Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Utility of Linkage Disequilibrium as a Statistic for Identifying Targets of Positive Selection in Nonequilibrium Populations

A critically important challenge in empirical population genetics is distinguishing neutral nonequilibrium processes from selective forces that produce similar patterns of variation. We here examine the extent to which linkage disequilibrium (i.e., nonrandom associations between markers) improves this discrimination. We show that patterns of linkage disequilibrium recently proposed to be unique to hitchhiking models are replicated under nonequilibrium neutral models. We also demonstrate that jointly considering spatial patterns of association among variants alongside the site-frequency spectrum is nonetheless of value. Through a comparison of models of equilibrium neutrality, nonequilibrium neutrality, equilibrium hitchhiking, nonequilibrium hitchhiking, and recurrent hitchhiking, we evaluate a linkage disequilibrium (LD) statistic (ωmax) that appears to have power to identify regions recently shaped by positive selection. Most notably, for demographic parameters relevant to non-African populations of Drosophila melanogaster, we demonstrate that selected loci are distinguishable from neutral loci using this statistic.
Is There a Clash of Civilizations? Evidence from Patterns of International Conflict Involvement, 1946-97

This article offers an empirical test of Huntington's thesis in The Clash of Civilizations. Huntington argues that states belonging to different civilizations will have a higher propensity to be involved in international conflict. This effect should be more prominent in the post-Cold War period. The civilization factor should also interact with membership in different Cold War blocs, border contiguity, regime type, and levels of modernization, magnifying or depressing the basic effects of these variables. To test these hypotheses, a logit specification with King & Zeng's solution for rareness of events is used on the Kosimo data. The Kosimo data allow for an extension of the empirical analysis from both a temporal and a substantive point of view. This study shows that state interactions across the civilizational divide are not more conflict prone. The first eight years of the post-Cold War era also fail to give support to Huntington's thesis. Moreover, while the civilization factor modifies the effects of border contiguity and regime type, this is not sufficient to generate conditions under which differences in civilizational heritage are associated with greater risks of conflict.
Fungal cell‐wall lytic enzymes, antifungal metabolite(s) production, and characterization from Streptomyces exfoliatus MT9 for controlling fruit‐rotting fungi

An antifungal actinomycete strain MT9 was isolated from Loktak Lake, Manipur, India and its cultural characteristics, fatty acid methyl ester, 16S rRNA gene analysis suggests that strain MT9 is identical to Streptomyces exfoliatus. Strain MT9 displayed strong and broad‐spectrum antagonism towards several fruit‐rotting fungi by mycelial growth suppression. Crude fungal cell‐wall lytic enzymes, i.e., chitinase, β‐1,3‐glucanase, and protease produced by S. exfoliatus MT9 were optimally active at pH 8.0 and 50 °C, pH 5.0 and 60 °C, pH 9.0 and 70 °C, respectively. All three mycolytic enzymes had good stability over a wide pH range of 5.0–10.0, with protease being more thermostable than both chitinase and β‐1,3‐glucanase. Interestingly zymogram analysis revealed that S. exfoliatus MT9 secretes six distinct chitinase isoenzymes with approximate molecular weights of 9.42, 13.93, 27.87, 36.43, 54.95, 103.27 kDa, six active protease isoenzymes with apparent molecular weights of 12.45, 30.20, 37.45, 46.32, 52.46, 131.46 kDa, and an active band of 119.39 kDa as β‐1,3‐glucanase enzyme. Extracellular fluid and its organic solvent extracts also exhibited inhibitory activity to various fruit‐rotting fungi. The MIC value of n‐butanol extract was 2–25 µg/ml against tested fruit‐rotting fungi. Antifungal secondary metabolite(s) was found to be polyene in nature. To the best of our knowledge, this is the first report on extracellular production of fungal cell‐wall lytic enzymes and antifungal metabolites by bioactive S. exfoliatus MT9 under submerged fermentation.
Mining social networks of open source CVE coordination

Coordination is one central tenet of software engineering practices and processes. In terms of software vulnerabilities, coordination is particularly evident in the processes used for obtaining Common Vulnerabilities and Exposures (CVEs) identifiers for discovered and disclosed vulnerabilities. As the central CVE tracking infrastructure maintained by the non-profit MITRE Corporation has recently been criticized for time delays in CVE assignment, almost an ideal case is available for studying software and security engineering coordination practices with practical relevance. Given this pragmatic motivation, this paper examines open source CVE coordination that occurs on the public oss-security mailing list. By combining social network analysis with a data-driven, exploratory research approach, the paper asks six data mining questions with practical relevance. By contemplating about answers to the questions asked by means of descriptive statistics, the paper consequently contributes not only to the contemporary industry debates, but also to the tradition of empirical vulnerability research. The perspective and the case are both novel in this tradition, thus opening new avenues for further empirical inquiries and practical improvements for the contemporary CVE coordination.
Réseaux de neurones et algorithmes génétiques : application à la modélisation et à l'optimisation de séchoirs industriels

