Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of serum C reactive protein and procalcitonin concentrations in addition to symptoms and signs to predict pneumonia in patients presenting to primary care with acute cough: diagnostic study

Objectives To quantify the diagnostic accuracy of selected inflammatory markers in addition to symptoms and signs for predicting pneumonia and to derive a diagnostic tool. Design Diagnostic study performed between 2007 and 2010. Participants had their history taken, underwent physical examination and measurement of C reactive protein (CRP) and procalcitonin in venous blood on the day they first consulted, and underwent chest radiography within seven days. Setting Primary care centres in 12 European countries. Participants Adults presenting with acute cough. Main outcome measures Pneumonia as determined by radiologists, who were blind to all other information when they judged chest radiographs. Results Of 3106 eligible patients, 286 were excluded because of missing or inadequate chest radiographs, leaving 2820 patients (mean age 50, 40% men) of whom 140 (5%) had pneumonia. Re-assessment of a subset of 1675 chest radiographs showed agreement in 94% (κ 0.45, 95% confidence interval 0.36 to 0.54). Six published “symptoms and signs models” varied in their discrimination (area under receiver operating characteristics curve (ROC) ranged from 0.55 (95% confidence interval 0.50 to 0.61) to 0.71 (0.66 to 0.76)). The optimal combination of clinical prediction items derived from our patients included absence of runny nose and presence of breathlessness, crackles and diminished breath sounds on auscultation, tachycardia, and fever, with an ROC area of 0.70 (0.65 to 0.75). Addition of CRP at the optimal cut off of >30 mg/L increased the ROC area to 0.77 (0.73 to 0.81) and improved the diagnostic classification (net reclassification improvement 28%). In the 1556 patients classified according to symptoms, signs, and CRP >30 mg/L as “low risk” (<2.5%) for pneumonia, the prevalence of pneumonia was 2%. In the 132 patients classified as “high risk” (>20%), the prevalence of pneumonia was 31%. The positive likelihood ratio of low, intermediate, and high risk for pneumonia was 0.4, 1.2, and 8.6 respectively. Measurement of procalcitonin added no relevant additional diagnostic information. A simplified diagnostic score based on symptoms, signs, and CRP >30 mg/L resulted in proportions of pneumonia of 0.7%, 3.8%, and 18.2% in the low, intermediate, and high risk group respectively. Conclusions A clinical rule based on symptoms and signs to predict pneumonia in patients presenting to primary care with acute cough performed best in patients with mild or severe clinical presentation. Addition of CRP concentration at the optimal cut off of >30 mg/L improved diagnostic information, but measurement of procalcitonin concentration did not add clinically relevant information in this group.
Disassembly of Shank and Homer Synaptic Clusters Is Driven by Soluble β-Amyloid1-40 through Divergent NMDAR-Dependent Signalling Pathways

Disruption of the postsynaptic density (PSD), a network of scaffold proteins located in dendritic spines, is thought to be responsible for synaptic dysfunction and loss in early-stage Alzheimer's disease (AD). Extending our previous demonstration that derangement of the PSD by soluble amyloid-β (Aβ) involves proteasomal degradation of PSD-95, a protein important for ionotropic glutamate receptor trafficking, we now show that Aβ also disrupts two other scaffold proteins, Homer1b and Shank1, that couple PSD-95 with ionotropic and metabotropic glutamate receptors. Treatment of fronto-cortical neurons with soluble Aβ results in rapid (within 1 h) and significant thinning of the PSD, decreased synaptic levels of Homer1b and Shank1, and reduced synaptic mGluR1 levels. We show that de novo protein synthesis is required for the declustering effects of Aβ on Homer1b (but not Shank1) and that, in contrast to PSD-95, Aβ-induced Homer1b and Shank1 cluster disassembly does not depend on proteasome activity. The regulation of Homer1b and Shank1 by Aβ diverges in two other respects: i) whereas the activity of both NMDAR and VDCC is required for Aβ-induced declustering of Homer1b, Aβ-induced declustering of Shank1 only requires NMDAR activity; and ii) whereas the effects of Aβ on Homer1b involve engagement of the PI-3K pathway and calcineurin phosphatase (PP2B) activity, those on Shank1 involve activation of the ERK pathway. In summary, soluble Aβ recruits discrete signalling pathways to rapidly reduce the synaptic localization of major components of the PSD and to regulate the availability of mGluR1 in the synapse.
Analysis of Heterogeneous Cellular Networks Under Frequency Diversity and Interference Correlation

