Local Installation Research Articles

NERDD: a web portal providing access to in silico tools for drug discovery.

The New E-Resource for Drug Discovery (NERDD) is a quickly expanding web portal focused on the provision of peer-reviewed in silico tools for drug discovery. NERDD currently hosts tools for predicting the sites of metabolism (FAME) and metabolites (GLORY) of small organic molecules, for flagging compounds that are likely to interfere with biological assays (Hit Dexter), and for identifying natural products and natural product derivatives in large compound collections (NP-Scout). Several additional models and components are currently in development. The NERDD web server is available at https://nerdd.zbh.uni-hamburg.de. Most tools are also available as software packages for local installation.

Pulsed Electrodeposition of Carbon Dioxide Reduction Electrocatalysts for Space Applications

Space programs around the globe have begun to consider the logistical demands of missions beyond the orbital neighborhood of Earth. Unlike local installations such as the International Space Station, long-range missions will not have the option to resupply critical materials from Earth. Thus, the development of capabilities for what is often termed "In-Situ Resource Utilization" (ISRU) have been a continuing focus of research through NASA and other agencies. One particular long-range mission of interest is to place human astronauts on Mars; the major component of the thin Martian atmosphere is carbon dioxide, making CO2 a natural input to ISRU technologies for production of carbon-containing materials. Production of mission consumables from in-situ Mars resources will be critical to enabling human exploration of Mars, in part by minimizing the number and size of descent/ascent vehicles. Potential ISRU products from CO2 include that seem likely to provide significant mission benefits with minimal infrastructure required are propellants (e.g., hydrocarbons), fuel cell reactants (e.g., formic acid, methanol, carbon monoxide), and life support consumables (e.g., oxygen). The first portion of this talk will comprise a high-level overview of the chemical transformations that can be imparted to CO2 via electrocatalysis on gas-diffusion electrodes (GDEs), in the form of a summary of literature reports on the catalytic performance of various single-metal and metal-alloy systems. The remainder will encompass an exposition of the electrocatalytic performance of tin and copper single-metal GDE electrocatalysts prepared by pulsed electrodeposition. These metals are well known for their ability to reduce carbon dioxide to formic acid and hydrocarbons/carbon monoxide, respectively, and are under active development to this end in numerous academic research groups and industrial entities. These experimental results clearly demonstrate the power and flexibility of the pulse/pulse-reverse electrodeposition approach to catalyst fabrication, as evidenced by the appreciable effects of the pulsed-waveform electrodeposition parameters on CO2 electroreduction product distribution and total current density.

Project-Based Learning Model Practicality on Local Network Devices Installation Subject

Abstract— The learning process in vocational high schools is the decisive factor for being able to give birth to vocational secondary education graduates that are in accordance with their competencies. The learning process will determine whether the learning goals will be achieved. This study aims to develop a project-based learning device on the subject of Local Network Devices Installation. The method used is the Instructional Development Institute (IDI) with processed data sourced from 2 teachers and 29 students. The result of this study is practical that a value of 77.87%. It is concluded that this model is very helpful in learning Local Network Device Installation and as a reference model for other subjects.

Thermal performance augmentation of metal foam infused phase change material using a partial filling strategy: An evaluation for fill height ratio and porosity

