Miracle-dz/UniFAR-FTUs huggingface dataset:
Pneumococcal finding in a sample from upper airways does not indicate pneumococcal infection of lower airways.

The presence of pneumococcus (Pnc) by antigen detection and culture was examined in nasopharyngeal aspirates (NPA) of 315 children hospitalized with middle or lower respiratory tract infection. Pnc was found in NPA from 115 (37%) patients, being demonstrated by antigen detection alone in 34 (30%), by culture alone in 26 (23%) and by both methods in 55 (48%) of Pnc-positive samples. Pnc findings in NPA were most common, 45-46%, in patients aged 1-4 years. Serological evidence of Pnc infection, based either on detection of Pnc antigen in serum or urine, or on demonstration of an antibody response to these antigens, was present in 31 (27%) of the 115 patients with and in 28 (14%) of the 200 patients without Pnc in NPA samples. In the 48 patients positive for Pnc in NPA samples both by antigen detection and culture the isolated Pnc strains were serotyped. In 45 (94%) of these the type/group of Pnc was the same by both methods indicating that the specificity of the antigen detection tests, latex particle agglutination and counterimmunoelectrophoresis, was high. To evaluate the diagnostic significance of Pnc antigen detection and culture in NPA, sensitivity, specificity and likelihood ratios were calculated; serological evidence of Pnc aetiology was used as a reference. For both methods, sensitivity was poor, less than 0.3, but specificity was good, greater than 0.8. It is concluded that the finding of Pnc by culture or antigen detection in NPA is no indication of Pnc respiratory infection. On the other hand, Pnc etiology is unprobable, if Pnc is not present in NPA. (ABSTRACT TRUNCATED AT 250 WORDS)
Analysis of the Fragile X Trinucleotide Repeat in Basques: Association of Premutation and Intermediate Sizes, Anchoring AGGs and Linked Microsatellites with Unstable Alleles

Fragile X Syndrome (FXS) is associated with an unstable CGG repeat sequence in the 5’ untranslated region in the first exon of the FMR1 gene which resides at chromosome position Xq27.3 and is coincident with the fragile site FRAXA. The CGG sequence is polymorphic with respect to size and purity of the repeat. Interpopulation variation in the polymorphism of the FMR1 gene and consequently, in the predisposition to FXS due to the prevalence of certain unstable alleles has been observed. Spanish Basque population is distributed among narrow valleys in northeastern Spain with little migration between them until recently. This characteristic may have had an effect on allelic frequency distributions. We had previously reported preliminary data on the existence of FMR1 allele differences between two Basque valleys (Markina and Arratia). In the present work we extended the study to Uribe, Gernika, Durango, Goierri and Larraun, another five isolated valleys enclosing the whole area within the Spanish Basque region. We analyzed the prevalence of FMR1 premutated and intermediate/grey zone alleles. With the aim to complete the previous investigation about the stability of the Fragile X CGG repeat in Basque valleys, we also analyzed the existence of potentially unstable alleles, not only in relation with size and purity of CGG repeat but also in relation with DXS548 and FRAXAC1 haplotypes implicated in repeat instability. The data show that differences in allele frequencies as well as in the distribution of the mutational pathways previously identified are present among Basques. The data also suggest that compared with the analyzed Basque valleys, Gernika had increased frequency of susceptibility to instability alleles, although the prevalence of premutation and intermediate/grey zone alleles in all the analyzed valleys was lower than that reported in Caucasian populations.
Acceptability attributes of crackers made from different types of composite flour

There is an increasing demand for fibre rich food and food ingredients. In this study, pumpkin pulp, unripe banana pulp, unripe mango pulp and peel which are high in dietary fibre were processed into flour and substituted at 5% level for wheat flour in a composite flour crackers formulation. The control crackers comprised of 100% wheat flour. Sensory evaluation was conducted using a 9-point hedonic scale with 31 panelists evaluating the crackers based on colour, crrispiness, taste and overall acceptance. Different types of composite flour crackers were not significantly different (p≤0.05) in term of crispiness. For colour, taste and overall acceptance, the pumpkin, banana and control crackers differ significantly (p≤0.05) with the mango pulp and mango peel crackers.
Statistical Metaphor Processing

