Miracle-dz/UniFAR-FTUs huggingface dataset:
Enlarged representative set of protein structures

TO reduce redundancy in the Protein Data Bank of 3D protein structures, which is caused by many homologous proteins in the data bank, we have selected a representative set of structures. The selection algorithm was designed to (1) select as many nonhomologous structures as possible, and (2) to select structures of good quality. The representative set may reduce time and effort in statistical analyses.
Skeletal muscle fiber composition is related to adiposity and in vitro glucose transport rate in humans.

The purpose of this study was to determine if a relationship exists among skeletal muscle fiber composition, adiposity, and in vitro muscle glucose transport rate in humans. Rectus abdominus muscle was obtained during elective abdominal surgery from nonobese control (n = 12), obese (n = 12), and obese non-insulin-dependent diabetes mellitus (NIDDM) patients (n = 10). The obese NIDDM group had a significantly lower percentage of type I muscle fibers (32.2 +/- 1.9%) than the obese group (40.4 +/- 2.7%), and both obese groups were significantly lower than the control group (50.0 +/- 2.6%). Insulin-stimulated glucose transport, determined on 28 subjects, was significantly lower in both the obese (3.83 +/- 0.48 nmol.min-1.mg-1) and NIDDM (3.93 +/- 1.0 nmol.min-1.mg-1) groups vs. the control group (7.35 +/- 1.50 nmol.min-1.mg-1). Body mass index (BMI) was inversely correlated to percent type I fibers (r = -0.50, P < 0.01) and to the insulin-stimulated glucose transport rate (r = -0.53, P < 0.01). The percentage of type I muscle fibers was related to the insulin-stimulated glucose transport rate (r = 0.57, P < 0.01), although this relationship was not significant after adjusting for BMI. Although these data do not support an independent relationship between fiber type and insulin action in obesity, a reduced skeletal muscle type I fiber population may be one component of a multifactorial process involved in the development of insulin resistance.
Experienced and inexperienced Internet users among pre-service teachers: Their use and attitudes toward the Internet

Much has been said about the benefits of the Internet as a teaching and learning tool but to realize these benefits, teachers must be willing and able to use the Internet effectively in their teaching. Studies have also clearly shown that the likeliness of teachers using the Internet effectively and the success of Internet utilization was very much related to the users’ attitudes toward the Internet (Liaw, 2002; Moon & Kim, 2001; Johnson & Hignite, 2000). This paper describes a study on pre-service teachers with differing levels of Internet experience, at one of the premier universities in Malaysia, to assess their Internet use and attitudes toward the Internet. The study is exploratory in essence and seeks to ascertain the comfort level of pre-service teachers where the Internet is concerned and hence to provide a glimpse of the future of the Internet in education within the Malaysian context.
Growth and cytochemistry of the adrenal gland of the mouse from birth to maturity

That the adrenal glands are essential to the maintenance of normal physiological conditions in the adults of higher vertebrates is soundly established, The importance of these glands in the mature state suggests that they might in early stages direct the development of the processes they later control. The literature on the adrenal contains however little that might implicate the fetal or juvenile gland in developmental events (see, for example, Hartmann and Brownell, '49). There have been, it is true, numerous studies on the growth, histology, and cytochemistry of the gland from juvenile stages, and we have cited some of the most useful of these in our discussion. Many of these investigations have contributed substantially to our knowledge of the growth and differentiation of the glands themselves; yet none was designed with the intention of correlating c.hanges within the adrenals with peripheral effects of their activity. In the young mouse the pituitary-adrenal axis has recently been shown to be responsible for the 15to 20-fold increase in alkaline phosphatase that occurs in the duodenum between the 15th and the 18th days of postnatal life (Moog, '53). This enzyme accumulation and other intestinal changes that
Colon cancer, physical activity, and occupational exposures. A case‐control study

A case‐control study on colon cancer was conducted encompassing 329 cases and 658 controls. Occupations and various exposures were assessed by questionnaires. A decreased risk was found in persons with physically active occupations. This effect was most pronounced in colon descendens and sigmoideum with an odds ratio (OR) of 0.49 whereas no reduced risk was found for right‐sided colon cancer. Regarding specific jobs, reduced ORs were found for agricultural, forestry, and saw mill workers and increased OR for railway employees. High‐grade exposure to asbestos or to organic solvents gave a two‐fold increased risk. Regarding exposure to trichloroethylene in general, a slightly increased risk was found whereas such exposure among dry cleaners gave a seven‐fold increase of the risk.
Feeding patterns of Triatoma infestans (Hemiptera: Reduviidae) in relation to transmission of American trypanosomiasis in Argentina.

