bluuebunny/crossref_metadata_2025_split huggingface dataset:
WormCat: An Online Tool for Annotation and Visualization of Caenorhabditis elegans Genome-Scale Data
Authors: Holdorf Amy D , Higgins Daniel P , Hart Anne C , Boag Peter R , Pazour Gregory J , Walhout Albertha J M , Walker Amy K 
Published: December 2019

Abstract
The emergence of large gene expression datasets has revealed the need for improved tools to identify enriched gene categories and visualize enrichment patterns. While gene ontogeny (GO) provides a valuable tool for gene set enrichment analysis, it has several limitations. First, it is difficult to graph multiple GO analyses for comparison. Second, genes from some model systems are not well represented. For example, ∼30% of Caenorhabditis elegans genes are missing from the analysis in commonly used databases. To allow categorization and visualization of enriched C. elegans gene sets in different types of genome-scale data, we developed WormCat, a web-based tool that uses a near-complete annotation of the C. elegans genome to identify coexpressed gene sets and scaled heat map for enrichment visualization. We tested the performance of WormCat using a variety of published transcriptomic datasets, and show that it reproduces major categories identified by GO. Importantly, we also found previously unidentified categories that are informative for interpreting phenotypes or predicting biological function. For example, we analyzed published RNA-seq data from C. elegans treated with combinations of lifespan-extending drugs, where one combination paradoxically shortened lifespan. Using WormCat, we identified sterol metabolism as a category that was not enriched in the single or double combinations, but emerged in a triple combination along with the lifespan shortening. Thus, WormCat identified a gene set with potential. phenotypic relevance not found with previous GO analysis. In conclusion, WormCat provides a powerful tool for the analysis and visualization of gene set enrichment in different types of C. elegans datasets.
Binding and Regulation of Transcription by Yeast Ste12 Variants To Drive Mating and Invasion Phenotypes
Authors: Zhou Wei , Dorrity Michael W , Bubb Kerry L , Queitsch Christine , Fields Stanley 
Published: December 2019

AbstractHere, Zhou et al. took advantage of Saccharomyces cerevisiae and its well-characterized mating and invasion pathways to explain how transcription factor variants alter motif recognition and gene expression, and ultimately, organismal phenotypes...Amino acid substitutions are commonly found in human transcription factors, yet the functional consequences of much of this variation remain unknown, even in well-characterized DNA-binding domains. Here, we examine how six single-amino acid variants in the DNA-binding domain of Ste12—a yeast transcription factor regulating mating and invasion—alter Ste12 genome binding, motif recognition, and gene expression to yield markedly different phenotypes. Using a combination of the “calling-card” method, RNA sequencing, and HT-SELEX (high throughput systematic evolution of ligands by exponential enrichment), we find that variants with dissimilar binding and expression profiles can converge onto similar cellular behaviors. Mating-defective variants led to decreased expression of distinct subsets of genes necessary for mating. Hyper-invasive variants also decreased expression of subsets of genes involved in mating, but increased the expression of other subsets of genes associated with the cellular response to osmotic stress. While single-amino acid changes in the coding region of this transcription factor result in complex regulatory reconfiguration, the major phenotypic consequences for the cell appear to depend on changes in the expression of a small number of genes with related functions.
Aplicación de la propuesta para fortalecer la vivencia de los valores de solidaridad y empatía con niños y niñas de 4 a 5 años, de una institución privada de Heredia, por medio de talleres lúdicos-creativos
Authors: Vargas Mora Mónika , Basten Michelle 
Published: December 2019

