Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of Oral Cholera Vaccine in Haiti: A Rural Demonstration Project

A cholera epidemic has claimed the lives of more than 8,000 Haitians and sickened 650,000 since the outbreak began in October 2010. Early intervention in the epidemic focused on case-finding, treatment, and water and sanitation interventions for prevention of transmission. Use of oral cholera vaccine (OCV) as part of a complementary set of control activities was considered but initially rejected by policymakers. In December 2011, the Minister of Health of Haiti called for a demonstration of the acceptability and feasibility of the use of OCV in urban and rural Haiti. This paper describes the collaborative activity that offered OCV to one region of the Artibonite Department of rural Haiti in addition to other ongoing treatment and control measures. Despite logistics and cold chain challenges, 45,417 persons were successfully vaccinated with OCV in the region, and 90.8% of these persons completed their second dose.
iPS Cells for Modelling and Treatment of Retinal Diseases

For many decades, we have relied on immortalised retinal cell lines, histology of enucleated human eyes, animal models, clinical observation, genetic studies and human clinical trials to learn more about the pathogenesis of retinal diseases and explore treatment options. The recent availability of patient-specific induced pluripotent stem cells (iPSC) for deriving retinal lineages has added a powerful alternative tool for discovering new disease-causing mutations, studying genotype-phenotype relationships, performing therapeutics-toxicity screening and developing personalised cell therapy. This review article provides a clinical perspective on the current and potential benefits of iPSC for managing the most common blinding diseases of the eye: inherited retinal diseases and age-related macular degeneration.
Targeted ablation and reorganization of the principal preplate neurons and their neuroblasts identified by golli promoter transgene expression in the neocortex of mice

The present study delineates the cellular responses of dorsal pallium to targeted genetic ablation of the principal preplate neurons of the neocortex. Ganciclovir treatment during prenatal development (E11–E13; where E is embryonic day) of mice selectively killed cells with shared S-phase vulnerability and targeted expression of a GPT [golli promoter transgene, linked to HSV-TK (herpes simplex virus-thymidine kinase), τ-eGFP (τ-enhanced green fluorescent protein) and lacZ (lacZ galactosidase) reporters] localized in preplate neurons. Morphogenetic fates of attacked neurons and neuroblasts, and their successors, were assessed by multiple labelling in time-series comparisons between ablated (HSV-TK+/0) and control (HSV-TK0/0) littermates. During ablation generation, neocortical growth was suppressed, and compensatory reorganization of non-GPT ventricular zone progenitors of dorsal pallium produced replacements for killed GPT neuroblasts. Replacement and surviving GPT neuroblasts then produced replacements for killed GPT neurons. Near-normal restoration of their complement delayed the settlement of GPT neurons into the reconstituted preplate, which curtailed the outgrowth of pioneer corticofugal axons. Based on this evidence, we conclude that specific cell killing in ablated mice can eliminate a major fraction of GPT neurons, with insignificant bystander killing. Also, replacement GPT neurons in ablated mice originate exclusively by proliferation from intermediate progenitor GPT neuroblasts, whose complement is maintained by non-GPT progenitors for inductive regulation of the total complement of GPT neurons. Finally, GPT neurons in both normal and ablated mice meet all morphogenetic criteria, including the ‘outside-in’ vertical gradient of settlement, presently used to identify principal preplate neurons. In ablated mice, delayed organization of these neurons desynchronizes and isolates developing neocortex from the rest of the brain, and permanently impairs its connectivity.
Chromatic aberration correction: an enhancement to the calibration of low‐cost digital dermoscopes

Background/purpose: We present a method for calibrating low‐cost digital dermoscopes that corrects for color and inconsistent lighting and also corrects for chromatic aberration. Chromatic aberration is a form of radial distortion that often occurs in inexpensive digital dermoscopes and creates red and blue halo‐like effects on edges. Being radial in nature, distortions due to chromatic aberration are not constant across the image, but rather vary in both magnitude and direction. As a result, distortions are not only visually distracting but could also mislead automated characterization techniques.
Improving accompanied Flamenco singing voice transcription by combining vocal detection and predominant melody extraction

