Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Interval Training-Based Glycolytic Capacity on Physical Fitness in Recreational Long-Distance Runners

Purpose. The aim of this study was to investigate the influence of 8-week-long interval training (targeting glycolytic capacity) on selected markers of physical fitness in amateur long-distance runners. Methods. The study involved 17 amateur long-distance runners randomly divided into an experimental ( n = 8) and control ( n = 9) group. The control group performed three or four continuous training sessions per week whereas the experimental group performed two interval running training sessions and one continuous running training session. A graded treadmill exercise test and the 12-min cooper test were performed pre- and post-training. Results. O 2 max and the rate of recovery increased in the experimental group. relative oxygen uptake, minute ventilation, and heart rate speed decreased in low- (6 km/h) and medium-intensity (12 km/h) running. Conclusions. both training modalities showed similar results. However, the significant differences in training volume (4–8 min interval training vs. 40–150 min continuous training) indicates that the modalities targeting glycolytic capacity may be more efficient for amateur runners prepare for long-distance events.
STUDIES ON THE EFFECT OF EXPERIMENTAL NONKETOTIC DIABETES MELLITUS ON ANTIBACTERIAL DEFENSE

Chronically diabetic nonketotic rats were shown to be more susceptible to experimental Type 25 pneumococcal pneumonia than nondiabetic rats. The cumulative mortality in the diabetic group was significantly higher at infecting doses of 103, 104, 105, and 106 organisms, and the LD 50 was less than one twentieth of that for the nondiabetic group. More than ten times as many viable pneumococci were found in the pneumonic lesions of the diabetic animals at 24 and 36 hr as were present in the lesions of the nondiabetic controls, and serial histologic studies revealed that phagocytosis was strikingly depressed in the alveolar exudates of the diabetic animals. The diabetic state was also found to cause a similar depression of in vivo phagocytosis in preformed peritoneal exudates. The results of in vitro experiments indicated that the principal defect in the diabetic animals resided in their serum rather than in their polymorphonuclear leukocytes. The depressive factor in the serum was identified as the abnormally high concentration of glucose. Since equivalent molar concentrations of unmetabolized sugars added to normal serum caused a similar depression of phagocytosis, it was tentatively concluded that the action of the glucose on the leukocytes was primarily osmotic. The sensitivity of the granulocytes to the glucose effect, however, depended upon the conditions of the phagocytic test. Only when the pneumococci were encapsulated and the leukocytes derived from inflammatory exudates were crowded together, as in vivo, was the depressive action of the glucose clearly demonstrable.
NEURAL CORRELATE OF VISUAL WORKING MEMORY IN THE MACAQUE MONKEY

ii Co-Authorship iv Acknowledgements v List of Tables viii List of Figures ix List of Abbreviations xi Chapter 1 – Introduction 1 1.1 Working Memory 1 1.2 Neurophysiological Measures of Working Memory 4 1.2.1 Single-Neuron Recordings 4 1.2.2 Functional Magnetic Resonance Imaging (fMRI) 7 1.2.3 Event-Related Potentials (ERPs) 10 1.3 Basis of Persistent Activity 18 1.3.1 Neurocomputational Models of Working Memory 18 1.3.2 Role of the NMDA Receptor in Working Memory 22 1.4 Scope of the Study 28 Chapter 2 – Materials and Methods 30 2.1 Subjects and Apparatus 30 2.2 Behavioral Paradigms 32 2.3 Experimental Procedures 36 2.4 EEG Recordings 36 2.5 Data Analysis 39 2.5. 1 Behavior 39 2.5. 2 ERP Analysis 41 Chapter 3 – Results 44 3.1 Behavior 45 3.1.1 Performance on the Memory-Guided Saccade Tasks 45 3.1.2 Control Performance on the Visual Sequential Comparison Task 45 vii 3.1.3 Effect of Ketamine on Performance on the Visual Sequential Comparison Task 50 3.2 ERPs 53 3.2.1 Contralateral and Ipsilateral ERPs 53 3.2.2 Correct and Error ERPs 60 3.2.3 Set Size Effect 66 3.2.4 Effect of Ketamine 71 Chapter 4 – Discussion 89 4.1 Results 89 4.1.1 Neural Correlate of Visual Working Memory 89 4.1.2 NMDA Receptor Blockade 93 4.1.3 Relevance to Schizophrenia 94 4.2 Limitations and Future Directions 98 4.3 Conclusion 101 References 103
Frequent walking, but not total physical activity, is associated with increased fracture incidence: A 5‐year follow‐up of an Australian population‐based prospective study (AusDiab)

