Miracle-dz/UniFAR-FTUs huggingface dataset:
The International Journal of Biostatistics Causal Effect Models for Realistic Individualized Treatment and Intention to Treat Rules

Marginal structural models (MSM) are an important class of models in causal inference. Given a longitudinal data structure observed on a sample of n independent and identically distributed experimental units, MSM model the counterfactual outcome distribution corresponding with a static treatment intervention, conditional on user-supplied baseline covariates. Identification of a static treatment regimen-specific outcome distribution based on observational data requires, beyond the standard sequential randomization assumption, the assumption that each experimental unit has positive probability of following the static treatment regimen. The latter assumption is called the experimental treatment assignment (ETA) assumption, and is parameter-specific. In many studies the ETA is violated because some of the static treatment interventions to be compared cannot be followed by all experimental units, due either to baseline characteristics or to the occurrence of certain events over time. For example, the development of adverse effects or contraindications can force a subject to stop an assigned treatment regimen. In this article we propose causal effect models for a user-supplied set of realistic individualized treatment rules. Realistic individualized treatment rules are defined as treatment rules which always map into the set of possible treatment options. Thus, causal effect models for realistic treatment rules do not rely on the ETA assumption and are fully identifiable from the data. Further, these models can be chosen to generalize marginal structural models for static treatment interventions. The estimating function methodology of Robins and Rotnitzky (1992) (analogue to its application in Murphy, et. al. (2001) for a single treatment rule) provides us with the corresponding locally efficient double robust inverse probability of treatment weighted estimator. In addition, we define causal effect models for “intention-to-treat” regimens. The proposed intention-to-treat interventions enforce a static intervention until the time point at which the next treatment does not belong to the set of possible treatment options, at which point the intervention is stopped. We provide locally efficient estimators of such intention-to-treat causal effects.
Dual function of UPF3B in early and late translation termination

Nonsense‐mediated mRNA decay (NMD) is a cellular surveillance pathway that recognizes and degrades mRNAs with premature termination codons (PTCs). The mechanisms underlying translation termination are key to the understanding of RNA surveillance mechanisms such as NMD and crucial for the development of therapeutic strategies for NMD‐related diseases. Here, we have used a fully reconstituted in vitro translation system to probe the NMD proteins for interaction with the termination apparatus. We discovered that UPF3B (i) interacts with the release factors, (ii) delays translation termination and (iii) dissociates post‐termination ribosomal complexes that are devoid of the nascent peptide. Furthermore, we identified UPF1 and ribosomes as new interaction partners of UPF3B. These previously unknown functions of UPF3B during the early and late phases of translation termination suggest that UPF3B is involved in the crosstalk between the NMD machinery and the PTC‐bound ribosome, a central mechanistic step of RNA surveillance.
Comparison of Genotypes and Serotypes of Campylobacter jejuni Isolated from Danish Wild Mammals and Birds and from Broiler Flocks and Humans

ABSTRACT The incidence of human infection with Campylobacter jejuni is increasing in most developed countries and the reason for this is largely unknown. Although poultry meat is considered to be a major source, it is evident that other reservoirs exist, possibly common to humans and poultry. Environmental sources are believed to be important reservoirs of Campylobacter infection in broiler chicken flocks. We investigated the potential importance of wildlife as a source of infection in commercial poultry flocks and in humans by comparing the serotype distributions, fla types, and macrorestriction profiles (MRPs) of C. jejuni isolates from different sources. The serotype distribution in wildlife was significantly different from the known distributions in broilers and humans. Considerable sero- and genotype diversity was found within the wildlife collection, although two major groups of isolates within serotype O:12 and the O:4 complex were found. Common clonal lines among wildlife, chicken, and/or human isolates were identified within serotype O:2 and the O:4 complex. However, MRPs of O:12 and O:38 strains isolated from wildlife and other sources indicated that some clonal lines propagated in a wide selection of animal species but were not detected in humans or broilers in this study. The applied typing methods successfully identified different clonal groups within a strain collection showing large genomic diversity. However, the relatively low number of wildlife strains with an inferred clonal relationship to human and chicken strains suggests that the importance of wildlife as a reservoir of infection is limited.
Antagonistic Process as Source of Visible-Light Suppression of Afterpotential in Limulus UV Photoreceptors

