Miracle-dz/UniFAR-FTUs huggingface dataset:
Current Trends in the Quality Assessment of Colorectal Cancer Practice and Treatment in South Korea during 2012–2017

Purpose Colorectal cancer (CRC) is increasing in South Korea due to westernized eating habits and regular health check-ups. The Korean Health Insurance Review and Assessment Service (HIRA) has conducted a national quality assessment of the treatment of CRC. This study examined the quality assessment report of the Korean HIRA and analyzed the status of practice pattern and the epidemiology of CRC in South Korea. Materials and Methods The number of subjects was determined based on the number of surgical procedures in each institution during 2012–2017. The institution types were classified according to the number of beds and the composition of oncologic specialists. Twenty-one indicators for diagnosis, chemotherapy, radiotherapy, surgery, pathology, and mortality were analyzed and the inter-institutional variation for each indicator was calculated. Results Among 21 evaluation indices, indicators related to medical records, receipt of chemotherapy with a high coefficient of variation of ≥ 0.1% were improved over 6 years until the survey in 2017. In the analysis of indices affecting surgical mortality, the regional lymph node resection and examination rate (p=0.022) showed a negative correlation with surgical mortality. Hospitalization stay (p < 0.001) and hospitalization cost (p=0.002) were positively correlated with surgical mortality. Conclusion This study showed that the treatment quality and examination status for CRC in South Korea were appropriate for improving relevant medical records, receipt of chemotherapy, maintaining the quality of treatment, and mortality. These analyses could be the basis for developing an improved quality assessment program worldwide.
Sex Chromatin Prevalence in Bengalee Hindu Females: A Comparative Study on Breast Cancer

X Chromosome inactivation refers to the developmentally regulated process of silencing gene expression from all but one X chromosome per cell in female mammals in order to equalize the levels of X chromosome derived gene expression between the sexes. In females, X Chromosome Inactivation (XCI) begins with the expression of the XIST gene from the X Chromosome destined to be inactivated (Xi) and the coating of XIST RNA in cis. The apparent cytological overlap between BRCA1 and XIST RNA across the Xi raised the possibility of a direct role of BRCA1 in localizing XIST. The present study was conducted to evaluate the comparison of prevalence of sex chromatin in Bengalee Hindu Breast Cancer patients with Normal Bengalee Hindu females. Material for the present study consisted of the samples of buccal smears of 70 normal females and 35 females of carcinoma of breast belonging to stage II, III, and IV. One hundred cells from each individual will be studied to ascertain the modal rate of incidences of sex chromatin. The present study demonstrated that the frequency of sex chromatin was significantly lower (P<0.05) among the breast cancer patients compared to the normal healthy females indicating reactivation of inactive X chromosome in case of malignancy. These results suggested the prognostic value of prevalence of sex chromatin in Breast Cancer patients.
Retrospective analysis of off‐label medication use at a plastic surgery hospital in China and evidence‐based evaluation

To retrospectively analyze the off‐label prescriptions at a plastic surgery hospital in China and conduct a literature review. The prescriptions in outpatient department from January 1, 2018 to December 31, 2018 were collected and compared with the related drug instructions in indications, dosage, frequency and route of administration to identify the off‐label prescriptions. According to related literatures, guidelines, and MICROMEDEX, the rationality of off‐label drug uses was evaluated. A total of 39 836 prescriptions were screened and 3395 (8.52%) off‐label prescriptions were identified. It involved 23 items off‐label medication uses. 20 items were off‐label used in indication and three items were in indication and administration route. These off‐label prescriptions involved 19 medicines and 12 indications and the dermatology related drug usage accounted for the largest proportion (91.3%). Additionally, five items (21.7%) were Chinese patent medicine related. Of the 23 items, seven (30.4%) have been recommended by guidelines and two (8.7%) by Thomson Grading System of Micromedex. All of them have been proved by literature evidence of level 1 to 4, in which 19 (82.6%) by Level 1 evidence, 21 (91.3%) by Level 1 to 2 evidence and 2 (8.7%) only by level 3 to 4 evidence. This can provide a theoretical basis to clinicians in prescribing. Our next work is to perfect some details about evidence assessment to improve the reliability.
Elucidating a novel WNT/?-CATENIN Signaling-Independent Environment that Precedes Villus Morphogenesis in the Embryonic Intestine