Infusion of a metal foam in a phase change material (PCM) used for a latent heat thermal energy storage (LHTES) system significantly improves the melting performance. The presence of metal foam in PCM, however, suppresses the natural convective transport, increases the cost, and depletes the TES capacity. An optimum thermal conductivity enhancer (TCE) density strategy is developed in the present study to determine the effective metal foam distribution and concentration. The primary objective of the strategy is the local installation of the metal foam mass at the high-temperature gradients region (high thermal potential) and elimination of the same at the region of low-temperature gradients (lower thermal potential) for the efficient use of the metal foam. Thus, the melting performance of the various fill height ratios (i.e. 0.25H, 0.5H, and 0.75H) and the metal foam porosities (0.97, 0.95, 0.92, and 0.90) are studied and comprehensively compared. To accomplish this, an in-house numerical code is developed using an enthalpy porosity approach supplemented with the local thermal non-equilibrium (LTNE) technique. Results show that the incorporation of the metal foam-PCM composite (MFPC) only at the lower portion of the enclosure enhances the total thermal transport. Further, the metal foam with the full height (H) and 0.75H require nearly the same total melting time and show that the total melting time increases as the fill height ratio further decreases. The influence of varying the porosities with the fixed fill height ratio of metal foam shows that if the porosity decreases, the total melting time decreases with a penalty of less TES capacity. By means of economic assessment, it is recommended that if the economy and TES capacity are major concerns of the thermal performance, a high porosity metal foam should be chosen with a compromise on the total melting time. Similarly, the LHTES systems targeting the higher melting rate can be designed with a low porosity metal foam, which increases the cost and reduces the TES capacity.

ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp.

BackgroundThe genus Paracoccidioides consists of thermodymorphic fungi responsible for Paracoccidioidomycosis (PCM), a systemic mycosis that has been registered to affect ~10 million people in Latin America. Biogeographical data subdivided the genus Paracoccidioides in five divergent subgroups, which have been recently classified as different species. Genomic sequencing of five Paracoccidioides isolates, representing each of these subgroups/species provided an important framework for the development of post-genomic studies with these fungi. However, functional annotations of these genomes have not been submitted to manual curation and, as a result, ~60–90% of the Paracoccidioides protein-coding genes (depending on isolate/annotation) are currently described as responsible for hypothetical proteins, without any further functional/structural description.Principal findingsThe present work reviews the functional assignment of Paracoccidioides genes, reducing the number of hypothetical proteins to ~25–28%. These results were compiled in a relational database called ParaDB, dedicated to the main representatives of Paracoccidioides spp. ParaDB can be accessed through a friendly graphical interface, which offers search tools based on keywords or protein/DNA sequences. All data contained in ParaDB can be partially or completely downloaded through spreadsheet, multi-fasta and GFF3-formatted files, which can be subsequently used in a variety of downstream functional analyses. Moreover, the entire ParaDB environment has been configured in a Docker service, which has been submitted to the GitHub repository, ensuring long-term data availability to researchers. This service can be downloaded and used to perform fully functional local installations of the database in alternative computing ecosystems, allowing users to conduct their data mining and analyses in a personal and stable working environment.ConclusionsThese new annotations greatly reduce the number of genes identified solely as hypothetical proteins and are integrated into a dedicated database, providing resources to assist researchers in this field to conduct post-genomic studies with this group of human pathogenic fungi.

Doc2Hpo: a web application for efficient and accurate HPO concept curation.

We present Doc2Hpo, an interactive web application that enables interactive and efficient phenotype concept curation from clinical text with automated concept normalization using the Human Phenotype Ontology (HPO). Users can edit the HPO concepts automatically extracted by Doc2Hpo in real time, and export the extracted HPO concepts into gene prioritization tools. Our evaluation showed that Doc2Hpo significantly reduced manual effort while achieving high accuracy in HPO concept curation. Doc2Hpo is freely available at https://impact2.dbmi.columbia.edu/doc2hpo/. The source code is available at https://github.com/stormliucong/doc2hpo for local installation for protected health data.

VirtualDose-IR: a cloud-based software for reporting organ doses in interventional radiology

