Miracle-dz/UniFAR-FTUs huggingface dataset:
BPAGS: a web application for bacteriocin prediction via feature evaluation using alternating decision tree, genetic algorithm, and linear support vector classifier

The use of bacteriocins has emerged as a propitious strategy in the development of new drugs to combat antibiotic resistance, given their ability to kill bacteria with both broad and narrow natural spectra. Hence, a compelling requirement arises for a precise and efficient computational model that can accurately predict novel bacteriocins. Machine learning’s ability to learn patterns and features from bacteriocin sequences that are difficult to capture using sequence matching-based methods makes it a potentially superior choice for accurate prediction. A web application for predicting bacteriocin was created in this study, utilizing a machine learning approach. The feature sets employed in the application were chosen using alternating decision tree (ADTree), genetic algorithm (GA), and linear support vector classifier (linear SVC)-based feature evaluation methods. Initially, potential features were extracted from the physicochemical, structural, and sequence-profile attributes of both bacteriocin and non-bacteriocin protein sequences. We assessed the candidate features first using the Pearson correlation coefficient, followed by separate evaluations with ADTree, GA, and linear SVC to eliminate unnecessary features. Finally, we constructed random forest (RF), support vector machine (SVM), decision tree (DT), logistic regression (LR), k-nearest neighbors (KNN), and Gaussian naïve Bayes (GNB) models using reduced feature sets. We obtained the overall top performing model using SVM with ADTree-reduced features, achieving an accuracy of 99.11% and an AUC value of 0.9984 on the testing dataset. We also assessed the predictive capabilities of our best-performing models for each reduced feature set relative to our previously developed software solution, a sequence alignment-based tool, and a deep-learning approach. A web application, titled BPAGS (Bacteriocin Prediction based on ADTree, GA, and linear SVC), was developed to incorporate the predictive models built using ADTree, GA, and linear SVC-based feature sets. Currently, the web-based tool provides classification results with associated probability values and has options to add new samples in the training data to improve the predictive efficacy. BPAGS is freely accessible at https://shiny.tricities. wsu.edu/bacteriocin-prediction/.
Land suitability assessment for locating industrial parks: a hybrid multi criteria decision‐making approach using Geographical Information System

Industrial areas play a critical role in urban and regional planning, especially for developing countries where reliable strategies for these areas can promote economic and environmental efficiency. The present study provides an integration of hybrid multi-criteria decision-making (MCDM) theories and Geographical Information System (GIS) processes in order to assess the suitability of an industrial location. Unlike traditional models, an efficient decision analysis demands handling uncertainties and considering dependencies between criteria. The proposed MCDM framework uses fuzzy theory because of the vagueness of experts' judgements. Moreover, Decision-Making Trial and Evaluation Laboratory (DEMATEL) is employed to investigate interrelationships among the criteria. In the proposed empirical solution, analytic network process (ANP) principles are used to deal with systematic interactions. We considered several factors such as accessibility, topography, proximity, and socioeconomic characteristics in the decision-making procedure for a sustainable industrial park. The system is applied to Hamadan province, Iran to determine appropriate locations that are the results of the aggregation of criteria maps in a GIS environment. The results demonstrate that accessibility and economic indicators are essential for choosing an industrial park's location. Additionally, the proposed method can be applied for an efficiency evaluation of available industrial parks.
Global testing of di(cid:27)erential gene expression

In studies about di(cid:27)erential gene expression between di(cid:27)erent clinical diagnoses the main interest may often not be in single genes but rather in groups of genes that are associated with a pathway or have a common location in the genome. In such cases it may be better to perform a global test because the problems of multiple testing can be avoided. The approach presented here is an ANCOVA global test on phenotype e(cid:27)ects and gene(cid:21)phenotype interaction. The test is generalized to groups of categorical variables (e.g. SNPs) and even mixed data by a likelihood ratio approach. Testing many groups simultaneously is also possible. This, of course, causes again need for correction for multiple testing. Besides the standard approaches for correction we introduce closed and hierarchical testing procedures in which the experiment(cid:21)wise error rate equals the required level of con(cid:28)dence of the overall test. This document was created using R version 4.3. 1 and versions 4.20. 0 and 5.56. 0 of the packages GlobalAncova and globaltest , respectively.
A modified paperfuge technique in evaluating anemia in phenylhydydrazine-induced ICR

