Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene expression analysis in breast cancer

Breast cancer is the most common type of cancer among females, both in incidence and death. As meaningful biological understanding of the disease is confounded by the existence of various molecular groups and sub-groups, the challenge for targeted drug development may lie in understanding the molecular mechanisms of various sub-groups in breast cancer. An in-house breast cancer gene expression dataset comprising 17 normal and 104 tumour samples was analysed to identify important genes and pathways relevant to various clinical parameters. Our results identified groups of patients with similar expression profiles, the possible biology driving them and the clinical implications. Comparing Normal and Cancer specimens’ gene expression profiles, TP53, along with cell cycle genes, were up-regulated in cancer samples. Embryonic stem cell pathway genes were up-regulated, while fatty acid biosynthesis pathways were down-regulated in tumors vs normal. The cancer specimens largely clustered with respect to ER status. Meta-analysis was performed on in-house datasets along with five public datasets to identify ER pathway genes. The analysis identified novel genes which had not been previously associated with ER-related pathways in cancer. Nuclear receptor pathways were up-regulated in ER-positive tumors/cell lines. Mining for ESR1-correlated genes across 5897 specimens identified FOXA1, SPDEF, C1ORF34 and GATA3 expression to be highly correlated. Three sub-clusters were identified among the ER-negative cluster. One represented ERBB2 over-expressing cluster. Additionally two unique groups of patients, with significant differences in survival, previously un-identified by other studies, were identified among the ER-negative cluster; a good prognosis cluster with high expression of Immune response genes; and a bad prognosis cluster with high expression of Ropporin, over-expression of which was also linked to high incidence of relapse in our study. siRNA knockdown of Ropporin (ROPN1 and ROPN1B) in the M14 melanoma cell line impaired cancer cell motility and invasion. Knockdown of ROPN1B in MDA-MB-435s reduced motility. In the first study of its kind our results validated the role of Ropporin in cancer cell motility and invasion. A list of 162 relapse-associated prognostically-important genes was used to develop a Neural Network back propagation model to predict the clinical outcomes. The model was successful in predicting relapse with 97.8% accuracy and outperformed existing models, indicating a strong possibility of its use as diagnostic model.
Prevalence of ocular manifestations of HIV/AIDS among patients attending adult infectious disease centre(AIDC)of excellence at the University Teaching Hospital in Lusaka,Zambia

Prevalence of ocular manifestations of HIV/AIDS among patients attending Adult Infectious Disease Centre (AIDC) of excellence at UTH, Lusaka. HIV and AIDS related ocular manifestations may affect 50-75% of HIV positive patients at some point in the course of their illness. Zambia has an HIV prevalence rate of 13.0%. This study was conducted in order to establish the prevalence and types of ocular manifestations in HIV/AIDS patients. This study was undertaken in order to determine the prevalence of ocular manifestations of HIV/AIDS in patients attending AIDC at UTH in Lusaka Zambia as well as to establish the types and categorize the HIV/AIDS ocular manifestations. Hospital based cross-sectional study. Adult Infectious Disease Centre (AIDC) of excellence at UTH, Lusaka. A total of 385 HIVAIDS patients attending routine clinic at the AIDC were randomly sampled and enrolled for the study. Patient’s medical records were used to obtain information on age, sex, HIV stage and CD4-T cell count. Ophthalmic examination included visual acuity assessment, anterior segment examination with slit-lamp biomicroscope and posterior segment examination using indirect ophthalmoscope and with the help of a 20D lens. Histopathological examinations were conducted on the specimen excised from patients who had conjunctival growths that were suspicious for Squamous Cell Carcinoma (SCC). The Statistical Package for Social Scientists (SPSS) version 22 was used to store and analyze the data. Inferential statistics was performed and a p<0.05 was considered significant. Ethical approval was obtained from UNZA Biomedical Research and Ethics Committee. The prevalence of ocular manifestations in this study was 74.0%. Out of the 385 participants (64.0%) were female and (36.0%) were males. Three hundred and Seventy Three 373 (96.9%) participants were on HAART for an average period of 7.8 months. A total of 211 (54.8%) participants had CD4 T-cell count ≥ 350 cells/μL, 79 (20.5%) had CD4 Tcell count between 200-350, and 88 (22.9%) had CD4 T-cell count below 200 cells/μL.
Known Phylogenies of Organisms Based on the Comparison of Homologous E2f Transcription Factors and how these Different Factors Changed Through Evolution