Current public health physical activity (PA) guidelines recommend that older adults accumulate ≥ 2.5 hours per week of moderate‐ to vigorous‐intensity PA to optimize health. The aim of this study was to examine (1) whether adults who meet the current PA guidelines are at reduced risk of fracture, (2) whether fracture risk varies by PA type/intensity and frequency, and (3) whether prolonged TV viewing, as a marker of sedentary behavior, is associated with fracture risk. This national, population‐based prospective study with a 5‐year follow‐up included 2780 postmenopausal women and 2129 men aged 50 years or older. Incident nontraumatic clinical fractures were self‐reported. Overall, 307 (6.3%) participants sustained at least one incident low‐trauma fracture (women 9.3%, men 2.3%). Multivariate logistic regression, adjusting for age, body mass index (BMI), physical function, previous fracture history, smoking, and dietary calcium and serum 25‐hydroxyvitamin D levels, showed that women who walked more than 3 hours per week or completed at least 6 weekly bouts of walking had a 51% and 56% increased fracture risk, respectively, compared with women who did no walking [odds ratio (OR) time = 1.51, 95% confidence interval (CI) 1.01–2.24; OR frequency = 1.56, 95% CI 1.07–2.27]. However, total and moderate to vigorous PA time and the accumulation of 2.5 hours per week or more of PA and TV viewing time were not associated with incident fractures. In men, there also was an increased fracture risk for those who walked more than 3 hours per week (OR = 2.30, 95% CI 1.06‐4.97) compared with those who reported no walking. In conclusion, older adults who adhered to the current PA guidelines were not protected against fragility fractures, but more frequent walking was associated with an increased fracture risk. © 2011 American Society for Bone and Mineral Research.
Identification of novel proteins associated with hepatocellular carcinomas using protein microarrays

Characterization of the protein profiles expressed by hepatocellular carcinomas (HCCs) may identify the genes involved in hepatocellular carcinogenesis and offers the possibility of elucidating clinical biomarkers. In an effort to discover such proteins and pathways that are deregulated in hepatocellular carcinogenesis, cellular proteomes of matched normal liver cells and carcinoma were analysed by tissue microdissection and protein microarrays. Using protein microarrays made up of 83 different antibodies, it was possible to monitor alterations of the protein levels in HCC and non‐neoplastic liver tissue. Further analysis of altered proteins was performed using western blot analysis and tissue microarrays (TMAs) containing 210 HCC specimens and corresponding liver tissue. The protein microarray approach revealed differential expression between HCC and normal liver of 32 of the 83 proteins examined: 21 of these were up‐regulated and 11 down‐regulated. IGF (insulin growth factor) II, ADAM (a disintegrin and metalloproteases) 9, STAT (signal transducers and activators of transcription) 3, SOCS (suppressors of cytokine signalling) 3, and cyclin D1 were significantly up‐regulated and collagen I, SMAD 4, FHIT (fragile histidine triad), and SOCS1 were down‐regulated. The differential expression of these proteins was confirmed using western blot analysis and TMAs. Correlation of differentially regulated proteins with clinico‐pathological data showed that cyclin D1 and SOCS1 were associated with tumour prognosis in univariate analysis, but not multivariate analysis. These data indicate that the development of an array‐based approach for the determination of protein profiles in HCC may facilitate the identification of new proteins associated with carcinogenesis or prognosis. Copyright © 2003 John Wiley & Sons, Ltd.
Zanamivir Pharmacokinetics and Pulmonary Penetration into Epithelial Lining Fluid following Intravenous or Oral Inhaled Administration to Healthy Adult Subjects

ABSTRACT Zanamivir serum and pulmonary pharmacokinetics were characterized following intravenous (i.v.) or oral inhaled administration. I.v. zanamivir was given as intermittent doses of 100 mg, 200 mg, and 600 mg every 12 h (q12h) for two doses or as a continuous infusion (6-mg loading dose followed by 3 mg/h for 12 h). Oral inhaled zanamivir (two 5-mg inhalations q12h for two doses) was evaluated as well. Each zanamivir regimen was administered to six healthy subjects with serial pharmacokinetic sampling. In addition, a single bronchoalveolar lavage (BAL) fluid sample was collected at various time points and used to calculate epithelial lining fluid (ELF) drug concentrations for each subject. For intermittent i.v. administration of 100 mg, 200 mg, and 600 mg zanamivir, the median zanamivir concentrations in ELF collected 12 h after dosing were 74, 146, and 419 ng/ml, respectively, each higher than the historic mean 50% inhibitory concentrations for the neuraminidases of wild-type strains of influenza A and B viruses. Median ELF/serum zanamivir concentration ratios ranged from 55 to 79% for intermittent i.v. administration (when sampled 12 h after the last dose) and 43 to 45% for continuous infusion (when sampled 6 to 12 h after the start of the infusion). For oral inhaled zanamivir, the median zanamivir concentrations in ELF were 891 ng/ml for the first BAL fluid collection and 326 ng/ml for subsequent BAL fluid collections (when sampled 12 h after the last dose); corresponding serum drug concentrations were undetectable. This study demonstrates zanamivir's penetration into the human pulmonary compartment and supports the doses selected for the continuing development of i.v. zanamivir in clinical studies of influenza.
Causality : Models , Reasoning , and Inference

