bluuebunny/crossref_metadata_2025_split huggingface dataset:
PENGEMBANGAN BUNDLE DALAM MENURUNKAN URINARY TRACT INFECTION (UTI) DI RSUD SEJIRAN SETASON MUNTOK
Authors: Syafriati Ani , Maria Rosa Elsye , Kurnia Sari Novita 
Published: December 2019

Background: Development of CAUTI bundle is very important to evaluate the nurse in implementing nursing practice related to urinary catheter which is one of prevention efforts and risk control of CAUTI.
Objective: The purpose of this study is to develop CAUTI bundle that is adjusted to hospital condition in Sejiran Setason Muntok Hospital.
Methods: In this study used qualitative method by conducting indepth interview and focus group discussion (FGD). It conducted for 3 weeks in Sejiran Setason Muntok Hospital, the total sample are 22 participants. The result produced the themes that used as the material for the development of the bundle or the observation sheet of CAUTI.
Results: There are 10 themes which become material for the development of CAUTI bundle. The CAUTI Bundle consists of bundle components such as indication of urinary catheter insertion, urinary catheter installation must comply with SOP, monitoring of urine output by regularly, emptying urine bag regularly, performing hand hygiene before and after procedure, using masks and handscoons, patients and families must be aware of their role in minimizing the risk of CAUTI.
Conclusion: Development of the bundle is very important as one of prevention of CAUTI incident in hospital.
Keyword : Bundle, CAUTI, Development.
Confounds in “failed” replications
Authors: Bressan Paola 
Published: December 2019

Reproducibility is essential to science, yet a distressingly large number of research findings do not seem to replicate. Here I discuss one underappreciated reason for this state of affairs. I make my case by noting that, due to artifacts, several of the replication failures of the vastly advertised Open Science Collaboration’s Reproducibility Project: Psychology turned out to be invalid. Although these artifacts would have been obvious on perusal of the data, such perusal was deemed undesirable because of its post hoc nature and was left out. However, while data do not lie, unforeseen confounds can render them unable to speak to the question of interest. I look further into one unusual case in which a major artifact could be removed statistically—the nonreplication of the effect of fertility on partnered women’s preference for single over attached men. I show that the “failed replication” datasets contain a gross bias in stimulus allocation which is absent in the original dataset; controlling for it replicates the original study’s main finding. I conclude that, before being used to make a scientific point, all data should undergo a minimal quality control—a provision, it appears, not always required of those collected for purpose of replication. Because unexpected confounds and biases can be laid bare only after the fact, we must get over our understandable reluctance to engage in anything post hoc. The reproach attached to p-hacking cannot exempt us from the obligation to (openly) take a good look at our data.
The Influence of Leadership, Organization Behavior, Compensation, And Work Discipline on Employee Performance in Non-Production Departments PT. Team Metal Indonesia
Authors: Bangun Rejeki , Ratnasari Sri Langgeng , Hakim Lukmanul 
Published: December 2019

This research is to get information about leadership, organization behavior, compensation, work discipline and four factors to employee performance in Non-Production Department PT. Team Metal Indonesia. This research used a questionnaire for 94 respondents and used SPSS version 20. This research is quantitative research, statistics analysis. Multiple Linear Regression method with quantitative analysis. Based on SPSS data analysis, the researcher got the result Multiple Linear Regression analysis to leadership (X1) is 2.071 with significant 0.041, organization behavior (X2) is 0.817 with significant 0.416, compensation (X3) is -0.726 with significant 0.470 and work discipline (X4) is 2.985 with significant number 0.004. Result of the simultaneous test (F test) 8.083. Conclusion for this research are first hypothesis leadership has influence to employee performance, second hypothesis organization behavior has influence on employee performance but not significant, third hypothesis compensation has influence to employee performance but not significant, fourth hypothesis work discipline has partial influence to employee performance and last hypothesis that these four variables (leadership, organization behavior, compensation, and work discipline) have simultaneous influence on employee performance
Molecular basis of the anti-cancer effects of genistein isoflavone in LNCaP prostate cancer cells
Authors: Merchant K. , Kumi-Diaka J. , Rathinavelu A. , Esiobu N. , Zoeller R. , Hartmann J. , Johnson M. 
Published: December 2019