While recent approaches to automatic voice melody transcription of accompanied flamenco singing give promising results regarding pitch accuracy, mistakenly transcribed guitar sections represent a major limitation for the obtained overall precision. With the aim of reducing the amount of false positives in the voicing detection, we propose a fundamental frequency contour estimation method which extends the pitch-salience based predominant melody extraction [3] with a vocal detection classifier based on timbre and pitch contour characteristics. Pitch contour segments estimated by the predominant melody extraction algorithm containing a high percentage of frames classified as non-vocal are rejected. After estimating the tuning frequency, the remaining pitch contour is segmented into single note events in an iterative approach. The resulting symbolic representations are evaluated with respect to manually corrected transcriptions on a frame-by-frame level. For two small flamenco dataset covering a variety of singers and audio quality, we observe a significant reduction of the voicing false alarm rate and an improved voicing F-Measure as well as an increased overall transcription accuracy. We furthermore demonstrate the advantage of vocal detection model trained on genre-specific material. The presented case study is limited to the transcription of Flamenco singing, but the general framework can be extended to other styles with genre-specific instrumentation.
Rate-compatible punctured serial concatenated convolutional codes

We propose and compare some good rate-compatible serial concatenated convolutional code (SCCC) families. To obtain rate-compatible SCCCs, the puncturing is limited to inner coded bits. However, and this is the novelty proposed, we do not limit the puncturing to inner parity bits only, but we extend it also to inner systematic bits, thus obtaining higher rate SCCCs (i.e., beyond the outer code rate). The two main applications of this technique are its use in hybrid ARQ/FEC schemes and to achieve unequal error protection (UEP) of an information sequence.
Preparing Meta-Analysis of Metamodel Understandability

Metamodels are designed to be used by machines and humans. For human users, the understandability of the metamodel is important. Experimental investigations of understandability in computer science have led to conflicting results. To resolve such conflicts and gain insights into the nature of some phenomenon beyond singular experiments, meta-analysis can be applied, i.e., the statistical analysis of results obtained by other (primary) empirical studies. This paper shows the current obstacles for a meta-analysis of metamodel understandability: They consist in the heterogeneity of the individual experiments and deficient reporting. The paper provides a framework to increase the comparability of experiments on understandability. Such comparability enables future meta-analysis.
Segmentation of the left and right cardiac ventricle using a combined bi-temporal statistical model

The manual segmentation and analysis of high-resolution multislice cardiac CT datasets is both labor intensive and time consuming. Therefore it is necessary to supply the cardiologist with powerful software tools to segment the myocardium as well as the cardiac cavities and to compute the relevant diagnostic parameters. In this paper we present an automatic cardiac segmentation procedure with minimal user interaction. It is based on a combined bi-temporal statistical model of the left and right ventricle using the principal component analysis (PCA) as well as the independent component analysis (ICA) to model global and local shape variation. To train the model we used manually drawn end-diastolic as well as end-systolic contours of the right epi- and of the left and right endocardium to create triangular surfaces of training datasets. These surfaces were used to build a mean triangular surface model of the left and right ventricle for the end-diastolic and end-systolic heart phase and to compute the PCA and ICA decorrelation matrices which are used in a point distribution model (PDM) to model the global and local shape variations. In contrast to many previous attempts of model based cardiac segmentation we do not create separate models for the left and the right ventricle and for different heart phases, but instead create one single parameter vector containing the information of both ventricles and both heart phases. This enables us to use the correlation between the phases and between left and right side to create a model which is more robust and less sensitive e.g. to poor contrast at the right ventricle.
Multiple sulfur isotopes reveal a magmatic origin for the Platreef platinum group element deposit, Bushveld Complex, South Africa

The Platreef ore horizon of the Bushveld Complex, South Africa, is the third largest platinum group element ore deposit in the world, but the origin of its ore remains enigmatic. A complex contact relationship between the igneous and footwall rocks of the Bushveld Complex, coupled with evidence for widespread late-stage hydrothermal processing, obscures the original mineralization history of the Platreef. We constrain the parental magmatic origin of the Platreef by exploiting multiple sulfur isotope contrasts across Bushveld Complex contact zones in order to see through the effects of postmineralization hydrothermal activity. We report S isotope measurements made on samples collected along two profi les through the Platreef into underlying metapelitic and metacarbonate footwall rocks. In both profi les, igneous rocks far from the contact have low Δ 33 S values (average Δ 33 S = 0.15‰), whereas metasedimentary rocks far from the contact have high Δ 33 S values (Δ 33 S to 5.04‰) with a smoothly varying profi le between the two end members. The midpoint in both isotope profi les is displaced into the footwall, defi ning a classic advective-dispersive tracer geometry. This geometry is not present in the associated δ 34 S values. The displacement of the Δ 33 S front suggests fl uid transport and advection of S into the country rocks; this was accompanied by back diffusion of the S isotope tracer into the Platreef. The Platreef magma was apparently S saturated prior to emplacement and, counterintuitively, lost S during the formation of the present Platreef ore horizon.
Abstract Spatial Concept Priming Dynamically Influences Real-World Actions