viii CHAPTER 1 – INTRODUCTION . 1 1.1: Intestine overview . 1 1.2: Models of the developing intestine . 3 1.3: Intestinal specification and gut tube patterning. 5 1.4: The WNT/β-CATENIN signaling pathway and its role in gut tube patterning . 8 1.5: Non-canonical WNT signaling as a regulator of gut tube elongation . 11 1.6: HH signaling and its role in the early intestine . 12 1.7: Early intestine development . 15 1.8: Villus formation . 18 1.9: Development and maturation of the intestine following villus formation . 24 1.10: Conclusion and goals of this thesis: . 29 References . 31 Figures . 48 CHAPTER 2 – A DYNAMIC WNT/β-CATENIN SIGNALING ENVIRONMENT LEADS TO WNTINDEPENDENT AND WNT-DEPENDENT PROLIFERATION OF EMBRYONIC INTESTINAL PROGENITOR CELLS. 55 2.1: Summary . 55 2.2: Introduction . 56 2.3: Results. 58
In Vitro Combined Effects of Zanthoxylum zanthoxyloides and Newbouldia laevis Methanolic Extracts on Three Life-Cycle Stages of the Parasitic Nematode, Haemonchus contortus

| Methanolic extracts of Zanthoxylum zanthoxyloides (Fagara), Newbouldia laevis and three of their combinations (50% N. laevis -50% Z. zanthoxyloides, 25% Z. zanthoxyloides -75% N. laevis and 75% Z. zanthoxyloides 25% N. laevis) were screened in vitro for potential anti-parasitic effects against eggs, infective larvae and adults of Haemonchus contortus. Significant effects were obtained but differences were observed depending on the parasitic stage. The effects of the two plant extracts and their combinations were no dose dependent on egg hatching and infective larvae although more potent effects were usually observed with low concentrations. In contrast, dose–response relationship was found for adult worms. On eggs hatching, the combined extracts 50% N. laevis 50% Z. zanthoxyloides and 25% Z. zanthoxyloides 75% N. laevis have showed the same effectiveness like Fagara and N. laevis extracts. Combined plant extracts seemed to be more effective than individual plant extracts on larval migration at less concentrations. Extracts of Fagara and two plant associations (i.e., 50% Z. zanthoxyloides 50% N. laevis and 75% Z. zanthoxyloides 25% N. laevis) reduced adult worm motility. Overall, the combination of 50% Z. zanthoxyloides -50% N. laevis was most effective on all three stages of H. contortus. These results showed that Z. zanthoxyloides (Fagara) and N. laevis used in combined form (50%:50%) were more effective on H. contortus thus both plants association could be used as potential alternative of synthetic drugs to control parasitic infections of H. contortus in small ruminants.
Weekly vagal modulations and their associations with physical fitness and physical activity

Abstract The root mean square of successive differences (RMSSD) of R-R intervals, the most robust vagal modulation parameter of heart rate variability (HRV), has been proposed as a marker of global health and training adaptations. The weekly averaging of RMSSD and its natural logarithm (LnRMSSD) has been adopted to enhance detection of training-induced adaptations. We assessed measures of aerobic fitness, body composition, objective physical activity (PA), and daily LnRMSSD recordings during different conditions, such as supine rest, seated rest, standing and walking at 5 km/h, over a week in 34 healthy young individuals of both sexes (age: 22 ± 4 yr; body fatness: 20 ± 8%; estimated VO2max: 40 ± 8 mL·kg−1·min−1). The day-to-day reliability and agreement among LnRMSSD averages over 5, 4, 3, 2 and a single-day value per condition were assessed, while correlations between LnRMSSD, aerobic fitness, body composition, and PA were also examined. Poor to good day-to-day reliability, and moderate to excellent agreement were observed for LnRMSSD recordings for diverse conditions with a minimum of two daily recordings in the supine condition, and three in the other conditions achieving excellent agreement for weekly HRV assessment. Several correlations between LnRMSSD, aerobic fitness, body composition, and PA were revealed, with stronger observed associations during walking. Utilisation of weekly HRV (average of 2–3 daily recordings), as described in the current study, may provide practitioners with a tool to assess weekly vagal modulations for health and performance purposes. Walking HRV recordings may be a practical alternative to other conditions for the investigation of cardiac autonomic function.
Evolution of solids in planet forming disks: The interplay of experiments, simulations, and observations

