DeePVP: Identification and classification of phage virion protein using deep learning

The poor annotation of phage virion protein (PVP) is the bottleneck of many areas of viral research, such as viral phylogenetic analysis, viral host identification and antibacterial drug design. Because of the high diversity of the PVP sequences, the PVP annotation remains a great challenging bioinformatic task. Based on deep learning, we present DeePVP that contains a main module and an extended module. The main module aims to identify the PVPs from non-PVP over a phage genome, while the extended module can further classify the predicted PVP into one of the ten major classes of PVP. Compared with the state-of-the-art tools that can distinguish PVP from non-PVP, DeePVP's main module performs much better, with an F1-score 9.05% higher in the PVP identification task. Compared with PhANNs, a tool that can further classify the predicted PVP into a specific class, the overall accuracy of DeePVP's extended module is approximately 3.72% higher in the PVP classification task. Two application cases on the genome of mycobacteriophage PDRPxv and Escherichia phage HP3 show that the predictions of DeePVP are much more reliable and can better reveal the compact PVP-enriched region, which may be conserved during the viral evolution process, over the phage genome.

Pembangunan Aplikasi Pengelolaan Data pada Rumah Sakit Berbasis Web

Hospital has a variety of facilities and services. Every day there are transactions recorded by the hospital in the form of documentation such as excel. Over time, if the transactions increase, the files that will be stored will be more and more large. Therefore, a website was created that can make it easier to manage data from these files. The web application is created using PHP and integrates with the MySQL database. The main module of the web application created is to import data from an excel file. The expected results from making this website are to make it easier for employees to manage data and view information in the form of tables or graphs. Data collection methods using observation, through interviews with the person in charge from hospital by giving a questionnaire about the interface of the application. Assessment of the results of interface improvements using a questionnaire from Post-Study System Usability Questionnaire version three, totalling 16 questions. The purpose of the User Interface and User Experience analysis is to assess and serve as a guide for improving the display that has been made whether it is in accordance with the standards requested by the hospital.

SwissPedData: Standardising hospital records for the benefit of paediatric research

Background Improvement of paediatric healthcare is hampered by inefficient processes of generating new evidence. Clinical research often requires extra encounters with patients, is costly, takes place in an artificial situation with a biased selection of patients, and entails long delays until new evidence is implemented into health care. Electronic health records (EHR) contain detailed information on real patients and cover the entirety of patients. However, the use of EHR for research is limited because they are not standardized between hospitals. This leads to disproportionate amounts of work for extracting data of interest and frequently data are incomplete and of poor quality. Aims SwissPedData aims to lay the foundation for a paediatric learning health system in Switzerland by facilitating EHR-based research. In this project, we aimed to assess the way routine clinical data are currently recorded in large paediatric clinics in Switzerland and to develop a national EHR-based common data model (CDM) that covers all processes of routine paediatric care in hospitals. Methods A taskforce of paediatricians from large Swiss children's hospitals reviewed the current status of routine data documentation in paediatric clinical care and the extent of digitalization. We then used a modified Delphi method to reach a broad consensus on a national EHR-based CDM. Results All Swiss children's hospitals use EHR to document some or all aspects of care. 119 paediatricians, representing eight hospitals and all paediatric subspecialties, participated in an extended Delphi process to create SwissPedData. The group agreed on a national CDM that comprises a main module with general paediatric data and sub-modules relevant to paediatric subspecialties. The data dictionary includes 336 common data elements (CDEs): 76 in the main module on general paediatrics and between 11 and 59 CDEs per subspecialty module. Among these, 266 were classified as mandatory, 52 as recommended and 18 as optional. Conclusion SwissPedData is a CDM for information to be collected in EHR of Swiss children's hospitals. It covers all care processes including clinical and paraclinical assessment, diagnosis, treatment, disposition and care site. All participating hospitals agreed to implement SwissPedData in their clinical routine and clinic information systems. This will pave the way for a national paediatric learning health system in Switzerland that enables fast and efficient answers to urgent clinical questions by facilitating high-quality nationwide retrospective and prospective observational studies and recruitment of patients for nested prospective studies and clinical trials.