the methodological community a major statement on causal inquiry. His account of the philosophy and history of causal analysis is a joy to read, especially his spirited 28-page epilogue, " The Art and Science of Cause and Effect. " The heart of Pearl's Causality is the set of ideas that he and his colleagues in computer science have developed over the past 20 years. They comprise a unified methodology for the graphical representation of joint probability distributions along with rules for inferring causality directly from such graphical representations. Reading Causality, however, feels a bit (I would imagine) like going for a hike in a rain forest with Judea Pearl as your guide. Initially, one's excitement is aroused by first contact with his causal flora and then further enchanted by his claims of all that lies ahead. But, before long, one is so deeply enveloped in his graphical vegetation that fear of ever finding a way out begins to take over. As I write this review, I must admit that I am still circling about in the counterfactual mangroves of Chapters 7 through 10. Nonetheless, I have come to a recommendation: Anyone who intends to teach causality in graduate methodology classes should read this book. Anyone who does not should avoid it, at least until the rest of us figure out which of its many ideas are unique and lasting contributions to causal analysis. That is to say, from the perspective of a sociologist, the work as a whole is a memorable tour de force, which succeeds admirably in provoking deep thoughts about (1) what social scientists can and should do with available observational data and (2) what sorts of theories and data sources we should be attempting to cultivate. But it is unclear which of Pearl's specific ideas should or
Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high‐quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high‐quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA‐based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n = 1510) of ultraconserved elements (UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome‐enabled hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support, although this result could be explained by factors such as taxon sampling. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders.
Genovariation Study of Hantavirus in Main Endemic Areas of Hemorrhagic Fever with Renal Syndrome in Hebei Province, China

Background Hemorrhagic fever with renal syndrome (HFRS) is an important infectious disease in Hebei Province. At present, cases from the northeast regions of the province account for >80% of the total incidences. However, studies that examine the region-specific genetic variations of the Hantavirus (HV), the causative pathogen for HFRS, have been lacking. Methods Rodents were collected in northeast Hebei Province from 2004 to 2013, and the HV strains used in this study were isolated in 1993. Lung tissues were isolated from the rodents and HV antigen was detected by indirect immunofluorescence. The M1 and M2 fragments of HV M region were amplified by reverse transcription polymerase chain reaction (RT-PCR), cloned into pMDl9-T vector, sequenced and compared with representative standard stains for homology and phylogenetic analysis. Result A total of 21 samples of HV antigen-positive were collected. Real-time PCR analysis revealed that the 19 rodent lungs and two HV strains were positive for the SEO virus. 11 samples were chosen to sequence, and they shared 95.8%–99.8% in nucleotide homology, and 83.6%–99.2% when compared to the standard strains of SEO virus. Phylogenetic analysis demonstrated that all strains were grouped into the same S3 subtype. Conclusion SEO was the major epidemic genotype of HV in the main HFRS endemic areas in Hebei Province, and S3 was the major subtype. There was minor genetic variation in HV over short term periods, while long term variations were higher.
Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data

Gene expression time-course experiments allow to study the dynamics of transcriptomic changes in cells exposed to different stimuli. However, most approaches for the reconstruction of gene association networks (GANs) do not propose prior-selection approaches tailored to time-course transcriptome data. Here, we present a workflow for the identification of GANs from time-course data using prior selection of genes differentially expressed over time identified by natural cubic spline regression modeling (NCSRM). The workflow comprises three major steps: 1) the identification of differentially expressed genes from time-course expression data by employing NCSRM, 2) the use of regularized dynamic partial correlation as implemented in GeneNet to infer GANs from differentially expressed genes and 3) the identification and functional characterization of the key nodes in the reconstructed networks. The approach was applied on a time-resolved transcriptome data set of radiation-perturbed cell culture models of non-tumor cells with normal and increased radiation sensitivity. NCSRM detected significantly more genes than another commonly used method for time-course transcriptome analysis (BETR). While most genes detected with BETR were also detected with NCSRM the false-detection rate of NCSRM was low (3%). The GANs reconstructed from genes detected with NCSRM showed a better overlap with the interactome network Reactome compared to GANs derived from BETR detected genes. After exposure to 1 Gy the normal sensitive cells showed only sparse response compared to cells with increased sensitivity, which exhibited a strong response mainly of genes related to the senescence pathway. After exposure to 10 Gy the response of the normal sensitive cells was mainly associated with senescence and that of cells with increased sensitivity with apoptosis. We discuss these results in a clinical context and underline the impact of senescence-associated pathways in acute radiation response of normal cells. The workflow of this novel approach is implemented in the open-source Bioconductor R-package splineTimeR.
Predictors of Public Support for Gender-Related Affirmative Action Interests, Gender Attitudes, and Stratification Beliefs

