Miracle-dz/UniFAR-FTUs huggingface dataset:
Retrospective comparative evaluation of the lasting impact of a community-based primary health care programme on under-5 mortality in villages around Jamkhed, India.

OBJECTIVE To conduct the first rigorous evaluation of the long-term effect of the Comprehensive Rural Health Project on childhood mortality in rural Maharashtra. METHODS Background information and full birth histories were collected by conducting household surveys and interviewing women. Control villages resembling project villages in terms of population size were randomly selected from an area enclosed by two ellipses centred around, but not including, the project area. An equal number of villages and approximately equal numbers of households and women were randomly sampled from both areas. Cox models with robust standard errors were used to compare the hazard of death among children under 5 years of age in project and control villages. FINDINGS The hazard of death was reduced by 30% (95% confidence interval, CI: 6% to 48%) after the neonatal period in the project villages compared with control villages after adjustment for caste and religion of subjects and for availability of irrigation in the villages. During the neonatal period there was an increase of 3% in the hazard of death, but it was not statistically significant (95% CI: -18% to 29%). CONCLUSION Our methods provide useful tools for evaluating long-running community-based primary health care programmes. Our findings add to the growing debate on the long-term sustainability of community-based interventions designed to reduce child mortality.
A Comparison of Full-Rate Full-Diversity 2x2 Space-Time Codes for WiMAX Systems

Multiple-input multiple-output (MIMO) techniques have become an essential part of broadband wireless communications systems. For example, the recently developed IEEE 802.16e specifications for broadband wireless access include three MIMO profiles employing 2 x 2 space-time codes (STCs), and two of these MIMO schemes are mandatory on the downlink of mobile WiMAX systems. One of these has full rate, and the other has full diversity, but neither of them has both of the desired features. The third profile, namely, Matrix C, which is not mandatory, is both a full rate and a full diversity code, but it has a high decoder complexity. Recently, the attention was turned to the decoder complexity issue and including this in the design criteria, several full-rate STCs were proposed as alternatives to Matrix C. In this paper, we review these different alternatives and compare them to Matrix C in terms of performances and the corresponding receiver complexities.
Institutions and Entrepreneurship Development in Russia: A Comparative Perspective

In this paper we use a comparative perspective to explore the ways in which institutions and networks have influenced entrepreneurial development in Russia. We utilize Global Entrepreneurship Monitor (GEM) data to study the effects of the weak institutional environment in Russia on entrepreneurship, comparing it first with all available GEM country samples and second, in more detail, with Brazil and Poland. Our results suggest that Russia's institutional environment is important in explaining its relatively low levels of entrepreneurship development, where the latter is measured in terms of both number of start-ups and of existing business owners. In addition, Russia's business environment and its consequences for the role of business networks contribute to the relative advantage of entrepreneurial insiders (those already in business) to entrepreneurial outsiders (newcomers) in terms of new business start-ups.
Effects of Class Imbalance in Test Suites: An Empirical Study of Spectrum-Based Fault Localization

Spectrum-based fault localization techniques (SBFLs) focus on the utilization of execution information provided by large number of test cases. How to use the cases effectively is an important issue for SBFLs. Related studies mainly focus on the effects of test suites' sizes on localization efficiency, while ignoring the class composition, especially a class imbalance phenomenon existing in test suites. In this paper, an empirical study is undertaken to explore two questions: (1) Does the class proportion between passed and failed cases have effects on SBFLs? (2) If yes, what are the effects? The research may construct a bridge in connecting software fault localization and class imbalance learning.
Multiparametric MR investigation of the motor pyramidal system in patients with ‘truly benign’ multiple sclerosis

One possible explanation for the mismatch between tissue damage and preservation of neurological functions in patients with benign multiple sclerosis (BMS) is that the pathophysiology differs from that occurring in other multiple sclerosis (MS) phenotypes. The objective of this study was to identify pathologically specific patterns of tissue integrity/damage characteristics of patients with BMS, and markers of potential prognostic value. The pyramidal system was investigated in 10 BMS patients and 20 controls using voxel-based morphometry to assess grey matter (GM) atrophy, and diffusion tractography and quantitative magnetization transfer to quantify the microstructural damage in the corticospinal tracts (CSTs). Widespread reductions in GM volume were found in patients compared with controls, including the primary motor cortex. A significant decrease was observed in the mean macromolecular pool ratio (F) of both CSTs, with no fractional anisotropy (FA) change. GM volume of the primary motor areas was associated with clinical scores but not with the CST parameters. The mismatch between F and FA suggests the presence of extensive demyelination in the CSTs of patients with BMS, in the absence of axonal damage. The lack of correlation with GM volume indicates a complex interaction between disruptive and reparative mechanisms in BMS.
Paneth cell ablation in the presence of Klebsiella pneumoniae induces necrotizing enterocolitis (NEC)-like injury in the small intestine of immature mice