Analyzing heterogeneous cellular networks (HCNs) has become increasingly complex, particularly due to irregular base station locations, massive deployment of small cells, and flexible resource allocation. The latter is usually not captured by existing stochastic models for analytical tractability. In this work, we develop a more realistic stochastic model for a generic K-tier HCN, where users are served in the downlink under frequency diversity. We derive the rate coverage probability for this case, taking into account the interference correlation across different parts of the allocated spectrum. Our results indicate that ignoring this type of correlation may considerably overestimate the offered date rate. Furthermore, the gain of spectrum diversification is significant, particularly at low to moderate target data rates.
The Tao of Hematopoietic Stem Cells: Toward a Unified Theory of Tissue Regeneration

Hematopoietic stem cells (HSCs) are the best studied of the tissue-specific stem cells. By definition, HSCs have long been regarded as restricted to formation of blood cells of both the lymphoid and myeloid lineages. HSCs residing in the bone marrow microenvironment have self-renewal capacity and can repopulate the hematopoietic system of irradiated transplant recipients for the lifetime of the individual. Therefore, HSCs are extremely important targets for gene therapy applications aimed toward the treatment of inherited and acquired blood disorders. However, recent studies have suggested that a subpopulation of HSCs may have the ability to contribute to diverse cell types such as hepatocytes, myocytes, and neuronal cells, especially following induced tissue damage. Preclinical amelioration of liver disease and myocardial infarcts by HSC-enriched bone marrow cell populations raises the possibility that HSC transplants have the potential to provide therapeutic benefit for a wide variety of diseases. These surprising findings contradict the dogma that adult stem cells are developmentally restricted. Extrapolation of these findings to the clinic will be facilitated by prospective identification of the stem cells that possess this developmental plasticity. Furthermore, characterization of the signaling pathways and molecular determinants regulating the remarkable transdifferentiation capacity of these stem cells may provide insight into novel approaches for modulating frequency of differentiative potential.
Scalable Approximate Bayesian Inference for Outlier Detection under Informative Sampling

Government surveys of business establishments receive a large volume of submissions where a small subset contain errors. Analysts need a fast-computing algorithm to ag this subset due to a short time window between collection and reporting. We offer a computationally-scalable optimization method based on non-parametric mixtures of hierarchical Dirichlet processes that allows discovery of multiple industry-indexed local partitions linked to a set of global cluster centers. Outliers are nominated as those clusters containing few observations. We extend an existing approach with a new "merge" step that reduces sensitivity to hyperparameter settings. Survey data are typically acquired under an informative sampling design where the probability of inclusion depends on the surveyed response such that the distribution for the observed sample is different from the population. We extend the derivation of a penalized objective function to use a pseudo-posterior that incorporates sampling weights that "undo" the informative design. We provide a simulation study to demonstrate that our approach produces unbiased estimation for the outlying cluster under informative sampling. The method is applied for outlier nomination for the Current Employment Statistics survey conducted by the Bureau of Labor Statistics.
Co-variation between autotrophy and heterotrophy in the Mediterranean coral Cladocora caespitosa

SUMMARY This study quantifies the relative contributions of autotrophy and heterotrophy to the energy budget of the temperate scleractinian species Cladocora caespitosa Linnaeus 1767. Colonies were incubated under different light and feeding regimes, and changes in carbon acquisition through photosynthesis and feeding were measured during a 2-month time period. This approach allowed us to quantify the rate at which adjustments to physiology occurred, as well as the magnitude of up- or downregulation of both feeding modes. In addition, we explored how shifts in carbon acquisition mode influenced tissue biomass (protein content), energy stores (lipid content) and colony growth (calcification). Increases in feeding capacity during prolonged exposure to darkness were correlated with decreases in photosynthetic capacity. However, feeding effort did not decrease when photosynthesis was high. In fact, feeding was maximal under high light conditions when food was not available. During starvation, colonies used their lipid stores to partially meet their metabolic requirements. Colonies kept in low light used nutrients from feeding to supplement calcification, whereas those kept at high light converted carbon from feeding into tissue biomass. This work provides the first estimates of rates of adjustment of heterotrophic feeding capacity in a Mediterranean scleractinian coral. For the study species, flexibility in carbon acquisition through heterotrophy was approximately equal to flexibility in photosynthesis both in magnitude and in the rate at which physiological adjustments occurred. The ability to alter feeding effort rapidly and strongly may explain the wide depth distribution of C. caespitosa, and its ability to survive in turbid coastal waters where light is often limited.
Parallel architecture for decoding LDPC Codes on high speed communication systems

This paper presents a novel parallel architecture for decoding LDPC codes. The proposed architecture has low memory and interconnection requirements, becoming attractive for high speed applications such as fiber optic communications and high density magnetic recording. As an example, the implementation on an FPGA of a TPC/SPC code using the proposed architecture will also be described.
A path planning heuristic for robotic manipulators

