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PregSS: Pregnancy Surveillance System Using Ontology for Interoperability
No full textPregSS: Pregnancy Surveillance System is an information system catering to the maternal care of women in barangay health centers in the Philippines. Since the maternal mortality rate of the country just increased prior the execution of this study, this aims to increase health care coverage by: being web-based, providing alerts on the patient’s health risks while recommending the level of care, also, generating monthly reports on maternal health indicators, and finally, incorporating an ontology for interoperability with other possible health services. This is achieved by mapping an existing medical ontology, named OpenGALEN, to the local database through the use of an RDF (Resource Description Framework)-to-RDB (Relational Database) mapping tool called D2RQ
Physic nut (Jatropha curcas) seed cake extract downregulates heat shock protein 70 expression in zebrafish (Danio rerio) liver.
No full textThe use of Jatropha curcas in biodiesel production is one of the emerging alternative sources of renewable energy. However, the extraction process leaves a seed cake waste and the lack of disposal protocols poses serious threat to ecosystems. This study aims to determine the toxicity of the seed cake extract to zebrafish through the analysis of heat shock protein 70 expression. The median lethal concentration (LC50) was first determined through an acute toxicity test coupled with probit analysis. For the HSP70 induction test, fishes were subjected to a nonexposed setup and sub-lethal concentration setups of detoxified, washed, and untreated seed cake. RNA was isolated and reverse transcribed followed by polymerase chain reaction and gel profiling. Results indicate an LC50 of 0.172% (w/v) or 1.72 g/L. The heat shock induction test showed a significant downregulation of HSP70 expression in fishes exposed to washed and untreated setups. This under-expression may be attributed to phytochemicals such as lectins which have been noted to interact with HSP70. Furthermore, mRNA levels in the detoxified setup have no significant difference with the non-exposed setup, possibly indicating a successful inactivation of toxic phytochemicals in the seed cake. Moreover, the present study shows that downregulation of HSP70 is also an indicator of stress, and low HSP70 levels may lead to decreased resistance to stress-inducing agents
VirHoLex 2.0 (Virus-Host Interaction Lexicon)
No full textElepaño et al. has successfully accomplished all features and functional requirements
necessary for the development of VirHoLex. However, the system was not thoroughly tested
after each module was integrated, generating a number of system bugs as a result. Though
Morales has partially refactored VirHoLex, specifically the Virho References and Virho
Hotspots modules, the modifications done were not sufficed to make the codes maintainable.
In order to preserve the credibility of the system, Struts framework was incorporated
into the program structure of VirHoLex after the system was debugged. Struts is built on
MVC design pattern that promotes separation of concerns, that is, separating business logic
from the user's view. The whole VirHoLex was refactored a) to remove jumbled and
redundant codes; b) to make the codes reusable and modular; and c) to promote programming
style uniformity for all modules. This will allow the future developers to easily understand
and modify the system.
In addition, the use of Subversion and Mantis Bug Tracking tool is pertinent to the
study since it permits the developers to easily track down the history of file changes, and to
have a proper documentation of system bugs and new features respectively. More
importantly, the second version of VirHoLex was deployed on MaxPlanck server so that
virologists can fully utilize the system
Woody plant species co-occurrence in the lowland forests of Puerto Princesa Subterranean River National Park, Palawan.
No full textThe Puerto Princesa Subterranean River National Park (PPSRNP) hosts an interestingly rich floral diversity (CEFP, 2001) in its lowland forest. In this forest, plant assemblages exist that are possibly governed by co-occurrence. To test for this, a null model analysis was implemented. A 2 km transect line was laid along the jungle trail of PPSRNP, which was divided into 40 sampling plots with 50-m interval. In each point, the trees were surveyed using a modified Point Center-Quarter Method wherein the diameter at breast height (DBH) and the global positioning system (GPS) coordinates of each trees were obtained. A matrix of the presence or absence of species in each sampling site was constructed and was analyzed for species co-occurrence using EcoSim version 7 (Gotelli and Entsminger, 2004). The results from the C-score, Combo, Checker and V-ratio indices show that woody plant species in the lowland forest of PPSRNP exhibit a non-random, segregated pattern, which could not be attributed to competition. The segregated pattern observed could be accounted for the heterogeneous soil type along the trail which might suggest habitat preference or association. A distribution map was also generated using DIVA-GIS version 5.2 (Hijman et al., 2005). The map generated showed segregation pattern, as distinctly exhibited by Dimorphocalyx murinus and Casearia grewiifolia. The results of this research have implications on the in-situ conservation of the area, providing basic framework for ecological studies such as habitat preferences
Microarray Data Clustering Using Self-Organizing Maps
No full textMicroarray is one of the technologies used in the interdisciplinary science of BioInformatics. Its primary objective is to discover biological knowledge among genes through their expressions. Gene expressions usually come in large and multi-dimensional data which makes computational and statistical analyses necessary. Clustering of microarray data is one of these. Grouping similar genes together unfolds relationships of the biological properties of the genes under specific condition and, if supported by visualization, serves as good decision support for researchers. MaSOM is a software that uses Self-Organizing Maps, an Artificial Neural Network suitable both for clustering and for visualization, as its clustering method. This tool can be used to analyse large data set by preprocessing, clustering, and visualizing two-color cDNA microarray data
Effect of the plant growth regulators, α-naphthaleneacetic acid (NAA) and 6-benzylaminopurine (BAP), on protocorm organogenesis of Spathoglottis plicata Blume.
