jimnoneill/paper-to-field-training huggingface dataset:
Data from Repositioning FDA-Approved Drugs in Combination with Epigenetic Drugs to Reprogram Colon Cancer Epigenome

&lt;div&gt;Abstract&lt;p&gt;Epigenetic drugs, such as DNA methylation inhibitors (DNMTi) or histone deacetylase inhibitors (HDACi), are approved in monotherapy for cancer treatment. These drugs reprogram gene expression profiles, reactivate tumor suppressor genes (TSG) producing cancer cell differentiation and apoptosis. Epigenetic drugs have been shown to synergize with other epigenetic drugs or various anticancer drugs. To discover new molecular entities that enhance epigenetic therapy, we performed a high-throughput screening using FDA-approved libraries in combination with DNMTi or HDACi. As a screening model, we used YB5 system, a human colon cancer cell line, which contains an epigenetically silenced &lt;i&gt;CMV-GFP&lt;/i&gt; locus, mimicking TSG silencing in cancer. &lt;i&gt;CMV-GFP&lt;/i&gt; reactivation is triggered by DNMTi or HDACi and responds synergistically to DNMTi/HDACi combination, which phenocopies TSG reactivation upon epigenetic therapy. GFP fluorescence was used as a quantitative readout for epigenetic activity. We discovered that 45 FDA-approved drugs (4% of all drugs tested) in our FDA-approved libraries enhanced DNMTi and HDACi activity, mainly belonging to anticancer and antiarrhythmic drug classes. Transcriptome analysis revealed that combination of decitabine (DNMTi) with the antiarrhythmic proscillaridin A produced profound gene expression reprogramming, which was associated with downregulation of 153 epigenetic regulators, including two known oncogenes in colon cancer (&lt;i&gt;SYMD3&lt;/i&gt; and &lt;i&gt;KDM8&lt;/i&gt;). Also, we identified about 85 FDA-approved drugs that antagonized DNMTi and HDACi activity through cytotoxic mechanisms, suggesting detrimental drug interactions for patients undergoing epigenetic therapy. Overall, our drug screening identified new combinations of epigenetic and FDA-approved drugs, which can be rapidly implemented into clinical trials. &lt;i&gt;Mol Cancer Ther; 16(2); 397–407. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

Topic: Pharmacogenetics and Drug Metabolism
Subfield: Pharmacology
Field: Pharmacology, Toxicology and Pharmaceutics
Domain: Life Sciences
The Effect of Probiotic Starter Culture Variation on the Quality of Yogurt Based on Indonesian National Standard

Yogurt is usually made by two lactic acid bacteria such as Streptococcus thermophilus and Lactobacillus bulgaricus. However, three to seven lactic acid bacteria are also used in several products. Therefore, this study aimed to examine the effect of variations in the number of starter bacteria and compare to Indonesian National Standard (SNI). The experimental method was used with starter variations, including a combination of two (Lactobacillus bulgaricus and Streptococcus thermophilus); three (Lactobacillus bulgaricus, Streptococcus thermophilus, Lactobacillus acidophilus); and seven bacteria (Lactobacillus bulgaricus, Streptococcus thermophilus, Lactobacillus acidophilus, Lactobacillus casei, Lactobacillus rhamnosus, Bifidobacterium longum, and Bifidobacterium infantis). The results showed that the yogurt with two and seven bacteria was within the range of SNI value standard. The pH, viscosity, syneresis, lactic acid content, total protein, and total number of bacteria for yogurt with two bacteria were 3.92, 453.76 cP, 88.05%, 1.27%, 3.26%, and 2.47 x 1012 Cfu/mL, respectively. The values for yogurt with seven bacteria were 4.11, 478.23 cP, 97,45%, 0,98%, 2.7%, and 1.53 x 1010, respectively, while formulas with three bacteria did not reach the pH standard. However, the atypical taste was given by the seven starter bacteria and the use of various bacteria starters affected the quality of yogurt. Specifically, formulas composed of two bacteria showed the best results according to SNI.

Topic: Food and Agricultural Sciences
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
The geriatric headache: a unique clinical ailment.