Metaphor is highly frequent in language, which makes its computational processing indispensable for real-world NLP applications addressing semantic tasks. Previous approaches to metaphor modeling rely on task-specific hand-coded knowledge and operate on a limited domain or a subset of phenomena. We present the first integrated open-domain statistical model of metaphor processing in unrestricted text. Our method first identifies metaphorical expressions in running text and then paraphrases them with their literal paraphrases. Such a text-to-text model of metaphor interpretation is compatible with other NLP applications that can benefit from metaphor resolution. Our approach is minimally supervised, relies on the state-of-the-art parsing and lexical acquisition technologies (distributional clustering and selectional preference induction), and operates with a high accuracy.
Inherited thrombocytopenias in the era of personalized medicine

Until 15 years ago, inherited thrombocytopenias (ITs) were quite an indistinct group of disorders, only a few forms of which had been clearly defined. Moreover, the genetic defect was known for only two disorders: Bernard-Soulier syndrome (BSS) and Wiskott Aldrich syndrome (WAS). Since then, our
Novel NAD(P)H Oxidase Inhibitor Suppresses Angioplasty-Induced Superoxide and Neointimal Hyperplasia of Rat Carotid Artery

Abstract— Neointimal proliferation occurring after vascular or endovascular procedures is a major complication leading to end-organ or limb ischemia. In experimental models, balloon injury has been shown to induce NAD(P)H oxidase to produce vascular superoxide anion (O2·−) production, which has been implicated in cell proliferation, but a direct link is still unclear. We postulated that inhibition of arterial NAD(P)H oxidase, resulting in decreased O2·−, would lessen the neointimal hyperplasia caused by balloon injury to the common carotid artery (CCA). Sprague-Dawley rats were implanted with osmotic minipumps containing either vehicle, a cell-permeant peptide that inhibits NAD(P)H oxidase (gp91ds-tat, 10 mg/kg per day), or a scrambled peptide control (scrmb-tat). Two days after pump implantation, the left CCA was injured using an intravascular balloon embolectomy catheter (2F Fogarty). Systolic blood pressure was monitored by tail cuff. Fourteen days after injury, CCAs were harvested and analyzed by digital morphometry. Rats in both groups remained normotensive, with no significant differences in systolic blood pressure. Reactive oxygen species measurements after injury indicated a significant reduction in vascular O2·− in rats infused with gp91ds-tat, and the neointima/media area and thickness ratios were significantly lower in their arteries compared with control. On the contrary, no significant change in overall CCA diameter was observed in any group. Our data indicate that in response to balloon injury of the rat carotid artery, NAD(P)H oxidase activity contributes to neointimal hyperplasia and is involved in vascular cell proliferation and migration during restenosis.
Simulated bidirectional texture functions with silhouette details

The representation of material appearance requires an understanding of the underlying structures of real surfaces, light-material interaction, and human visual system. The Bidirectional Texture Function (BTF) describes real-world materials as a spatial variation of reflectance, which depends on view and light directions. Real BTFs integrate all optical phenomena occurring in a complex material, such as self-occlusions, interreflections, subsurface scattering, etc., independently of the mesoscopic surface geometry. In this paper, we revisit BTF simulation to improve the modeling of surface appearance. In the recent years, computer graphics has achieved very good levels of image realism on geometrical appearance of 3D scenes. It is therefore logical to think that using this technology to simulate visual effects at the level of the mesoscopic geometry should provide even more realistic simulated BTFs. Our ultimate goal here is thus to produce material appearance as rich and as similar as those in reality, but relying more on the intuition and skills of artists, and on the rendering capacity of today's computer graphics. We have designed a virtual parallel-projection/directional incident illumination framework that exploits rendering coherency in order to produce, in reasonable rendering times and with good compression ratios, BTFs of complex mesoscopic geometry, and this, even at grazing angles. Our current framework can simulate efficiently local interreflections effects within mesoscopic structures, as well as effects due to transparency, silhouettes, and surface curvatures. Our general simulation framework should also prove extensible to several other visual phenomena.
A lambda-calculus foundation for universal probabilistic programming

