Miracle-dz/UniFAR-FTUs huggingface dataset:
The activity of the HIV-1 IRES is stimulated by oxidative stress and controlled by a negative regulatory element

Initiation of translation of the full-length messenger RNA of HIV-1, which generates the viral structural proteins and enzymes, is cap-dependent but can also use an internal ribosome entry site (IRES) located in the 5′ untranslated region. Our aim was to define, through a mutational analysis, regions of HIV-1 IRES that are important for its activity. A dual-luciferase reporter construct where the Renilla luciferase (Rluc) translation is cap-dependent while the firefly luciferase (Fluc) translation depends on HIV-1 IRES was used. The Fluc/Rluc ratio was measured in lysates of Jurkat T cells transfected with the dual-luciferase plasmid bearing either the wild-type or a mutated IRES. Deletions or mutations in three regions decreased the IRES activity but deletion or mutations of a stem-loop preceding the primer binding site increased the IRES activity. The wild-type IRES activity, but not that of an IRES with a mutated stem-loop, was increased when cells were treated with agents that induce oxidative stress. Such stress is known to be caused by HIV-1 infection and we propose that this stem-loop is involved in a switch that stimulates the IRES activity in cells infected with HIV-1, supporting the suggestion that the IRES activity is up-regulated in the course of HIV-1 replication cycle.
Priming effect of platelet activating factor on leukotriene C4 from stimulated eosinophils of asthmatic patients.

BACKGROUND Eosinophils from asthmatic patients are known to release greater amounts of leukotrienes than normal eosinophils when stimulated by the calcium ionophore A23187. The effect of platelet activating factor (PAF) in priming eosinophils was investigated. METHODS Eosinophils were obtained from 18 asthmatic patients and 18 healthy donors. Cells separated by the Percoll gradients were incubated with PAF (C-18) for 30 minutes and then stimulated with the calcium ionophore A23187 (2.5 microM) for 15 minutes. The amount of leukotriene C4 (LTC4) in supernatants was measured using a combination of high pressure liquid chromatography and radioimmunoassay. RESULTS The mean (SD) amount of LTC4 released by eosinophils from asthmatic patients upon stimulation with the calcium ionophore A23187 alone was 27.9 (9.9) ng/10(6) cells (n = 6). The amount of LTC4 released following stimulation with the calcium ionophore A23187 after pretreatment with PAF (1, 5, and 10 microM) was 57.2 (8.9), 75.1 (14.3), and 52.6 (10.7) ng/10(6) cells (n = 6), respectively. Trace amounts of LTC4 (0.9 (0.02) ng/10(6) cells, n = 6) were detected in the supernatant of the cells after stimulation by PAF alone (5 microM). The amount of LTC4 released upon stimulation by calcium ionophore A23187 alone in eosinophils from healthy donors was 10.3 (3.7) ng/10(6) cells (n = 4). The amounts of LTC4 released upon stimulation with calcium ionophore A23187 after pretreatment with PAF at concentrations of 1, 5, and 10 microM were 11.9 (3.5), 17.8 (5.6), and 12.7 (5.1) ng/10(6) cells (n = 4), respectively. Trace amounts of LTC4 (0.6 (0.02) ng/10(6) cells, n = 4) were detected in the supernatant of the cells upon stimulation with PAF alone (5 microM). The amounts of LTC4 released upon stimulation with calcium ionophore A23187 after pretreatment with lyso-PAF at concentrations of 1, 5, and 10 microM (n = 4 or 6) were 30.8 (5.2), 22.9 (5.1), and 27.3 (4.3) ng/10(6) cells (n = 6) from the eosinophils of asthmatic patients and 13.7 (3.3), 15.2 (4.9), and 14.7 (3.8) ng/10(6) cells (n = 4) from the eosinophils of healthy donors. CONCLUSIONS The results indicated that PAF enhanced LTC4 formation by eosinophils obtained from asthmatic patients stimulated with the calcium ionophore A23187, but not those obtained from normal subjects.
Grading of Clear Cell Renal Cell Carcinoma Should be Based on Nucleolar Prominence