L'optimisation de sechoirs necessite deux types d'outils pour, dans un premier temps, representer efficacement le comportement du systeme et, par la suite, optimiser simultanement sa structure, ses dimensions et ses parametres de fonctionnement. Dans cette these, une nouvelle approche globale d'optimisation est developpee. Les reseaux de neurones artificiels y sont utilises pour representer efficacement les phenomenes physiques apparaissant lors du sechage et les algorithmes genetiques permettent d'optimiser differents problemes. L'approche est validee sur deux exemples de sechoirs industriels convectifs. Les applications developpees dans cette these sortent du champ de competences classique des reseaux de neurones en permettant la representation des resultats fournis par un modele de sechage mathematique. Pour une meme precision, les rn offrent ainsi la possibilite de diminuer les temps de simulations dans des rapports variant de 100 a 1000 par rapport a des approches plus classiques (differences finies, methode pre-integree). Par ailleurs, il devient possible de controler le niveau de connaissances sur le processus ou sur le produit a traiter pendant la constitution de la representation neuronale. Enfin, l'application simultanee de la representation neuronale et de la recherche par algorithme genetique nous a permis de mener une approche d'optimisation globale multi-criteres sur des installations de sechage. L'application finale utilise les capacites de chacun de ces outils afin de determiner les parametres de conception et de conduite des benefice). Cette approche permet aussi d'aboutir a des solutions technologiques adaptees aux contraintes imposees par l'environement industriel. De plus, la globalite du probleme traite nous permet de nous affranchir de la demarche lineaire et reductrice generalement utilisee pendant la phase de conception d'un systeme : les solutions obtenus sont par ce fait plus riche et plu representatives. Les outils et la demarche developpes dans ce travail se tournent resolement vers une approche de c. A. O. (conception assistee par ordinateur) utilisable pour etudier de nombreux systemes industriels complexes.
Key Strategies to Further Reduce Stunting in Southeast Asia: Lessons from the ASEAN Countries Workshop

Background To further reduce stunting in Southeast Asia, a rapidly changing region, its main causes need to be identified. Objective Assess the relationship between different causes of stunting and stunting prevalence over time in Southeast Asia. Methods Review trends in mortality, stunting, economic development, and access to nutritious foods over time and among different subgroups in Southeast Asian countries. Results Between 1990–2011, mortality among under-five children declined from 69/1,000 to 29/1,000 live births. Although disease reduction, one of two direct causes of stunting, has played an important role which should be maintained, improvement in meeting nutrient requirements, the other direct cause, is necessary to reduce stunting further. This requires dietary diversity, which is affected by rapidly changing factors: economic development; urbanization, giving greater access to larger variety of foods, including processed and fortified foods; parental education; and modernizing food systems, with increased distance between food producers and consumers. Wealthier consumers are increasingly able to access a more nutritious diet, while poorer consumers need support to improve access, and may also still need better hygiene and sanitation. Conclusions In order to accelerate stunting reduction in Southeast Asia, availability and access to nutritious foods should be increased by collaboration between private and public sectors, and the Association of Southeast Asian Nations (ASEAN) can play a facilitating role. The private sector can produce and market nutritious foods, while the public sector sets standards, promotes healthy food choices, and ensures access to nutritious foods for the poorest, e.g, through social safety net programs.
Positive selection of cytotoxic T lymphocyte escape variants during acute hepatitis C virus infection

Cellular immune responses are induced during hepatitis C virus (HCV) infection and acute‐phase CD8+ T cells are supposed to play an important role in controlling viral replication. In chimpanzees, failure of CD8+ T cells to control HCV replication has been associated with acquisition of mutations in MHC class I‐restricted epitopes. In humans, although selection of escape mutations in an immunodominant CTL epitope has been recently described, the overall impact of immune escape during acute HCV infection is unclear. Here, by performing an in depth analysis of the relationship between early cellular immune responses and viral evolution in a chronically evolving HCV acutely infected individual, we demonstrate: (i) the presence of a potent and focused CD8+ T cell response against a novel epitope in the NS3 protein, (ii) the elimination of the quasi‐species harboring the original amino acid sequence within this epitope, and (iii) the selection for a virus population bearing amino acid changes at a single residue within the cytotoxic T cell epitope that strongly diminished T cell recognition. These results support the view that acute‐phase CD8+ T cell responses exert a biologically relevant pressure on HCV replication and that viruses escaping this host response could have a significant survival advantage.
Association of PAX2 with Cell Apoptosis in Unilateral Ureteral Obstruction Rats

