Miracle-dz/UniFAR-FTUs huggingface dataset:
Equity and efficiency in the scaled-up implementation of integrated neglected tropical disease control: the health economics protocol of the COUNTDOWN multicountry observational study in Ghana, Cameroon and Liberia

Introduction Worldwide, millions of individuals are affected by neglected tropical diseases (NTDs). They are frequently the poorest and most marginalised members of society. Their living conditions, among other things, make them susceptible to such diseases. Historically, several large-scale treatment programmes providing mass drug administrations (MDAs) were carried out per single disease but over the last decade there has been an increasing trend towards co-implementation of MDA activities given the resources used for such programmes are often the same. The COUNTDOWN multicountry studies focus on scaled-up implementation of integrated control strategies against four diseases: lymphatic filariasis, onchocerciasis, schistosomiasis and soil-transmitted helminthiasis. The objective of the COUNTDOWN economic study is to assess the multicountry implementation of control interventions in terms of equity, impact and efficiency. Methods The health economic study uses different analytical methods to assess the relationship between NTDs and poverty and the cost-effectiveness of different large-scale intervention options. Regression analysis will be used to study the determinants of NTD occurrence, the impact of NTDs on poverty, factors that hinder access to MDAs and the effect of NTDs on quality-of-life of those affected, including disability. Cost-effectiveness analyses of various integration methods will be performed using health economic modelling to estimate the cost and programme impact of different integration options. Here, cost-effectiveness ratios will be calculated, including multivariate sensitivity analyses, using Bayesian analysis. Ethics and dissemination Ethics approval has been received both at the Liverpool School of Tropical Medicine and in all participating countries. Results of the various substudies will be presented for publication in peer-reviewed journals. Study dates 1 July 2016 to 30 June-October 2019.
A variational method for analyzing limit cycle oscillations in stochastic hybrid systems.

Many systems in biology can be modeled through ordinary differential equations, which are piece-wise continuous, and switch between different states according to a Markov jump process known as a stochastic hybrid system or piecewise deterministic Markov process (PDMP). In the fast switching limit, the dynamics converges to a deterministic ODE. In this paper, we develop a phase reduction method for stochastic hybrid systems that support a stable limit cycle in the deterministic limit. A classic example is the Morris-Lecar model of a neuron, where the switching Markov process is the number of open ion channels and the continuous process is the membrane voltage. We outline a variational principle for the phase reduction, yielding an exact analytic expression for the resulting phase dynamics. We demonstrate that this decomposition is accurate over timescales that are exponential in the switching rate ϵ-1. That is, we show that for a constant C, the probability that the expected time to leave an O(a) neighborhood of the limit cycle is less than T scales as T exp (-Ca/ϵ).
Syntax and Semantics of Quantitative Type Theory

We present Quantitative Type Theory, a Type Theory that records usage information for each variable in a judgement, based on a previous system by McBride. The usage information is used to give a realizability semantics using a variant of Linear Combinatory Algebras, refining the usual realizability semantics of Type Theory by accurately tracking resource behaviour. We define the semantics in terms of Quantitative Categories with Families, a novel extension of Categories with Families for modelling resource sensitive type theories.
Visual object tracking in a parking garage using compressed domain analysis

Modern driver assistance systems enable a variety of use cases which rely on accurate localization information of all traffic participants. Due to the unavailability of satellite-based localization, the use of infrastructure cameras is a promising alternative in indoor spaces such as parking garages. This paper presents a parking management system which extends the previous work of the eValet system with a low-complexity tracking functionality on compressed video bitstreams (compressed-domain tracking). The advantages of this approach include the improved robustness to partial occlusions as well as a resource-efficient processing of compressed video bit-streams. We have separated the tasks into different modules which are integrated into a comprehensive architecture. The demonstrator setup includes a 2D visualizer illustrating the operation of the algorithms on a single camera stream and a 3D visualizer displaying the abstract object detections in a global reference frame.
Assessing emotional responses induced in virtual reality using a consumer EEG headset: A preliminary report

We report on a pilot study involving emotion elicitation in virtual reality (VR) and assessment of emotional responses with a consumer-grade EEG device. The stimulation used HTC Vive VR system showing pictures from NAPS database within a specifically designed virtual environment. The stimulation consisted of two distinct sequences with 10 pictures of happiness and 10 pictures of fear. Each picture was contained in a separate virtual room that the participants traveled through along a preset path. The estimation employed EMOTIV EPOC+ 14-channel EEG headset and a custom-developed application. The software wirelessly received EEG signals from alpha, beta low, beta high, gamma and theta bands, time-stamped them and dynamically stored in a relational database for subsequent analysis. Our preliminary results show that statistically significant correlations between valence and arousal ratings of pictures and EEG bands are present but highly personalized. Simultaneous correct placement of VR and EEG headsets is demanding and precise localization of electrodes is difficult. In fact, if emotion estimation is not strictly necessary we recommend using devices with fewer electrodes. Nevertheless, we found the EEG to be effective. By acknowledging its limitations, and using the headset in the correct context, experiments involving emotions may be significantly amended.
Bridging the Gap: A 20-Year Experience with Vein Grafts for Free Flap Reconstruction. The Odds for Success