No full textSpathoglottis plicata Blume is known to be difficult to propagate by natural methods. The use of in vitro culture methods would result to a faster, more practical and more efficient means for its propagation. In this study, the appropriate concentrations of plant growth regulators (PGRs) on plantlet regeneration from Spa. plicata protocorms were investigated. Protocorms obtained from in vitro germinated seeds were cultured in halfstrength Murashige and Skoog (MS) basal medium with modified Nitsch & Nitsch (N&N) vitamins, 3% sucrose, 0.2% activated charcoal and 0.55% pharmaceutical agar. The culture medium was supplemented with α-naphthaleneacetic acid (NAA) and 6-benzylaminopurine (BAP) at different concentrations. The effects of NAA and BAP on protocorm cultures were evaluated based on their shoot length, number of leaves, root length and number of roots. Cultures responded positively to half-strength MS basal medium without PGRs based on their morphological characteristics. The maximum shoot length (29.87 ± 1.521 mm) was obtained at 0.5 mg/L BAP. It was generally observed that low concentrations of BAP, with little to no NAA, favored the elongation of shoots in culture. The number of leaves per plantlet was not significantly affected even with the addition of combinations of BAP and NAA. For root length, the highest obtained (16.40 ± 1.479 mm) were observed in media having 0.5 mg/L NAA and in 1.0 mg/L NAA and 0.5 mg/L BAP. Root length was observed to be high in cultures with low concentrations of NAA and BAP combinations. The greatest frequency of rooting (2.8 ± 0.175) was observed in media supplemented with only 2.0 g/L NAA. Medium containing predominantly NAA, with low concentrations of BAP, was observed to favor root formation in cultures
WASMS: Web-based Application for Soccer Motivation using Simulations applying Artificial Neural Network
No full textSoccer is not yet a renowned sport in the Philippines and we lack efficient ways in introducing it
to the people, particularly the youth. In this study, a web-based application for soccer motivation using
simulations, or WASMS, is created. It renders both introductory and advanced information about the
sport in enticing manners. It features primarily soccer simulations implemented in a Java applet. These
simulations are incorporated in a highly graphical and smoothly animated game to provide a more
effective encouragement for the target users. The simulations are inspired by the RoboCup Simulation
League, a testbed for developing new methods of artificial intelligence and machine learning. In these
simulations, an artificial neural network is applied to the decision-making process of AI players when
trying to score a goal. The trained neural net is capable of answering two classification problems: when
to shoot the ball and where to shoot it
Antioxidant effect of Peperomia pellucida (L.) HBK decoction on the liver histopathology of trichloroethylene-exposed rats.
No full textOxidative stress has harmful effects in different body organs which could lead to the occurrence of severe diseases such as hypertension and cancer. In search of an alternative medicine that is accessible and inexpensive, this study was conducted to determine the effect of Peperomia pellucida decoction in the liver histopathology of rats under trichloroethylene (TCE)-induced stress. Twenty five rats were distributed among five groups: negative and positive control groups, and three groups orally given with P. pellucida decoction at concentrations 5, 10, and 15 ml/kg. TCE was also orally administered to the latter four groups to induce stress. Liver histopathological analysis of the rats has shown that P. pellucida decoction possesses hepatoprotective effect against hepatocyte apoptosis, cytolytic necrosis, and fibrosis caused by oxidative stress. This is due to the plant’s ability to elevate antioxidant enzymes, caused by its bioactive compounds such as flavonoids. The 5 ml/kg concentration was the effective dose, with the 10 and 15 ml/kg concentrations showing increasing damage due to the counteracting effects of H2O2 also formed by antioxidants, and the presence of antagonistic compounds such as apiols at higher concentrations. The most effective dose of the decoction lies within the 5 to 10 ml/kg range
CSCoRE: Computer Science Collaborative Research Environment 2.0
No full textCollaboration is the cooperation of individuals in order to attain a common
goal. In line with this concept, work
ows may be employed to systematize cer-
tain procedures necessary to conduct a research or a project. Using work
ows
relative to collaboration yields increased e ciency, better process control,
exibil-
ity and process optimization. Meanwhile to adapt with the distributed model of
organization of most software development teams, distributed version control sys-
tems (DVCSs) are rapidly gaining ground as the preferred architecture of projects
over the traditional centralized systems. O ine operations, experimental branches
and easy peer-to-peer collaboration are but some of the reasons why developers
are making the switch.
Although CSCoRE integrates e ective project management and availability
of tools in one collaborative environment, it fairly lacks two substantial features
relevant to research and development in Computer Science. First, it has no support
for work
ow management and second, it does not o er Git DVCS.
With the Computer Science Collaborative Research Environment (CSCoRE)
2.0, the collaboratory gains a step up on its purpose of being a bene cial tool for
collaboration speci cally for projects in the eld of Computer Science through the
addition of the modules ProcessMaker and Git repository. ProcessMaker provides
CSCoRE with an embedded work
ow management system in which pertinent
work
ows tailored to the needs of a project can be utilized to streamline the
ow
of information among members of the team. The Git repository on the other hand,
o ers users the ability to conveniently browse and obtain version controlled les
of a project. Through this, the distributed nature of Git gives enough
exibility
to t well with the structure on how most software development teams collaborate
and contribute
Fine Grained Access Security Module for DentISt: Dental Information System (DentISt) 3.0
No full textDentISt 3.0 is the third version of the electronic patient record of UPCD. Compare to earlier version, the new one no longer uses OpenMRS as its EMR engine thus fixing the compatibility issues that was seen in the earlier version and give a more student-teacher approach.
As security in a system is one of the main concerns in converting from paper-based to electronic-based; DentISt has one module concerning the fine-grained access control of the system. To strengthen the access control, the usual placement of the access control in the application layer is change to the database layer and also using some HIPAA policies for sensitive data. Having the access control in the database layer helps us to have a multi-user database login and the use of stored procedure to avoid SQL injection. Some policies also provide us to provide three important security features - data integrity, confidentiality and availability, and audit trail of the system