Recibido 29 de noviembre de 2012 • Corregido 01 de mayo de 2013 • Aceptado 19 de junio de 2013El objetivo fue analizar, en qué forma, el desarrollo de talleres lúdico-creativos fortalecen la vivencia de los valores de solidaridad y empatía con niños y niñas de 4 a 5 años que asisten a una institución privada en Heredia. Esta investigación fue de tipo cualitativa y se desarrolló en tres etapas. Una etapa diagnóstica para describir los conocimientos previos de las personas participantes con dichos valores, la cual se llevó a cabo por medio de entrevistas y observaciones no participantes. La segunda etapa consistió en formular y aplicar talleres lúdico-creativos que fortalecieran estos valores en el estudiantado. La última etapa fue un análisis comparativo entre la información recolectada inicialmente y los datos recopilados después de implementada la propuesta, para así verificar si la aplicación de dichos talleres influye en la vivencia de los valores de empatía y solidaridad en la niñez participante. Una de las principales conclusiones consiste en que al poder compartir y trabajar con los estudiantes y las estudiantes con esta metodología, se logró implementar una conciencia respecto a los sentimientos de las personas que los rodean, así como mejorar la convivencia de los niños y niñas con los demás.
Elevated Colonic Mucin Expression Correlates with Extended Time to Surgery for Ulcerative Colitis Patients
Authors: Eshelman Melanie A , Jeganathan N Arjun , Schieffer Kathleen M , Kline Bryan P , Mendenhall Megan , Deiling Sue , Harris Leonard , Koltun Walter A , Yochum Gregory S 
Published: December 2019

Background and Aims: Both genetic and environmental factors contribute to the development and persistence of ulcerative colitis (UC). As supported by differential responses to therapy, multiple subclasses of disease likely comprise UC. We reasoned that profiling the colonic transcriptomes may offer one approach to molecular subtype UC.
Methods: We conducted RNA-sequencing (RNA-seq) on full-thickness colonic tissues from 26 UC patients undergoing colectomy. Hierarchal clustering from transcriptomic data identified disease subsets. Subsets were characterized using differential gene expression analysis, cell type deconvolution, and network analysis.
Results: We identified two UC subsets that were distinguished by 957 differentially expressed genes. Cluster 1 was enriched in genes associated with intestinal epithelial cell (IEC) differentiation, while cluster 2 was enriched in genes associated with epithelial-to-mesenchymal transition (EMT) and inflammatory responses. Cluster 1 was associated with an extended time from diagnosis to colectomy [hazard ratio = 0.45 (95% CI: 0.14-0.88); p=0.03]. Of cluster 1 genes, elevated MUC5B, MUC4, and MUC2 expression displayed the strongest correlation with increased time to surgery [hazard ratio = 0.37 (95% CI: 0.11-0.61); p=0.0044].
Conclusions: Our transcriptome analysis indicates that UC can be sub-classified into at least two molecular signatures. We found that elevated mucin gene expression correlated with prolonged time to colectomy following diagnosis. This work identified MUC5B, MUC4, and MUC2 as potential prognostic indicators of disease severity, as reflected in time to surgery after diagnosis.
Impact of cortical mastoidectomy on tympanoplasty for recurrent suppurative otitis media: a prospective study
Authors: Sisodia Shalini Singh , Sriprakash Vinnakota 
Published: December 2019

<p class="abstract"><strong>Background:</strong> Chronic suppurative otitis media condition is characterized by an ear discharge and a perforation in the tympanic membrane. Tympanoplasty and tympanoplasty with mastoidectomy are the two common surgeries performed to manage this condition.</p><p class="abstract"><strong>Methods:</strong> 50 patients were divided into two groups of 25 each. On Group I, tympanoplasty alone was done and on Group II tympanoplasty along with mastoidectomy was performed and outcome was noted. </p><p class="abstract"><strong>Results:</strong> The most common age group to be affected was 21-30 years. Discharge of 1-3 years was observed in 32% in Group I and 36% in Group II. 84% in Group I and 72% in Group II had mild hearing loss, and in both the groups, moderate perforations were more common. 84% of the patients in Group I and 88% in group II showed acceptance to the surgeries and the hearing gain in both the groups was around 10.</p><p class="abstract"><strong>Conclusions:</strong> This study shows that tympanoplasty with mastoidectomy has no added advantage over tympanoplasty alone in the patients with chronic suppurative otitis media.</p>
Suspension damping optimization using genetic algorithms
Authors: HEMATİ Ali , SHOOSHTARİ Alireza 
Published: December 2019

Vehicle
ride comfort is a function of the frequency of transmitting vibrations to
passengers from road irregularities. The objective of this research is to provide a systematic method into the requirement
of the passive suspension based on genetic algorithm (GA). Objective function of GA method is driver’s seat acceleration to
provide driver ride comfort. The passive suspension damping coefficient and
driver’s seat suspension damping coefficient have been optimized. In this
paper, a vehicle with eight degrees of freedom has been simulated to achieve
driver’s seat comfort. Analytical
results explained by mathematical equations presented in the graphical form
have been included.
Role of Virechana Karma In Mrit Bhakshana Janya Pandu Roga W.S.R. Gandupada Krimi
Authors: Kaushik Dr. Devender , Sahay Dr. Sweta 
Published: December 2019