This study introduces the methods used to determine the phylogeny of different E2f factors as they might have evolved over time in different organisms, diverging into the wide array shown today. It also represents a method to find new, putative E2f factors in the known genomic database through in silico analysis. To do this, techniques such as BLAST searches, sequence homology alignment, and phylogenetic comparisons were used. The findings of this study suggest that these factors may have evolved through the basis of function, although convergent evolution may be a distinct possibility in some cases. From these finds, the activator groups may have evolved separately from the repressor groups, but with different groupings than those found when the factors were independently analyzed. To make this conclusion, we also used potential factors that were found in some metazoans like Arabidopsis or Danio rerio. Further investigation may be needed to determine whether these factors may really function in the way that E2fs are known to do.
EFEKTIVITAS EDUKASI FLIPCHART TERHADAP PENGETAHUAN, SIKAP, PERSEPSI DAN GULA DARAH PASIEN DM TIPE 2 DENGAN TERAPI INSULIN

ABSTRAK Latar belakang: Diabetes Mellitus (DM) merupakan penyakit metabolik yang ditandai hiperglikemia dan gangguan metabolisme karbohidrat, protein, dan lemak akibat gangguan insulin, baik sekresi,kerja atau keduanya. Edukasi merupakan salah satu cara yang efektif untuk mengurangi komplikasi dan meningkatkan pengelolaan DM. Penelitian terdahulu menunjukan bahwa edukasi dengan flipchart memberikan pengaruh terhadap pengelolaan diabetes mellitus. Tujuan dari penelitian ini adalah untuk mengetahui efektivitas dari pemberian edukasi flipchart terhadap pengetahuan pasien DM tipe 2. Metode: Survey dilakukan menggunakan metode penelitian pre-experimental dengan desain pre-posttest study. Kuesioner digunakan untuk mengukur tingkat pengetahuan,sikap, persepsi pasien. Sampel adalah pasien diabetes mellitus tipe 2 di RSUD Sanjiwani Gianyar yang memenuhi kriteria inklusi. Penelitian dilakukan Juni-November 2017. Hasil data dianalisis menggunakan Wilcoxon Signed Ranks Test. Hasil: analisa pada empat puluh pasien diabetes mellitus tipe 2 menunjukkan terdapat perbedaan signifikan (p<0,005 ) pada pengetahuan, sikap, persepsi dan kadar gula darah acak sebelum dan setelah diberikan edukasi flipchart. Kesimpulan: Pemberian edukasi terapi insulin dengan media flipchart pada pasien diabetes mellitus tipe 2 dapat meningkatkan pengetahuan, sikap, persepsi dan kadar gula darah acak. Kata Kunci: Diabetes Mellitus tipe 2, Pengetahuan, Sikap, Persepsi, Gula darah acak Background: Diabetes Mellitus (DM) is a metabolic disease characterized by hyperglycemia and metabolic disorders of carbohydrates, proteins, and fats due to insulin disorders, secretions, work or both. Education is one effective way to reduce complications and improve the management of DM. Previous research has shown that education with flipcharts has an effect on the management of diabetes mellitus. The purpose of this study is to determine the effectiveness of flipchart education on the knowledge of patients with type 2 diabetes mellitus. Methods: The survey was conducted using pre-experimental research method with preposttest study design. Questionnaires were used to measure the level of patient knowledge, attitude, and perception. The sample was a patient of type 2 diabetes mellitus at RSUD Sanjiwani Gianyar who fulfilled the inclusion criteria. The study was conducted from June to November 2017. The results were analyzed using Wilcoxon Signed Ranks Test. Result: The results of analysis on forty patients with type 2 diabetes mellitus showed significant differences (p<0,005) in knowledge, attitude, perception, and blood glucose before and after given flipchart education. Conclution: Provision of insulin therapy education with flipchart media in patients with type 2 diabetes mellitus can improve patient knowledge, attitude, perception, and random blood glucose. Keywords: Type 2 Diabetes Mellitus, Knowledge, Attitude, Perception, Blood Glucose
Genetic analysis of diarrhea and respiratory diseases in Austrian Fleckvieh heifer calves