Agar double diffusion tests were used to analyze the origin of blood meals from 720 Triatoma infestans bugs collected from bedrooms and peridomestic structures of 9 households near Guanaco Muerto in the Province of Cordoba, Argentina. The intestinal contents of 332 (46.1%) of the bugs reacted to 1 or more of 11 antisera tested. Dog was the most frequently identified host in bugs collected from bedrooms (48.9%), followed by chicken (34.8%) and man (11.9%). A significantly higher number of blood meals from dogs were identified in nymphs than in adults. A predominance of identified feedings from goat (43.8%) and chicken (33.3%) were found in bugs from peridomestic structures. Movement of T. infestans between domestic and peridomestic structures is apparently minimal, since identified blood meals in bugs from bedrooms included only 1.8% from wild cavies, 0.4% from goats and 0.4% from horses, while only 3.3% of the total identified feedings from peridomestically collected bugs were from man. Since only a small number of bugs collected from goat pens and chicken houses contained blood meals from opossum (1.9%) and rodents (4.5%), these animals were considered to be of little importance in the maintenance of domestic populations of T. infestans . The highest rates of infection with Trypanosoma cruzi were found in bugs from bedrooms (63.6%). Peridomestically collected bugs from storerooms, chicken houses and goat pens showed significantly lower rates of infection (25, 2.4 and 1.4%, respectively). In bugs collected from bedrooms, a high correlation occurred between identified feedings from dogs and the rate of infection with T. cruzi . Dogs were considered the most important host, both as a reservoir source of T. cruzi and in the maintenance of domiciliary T. infestans in the study area.
Neonatal Outcomes of Small for Gestational Age Preterm Infants in Canada

Abstract To compare the effect of small for gestational age (SGA) on mortality, major morbidity and resource utilization among singleton very preterm infants (<33 weeks gestation) admitted to neonatal intensive care units (NICUs) across Canada. Infants admitted to participating NICUs from 2003 to 2008 were divided into SGA (defined as birth weight <10th percentile for gestational age and sex) and non-small gestational age (non-SGA) groups. The risk-adjusted effects of SGA on neonatal outcomes and resource utilization were examined using multivariable analyses. SGA infants (n = 1249 from a cohort of 11,909) had a higher odds of mortality (adjusted odds ratio [AOR] 2.46; 95% confidence interval [CI], 1.93–3.14), necrotizing enterocolitis (AOR 1.57; 95% CI, 1.22–2.03), bronchopulmonary dysplasia (AOR 1.78; 95% CI, 1.48–2.13), and severe retinopathy of prematurity (AOR 2.34; 95% CI, 1.71–3.19). These infants also had lower odds of survival free of major morbidity (AOR 0.50; 95% CI, 0.43–0.58) and respiratory distress syndrome (AOR 0.79; 95% CI, 0.68–0.93). In addition, SGA infants had a more prolonged stay in the NICU, and longer use of ventilation continuous positive airway pressure, and supplemental oxygen (p < 0.01 for all). SGA infants had a higher risk of mortality, major morbidities, and higher resource utilization compared with non-SGA infants.
Respiratory protection of nitrogenase in Azotobacter species: is a widely held hypothesis unequivocally supported by experimental evidence?