Background: Successful free tissue transfer requires tension-free microvascular anastomosis. Vein grafts are used when this cannot be obtained, which increases microsurgical complexity and the chance of vessel thrombosis. Previous studies on vein grafts are limited to low numbers and selected techniques, making it difficult to draw conclusions. Methods: A retrospective chart review was performed for all patients who underwent vein grafts in free flap reconstruction from 1995 to 2015. Information on patient and flap characteristics, returns to the operating room, and flap loss was analyzed. Results: Seventy-two free flap reconstructions requiring 122 vein grafts were performed in the genitourinary/perineal (49 percent) and head and neck (38 percent) regions. The majority were performed in the initial operation (82 percent) and, of those, the majority were planned (71 percent). The most common vein graft types used were transposition arteriovenous loops (57 percent) and interpositions (26 percent). Of the initial cases, 22 percent returned to the operating room, resulting in a 7 percent total flap loss rate and a 7 percent partial flap loss rate. On univariate analysis, graft timing/planning, gap type, vein graft type, and reconstruction location were significantly associated with take-backs and flap loss. However, gap type and location seem to be strongly associated with graft timing/planning and vein graft type. Graft type and planning/timing do not have as strong a relationship and seem to independently relate to flap loss. Conclusions: Vein grafts are more successful when planned and when performing transpositions and arteriovenous loops over interpositions. These graft types should be considered over interpositions when possible. CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, IV.
Combining skeletal poses for 3D human model generation using multiple kinects

RGB-D cameras, such as the Microsoft Kinect, provide us with the 3D information, color and depth, associated with the scene. Interactive 3D Tele-Immersion (i3DTI) systems use such RGB-D cameras to capture the person present in the scene in order to collaborate with other remote users and interact with the virtual objects present in the environment. Using a single camera, it becomes difficult to estimate an accurate skeletal pose and complete 3D model of the person, especially when the person is not in the complete view of the camera. With multiple cameras, even with partial views, it is possible to get a more accurate estimate of the skeleton of the person leading to a better and complete 3D model. In this paper, we present a real-time skeletal pose identification approach that leverages on the inaccurate skeletons of the individual Kinects, and provides a combined optimized skeleton. We estimate the Probability of an Accurate Joint (PAJ) for each joint from all of the Kinect skeletons. We determine the correct direction of the person and assign the correct joint sides for each skeleton. We then use a greedy consensus approach to combine the highly probable and accurate joints to estimate the combined skeleton. Using the individual skeletons, we segment the point clouds from all the cameras. We use the already computed PAJ values to obtain the Probability of an Accurate Bone (PAB). The individual point clouds are then combined one segment after another using the calculated PAB values. The generated combined point cloud is a complete and accurate 3D representation of the person present in the scene. We validate our estimated skeleton against two well-known methods by computing the error distance between the best view Kinect skeleton and the estimated skeleton. An exhaustive analysis is performed by using around 500000 skeletal frames in total, captured using 7 users and 7 cameras. Visual analysis is performed by checking whether the estimated skeleton is completely present within the human model. We also develop a 3D Holo-Bubble game to showcase the real-time performance of the combined skeleton and point cloud. Our results show that our method performs better than the state-of-the-art approaches that use multiple Kinects, in terms of objective error, visual quality and real-time user performance.
Replication, Registration, and Scientific Creativity

The bureaucratization of psychological science exacts intellectual costs that go beyond the sheer amount of time that is drained away from creative scientific activity. Additional administrative hurdles are now being generated in an attempt to ensure the replicability of psychological effects. A cognitive analysis of those hurdles shows that impairment of scientific creativity is a foreseeable consequence, owing to their frequent verbatim-processing focus and the negative emotional context in which they are embedded. We consider whether it is possible to enhance replicability without increasing bureaucratic obstacles and to enhance scientific creativity in the presence of such obstacles.
Gene Regulation by Redox-Sensitive Burkholderia thailandensis OhrR and Its Role in Bacterial Killing of Caenorhabditis elegans