Background: Prostate cancer is the most common form of non-skin cancer within the United States and the second leading cause of cancer deaths. Survival rates for the advanced disease remain relatively low, and conventional treatments may be accompanied by significant side effects. As a result, current research is aimed at alternative or adjuvant treatments that will target components of the signal transduction, cell-cycle and apoptosis pathways, to induce cell death with little or no toxic side effects to the patient. In this study, we investigated the effect of genistein isoflavone, a soy derivative, on expression levels of genes involved in these pathways. The mechanism of genistein-induced cell death was also investigated. The chemosensitivity of the LNCaP prostate cancer cells to genistein was investigated using ATP and MTS assays, and a caspase binding assay was used to determine apoptosis induction. Several molecular targets were determined using cDNA microarray and RT-PCR analysis.Results: The overall data revealed that genistein induces cell death in a time- and dose-dependent manner, and regulates expression levels of several genes involved in carcinogenesis and immunity. Several cell-cycle genes were down-regulated, including the mitotic kinesins, cyclins and cyclin-dependent kinases. Various members of the Bcl-2 family of apoptotic proteins were also affected. The DefB1 and the HLA membrane receptor genes involved in immunogenicity were also up-regulated. Conclusion: The results indicate that genistein inhibits growth of the hormone-dependent prostate cancer cells, LNCaP, via apoptosis induction through regulation of some of the genes involved in carcinogenesis of many tumors, and immunogenicity. This study augments the potential phytotherapeutic and immunotherapeutic significance of genistein isoflavone. Key words: Genistein isoflavone, prostate cancer, expression of genes, phytotherapeutic adjuvant, immunotherapy and chemotherapy
Antioxidant Protection against Pathological Mycotoxins Alterations on Proximal Tubules in Rat Kidney
Authors: Ali Awatef , Abdu Susan 
Published: December 2019

Background: Ochratoxin A (OTA) was one of the mycotoxins and received attention worldwide because of the hazard it posed to human and animal health, where the kidney was the primary target organ for OTA toxicity. In the other hand, dates served as a good source of natural antioxidants and could potentially be considered as a functional food.Methods: The study was performed in the department of biology in King Abdulaziz University. Animals were gavage administrated and divided into four groups: first group received (sodium bicarbonate), second group received (289 µg OTA /kg B.W. /day), third group received (1mg Ajwa/kg B.W. / day) and fourth group received (289 µg OTA /kg B.W./day+ 1mg Ajwa /kg B.W. / day). Serum (creatinine - urea) levels were measured in each group at the time of tissue collection, some biopsies were fixed in 10% buffered formalin solution for light microscopy processing stained with Haematoxylin and Eosin (H& E.), Periodic Acid-Schiff (PAS) and Masson´s Trichrome (M.T.).Other biopsies were immediately collected into electron microscopy processing. Results: After 28 days, a significant decrease in body weight, kidney weight and relative weight was detected in OTA treated group. Also, Serum (creatinine-urea) level were elevated. The normal cyto-architecture of proximal tubules were lost exhibiting damaged bruch border, degenerated, binucleated and karyomegalic cells. The most destructed ultra-structure was the mitochondria which severely swollen with disintegrated membranes. In Ajwa Date extract-group the proximal tubules were normal, whereas in Ajwa date extract + OTA -group the severity of the lesions was significantly reduced. Conclusion: The present results indicated that, Ajwa date have protective effects and ameliorated the lesions of Ochratoxin nepherotoxicity which might lead to kidney failure. Key words: Ochratoxin A., Ajwa date, proximal tubules, light –structure, ultra –structure, biochemical analysis, morphometry.
Dietary Supplementation of Fructooligosaccharides Reduces Hepatic Steatosis Associated with Insulin Resistance in Obese Zucker Rats
Authors: Kaume Lydia , Gilbert William , Gadang Vidya , Devareddy Latha 
Published: December 2019