The "geriatric headache" may be a unique clinical ailment. A change in a chronic headache pattern or a new onset headache should raise suspicion immediately in an elderly patient. Temporal arteritis occurs almost exclusively in the elderly population. Because of its grave prognosis and ease of treatment, this condition should always be considered a possibility in the elderly patient with headache. A throbbing non-migranous headache may indicate an impending cerebrovascular event. Other causes of headache, such as mass lesions (tumours, subdural hematomas), drugs (nitrates, estrogens) and depression, take on greater significance in the elderly. While migraine and cluster headaches are more common in young adults, they may begin in older persons; indeed, transient migraine accompaniments are "TIA mimics". The authors hope that this overview of the "geriatric headache" will facilitate early recognition of this ailment which often leads to diagnostic confusion.

Topic: Migraine and Headache Studies
Subfield: Psychiatry and Mental health
Field: Medicine
Domain: Health Sciences
Contemporary Research Issues in Business—IT Alignment

The importance and the Strategic (Business and information technology (FI) alignment has been wed established For die past 20 years the researchers and practitioners are working hard for achieving alignment In this chapter an effort has been made to emphasize the need and importance of strategic alignment derive its definition from research literature and explore various contemporary research issues. Design/ Methodology/Approach: In this chapter an attempt has been made to conceptualize and present die various research issues with their meanings and notions adopted By various researchers in this field. These will help those researchers who want to pursue research in this field. Research limitations/Implications: The study is Based on few research articles only. It is possible to identify more research By more intensively reviewing the existing research literature. Originality/Value: This is important because the many research issues in this research area have contradictory and chaotic existence. Here the authors have a strong notion that presently there is a shortage of research articles in die existing literature presenting these research issues in a systematic and comprehensive manner.

Topic: Information Technology Governance and Strategy
Subfield: Management Information Systems
Field: Business, Management and Accounting
Domain: Social Sciences
Chemo-mechanical coupling in clays : from nano-scale to engineering applications

The main operational parameters controlling borehole stability in drilling shales with environmentally acceptable water-based drilling fluids are the density and the chemical composition of the fluid. An electro-chemo-poro-elastic model for saturated shale is presented, which describes the interaction between the drilling fluid composition and the mechanical behaviour ofthc shale. Based on the theory ofmixtures, the model for the shale distinguishes four constituents: a compressible charged porous solid, compressible fluid, cations and anions. Each constituent is described by its individual balance cquation, which allows for the necessary intcraction between the constituents. The model includes osmotic swelling of the charged porous matrix and the flows of the fluid, ions and the current through the matrix are all fully coupled. Exact analytical solutions for the electro-chemical loading of a confined cylindrical shale sample are presented for the simplified near case.

Topic: Clay minerals and soil interactions
Subfield: Biomaterials
Field: Materials Science
Domain: Physical Sciences
HPTLC quantification of garcinol in three endemic Garcinia species of Assam, estimation of secondary metabolites and evaluation of in vitro antioxidant activity

Abstract Garcinol, the main polyisoprenylated benzophenone present in Garcinia species. A simple, rapid, reliable high-performance thin-layer chromatography (HPTLC) technique has been developed for simultaneous detection and quantification of garcinol in three endemic Garcinia sp. of Assam, India. While G. mangostana and G. indica have garnered extensive recognition, these lesser-known species have not received proportionate level of scientific exploration, therefore has served as the subject of investigation. Chromatographic separation was achieved using pre-coated silica gel 60 F 254 plates. The optimized mobile phase (Toluene-Ethyl acetate-Formic acid, 5:4:1 V/V ) at 276 nm produced well-defined and sharp peaks of garcinol, maintaining a constant R F value of 0.75. The regression equation demonstrated a linear relationship with a correlation coefficient of 0.9955. The method was validated in accordance with International Conference of Harmonization guidelines (ICH), encompassing assessments for precision, accuracy, repeatability and robustness, all of which yielded low percentage of relative standard deviation values, attesting to its excellent performance. The content of garcinol found in the extracts were in the range of 0.58–0.98 % w/w . In secondary metabolite analysis, significant amount of phenols (26.06 ± 1.65–57.51 ± 2.62 gallic acid equivalent mg g −1 ), flavonoids (11.27 ± 1.06–21.09 ± 1.34 quercetin equivalent mg g −1 ) and ascorbic acid (3.56 ± 0.12–3.65 ± 0.11 mg/10 g) contents were detected in the extracts. Further, the extracts exhibited good anti-radical activity, which may be attributed to the presence of important secondary metabolites. Therefore, this research establishes the three endemic Garcinia sp. as promising source of garcinol. Additionally, the developed method can be applied for routine quality control analysis of herbal formulations containing garcinol.