Abstract Renal interstitial fibrosis (RIF) is the final common pathway for chronic kidney disease. Cell apoptosis is a critical detrimental event that leads to renal fibrosis. Paired box 2 (PAX2) plays a major role in the development of the kidney. This study was performed to investigate whether PAX2 was associated with cell apoptosis in the progression of RIF in unilateral ureteral obstruction (UUO) rats. Eighty Wistar male rats were divided into two groups randomly: sham operation group (SHO) and model group subjected to UUO (GU), n = 40, respectively. The model was established by left ureteral ligation. Renal tissues were collected 14 and 28 days after surgery. Protein expressions of PAX2, transforming growth factor-β1 (TGF-β1), α-smooth muscle actin (α-SMA), collagen-IV (Col-IV), fibronectin (FN), and caspase-3 were detected using immunohistochemical analysis; mRNA expression of PAX2 in renal tissue was detected by real-time reverse transcription polymerase chain reaction; and RIF index and cell apoptosis index in renal interstitium were also calculated. When compared with those in the SHO group, expressions of PAX2 (protein and mRNA) were markedly increased in the GU group (each p < 0.01). Protein expressions of TGF-β1, α-SMA, Col-IV, FN, and caspase-3 and RIF index and cell apoptosis index in the GU group were remarkably increased when compared with those in the SHO group (each p < 0.01). The protein expression of PAX2 was positively correlated with the protein expressions of TGF-β1, α-SMA, Col-IV, FN, and caspase-3 and with RIF index and cell apoptosis index (all p < 0.01). The apoptotic cell in our observation was mainly derived from renal tubular epithelial cells. In conclusion, the increased expression of PAX2 is associated with cell apoptosis in the progression of RIF in UUO rats, suggesting that PAX2 is a potentially therapeutic target for prevention of RIF. Tian-Biao Zhou and Yuan-Han Qin wish it to be known that, in their opinion, they should be regarded as joint first authors.
The case for development of a new test of health literacy.

PURPOSE/OBJECTIVES To review the need for reading assessments for patients with cancer, review existing reading assessment tools, and make a case for a new tool specific to patients with cancer. DATA SOURCES Published articles, experiences, and discussions with published authors in the field of literacy. DATA SYNTHESIS Valid and reliable tools that assess word recognition and comprehension exist for general use in health care. Word-recognition tests do not always predict comprehension, and a commonly used comprehension test has sections assessing only very low, second year of high school, and graduate-level skills. CONCLUSIONS A new tool, developed specifically for patients with cancer, may better capture reading ability and comprehension. It is being evaluated for use in a clinical setting. IMPLICATIONS FOR NURSING If nurses know their patients' reading levels, they can plan more effectively for teaching self-care and discussing decision making. Outcomes related to health and satisfaction may improve if poor readers are given materials they can understand.
Determination of cocaine and heroin with their respective metabolites in meconium by gas chromatography‐mass spectrometry

The analysis of meconium specimens is a relatively accurate method for the detection of fetal exposure to drugs. The purpose of this study was to develop and validate a method for meconium sample preparation for a gas chromatography‐mass spectrometry (GC‐MS) confirmation of meconium extracts for cocaine, benzoylecgonine, codeine, morphine and 6‐monoacetylmorphine. The analytes were initially extracted from the matrix by methanol. Subsequently a solid‐phase extraction with Waters Oasis® HLB cartridges was applied. Analytes were determined in GC‐MS single monitoring mode. The method was validated in the range 40–2000 ng g−1 using 0.5 g of meconium per assay. The detector response was linear over the studied range, and limits of quantitation and detection were found to be acceptable. Intra‐ and inter‐batch coefficients of variation oscillated between 2.54% and 20.5%, and mean relative errors were in the range 0.79%–19.9%. The recoveries were higher than 42.1% in all cases. Finally the method was applied to analysis of meconium in newborns to assess fetal exposure to cocaine and opiates. Copyright © 2007 John Wiley & Sons, Ltd.
PDF optimized parametric vector quantization of speech line spectral frequencies

A computationally efficient, high quality, vector quantization scheme based on a parametric probability density function (PDF) is developed for encoding speech line spectral frequencies (LSF). For this purpose, speech LSFs are modeled as i.i. d realizations of a multivariate normal mixture density. The mixture model parameters are efficiently estimated from the training data using the expectation maximization (EM) algorithm. The estimated density is suitably quantized using transform coding and bit-allocation techniques for both fixed rate and variable rate systems. Source encoding using the resultant codebook involves no searches and its computational complexity is minimal and independent of the rate of the system. Experimental results show that the proposed scheme provides 2-3 bits gain over conventional MSVQ schemes. The proposed memoryless quantizer is enhanced to form a quantizer with memory. The quantizer with memory provides transparent quality speech at 20 bits/frame.
Synthesized Compact Models and Experimental Verifications for Substrate Noise Coupling in Mixed-Signal ICs