SHOOT FORMATION OF EPILOBIUM HIRSUTUM L. IN CONNECTION WITH THE ADAPTATION OF HERBS OF THE SEASONAL CLIMATE TO THE CONDITIONS OF VARIABLE HUMIDIFICATION / WATERING

One of the fundamental problems of modern biology is the identification of adaptations of organisms to existence in different environments of the biosphere, the mechanisms and methods of the formation of their adaptations. A comparative analysis of shoot formation and ontogenesis of individuals makes it possible to reveal these features in plant biomorphs, including during the development of reservoirs by herbs by mesophytes. The article describes the shoot formation of the hygromesophyte Epilobium hirsutum L. The development and structural-functional zoning of shoots were assessed from the standpoint of modular organization and compared with the peculiarities of shoots formation in mesophytic and hydrophyte grasses. Shown: their similarity with monocarpic shoots of mesophytic herbs at the initial stages; further prolongation in the form of basipetal development through heterochronies and heterotopies with the development of lateral sylleptic shoots as in hydrophytes; increasing the area of the assimilating surface of an individual and ensuring the autonomy of individual shoot systems due to this with early morphological disintegration of the individual. It is proposed to distinguish the following stages in the development of the terrestrial part of the shoot system: vegetative uniaxial shoot - monocarpic shoot - disjunctive system of monopodial shoot - synflorescence system (double heterothetical frondose-frondular brush) at the shoot apex and replacement shoots in the transitional phase of its development in the zone of renewal , broken by the middle zone of inhibition, is more multicomponent and branched in comparison with those in mesohygrophytes like Veronica longifolia L., but less complexity than in hydrophytes - the aquatic form of V. anagallis-aquatica L. It is noted that the early transformation of the universal module (monocarpic shoot) into the main module (the shoot system formed on its basis) is provided by polyvariance in the development of leaf rudiments and axillary structures of elementary modules (elementary metameres) in connection with the conditions of the location of the apex and demonstrates possible mechanisms of adaptation of flowering plants with a sympodial long-shoot model of shoot formation to life in water bodies: abbreviation of ontogeny of an individual and monocarpity of ramet with polycarpicity of an organism (prolongation of ontogeny of an individual).

Genetic Characteristics of Systematic Juvenile Idiopathic Arthritis and The Bioinformatics Basis for Treatment

Objective Systemic Juvenile Idiopathic Arthritis (sJIA) is a distinctive subtype of Juvenile Idiopathic Arthritis (JIA). The pathogenesis of sJIA is still unclear with the treatment options limited. Although previous bioinformatics analyses have identified some genetic factors underlying sJIA, these studies were mostly single center with a small sample size and the results were often inconsistent. Herein, we combined two datasets of GSE20307 and GSE21521 and select the matrix of patients diagnosed as sJIA in it for further analysis. Methods The GSE20307 and GSE21521 matrixs downloaded from the Gene Expression Omnibus (GEO) were analyzed using online-tool GEO2R, Venny, Metascape, STRING, and Cytoscape to identify differentially expressed genes (DEGs), enrichment pathways, protein-protein interaction (PPI), main Module and hub genes between sJIA individuals and healthy controls. Results A total of 289 overlapping genes (consisting of 41 downregulated genes and 248 upregulated genes) were identified. Hub genes were primarily related to erythropoiesis. And the KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of overlapping DEGs were maily involved in Malaria and non-small cell lung cancer. Besides, DEGs in main module were involved in ubiquitin mediated proteolysis. Conclusions our study suggests that the erythropoiesis signature indeed exists in sJIA similar to previous reports. And combining previous research and our results, we provide a basis for the application of proteasome inhibitors, hydroxychloroquine and kinase inhibitors in patients with sJIA from the perspective of bioinformatics.

TCDNet: Trilateral Change Detection Network for Google Earth Image

Change detection is a very important technique for remote sensing data analysis. Its mainstream solutions are either supervised or unsupervised. In supervised methods, most of the existing change detection methods using deep learning are related to semantic segmentation. However, these methods only use deep learning models to process the global information of an image but do not carry out specific trainings on changed and unchanged areas. As a result, many details of local changes could not be detected. In this work, a trilateral change detection network is proposed. The proposed network has three branches (a main module and two auxiliary modules, all of them are composed of convolutional neural networks (CNNs)), which focus on the overall information of bitemporal Google Earth image pairs, the changed areas and the unchanged areas, respectively. The proposed method is end-to-end trainable, and each component in the network does not need to be trained separately.