SUMMARY Necrotizing enterocolitis (NEC) is a leading cause of morbidity and mortality in premature infants. During NEC pathogenesis, bacteria are able to penetrate innate immune defenses and invade the intestinal epithelial layer, causing subsequent inflammation and tissue necrosis. Normally, Paneth cells appear in the intestinal crypts during the first trimester of human pregnancy. Paneth cells constitute a major component of the innate immune system by producing multiple antimicrobial peptides and proinflammatory mediators. To better understand the possible role of Paneth cell disruption in NEC, we quantified the number of Paneth cells present in infants with NEC and found that they were significantly decreased compared with age-matched controls. We were able to model this loss in the intestine of postnatal day (P)14-P16 (immature) mice by treating them with the zinc chelator dithizone. Intestines from dithizone-treated animals retained approximately half the number of Paneth cells compared with controls. Furthermore, by combining dithizone treatment with exposure to Klebsiella pneumoniae, we were able to induce intestinal injury and inflammatory induction that resembles human NEC. Additionally, this novel Paneth cell ablation model produces NEC-like pathology that is consistent with other currently used animal models, but this technique is simpler to use, can be used in older animals that have been dam fed, and represents a novel line of investigation to study NEC pathogenesis and treatment.
The Pitch of Vibrato Tones

We study vibrato as the more ubiquitous manifestation of a nonstationary tone that can evoke a single overall pitch. Some recent results using nonsymmetrical vibrato tones suggest that the perceived pitch could be governed by some stability‐sensitive mechanism. For nonstationary sounds the adequate tools are time–frequency representations (TFRs). We show that a recently proposed TFR could be the simplest framework to explain this hypothetical stability‐sensitive mechanism. We propose a one‐parameter model within this framework that is able to predict previously reported results and we present new results obtained from psychophysical experiments performed in our laboratory.
A Phase II Study of the Efficacy and Safety of the Combination Therapy of the MEK Inhibitor Refametinib (BAY 86-9766) Plus Sorafenib for Asian Patients with Unresectable Hepatocellular Carcinoma

Purpose: There is an unmet need for treatment options in hepatocellular carcinoma (HCC). Sorafenib is currently the only approved systemic treatment for HCC. Refametinib, an oral, allosteric MEK inhibitor, has demonstrated antitumor activity in combination with sorafenib in vitro and in vivo. A phase II study evaluated efficacy and safety of refametinib plus sorafenib in Asian patients with HCC (NCT01204177). Experimental Design: Eligible patients received twice-daily refametinib 50 mg plus twice-daily sorafenib 200 mg (morning)/400 mg (evening), with dose escalation to sorafenib 400 mg twice daily from cycle 2 if no grade ≥2 hand-foot skin reaction, fatigue, or gastrointestinal toxicity occurred. Primary efficacy endpoint: disease control rate. Secondary endpoints: time to progression, overall survival, pharmacokinetic assessment, biomarker analysis, safety, and tolerability. Results: Of 95 enrolled patients, 70 received study treatment. Most patients had liver cirrhosis (82.9%) and hepatitis B viral infection (75.7%). Disease control rate was 44.8% (primary efficacy analysis; n = 58). Median time to progression was 122 days, median overall survival was 290 days (n = 70). Best clinical responders had RAS mutations; majority of poor responders had wild-type RAS. Most frequent drug-related adverse events were diarrhea, rash, aspartate aminotransferase elevation, vomiting, and nausea. Dose modifications due to adverse events were necessary in almost all patients. Conclusions: Refametinib plus sorafenib showed antitumor activity in patients with HCC and was tolerated at reduced doses by most patients. Frequent dose modifications due to grade 3 adverse events may have contributed to limited treatment effect. Patients with RAS mutations appear to benefit from refametinib/sorafenib combination. Clin Cancer Res; 20(23); 5976–85. ©2014 AACR.
Chest Radiographic Patterns and the Transmission of Tuberculosis: Implications for Automated Systems