A cloud-based software, VirtualDose-IR (Virtual Phantoms Inc., Albany, New York, USA), designed to report organ doses and effective doses for a diverse patient population from interventional radiology (IR) procedures has been developed and tested. This software is based on a comprehensive database of Monte Carlo-generated organ dose built with a set of 21 anatomically realistic patient phantoms. The patient types included in this database are both male and female people with different ages reflecting reference adults, obese people with different BMIs and pregnant women at different gestational stages. Selectable parameters such as patient type, tube voltage, filtration thickness, beam direction, field size, and irradiation site are also considered in VirtualDose-IR. The software has been implemented using the ‘Software as a Service (SaaS)’ delivery concept permitting simultaneous multi-user, multi-platform access without requiring local installation. The patient doses resulting from different target sites and patient populations were reported using the VirtualDose-IR system. The patient doses under different source to surface distances (SSD) and beam angles calculated by VirtualDose-IR and Monte Carlo simulations were compared. For most organs, the dose differences between VirtualDose-IR results and Monte Carlo results were less than 0.3 mGy at 15 000 mGy * cm2 kerma-area product (KAP). The organ dose results were compared with measurement data previously reported in literatures. The doses to organs that were located within the irradiation field match closely with experimental measurement data. The differences in the effective dose values between calculated using VirtualDose-IR and those measured were less than 2.5%. The dose errors of most organs between VirtualDose-IR and literature results were less than 40%. These results validate the accuracy of organ doses reported by VirtualDose-IR. With the inclusion of pre-specified clinical IR examination parameters (such as beam direction, target location, field of view and beam quality) and the latest anatomically realistic patient phantoms in Monte Carlo simulations, VirtualDose-IR provides users with accurate dose information in order to systematically compare, evaluate, and optimize IR plans.

Thermal transport augmentation in latent heat thermal energy storage system by partially filled metal foam: A novel configuration

Abstract Thermal transport augmentation in latent heat thermal energy storage (LHTES) system by local installation of metal foam-phase change material (PCM) composite is presented in the current work. The study highlights an optimal concentration and position of metal foam-PCM composite (MFPC) to elevate thermal performance without altering an overall melting time. Thus, a novel configuration MFPC is proposed according to the optimum thermal conductivity enhancer (TCE) density, a criterion defined based on the temporal variation of local temperature gradient during the melting process. The fundamental principle of the criterion is positioning the metal foam only at the maximum thermal potential region for the effective utilization efficiency of the metal foam. A numerical code based on a local thermal non-equilibrium coupled enthalpy porosity approach is developed and validated. The numerical results showed that the proposed configuration with the provision of MFPC at a high thermal potential region alleviates local conductive transport with enhancement in the overall melting rate. It is seen that the withdrawal of metal mass at low thermal potential region encompasses the beneficial influence of natural convective transport, which is observed to be impeded in the previous configuration. The total melting time is observed to be equal for the proposed configuration when compared to the LHTES with the full volume of metal foam. The elimination of metal mass can increase the mass of PCM and thermal energy storage capacity. Additionally, it can assist to reduce weight and economy of the LHTES system.

ПРОБЛЕМЫ ОБЕСПЕЧЕНИЯ НАСЕЛЕНИЯ БОХТАРСКОГО РЕГИОНА ХАТЛОНСКОЙ ОБЛАСТИ ДОБРОКАЧЕСТВЕННОЙ ПИТЬЕВОЙ ВОДОЙ

Objective: To study the state of providing safe drinking water to the population of the Bohkhtar area of Khatlon region Methods: The objects of the study were: sources of drinking water supply, centralized systems of household and drinking water supply, water networks of 15 districts of the Bokhtar area. The hygienic assessment of drinking water sources, centralized water systems, sanitation zones and the quality of drinking water was carried out in accordance with Tajikistan’s water legislation. Results: The Bokhtar area population for 01.01.2019 is 2126494 people. Only 30% of the population of the region is provided with piped drinking water, and another part of the population (70%) use water from open water sources (rivers, canals, aryks, hauzi, etc.), therefore, there is high incidence of acute intestinal infections, which is more common in remote districts of rural areas. Of the total number of 125 functioning water pipes, 63% do not fully comply with sanitary regulations and norms. Water treatment and decontamination system are not implemented. The wear and breeding of water supply networks today fluctuates between 60-80%. It should be noted that about 40% of the population of the Bokhtar area uses water from irrigation canals that flow through their territory and are the main source of drinking water. Conclusion: In the cities and districts of the Bokhtar area, the issue of providing the population with good-quality drinking water is still low, especially in remote areas. Its solution is related to the implementation of a set of measures, such as: the improvement of water facilities, the construction and reconstruction of water pipes, the establishment of modern technologies to transport and purify water, to use local installations for water treatment, treatment and disposal, to carry out informational work with the population. Keywords: Bokhtar area, population, water supply problem, quality of drinking water, state of water pipes.