Experienced regularities in our perceptions and actions play important roles in grounding abstract concepts such as social status, time, and emotion. Might we similarly ground abstract spatial concepts in more experienced-based domains? The present experiment explores this possibility by implicitly priming abstract spatial terms (north, south, east, west) and then measuring participants’ hand movement trajectories while they respond to a body-referenced spatial target (up, down, left, right) in a verbal (Exp. 1) or spatial (Exp. 2) format. Results from two experiments demonstrate temporally dynamic and prime biased movement trajectories when the primes are incongruent with the targets (e.g., north – left, west – up). That is, priming abstract coordinate directions influences subsequent actions in response to concrete target directions. These findings provide the first evidence that abstract concepts of world-centered coordinate axes are implicitly understood in the context of concrete body-referenced axes; critically, this abstract-concrete relationship manifests in motor movements, and may have implications for spatial memory organization.
Role of Electron-Driven Proton-Transfer Processes in the Ultrafast Deactivation of Photoexcited Anionic 8-oxoGuanine-Adenine and 8-oxoGuanine-Cytosine Base Pairs

It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the 8-oxo-G nucleoside may have been a primordial precursor of present-day flavins in DNA or RNA repair. Because the electron transfer leading to the splitting of a thymine-thymine pair in a CPD lesion occurs in the photoexcited state, a reasonably long excited-state lifetime of 8-oxo-G is required. The neutral (protonated) form of 8-oxo-G exhibits a very short (sub-picosecond) intrinsic excited-state lifetime which is unfavorable for repair. It has therefore been argued that the anionic (deprotonated) form of 8-oxo-G, which exhibits a much longer excited-state lifetime, is more likely to be a suitable cofactor for DNA repair. Herein, we have investigated the exited-state quenching mechanisms in the hydrogen-bonded complexes of deprotonated 8-oxo-G− with adenine (A) and cytosine (C) using ab initio wave-function-based electronic-structure calculations. The calculated reaction paths and potential-energy profiles reveal the existence of barrierless electron-driven inter-base proton-transfer reactions which lead to low-lying S1/S0 conical intersections. The latter can promote ultrafast excited-state deactivation of the anionic base pairs. While the isolated deprotonated 8-oxo-G− nucleoside may have been an efficient primordial repair cofactor, the excited states of the 8-oxo-G−-A and 8-oxo-G−-C base pairs are likely too short-lived to be efficient electron-transfer repair agents.
Cross-dataset learning and person-specific normalisation for automatic Action Unit detection

Automatic detection of Facial Action Units (AUs) is crucial for facial analysis systems. Due to the large individual differences, performance of AU classifiers depends largely on training data and the ability to estimate facial expressions of a neutral face. In this paper, we present a real-time Facial Action Unit intensity estimation and occurrence detection system based on appearance (Histograms of Oriented Gradients) and geometry features (shape parameters and landmark locations). Our experiments show the benefits of using additional labelled data from different datasets, which demonstrates the generalisability of our approach. This holds both when training for a specific dataset or when a generic model is needed. We also demonstrate the benefits of using a simple and efficient median based feature normalisation technique that accounts for person-specific neutral expressions. Finally, we show that our results outperform the FERA 2015 baselines in all three challenge tasks - AU occurrence detection, fully automatic AU intensity and pre-segmented AU intensity estimation.
Amyloid beta oligomers induce impairment of neuronal insulin receptors

Recent studies have indicated an association between Alzheimer's disease (AD) and central nervous system (CNS) insulin resistance. However’ the cellular mechanisms underlying the link between these two pathologies have not been elucidated. Here we show that signal transduction by neuronal insulin receptors (IR) is strikingly sensitive to disruption by soluble Aβ oligomers (also known as ADDLs). ADDLs are known to accumulate in AD brain and have recently been implicated as primary candidates for initiating deterioration of synapse function, composition, and structure. Using mature cultures of hippocampal neurons, a preferred model for studies of synaptic cell biology, we found that ADDLs caused a rapid and substantial loss of neuronal surface IRs specifically on dendrites bound by ADDLs. Removal of dendritic IRs was associated with increased receptor immunoreactiv‐ity in the cell body, indicating redistribution of the receptors. The neuronal response to insulin, measured by evoked IR tyrosine autophosphorylation, was greatly inhibited by ADDLs. Inhibition also was seen with added glutamate or potassium‐induced depolarization. The effects on IR function were completely blocked by NMDA receptor antagonists, tetrodotoxin, and calcium chelator BAPTA‐AM. Downstream from the IR, ADDLs induced a phosphorylation of Akt at serine473, a modification associated with neurodegenerative and insulin resistance diseases. These results identify novel factors that affect neuronal IR signaling and suggest that insulin resistance in AD brain is a response to ADDLs, which disrupt insulin signaling and may cause a brain‐specific form of diabetes as part of an overall pathogenic impact on CNS synapses. — Zhao, W. Q. , De Felice, F. G. , Fernandez, S. , Chen, H. , Lambert, M. P., Quon, M. J., Krafft, G. A. , Klein, W. L. Amyloid beta oligomers induce impairment of neuronal insulin receptors. FASEB J. 22, 246–260 (2008)
Approximate similarity search in genomic sequence databases using landmark-guided embedding