Fuhrman grading of renal cell carcinoma focuses on features of nuclear size, nuclear shape, and nucleolar prominence. Despite the reported widespread usage of Fuhrman grading in clinical studies, there is debate as to the prognostic significance and reproducibility of its criteria. It has been noted that many pathologists rely on assessment of nucleolar prominence alone when grading renal cell carcinoma; however, the validity of this remains unconfirmed. This study was undertaken to determine the relationship of the 3 morphologic components of the Fuhrman grading system with one another and to determine which, if any of these, can be correlated with outcome for clear cell renal cell carcinoma. One hundred twenty-one organ-confined clear cell renal cell carcinomas were examined in this study. Parameters of nuclear size (area, major axis, perimeter) and nuclear shape (shape factor, nuclear compactness) were assessed by image analysis, whereas nucleolar prominence was assigned (grades 1 to 3) using the criteria of Fuhrman. On the basis of the predominant grade present, there were 17 nucleolar grade 1, 90 nucleolar grade 2, and 14 nucleolar grade 3 tumors. When the high-power field in each tumor with the worst nucleolar grade was assessed, there was 1 nucleolar grade 1, 68 nucleolar grade 2, and 52 nucleolar grade 3 tumors. Predominant and worst nucleolar grade correlated with all measures of nuclear size, but not nuclear shape. Worst nucleolar grade and all parameters of nuclear size were significantly associated with outcome. On multivariate analysis, worst nucleolar grade retained a significant association with survival when modeled with nuclear area. Neither worst nucleolar grade nor major nuclear axis/nuclear perimeter was significantly associated with survival when modeled together. In this study, we have shown that worst nucleolar grade and nuclear size are of prognostic significance for clear cell renal cell carcinoma. We have further shown the association of worst nucleolar grade with outcome to be independent of nuclear area, whereas it is a dependent variable when tested against other parameters of nuclear size. These findings indicate that worst nucleolar grading alone is a valid grading parameter for clear cell renal cell carcinoma.
Assessing Tuberculosis Case Fatality Ratio: A Meta-Analysis

Background Recently, the tuberculosis (TB) Task Force Impact Measurement acknowledged the need to review the assumptions underlying the TB mortality estimates published annually by the World Health Organization (WHO). TB mortality is indirectly measured by multiplying estimated TB incidence with estimated case fatality ratio (CFR). We conducted a meta-analysis to estimate the TB case fatality ratio in TB patients having initiated TB treatment. Methods We searched for eligible studies in the PubMed and Embase databases through March 4th 2011 and by reference listing of relevant review articles. Main analyses included the estimation of the pooled percentages of: a) TB patients dying due to TB after having initiated TB treatment and b) TB patients dying during TB treatment. Pooled percentages were estimated using random effects regression models on the combined patient population from all studies. Main Results We identified 69 relevant studies of which 22 provided data on mortality due to TB and 59 provided data on mortality during TB treatment. Among HIV infected persons the pooled percentage of TB patients dying due to TB was 9.2% (95% Confidence Interval (CI): 3.7%–14.7%) and among HIV uninfected persons 3.0% (95% CI: −1.2%–7.4%) based on the results of eight and three studies respectively providing data for this analyses. The pooled percentage of TB patients dying during TB treatment was 18.8% (95% CI: 14.8%–22.8%) among HIV infected patients and 3.5% (95% CI: 2.0%–4.92%) among HIV uninfected patients based on the results of 27 and 19 studies respectively. Conclusion The results of the literature review are useful in generating prior distributions of CFR in countries with vital registration systems and have contributed towards revised estimates of TB mortality This literature review did not provide us with all data needed for a valid estimation of TB CFR in TB patients initiating TB treatment.
Active Imitation Learning via Reduction to I.I.D. Active Learning