A routine registration system is an essential prerequisite for the reduction of disease frequencies by both, management and breeding. However, in Scandinavian countries with a long history of health registration and also in Austria, where health registration just started recently, the main focus is on lactating cows. While support for management (Egger-Danner et al. (2007a)) is also provided for replacement stock, no routine breeding value estimation exists for this group of animals in either country. Continued non-consideration of calfhood diseases could however lead to increased disease incidence. Gastrointestinal and respiratory diseases were shown to be among the main health problems during the calves’ first months of life (e.g. Gulliksen et al. (2009); Svensson et al. (2003)). In dairy cattle, genetic parameters were only estimated for respiratory diseases in Norwegian Red calves (intraherd heritability 0.05 on the underlying scale; Heringstad et al. (2008)). The aim of this study thus was the genetic analysis of diarrhea and respiratory diseases in female Austrian Fleckvieh (dual purpose Simmental) calves by means of a Bayesian probit threshold sire model.
Cardiovascular Risk Factors at a National Heart Referral Center in Sudan

عل ةيلاع تلادعم دوجو يلا ثحبلا صلخو يلع أرط يذلا رييغتلا يلا اهمظعم دوعي ةددعتم بابسا نع ةجتان ةيئاعولا ةيبلقلا ةروطخلا لماو ددعتملا نوهدلا نم ةريبك تايمك يلع يوتحت يتلاو فايللاا ةليلق ةيذغلاا نم عاونا كلاهتسا و ةقباسلا ةثلاثلا دوقعلا للاخ هايحلا طمن ة سلا تابجولاو ةرركملا تايوشنلا و عبشتلالا ةيلاع تلادعمب نيخدتلا ةرهاظراشتنا يلا ةفاضلااب نوهدلاو حلملا نم ةيلاعلا تايمكلا تاذ ةعير بابشلا طاسوا نيب . طمن عابتا ةيمهاو لماوعلا هذه هاجت ناكسلا نيب يعولا عفرب مامتهلاا ةيحصلا تاهجلا ثح يلع ةيصوتب ثحبلا متخيو لا يندبلا طاشنلاب مامتهلااو يحص يئاذغو يتايح يموي .
Frequent pattern finding in integrated biological networks

Biomedical research is undergoing a revolution with the advance of high-throughput technologies. A major challenge in the post-genomic era is to understand how genes, proteins and small molecules are organized into signaling pathways and regulatory networks. To simplify the analysis of large complex molecular networks, strategies are sought to break them down into small yet relatively independent network modules, e.g. pathways and protein complexes. In fulfillment of the motivation to find evolutionary origins of network modules, a novel strategy has been developed to uncover duplicated pathways and protein complexes. This search was first formulated into a computational problem which finds frequent patterns in integrated graphs. The whole framework was then successfully implemented as the software package BLUNT, which includes a parallelized version. To evaluate the biological significance of the work, several large datasets were chosen, with each dataset targeting a different biological question. An application of BLUNT was performed on the yeast protein-protein interaction network, which is described. A large number of frequent patterns were discovered and predicted to be duplicated pathways. To explore how these pathways may have diverged since duplication, the differential regulation of duplicated pathways was studied at the transcriptional level, both in terms of time and location. As demonstrated, this algorithm can be used as new data mining tool for large scale biological data in general. It also provides a novel strategy to study the evolution of pathways and protein complexes in a systematic way. Understanding how pathways and protein complexes evolve will greatly benefit the fundamentals of biomedical research.
The Energetics of Estivating Sirenid Salamanders