Similarity search in sequence databases is of paramount importance in bioinformatics research. As the size of the genomic databases increases, similarity search of proteins in these databases becomes a bottle-neck in large-scale studies, calling for more efficient methods of content-based retrieval. In this study, we present a metric-preserving, landmark-guided embedding approach to represent sequences in the vector domain in order to allow efficient indexing and similarity search. We analyze various properties of the embedding and show that the approximation achieved by the embedded representation is sufficient to achieve biologically relevant results. The approximate representation is shown to provide several orders of magnitude speed-up in similarity search compared to the exact representation, while maintaining comparable search accuracy.
A practical theory of language-integrated query

Language-integrated query is receiving renewed attention, in part because of its support through Microsoft's LINQ framework. We present a practical theory of language-integrated query based on quotation and normalisation of quoted terms. Our technique supports join queries, abstraction over values and predicates, composition of queries, dynamic generation of queries, and queries with nested intermediate data. Higher-order features prove useful even for constructing first-order queries. We prove a theorem characterising when a host query is guaranteed to generate a single SQL query. We present experimental results confirming our technique works, even in situations where Microsoft's LINQ framework either fails to produce an SQL query or, in one case, produces an avalanche of SQL queries.
Factors Associated With School Dropouts and Juvenile Delinquency Among Lower-Class Children

IT IS WELL KNOWN that the lower socioeconomic classes have markedly higher rates of school dropouts and juvenile delinquency than do those in the upper levels of income and affluence.l Less understood are the factors associated with clropouts and delinquency within these lower classes. Despite the higher rates, a majority of these youths do not leave school or become delinquent. By itself, being poor is not, enough to explain the occurrence of dropping out and delinquency ; other influences are involved. What factors can explain why some of these youths leave school early but most do not) ; why some of them are picked up by the police and juvenile courts but most are not? To explore these questions it was decided to do a retrospective cohort study of a known group of lower-class juveniles. The study was designed to explore the characteristics and records of a sample of lower-class children who were reaching school age in 1950 and who would have passed their juvenile years by the time of the study in 1962. We were fortunate at Yale University in having access to the results of the 1950 New Haven Five Percent Sample. This was a survey of 5 percent of the total New Haven population in 1950, conducted by Yale Universit.y to establish a baseline for extensive studies of social class and mental
Evaluation of the Therapeutic Potential of Bone Marrow-Derived Myeloid Suppressor Cell (MDSC) Adoptive Transfer in Mouse Models of Autoimmunity and Allograft Rejection

Therapeutic use of immunoregulatory cells represents a promising approach for the treatment of uncontrolled immunity. During the last decade, myeloid-derived suppressor cells (MDSC) have emerged as novel key regulatory players in the context of tumor growth, inflammation, transplantation or autoimmunity. Recently, MDSC have been successfully generated in vitro from naive mouse bone marrow cells or healthy human PBMCs using minimal cytokine combinations. In this study, we aimed to evaluate the potential of adoptive transfer of such cells to control auto- and allo-immunity in the mouse. Culture of bone marrow cells with GM-CSF and IL-6 consistently yielded a majority of CD11b+Gr1hi/lo cells exhibiting strong inhibition of CD8+ T cell proliferation in vitro. However, adoptive transfer of these cells failed to alter antigen-specific CD8+ T cell proliferation and cytotoxicity in vivo. Furthermore, MDSC could not prevent the development of autoimmunity in a stringent model of type 1 diabetes. Rather, loading the cells prior to injection with a pancreatic neo-antigen peptide accelerated the development of the disease. Contrastingly, in a model of skin transplantation, repeated injection of MDSC or single injection of LPS-activated MDSC resulted in a significant prolongation of allograft survival. The beneficial effect of MDSC infusions on skin graft survival was paradoxically not explained by a decrease of donor-specific T cell response but associated with a systemic over-activation of T cells and antigen presenting cells, prominently in the spleen. Taken together, our results indicate that in vitro generated MDSC bear therapeutic potential but will require additional in vitro factors or adjunct immunosuppressive treatments to achieve safe and more robust immunomodulation upon adoptive transfer.