Anemia is a common observation in several diseases in humans and animals. This condition is evaluated through the blood using parameters, including the packed cell volume (PCV). However, quick diagnosis might take longer, especially in resource limited areas, as blood samples still need to be processed in the laboratory. In this experimental study, a modified paperfuge technique was evaluated to assess anemia in an animal model. A total of 16 ICR mice were used. After animal acclimatization for ten days, persistent anemia (hemolytic) was induced in nine mice by administering phenylhydrazine every other day for three times. Only distilled water was used in the control mice. After seven days, blood was extracted from the mice. Complete blood count using a species specific hematology machine was performed. PCV was further evaluated using the centrifuge machine and the modified paperfuge technique. Results using the hematology machine showed that the phenylhydrazine-induced mice had lower red blood cell count (x= 4.26 x 10^6/µL, SD=0.93) and PCV (x=32.5, SD=7.5) than the red blood cell count (x=5.26 x 10^6/µL, SD=1.1) and PCV (x=36.5, SD=5.8) of the control mice. PCV readings from the three methods were strongly correlated with the RBC count. On the other hand, PCV readings from the paperfuge technique were also strongly and significantly correlated with the centrifuge (R=0.99, p=0.000) and hematology machine (R=0.89, p=0.000) results. Further analysis revealed that there was no significant difference observed between the PCV readings of the CBC machine, the centrifuge and the modified paperfuge (treatment group: p=0.39, control group: p=0.09). Results suggest that the modified paperfuge technique can be reliable in measuring PCV to evaluate anemia. Further studies are recommended to compare results in anemic animals and humans.
Changes in instrumental activities daily living limitations and their associated factors according to gender in community-residing older adults: A longitudinal cohort study

Background Increases in dependence among older adults cause increases in care needs and social care burden. Instrumental activities of daily living (IADL) are often used to assess the independence of older adults residing in communities. Various factors affect IADL limitations, but few studies confirm gender differences in IADL limitations in older adults. This study explored the changes in incidence of IADL limitations across 14 years and identified the factors associated with IADL limitations according to gender among older adults in Korea. Method This study uses secondary data analysis with 2006–2020 data from the Korean Longitudinal Study of Aging (KLoSA), a longitudinal cohort study. Among the total 10,254 participants, 1,230 adults aged 65 years and over who met the criteria were included in the final analysis. For each IADL item, a limitation was defined when the response was partial or complete dependence. Multivariate logistic regression was performed to identify the factors (in 2006) associated with IADL limitations in 2020. Results The mean age of the participants at baseline was 69.64 years (SD 3.93), and 61.0% of participants were female. Total scores for IADL limitations increased gradually across 14 years in all participants, and observed changes were statistically significant. The top three ranked items of IADL limitations differed according to gender in 2020: the top limitations in men were preparing meals, laundry, and using public transportation, and the top limitations in women were using public transportation, going out, and handling money. Factors associated with total IADL limitations were grip strength in men and age, dementia, fear of fall, and grip strength in women. Factors associated with the top three ranked items of IADL limitations differed according to gender. Conclusion The incidence of IADL limitations gradually increased in all participants over a 14-year period. In older adults in Korea, gender differences were confirmed in the factors associated with IADL limitations, as well as in the main limited activities. To minimize IADL limitations in community-residing older adults, it is necessary to plan tailored interventions.
Exploring the mechanisms between socio-economic status and health: Mediating roles of health-related behaviors before and during COVID-19