Siren lacertina and Pseudobranchus striatus are aquatic salamanders that inhabit drought-prone waters in the southeastern United States. When drought occurs, sirenids burrow into the substratum and remain inactive until the habitat is reflooded. The energetics of estivating sirenids were studied by inducing animals to estivate in the laboratory and measuring rates of oxygen consumption and blood lactate levels. Lipid stores were measured to determine energy reserves of fresh-caught animals. In both species, resting metabolic rates are 60-70% lower in estivators than in aquatic animals. At these low metabolic rates, adult S. lacertina (>500 g body mass) could survive 2-3 yr on stored energy. Smaller S. lacertina and P. striatus have higher massspecific metabolic rates during estivation, but even a 1 g sirenid could survive for several months without food. Ventilation rates decrease during estivation, but low blood lactate levels indicate that respiration is aerobic.
Comparison of delayed cord clamping and umbilical cord milking in late preterm and term Infants – An Open Label Randomised Control Trial.

The umbilical cord is the lifeline that connects the placenta to the fetus. It contains umbilical arteries that carry blood from the infant to the placenta and umbilical veins which carry blood from the placenta to the infant. Following birth, blood continues to flow through umbilical arteries (from the infant to the placenta) for approximately 20-25 seconds and is negligible by 45 seconds (Yao and Lind, 1974). In the umbilical vein, however, blood continues to flow from the placenta to the infant for up to 3 minutes after delivery (Dewey and Chaparro, 2007). 1. Umbilical cord milking is as effective as delaying the umbilical cord clamping in achieving higher haemoglobin levels at two months of age in late preterm and term infants delivered both by caesarean section and vaginal route. 2. Umbilical cord milking and delayed cord clamping resulted in comparable levels of haemoglobin and hematocrit at 48 hours of life implying that similar amount of placental transfusion occurs in both the groups. 3. Milking the umbilical cord resulted in similar iron stores when compared to that of the delayed cord clamping. 4. Umbilical cord milking does not produce significant hemodynamic disturbances. 5. Frequency of adverse effects like significant hyperbilirubinemia requiring phototherapy, respiratory distress and Polycythemia were similar in both the groups.
Assessment of a Brief Intervention with Parents to Prevent Shaken Baby Syndrome

Abstract Shaken Baby Syndrome (SBS) is a form of physical abuse, which may result in serious consequences for child development. Despite its severity, SBS can be prevented through parent training. This study aimed to evaluate the effectiveness of a brief intervention to increase knowledge on SBS with 252 parents. Participants were randomly assigned into two conditions: Experimental Group (EG) and a waiting Control Group (CG). The intervention consisted of exhibition of an educational video and reading a pamphlet on SBS. To measure parental knowledge, the Attitudes towards the Infant Crying Scale was used. An increase in participants’ knowledge about consequences of shaking, caregiver’s wellbeing, caregiver strategies to deal with crying, beliefs about infant care and about characteristics of infant crying were observed in the EG at posttest, indicating the effectiveness of the intervention.
Wystepowanie i charakterystyka gronkowcow wyizolowanych od drobiu

The paper presents the results of studies on staphylococci infections in poultry and the phenotype properties of isolated strains. A total of 572 studies were carried out from October 2000 to July 2001, and the percent-age of the samples collected for examination was as followed: 70% - layers and broilers, 14% - ducks and geese, 12.4% - turkeys, and 3.6% - pigeons, ostriches and parrots. Staphylococci were isolated from birds' organs (liver, spleen and lungs) and joints (tarsal and digits). The isolated staphylococci were identified with ID32 STAPH kit (bioMerieux) and other tests (e.g. coagulase and DNase test, clumping factor", pigmentation and haemolytic activities). Additionally, susceptibility to chemotherapy was determined in-vitro. The sensitivity of S. aureus strains to methycillin was also determined. A high percentage of microbial infections caused by the micro-organisms of Staphylococcus genus were recorded. Staphylococei were isolated in 60 out of the 572 eases examined (10,5%) and the strains'distribution was as follows: 43 strains (71.7%) found in layers and broilers, 8 (13.3%) in ducks and geese, and 9 (15.0%) in turkeys. The staphytococci isolated from poultry belonged to 10 species, amongst which the most common were: S. aureus (48,3%), S. xylosus (15,0%), S. lentus (8,3%), S. cohni and S. saprophiticus (po 5%). Birds* joints afflicted with lesions showed a total of 18 strains (30% of all isolates) belonging to 2 species, namely: S. aureus (83,3%) and S. lentus (16,7%). All staphylococci strains were characterised in vitro by a high sensitivity to amoxyeillin and amoxycillin with clavulanic acid (100%) and ampicillin, neomycin and gentamicin (over 90%). All S. aureus strains proved to be sensitive to methycillin.
Valeur nutritionnelle de la viande de lapin