The hypothesis of respiratory protection, originally formulated on the basis of results obtained with Azotobacter species, postulates that consumption of O(2) at the surface of diazotrophic prokaryotes protects nitrogenase from inactivation by O(2). Accordingly, it is assumed that, at increased ambient O(2) concentrations, nitrogenase activity depends on increased activities of a largely uncoupled respiratory electron transport system. The present review compiles evidence indicating that cellular O(2) consumption as well as both the activity and the formation of the respiratory system of Azotobacter vinelandii are controlled by the C/N ratio, that is to say the ratio at which the organism consumes the substrate (i.e. the source of carbon, reducing equivalents and ATP) per source of compound nitrogen. The maximal respiratory capacity which can be attained at increased C/N ratios, however, is controlled, within limits, by the ambient O(2) concentration. When growth becomes N-limited at increased C/N ratios, cells synthesize nitrogenase and fix N(2). Under these diazotrophic conditions, cellular O(2) consumption remains constant at a level controlled by the O(2) concentration. Control by O(2) has been studied on the basis of both whole cell respiration and defined segments of the respiratory electron transport chain. The results demonstrate that the effect of O(2) on the respiratory system is restricted to the lower range of O(2) concentrations up to about 70 microM. Nevertheless, azotobacters are able to grow diazotrophically at dissolved O(2) concentrations of up to about 230 microM indicating that respiratory protection is not warranted at increased ambient O(2) concentrations. This conclusion is supported and extended by a number of results largely excluding an obvious relationship between nitrogenase activity and the actual rate of cellular O(2) consumption. On the basis of theoretical calculations, it is assumed that the rate of O(2) diffusion into the cells is not significantly affected by respiration. All of these results lead to the conclusion that, in the protection of nitrogenase from O(2) damage, O(2) consumption at the cell surface is less effective than generally assumed. It is proposed that alternative factors like the supply of ATP and reducing equivalents are more important.
Quality‐adjusted life years: how useful in medico economic studies

Cost‐effectiveness analysis has evolved as a practical response to the need to allocate limited resources for health care. It can be used to compare interventions whose effects on health are different if the measure of effectiveness captures all the important health dimensions of the effects of the interventions. Using the quality‐adjusted life year (QALY) as the unit of effectiveness attempts to approach this ideal and is currently the approach recommended by many consensus groups. Conventional QALYs represent time spend in a series of “quality‐weighted” health states, where the quality weights reflect the desirability of living in the state. Many challenges arise when preferences are incorporated into an economic analysis. The purpose of this paper is to highlight some of the issues surrounding the use of QALYs and to encourage researchers to present their methodology in a clear and transparent way.
Coping with unemployment: Does educational attainment make any difference?

Aims: The aim of this study was to examine the cross-sectional association between educational attainment and coping strategies with unemployment in a random sample of 37- to 56-year-old Danish men and women in long-term unemployment. Methods: Data were based on a survey among 575 men and 1,064 women who had been unemployed at least 70% of the time during a three-year period (October 1996 to October 1999). The outcome measures were two scales for coping with unemployment, one for problem-solving coping, and one for avoidant coping. Educational attainment was measured by years of vocational training. Results: A significant association was found between low educational attainment and low use of problem-solving coping among both men, OR=1.81 (95% CI 1.19—2.75), and women, OR=1.57 (1.13— 2.18). Adjustment for cohabitation status, self rated health, economic strain, and unemployment status did not change this association substantially. High use of avoidant coping was associated with low educational attainment among men, OR=1.57 (0.98—2.51). For women, medium educational attainment was significantly associated with low use of avoidant coping, OR=0.60 (0.42—0.85). This result was not affected by adjustment for the covariates. Conclusions: Coping strategies are considered a potential modifier of the impact of unemployment on health and well-being. In this study, differences in coping strategies with unemployment were associated with educational attainment.
Structural and morphological changes in rat ventricular myocardium induced by chronic systemic hypoxi.