A practical solution to path planning problem for a six-degree-of-freedom robotic manipulator with arbitary payload has been implemented. This problem in its most general form has been shown to be intractable, so most researchers in the field simplify the problem in some way. Often these simplifications make the resulting path planner of little practical use. In this paper an overview of a practical path planner is given. Heuristics are used to plan for the last three degrees of freedom of the robot and its payload, and the details of one of these heuristics is described. The use of heuristics makes the planner incomplete, but for all tasks programmed for the robot the planner has not failed to find a path.
Shared Subgenome Dominance Following Polyploidization Explains Grass Genome Evolutionary Plasticity from a Seven Protochromosome Ancestor with 16K Protogenes

Modern plant genomes are diploidized paleopolyploids. We revisited grass genome paleohistory in response to the diploidization process through a detailed investigation of the evolutionary fate of duplicated blocks. Ancestrally duplicated genes can be conserved, deleted, and shuffled, defining dominant (bias toward duplicate retention) and sensitive (bias toward duplicate erosion) chromosomal fragments. We propose a new grass genome paleohistory deriving from an ancestral karyotype structured in seven protochromosomes containing 16,464 protogenes and following evolutionary rules where 1) ancestral shared polyploidizations shaped conserved dominant (D) and sensitive (S) subgenomes, 2) subgenome dominance is revealed by both gene deletion and shuffling from the S blocks, 3) duplicate deletion/movement may have been mediated by single-/double-stranded illegitimate recombination mechanisms, 4) modern genomes arose through centromeric fusion of protochromosomes, leading to functional monocentric neochromosomes, 5) the fusion of two dominant blocks leads to supradominant neochromosomes (D + D = D) with higher ancestral gene retention compared with D + S = D (i.e., fusion of blocks with opposite sensitivity) or even S + S = S (i.e., fusion of two sensitive ancestral blocks). A new user-friendly online tool named “PlantSyntenyViewer,” available at http://urgi.versailles. inra.fr/synteny-cereal, presents the refined comparative genomics data.
Differentiated Service Pricing on Social Networks Using Stochastic Optimization

This paper develops a combined simulation and optimization model that allows to optimize different service pricing strategies defined on the social networks under uncertainty. For a specific reference problem we consider a telecom service provider whose customers are connected in such network. Besides the service price, the acceptance of this service by a given customer depends on the popularity of this service among the customer's neighbors in the network. One strategy that the service provider can pursue in this situation is to stimulate the demand by offering the price incentives to the most connected customers whose opinion can influence many other participants in the social network. We develop a simulation model of such social network and show how this model can be integrated with stochastic optimization in order to obtain the optimal pricing strategy. Our results show that the differentiated pricing strategies can increase substantially the revenue of a service provider operating on a social network.
A Workflow for Automated Satellite Image Processing: from Raw VHSR Data to Object-Based Spectral Information for Smallholder Agriculture

Earth Observation has become a progressively important source of information for land use and land cover services over the past decades. At the same time, an increasing number of reconnaissance satellites have been set in orbit with ever increasing spatial, temporal, spectral, and radiometric resolutions. The available bulk of data, fostered by open access policies adopted by several agencies, is setting a new landscape in remote sensing in which timeliness and efficiency are important aspects of data processing. This study presents a fully automated workflow able to process a large collection of very high spatial resolution satellite images to produce actionable information in the application framework of smallholder farming. The workflow applies sequential image processing, extracts meaningful statistical information from agricultural parcels, and stores them in a crop spectrotemporal signature library. An important objective is to follow crop development through the season by analyzing multi—temporal and multi—sensor images. The workflow is based on free and open—source software, namely R, Python, Linux shell scripts, the Geospatial Data Abstraction Library, custom FORTRAN, C++, and the GNU Make utilities. We tested and applied this workflow on a multi—sensor image archive of over 270 VHSR WorldView—2, —3, QuickBird, GeoEye, and RapidEye images acquired over five different study areas where smallholder agriculture prevails.
An outbreak of hepatitis A associated with a bakery, New York, 1994: The 1968 ‘West Branch, Michigan’ outbreak repeated

Summary In a community hepatitis A outbreak in the Rochester, New York area, 64 of 79 (81 %) people with anti-hepatitis A 1gM-antibodies and onset of symptoms from 9 April–31 May 1994, recalled eating food obtained from a retail buyer's club. Eleven (65%) of 17 households with cases contained club members compared with 7 (21%) of 34 neighbourhood-matched control-households (matched odds ratio 8·5; 95% CI 1·7–41·6). Club employees who ate sugar-glazed baked goods were at fourfold increased risk for hepatitis. The source of infection was an 1gM- positive baker who contaminated baked goods while applying sugar glaze. Computer-generated purchase lists implicated 11–12 March and 21–24 March as the most likely dates when contamination occurred. This investigation demonstrates the importance of food workers adhering to established hygiene practices. Computer-generated commercial datasets can be useful in epidemiologic investigations.
Mitochondrial oxidative phosphorylation is a downstream regulator of nitric oxide effects on chondrocyte matrix synthesis and mineralization.

