Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comparison of Methods for Estimating the Causal Effect of a Treatment in Randomized Clinical Trials Subject to Noncompliance

Summary We consider the analysis of clinical trials that involve randomization to an active treatment (T = 1) or a control treatment (T = 0), when the active treatment is subject to all‐or‐nothing compliance. We compare three approaches to estimating treatment efficacy in this situation: as‐treated analysis, per‐protocol analysis, and instrumental variable (IV) estimation, where the treatment effect is estimated using the randomization indicator as an IV. Both model‐ and method‐of‐moment based IV estimators are considered. The assumptions underlying these estimators are assessed, standard errors and mean squared errors of the estimates are compared, and design implications of the three methods are examined. Extensions of the methods to include observed covariates are then discussed, emphasizing the role of compliance propensity methods and the contrasting role of covariates in these extensions. Methods are illustrated on data from the Women Take Pride study, an assessment of behavioral treatments for women with heart disease.
Parental Involvement: The Missing Link in Academic Performance, Socialization and Coping Behavior of Students at St. Louis High School in Natore, Bangladesh

Parental involvement in school settings has been associated with a number of positive outcomes. The purpose of this study is to examine the relationships between parental involvement and academic performance, socialization, and coping behavior of students at St. Louis High School in Natore, Bangladesh. Data was collated from the accomplished student questionnaires of tenth-grade students (N=86), their parents (N=86) and teachers (N=10). The data were processed to investigate the relationship between the predictor variable and the criterion variables. This study employed a simple linear regression analysis. The significance of the study is defined by the influence of parental involvement and values for much more effective academic performance, socialization, and coping behaviour of the students. The significant findings of the study reveal that parental involvement and students’ socialization are important and necessary for the well-being of the students. However, academic performance and coping behavior did not factor much in parental involvement.
Development and Application of Novel Constructs to Score C:G-to-T:A Transitions and Homologous Recombination in Arabidopsis1[W]

We report on the development of five missense mutants and one recombination substrate of the β-glucuronidase (GUS)-encoding gene of Escherichia coli and their use for detecting mutation and recombination events in transgenic Arabidopsis (Arabidopsis thaliana) plants by reactivation of GUS activity in clonal sectors. The missense mutants were designed to find C:G-to-T:A transitions in a symmetrical sequence context and are in that respect complementary to previously published GUS point mutants. Small peptide tags (hemagglutinin tag and Strep tag II) and green fluorescent protein were translationally fused to GUS, which offers possibilities to check for mutant GUS production levels. We show that spontaneous mutation and recombination events took place. Mutagenic treatment of the plants with ethyl methanesulfonate and ultraviolet-C increased the number of mutations, validating the use of these constructs to measure mutation and recombination frequencies in plants exposed to biotic or abiotic stress conditions, or in response to different genetic backgrounds. Plants were also subjected to heavy metals, methyl jasmonate, salicylic acid, and heat stress, for which no effect could be seen. Together with an ethyl methanesulfonate mutation induction level much higher than previously described, the need is illustrated for many available scoring systems in parallel. Because all GUS missense mutants were cloned in a bacterial expression vector, they can also be used to score mutation events in E. coli.
Deep View Morphing

View morphing takes two views of a 3D object and infers the appearance of the object at intermediary views. This problem is traditionally approached through the lens of epipolar geometry, but such techniques require computing pixel correspondences, and are brittle to changes in visibility. This work introduces a neural network based approach for learning to generate morphs of 3D objects. Three experiments are performed to assess the model’s ability to reconstruct images and generalize to unseen objects.
Nitrogen Availability From Manure in Years Following a One-Time Application

