occur in many oil and gas wells is the failure of the cement sheath because of debonding from the casing string or from the formation. This results in the formation of microannuli, which can become pathways for fluid migration. Cement shrinkage during setting is regarded as one of the main causes of the formation of microannuli. In this paper, a new class of polymer-based expandable additives in the form of fibers is incorporated into the cement to compensate for shrinkage and thereby help prevent the formation of microannuli in oil and gas wells. The proposed fiber additives are made from shape-memory polymers (SMPs) and expand when exposed to temperatures above a specific value that is, by design, below the downhole temperature of the cemented zone. Fiber expansion occurs after the placement of the cement slurry but before its setting to avoid the inducement of any microfractures. As a result of the expansion of the cement paste, flow channels and fluid migration may significantly decrease while preserving the mechanical properties required for the mechanical integrity of the cement sheath. The bridging effect of fibers across individual microcracks helps control the propagation and coalescence of small fractures. Considering the inert property of the proposed additive, the water-cement ratio and its chemical properties do not need to be revisited. The measured increase in cement ductility makes the cement system more resistant to cracking. The cement expansion, fluid loss, gel strength, compressive strength, ductility, and tensile strength of the samples containing these fibers are examined using destructive and nondestructive methods, as reported here. The proposed class of expandable additives can help operators reach sustainable well integrity by increasing the contact stress at the cement–casing and the cement–formation interfaces to prevent fluid migration and the propagation of cracks.
Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads
Authors: Pearman William S , Freed Nikki E , Silander Olin K
Published: April 2020

Background The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly increasing popularity of this approach, a large number of computational tools and pipelines are available for analysing metagenomic data. However, the majority of these tools have been designed and benchmarked using highly accurate short read data (i.e. Illumina), with few studies benchmarking classification accuracy for long error-prone reads (PacBio or Oxford Nanopore). In addition, few tools have been benchmarked for non-microbial communities. Results Here we compare simulated long reads from Oxford Nanopore and Pacific Biosciences with high accuracy Illumina read sets to systematically investigate the effects of sequence length and taxon type on classification accuracy for metagenomic data from both microbial and non-microbial communities. We show that very generally, classification accuracy is far lower for non-microbial communities, even at low taxonomic resolution (e.g. family rather than genus). We then show that for two popular taxonomic classifiers, long reads can significantly increase classification accuracy, and this is most pronounced for non-microbial communities. Conclusions This work provides insight on the expected accuracy for metagenomic analyses for different taxonomic groups, and establishes the point at which read length becomes more important than error rate for assigning the correct taxon.
Combined use of apatinib mesylate and vinorelbine versus vinorelbine alone in recurrent or metastatic triple-negative breast cancer: study protocol for a randomized controlled clinical trial
Authors: Wu Shuo , Zhang Liang , Li Huan , Xu Junnan , Jiang Cui , Sun Tao
Published: April 2020

Background: The emergence of new molecular targeted drugs provides new prospects for the treatment of advanced breast cancer; the future therapeutic trend includes chemotherapy combined with molecular targeted therapy. Apatinib mesylate, a novel, small anti-angiogenic agent, highly selectively inhibits the activity of vascular endothelial growth factor receptor-2 tyrosine kinase. Apatinib mesylate also blocks the signaling of vascular endothelial growth factor binding to its receptor, thereby strongly inhibiting tumor angiogenesis and exerting an anti-tumor effect. However, a randomized controlled clinical trial of apatinib combined with vinorelbine for triple-negative breast cancer (TNBC) has not been reported. We will compare the therapeutic effect of vinorelbine alone, or in combination with apatinib mesylate, in patients with recurrent or metastatic TNBC in North China who have received at least two drug treatments, including anthracyclines and taxanes.Methods/analysis: This study is a triple-blind, randomized, placebo-controlled, parallel-group clinical trial. We plan to include 238 female patients with locally recurrent or metastatic TNBC, admitted at the Liaoning Cancer Hospital & Institute, Northeast China. All enrolled patients will be randomized to oral vinorelbine alone (40 mg, thrice a week [Mondays, Wednesdays, and Fridays] in each 3-week cycle), or in combination with oral apatinib mesylate (500 mg, once daily in each 3-week cycle). Radiographic assessment will be performed every 6 weeks for 36 weeks, and every 9 weeks thereafter. The primary outcome is progression-free survival, and secondary outcomes include overall survival, disease control rate, objective response rate, and incidence of adverse events at grades 3 and 4, as defined by the National Cancer Institute Common Toxicity Criteria Version 4.0. Outcome measures will be evaluated at baseline (< 2 weeks before starting treatment), every 6 weeks during treatment, and at 4 weeks and every 3 months after treatment discontinuation.Discussion: Based on the data from this trial, we hope to identify a treatment plan that is suitable for female TNBC patients in Northeast China who have been treated with anthracyclines and taxanes.Trial registration: ClinicalTrials.gov (identifier: NCT03932526). Registered on April 30, 2019.
Nurses’ knowledge of pressure ulcer and its associated factors at Hawassa University Comprehensive Specialized Hospital Hawassa, Ethiopia, 2018.
Authors: Muhammed Ezedin Molla , Bifftu Berhanu Boru , Temachu Yemataw Zewdu , Walle Tarkie Abebe
Published: April 2020