Fatty acid hydroperoxides are involved in host-pathogen interactions. In both plants and mammals, polyunsaturated fatty acids are liberated during infection and enzymatically oxidized to the corresponding toxic hydroperoxides during the defensive oxidative burst that is designed to thwart the infection. ABSTRACT Fatty acid hydroperoxides are involved in host-pathogen interactions. In both plants and mammals, polyunsaturated fatty acids are liberated during infection and enzymatically oxidized to the corresponding toxic hydroperoxides during the defensive oxidative burst that is designed to thwart the infection. The bacterial transcription factor OhrR (organic hydroperoxide reductase regulator) is oxidized by organic hydroperoxides, as a result of which the ohr gene encoding organic hydroperoxide reductase is induced. This enzyme converts the hydroperoxides to less toxic alcohols. We show here that OhrR from Burkholderia thailandensis represses expression of ohr. Gene expression is induced by cumene hydroperoxide and to a lesser extent by inorganic oxidants; however, Ohr contributes to degradation only of the organic hydroperoxide. B. thailandensis OhrR, which binds specific sites in both ohr and ohrR promoters, as evidenced by DNase I footprinting, belongs to the 2-Cys subfamily of OhrR proteins, and its oxidation leads to reversible disulfide bond formation between conserved N- and C-terminal cysteines in separate monomers. Oxidation of the N-terminal Cys is sufficient for attenuation of DNA binding in vitro, with complete restoration of DNA binding occurring on addition of a reducing agent. Surprisingly, both overexpression of ohr and deletion of ohr results in enhanced survival on exposure to organic hydroperoxide in vitro. While Δohr cells are more virulent in a Caenorhabditis elegans model of infection, ΔohrR cells are less so. Taken together, our data suggest that B. thailandensis OhrR has several unconventional features and that both OhrR and organic hydroperoxides may contribute to virulence.
Energy Consumption Model for Sensor Nodes Based on LoRa and LoRaWAN

Energy efficiency is the key requirement to maximize sensor node lifetime. Sensor nodes are typically powered by a battery source that has finite lifetime. Most Internet of Thing (IoT) applications require sensor nodes to operate reliably for an extended period of time. To design an autonomous sensor node, it is important to model its energy consumption for different tasks. Each task consumes a power consumption amount for a period of time. To optimize the consumed energy of the sensor node and have long communication range, Low Power Wide Area Network technology is considered. This paper describes an energy consumption model based on LoRa and LoRaWAN, which allows estimating the consumed power of each sensor node element. The definition of the different node units is first introduced. Then, a full energy model for communicating sensors is proposed. This model can be used to compare different LoRaWAN modes to find the best sensor node design to achieve its energy autonomy.
SIGIR 2018 Tutorial on Health Search (HS2018): A Full-day from Consumers to Clinicians

The HS2018 tutorial will cover topics from an area of information retrieval (IR) with significant societal impact --- health search. Whether it is searching patient records, helping medical professionals find best-practice evidence, or helping the public locate reliable and readable health information online, health search is a challenging area for IR research with an actively growing community and many open problems. This tutorial will provide attendees with a full stack of knowledge on health search, from understanding users and their problems to practical, hands-on sessions on current tools and techniques, current campaigns and evaluation resources, as well as important open questions and future directions.
A simple magnetoencephalographic auditory paradigm may aid in confirming left-hemispheric language dominance in epilepsy patients

Objective The intracarotid amobarbital procedure (IAP) is the current “gold standard” in the preoperative assessment of language lateralization in epilepsy surgery candidates. It is, however, invasive and has several limitations. Here we tested a simple noninvasive language lateralization test performed with magnetoencephalography (MEG). Methods We recorded auditory MEG responses to pairs of vowels and pure tones in 16 epilepsy surgery candidates who had undergone IAP. For each individual, we selected the pair of planar gradiometer sensors with the strongest N100m response to vowels in each hemisphere and—from the vector sum of signals of this gradiometer pair—calculated the vowel/tone amplitude ratio in the left (L) and right (R) hemisphere and, subsequently, the laterality index: LI = (L–R)/(L+R). In addition to the analysis using a single sensor pair, an alternative analysis was performed using averaged responses over 18 temporal sensor pairs in both hemispheres. Results The laterality index did not correlate significantly with the lateralization data obtained from the IAP. However, an MEG pattern of stronger responses to vowels than tones in the left hemisphere and stronger responses to tones than vowels in the right hemisphere was associated with left-hemispheric language dominance in the IAP in all the six patients who showed this pattern. This results in a specificity of 100% and a sensitivity of 67% of this MEG pattern in predicting left-hemispheric language dominance (p = 0.01, Fisher's exact test). In the analysis using averaged responses over temporal channels, one additional patient who was left-dominant in IAP showed this particular MEG pattern, increasing the sensitivity to 78% (p = 0.003). Significance This simple MEG paradigm shows promise in feasibly and noninvasively confirming left-hemispheric language dominance in epilepsy surgery candidates. It may aid in reducing the need for the IAP, if the results are confirmed in larger patient samples.
Co-Creating Value from IT in a Contracted Public Sector Service Environment: Perspectives on COBIT and Val IT