In standard passive imitation learning, the goal is to learn a target policy by passively observing full execution trajectories of it. Unfortunately, generating such trajectories can require substantial expert effort and be impractical in some cases. In this paper, we consider active imitation learning with the goal of reducing this effort by querying the expert about the desired action at individual states, which are selected based on answers to past queries and the learner's interactions with an environment simulator. We introduce a new approach based on reducing active imitation learning to i.i. d. active learning, which can leverage progress in the i.i. d. setting. Our first contribution, is to analyze reductions for both non-stationary and stationary policies, showing that the label complexity (number of queries) of active imitation learning can be substantially less than passive learning. Our second contribution, is to introduce a practical algorithm inspired by the reductions, which is shown to be highly effective in four test domains compared to a number of alternatives.
Outstanding quality factors of bulk acoustic wave resonators at cryogenic temperature

Bulk acoustic wave resonators have already been tested at cryogenic temperature and high quality factors (Q-factors) have been observed in such conditions. Main results obtained at this time, and confirmed latter. So, it was tempting to investigate again this domain, with more accurate and easy-to-use means of measurements than in the years 60's - 70's, and even up to the years 90's. As a matter of course, specific means of investigation have been set up in this way. The Q-factor behavior of a quartz crystal resonator versus temperature when the temperature decreases from the ambient to cryogenic temperatures is quite well described at least up to above 10K. The Q-factor first increases, then goes down in a first peak at about 50 K, before increasing again with just a disturbance around 20 K. The increasing is essentially noticeable below this temperature. In the area of 50 K, the increasing of the Q-factor is attributed to a relaxation phenomenon due to the presence of Na+ impurities. These ions are combined with Al3+ ions substituted to some silicon ions Si4+ in the lattice. Interactions of the acoustic wave with acoustic phonons would be responsible of the deterioration of the Q-factor near 20 K. When the temperature decreases below 10 K, the increasing of the Q-factor can sometimes slow down because of the presence to the amorphous layer of silica at the resonator surface. In 1988, J. J. Suter has shown that an electrodeless resonator of the BVA type exhibits higher Q-factor than a conventional electrode-deposited resonator, at low temperature, especially below 5K. The fact that a metallised resonator has a lowest Q-factor has also been mentioned by Fraser.
The evaluation of the correlation between histomorphometric analysis and micro-computed tomography analysis in AdBMP-2 induced bone regeneration in rat calvarial defects

Purpose Micro-computed tomography (micro-CT) has been widely used in the evaluation of regenerated bone tissue but the reliability of micro-CT has not yet been established. This study evaluated the correlation between histomorphometric analysis and micro-CT analysis in performing new bone formation measurement. Methods Critical-size calvarial defects were created using a 8 mm trephine bur in a total of 24 Sprague-Dawley rats, and collagen gel mixed with autogenous rat bone marrow stromal cells (BMSCs) or autogenous rat BMSCs transduced by adenovirus containing bone morphogenic protein-2 (BMP-2) genes was loaded into the defect site. In the control group, collagen gel alone was loaded into the defect. After 2 and 4 weeks, the animals were euthanized and calvaria containing defects were harvested. Micro-CT analysis and histomorphometric analysis of each sample were accomplished and the statistical evaluation about the correlation between both analyses was performed. Results New bone formation of the BMP-2 group was greater than that of the other groups at 2 and 4 weeks in both histomorphometric analysis and micro-CT analysis (P=0.026, P=0.034). Histomorphometric analysis of representative sections showed similar results to histomorphometric analysis with a mean value of 3 sections. Measurement of new bone formation was highly correlated between histomorphometric analysis and micro-CT analysis, especially at the low lower threshold level at 2 weeks (adjusted r2=0.907, P<0.001). New bone formation of the BMP-2 group analyzed by micro-CT tended to decline sharply with an increasing lower threshold level, and it was statistically significant (P<0.001). Conclusions Both histomorphometric analysis and micro-CT analysis were valid methods for measurement of the new bone in rat calvarial defects and the ability to detect the new bone in micro-CT analysis was highly influenced by the threshold level in the BMP-2 group at early stage.
Taenia solium: the complex interactions, of biological, social, geographical and commercial factors, involved in the transmission dynamics of pig cysticercosis in highly endemic areas