Drawing on data from the General Social Survey during the period from 1996 through 2006, we explore predictors of support for gender-related affirmative action in the United States. Following the literature on race-based affirmative action, we identify three main domains of predictors, each of which also resonates well with themes within scholarship on gender: interests; gender-related attitudes; and general stratification beliefs. In multivariate analyses, at least some predictors within each domain are significant. We conclude that like support for race-based affirmative action, support for gender-based affirmative action is based on a combination of interests, gender attitudes, and general stratification beliefs, but that gender attitudes are less important in shaping such support than racial beliefs are in shaping support for race-based affirmative action. The implications of these findings for the literature on race-related affirmative action as well as for the literature on gender-related attitudes are considered.
A Benchmark for Endoluminal Scene Segmentation of Colonoscopy Images

Colorectal cancer (CRC) is the third cause of cancer death worldwide. Currently, the standard approach to reduce CRC-related mortality is to perform regular screening in search for polyps and colonoscopy is the screening tool of choice. The main limitations of this screening procedure are polyp miss rate and the inability to perform visual assessment of polyp malignancy. These drawbacks can be reduced by designing decision support systems (DSS) aiming to help clinicians in the different stages of the procedure by providing endoluminal scene segmentation. Thus, in this paper, we introduce an extended benchmark of colonoscopy image segmentation, with the hope of establishing a new strong benchmark for colonoscopy image analysis research. The proposed dataset consists of 4 relevant classes to inspect the endoluminal scene, targeting different clinical needs. Together with the dataset and taking advantage of advances in semantic segmentation literature, we provide new baselines by training standard fully convolutional networks (FCNs). We perform a comparative study to show that FCNs significantly outperform, without any further postprocessing, prior results in endoluminal scene segmentation, especially with respect to polyp segmentation and localization.
Clinical course of hepatitis C virus during the first decade of infection: cohort study

Abstract Objective: To determine the clinical course of hepatitis C virus in the first decade of infection in a group of patients who acquired their infections on a known date. Design: Cohort study. Setting: Clinical centres throughout the United Kingdom. Participants: 924 transfusion recipients infected with the hepatitis C virus (HCV) traced during the HCV lookback programme and 475 transfusion recipients who tested negative for antibodies to HCV (controls). Main outcome measures: Clinical evidence of liver disease and survival after 10 years of infection. Results: All cause mortality was not significantly different between patients and controls (Cox's hazards ratio 1.41, 95% confidence interval 0.95 to 2.08). Patients were more likely to be certified with a death related to liver disease than were controls (12.84, 1.73 to 95.44), but although the risk of death directly from liver disease was higher in patients than controls this difference was not significant (5.78, 0.72 to 46.70). Forty per cent of the patients who died directly from liver disease were known to have consumed excess alcohol. Clinical follow up of 826 patients showed that liver function was abnormal in 307 (37.2%), and 115 (13.9%) reported physical signs or symptoms of liver disease. Factors associated with developing liver disease were testing positive for HCV ribonucleic acid (odds ratio 6.44, 2.67 to 15.48), having acquired infection when older (at age ≥ 40 years; 1.80, 1.14 to 2.85), and years since transfusion (odds ratio 1.096 per year, 1.00 to 1.20). For patients with severe disease, sex was also significant (odds ratio for women 0.38, 0.17 to 0.88). Of the 362 patients who had undergone liver biopsy, 328 (91%) had abnormal histological results and 35 (10%) of these were cirrhotic. Conclusions: Hepatitis C virus infection did not have a great impact on all cause mortality in the first decade of infection. Infected patients were at increased risk of dying directly from liver disease, particularly if they consumed excess alcohol, but this difference was not statistically significant. What is already known on this topic The clinical course of HCV infection is unclear because most information has come from studies of patients with established chronic liver disease Studies that follow patients from disease onset are rare because most HCV infections are asymptomatic What this study adds HCV infection does not have a great impact on all cause mortality in the first decade of infection Infected patients have an increased risk of dying from a liver related cause, particularly if they consumed excess alcohol