ABSTRACT: Research that examines Information Technology (IT) value has called for studies to explore the co-creation of value, including in multi-firm environments. This study draws upon the practice of IT governance in a successful large-scale IT deployment, wherein private and public firms were involved as customer service providers with the principal, a large government department. Drawing on customer-centric co-creation concepts from marketing research, through comparative analysis and related application to our case study, we detail the merit of a service-oriented approach to co-creating value from IT and the assistance COBIT and Val IT can provide. Importantly, we identified determinates of co-created value in a multi-firm environment, although our analysis reveals some need to evolve COBIT and Val IT to improve guidance regarding the mechanisms required to achieve this in such environments.
Genome-Wide Association and Regional Heritability Mapping of Plant Architecture, Lodging and Productivity in Phaseolus vulgaris

The availability of high-density molecular markers in common bean has allowed to explore the genetic basis of important complex agronomic traits with increased resolution. Genome-Wide Association Studies (GWAS) and Regional Heritability Mapping (RHM) are two analytical approaches for the detection of genetic variants. We carried out GWAS and RHM for plant architecture, lodging and productivity across two important growing environments in Brazil in a germplasm of 188 common bean varieties using DArTseq genotyping strategies. The coefficient of determination of G × E interaction (c2int) was equal to 17, 21 and 41%, respectively for the traits architecture, lodging, and productivity. Trait heritabilities were estimated at 0.81 (architecture), 0.79 (lodging) and 0.43 (productivity), and total genomic heritability accounted for large proportions (72% to ≈100%) of trait heritability. At the same probability threshold, three marker–trait associations were detected using GWAS, while RHM detected eight QTL encompassing 145 markers along five chromosomes. The proportion of genomic heritability explained by RHM was considerably higher (35.48 to 58.02) than that explained by GWAS (28.39 to 30.37). In general, RHM accounted for larger fractions of the additive genetic variance being captured by markers effects inside the defined regions. Nevertheless, a considerable proportion of the heritability is still missing (∼42% to ∼64%), probably due to LD between markers and genes and/or rare allele variants not sampled. RHM in autogamous species had the potential to identify larger-effect QTL combining allelic variants that could be effectively incorporated into whole-genome prediction models and tracked through breeding generations using marker-assisted selection.
Elucidating Gene-by-Environment Interactions Associated with Differential Susceptibility to Chemical Exposure

Background: Modern societies are exposed to vast numbers of potentially hazardous chemicals. Despite demonstrated linkages between chemical exposure and severe health effects, there are limited, often conflicting, data on how adverse health effects of exposure differ across individuals. Objectives: We tested the hypothesis that population variability in response to certain chemicals could elucidate a role for gene–environment interactions (GxE) in differential susceptibility. Methods: High-throughput screening (HTS) data on thousands of chemicals in genetically heterogeneous zebrafish were leveraged to identify a candidate chemical (Abamectin) with response patterns indicative of population susceptibility differences. We tested the prediction by generating genome-wide sequence data for 276 individual zebrafish displaying susceptible (Affected) vs. resistant (Unaffected) phenotypes following identical chemical exposure. Results: We found GxE associated with differential susceptibility in the sox7 promoter region and then confirmed gene expression differences between phenotypic response classes. Conclusions: The results for Abamectin in zebrafish demonstrate that GxE associated with naturally occurring, population genetic variation play a significant role in mediating individual response to chemical exposure. https://doi.org/10.1289/EHP2662
Mitochondrial dysfunction and altered ribostasis in hippocampal neurons with cytoplasmic inclusions of multiple system atrophy

Multiple system atrophy (MSA) is a sporadic adult‐onset neurodegenerative disease. It has recently been shown that patients with MSA accompanied by cognitive decline display numerous neuronal cytoplasmic inclusions (NCIs) in the limbic neurons. We examined potential mechanisms underlying the formation of these NCIs by determining of mitochondrial function and statuses of RNA processing by analyzing 12 pathologically confirmed cases of MSA. Among them, four had cognitive impairment Semiquantitative evaluation using immunohistochemistry analyses revealed a significantly greater NCI burden in the hippocampal cornu ammonis 1 (CA1) subfield, subiculum, and amygdala in the cases with cognitive impairments compared with those without cognitive impairment. Immunofluorescent staining revealed that limbic neurons with NCIs often accelerated production of reactive oxygen species (ROS) and degraded mitochondrial quality control. Immunofluorescent staining also revealed that neurons with these NCIs translocated heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1) from the nucleus and aggregated abnormally at the perinuclear rim. Since the NCIs in the hippocampal neurons of MSA with cognitive impairments were more numerous, the neuronal mitochondrial dysfunction and altered ribostasis observed in NCI formation may be involved in the hippocampal degeneration of MSA.