The relationship between individuals’ socioeconomic characteristics and their health outcomes is widely acknowledged. However, the specific mechanisms through which these factors are interconnected have not been studied sufficiently. The current study investigated the association among socio-economic status (education of parents, economic status of family) and perceived health mediated by physical activity and sedentary time (purpose for study or not), before and during Covid-19. Three cross-sectional and population-based representative surveys from 2019, 2020, and 2021 were utilized. Overall, 167,099 Korean adolescents (57,303 in 2019, 54,948 in 2020, 54,848 in 2021) participated. A multi-group structural equation model showed that socio-economic status was associated with perceived health through physical activity and sedentary behaviors. Both measures of socio-economic status were positively associated with sedentary time for study purposes, but negatively associated with purposes other than study. Higher education of parents negatively predicted physical activity, whereas higher economic status of family positively predicted physical activity. The impact of socio-economic status on sedentary time tended to increase after the pandemic. Covid-19 significantly affected adolescents’ health and health-related behaviors. Comprehensive policies considering adolescents’ socio-economic status and their physical activity and sedentary time would mitigate the health effects of the pandemic.
Quantitative Speciation of Insoluble Chlorine in Environmental Solid Samples

Since organically bound chlorine (organo-Cl) has been determined by different methods depending on samples and study fields, it has been difficult to compare organo-Cl in different environments. Here, we focused on Cl in water-insoluble fractions (insoluble Cl) and applied Cl K-edge X-ray absorption spectroscopy in conjunction with combustion ion chromatography. Quantitative speciation of insoluble Cl enabled us to compare the concentrations of Cl bonded with aromatic carbon (aromatic-Cl) and aliphatic carbon (aliphatic-Cl) as well as organo-Cl across different types of environmental solid samples (soils, particulate matter, dust, and ashes). The concentrations of organo-Cl in house dust and urban particulate matter exceeded those in forest soils, suggesting that house dust and urban particulate matter may be important pools of organochlorine compounds (OCs). Further, by studying representative samples with concentrations of some individual organochlorine compounds (OCs), we evaluated the mass balance of .
PEMBOBOTAN KATA BERDASARKAN KLASTER PADA OPTIMISASI COVERAGE, DIVERSITY DAN COHERENCE UNTUK PERINGKASAN MULTI DOKUMEN

[Id]Peringkasan yang baik dapat diperoleh dengan coverage, diversity dan coherence yang optimal. Namun, terkadang sub-sub topik yang terkandug dalam dokumen tidak terekstrak dengan baik, sehingga keterwakilan setiap sub-sub topik tersebut tidak ada dalam hasil peringkasan dokumen. Pada paper ini diusulkan metode baru pembobotan kata berdasarkan klaster pada optimisasi coverage, diversity dan coherence untuk peringkasan multi-dokumen. Metode optimasi yang digunakan ialah self-adaptive differential evolution (SaDE) dengan penambahan pembobotan kata berdasarkan hasil dari pembentukan cluster dengan metode Similarity Based Histogram Clustering (SHC). Metode SHC digunakan untuk mengklaster kalimat sehingga setiap sub-topik pada dokumen bisa terwakili dalam hasil peringkasan. Metode SaDE digunakan untuk mencari solusi hasil ringkasan yang memiliki tingkat coverage, diversity, dan coherence paling tinggi. Uji coba dilakukan pada 15 topik dataset Text Analysis Conference (TAC) 2008. Hasil uji coba menunjukkan bahwa metode yang diusulkan dapat menghasilkan ringkasan skor ROUGE-1 sebesar 0.6704, ROUGE-2 sebesar 0.2051, ROUGE-L sebesar 0.6271 dan ROUGE-SU sebesar 0.3951. Kata kunci : peringkasan multi dokumen, similarity based histogram clustering, coverage, diversity, coherence[En]Good summary can be obtained with optimizing coverage, diversity, and coherence. Nevertheless, sometime sub-topics wich is contained in the document is not extracted well, so that the representation of each sub-topic is appear in docment summarizarion result. In this paper, we propose new of term weighting based on? cluster in optimizing coverage, diversity, and coherence for multi-document summarization. Optimization method which is used is self-adaptive differential evolution (SaDE) with additional term weighting based on clustering result with Similarity Based Histogram Clustering (SHC). SHC is used to cluster sentence so that every sub-topic in the document can be represented in summarization result. SaDE is used to search summarization result solution which has high coverage, diversity, and coherence level. Experiment is done on 15 topics in Text Analysis Conference (TAC) 2008 dataset. Experimental results show that this proposed method can produce summarization score? ROUGE-1 0.6704, ROUGE-2 0.2051, ROUGE-L 0.6271 and ROUGE-SU 0.3951. Keywords: multy-document summarization, similarity based histogram clustering, coverage, diversity, coherence.
Training Induced Oxidative Stress-Derived DNA and Muscle Damage in Triathletes.