AIM to explore the effects of chronic systemic hypoxia on myocardial structure and morphology. In addition, the goal of present study is to develop a hypoxia-induced heart failure model in rats. METHODS Sprague-Dawley male rats, weighing 220-250 g at the time of recruitment were randomly allocated into 7 groups (n = 4 per group), the control normoxia group was exposed to room air, while the hypoxia groups were caged in a plexiglas hypoxic chamber (8% O2 and 92% N2) for 28 days. Structural and morphological changes of ventricular myocardium were determined at day 28, while blood gas parameters were measured at day 1, 3, 7, 14, 21, and 28. RESULTS histopathologic and morphologic evaluation showed massive hypertrophy accompanied by damage of the intercalated disk (ID) structure, angiogenesis, necrosis, fibrosis, and apoptosis as a hallmark of ventricular remodeling. At the end of treatment, there were increases of LV (2.79 vs 3.71) and RV (1.72 vs 2.54) wall thicknesses, and also in hypertrophy index (from 3.19 to 5.74). Blood gas analysis revealed metabolic acidosis compensated by respiratory alkalosis. There was an observed decrease of blood gas parameters in hypoxia group compared to control group: PO2 (24.7 vs 96.4 mm Hg), PCO2 (18.2 vs 40.4 mm Hg), O2 saturation (25.5 vs 94.1 %), and HCO3 (10.1 vs 23.4 mmol/L). On the other hand an increase in hemoglobin level (221.5 vs 120.3 g/L), haematocrit level (68.6 vs 45.2 %), and red blood cell count (10.4 vs 6.9 μL/1000) could be observed. CONCLUSION our data clearly show that chronic systemic hypoxia causes massive ventricular hypertrophy accompanied by severe structural and morphological impairment of ventricular myocardium, which eventually results in cardiac failure.
IL-7 Receptor Expression Provides the Potential for Long-Term Survival of Both CD62Lhigh Central Memory T Cells and Th1 Effector Cells during Leishmania major Infection1

Infection with the intracellular protozoan parasite Leishmania major induces a state of concomitant immunity wherein secondary immunity is dependent upon the persistence of the original pathogen. Our laboratory has described two populations of Leishmania-induced CD4+ T cells that contribute to immunity: CD62Lhigh central memory T (TCM) cells and CD62Llow effector T cells. To determine whether the prosurvival cytokine IL-7 contributes to maintaining these T cells, we examined expression of the IL7R on CD4+ T cells activated during L. major infection. We found that TCM cells present in chronically infected mice expressed high levels of the IL7R. However, in addition to the expression of the IL7R by TCM cells, CD62Llow cells responding to L. major infection expressed the IL7R. Additional experiments revealed that a large percentage of the IL7RhighCD62Llow cells were Th1 cells, based on transcription at the IFN-γ locus and up-regulation of the Th1-promoting transcription factor T-bet. The up-regulation of T-bet did not prevent IL7R expression by L. major-responding CD4+ T cells, nor did the absence of T-bet result in increased IL7R expression. Finally, blockade of IL7R signaling decreased the number of T-bet+CD4+ T cells, reduced IFN-γ production, and inhibited delayed-type hypersensitivity responses in immune mice challenged with L. major, indicating that IL7R signaling contributes to the maintenance of Th1 effector cells. Thus, both TCM and Th1 effector cells can express the IL7R during chronic L. major infection, which provides a potential means for their long-term survival in addition to the presence of persisting parasites.
beta(2)-Microglobulin modified with advanced glycation end products delays monocyte apoptosis.

BACKGROUND A local inflammatory reaction to beta(2)-microglobulin (beta(2)m) amyloid deposits by monocytes/macrophages is a characteristic histologic feature of dialysis-related amyloidosis (DRA). Since beta(2)m modified with advanced glycation end products (AGE-beta(2)m) is a major constituent of amyloid in DRA, we tested the hypothesis that AGE-beta(2)m affects apoptosis and phenotype of human monocytes. METHODS Human peripheral blood monocytes were incubated with or without in vitro-derived AGE-beta(2)m, and their viability, extent of apoptosis, morphology, and function examined over the subsequent four days. RESULTS AGE-modified but not unmodified beta(2)m significantly delayed spontaneous apoptosis of human peripheral blood monocytes in adherent and nonadherent cultures. The effect of AGE-beta(2)m on monocytes apoptosis was time- and dose-dependent and was attenuated by a blocking antibody directed against the human AGE receptor (RAGE). There was no difference in effect between AGE-beta(2)m and that of AGE-modified human serum albumin. Culture of monocytes with AGE-beta(2)m did not alter membrane expression of Fas or Fas ligand. Monocytes cultured with AGE-beta(2)m underwent substantial changes in morphology similar to those observed when monocytes differentiate into macrophages. The cultured cells increased in size and vacuolization, and their content of beta-glucuronidase and acid phosphatase increased by 5- to 10-fold at day 4. Expression of the monocyte--macrophage membrane antigens HLA-DR, CD11b, and CD11c also increased at day 4. Although exhibiting phenotypic characteristics of macrophages, monocytes cultured with AGE-beta(2)m functioned differently than macrophages cultured with serum. Superoxide production in response to phorbol myristic acetate was maintained in monocytes cultured with AGE-beta(2)m, but declined with time in cells cultured with serum. Constitutive synthesis of tumor necrosis factor-alpha (TNF-alpha), interleukin-1 beta (IL-1 beta) and prostaglandin E2 (PGE2) increased in monocytes cultured for four to six days with AGE-beta(2)m. CONCLUSIONS These findings support a novel role for AGE-modified proteins such as AGE-beta(2)m that may contribute to the development of a local inflammatory response, with predominant accumulation of monocytes/macrophages, in DRA.
A Bayesian approach for instrumental variable analysis with censored time‐to‐event outcome