Abstract Circumstellar dust analogues can be studied experimentally to determine their collisional behavior and their optical properties. These results affect simulations of circumstellar disks in various, substantial ways: Collision results determine how dust aggregates grow and how their aerodynamic properties change with time. This determines how solids move throughout the disk, how they accumulate, and how planetesimals might be formed. The optical properties determine the observational signature of these effects and allow us to constrain the spatial distribution of dust in disks, the sizes of the aggregates, as well as the temperature and optical depth of the dust emission. In this contribution, it is discussed how theoretical models and their predictions depend on laboratory results and what we learned about disks from high spatial resolution radio interferometry.
Dosimetric and mechanical equivalency of Varian TrueBeam linear accelerators

Abstract Purpose To investigate and improve the level of equivalency of Varian TrueBeam linear accelerators (linacs) in energy‐, dosimetric leaf gap‐ (DLG) and jaw calibration. Methods Eight linacs with four photon energies: 6 MV, 6 MV FFF, 10 MV FFF, and 15 MV, and three electron energies (on two linacs): 6, 9, and 12 MeV were commisioned and beam‐matched. Initially, symmetry of lateral profiles was calibrated for maximum field size. Energy‐matching was then performed for photons by adjusting diagonal profiles at maximum field size and depth of maximum dose to coincide with the reference linac, and for electrons by matching the range at percentage depth of ionization of 90%, 80%, and 50%. Calibration of DLG was performed for 6 MV and evaluated among the linacs. The relationship between DLG and the Gap value was investigated. A method using electronic portal imaging device (EPID) was developed and implemented for jaw calibration. Results Symmetry calibration for photons (electrons) was within 1% (0.7%), further improving the vendor's acceptance criteria. Photon and electron energy‐matching was within 0.5% and 0.1 mm, respectively. Calibration of DLG was within 0.032 mm among the linacs and utilizing the relationship between DLG and the Gap value resulted in an empirical calibration method which was implemented to simplify DLG adjustment. Using EPID‐based method of calibration, evaluation of the jaw‐positioning among the linacs for 30 cm × 30 cm field size was within 0.4 mm and in the junction area within 0.2 mm. Dose delivery error of VMAT‐plans were at least 99.2% gamma pass rate (1%, 1 mm). Conclusions High level of equivalency, beyond clinically accepted criteria, of TrueBeam linacs could be achieved which reduced dose delivery systematic errors and increased confidence in interchanging patients among linacs.
Tailored Web-Based Smoking Interventions and Reduced Attrition: Systematic Review and Meta-Analysis

Background The increasing number of internet users presents an opportunity to deliver health interventions to large populations. Despite their potential, many web-based interventions, including those for smoking cessation, face high rates of attrition. Further consideration of how intervention features impact attrition is needed. Objective The aim of this systematic review is to investigate whether tailored web-based smoking cessation interventions for smokers are associated with reduced rates of attrition compared with active or passive untailored web-based interventions. The outcomes of interest were dropout attrition at 1-, 3-, 6-, and 12-month follow-ups. Methods Literature searches were conducted in May 2018 and updated in May 2020 on MEDLINE (Medical Literature Analysis and Retrieval System Online), PsycINFO (Psychological Information), EMBASE (Excerpta Medica dataBASE), CINAHL (Cumulated Index to Nursing and Allied Health Literature), Scopus, and the Cochrane Tobacco Addiction Group Specialized Register with the following search terms: smoking cessation, tailored, or web- or internet-based. Included studies were published in English before or in May 2020 using a randomized controlled trial design. Studies were restricted to those with web-based delivery, a tailored intervention group, an untailored control group, and a reported outcome of smoking cessation. Studies were assessed for methodological quality using the Cochrane Risk of Bias tool. Two reviewers independently extracted the study characteristics and the number of participants lost to follow-up for each treatment group. Results A total of 13 studies were included in the systematic review, of which 11 (85%) were included in the meta-analysis. Tailoring had no statistically significant effect on dropout attrition at 1-month (risk ratio [RR]=1.02, 95% CI 0.95-1.09; P=.58; I2=78%), 3-month (RR=0.99, 95% CI 0.95-1.04; P=.80; I2=73%), 6-month (RR=1.00, 95% CI 0.95-1.05; P=.90; I2=43%), or 12-month (RR=0.97, 95% CI 0.92-1.02; P=.26; I2=28%) follow-ups. Subgroup analyses suggested that there was a statistically significant effect of tailoring between the active and passive subgroups at 1-month (P=.03), 3-month (P<.001), and 6-month (P=.02) follow-ups but not at 12-month follow-up (P=.25). Conclusions The results suggest that tailoring of web-based smoking cessation interventions may not be associated with reduced rates of dropout attrition at 1-, 3-, 6-, or 12-month follow-ups. Significant differences between studies that include untailored active and passive control groups suggest that the role of tailoring may be more prominent when studies include a passive control group. These findings may be because of variability in the presence of additional features, the definition of smokers used, and the duration of smoking abstinence measured. Future studies should incorporate active web-based controls, compare the impact of different tailoring strategies, and include populations outside of the Western countries.
Responses of interspecific associations in mixed‐species bird flocks to selective logging