Topic: Natural Compound Pharmacology Studies
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Essays in Applied Microeconomics: Dissertation Summary

In the United States, like many developed countries, government provides substantial support for primary, secondary, and postsecondary education. In 2011, expenditures on education are expected to equal 7.6 percent of GDP (National Center for Education Statistics 2011). At the postsecondary level, federal grants and loans for college students aim to ameliorate credit market imperfections. Publicly provided K–12 education insures universal access to human capital development for all children. The three essays that make up this dissertation broadly focus on the role government should play in financing and providing education.

Topic: Monetary Policy and Economic Impact
Subfield: General Economics, Econometrics and Finance
Field: Economics, Econometrics and Finance
Domain: Social Sciences
Recovery of multi-drug resistant, multiple antibiotic resistance genes-carrying non-typhoidal Salmonella from antibiotic-free and conventional chicken meat: A comparative study in Delhi, India

Food-associated Salmonella spp. are regularly implicated in diarrhoeal illnesses. Emergence of antibiotic resistance (AR) among Salmonella enterica (S. enterica) has become a global healthcare problem, necessitating an AR risk assessment along the food-chain network. Considering the growing trend of selling alternatively labelled meat products in low- and middle-income countries like India, a comprehensive evaluation of AR in non-typhoidal Salmonella (NTS) isolates associated with antibiotic-free (AF) labelled chicken meat was carried out. Additionally, the resistance profile of AF chicken meat-derived microbes was compared to the conventional (CL) chicken meat-derived ones. Results highlighted high degree of resistance in AF-derived NTS isolates to tetracycline (87.0 %), nalidixic-acid (53.0 %) and ampicillin (41.0 %), and moderate degree of resistance to imipenem (28.0 %), co-trimoxazole (27.0 %), cefazolin (23.0 %) and ciprofloxacin (15 %). Horizontally-transmissible AR genes (ARGs), such as, tetA (77.0 %), qnrS (53.0 %), ampC (41.0 %), sul3, (21.0 %) etc. were also prevalent among screened isolates. Overall, 74.0 % of S. enterica were multi-drug resistant (MDR) and 45.0 % harboured ≥ 3 ARGs. There was no difference in resistance profile and multiple antibiotic resistance (MAR) index of isolates derived from AF and CL chicken meat (two-way ANOVA, unpaired t-test, respectively; p < 0.05). Correlation analysis showed a positive relationship between various AR phenotypes and ARGs that provide the corresponding resistance (p < 0.05). This means that the prevalence of positively correlating ARGs could be used to predict physical resistance. Our study illustrates that choosing AF chicken meat in markets of Delhi may not effectively minimise the exposure of resistant NTS to consumers. Observations also recommend a systematic AR risk assessment of foodstuffs across the region for a more informed assistance to the authorities in distributing relevant labels to food products.

Topic: Salmonella and Campylobacter epidemiology
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Cardiac gene expression profile and lipid accumulation in response to starvation

Starvation induces many biochemical and histological changes in the heart; however, the molecular events underlying these changes have not been fully elucidated. To explore the molecular response of the heart to starvation, microarray analysis was performed together with biochemical and histological investigations. Serum free fatty acids increased twofold in both 16- and 48-h-fasted mice, and cardiac triglyceride content increased threefold and sixfold in 16- and 48-h-fasted mice, respectively. Electron microscopy showed numerous lipid droplets in hearts of 48-h-fasted mice, whereas fewer numbers of droplets were seen in hearts from 16-h-fasted mice. Expression of 11,000 cardiac genes was screened by microarrays. More than 50 and 150 known genes were detected by differential expression analysis after 16- and 48-h-fasts, respectively. Genes for fatty acid oxidation and gluconeogenesis were increased, and genes for glycolysis were decreased. Many other genes for metabolism, signaling/cell cycle, cytoskeleton, and tissue antigens were affected by fasting. These data provide a broad perspective of the molecular events occurring physiologically in the heart in response to starvation.