OBJECTIVE Increased chondrocyte nitric oxide (NO) and peroxynitrite production appears to modulate decreased matrix synthesis and increased mineralization in osteoarthritis (OA). Because NO inhibits mitochondrial respiration, this study was undertaken to directly assess the potential role of chondrocyte mitochondrial oxidative phosphorylation (OXPHOS) in matrix synthesis and mineralization. METHODS We studied cultured human articular chondrocytes and immortalized costal chondrocytes (TC28 cells). We also assessed the effects of antimycin A and oligomycin (inhibitors of mitochondrial complexes III and V, respectively) on chondrocyte mitochondrial respiration, ATP synthesis, and inorganic pyrophosphate (PPi) generation, and the mineralizing potential of released matrix vesicles (MV). RESULTS Articular chondrocytes and TC28 cells respired at comparable rates. Peroxynitrite and NO donors markedly suppressed respiration and ATP generation in chondrocytes. Because NO exerts multiple effects on chondrocytes, we investigated the primary functions of mitochondrial respiration and OXPHOS. To do so, we identified minimally cytotoxic doses of antimycin and oligomycin, which both induced intracellular ATP depletion (by 50-80%), attenuated collagen and proteoglycan synthesis, and blocked transforming growth factor beta from increasing intracellular ATP and elaboration of PPi, a critical inhibitor of hydroxyapatite deposition. Antimycin and oligomycin also abrogated the ability of the ATP-hydrolyzing enzyme plasma cell membrane glycoprotein 1 (PC-1) to increase chondrocyte PPi generation. Finally, MV from cells treated with antimycin or oligomycin contained less PPi and precipitated >50% more 45Ca. CONCLUSION Chondrocyte mitochondrial reserve, as NO-sensitive mitochondrial respiration-mediated ATP production, appears to support matrix synthesis and PPi elaboration and to regulate MV composition and mineralizing activity. NO-induced depression of chondrocyte respiration could modulate matrix loss and secondary cartilage mineralization in OA.
Enterovirus infections as a possible risk factor for myocardial infarction.

BACKGROUND An increasing body of evidence suggests that, in addition to the well-known classic risk factors, some microbial infections may be associated with the development of atherosclerosis and myocardial infarction (MI). The aim of our study was to evaluate the possible role of enteroviral infections in the pathogenesis of MI. METHODS AND RESULTS Stored sera, collected in Eastern Finland in 1977, from a set of 12 155 randomly selected men and women aged 25 to 64 years were used in prospective, nested case-control study. The study sample comprised 183 men and 81 women with MI and matched controls. The sera were tested for IgG antibodies to a newly identified enterovirus-common (EVC) antigen, to heat-denatured coxsackievirus B5 (CBV-5), and to adenovirus hexon protein. Raw data from enzyme immunoassays were converted to relative units before analysis. In univariate analysis, EVC antibodies were significantly associated with the risk of MI in men (P=0.009) but not in women. Men with MI had a significantly higher mean level of EVC antibodies than matched controls (P=0.014). High antibody levels to EVC were associated with an increased risk of MI in men aged 25 to 49 years (relative risk [RR] 4.34, P<0.001) but not in older men (>50 years of age). Women with MI also showed a trend toward higher antibody levels than control women, but the difference was not statistically significant. Antibody levels to whole CBV-5 or adenovirus hexon protein appeared to be no different among case patients versus control subjects. CONCLUSIONS If we assume that a high level of EVC antibodies reflects a history of relatively frequent enterovirus infections, the present observation might suggest that enterovirus infections increase the risk of MI at least in middle-aged men. Further studies are needed to understand possible clinical significance of this observation.
Time-Scale Information Measures for Text-Independent Phone Segmentation

In this work, speech parameterization based on the continuous multiresolution divergence is used to modify a textindependent phone segmentation algorithm. This encoding is employed as input and also replaces an stage of the segmentation procedure responsible for the estimation of the intensity of changes in signal features. The segmentation performance of this representation has been compared with the original algorithm using as input a classical Melbank parameterization and speech representation based on the continuous multiresolution divergence. The results indicate that the modification here proposed increases the ability of the algorithm to perform the segmentation task. This suggests that continuous multiresolution divergence provides valuable information related to acoustic features that take into account phoneme transitions. Moreover, this parameterization gives enough information for its direct use without further processing. Keywords— Information measures, Divergence, Multiresolution analysis, Automatic speech segmentation.