Manure from the semiarid West’s dairy industries is a rich nutrient source, but its use for crops can be problematic because soil N availability from manure may vary substantially depending on the year of application. Experimental plots established in Idaho on a Portneuf silt loam (coarse silty, mixed, superactive, mesic Durinodic Xeric Haplocalcid) included six manure treatments and two non-manure treatments with four replicates. The six manure treatments included combinations of two manure rates, Man-1x (277 lbs total N/ac) and Man-3x (866 lbs total N/ac) applied in the fall either 1, 2, or 3 years previously. The two non-manure treatments were urea fertilizer applied per soil test (Fert) and a control with no amendment. We measured net N mineralization (0-12 in) in the plots using buried bags in 2006, 2007, and 2009 for a sprinkler-irrigated barley, sugarbeet, and dry bean crop, respectively. This resulted in i) two years of net N mineralization data for each manure rate applied 1, 2, or 3 years prior to measurement; and ii) one year of data for each manure rate applied 4 or 5 years previous to the measurement year. A 5-year decay series for each of the two manure rates was derived from functions fitted to the net N mineralization data, expressed as a fraction of total manure-N applied. The decay series (y1-y5) for the manure-1x treatment was 0.23, 0.12, 0.10, 0.09, and 0.08 while that for the manure-3x rate was 0.20, 0.08, 0.05, 0.04, and 0.03. Soil at the 12-to-24-in depth contributed up to 28% of the total N mineralized in the 0-to-60-cm soil layer of manure-amended soils in the 3rd year after application, with lesser amounts contributed in earlier years due to immobilization. The efficacy of N mineralization processes decreased as the manure application increased, thus using a single decay series to predict N availability across a range of manure application rates could lead to substantial estimation errors.
Development of structure-activity modelling of carboxamides compounds for Aedes aegypti repellents

Article history: Received 21 May 2017 Received in revised form 17 July 2017 Accepted 2 August 2017 Available online 14 August 2017 Recently, research has been critically focused on finding new compounds with antirepellent activity due to the rising of new types of mosquito-borne diseases. Mosquito repellents are the safer and cleaner alternative to fight the anthropods from bitten human skins, hence reduce the spread of diseases. This study investigated the relationships between biological activity and structure of carboxamides by using Quantitative Structure-Activity Relationship (QSAR) analysis. The data set used in this study comprised of 40 carboxamide compounds taken from the literature with their activities expressed as log PT (protection time). These compounds were split into training set for model building and test set for external validation using activity-based ranking method. The training set contained approximately 75% of the compounds while the remaining compounds were then used as the validation set to verify the accuracy of the model. DRAGON software was employed to generate molecular descriptors. The important relevant descriptors were further selected and reduced by using Genetic Algorithm (GA) as variable selection method. Two QSAR models were developed by combining GA method with two different modelling techniques that are multiple linear regressions (MLR) and partial least square (PLS). All the models are robust with good correlation coefficient (r2) greater than 0.6 and external validation r2test more than 0.5. Statistics of the GA-MLR model are r2 = 0.779 and r2test = 0.646. Whereas, the second model generated from GA and PLS shows good r2 with value of 0.775 and r2test = 0.563. These results could be useful in finding new, safe, and more effective repellents against Aedes Aegypti in a short time by providing guidance for further laboratory work as well as prediction of external compounds and help to understand the factors affecting their activity.
Net Greenhouse Gas Budget and Soil Carbon Storage in a Field with Paddy–Upland Rotation with Different History of Manure Application

Methane (CH4) and nitrous oxide (N2O) fluxes were measured from paddy–upland rotation (three years for soybean and three years for rice) with different soil fertility due to preceding compost application for four years (i.e., 3 kg FW m−2 year−1 of immature or mature compost application plots and a control plot without compost). Net greenhouse gas (GHG) balance was evaluated by integrating CH4 and N2O emissions and carbon dioxide (CO2) emissions calculated from a decline in soil carbon storage. N2O emissions from the soybean upland tended to be higher in the immature compost plot. CH4 emissions from the rice paddy increased every year and tended to be higher in the mature compost plot. Fifty-two to 68% of the increased soil carbon by preceding compost application was estimated to be lost during soybean cultivation. The major component of net GHG emission was CO2 (82–94%) and CH4 (72–84%) during the soybean and rice cultivations, respectively. Net GHG emissions during the soybean and rice cultivations were comparable. Consequently, the effects of compost application on the net GHG balance from the paddy–upland rotation should be carefully evaluated with regards to both advantages (initial input to the soil) and disadvantages (following increases in GHG).
The Endogenous Cannabinoid System Regulates Seizure Frequency and Duration in a Model of Temporal Lobe Epilepsy