Abstract If a programme for the control of pig cysticercosis is to be effective it has to be based on good data on the local epidemiology of Taenia solium. In 2002–2003, in a cross-sectional study of pig cysticercosis in the Mexican state of Morelos, 1747 pigs that had been born and reared in rural areas of the state were checked for T. solium infection by tongue inspection. The prevalence of cysticercosis in the pigs was found to vary from 0% to 30% according to the municipality from which the pigs came. Although prevalence appeared to be unaffected by the socio–economic status of the municipality, it was relatively high in areas that lacked latrines, and in pigs that were castrated, pregnant and/or of the native (rather than an imported) breed. The results of questionnaire-based interviews with pig owners revealed that most (64.5%) of the rural pigs, whether infected or not, are slaughtered and consumed within the locality where they were reared. The other pigs are sold at low prices to organised traffickers who take the uninspected pigs to neighbouring urban areas for sale. The observed complexity in the factors affecting the transmission of T. solium to the pigs of Morelos state calls for an intervention strategy of matching complexity, initially targeted at those villages with the highest prevalences of pig cysticercosis. The road transport of pigs needs to be better regulated, and the vaccination and genetic improvement of the rural pigs, and delaying the castration of the boars, should all be considered.
Impact of the year 2000 Medicare policy change on older patient enrollment to cancer clinical trials.

PURPOSE A prior analysis by the Southwest Oncology Group (SWOG) showed that women and African American patients were adequately represented on cancer clinical treatment trials but that older patients were substantially underrepresented. Twenty-five percent of patients > or = 65 years old were enrolled onto SWOG trials from 1993 to 1996, whereas 63% of all patients with cancer were > or = 65 years old. Recognition of this under-representation led to a change in Medicare policy in 2000 to include coverage of routine patient care costs of clinical trials. We conducted an updated analysis of accrual trends. METHODS The proportions of enrollment onto SWOG treatment trials by sex, race/ethnicity, and age (> or = 65 years) were computed for the years 1997 to 2000; corresponding rates in the United States were derived from US Census and National Cancer Institute Surveillance, Epidemiology, and End results data. Additionally, method of payment data were analyzed over time (1993 to 2003) to assess whether patterns in method of payment changed with the new Year 2000 Medicare policy on clinical trials coverage. RESULTS The results showed continued adequate representation by sex and race/ethnicity. Older patient accrual on SWOG trials increased significantly since 2000, with 31% of patients > or = 65 years old enrolled from 1997 to 2000 and 38% enrolled from 2001 to 2003 (v 25% from 1993 to 1996). The percentage of patients using Medicare plus supplemental insurance also increased beginning in 2000, whereas the percentage of patients using Medicare alone remained the same. CONCLUSION Method of payment analyses provided evidence that the Year 2000 Medicare policy change had a positive impact, but only for those patients with supplemental private coverage of coinsurance costs. Improvements in the Medicare payment structure could further increase older patient participation in clinical trials.
Tenderness classification of beef: III. Effect of the interaction between end point temperature and tenderness on Warner-Bratzler shear force of beef longissimus.

The objectives of this experiment were to determine 1) whether end point temperature interacts with tenderness to affect Warner-Bratzler shear force of beef longissimus and 2) if so, what impact that interaction would have on tenderness classification. Warner-Bratzler shear force was determined on longissimus thoracis cooked to either 60, 70, or 80 degrees C after 3 and 14 d of aging from carcasses of 100 steers and heifers. Warner-Bratzler shear force values (3- and 14-d aged steaks pooled) for steaks cooked to 70 degrees C were used to create five tenderness classes. The interaction of tenderness class and end point temperature was significant (P < .05). The increase in Warner-Bratzler shear force as end point temperature increased was greater (P < .05) for less-tender longissimus than more-tender longissimus (Tenderness Class 5 = 5.1, 7.2, and 8.5 kg and Tenderness Class 1 = 2.4, 3.1, and 3.7 kg, respectively, for 60, 70, and 80 degrees C). The slopes of the regressions of Warner-Bratzler shear force of longissimus cooked to 60 or 80 degrees C against Warner-Bratzler shear force of longissimus cooked to 70 degrees C were different (P < .05), providing additional evidence for this interaction. Correlations of Warner-Bratzler shear force of longissimus cooked to 60 or 80 degrees C with Warner-Bratzler shear force of longissimus cooked to 70 degrees C were . 90 and . 86, respectively. One effect of the interaction of tenderness with end point temperature on tenderness classification was to increase (P < .01) the advantage in shear force of a "Tender" class of beef over "Commodity" beef as end point temperature increased (.24 vs .42 vs .60 kg at 14 d for 60, 70, and 80 degrees C, respectively). When aged 14 d and cooked to 80 degrees C, "Commodity" steaks were six times more likely (P < .01) than "Tender" steaks to have shear force values > or = 5 kg (24 vs 4%). The end point temperature used to conduct tenderness classification did not affect classification accuracy, as long as the criterion for "Tender" was adjusted accordingly. However, cooking steaks to a greater end point temperature than was used for classification may reduce classification accuracy. The beef industry could alleviate the detrimental effects on palatability of consumers cooking beef to elevated degrees of doneness by identifying and marketing "Tender" longissimus.
TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems

TensorFlow is an interface for expressing machine learning algorithms, and an implementation for executing such algorithms. A computation expressed using TensorFlow can be executed with little or no change on a wide variety of heterogeneous systems, ranging from mobile devices such as phones and tablets up to large-scale distributed systems of hundreds of machines and thousands of computational devices such as GPU cards. The system is flexible and can be used to express a wide variety of algorithms, including training and inference algorithms for deep neural network models, and it has been used for conducting research and for deploying machine learning systems into production across more than a dozen areas of computer science and other fields, including speech recognition, computer vision, robotics, information retrieval, natural language processing, geographic information extraction, and computational drug discovery. This paper describes the TensorFlow interface and an implementation of that interface that we have built at Google. The TensorFlow API and a reference implementation were released as an open-source package under the Apache 2.0 license in November, 2015 and are available at www.tensorflow. org.
Surface energy effect on nonlinear buckling and postbuckling behavior of functionally graded piezoelectric cylindrical nanoshells under lateral pressure

In this paper, the surface energy effect on the nonlinear buckling and postbuckling behavior of functionally graded piezoelectric (FGP) cylindrical nanoshells subjected to lateral pressure is studied based on the electro-elastic surface/interface theory together with von-Kármán-Donnell-type kinematics of nonlinearity. The total strain energy of the FGP nanoshell, including surface energy, is derived by considering the constitutive formulations of surface phase. The principle of minimum potential energy is utilized to establish the nonlinear governing differential equations, and the singular perturbation technique is employed to obtain the asymptotic solutions. Then, two sets of comparison are conducted to validate the present work, and some numerical examples are given to study the effects of surface parameters, power law index and aspect ratio on the buckling and postbuckling behavior of FGP nanoshells. The results show that the critical buckling load and postbuckling path of FGP nanoshell are significantly size-dependent.
Reproductive seasonality in the female scimitar‐horned oryx (Oryx dammah)

Faecal oestrogen and progestin analyses were used to assess ovarian activity in non‐pregnant scimitar‐horned oryx (Oryx dammah) during a 13‐month interval. Mean (± SE) luteal phase, interluteal phase and oestrous cycle duration were 18.8 (± 0.5), 5.1 (± 0.2) and 23.8 (± 1.3) days, respectively. All females exhibited a synchronized anovulatory period that ranged from 36–95 days during spring. Short ovarian cycles (10.6 (± 0.8) days) were observed intermittently throughout the year and before the spontaneous resumption of oestrous cyclicity. Periovulatory peaks in oestrogen concentrations were detected for 42.5% (31/73) of ovarian cycles. A parallel analysis of reproductive data from the North American studbook (1985–1994) revealed that captive‐held scimitar‐horned oryx gave birth throughout the year. Sex ratio at birth was male‐biased (54.4%), and 19.1% of all calves failed to survive to 6 months of age (220 out of 1149 births). Only 0.7% of births resulted in twins. Median interbirth interval was 277 days, and 75% of these intervals were less than 332 days. Interbirth interval was extended (P < 0.05) if parturition occurred from January through May. In summary, the scimitar‐horned oryx is a seasonally polyoestrous species that experiences a distinct anovulatory period during spring in north‐east America.