Topic: Hormonal Regulation and Hypertension
Subfield: Endocrinology, Diabetes and Metabolism
Field: Medicine
Domain: Health Sciences
Culture strategies, diseases and their mitigations in mono-sex Nile tilapia farming in Jessore sadar region, Bangladesh

A survey was carried out to investigate culture strategies, disease patterns and mitigations in mono-sex Nile tilapia in Jessore sadar region. Data obtained by questionnaire interview, individual interview, telephonic interview, PRA method, mono-sex Nile tilapia farm survey from four villages. It was observed that 30.769% farmers and farm owner had no training about culture of mono-sex Nile tilapia while 69.230% farmers and farm owner received short term training from different Department of Fisheries, different NGOs. Mono-sex Nile tilapia culture in ponds was basically a three-tier culture system. Pre-stocking management of ponds in the study area comprised dike repairing, aquatic weed control, waste soil removal and undesirable species (predator and trash fish) control. Majority (85%) of the farm owners and farmers depends on ground water and only (15%) depends on surface water. About 95% of farm of farm owners controlled aquatic weeds manually. Removal of predatory and undesired fish from pond used different types of chemicals but most used rotenone (80%). Fertilizer of pond preparation (Organic and inorganic) in the study area but mostly used cases inorganic fertilizers had applied at the rate of urea 114 kg/ha and triple superphosphate 60 kg/ha in 4-5 installments. Stocking density of mono-sex Nile tilapia was 200-380 fry per decimal. It was recorded that 85% of mono-sex Nile tilapia farmers and farm owner applied supplementary such as commercially manufactured feed and 12% are applied of farm made feed. It was observed,they provided heavy fertilizer, high stocking density, over feed provided, provided over dose drugs so ultimated result of disease occured. Parasitic related disease, bacterial diseases, fungal diseases, viral diseases were attacked in mono-sex Nile tilapia. Argulosis and Streptococcus were mostly common disease in this mono-sex Nile tilapia farm.

Topic: Fish Biology and Ecology Studies
Subfield: Aquatic Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Electronic Medical Record (EMR) Informatics Security

Medical records, once archived on paper and stored in filing cabinets, are now housed in electronic data repositories. While converting medical information into electronic format yields enormous benefits, it also raises new privacy and security concerns. The fact that medical information is now accessed, stored, processed, and transmitted through multiple organizations has led to the need for medical informatics security. In this paper, we examine the evolution of electronic medical records, review relevant legislation, and examine issues of privacy and security as it relates to medical information.

Topic: Electronic Health Records Systems
Subfield: Health Information Management
Field: Health Professions
Domain: Health Sciences
Type 2 diabetes and physical activity: barriers and enablers to diabetes control in Eastern India

Abstract Introduction: Type 2 diabetes (T2D) has tremendous morbidity burden owing to disease management and complication prevention. Behavior modification identified as a key to management includes healthy diet and regular physical activity (PA). This study aims to identify patterns and preferences of PA of T2D patients and explore perceived enablers and barriers for diabetes control in Bhubaneswar. Methods: Cross-sectional, facility-based study conducted in the private sector from June to August 2014 recruited 321 T2D patients using semi-structured questionnaires. Descriptive statistics and associations of PA were computed. Results: Almost two-thirds of patients (59%) were reported performing PA frequently. Majority patients cited walking as the most preferred mode of PA (79%) with 41% performing PA daily. Actual versus perceived weight was a complete mismatch with most patients misjudging their weight. Reasons for enabling PA included ‘controlling diabetes’ and ‘doctor’s advice’ as key factors, while ‘lack of time’ and ‘unwillingness’ were main barriers among inactive patients. Conclusion: Counseling on PA by physicians during routine visits, along with tailored or patient-specific interventions should be considered. Focus on social support for positive behavioral changes and motivation play a central role in diabetes control.