Objective Regular moderate-intensity exercise has beneficial health effects, whereas regular strenuous exercise increases the production of oxidants that may lead to DNA, skeletal, and cardiac muscle damages. Triathletes experience strenuous muscular activity both during competition and training, being at risk of developing these tissue damages. The objective of the present study was to estimate DNA, skeletal, and cardiac muscle damages using blood biomarkers, 8-hydroxy-2'-deoxyguanosine (8-OHdG), myoglobin, and cardiac troponin I (cTnI) among young triathletes. Materials and Methods Age-matched seven male and seven female triathletes were recruited for the study. They were on a standardized training regimen and on average competed in at least one endurance event every month for the past 3-4 years. Serum biomarkers were measured using enzyme-linked immunosorbent assay at the start and at end of the racing season. Results Both male and female triathletes showed a statistically significant increase in 8-OHdG. A similar pattern of increase was seen with serum myoglobin, which was not statistically significant in both male and female triathletes. cTnI levels did not show any change in both sexes. Conclusion Our study shows that there could be an increased evidence of DNA damage among triathletes. However, similar effects were not observed with skeletal and cardiac muscle biomarkers.
Propolis alleviates ulcerative colitis injury by inhibiting the protein kinase C ‐ transient receptor potential cation channel subfamily V member 1 ‐ calcitonin gene-related peptide/substance P (PKC-TRPV1-CGRP/SP) signaling axis

This study investigated the protective effect of water-soluble propolis (WSP) on colonic tissues in ulcerative colitis (UC) and the role of the protein kinase C ‐ transient receptor potential cation channel subfamily V member 1 ‐ calcitonin gene-related peptide/substance P (PKC-TRPV1-CGRP/SP) signaling pathway. Male SD rats were divided into a control group, a UC model group, various WSP groups (Low-WSP, Medium-WSP, and High-WSP) with UC, and a salazosulfapyridine (SASP) positive control group with UC. After UC was established, the WSP and SASP groups were treated with WSP or SASP, respectively, for 7 d. Each day, body weight measurements were obtained, and the disease activity index (DAI) was recorded by observing fecal characteristics and blood in the stool. After the experiment, hematoxylin and eosin (HE) colonic tissue staining was performed to observe pathological changes, western blotting and immunohistochemistry were performed to detect PKC, TRPV1, CGRP, and SP expression in colonic tissues, and laser confocal microscopy was performed to observe the fluorescence colocalization of PKC/TRPV1, TRPV1/CGRP, and TRPV1/SP. HE staining showed significant colonic tissue structure disruption and inflammatory infiltration in the UC group. Western blotting and immunohistochemistry showed that the expression of PKC, TRPV1, CGRP, and SP in the colonic tissues of the UC group increased significantly compared with that of the control group. Compared with the UC group, the expression of PKC, TRPV1, CGRP, and SP in colonic tissues was significantly reduced in the High-WSP, Medium-WSP, and SASP groups. Immunofluorescence showed the colocalized expression of PKC/TRPV1, TRPV1/CGRP, and TRPV1/SP proteins in the colon tissue of the UC group was significantly reduced after WSP and SASP interventions compared with that of the control group. The results suggest that the mechanism of UC alleviation by propolis may inhibit the PKC-TRPV1-CGRP/SP signaling pathway and the release of inflammatory mediators, thus alleviating inflammation.
Physico-Chemical Characteristics and Rheolgical Properties of Different Wheat Varieties Grown in Sindh