Background: Pressure ulcer is largely avoidable, but its prevalence rate increased more than 80% in a thirteen years study. Nurses have a great position to advance best practices towards the prevention of pressure ulcers. Therefore they should be knowledgeable of the signs and symptoms of pressure ulcers, and preventive strategies to reduce its incidence, but there is limited evidence on nurses’ knowledge and its associated factors to prevent pressure ulcer in Ethiopia. Methods: A hospital-based cross-sectional study was conducted from March 25 – April 23/ 2018. A total of 356 nurses were selected by stratification with a simple random sampling technique. Pretested structured questionnaire with closed and open-ended questions was used to collect data. Frequency distribution and percentage were computed to describe each variable. Bivariate and multivariable logistic regression with a 95% confidence interval was also carried out to see the effect of each independent variable on the dependent variable and declared statistical significant association with P< 0.05. Result: The mean knowledge score of nurses was 25.22 out of 41 item questions. Fifty-two point five percent of nurses score above the mean. Males [AOR=0.44, 95% CI (0.26 – 0.73)], working a maximum of eight hours [AOR= 3.57, 95% CI (1.48 – 8.61), not having training [(AOR= 2.31, 95% CI (1.14 – 4.61)], Low salary [AOR= 3.47, 95% CI (1.03 – 11.67)] were significantly associated with inadequate knowledge. Conclusion: Generally a nurse's knowledge of pressure ulcer was inadequate. Being female, working less than or equal to eight hours, not having the training and low working salary are contributors to a low level of knowledge for pressure ulcer.
Increasing questionnaire response: evidence from a nested RCT within a longitudinal birth cohort study
Authors: Goodwin Michaela , Walsh Tanya , Whittaker William , Emsley Richard , Sutton Matthew , Tickle Martin , Kelly Michael , Pretty Iain
Published: April 2020

Background: High response rates are essential when questionnaires are used within research, as representativeness can affect the validity of studies and the ability to generalise the findings to a wider population. Aims: The study measured the response rate to questionnaires from a large longitudinal epidemiological study and sought to determine if any changes made throughout data collection had a positive impact on the response to questionnaires and readdressed any imbalance in response rates by participants’ levels of deprivation. Methods: Data were taken from a prospective, comparative study, designed to examine the effects of the reintroduction of water fluoridation on children’s oral health over a five-year period. Response rates were analysed for the first year of data collection. During this year changes were made to the questionnaire layout and cover letter to attempt to increase response rates. Additionally a nested randomised control trial compared the effect on response rates of three different reminders to complete questionnaires.Results: Data were available for 1824 individuals. Sending the complete questionnaire again to non responders resulted in the highest level of response (25%). A telephone call to participants was the only method that appeared to address the imbalance in deprivation, with a mean difference in deprivation score of 2.65 (95% CI -15.50 to 10.20) between the responders and non responders . Conclusions: Initially, low response rates were recorded within this large, longitudinal study giving rise to concerns about non-response bias. Resending the entire questionnaire again was the most effective way of reminding participants to complete the questionnaire. As this is a less labour intensive method than for example, calling participants, more time can then be spent targeting groups who are underrepresented In order to address these biases, data can be weighted in order to draw conclusions about the population.
Marital Status, An Independent Predictor for Survival of Gastric Neuroendocrine Neoplasm Patients: A Population-based, Propensity Score-matched Study
Authors: Zhou Yu-Jie , Lu Xiao-Fan , Zheng Kenneth I. , Wang Qi-Wen , Chen Jin-Nan , Zhang Qing-Wei , Yan Fang-Rong , Li Xiaobo
Published: April 2020