Dear Sir: The relation between the visual pigment cascade and the membrane potential changes which result from the absorption of photons in photoreceptors is still unclear. Nolte and Brown (1), working on the UV cells of the median eye of Limulus, have recently established an interesting correlation between the induction and suppression by light of a prolonged depolarizing afterpotential (PDA) and the hypothetical photoconversion of the visual pigment from the primary state (VP360) to a metastable photoproduct (M480) and the reverse photoconversion, respectively. However, they offered a tentative model relating the depolarization directly to the presence of M480 or dark conversion of M480 into VP360. We present evidence suggesting that (a) no pigment change takes place during the dark decline of the PDA, and (b) the pigment does not return in the dark to its original state at least for hours at room temperature. (We assume, as do Nolte and Brown, that this cell contains only one visual pigment. No cells are known to contain more than one.) The observations (1, 2) on which Nolte and Brown based their model relate to the very slow repolarization in the dark of a UV cell depolarized by strong UV stimulation (see trace A of Fig. 1). This PDA can be rapidly suppressed by visible light (as in trace D of Fig. 1). The model suggests that the dark decay and the suppression by light of the PDA are due to the return of the pigment to the VP360 state, by slow conversion in the dark, or by photoregeneration. If the dark decay of the PDA were directly linked to the return of the pigment to its primary state, however, one would expect that further UV stimulation of a cell in which a maximal PDA has declined to base line would again induce a PDA. This turns out not to be the case. Trace A of Fig. 1 (see reference 3 for Methods) shows the intracellular response to UV light (360 nm) of a cell which had been exposed 5 min earlier to strong visible light (550 nm), and resembles the third trace of Fig. 1 of reference (1). Trace B
Distribution of intracellular and secreted surfactant during postnatal rat lung development

Pulmonary surfactant prevents alveolar collapse via reduction of surface tension. In contrast to human neonates, rats are born with saccular lungs. Therefore, rat lungs serve as a model for investigation of the surfactant system during postnatal alveolar formation. We hypothesized that this process is associated with characteristic structural and biochemical surfactant alterations. We aimed to discriminate changes related to alveolarization from those being either invariable or follow continuous patterns of postnatal changes. Secreted active (mainly tubular myelin (tm)) and inactive (unilamellar vesicles (ulv)) surfactant subtypes as well as intracellular surfactant (lamellar bodies (lb)) in type II pneumocytes (PNII) were quantified before (day (d) 1), during (d 7), at the end of alveolarization (d 14), and after completion of lung maturation (d 42) using electron microscopic methods supplemented by biochemical analyses (phospholipid quantification, immunoblotting for SP‐A). Immunoelectron microscopy determined the localization of surfactant protein A (SP‐A). (1) At d 1 secreted surfactant was increased relative to d 7–42 and then decreased significantly. (2) Air spaces of neonatal lungs comprised lower fractions of tm and increased ulv, which correlated with low SP‐A concentrations in lung lavage fluid (LLF) and increased respiratory rates, respectively. (3) Alveolarization (d 7–14) was associated with decreasing PNII size although volume and sizes of Lb continuously increased. (4) The volume fractions of Lb correlated well with the pool sizes of phospholipids in lavaged lungs. Our study emphasizes differential patterns of developmental changes of the surfactant system relative to postnatal alveolarization. Pediatr Pulmonol. 2007; 42:548–562. © 2007 Wiley‐Liss, Inc.
The WAM - Definition and Compiler Correctness