English

The photovoltaic (PV) lifetime and the return-on-investment for local PV system installation rely on long-term device performance. Understanding the efficient degradation behavior under a given set of environmental conditions is, therefore, a primary goal for experimental research and economic analysis. The modules were characterized with measurement of their I-V features under similar outdoor condition. Moreover, measurement of different meteorological parameters like humidity and temperature is done from the weather station. The present study aims to measure electrical characteristics (Isc, Voc, Pmax and FF) in monocrystalline and amorphous silicon modules exposed for 5 years in a sub-oceanique climate in Cologne. The results show the Pmax of monocrystalline silicone has more degradation (3.41%/year) than the amorphous silicon (1.76%/year).   Key words: PV module, amorphous, crystalline, degradation.

56 Spatial analysis of transcriptome changes in porcine endometrium on Day 14 of pregnancy

During the conception cycle, the embryo undergoes a series of developmental processes including cell division, cellular reorganization, and oestrogen secretion before attaching to the uterine epithelium. The uterine endometrium is complex and consists of various layers and cell types [i.e. luminal epithelium (LE), glandular epithelium (GE), blood cells (B), and stromal areas (S)]. The objective of this study was to characterise the complex transcriptome changes in porcine endometrium during the time of conceptus attachment with respect to localization in different endometrial cell types. RNA-sequencing (RNA-Seq) was conducted for LE, GE, B, and S samples isolated from endometrial tissue collected on Day 14 of pregnancy and the oestrous cycle, respectively (each group n=4), by laser capture microdissection (PALM LCM microscope, Zeiss, Jena, Germany). Total RNA was isolated (RNA integrity number>6.5) and used for the preparation of 32 RNA-seq libraries (Ovation SoLo RNA-Seq System, NuGEN Technologies, San Carlos, CA, USA). Multiplexed (barcode-tagged) libraries were run on an Illumina HiSEqn 2500 (Illumina, San Diego, CA, USA). The obtained sequence data were analysed with a RNA-Seq data analysis pipeline on a local Galaxy server installation. The resulting read counts were used for statistical analysis in EdgeR to identify differentially expressed genes (DEG). Furthermore, an RNA-seq dataset for complete Day 14 endometrial tissue samples from a previous study was analysed using the same pipeline. A total of 14297 genes were detectable in complete endometria, and 12000, 11903, 11094, and 11933 genes in LE, GE, B, and S, respectively. Differential expression analysis was performed between the pregnant and the cyclic nonpregnant group for each cell type and the complete tissue. The highest number of DEG was found for LE (1410) when compared with GE, B, and S (800, 1216, and 384, respectively). In total, 3262 DEG were obtained for the complete tissue between pregnant and nonpregnant gilts. The DEG were assigned to Gene Ontology (GO) terms to characterise overrepresented functional categories and pathways specific for the individual endometrial compartments. The GO classification revealed that most DEG in LE were involved in cell communication, such as ‘extracellular exosome’, ‘extracellular vesicle’, ‘homeostatic process’, whereas the ‘response to organic substance’ and ‘regulation of cell migration’ categories were enriched in GE. In blood vessels, categories such as ‘membrane-bounded vesicle’, ‘cell junction’, ‘cell development’, ‘cell adhesion’ and ‘blood vessel morphogenesis’ were found as overrepresented, whereas in stromal regions, most DEG were assigned to ‘cell communication’ and ‘secretion’. These results confirmed the hypothesis that conceptus signals induce specific transcriptomic regulations in the endometrial compartments/cell types related to their functions during recognition of pregnancy adding a new level of spatial gene expression regulation to endometrial transcriptome analysis.