Background: Marital status proves to be an independent prognostic factor in a variety of cancers. However, its prognostic impact on gastric neuroendocrine neoplasms (G-NEN) has not been investigated.Methods: We identified 3947 G-NEN patients from the Surveillance, Epidemiology, and End Results (SEER) database. Meanwhile, propensity scores for marital status were used to match 506 unmarried patients with 506 married patients. We used Kaplan–Meier method and multivariate Cox regression to analyse the association between marital status and the overall survival (OS) and G-NEN cause-specific survival (CSS) before matching and after matching.Results: Married patients enjoyed better OS and CSS, compared with divorced/separated, single, and widowed patients. Multivariate Cox regression analysis indicated that unmarried status was associated with higher mortality hazards for both OS and CSS among G-NEN patients. Additionally, widowed individuals had the highest risks of overall and cancer-specific mortality compared to other unmarried groups in both males and females. Furthermore, marital status remained an independent prognostic and protective factor for both OS and CSS in 1:1 propensity score-matched analysis.Conclusion: Marital status was an independent prognostic factor for G-NEN. Meanwhile, widowed patients with G-NEN had the highest risk of death compared with single, married, and divorced/separated patients.
Resilient Health Care: a systematic review of conceptualisations, study methods and factors that develop resilience.
Authors: Iflaifel Mais HM , Lim Rosemary , Ryan Kath M , Crowley Clare
Published: April 2020

Background Traditional approaches to safety management in health care have focused primarily on counting errors and understanding how things go wrong. Resilient Health Care (RHC) provides an alternative complementary perspective of learning from incidents and understanding how, most of the time, work is safe. The aim of this review was to identify how RHC is conceptualised, described and interpreted in the published literature, to describe the methods used to study RHC, and to identify factors that develop RHC.Methods Electronic searches of PubMed, Scopus and Cochrane databases were performed to identify relevant peer-reviewed studies, and a hand search undertaken for studies published in books that explained how RHC as a concept has been interpreted, what methods have been used to study it, and what factors have been important to its development. Studies were evaluated independently by two researchers. Data was synthesised using a thematic approach.Results Thirty-six studies were included; they shared similar descriptions of RHC which was the ability to adjust its functioning prior to, during, or following events and thereby sustain required operations under both expected and unexpected conditions. Qualitative methods were mainly used to study RHC. Two types of data sources have been used: direct (e.g. focus groups and surveys) and indirect (e.g. observations and simulations) data sources. Most of the tools for studying RHC were developed based on predefined resilient constructs and have been categorised into three categories: performance variability and Work As Done, cornerstone capabilities for resilience, and integration with other safety management paradigms. Tools for studying RHC currently exist but have yet to be fully implemented. Effective team relationships, trade-offs and health care ‘resilience’ training of health care professionals were factors used to develop RHC. Conclusions Although there was consistency in the conceptualisation of RHC, methods used to study and the factors used to develop it, several questions remain to be answered before a gold standard strategy for studying RHC can confidently be identified. These include operationalising RHC assessment methods in multi-level and diverse settings and developing, testing and evaluating interventions to address the wider safety implications of RHC amidst organisational and institutional change.
Clinical audit in the Pediatric primary care office and overweight prevention in toddlers.
Authors: Limauro Raffaele , Gallo Patrizia , Cioffi Luigi , Antignani Angelo , Cioffi Valentina , Calella Patrizia , Valerio Giuliana
Published: April 2020