This paper provides a mathematical analysis of the Warren Abstract Machine for executing Prolog and a correctness proof for a general compilation scheme of Prolog for the WAM. Starting from an abstract Prolog model which is close to the programmer's intuition, we derive the WAM methodically by stepwise reenement of Prolog models, proving correctness and completeness for each reenement step. Along the way we explicitely formulate, as proof assumptions, a set of natural conditions for a compiler to be correct, thus making our proof applicable to a whole class of compilers. The proof method provides a rigorous mathematical framework for the study of Prolog compilation techniques. It can be applied in a natural way to extensions and variants of Prolog and related WAMs allowing for parallelism, constraint handling, types, functional components|in some cases it has in fact been successfully extended. Our exposition assumes only a general understanding of Prolog. We reach full mathematical rigour, without heavy methodological overhead, by using Gurevich's notion of evolving algebras.
Potential Impact of the Tropical Indian Ocean–Indonesian Seas on El Niño Characteristics*

Diagnostics performed with twentieth-century (1861-2000) ensemble integrations of the Geophysical Fluid Dynamics Laboratory Climate Model, version 2.1 (CM2.1) suggest that, during the developing phase, El Nino events that co-occur with the Indian Ocean Dipole Zonal Mode (IODZM; class 1) are stronger than those without (class 2). Also, during class 1 events coherent sea surface temperature (SST) anomalies develop in the Indonesian seas that closely follow the life cycle of IODZM. This study investigates the effect of these regional SST anomalies (equatorial Indian Ocean and Indonesian seas) on the amplitude of the developing El Nino. An examination of class 1 minus class 2 composites suggests two conditions that could lead to a strong El Nino in class 1 events: (i) during January, ocean-atmosphere conditions internal to the equatorial Pacific are favorable for the development of a stronger El Nino and (ii) during May-June, coinciding with the development of regional SST anomalies, an abrupt increase in westerly wind anomalies is noticeable over the equatorial western Pacific with a subsequent increase in thermocline and SST anomalies over the eastern equatorial Pacific. This paper posits the hypothesis that, under favorable conditions in the equatorial Pacific, regional SST anomalies may enable the development of a stronger El Nino. Owing to a wealth of feedbacks in CM2.1, solutions from a linear atmosphere model forced with May-June anomalous precipitation and anomalous SST from selected areas over the equatorial Indo-Pacific are examined. Consistent with our earlier study, the net Kelvin wave response to contrasting tropical Indian Ocean heating anomalies cancels over the equatorial western Pacific. In contrast, Indonesian seas SST anomalies account for about 60%-80% of the westerly wind anomalies over the equatorial western Pacific and also induce anomalous precipitation over the equatorial central Pacific. It is argued that the feedback between the precipitation and circulation anomalies results in an abrupt increase in zonal wind anomalies over the equatorial western Pacific. Encouraged by these results, the authors further examined the processes that cause cold SST anomalies over the Indonesian seas using an ocean model. Sensitivity experiments suggest that local wind anomalies, through stronger surface heat loss and evaporation, and subsurface upwelling are the primary causes. The present results imply that in coupled models, a proper representation of regional air-sea interactions over the equatorial Indo-Pacific warm pool may be important to understand and predict the amplitude of El Nino.
Performance Responses, Nutrient Digestibility, Blood Characteristics, and Measures of Gastrointestinal Health in Weanling Pigs Fed Protease Enzyme