Several lines of evidence suggest that cannabinoid compounds are anticonvulsant. However, the anticonvulsant potential of cannabinoids and, moreover, the role of the endogenous cannabinoid system in regulating seizure activity has not been tested in an in vivo model of epilepsy that is characterized by spontaneous, recurrent seizures. Here, using the rat pilocarpine model of epilepsy, we show that the marijuana extract Δ9-tetrahydrocannabinol (10 mg/kg) as well as the cannabimimetic, 4,5-dihydro-2-methyl-4(4-morpholinylmethyl)-1-(1-naphthalenyl-carbonyl)-6H-pyrrolo[3,2,1-i,j]quinolin-6-one [R(+)WIN55,212 (5 mg/kg)], completely abolished spontaneous epileptic seizures. Conversely, application of the cannabinoid CB1 receptor (CB1) antagonist, N-(piperidin-1-yl-5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamidehydrochloride (SR141716A), significantly increased both seizure duration and frequency. In some animals, CB1 receptor antagonism resulted in seizure durations that were protracted to a level consistent with the clinical condition status epilepticus. Furthermore, we determined that during an short-term pilocarpine-induced seizure, levels of the endogenous CB1 ligand 2-arachidonylglycerol increased significantly within the hippocampal brain region. These data indicate not only anticonvulsant activity of exogenously applied cannabinoids but also suggest that endogenous cannabinoid tone modulates seizure termination and duration through activation of the CB1 receptor. Furthermore, Western blot and immunohistochemical analyses revealed that CB1 receptor protein expression was significantly increased throughout the CA regions of epileptic hippocampi. By demonstrating a role for the endogenous cannabinoid system in regulating seizure activity, these studies define a role for the endogenous cannabinoid system in modulating neuroexcitation and suggest that plasticity of the CB1 receptor occurs with epilepsy.
Error analysis of a class of derivative estimators for noisy signals and applications. (Analyse d'Erreurs d'Estimateurs des Dérivées de Signaux Bruités et Applications)

Recent algebraic parametric estimation techniques (see (10,11)) led to point-wise derivative estimates by using only the iterated integral of a noisy observation signal (see (24,25)). In this paper, we extend such differentiation methods by providing a larger choice of parameters in these integrals: they can be reals. For this, the extension is done via a truncated Jacobi orthogonal series expansion. Then, the noise error contribution of these derivative estimations is investigated: after proving the existence of such integral with a stochastic process noise, their statistical properties (mean value, variance and covariance) are analyzed. In particular, the following important results are obtained: a) the bias error term, due to the truncation, can be reduced by tuning the parameters, b) such estimators can cope with a large class of noises for which the mean and covariance are polynomials in time (with degree smaller than the order of derivative to be estimated), c) the variance of the noise error is shown to be smaller in the case of negative real parameters than it was in (24,25) for integer values.
Hesperidin contributes to the vascular protective effects of orange juice: a randomized crossover study in healthy volunteers.

BACKGROUND Although numerous human studies have shown consistent effects of some polyphenol-rich foods on several intermediate markers for cardiovascular diseases, it is still unknown whether their action could be specifically related to polyphenols. OBJECTIVE We investigated the effect of orange juice and its major flavonoid, hesperidin, on microvascular reactivity, blood pressure, and cardiovascular risk biomarkers through both postprandial and chronic intervention studies. DESIGN Twenty-four healthy, overweight men (age 50-65 y) were included in a randomized, controlled, crossover study. Throughout the three 4-wk periods, volunteers daily consumed 500 mL orange juice, 500 mL control drink plus hesperidin (CDH), or 500 mL control drink plus placebo (CDP). All measurements and blood collections were performed in overnight-fasted subjects before and after the 4-wk treatment periods. The postprandial study was conducted at the beginning of each experimental period. RESULTS Diastolic blood pressure (DBP) was significantly lower after 4 wk consumption of orange juice or CDH than after consumption of CDP (P = 0.02), whereas microvascular endothelium-related reactivity was not significantly affected when measured after an overnight fast. However, both orange juice and CDH ingestion significantly improved postprandial microvascular endothelial reactivity compared with CDP (P < 0.05) when measured at the peak of plasma hesperetin concentration. CONCLUSIONS In healthy, middle-aged, moderately overweight men, orange juice decreases DBP when regularly consumed and postprandially increases endothelium-dependent microvascular reactivity. Our study suggests that hesperidin could be causally linked to the beneficial effect of orange juice. This trial is registered at clinicaltrials.gov as NCT00983086.
Nutrient cycling in mango trees Ciclagem de nutrientes em mangueira