Background: Clinical audit is a process by which physicians or other health care professionals perform a regular and systematic review of their clinical practice and amend it, when necessary. An internal audit allows to review the activities carried out by professionals, in order to assess the appropriateness, effectiveness, efficiency and safety of the services provided. Aim of this study was to apply the process of clinical audit to the obesity/overweight care in toddlers. After the correction of the nutritional errors that were considered potentially responsible for the excess weight gain, the effect of the changes of dietary advice s on the frequency of overweight/obesity was assessed in a cohort of children aged 24-36 months. Methods: Three Italian primary care pediatricians set up the audit strategy by recognizing the high prevalence of overweight and obesity in the entire cohort of toddlers born in 2005, 2006 and 2007 (Pre-Audit group, age 24-36 months old) under their care. By reviewing their clinical practice, they changed the protocol of weaning and feeding up to 36 months, mainly reducing protein and sugar excess. The change involved the cohorts of toddlers born in the years 2010, 2011 and 2012 (Post-Audit group). Results: Change in the approach of pediatricians to children’s diet yielded a reduction of the frequency of overweight/obesity in children between 24 and 36 months of life from 26.3% in the Pre-Audit group to 13.9% in the Post-Audit group (p<0.0001). Conclusion: Clinical audit revealed high rates of obesity/overweight among toddlers. The practice developed a new strategy for nutritional counseling, which was effective in reducing the frequency of overweight/obesity in young children.
The diagnostic yield of intellectual disability: Combined whole genome low-coverage sequencing and medical exome sequencing
Authors: Wang Jun , Wang Yan , Wang Liwen , Chen Wangyang , Sheng Min
Published: April 2020

Background: Intellectual disability (ID) is a heterogeneous neurodevelopmental disorder with a complex genetic underpinning in its etiology. Chromosome microarray (CMA) is recommended as the first-tier diagnostic test for ID due to high detection rate of copy number variation (CNV). Methods: To identify an appropriate clinical detection scheme for ID in Han Chinese patients, whole genome low-coverage sequencing was performed as the first-tier diagnostic test, and medical exome sequencing (MES) as the second-tier diagnostic test for patients with negative results of CNVs.Results: A total of 19 pathogenic CNVs in 16/95(16.84%) ID patients and 10 pathogenic single-nucleotide variations (SNVs), including 6 novel mutations in 8/95(8.42%) ID patients were identified on whom no pathogenic CNVs were discovered. The detection rate of CNVs in ID with multiple congenital anomalies (MCA) subgroup was significantly higher than ID with autism spectrum disorders and other IDs subgroups. And the single-nucleotide variations showed a higher occurrence rate in the other IDs subgroup.Conclusions: There were differences in the diagnostic yields of different variation types among the three ID subgroups. Our findings provided a new perspective on appropriate clinical detection scheme in different ID subgroups based on statistically significant differences among the three ID subgroups. The application of whole genome low-coverage sequencing as the first-tier diagnostic test for ID with MCA subgroup and MES as the first-tier diagnostic test for other ID subgroup was considered as an efficient clinical detection scheme.
Examining correlations between opioid dispensing and opioid-related hospitalizations in Canada, 2007 - 2016
Authors: Jones Wayne , Kurdyak Paul , Fischer Benedikt
Published: April 2020

Background: High levels of opioid-related mortality, as well as morbidity, contribute to the excessive opioid-related disease burden in North America, induced by high availability of opioids. While correlations between opioid dispensing levels and mortality outcomes are well-established, fewer evidence exists on correlations with morbidity (e.g., hospitalizations).Methods: We examined possible overtime correlations between medical opioid dispensing and opioid-related hospitalizations in Canada, by province, 2007 – 2016. For dispensing, we examined annual volumes of medical opioid dispensing from a representative, stratified sample of retail pharmacies across Canada. Raw dispensing information for ‘strong opioids’ was converted into Defined Daily Doses per 1,000 population per day (DDD/1,000/day). Opioid-related hospitalization rates referred to opioid poisoning-related admissions by province, for fiscal years 2007-08 to 2016-17, drawn from the national Hospital Morbidity Database. We assessed possible correlations between opioid dispensing and hospitalizations by province using the Pearson product moment correlation; correlation values (r) and confidence intervals were reported.Results: Significant correlations for overtime correlations between population-levels of opioid dispensing and opioid-related hospitalizations were observed for three provinces: Quebec (r=0.87, CI: 0.49–0.97; p=0.002); New Brunswick (r=0.85;CI: 0.43–0.97; p=0.004) and Nova Scotia (r=0.78; CI:0.25–0.95; p=0.012), with Saskatchewan (r=0.073; CI:-0.07–0.91;p=0.073) featuring borderline significance.Conclusions: The correlations observed further contribute to evidence on opioid dispensing levels as a systemic driver of population-level harms. Notably, correlations were not identified principally in provinces with reported high contribution levels (>50%) of illicit opioids to mortality, which are not captured by dispensing data and so may have distorted potential effects due to contamination.