The Impact of Mechanically-Imposed Shear on Clogging, Fouling and Energy Demand for an Immersed Membrane Bioreactor.

The impact of the application of mechanically-imposed shear on the propensity for fouling and clogging (or “sludging”—the agglomeration of sludge solids in the membrane channel) of an immersed flat sheet (iFS) membrane bioreactor (MBR) was studied. The bench-scale test cell used contained a single flat sheet fitted with a crank and motor to allow the membrane to be oscillated (or reciprocated) vertically at a low rate (20 RPM). The membrane was challenged with sludge samples from a local MBR installation treating petroleum industry effluent, the sludge having previously been demonstrated as having a high sludging propensity. Sludging was measured by direct visual observation of membrane surface occlusion by the agglomerated solids, with fouling being notionally represented by the rate of transmembrane pressure increase. Results demonstrated membrane reciprocation to have a more beneficial impact on sludging amelioration than on suppressing fouling. Compared with the stationary membrane, sludging was reduced by an average of 45% compared with only 13% for fouling suppression at the reference flux of 15 L·m−2·h−1 applied. The specific energy demand of the mechanical shear application was calculated as being around 0.0081 kWh·m−3, significantly lower than values reported from a recent pilot scale study on a reciprocated immersed hollow fibre MBR. Whilst results appear promising in terms of energy efficiency, it is likely that the mechanical complexity of applying membrane movement would limit the practical application to low flows, and a correspondingly small number of membrane modules.

Towards systematic, data-driven validation of a collaborative, multi-scale model of Caenorhabditis elegans.

The OpenWorm Project is an international open-source collaboration to create a multi-scale model of the organism Caenorhabditis elegans At each scale, including subcellular, cellular, network and behaviour, this project employs one or more computational models that aim to recapitulate the corresponding biological system at that scale. This requires that the simulated behaviour of each model be compared with experimental data both as the model is continuously refined and as new experimental data become available. Here we report the use of SciUnit, a software framework for model validation, to attempt to achieve these goals. During project development, each model is continuously subjected to data-driven 'unit tests' that quantitatively summarize model-data agreement, identifying modelling progress and highlighting particular aspects of each model that fail to adequately reproduce known features of the biological organism and its components. This workflow is publicly visible via both GitHub and a web application and accepts community contributions to ensure that modelling goals are transparent and well-informed.This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.

Hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.

The Human Genome Variation Society (HGVS) nomenclature guidelines encourage the accurate and standard description of DNA, RNA, and protein sequence variants in public variant databases and the scientific literature. Inconsistent application of the HGVS guidelines can lead to misinterpretation of variants in clinical settings. Reliable software tools are essential to ensure consistent application of the HGVS guidelines when reporting and interpreting variants. We present the hgvs Python package, a comprehensive tool for manipulating sequence variants according to the HGVS nomenclature guidelines. Distinguishing features of the hgvs package include: (1) parsing, formatting, validating, and normalizing variants on genome, transcript, and protein sequences; (2) projecting variants between aligned sequences, including those with gapped alignments; (3) flexible installation using remote or local data (fully local installations eliminate network dependencies); (4) extensive automated tests; and (5) open source development by a community from eight organizations worldwide. This report summarizes recent and significant updates to the hgvs package since its original release in 2014, and presents results of extensive validation using clinical relevant variants from ClinVar and HGMD.

Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services.

Database identifier mapping services are important to make database information interoperable. BridgeDb offers such a service. Available mapping for BridgeDb link 1. genes and gene products identifiers, 2. metabolite identifiers and InChI structure description, and 3. identifiers for biochemical reactions and interactions between multiple resources that use such IDs while the mappings are obtained from multiple sources. In this study we created BridgeDb mapping databases for selections of genes-to-variants (and variants-to-genes) based on the variants described in Ensembl. Moreover, we demonstrated the use of these mappings in different software tools like R, PathVisio, Cytoscape and a local installation using Docker. The variant mapping databases are now described on the BridgeDb website and are available from the BridgeDb mapping database repository and updated according to the regular BridgeDb mapping update schedule.