Les aliments pour l'homme, outre leurs aspects nutritionnels de couverture des besoins, ont acquis depuis peu une valeur sante. Face a ce phenomene, de nouveaux besoins de connaissances concernant les constituantsdes aliments sont apparus. Cet article a pour objet de montrer les points forts et les lacunes dans les connaissances relatives a la valeur nutritionnelle de la viande de lapin. 50 publications ont ete selectionnees. Pour des lapins aux âges et poids commerciaux d'abattage, les teneurs en proteines (21 ′ 1,5 % de viande fraiche), eau (72,5 ′ 2,5 % de viande fraiche) et mineraux totaux (1,2 ′ 0,1 % de viande fraiche) sont similaires dans les differents travaux et ne necessitent pas d'autres investigations. Les principales causes de variations de la teneur en lipides (5 ′ 3,3 % de viande fraiche) sont connues et bien decrites (region anatomique et alimentation principalement). La viande de lapin est pauvre en sodium (49 mg/100 g) mais riche en phosphore (277 mg/100 g). Les teneurs en certains elements tels le fer (1,4 mg/100 g), le cuivre ou le selenium ne sont pas suffisamment bien etablies. Par ailleurs les teneurs d'autres oligo-elements n'ont a notre connaissance jamais ete evaluees. Enfin, les donnees disponibles semblent indiquer que la viande de lapin montre un profil global en vitamines proche de celui observe chez le poulet. Il est cependant necessaire de confirmer ces observations. La viande de lapin presente une teneur en cholesterol relativement basse comparativement aux autres viandes de 59 mg/100g et un ratio en acides gras omega 6 / omega 3 avantageux de 5,9. L'equilibre en acide gras de la viande de lapin, animal monogastrique et herbivore, montre par ailleurs une remarquable plasticite en fonction de l'equilibre en acide gras de la ration.
Possible Role of Brain-Derived Neurotrophic Factor in the Pathogenesis of Coronary Artery Disease

Background— The neurotrophin (NT) family, including nerve growth factor NT-3 and brain-derived neurotrophic factor (BDNF), has a critical role in the survival, growth, maintenance, and death of central and peripheral neurons. NTs and their receptors are expressed in atherosclerotic lesions; however, their significance in cardiovascular disease remains unclear. Methods and Results— To clarify the role of NTs in the pathogenesis of coronary artery disease, NT plasma levels in the aorta, coronary sinus, and peripheral veins of patients with unstable angina (n=38), stable effort angina (n=45), and non–coronary artery disease (n=24) were examined. In addition, regional expression of BDNF in coronary arteries was examined in autopsy cases and patients with angina pectoris by directional coronary atherectomy. The difference in BDNF levels, but not NT-3, between the coronary sinus and aorta was significantly greater in the unstable angina group compared with the stable effort angina and non–coronary artery diseas.
Assessing Malaria Vaccine Efficacy

After many years of silence, eradication of malaria is, once again, one of the top priorities on the agenda of many international health and development agencies. To meet this idealistic goal, a combination of control tools is needed. From this armentarium, a malaria vaccine is central to prevent infection and/or disease. However, numerous malaria vaccine candidates have shown limited efficacy in Phase II and III studies. One reason for these failures has been that the assessment of efficacy in the context of malaria has been difficult to standardize. In this article, we have reviewed and discussed the different ways to assess the outcome of a malaria vaccination.