Estimates of nutrient amounts both shedding and demanding replacement in the maintenance of productivity of fruit trees require studies on element dynamics within the many ecosystem components generally made up of nutrient cycling. Thus, it was the objective of this study to evaluate the nutrient biochemical cycling in a mango tree (Mangifera indica L.) orchard, Palmer variety. Macronutrients [nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S)] had their contents evaluated in leaves at different stages: new, mature, senescent, and litter. First exploratory analysis was performed for main components which preserve the multivariate structure shown by the data. It was possible to observe the association of new leaves with N, P, K, Mg, and S; senescent leaves and the leaves from the litter were associated to Ca, while mature leaves, to K. As a complement, taking the independent variables into consideration, Tukey test (p≤0.01) showed that the averages of N, P, and Ca differ between the new and the mature leaves; average of Mg in new leaves differs from the others, and S does not differ along the stages. Also observed was the re-translocation of 41%, 63% and 57% of N, P, and K, respectively, when comparison was made among the contents of the elements in mature leaves as well as in litter, which indicates that the biochemical cycling is important for the mango tree cultivation.
Safety and efficacy of switching from dorzolamide 1.0%/timolol maleate 0.5% eye drops to brinzolamide 1.0%/timolol maleate 0.5% eye drops

Purpose To evaluate the safety and efficacy of switching from dorzolamide 1.0%/timolol maleate 0.5% fixed-combination (DTFC) eye drops to brinzolamide 1.0%/timolol maleate 0.5% fixed-combination (BTFC) eye drops in patients with primary open-angle glaucoma or ocular hypertension. Methods A total of 35 eyes of 35 patients with primary open-angle glaucoma or ocular hypertension using DTFC eye drops were included. Participants discontinued DTFC drops and immediately began using BTFC drops. All other eye drops currently being used were continued. Intraocular pressure (IOP) 1 and 3 months after switching medications was compared with baseline IOP. One month after switching medications, participant preference and adherence were evaluated. Adverse reactions were monitored at each study visit. Results The IOP was 17.9±2.6 mmHg at baseline and 18.3±4.1 mmHg and 17.8±3.4 mmHg 1 month and 3 months after switching medications, respectively (P=0.633). The frequency of missing a dose was not different before (6.1%) and after (6.1%) switching to BTFC. Significantly fewer participants reported stinging after switching to BTFC (15.2%) than while using DTFC (51.5%, P,0.01). Blurred vision was reported with the same frequency before (39.4%) and after (42.4%) switching to BTFC. A total of 33.3% and 27.3% of patients preferred DTFC and BTFC, respectively. Several patients withdrew from the study because of discomfort (n=2, 5.7%), discharge (n=1, 2.9%), dizziness (n=1, 2.9%), or increased IOP (n=2, 5.7%). Conclusion Switching from DTFC to BTFC was well tolerated and did not result in IOP changes or a decreased patient adherence. When glaucoma patients complain of stinging with DTFC administration, switching to BTFC is an acceptable treatment option.
Meshless simulation of brittle fracture

We propose a meshless method to simulate brittle fracture. For brittle solids, stress computation can be difficult because brittle materials generally require small timesteps which bring about heavy computational burden. Furthermore, treating the brittle objects as deformable bodies will cause inevitable visual artifact. We treat the brittle objects as fully rigid bodies and solve the brittle stress distribution with Meshless Local Petrov‐Galerkin as a quasistatic problem, so visual artifact disppears and no timestep restriction exists. As a meshless framework, our method has the advantage of easy‐resampling around high stress areas to improve computation accuracy. To generate fractured pieces, unlike previous methods which explicitly track the crack propagation, we also present a novel damage based model. Our model supports user‐control of the fracture pattern which is especially useful when simulating anisotropic materials such as glass or wood. Results show that our meshless framework is physically feasible and user controllable. Copyright © 2011 John Wiley & Sons, Ltd.
Program Participation and Farm-Level Adoption of Conservation Tillage: Estimates from a Multinomial Logit Model