Background: One in five adults in the United States is obese as defined by a body mass index of 30 kg/m2. Obesity is associated with metabolic syndrome, a combination of medical conditions including cardiovascular disease, type 2 diabetes, hypertension, hypercholesterolemia, and hypertriglyceridemia. These conditions present challenges to the medical care system and require a multifaceted approach through a variety of interventions. This study investigated the effects of fructooligosaccharides (FOS) at the level of 5 % (w/w) in alleviating the complications associated with metabolic syndrome.Methods: The study was carried out using thirty-six, three-month old female lean and obese Zucker rats housed in an environmentally controlled laboratory. The Zucker rats were divided into three groups (N=12): Lean (L-CTRL) and obese controls (O-CTRL) and obese-FOS (O-FOS). The controls received AIN-93M purified rodent diet and the animals in the O-FOS group were fed AIN-93M diet modified to contain 5.0% FOS (w/w). After 100 days of treatment, the rats were fasted for 12 hours and sacrificed. Tissue and organs of interest, and blood were collected for analysis. Serum concentrations of the following were determined: glucose, glycosylated hemoglobin (HbA1c), total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-C), high-density lipoprotein-cholesterol (HDL-C), triglycerides (TG), and insulin. Gravimetric quantification of liver lipids was performed and peroxisome proliferator-activated receptor-γ (PPAR-γ) gene expression was determined in white adipose tissue by qRT-PCR.Results: No significant differences were observed in the serum lipids, fasting blood glucose, HbA1c and PPAR-γ gene expression in white adipose tissue of O-FOS group compared to O-CTRL group. FOS supplementation significantly lowered the percent total liver lipids by 12% with a subsequent reduction in the liver weights compared to O-CTRL rats. Serum insulin concentrations were lowered 3.6 fold in O-FOS group compared to O-CTRL (P < 0.05). Conclusion: Based on these findings we conclude that dietary supplementation of 5% FOS (w/w) may reduce hepatic steatosis and the risk for non-alcoholic fatty liver disease (NAFLD) associated with insulin resistance without changes in blood lipids and glucose levels.Key words: Dietary fiber, Fructooligosaccharide, Hepatosteatosis, Liver lipids, Non-alcoholic fatty liver disease (NAFLD), Zucker.
Antioxidant Activity and Mechanism of Protocatechuic Acid in vitro
Authors: Li Xican , Wang Xiaozhen , Chen Dongfeng , Chen Shuzhi 
Published: December 2019

Background: Protocatechuic acid (PCA) is a natural phenolic acid widely distributed in plants and is considered as an active component of some traditional Chinese herbal medicines such as Cibotium barometz (L.) J.Sm, Stenoloma chusanum (L.) Ching, Ilex chinensis Sims. PCA was reported to possess various pharmacological effects which may be closely correlated with its antioxidant activities. However, the antioxidant of PCA has not been investigated systematically yet. Methods: In the study, the antioxidant activities of protocatechuic acid were measured in vitro using various antioxidant assays including 1,1-diphenyl-2-picryl-hydrazyl (DPPH•), 2,2’-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS+•), superoxide anion radicals (•O2-) and hydroxyl radical (•OH) scavenging activity, ferric ions (Fe3+) and cupric ions (Cu2+) reducing power, ferrous ions (Fe2+) and cupric ions (Cu2+) chelating activity, compared with the positive controls Trolox or BHT.Results: In all assays, PCA along with positive controls exhibited dose-dependently antioxidant ability. Comparing to a standard antioxidant Trolox, the relative antioxidant activity of PCA (i.e. the ratio of IC50(Trolox)/IC50(PCA) ) was calculated as 2.8, 2.3, 3.7, 6.1, 4.2, 1.0, 2.7, 1.5, respectively, for DPPH, ABTS, reducing power (Fe3+), reducing power (Cu2+), superoxide anion radical-scavenging, hydroxyl radical-scavenging, chelating ability (Fe2+) and chelating ability (Cu2+). Conclusion: Comparing to Trolox, PCA shows much more effective antioxidant activity in vitro in both lipid and aqueous media. Hence, it could therefore be used in pharmacological or food industry as a natural antioxidant. It may exhibit antioxidant activity by both chelating metal transition ions as well as by scavenging free radicals via donating hydrogen atom (H•) or electron (e).Keywords: Protocatechuic acid, antioxidant, reducing power, free radical-scavenging, chelating ability.
Towards a Formal Semantics for the Process Model of the Taverna	Workbench. Part I
Authors: Sroka Jacek , Hidders Jan 
Published: December 2019