Although exogenous protease enzymes have been used in poultry diets quite extensively, this has not been the case for pig diets. In general, due to their better gut fermentative capacity and longer transit time, pigs have greater capacity to digest dietary proteins than poultry. However, in early-weaned piglets, the stress brought about by weaning adversely affects the digestion of dietary proteins. Therefore, a study was conducted to determine the effects of a commercial protease enzyme in weanling pigs. Indices of growth, nutrient digestibility, blood profiles, fecal microflora, fecal gas emission and fecal scores were measured during the study. A total of 50 weanling pigs (6.42±0.12 kg) at 28 d of age were randomly assigned to receive 1 of 2 dietary treatments: i) control diet (corn-soy based) with no supplemental protease (CON), and ii) control diet+200 g/ton protease (PROT) for 42 d. A completely randomized design consisting of 2 treatments, 5 replicates, and 5 pigs in each replicate was used. Growth performance in terms of body weight (27.04±0.38 kg vs 25.75±0.39 kg; p<0.05) and average daily gain (491±7.40 g vs 460±7.46 g; p<0.05) in PROT fed pigs were increased significantly, but gain per feed (0.700±0.01 vs 0.678±0.01; p>0.05) was similar between treatments at d 42. Relative to CON pigs, PROT fed pigs had increased (p<0.05) apparent total tract digestibility (84.66%±0.65% vs 81.21%±1.13% dry matter and 84.02%±0.52% vs 80.47%±1.22% nitrogen) and decreased (p<0.05) NH3 emission (2.0±0.16 ppm vs 1.2±0.12 ppm) in the feces at d 42. Except for a decreased (p<0.05) in blood creatinine level, no differences were observed in red blood cell, white blood cell, lymphocyte, urea nitrogen, and IgG concentrations between treatments. Fecal score and fecal microflora (Lactobacillus and E. coli) were also similar between CON and PROT groups. Overall, the supplementation of protease enzyme in weanling pigs resulted in improved growth rate and nutrient digestibility. Exogenous protease enzyme reduced fecal NH3 emission, thus, potentially serving as a tool in lowering noxious gas contribution of livestock production in the environment.
Private spatial data aggregation in the local setting

With the deep penetration of the Internet and mobile devices, privacy preservation in the local setting has become increasingly relevant. The local setting refers to the scenario where a user is willing to share his/her information only if it has been properly sanitized before leaving his/her own device. Moreover, a user may hold only a single data element to share, instead of a database. Despite its ubiquitousness, the above constraints make the local setting substantially more challenging than the traditional centralized or distributed settings. In this paper, we initiate the study of private spatial data aggregation in the local setting, which finds its way in many real-world applications, such as Waze and Google Maps. In response to users' varied privacy requirements that are natural in the local setting, we propose a new privacy model called personalized local differential privacy (PLDP) that allows to achieve desirable utility while still providing rigorous privacy guarantees. We design an efficient personalized count estimation protocol as a building block for achieving PLDP and give theoretical analysis of its utility, privacy and complexity. We then present a novel framework that allows an untrusted server to accurately learn the user distribution over a spatial domain while satisfying PLDP for each user. This is mainly achieved by designing a novel user group clustering algorithm tailored to our problem. We confirm the effectiveness and efficiency of our framework through extensive experiments on multiple real benchmark datasets.
THE SLOAN DIGITAL SKY SURVEY DATA RELEASE 7 SPECTROSCOPIC M DWARF CATALOG. III. THE SPATIAL DEPENDENCE OF MAGNETIC ACTIVITY IN THE GALAXY

We analyze the magnetic activity of 59,318 M dwarfs from the Sloan Digital Sky Survey Data Release 7. This analysis explores the spatial distribution of M dwarf activity as a function of both vertical distance from the Galactic plane (Z) and planar distance from the Galactic center (R). We confirm the established trends of decreasing magnetic activity (as measured by Hα emission) with increasing distance from the mid-plane of the disk and find evidence of a trend in Galactocentric radii. We measure a non-zero radial gradient in the activity fraction in our analysis of stars with spectral types dM3 and dM4. The activity fraction increases with R and can be explained by a decreasing mean stellar age with increasing distance from the Galactic center.
WCET analysis for multi-core processors with shared buses and event-driven bus arbitration