Background: Krimi roga is one of the most common diseases.in Ayurvedic classics most of the Acharyas gave extensive explainations regarding the krimi roga. Gandupada krimi is one of the pureeshaja krimi mentioned in classics. Ascaris Lumbricoides has the close resemblance to the Gandupada krimi, it is the most common Helminthic infestations. It has a world- wide distribution, but the highest prevalence occurs in tropical & sub- tropical regions and areas with inadequate sanitation, Poverty, ignorance, lack of hygiene maintenance, bad sanitation and use of un cooked food or improper washing of food materials, eating soil etc. are the important factors for spreading helminthic infection in developing countries like India. In Ayurveda Virechana Karma is mentioned as the ideal treatment for krimi kostha & pandu.
Objective : To study the role of Virechana karma in Mritbhakshana janya Pandu roga w.s.r. Gandupada krimi (Ascariasis)
Design: Randomized open angle clinical study.
Study: The study took place at Gaur Brahaman Ayurvedic College Brahamanwas Rohtak India.
Participant: The 40 participants were registered for study irrespective of their sex, cast, race etc.
Intervention: Role of virechana in Mritbhakshana janya panduroga WSR Gandupada krimi.
Result: 100% result of virechana found in Gandupada krimi.
Conclusion: In the present clinical study Role of Virechana karma in Mridbhakshana janya pandu offered better results in pacifying almost entire range of symptomatology.
The role of education in human nature and future human design according to Edgar Morin
Authors: Demirel Funda 
Published: December 2019

Understanding the structure of human nature is an important element in determining educational practices. Recent developments in the field of science, culture and technology today require us to reconsider the developments and changes in human nature. Therefore, while determining the qualifications and principles that should play a role in the education of the future, it is necessary to first evaluate how human that is both the subject and object of education in perceived in the 21st century. While all the disciplines are essentially examining human being from different perspectives and trying to understand its nature, Edgar Morin, a contemporary philosopher and sociologist, considers the issue from a different perspective and thinks that the reality of human nature can be reached only when the disciplines are considered as a whole. Morin, who thinks that uncertainties will be clarified with an integrated education, has suggestions for the education of the future.
Keywords: Edgar Morin, philosophy of education, education of future, human nature.
Design of smart stick for visually impaired people using Arduino
Authors: Salama Ramiz , Ayoub Ahmad 
Published: December 2019

Nowadays, blind or impaired people are facing a lot of problems in their daily life since it is not easy for them to move, which is very dangerous. There are about 37 million visually impaired people across the globe according to the World Health Organization. People with these problems mostly depend on others, for example, a friend, or their trained dog while movÄ±ng outside. Thus, we were motivated to develop a smart stick to solve this problem. The smart stick, integrated with an ultrasonic sensor, buzzer and vibrator, can detect obstacles in the path of the blind people. The buzzer and vibration motor are activated when any obstacle is detected to alert the blind person. This work proposes a low-cost ultrasonic smart blind stick for blind people so that they can move from one place to another in an easy, safe and independent manner. The system was designed and programmed using C language.
Keywords: Arduino Uno, Arduino IDE, ultrasonic sensor, buzzer, motor.
Post-partum Hemorrhage and Anemia as its Modifiable Risk Factor: A Literature Review
Authors: Anggraeni Mekar Dwi , Setiyani Rahmi , Setiawati Nina 
Published: December 2019