Workflow development and enactment workbenches are becoming a standard tool for conducting in silico experiments. Their main advantages are easy to operate user interfaces, specialized and expressive graphical workflow specification languages and integration with a huge number of bioinformatic services. A popular example of such a workbench is Taverna, which has many additional useful features like service discovery, storing intermediate results and tracking data provenance. We discuss a detailed formal semantics for Scufl - the workflow definition language of the Taverna workbench. It has several interesting features that are notmet in other models including dynamic and transparent type coercion and implicit iteration, control edges, failure mechanisms, and incominglinks strategies. We study these features and investigate their usefulness separately as well as in combination, and discuss alternatives. The formal definition of such a detailed semantics not only allows to exactly understand what is being done in a given experiment, but is also the first step toward automatic correctness verification and allows the creation of auxiliary tools that would detect potential errors and suggest possible solutions to workflow creators, the same way as Integrated Development Environments aid modern programmers. A formal semantics is also essential for work on enactment optimization and in designing the means to effectively query workflow repositories. This paper is the first of two. It defines, explains and discusses fundamental notions for describing Scufl graphs and their semantics. Then, in the second part, we use these notions to define the semantics and show that our definition can be used to prove properties of Scufl graphs.
Avoiding Irreducible CSC Conflicts by Internal Communication
Authors: Wist Dominic , Wollowski Ralf , Schaefer Mark , Vogler Walter 
Published: December 2019

Resynthesis of handshake specifications obtained e.g. from BALSA or TANGRAM with speed-independent logic synthesis from STGs is a promising approach. To deal with state-space explosion,we suggested STG decomposition; a problemis that decomposition can lead to irreducible CSC conflicts. Here, we present a new approach to solve such conflicts by introducing internal communication between the components. We give some first, very encouraging results for very large STGs concerning synthesis time and circuit area.
Mathematical Modeling of Regulation of Type III Secretion System	in Salmonella enterica Serovar Typhimurium by SirA
Authors: Ganesh Aparna B. , Rajasingh Hannah , Mande Sharmila S. 
Published: December 2019

Salmonella enterica serovar Typhimurium invades the intestinal epithelial cells using type three secretion system (TTSS) encoded on Salmonella pathogenicity island-1 (SPI-1). The key regulator of this secretion system is HilA, which is in turn regulated by HilD, HilC and RtsA. It is also known that SirA/BarA system, a two-component regulatory system plays a crucial role in regulating HilA. There are two different mechanisms that have been proposed earlier for regulation of HilD-HilC-RtsA-HilA network by SirA. One considers SirA to be acting through HilA and HilC, whereas the other considers SirA to be acting through HilD. In this paper, we have built mathematical models corresponding to both these scenarios and carried out simulations under different gene knock-out conditions. Additionally, since the two proposed mechanisms based on the experimental data are equally likely, we also considered a mechanism which is a combination of the two proposed mechanisms. The simulations were carried out to check the levels of HilA, the factor regulating the virulence, as well as the levels of the intermediate components in the network, namely HilC and RtsA. The simulation results were used to check the consistency of various models and also to suggest the most probable mechanism of hilA regulation. The results of our study show that while most of the mathematical models are able to predict the virulence data, the models considering SirA to regulate through HilA and HilC fail to predict the levels of intermediate components, HilC and RtsA. Nevertheless, one of the models considering regulation of virulence by SirA via HilD was able to predict results comparable to the experimental data. In addition, combination of this model (regulation by SirA via HilD) with the model considering regulation by SirA through HilA and HilC, also predicted results consistent with experimental observations. Our conclusions were further validated by testing the stability of the results against changes in parameter values, thus confirming the relative robustness of the proposed modeling system.
A Naive Bayes Classifier for Protein Function Prediction
Authors: Kohonen Jukka , Talikota Sarish , Corander Jukka , Auvinen Petri , Arjas Elja 
Published: December 2019