1Post-graduate Program in Wildlife Biology & Conservation, Wildlife Conservation Society – India Program &National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India 2Centre for Wildlife Studies, Bangalore, Karnataka, India 3Nature Conservation Foundations, Mysore, Karnataka, India 4Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, USA
Functional soluble dietary fiber from ginseng residue: Polysaccharide characterization, structure, antioxidant, and enzyme inhibitory activity.

Ginseng (Panax ginseng C.A. Meyer) is the most famous edible Chinese herbal medicine. In the present study, soluble dietary fiber of ginseng (ginseng-SDF, 8.98% content) was extracted from ginseng residue, and its physicochemical characterization, structure, and biological activities were studied. Ginseng-SDF was an acidic heteropolysaccharide (uronic acid, 4.42% content) rich in protein, amino acids, and mineral elements. Glucose was its main monosaccharide composition (58.03%). Ginseng-SDF had a porous microstructure, a typical cellulose I structure and a large number of hydroxyl functional groups. These chemical composition and structural characteristics gave ginseng-SDF a good water solubility (98.56%), oil-holding capacity (OHC) (3.01 g/g), and biological activities, as the antioxidant activity (13.35 μM TE/g, 105.17 μM TE/g, 54.20 μM TE/g for DPPH, ABTs, and FRAP assays, respectively), glucose diffusion retardation index (GDRI, 33.33%-7.43%), and α-amylase/α-glucosidase inhibitory activities (IC50 , 6.70 mg/ml, and 4.89 mg/ml, respectively). The results suggested that ginseng residue is a valuable source of functional dietary fiber, and the ginseng-SDF has a potential use in antioxidant and hypoglycemic foods. PRACTICAL APPLICATIONS: Ginseng has long been popular as a health food in Asia, North America, and Europe. Ginseng residue is rich in polysaccharides, dietary fiber, proteins, and other components, which is also of great research value. However, there are few studies focus on the soluble dietary fiber of ginseng at present. The research shows that ginseng residue is a valuable source of functional dietary fiber. The chemical components and structural characteristics give ginseng-SDF a noteworthy antioxidant activity and enzyme inhibitory activity in vitro. These properties and biological activities indicate that ginseng-SDF has application value in antioxidant and hypoglycemic foods.
Repurposed kinase inhibitors and β-lactams as a novel therapy for antibiotic resistant bacteria

Antibiotic resistant bacteria are an increasing global problem, and pathogenic actinomycetes and firmicutes are particularly challenging obstacles. These pathogens share several eukaryotic-like kinases that present antibiotic development opportunities. We used computational modelling to identify human kinase inhibitors that could be repurposed towards bacteria as part of a novel combination therapy. The computational model suggested a family of inhibitors, the imidazopyridine aminofurazans (IPAs), bind PknB with high affinity. We found that these inhibitors biochemically inhibit PknB, with potency roughly following the predicted models. A novel x-ray structure confirmed that the inhibitors bind as predicted and made favorable protein contacts with the target. These inhibitors also have antimicrobial activity towards Mycobacteria and Nocardia, and normally ineffective β-lactams can potentiate IPAs to more efficiently inhibit growth of these pathogens. Collectively, our data show that in silico modeling can be used as a tool to discover promising drug leads, and the inhibitors we discovered can synergize with clinically relevant antibiotics to restore their efficacy against bacteria with limited treatment options.
Hooked on a Feeling: Influence of Brief Exposure to Familiar Music on Feelings of Emotion in Individuals with Alzheimer's Disease.