We develop the operational semantics of an untyped probabilistic λ-calculus with continuous distributions, and both hard and soft constraints,as a foundation for universal probabilistic programming languages such as Church, Anglican, and Venture. Our first contribution is to adapt the classic operational semantics of λ-calculus to a continuous setting via creating a measure space on terms and defining step-indexed approximations. We prove equivalence of big-step and small-step formulations of this distribution-based semantics. To move closer to inference techniques, we also define the sampling-based semantics of a term as a function from a trace of random samples to a value. We show that the distribution induced by integration over the space of traces equals the distribution-based semantics. Our second contribution is to formalize the implementation technique of trace Markov chain Monte Carlo (MCMC) for our calculus and to show its correctness. A key step is defining sufficient conditions for the distribution induced by trace MCMC to converge to the distribution-based semantics. To the best of our knowledge, this is the first rigorous correctness proof for trace MCMC for a higher-order functional language, or for a language with soft constraints.
Genome‐based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species

Analysis of microbial genome sequences have revealed numerous genes involved in antibiotic biosynthesis. In Pseudomonads, several gene clusters encoding non‐ribosomal peptide synthetases (NRPSs) were predicted to be involved in the synthesis of cyclic lipopeptide (CLP) antibiotics. Most of these predictions, however, are untested and the association between genome sequence and biological function of the predicted metabolite is lacking. Here we report the genome‐based identification of previously unknown CLP gene clusters in plant pathogenic Pseudomonas syringae strains B728a and DC3000 and in plant beneficial Pseudomonas fluorescens Pf0‐1 and SBW25. For P. fluorescens SBW25, a model strain in studying bacterial evolution and adaptation, the structure of the CLP with a predicted 9‐amino acid peptide moiety was confirmed by chemical analyses. Mutagenesis confirmed that the three identified NRPS genes are essential for CLP synthesis in strain SBW25. CLP production was shown to play a key role in motility, biofilm formation and in activity of SBW25 against zoospores of Phytophthora infestans. This is the first time that an antimicrobial metabolite is identified from strain SBW25. The results indicate that genome mining may enable the discovery of unknown gene clusters and traits that are highly relevant in the lifestyle of plant beneficial and plant pathogenic bacteria.
Spatio-temporal Patterns and Landscape-Associated Risk of Buruli Ulcer in Akonolinga, Cameroon

Background Buruli ulcer (BU) is an extensively damaging skin infection caused by Mycobacterium ulcerans, whose transmission mode is still unknown. The focal distribution of BU and the absence of interpersonal transmission suggest a major role of environmental factors, which remain unidentified. This study provides the first description of the spatio-temporal variations of BU in an endemic African region, in Akonolinga, Cameroon. We quantify landscape-associated risk of BU, and reveal local patterns of endemicity. Methodology/Principal Findings From January 2002 to May 2012, 787 new BU cases were recorded in 154 villages of the district of Akonolinga. Incidence per village ranged from 0 (n = 59 villages) to 10.4 cases/1000 person.years (py); median incidence was 0.4 cases/1,000py. Villages neighbouring the Nyong River flood plain near Akonolinga town were identified as the highest risk zone using the SPODT algorithm. We found a decreasing risk with increasing distance to the Nyong and identified 4 time phases with changes in spatial distribution. We classified the villages into 8 groups according to landscape characteristics using principal component analysis and hierarchical clustering. We estimated the incidence ratio (IR) associated with each landscape using a generalised linear model. BU risk was highest in landscapes with abundant wetlands, especially cultivated ones (IR = 15.7, 95% confidence interval [95%CI] = 15.7[4.2–59.2]), and lowest in reference landscape where primary and secondary forest cover was abundant. In intermediate-risk landscapes, risk decreased with agriculture pressure (from IR[95%CI] = 7.9[2.2–28.8] to 2.0[0.6–6.6]). We identified landscapes where endemicity was stable and landscapes where incidence increased with time. Conclusion/Significance Our study on the largest series of BU cases recorded in a single endemic region illustrates the local evolution of BU and identifies the Nyong River as the major driver of BU incidence. Local differences along the river are explained by wetland abundance and human modification of the environment.
Akt Inhibitors MK-2206 and Nelfinavir Overcome mTOR Inhibitor Resistance in Diffuse Large B-cell Lymphoma