Over the past decade, conservation compliance has reduced soil erosion. What will happen to these erosion benefits if commodity programs are eliminated or if the subsidy level is greatly reduced? This study investigates whether there will be a significant decline in the amount of acreage on which conservation practices are adopted if future farm program benefits are not tied to conservation compliance.
Impact of type of procedure and surgeon on EuroSCORE operative risk validation

Objective EuroSCORE has been used in cardiac surgery operative risk assessment, despite important variables were not included. The objective of this study was to validate EuroSCORE on mortality prediction in a Brazilian cardiovascular surgery center, defining the influence of type of procedure and surgical team. Methods Between January 2006 and June 2011, 2320 consecutive adult patients were studied. According to additive EuroSCORE, patients were divided into low risk (score<2), medium risk (3 - 5), high risk (6 - 11) and very high risk (>12). The relation between observed mortality (O) and expected mortality (E) according to logistic EuroSCORE was calculated for each of the groups, types of procedures and surgeons with > 150 operations, and analyzed by logistic regression. Results EuroSCORE correlated to the observed mortality (O/E=0.94; P<0.0001; area under the curve 0.78). However, it overestimated the mortality in very high risk patients (O/E=0.74; P=0.001). EuroSCORE tended to overestimate isolated myocardial revascularization mortality (O/E=0.81; P=0.0001) and valve surgery mortality (O/E=0.89; P=0.007) and it tended to underestimate combined procedures mortality (O/E=1.09; P<0.0001). EuroSCORE overestimated surgeon A mortality (O/E=0.46; P<0.0001) and underestimated surgeon B mortality (O/E=1.3; P<0.0001), in every risk category. Conclusion In the present population, EuroSCORE overestimates mortality in very high risk patients, being influenced by type of procedure and surgical team. The most appropriate surgical team may minimize risks imposed by preoperative profiles.
Hedgehog signaling regulates the generation of ameloblast progenitors in the continuously growing mouse incisor

In many organ systems such as the skin, gastrointestinal tract and hematopoietic system, homeostasis is dependent on the continuous generation of differentiated progeny from stem cells. The rodent incisor, unlike human teeth, grows throughout the life of the animal and provides a prime example of an organ that rapidly deteriorates if newly differentiated cells cease to form from adult stem cells. Hedgehog (Hh) signaling has been proposed to regulate self-renewal, survival, proliferation and/or differentiation of stem cells in several systems, but to date there is little evidence supporting a role for Hh signaling in adult stem cells. We used in vivo genetic lineage tracing to identify Hh-responsive stem cells in the mouse incisor and we show that sonic hedgehog (SHH), which is produced by the differentiating progeny of the stem cells, signals to several regions of the incisor. Using a hedgehog pathway inhibitor (HPI), we demonstrate that Hh signaling is not required for stem cell survival but is essential for the generation of ameloblasts, one of the major differentiated cell types in the tooth, from the stem cells. These results therefore reveal the existence of a positive-feedback loop in which differentiating progeny produce the signal that in turn allows them to be generated from stem cells.
Venous Function and Central Venous Pressure: A Physiologic Story

The veins contain approximately 70% of total blood volume and are 30 times more compliant than arteries; therefore, changes in blood volume within the veins are associated with relatively small changes in venous pressure. The terms venous capacity, compliance, and stressed and unstressed volumes are defined. Decreases in flow into a vein are associated with decreases in intravenous pressure and volume, and vice versa. Changes in resistance in the small arteries and arterioles may affect venous return in opposite directions; this is explained by a two-compartment model: compliant (mainly splanchnic veins) and noncompliant (nonsplanchnic veins). Effects of intrathoracic and intraabdominal pressures on venous return and central venous pressure as well as the value of central venous pressure as a diagnostic variable are discussed.