Customizing Stata Graphs made Easy (Part 1)

The overall look of Stata's graphs is determined by so-called scheme files. Scheme files are system components; that is, they are part of the local Stata installation. In this article, I argue that style settings deviating from default schemes should be part of the script producing the graphs, rather than being kept in separate scheme files, and I present a simple tool called grstyle that supports such practice.

BED: a Biological Entity Dictionary based on a graph data model.

The understanding of molecular processes involved in a specific biological system can be significantly improved by combining and comparing different data sets and knowledge resources. However, these information sources often use different identification systems and an identifier conversion step is required before any integration effort. Mapping between identifiers is often provided by the reference information resources and several tools have been implemented to simplify their use. However, most of these tools do not combine the information provided by individual resources to increase the completeness of the mapping process. Also, deprecated identifiers from former versions of databases are not taken into account. Finally, finding automatically the most relevant path to map identifiers from one scope to the other is often not trivial. The Biological Entity Dictionary (BED) addresses these three challenges by relying on a graph data model describing possible relationships between entities and their identifiers. This model has been implemented using Neo4j and an R package provides functions to query the graph but also to create and feed a custom instance of the database. This design combined with a local installation of the graph database and a cache system make BED very efficient to convert large lists of identifiers.

Customizing Stata graphs made easy

In Jann (2018b, Stata Journal 18: 491–502), I presented a command called grstyle that simplifies changing the default look of Stata graphs. The command, however, still relies on idiosyncratic scheme file syntax, which may not be well known to many users. In this article, I therefore present an extension called grstyle set that automates the creation of sets of scheme file entries for a number of potentially useful adjustments, without much typing and without requiring much knowledge about scheme file syntax. Covered topics include, for example, the rendering of the background and coordinate system, the placement and look of the legend, the assignment of colors, symbols, and line patterns, and the assignment of relative or absolute sizes.

MakeCode and CODAL: intuitive and efficient embedded systems programming for education

Across the globe, it is now commonplace for educators to engage in the making (design and development) of embedded systems in the classroom to motivate and excite their students. This new domain brings its own set of unique requirements. Historically, embedded systems development requires knowledge of low-level programming languages, local installation of compilation toolchains, device drivers, and applications. For students and educators, these requirements can introduce insurmountable barriers. We present the motivation, requirements, implementation, and evaluation of a new programming platform that enables novice users to create software for embedded systems. The platform has two major components: 1) Microsoft MakeCode ( www.makecode.com ), a web app that encapsulates an entire beginner IDE for microcontrollers; and 2) CODAL, an efficient component-oriented C++ runtime for microcontrollers. We show how MakeCode and CODAL provide an accessible, cross-platform, installation-free programming experience for the BBC micro:bit and other embedded devices.

BED: a Biological Entity Dictionary based on a graph data model

The understanding of molecular processes involved in a specific biological system can be significantly improved by combining and comparing different data sets and knowledge resources. However, these information sources often use different identification systems and an identifier conversion step is required before any integration effort. Mapping between identifiers is often provided by the reference information resources and several tools have been implemented to simplify their use. However, most of these tools do not combine the information provided by individual resources to increase the completeness of the mapping process. Also, deprecated identifiers from former versions of databases are not taken into account. Finally, finding automatically the most relevant path to map identifiers from one scope to the other is often not trivial. The Biological Entity Dictionary (BED) addresses these three challenges by relying on a graph data model describing possible relationships between entities and their identifiers. This model has been implemented using Neo4j and an R package provides functions to query the graph but also to create and feed a custom instance of the database. This design combined with a local installation of the graph database and a cache system make BED very efficient to convert large lists of identifiers.