BACKGROUND Research has indicated that individuals with Alzheimer's-type dementia (AD) can experience prolonged emotions, even when they cannot recall the eliciting event. Less is known about whether music can modify the emotional state of individuals with AD and whether emotions evoked by music linger in the absence of a declarative memory for the eliciting event. OBJECTIVE We examined the effects of participant-selected recorded music on self-reported feelings of emotion in individuals with AD, and whether these feelings persisted irrespective of declarative memory for the emotion-inducing stimuli. METHODS Twenty participants with AD and 19 healthy comparisons (HCs) listened to two 4.5-minute blocks of self-selected music that aimed to induce either sadness or happiness. Participants reported their feelings at baseline and three times post-induction and completed recall and recognition tests for the music selections after each induction. RESULTS Participants with AD had impaired memory for music selections compared to HCs. Both groups reported elevated sadness and negative affect after listening to sad music and increased happiness and positive affect after listening to happy music, relative to baseline. Sad/negative and happy/positive emotions endured up to 20 minutes post-induction. CONCLUSION Brief exposure to music can induce strong and lingering emotions in individuals with AD. These findings extend the intriguing phenomenon whereby lasting emotions can be prompted by stimuli that are not remembered declaratively. Our results underscore the utility of familiar music for inducing emotions in individuals with AD and may ultimately inform strategies for using music listening as a therapeutic tool with this population.
Evaluation of nutritional behaviour related to COVID-19

Abstract Objective: It is known that social isolation process has an impact on individuals’ eating behaviours. Continuing nutritional behaviour resulting from emotional eating, uncontrolled eating and cognitive restriction may turn into eating disorders in the future. The purpose of this study is to evaluate the possible effects of Corona Virus Disease-2019 (COVID-19) pandemic and social isolation process on individuals’ nutritional behaviours and body weight changes. Design: Retrospective cohort study. Setting: Nutritional behaviours of the participants before the COVID-19 pandemic and in the social isolation process were evaluated with the Three Factor Nutrition Questionnaire. The changes in individuals’ body weight during this period were also evaluated. Participants: A total of 1036 volunteer individuals (827 women, 209 men) aged 18 years and over participated in the study. Results: During the COVID-19 pandemic and social isolation process, there was an increase in emotional eating and uncontrolled eating behaviours of individuals, but no significant change in cognitive restriction behaviour occurred (P = <0·00; P = <0·00 and P = 0·53, respectively). It was reported that the body weight of 35 % of the individuals who participated in the study increased during this period. Conclusion: Social isolation process practiced as a result of COVID-19 pandemic may lead to changes in some nutritional behaviours. Some precautions should be taken to prevent this situation that occurs in nutritional behaviours from causing negative health problems in the future.
Nucleosome positioning dynamics in evolution and disease

ii Lay Summary . iv Acknowledgements . vi List of Figures . x List of Tables . xii Abbreviations . xiii Chapter 1: Introduction . 1 1.1 Chromatin structure and the nucleosome . 1 1.1.1 Different layers of chromatin structure in eukaryotes . 1 1.1.2 Nucleosome structure and its biological importance . 1 1.1.3 Determinants of nucleosome positioning . 3 1.1. 4 Personal summary . 18 1.2 Mutation spectra and chromatin structure . 18 1.2. 1 Central importance of mutations in the evolutionary process and human diseases . 18 1.2. 2 Variations in mutation spectra . 20 1.2. 3 Chromatin structure and mutation rates . 21 1.2. 4 Personal summary . 23 1.3 Goals of investigation . 23 Chapter 2: Nucleosome Positioning Dynamics in Evolution . 25 2.