Topic: Diabetes Management and Education
Subfield: Endocrinology, Diabetes and Metabolism
Field: Medicine
Domain: Health Sciences
Histone H3 Lysine 4 and 27 Trimethylation Landscape of Human Alzheimer’s Disease

Background: Epigenetic remodeling is emerging as a critical process for both the onset and progression of Alzheimer’s disease (AD), the most common form of neurodegenerative dementia. However, it is not clear to what extent the distribution of histone modifications is involved in AD. Methods: To investigate histone H3 modifications in AD, we compared the genome-wide distributions of H3K4me3 and H3K27me3 in entorhinal cortices from severe sporadic AD patients and from age-matched healthy individuals of both sexes. Results: AD samples were characterized by typical average levels and distributions of the H3K4me3 and H3K27me3 signals. However, AD patients showed a lower H3K4me3 and higher H3K27me3 signal, particularly in males. Interestingly, the genomic sites found differentially trimethylated at the H3K4 between healthy and AD samples involve promoter regions of genes belonging to AD-related pathways such as glutamate receptor signaling. Conclusions: The signatures of H3K4me3 and H3K27me3 identified in AD patients validate the role of epigenetic chromatin remodeling in neurodegenerative disease and shed light on the genomic adaptive mechanisms involved in AD.

Topic: Epigenetics and DNA Methylation
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Does Security Imply Safety? On the (Lack of) Correlation Between Different Aspects of Security

This paper investigates to what extent different aspects of security correlate. It distinguishes four concepts covered by the term ‘security’: technical safety, perceived safety, technical security and perceived security. It is shown that these concepts need not correlate conceptually. Furthermore, the paper shows empirically that these concepts correlate weakly in two cases. This has implications for policy and research. First, it leaves open the possibility that interventions targeting one aspect of security do not affect, or even adversely affect, another aspect of security: an expression of a security gap. Second, research is commonly motivated by individual-level arguments relating to safety, whilst relying on aggregate indicators more likely capturing security.

Topic: Terrorism, Counterterrorism, and Political Violence
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
Islamic Education Values in Minangkabau Wedding Ceremony (Study of Traditional Mariage in Pauh, Padang, West Sumatera)

The aim of the research is to describe the processions of wedding ceremony that done by Pauh society. It also aims to find out whether the values of Islamic education are still carried out by the society in the wedding processions. The research was descriptive qualitative method using naturalistic approach where the data were obtained through observation and interview. The subjects of the research were the head of KAN Kerapatan Adat Nagari in Pauh, ninik mamak, cerdik pandai, the head of KUA, and religious leaders. Snowballing sampling technique was used and the head of the KAN of Pauh was decided to be the first key informant. Based on the information gathered from the key informants, it was found that Islamic education values were reflected in the procession of wedding ceremony. It is recommended that wedding ceremony in West Sumatra should be held properly based on the Isamic teaching.

Topic: Cultural and Religious Practices in Indonesia
Subfield: Cultural Studies
Field: Social Sciences
Domain: Social Sciences
Cloning by Gibson Assembly v1

Gibson assembly is a molecular cloning method that allows for the joining of multiple DNA fragments in a single, isothermal reaction. It is named after its creator, Daniel G. Gibson, who is the chief technology officer and co-founder of the synthetic biology company, Telesis Bio. - Wikipedia Daniel G. Gibson, of the J. Craig Venter Institute, described a robust exonuclease-based method to assemble DNA seamlessly and in the correct order, eponymously known as Gibson Assembly. The reaction is carried out under isothermal conditions using three enzymatic activities: a 5’ exonuclease generates long overhangs, a polymerase fills in the gaps of the annealed single strand regions, and a DNA ligase seals the nicks of the annealed and filled-in gaps. This method has been widely adopted and is a major workhorse of synthetic biology projects worldwide.

Topic: CRISPR and Genetic Engineering
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
[Impact of pretreatment variables on the outcome of standardized 131I therapy with 150 Gray in Graves' disease].

Radioiodine treatment with 150 Gray causes a considerable decrease in thyroid size in most patients with Graves' disease. Age and initial thyroid volume are important determinants of thyroid function and size after therapy and should be considered in dose calculation.

Topic: Thyroid Disorders and Treatments
Subfield: Endocrinology, Diabetes and Metabolism
Field: Medicine
Domain: Health Sciences