Instrumental variable (IV) analysis has been widely used in economics, epidemiology, and other fields to estimate the causal effects of covariates on outcomes, in the presence of unobserved confounders and/or measurement errors in covariates. However, IV methods for time‐to‐event outcome with censored data remain underdeveloped. This paper proposes a Bayesian approach for IV analysis with censored time‐to‐event outcome by using a two‐stage linear model. A Markov chain Monte Carlo sampling method is developed for parameter estimation for both normal and non‐normal linear models with elliptically contoured error distributions. The performance of our method is examined by simulation studies. Our method largely reduces bias and greatly improves coverage probability of the estimated causal effect, compared with the method that ignores the unobserved confounders and measurement errors. We illustrate our method on the Women's Health Initiative Observational Study and the Atherosclerosis Risk in Communities Study. Copyright © 2014 John Wiley & Sons, Ltd.
The Phenomenon of Taking Life Day-by-Day: Using Parse's Research Method

Parse's research method informed the exploration of the phenomenon of taking life day-by-day as viewed through the conceptual lens of the human becoming theory. From the perspective of human becoming, taking life day-by-day is a universal lived experience of health and quality of life. The participants in this study were 10 men between 35 and 60 years who had experienced depression and were willing to share their lived world of taking life day-by-day. Three core concepts were explicated from the participants' dialogues, enduring with the burdensome, envisioning the possibles, and sure-unsure. The findings of this study represent a tapestry of the participants' experiences woven with the human becoming theory, this researcher's engagement with an exacting process of inquiry, and his personal journey into the landscape of the human becoming school of thought.
Primary stability of a hybrid self-tapping implant compared to a cylindrical non-self-tapping implant with respect to drilling protocols in an ex vivo model.

BACKGROUND Modifications of implant design have been intending to improve primary stability. However, little is known about investigation of a hybrid self-tapping implant on primary stability. PURPOSES The aims of this study were to evaluate the primary stability of two hybrid self-tapping implants compared to one cylindrical non-self-tapping implant, and to elucidate the relevance of drilling protocols on primary stability in an ex vivo model. MATERIALS AND METHODS Two types of hybrid self-tapping implants (Straumann® Bone Level implant [BL], Straumann® Tapered Effect implant [TE]) and one type of cylindrical non-self-tapping implant (Straumann® Standard Plus implant [SP]) were investigated in the study. In porcine iliac cancellous bones, 10 implants each were inserted either using standard drilling or under-dimensioned drilling protocol. The evaluation of implant-bone interface stability was carried out by records of maximum insertion torque, the Periotest® (Siemens, Bensheim, Germany), the resonance frequency analysis (RFA), and the push-out test. RESULTS In each drilling group, the maximum insertion torque values of BL and TE were significantly higher than SP (p=.014 and p=.047, respectively). In each group, the Periotest values of TE were significantly lower than SP (p=.036 and p=.033, respectively). The Periotest values of BL and TE were significantly lower in the group of under-dimensioned drilling than standard drilling (p=.002 and p=.02, respectively). In the RFA, no statistical significances were found in implants between two groups and between implants in each group. In each group, the push-out values of BL and TE were significantly higher than SP (p=.006 and p=.049, respectively). CONCLUSION Hybrid self-tapping implants could achieve a high primary stability which predicts them for use in low-density bone. However, there is still a debate to clarify the influence of under-dimensioned drilling on primary stability.