<p>Maternal mortality is an indicator of a country’s health status. Postpartum hemorrhage is the main cause of maternal mortality. Understanding the postpartum hemorrhage risk factors useful to develop strategy in order to reduce maternal mortality. The aim of this study was to find modifiable postpartum hemorrhage's risk factors. This study used 6 steps which include formulating the research questions and objectives, searching the extant literature, screening for inclusion, assessing the quality of primary studies, extracting data, and analyzing data. The article was searched from Google Scholar and NCBI databases using bilingual keywords: "faktor-faktor, perdarahan postpartum, risk factors, and postpartum hemorrhage". There were 1736 papers founded and only 14 articles met the inclusion criteria and included in the analysis. The review revealed that anemia, age, parity, birth passage laceration, obstetric history, multiple pregnancy, placental retention, prolonged labor, atonia uteri, pre-eclampsia, pregnancy induced hypertension, section caesarian, placental complication, history of post-partum hemorrhage, episiotomy, high neonatal birth weight. Anemia is the only modifiable risk factor which may be prevented by nurses. </p>
PERAN MAJAS SARKASME DAN NILAI PENDIDIKAN KARAKTER DALAM PUISI MENCARI TANAH LAPANG KARYA WIJI THUKUL DAN RELEVANSINYA DENGAN PENGAJARAN SASTRA DI PERGURUAN TINGGI
Authors: Hartavi Andromeda Nova , Suwandi Sarwiji , Hastuti Sri 
Published: December 2019

<em>This research aims to describe and explain the role of sarcasm, the value of character education in the collection of poetry Mencari Tanah Lapang by Wiji Thukul, and the relevance the role of sarcasm and the value of character education in the collection of poetry Mencari Tanah Lapang by Wiji Thukul on the teaching of literature in universities. Technique of subject sampling is purposive sampling. Data collection techniques used are document analysis and interviews. The validity of data in this study is done by using critical discourse analysis techniques. The results of this research are: (1) there are 62 sarcasm in the collection of poetry Mencari Tanah Lapang that serve as satirical of rules, satire of politics, satire of development, satire of education, satire of social inequality, and satire world health; (2) the value of character education contained in the collection of poetry Mencari Tanah Lapang is religious values, honesty, tolerance, hard work, democracy, reading, and social care;(3) the role of sarcasm majors and the value of character education contained in the collection of poetry Mencari Tanah Lapang can be used as a literary teaching material with the subject of poetry in the study program of Indonesian literature.</em>
PENGOLAHAN HASIL PERKEBUNAN UNTUK PENINGKATAN EKONOMI MASYARAKAT DESA WOLOGAI TENGAH KECAMATAN DETUSOKO KABUPATEN ENDE
Authors: Priska Melania , Peni Natalia , Carvallo Ludovicus 
Published: December 2019

Program KKN-PPM bertujuan untuk meningkatkan pengetahuan, ketrampilan, dan ekonomi masyarakat desa Wologai Tengah tentang pengolahan buah kopi dan kemiri menjadi kopi jahe dan minyak kemiri yang bernilai jual tinggi. Adapun metode pelaksanaan program KKN-PPM ini adalah berupa workshop pada aspek teknis maupun manajemen dan pemasarannya, dalam bentuk: workshop pembuatan kopi jahe dan minyak kemiri; workshop enterpreuner motivation; workshop manajemen home industry dan pemasaran hasil produksi. Dari kegiatan tersebut menunjukkan bahwa workshop dapat meningkatkan pengetahuan dan ketrampilan masyarakat. Selain itu, masyarakat juga dapat berwirausaha secara home industry kopi jahe dan minyak kemiri sebagai buah tangan khas desa Wologai Tengah. Hasil dari home industry kopi jahe dan minyak kemiri dapat meningkatkan ekonomi masyarakat dan membuka lapangan pekerjaan bagi masyarakat desa Wologai Tengah.
Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm
Authors: NAM Kiwoong , Nhim Sandra , Robin Stéphanie , Bretaudeau Anthony , Nègre Nicolas , d'Alençon Emmanuelle 
Published: December 2019