Purpose: The mTOR pathway is constitutively activated in diffuse large B-cell lymphoma (DLBCL). mTOR inhibitors have activity in DLBCL, although response rates remain low. We evaluated DLBCL cell lines with differential resistance to the mTOR inhibitor rapamycin: (i) to identify gene expression profile(s) (GEP) associated with resistance to rapamycin, (ii) to understand mechanisms of rapamycin resistance, and (iii) to identify compounds likely to synergize with mTOR inhibitor. Experimental Design: We sought to identify a GEP of mTOR inhibitor resistance by stratification of eight DLBCL cell lines with respect to response to rapamycin. Then, using pathway analysis and connectivity mapping, we sought targets likely accounting for this resistance and compounds likely to overcome it. We then evaluated two compounds thus identified for their potential to synergize with rapamycin in DLBCL and confirmed mechanisms of activity with standard immunoassays. Results: We identified a GEP capable of reliably distinguishing rapamycin-resistant from rapamycin-sensitive DLBCL cell lines. Pathway analysis identified Akt as central to the differentially expressed gene network. Connectivity mapping identified compounds targeting Akt as having a high likelihood of reversing the GEP associated with mTOR inhibitor resistance. Nelfinavir and MK-2206, chosen for their Akt-inhibitory properties, yielded synergistic inhibition of cell viability in combination with rapamycin in DLBCL cell lines, and potently inhibited phosphorylation of Akt and downstream targets of activated mTOR. Conclusions: GEP identifies DLBCL subsets resistant to mTOR inhibitor therapy. Combined targeting of mTOR and Akt suppresses activation of key components of the Akt/mTOR pathway and results in synergistic cytotoxicity. These findings are readily adaptable to clinical trials. Clin Cancer Res; 18(9); 2534–44. ©2012 AACR.
Global Distribution of Nighttime Medium‐Scale Traveling Ionospheric Disturbances Seen by Swarm Satellites

The activity of nighttime medium‐scale traveling ionospheric disturbance (MSTID) in middle latitudes (±25°–40° magnetic latitudes) is investigated using the measurements of the electron density by Swarm satellites. Fractional electron density fluctuation is used as a proxy for MSTIDs, and the MSTID distribution is derived from the observations in December 2013–January 2017. The MSTID activity shows a semiannual variation in most longitudes with the primary and secondary peaks during the June and December solstices, respectively. The distinguishing feature in the MSTID distribution is the high occurrence rate of MSTIDs around 150°E longitude in June–August. The longitudinal and annual distribution of MSTIDs shows a hemispheric symmetry, which we interpret as the demonstration of conjugacy in MSTIDs.
Claims of sex differences: an empirical assessment in genetic associations.

CONTEXT Many studies try to probe for differences in risks between men and women, and this is a major challenge in the expanding literature of associations between genetic variants and common diseases or traits. OBJECTIVE To evaluate whether prominently claimed sex differences for genetic effects have sufficient internal and external validity. DATA SOURCES We searched PubMed through July 6, 2007, for genetic association studies claiming sex-related differences in the articles' titles. Titles and abstracts and, if necessary, the full text of the article were assessed for eligibility. STUDY SELECTION Two hundred fifteen articles were retrieved by the search. We considered eligible all retrieved association studies that claimed different genetic effects across sexes of 1 or more gene variants for any human disease or phenotype. We considered both biallelic and multiallelic markers (including haplotypes) and both binary and continuous phenotypes and traits. We excluded non-English-language studies; studies evaluating only 1 sex; studies in which sex was treated only as an independent predictor of disease; studies that did not address any association of the investigated genetic variant with a disease or trait; studies not involving humans; and studies in which the authors did not claim any sex difference. DATA EXTRACTION Two evaluators independently extracted data with a third evaluator arbitrating their discrepancies. Data evaluation included whether analyses were stated to have been specified a priori; whether sex effects were evaluated in the whole study or subgroups thereof; and whether the claims were appropriately documented, insufficiently documented, or spurious. For appropriately and insufficiently documented claims we performed the calculations for gene-sex interaction whenever raw data were available. Finally, we compared the sex-difference claims with the best internal validity against the results of other studies addressing the same interaction. RESULTS We appraised 432 sex-difference claims in 77 eligible articles. Authors stated that sex comparisons were decided a priori for 286 claims (66.2%), while the entire sample size was used in 210 (48.6%) claims. Appropriate documentation of gene-sex interaction was recorded in 55 claims (12.7%); documentation was insufficient for 303 claims and spurious for the other 74. Data for reanalysis of claims were available for 188 comparisons. Of these, 83 (44.1%) were nominally statistically significant at a P = . 05 threshold, and more than half of them (n = 44) had modest P values between . 01 and . 05. Of 60 claims with seemingly the best internal validity, only 1 was consistently replicated in at least 2 other studies. CONCLUSION In this sample of highly prominent claims of sex-related differences in genetic associations, most claims were insufficiently documented or spurious, and claims with documented good internal and external validity were uncommon.
Antibiotic prescription behaviours in Lao People's Democratic Republic: a knowledge, attitude and practice survey