Background Computer-aided detection to identify and diagnose pulmonary tuberculosis is being explored. While both cavitation on chest radiograph and smear-positivity on microscopy are independent risk factors for the infectiousness of pulmonary tuberculosis it is unknown which radiographic pattern, were it detectable, would provide the greatest public health benefit; i.e. reduced transmission. Herein we provide that evidence. Objectives 1) to determine whether pulmonary tuberculosis in a high income, low incidence country is more likely to present with “typical” adult-type pulmonary tuberculosis radiographic features and 2) to determine whether those with “typical” radiographic features are more likely than those without such features to transmit the organism and/or cause secondary cases. Methods Over a three-year period beginning January 1, 2006 consecutive adults with smear-positive pulmonary tuberculosis in the Province of Alberta, Canada, were identified and their pre-treatment radiographs scored by three independent readers as “typical” (having an upper lung zone predominant infiltrate, with or without cavitation but no discernable adenopathy) or “atypical” (all others). Each patient’s pre-treatment bacillary burden was carefully documented and, during a 30-month transmission window, each patient’s transmission events were recorded. Mycobacteriology, radiology and transmission were compared in those with “typical” versus “atypical” radiographs. Findings A total of 97 smear-positive pulmonary tuberculosis cases were identified, 69 (71.1%) with and 28 (28.9%) without “typical” chest radiographs. “Typical” cases were more likely to have high bacillary burdens and cavitation (Odds Ratios and 95% Confidence Intervals: 2.75 [1.04–7.31] and 9.10 [2.51–32.94], respectively). Typical cases were also responsible for most transmission events—78% of tuberculin skin test conversions (p<0.002) and 95% of secondary cases in reported close contacts (p<0.01); 94% of secondary cases in “unreported” contacts (p<0.02). Conclusion As a group, smear-positive pulmonary tuberculosis patients with typical radiographic features constitute the greatest public health risk. This may have implications for automated detection systems.
Development of the stapes and associated structures in human embryos

The objective of this study was to clarify the development of the stapes in humans and its relationship with the cartilage of the second branchial arch. The study was carried out in 25 human embryos between 6 and 28 mm crown–rump length. The stapes develops at the cranial end of the second branchial arch through an independent anlage of the cartilage of this arch. Between the stapedial anlage and the cranial end of the Reichert's cartilage there is a formation called the interhyale, the internal segment of which gives rise to the tendon of the stapedial muscle. The stapedial anlage is a unique formation with two distinct parts: the superior part that will comprise the base and the inferior part that will be crossed by the stapedial artery during embryonic development and will constitute the limbs and the head of the stapes. According to the results, the otic capsule is not involved in formation of the base of the stapes.
Visual localization within LIDAR maps for automated urban driving

This paper reports on the problem of map-based visual localization in urban environments for autonomous vehicles. Self-driving cars have become a reality on roadways and are going to be a consumer product in the near future. One of the most significant road-blocks to autonomous vehicles is the prohibitive cost of the sensor suites necessary for localization. The most common sensor on these platforms, a three-dimensional (3D) light detection and ranging (LIDAR) scanner, generates dense point clouds with measures of surface reflectivity-which other state-of-the-art localization methods have shown are capable of centimeter-level accuracy. Alternatively, we seek to obtain comparable localization accuracy with significantly cheaper, commodity cameras. We propose to localize a single monocular camera within a 3D prior ground-map, generated by a survey vehicle equipped with 3D LIDAR scanners. To do so, we exploit a graphics processing unit to generate several synthetic views of our belief environment. We then seek to maximize the normalized mutual information between our real camera measurements and these synthetic views. Results are shown for two different datasets, a 3.0 km and a 1.5 km trajectory, where we also compare against the state-of-the-art in LIDAR map-based localization.
Extracellular matrix composition determines the transcriptional response to epidermal growth factor receptor activation

The transcriptional response to epidermal growth factor (EGF) was examined in a cultured cell model of adhesion. Gene expression was monitored in human embryonic kidney cells (HEK293) after attachment of cells to the extracellular matrix (ECM) proteins, laminin, and fibronectin, by using complementary DNA micorarrays printed with 1,718 individual human genes. Cluster analysis revealed that the influence of EGF on gene expression, either positive or negative, was largely independent of ECM composition. However, clusters of EGF-regulated genes were identified that were diagnostic of the type of ECM proteins to which cells were attached. In these clusters, attachment of cells to a laminin or fibronectin substrata specifically modified the direction of gene expression changes in response to EGF stimulation. For example, in HEK293 cells attached to fibronectin, EGF stimulated an increase in the expression of some genes; however, genes in the same group were nonresponsive or even suppressed in cells attached to laminin. Many of the genes regulated by EGF and ECM proteins in this manner are involved in ECM and cytoskeletal architecture, protein synthesis, and cell cycle control, indicating that cell responses to EGF stimulation can be dramatically affected by ECM composition.
The analysis of visual motion: a comparison of neuronal and psychophysical performance

We compared the ability of psychophysical observers and single cortical neurons to discriminate weak motion signals in a stochastic visual display. All data were obtained from rhesus monkeys trained to perform a direction discrimination task near psychophysical threshold. The conditions for such a comparison were ideal in that both psychophysical and physiological data were obtained in the same animals, on the same sets of trials, and using the same visual display. In addition, the psychophysical task was tailored in each experiment to the physiological properties of the neuron under study; the visual display was matched to each neuron's preference for size, speed, and direction of motion. Under these conditions, the sensitivity of most MT neurons was very similar to the psychophysical sensitivity of the animal observers. In fact, the responses of single neurons typically provided a satisfactory account of both absolute psychophysical threshold and the shape of the psychometric function relating performance to the strength of the motion signal. Thus, psychophysical decisions in our task are likely to be based upon a relatively small number of neural signals. These signals could be carried by a small number of neurons if the responses of the pooled neurons are statistically independent. Alternatively, the signals may be carried by a much larger pool of neurons if their responses are partially intercorrelated.
Visual Analytics for Mobile Eye Tracking