Multi-core processors share common hardware resources between several processor cores. As a consequence, a program executed on one processor core may influence the execution time of the programs executed on the concurrent cores. This effect is commonly referred to as shared-resource interference. Worst-case execution time (WCET) analysis for multi-core processors has to take into account the shared-resource interference. Most existing approaches to WCET analysis for multi-core processors with shared buses and event-driven bus arbitration rely on compositionality. These approaches, however, do not support complex processor core pipelines. The existing approaches that support complex pipelines perform an exhaustive enumeration of possible interleavings of accesses to the shared bus by the different cores. Such an enumeration is infeasible in most cases. Our approach extends the state of the art in WCET analysis for single-core processors in such a way that it can deal with shared-bus interference. It does not rely on compositionality or enumeration of interleavings. Our approach calculates co-runner-insensitive WCET bounds, that are independent of the programs executed in parallel. Furthermore, it is able to improve those bounds by taking into account the bus access behavior of the concurrent cores and, thus, to calculate co-runner-sensitive WCET bounds. The implementation of our approach is evaluated for different multi-core processors. Our calculation of co-runner-insensitive WCET bounds is shown to be almost independent of the number of processor cores in terms of runtime and memory consumption. The co-runner-sensitive WCET bounds are up to 12.5% smaller than the co-runner-insensitive ones for a dual-core processor.
A Combined Random Forest and OBIA Classification Scheme for Mapping Smallholder Agriculture at Different Nomenclature Levels Using Multisource Data (Simulated Sentinel-2 Time Series, VHRS and DEM)

Sentinel-2 images are expected to improve global crop monitoring even in challenging tropical small agricultural systems that are characterized by high intra- and inter-field spatial variability and where satellite observations are disturbed by the presence of clouds. To overcome these constraints, we analyzed and optimized the performance of a combined Random Forest (RF) classifier/object-based approach and applied it to multisource satellite data to produce land use maps of a smallholder agricultural zone in Madagascar at five different nomenclature levels. The RF classifier was first optimized by reducing the number of input variables. Experiments were then carried out to (i) test cropland masking prior to the classification of more detailed nomenclature levels, (ii) analyze the importance of each data source (a high spatial resolution (HSR) time series, a very high spatial resolution (VHSR) coverage and a digital elevation model (DEM)) and data type (spectral, textural or other), and (iii) quantify their contributions to classification accuracy levels. The results show that RF classifier optimization allowed for a reduction in the number of variables by 1.5- to 6-fold (depending on the classification level) and thus a reduction in the data processing time. Classification results were improved via the hierarchical approach at all classification levels, achieving an overall accuracy of 91.7% and 64.4% for the cropland and crop subclass levels, respectively. Spectral variables derived from an HSR time series were shown to be the most discriminating, with a better score for spectral indices over the reflectances. VHSR data were only found to be essential when implementing the segmentation of the area into objects and not for the spectral or textural features they can provide during classification.
Evaluation of a technical revegetation action performed on foredunes at Devesa de la Albufera, Valencia, Spain

We have evaluated the level of restoration achieved by a technical revegetation action carried out on reconstructed foredunes at the Devesa de la Albufera and compared this level with that achieved by spontaneous succession. Foredunes 1, 3, 6 and 20 y old since revegetated (1, 3, 6 and 20 y, respectively) were considered as spatially separated stages representing a successional trend in the development of the restored plant community. Lower and similar levels of diversity (richness and H´ and Pielou´s indexes) and coverage, respectively, were found on dunes corresponding to the oldest stage of technical revegetation compared with that of the reference site. Diversity and coverage parameters increased during the first 6 y of the technical succession and decreased after 20 y of revegetation. Moreover, that increase was quite obvious as early as 3 y after the onset of revegetation. Results also showed that the Devesa de la Albufera has its own capacity for revegetation. According to the Jaccard and Sørensen indexes, these dunes were more similar to the reference than those from the 20 y old site. Beyond the current functionality of the revegetated sites, it is concluded that the natural and aesthetic values may be restored at the Valencian Devesa de la Albufera. Copyright © 2010 John Wiley & Sons, Ltd.