Abstract
Background: The process of speciation inherently involves the transition from genetic to genomic differentiation. In the absence of a geographic barrier, the whole genome differentiation may occur only when the homogenizing effect of recombination is overcome across the whole genome. The fall armyworm is observed as two sympatric strains with different host-plant preferences across the entire habitat. These two strains exhibit a very low level of genetic differentiation across the whole genome, suggesting that whole genome differentiation occurred at an early stage of speciation. In this study, we aim at identifying critical evolutionary forces responsible for the whole genome differentiation in the fall armyworm. Results: We found that these two strains exhibit a low level of genomic differentiation (Fst = 0.0176), while 91.3% of 10kb windows have genetically differentiated sequences (Fst > 0). We observed that a genomic reduction in migration rate due to combined effects of mild positive selection and genetic linkages to selectively targeted loci are responsible for the whole genome differentiation. Phylogenetic analysis shows that positive selection generates the whole genome differentiation by sub-setting of variants in one strain from the other. Conclusions: From these results, we concluded that positive selection alone is sufficient for whole genome differentiation during the process of speciation. This study demonstrates that the propensity of adaptation alone determines the speciation events, suggesting that adaptive evolution is a single critical driving force for species diversity.
Risk and Protective Factors Associated Mental Health among Female Military Veterans: Results from the Veterans’ Health Study
Authors: Adams Richard , Hu Yirui , Figley Charles R. , Urosevich Thomas G. , Hoffman Stuart N. , Kirchner H. Lester , Dugan Ryan J. , Boscarino Joseph J. , Withey Carrie A. , Boscarino Joseph A. 
Published: December 2019

Abstract
Background: This study focuses on factors that may affect female veterans’ mental health, compared to men, and is part of a large study assessing the prevalence of mental health disorders and treatment seeking among formerly deployed US military service members. Methods: We surveyed a random sample of 1,730 veterans who were patients in a large non-VA hospital system in the US. Based on previous research, women were hypothesized to be at higher risk for psychological problems. We adjusted our models for confounding factors, including history of childhood abuse, combat exposure, stressful life events, alcohol misuse, psychological resources, and social support. Results: Among the veterans studied, 5% (N=85) were female, 96% were White, 22.9% were Iraq/Afghanistan veterans, and the mean age was 59 years old. Compared to males, female veterans were younger, unmarried, college graduates, have less combat exposure, but more likely to have lifetime PTSD (29% vs. 12%.), lifetime depression (46% vs. 21%), and lifetime suicide ideation (27% vs. 11%). Females were more likely to have low psychological resilience and use psychotropic medicines and psychiatric services in the past year. Using multivariate logistic regression analyses that controlled for risk and protective factors, female veterans had greater risk for lifetime PTSD, lifetime depression, and lifetime suicidal thoughts, compared to men. Since the 95% of the population in this study were men and these results may have been statistically biased, we reran our analyses using propensity score matching. The results were the same. Conclusion: Using a sample of post-deployment veterans receiving services from a non-VA healthcare system, we find that female veterans are at greater risk for lifetime psychological problems, compared to male veterans. We discuss these findings and their implications for service providers.
Evaluation of three different vectors on human iLRP expression in Escherichia coli
Authors: Liu Bainan , Zhang Dong , Yan Lingli , Zhou Ming 
Published: December 2019

Abstract
Background: iLRP (immature laminin receptor protein) is a tumor associated antigen over-expressed on the surface of most human cancer cells and plays an important role in the process of tumorigenesis and development. It has strong auto-immunogenicity in patients and is a good target protein for tumor immunotherapy. The aim of this study is to find a practical and an efficient method for the production of recombinant iLRP, and to provide enough recombinant protein for further study of its potential applications.Results: In this report, three different expression vectors based on pET-30a(+) from pET expression systems were constructed. The first one is to add a 6xHis-Tag to the N-terminal of natural iLRP, which is called as pET-His-iLRP. The second one is to include an S-Tag between the C-terminal of 6xHis-Tag and the N-terminal of natural iLRP, which is called as pET-His-S-iLRP. The third one only contains the 6xHis-Tag in front of the N-terminal of iLRP, but the natural iLRP gene was first optimized according to the bacterial genome, and the constructed vector was named as pET-His-Opt-iLRP. Then the expression of three vectors in Escherichia coli (E. coli) BL21 (DE3) was analyzed. Results demonstrated that the expression of iLRP was the highest in the vector of pET-His-Opt-iLRP, followed by the vector of pET-His-S-iLRP, and the vector of pET-His-iLRP expressed the lowest iLRP.Conclusions: According to the results, it was concluded that the vetor pET-His-Opt-iLRP combining the codon-optimized iLRP gene with a 6xHis-Tag had the best effect on the expression of iLRP, and the expression in vectors with the natural iLRP gene depends on its leader sequences in the expression frame. The longer leader sequences accommodate to the host E. coli, the higher expression the engineered gene would be.