A synthesized compact modeling (SCM) approach for substrate coupling analysis is presented. The SCM is formulated using a scalable Z matrix approach for heavily doped substrates with a lightly doped epitaxial layer and using a nodal lumped resistance approach for lightly doped substrates. The SCM models require a set of process-dependent fitting coefficients and incorporate geometrical parameters of the substrate ports in a compact form that includes size, perimeter, and separation defined using the geometric mean distance to accommodate both far-field and near-field effects. The SCM approach is verified based on measurement data from two test chips, one in a custom lightly doped process and the other one using a 0.18-mum BiCMOS lightly doped foundry process. The model accuracy is shown to be within 15% compared to measured data extracted from the test patterns. The SCM is exploited with application examples to show substrate model generation efficiency and accuracy at different levels of complexity, including a full chip substrate noise distribution analysis for a 2 mm by 2 mm chip with 319 substrate contacts
Guides nanophotoniques III-V/polymère

Les composants photoniques peuvent s'etendre sur des longueurs allant jusqu'a plusieurs centimetres. Ceci est vrai aussi bien dans le cas de composants actifs et passifs tels que les filtres ou les (de)multiplexeurs que pour l'ensemble des interconnexions optiques. Pour reduire la taille des circuits photoniques integres, il est necessaire de faire appel a des guides d'onde optiques monomodes presentant un fort confinement lie a un contraste d'indices eleve des structures. Les dimensions laterales de ces guides sont alors typiquement inferieures a 500 nm. C'est dans cette optique que nous presentons une etude numerique de ces guides dans le but notamment d'ameliorer l'injection de la lumiere. Le fort confinement est realise par le biais d'un fil optique a base de GaAs insere dans une matrice polymere (fig.1) dont nous presentons les differentes etapes technologiques necessaires a leur realisation. Il est alors technologiquement envisageable d'incorporer au sein du circuit des fonctions de multiplexage par l'intermediaire de reseaux de Bragg.
Life in a Pill Bottle: The Experience of Taking HIV Medications

The purpose of this phenomenological study was to describe the experience of taking HIV medications (HAART) and identify factors affecting adherence. Participants were 10 middle-aged and older (35 to 58) HIV-positive adults (four homosexual men and six women with a history of substance abuse) who were asked to describe the daily experience of taking HAART. The metaphor that emerged from the data was Life In a Pill Bottle, which reflected the central focus of HAART in participants’ lives and also described the complex relationships that evolved between and among the person, the medications, and the virus. Three themes comprised the experience: commitment versus perseverance, feeling bad, and healing helpers. Similarities and differences were noted between men and women.
Safety and pharmacokinetics of rimantadine small-particle aerosol

The safety and pharmacokinetics of rimantadine administered by small-particle aerosol were assessed in healthy adults and adults with acute influenza virus infection. Aerosolized rimantadine delivered at a concentration of 40 micrograms/liter of air was associated with nasal burning and irritation in normal volunteers. A concentration of 20 micrograms/liter of air was well tolerated for up to 12 h by normal volunteers and was not associated with any changes in pulmonary function, as measured by routine spirometry, plethysmography, or diffusion capacity of carbon monoxide. Mean peak levels of drug in serum were approximately 10-fold lower after 12 h of aerosol administration than they were after oral administration of 200 mg (29.7 versus 255 ng/ml, respectively), while mean nasal wash levels were approximately 100-fold higher (6,650 versus 66.6 ng/ml, respectively). Elimination half-lives were similar after both aerosol and oral administration (24.1 and 25.2 h, respectively), and rimantadine urinary excretion was less than 1% per 24 h in both groups. Twenty micrograms of aerosolized rimantadine per liter of air given 12 h daily for 3 days to nine adults with acute influenza virus infection was well tolerated. Levels in plasma after 12 h of aerosol inhalation were similar to those in normal volunteers, but were higher at the end of the third treatment than they were at the end of the first treatment (88.3 versus 47.9 ng/ml, respectively). Thus, rimantadine delivered via small-particle aerosol at a dose of 20 micrograms/liter of air was well tolerated in normal volunteers and in those with acute influenza and was associated with high local concentrations.
Spin Injection and Detection in Semiconductors—Electrical Issues and Device Aspects

Spin selectivity has already been demonstrated for both injection and (recently) detection contacts on semiconductors, but a clear demonstration of a magnetoresistance signal is still lacking. After outlining the various categories of device proposals and the associated choice of semiconductor material, we summarize the various injection contact technologies that have been reported and assess their potential for practical device applications in terms of electrical efficiency, bias dependence (both intrinsic and extrinsic), and performance in unipolar devices. We then focus on the design of an all-electrical injection-detection device in GaAs and demonstrate that a correct design of the semiconductor channel and contact regions is the key for preserving the spin sensitivity that is provided by the contacts