Abstract Objective To assess the antibiotic prescribing practices of doctors working in the Lao People's Democratic Republic and their knowledge of local antibiotic resistance patterns. Methods Doctors attending morning meetings in 25 public hospitals in four provinces were asked to complete a knowledge, attitude and practice survey. The questionnaire contained 43 multiple choice questions that the doctor answered at the time of the meeting. Findings The response rate was 83.4% (386/463). Two hundred and seventy doctors (59.8%) declared that they had insufficient information about antibiotics. Only 14.0% (54/386) recognized the possibility of cephalosporin cross-resistance in methicillin-resistant Staphylococcus aureus. Most participants had no information about local antibiotic resistance for Salmonella Typhi (211/385, 54.8%) and hospital-acquired pneumonia (253/384, 65.9%). Unnecessary antibiotic prescriptions were considered as harmless by 115 participants and 148 considered locally-available generic antibiotics to be of poor quality. Nearly three-quarters (280/386) of participants agreed that it was difficult to select the correct antibiotics. Most participants (373/386) welcomed educational programmes on antibiotic prescribing and 65.0% (249/383) preferred local over international antibiotic guidelines. Conclusion Doctors in the Lao People's Democratic Republic seem to favour antibiotic prescribing interventions. Health authorities should consider a capacity building programme that incorporates antibiotic prescribing and hospital infection control.
Bayesian Estimates of the Prevalence of β-Thalassemia Trait in Voluntary Blood Donors of Central India: A Survey

Early detection of β-thalassemia (β-thal) trait is important. Voluntary blood donors represent an important group who are accessible and cooperative for this purpose. However, the usefulness of this population in β-thal trait detection programs has not been studied in India. We conducted a hematological survey of 5,045 blood donors who visited the Bhopal Memorial Hospital & Research Centre, Bhopal in central India. Using robust Bayesian methods, we estimated the prevalence of β-thal trait. The overall prevalence of β-thal trait in the study population was 9.59% [95% confidence interval (95% CI) 8.78–10.4%]. The prevalence of β-thal trait varied across the states of origin and within the state of Madhya Pradesh. We observed a cline effect for β-thal trait prevalence in relation to the latitude (p = 0.024). We conclude that blood donors offer an attractive adjunct to β-thal trait detection in national programs. Our study also offers insights into the β-thal trait gene flow and migration in India.
Recursive bi-partitioning of netlists for large number of partitions

In many application in VLSI CAD, a given netlist has to be partitioned into smaller sub-designs which can be handled much better. In this paper we present a new recursive bi-partitioning algorithm that is especially applicable, if a large number of final partitions, e.g. more than 1000, has to be computed. The algorithm consists of two steps. Based on recursive splits the problem is divided into several sub-problems, but with increasing recursion depth more run time is invested. By this an initial solution is determined very fast. The core of the method is a second step, where a very powerful greedy algorithm is applied to refine the partitions. Experimental results are given that compare the new approach to state-of-the-art tools. The experiments show that the new approach outperforms the standard techniques with respect to run time and quality. Furthermore, the memory usage is very low and is reduced in comparison to other methods by more than a factor of four.