DEVELOPMENT OF GIS DATABASE AND FACILITY MANAGEMENT SYSTEM: ASSET AND SPACE IN UKM

Facility Management (FM) has becoming a crucial aspect in providing better service to the client/tenant or public as well as to minimize the maintenance cost. Group of buildings bounded by a defined boundary/spatial space such as a college, university, city or even a country have to manage their assets and space systematically with maximum potential/usage and minimum maintenance cost. Incorporating GIS plays innovative and effective role in asset and space FM especially. There are a lot of research and suggestions for it, but implementation is still average and quite new in Malaysia. University Kebangsaan Malaysia (UKM Bangi) has taken initiative to perform such idea with a full scale implementation. Currently, UKM utilizes GIS in nine modules, where one of the main module called SEPADU, an internal use module system for asset and space information system. This paper describes the implementation of integrated GIS solution in information system. Spatial data acquisition, database development and system for FM will be discussed in this paper.

A method of identifying the durability indicator of microcircuitry

The Aim of this paper is to ensure the compliance of the requirements for the durability of long-life space technology with the fact that regulatory documents for microcircuitry do not contain durability indicators. Thus, in accordance with OST V 11 0998-99, the dependability requirements only contain indicators of reliability and storability. On the other hand, along with the requirements for reliability and storability, the dependability specifications for space technology feature requirements for durability in operation that are usually equal to the gamma-percentile life Тl.г = 100 000 h and more if г = 99.9%. Therefore, for such long-life systems one must define durability indicators that are now absent in the technical conditions or other delivery documents. The definition of such indicators by means of durability testing is costly and time-consuming. Thus, an analytical method was proposed, according to which the lower estimate boundary for the gamma-percentile life Тl.г of microcircuitry can be obtained by equalizing the probability of no-failure of the microcircuit over time Тl.г to the probability of non-occurrence of life failures that put the microcircuit into the limit state, upon which its operation shall be terminated. In this case, in order to obtain Тl.г = 99.9% = 100 000 h, a nonredundant microcircuit or another product must have the failure rate of 10-8 1/h. In the case of more complex microcircuits, it does not appear to be possible to obtain the required value of Тl.г=99.9% = 100 000 h. The paper suggests extending the use of the proposed method of durability indicator identification taking into consideration the fact that in the systems under consideration the failure of any one product is not allowed and, in this view, various ways of ensuring equipment redundancy are used. Hot standby is understood as a redundancy with one or several backup modules that operate similarly to the main module. Warm standby is understood as a redundancy with one or several modules that operate at a lower rate that the main module until they start functioning as the main module. The paper considers a number of redundancy architectures of a complex microcircuit that enable the specified high durability indicators. The formula was obtained for calculation of the durability indicator for more general cases, when the microcircuit is part of a module backed-up by another identical module. In this case, if the second module is in warm standby, a high durability indicator can be ensured for the microcircuit. If the second module is in hot standby, the specified durability indicator of the microcircuit is not ensured. The considered method of durability indicator identification can be used for other redundancy architectures of modules in a system.

Groundwater flow simulation through the application of the FREEWAT modeling platform

FREEWAT is a free and open source QGIS-integrated platform, developed to simulate several hydrological processes by combining the capabilities of geographic information system (GIS) for geo-processing and post-processing tools with several codes of the well-known USGS MODFLOW ‘family’. FREEWAT platform was applied for the groundwater flow simulation of a coastal aquifer system, located in northern Greece. The simulation was conducted using the MODFLOW_2005 code, the Observation Analysis Tool (a FREEWAT module facilitating the integration of time series observations into modeling), while the UCODE_2014 code was used as the main module for the sensitivity analysis and parameter estimation. The statistics used include composite scaled sensitivities, parameter correlation coefficients, and leverage. The simulation of the investigated aquifer system was found to be satisfactory, indicating that the simulated level values were slightly greater than the observed values after the optimization.

A semi-automatic dispenser for solid and liquid food in aquatic facilities

We present a novel, low-footprint and low-cost semi-automatic system for delivering solid and liquid food to zebrafish, and more generally to aquatic animals raised in racks of tanks. It is composed of a portable main module equipped with a contactless reader that adjusts the quantity to deliver for each tank, and either a solid food module or a liquid food module. Solid food comprises virtually any kind of dry powder or grains below two millimeters in diameter, and, for liquid-mediated food, brine shrimps (Artemia salina) and rotifers (Rotifera) have been successfully tested. Real-world testing, feedback and validation have been performed in a zebrafish facility for several months. In comparison with manual feeding this system mitigates the appearance of musculoskeletal disorders among regularly-feeding staff, and let operators observe the animals’ behavior instead of being focused on quantities to deliver. We also tested the accuracy of both humans and our dispenser and found that the semi-automatic system is much more reliable, with respectively 7-fold and 84-fold drops in standard deviation for solid and liquid food.