The analysis of eye tracking data often requires the annotation of areas of interest (AOIs) to derive semantic interpretations of human viewing behavior during experiments. This annotation is typically the most time-consuming step of the analysis process. Especially for data from wearable eye tracking glasses, every independently recorded video has to be annotated individually and corresponding AOIs between videos have to be identified. We provide a novel visual analytics approach to ease this annotation process by image-based, automatic clustering of eye tracking data integrated in an interactive labeling and analysis system. The annotation and analysis are tightly coupled by multiple linked views that allow for a direct interpretation of the labeled data in the context of the recorded video stimuli. The components of our analytics environment were developed with a user-centered design approach in close cooperation with an eye tracking expert. We demonstrate our approach with eye tracking data from a real experiment and compare it to an analysis of the data by manual annotation of dynamic AOIs. Furthermore, we conducted an expert user study with 6 external eye tracking researchers to collect feedback and identify analysis strategies they used while working with our application.
Identification of Novel in vivo MAP Kinase Substrates in Arabidopsis thaliana Through Use of Tandem Metal Oxide Affinity Chromatography*

Mitogen-activated protein kinase (MPK) cascades are important for eukaryotic signal transduction. They convert extracellular stimuli (e.g. some hormones, growth factors, cytokines, microbe- or damage-associated molecular patterns) into intracellular responses while at the same time amplifying the transmitting signal. By doing so, they ensure proper performance, and eventually survival, of a given organism, for example in times of stress. MPK cascades function via reversible phosphorylation of cascade components MEKKs, MEKs, and MPKs. In plants the identity of most MPK substrates remained elusive until now. Here, we provide a robust and powerful approach to identify and quantify, with high selectivity, site-specific phosphorylation of MPK substrate candidates in the model plant Arabidopsis thaliana. Our approach represents a two-step chromatography combining phosphoprotein enrichment using Al(OH)3-based metal oxide affinity chromatography, tryptic digest of enriched phosphoproteins, and TiO2-based metal oxide affinity chromatography to enrich phosphopeptides from complex protein samples. When applied to transgenic conditional gain-of-function Arabidopsis plants supporting in planta activation of MPKs, the approach allows direct measurement and quantification ex vivo of site-specific phosphorylation of several reported and many yet unknown putative MPK substrates in just a single experiment.
Lymphocytic choriomeningitis virus killer T cells are lethal only in weakly disseminated murine infections

Two types of lymphocytic choriomeningitis (LCM) viruses were studied which, upon intracerebral injection into adult C3H mice, provoked either (a) acute fatal central nervous system (CNS) disease or (b) life- long persistent infection. Both virus types, (a) aggressive and (b) docile, had been found to induce LCM-specific lymphocytes with comparable in vitro lytic activity (11). Because the requirement for T cells in the development of adult LCM disease has been extensively documented, we sought other reasons for the lack of acute disease in mice infected with docile virus. A striking correlation was found between the outcome of the infection and spread of virus to visceral organs. Adoptive transfer experiments showed that a 300-plaque forming unit inoculum of docile virus induced a population of T cells in donor mice fully capable of causing CNS disease in identically infected recipients. This disease causing ability was lost if the interaction was delayed beyond 3 d after infection of the recipients, but could be preserved by lowering the size of the viral inoculum in the recipients. Furthermore, without adoptive transfer, very low intracerebral doses of docile virus (which mimicked the normally slow spread of aggressive virus) were lethal. On the other hand, very high doses of aggressive virus, which mimicked the normally rapid spread of docile virus, did not induce fatal CNS disease. The results suggest that rapid dissemination of the LCM infection creates multiple target organs which divert the focused lethal T cell attack on the brain.
Reduction in CS: A (Mostly) Quantitative Analysis of Reductive Solutions to Algorithmic Problems

Reduction is a problem-solving strategy, relevant to various areas of computer science, and strongly connected to abstraction: a reductive solution necessitates establishing a connection among problems that may seem totally disconnected at first sight, and abstracts the solution to the reduced-to problem by encapsulating it as a black box. The study described in this article continues a previous, qualitative study that examined the ways undergraduate computer science students perceive, experience, and use reduction as a problem-solving strategy. The current study examines the same issue, but in the context of a larger population, using also quantitative analysis, and focusing on algorithmic problems. The findings indicate difficulties students have with the abstract characteristics of reduction and with acknowledging reduction as a general problem-solving strategy.