A Naive Bayes classifier tool is presented for annotating proteins on the basis of amino acid motifs, cellular localization and protein-protein interactions. Annotations take the form of posterior probabilities within the Molecular Function hierarchy of the Gene Ontology (GO). Experiments with the data available for yeast, Saccharomyces cerevisiae, show that our prediction method can yield a relatively high level of accuracy. Several apparent challenges and possibilities for future developments are also discussed. A common approach to functional characterization is to use sequence similarities at varying levels, by utilizing several existing databases and local alignment/identification algorithms. Such an approach is typically quite labor-intensive when performed by an expert in a manual fashion. Integration of several sources of information is in this context generally considered as the only possibility to obtain valuable predictions with practical implications. However, some improvements in the prediction accuracy of the molecular functions, and thereby also savings in the computational effort, can be achieved by restricting attention to only those data sources that involve a higher degree of specificity. We employ here a Naive Bayes model in order to provide probabilistic predictions, and to enable a computationally efficient approach to data integration.
SubCellProt: Predicting Protein Subcellular Localization Using	Machine Learning Approaches
Authors: Garg Prabha , Sharma Virag , Chaudhari Pradeep , Roy Nilanjan 
Published: December 2019

High-throughput genome sequencing projects continue to churn out enormous amounts of raw sequence data. However, most of this raw sequence data is unannotated and, hence, not very useful. Among the various approaches to decipher the function of a protein, one is to determine its localization. Experimental approaches for proteome annotation including determination of a protein's subcellular localizations are very costly and labor intensive. Besides the available experimental methods, in silico methods present alternative approaches to accomplish this task. Here, we present two machine learning approaches for prediction of the subcellular localization of a protein from the primary sequence information. Two machine learning algorithms, k Nearest Neighbor (k-NN) and Probabilistic Neural Network (PNN) were used to classify an unknown protein into one of the 11 subcellular localizations. The final prediction is made on the basis of a consensus of the predictions made by two algorithms and a probability is assigned to it. The results indicate that the primary sequence derived features like amino acid composition, sequence order and physicochemical properties can be used to assign subcellular localization with a fair degree of accuracy. Moreover, with the enhanced accuracy of our approach and the definition of a prediction domain, this method can be used for proteome annotation in a high throughput manner. SubCellProt is available at www.databases.niper.ac.in/SubCellProt.
Empowering Spot Detection in 2DE Images by Wavelet Denoising
Authors: Soggiu Alessio , Marullo Osvaldo , Roncada Paola , Capobianco Enrico 
Published: December 2019

Typical high-abundant proteins, including albumin, IgG, IgA and others, are the target of depletion methods usually applied to two-dimensional electrophoresis (2DE) of human biological fluids like serum and plasma. Detection of low-abundant proteins is of interest with regard to biomarkers for disease when being studied by 2DE or liquid chromatography-mass spectrometry (LC/MS). After depletion of very abundant proteins, serum samples consist of an enriched pool of low-abundant proteins that can be further studied without significant interferences, thus allowing for a full identification of the low abundant proteins, whose spots become now more visible. We have employed wavelet-based techniques and their derived denoisers to explore 2DE from disease-control human samples. We have pursued the goal of mimicking in silico the spot detection performance experimentally obtained by depletion methods, thus hoping to read through the critical high-abundant protein regions. Our results suggest that an efficient and effective computational tool has been added to other ones performing 2DE image analysis, such as decomposition and segmentation, but with the advantage of being specifically targeted to the depletion task.