This study was designed to investigate the physico-chemical and rheological properties of 17 wheat varieties (TJ-83, Jouhar, TD-1, Anmool, Mehran, Indus-66, Sindh B-1, Abadgar, Bhittai, Imdad, Mexi-Pak, Soughat, Blue Silver, Moomal, Marvi, Kiran, and Pak-70 ) commercially grown on experimental field of Agriculture Research Institute, Tandojam. The results revealed that moisture % were in range of 11 to 12 among all varieties, high protein content of about 15.2% was found in Mehran and Blue silver varieties, starch was found high in Maxi-pak (70.6%), high hardness values in Imdad (70.1%) and Jouhar (70.2%). However, zeleny content was found high in Marvi, Abadgaar and Mehran i.e. 71%. Amylographic results showed that among all varieties the Bhittai variety required maximum temperature up to 65.7 o C for the beginning of gelatinization as compared to other varieties. The highest gelatinization temperature was noted up to 96.7 o C in Moomal whereas others had temperature from 82.7 to 89.0 o C. Highest gelatinization maxima (1782AU) acquired by T.J-83 variety. The results of Farinograph showed that highest water absorption was noted in Anmool variety. The highest dough development time and dough stability were found highest in Kiran and Indus-66, respectively. T.D-1 and Jouhar varieties had highest break down time as well as highest Farinograph quality.
Sistem Pakar Identifikasi Varietas Ikan Mas (Cyprinus carpio) Berdasarkan Karakteristik Morfologi dan Tingkah Laku

Penelitian ini mengidentifikasi 6 varietas ikan mas menggunakan 8 parameter input yang meliputi karakteristik morfologi dan tingkah laku. Pembagian data latih dan data uji dilakukan menggunakan metode k-fold cross validation . Variabel yang bersifat nominal diolah menggunakan jarak nominal, sedangkan variabel numerik dan ordinal diolah dengan menggunakan jarak Euclid. Sebelum menghitung jarak Euclid, metode normalisasi min-max diterapkan pada variabel numerik dan ordinal. Hasil perhitungan jarak Euclid dan jarak nominal digabung dengan menggunakan rumus agregat. Metode klasifikasi yang digunakan untuk identifikasi ialah metode k-nearest neighbour (KNN). Akurasi rata-rata terbaik untuk percobaan tanpa normalisasi ialah 94.58% dan untuk percobaan dengan normalisasi ialah 98.54% saat k = 3. Sistem ini dapat diakses pada alamat http://apps.cs. ipb.ac. id/spivim . Kata kunci: ikan mas, jarak Euclidean, k-nearest neighbour, nominal distance, normalisasi min-max.
Precipitation Predictability of MM5 in the Simulation of Heavy Rainfall over Korea

In the heavy rainfall prediction in Korea, one of major deficient components is lack of mesoscale data for the model initial conditions. However, potential predictability of MM5 in heavy rainfall simulations can be estimated using synoptic-scale data such as the NCEP/NCAR reanalysis, because mesoscale models using sophisticated physical processes have potential ability to evolve internal variability of mesoscale features under synoptic-scale situation. Using the NCEP/NCAR reanalysis data the MM5 model has reproduced, to a certain degree, the amount and pattern of heavy rainfall through the simulation of heavy rainfall cases over Korea (Lee et al., 2001). One of the issues would be how much quantitatively reproduce intense precipitation. Cumulus parameterization schemes (CPSs) and grid-scale resolvable schemes (GRSs) in the MM5 have showed successful performances in specific convective environments through case studies. However, the general applicability of physical process schemes in a mesoscale model to intense precipitation in heavy rainfall events is still uncertain. Wang and Seaman (1997) conducted a comparison study of four CPSs. Yang and Tung (2003) tested the same four CPSs for six heavy rainfall cases occurring over Taiwan. Lee et al. (2001) compared four CPSs in different horizontal resolutions with four heavy rainfall cases over Korea in the monsoon season. The objective of this study is to investigate precipitation predictability and CPS performance of the MM5 through the simulations of thirty heavy rainfall events occurring over the Korean Peninsula during the summer monsoon season.