Miracle-dz/UniFAR-FTUs huggingface dataset:
Population Genetic Structure of Clinical and Environmental Isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers

ABSTRACT Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n=112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and α-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species.
Particle size analysis: AAPS workshop report, cosponsored by the Food and Drug Administration and the United States Pharmacopeia

The concepts of particle engineering and dosage form design have become dominant themes in pharmaceutical manufacturing. This trend is not simply a reflection of the development of new, more sophisticated manufacturing methods of particles or dispersed systems but also recognition of the importance of quality control even in more traditional manufacturing processes. However, the diversity of particle treatments, methods of particle size analysis, expression and interpretation of data, and process applications results in complicated and sometimes confusing criteria for selection, adoption, or relevance of the available techniques.
Microwave remote sensing of multi-layered rough-surface snow-covered sea ice dielectric profile: Sensitivity analysis and inversion

The goal of this paper is to investigate the sensitivity of the normalized radar cross section data collected from a given arctic profile of interest with respect to snow and ice complex permittivities and their thickness values. To calculate this sensitivity, the recently-developed boundary perturbation theory is used as a forward scattering solver. This sensitivity analysis is then used to set some guideline for appropriate data collection schemes to be used for arctic dielectric profile inversion. Finally, the inversion of two different data sets having different sensitivities to the unknown model parameters are presented and compared.
Negotiation of identity in group therapy for aphasia: the Aphasia Café.

BACKGROUND There has been increasing interest in ensuring that aphasia intervention includes attention to the negotiation of a robust identity after the life-altering changes that often accompany the onset of aphasia. But how does one go about simultaneously improving communication and positive identity development within aphasia therapy? Socially oriented group therapy for aphasia has been touted as one means of addressing both psychosocial and communicative goals in aphasia. AIMS This article describes the results of a sociolinguistic analysis of group therapy for aphasia in which positive personal and group identity are skilfully negotiated. METHODS & PROCEDURES Sociolinguistic microanalysis of discourse in a group therapy session was undertaken. The session, described as group conversation therapy, included eight adults with aphasia, a speech-language pathologist and an assistant. The session was videotaped and transcribed, and the data were analysed to identify 'indices of identity' within the discourse. This included discourse that exposed members' roles, values or beliefs about themselves or others. The data were further analysed to identify 'patterns' of discourse associated with identity. The result is a detailed description of identity-enhancing discourse within group therapy for aphasia. OUTCOMES & RESULTS The findings included several categories associated with the negotiation of identity in therapy including: (1) discourse demonstrating that group members were 'being heard', (2) that the competence of group members was assumed, (3) that 'solidarity' existed in the group, (4) that saving face and promoting positive personal identity was important, and (5) that markers of group identity were made visible via discourse that referenced both member inclusion as well as non-member exclusion. CONCLUSIONS & IMPLICATIONS The results suggest that it is possible to create identity-enhancing interactions as part of therapy for aphasia; the analysis demonstrates the potential role of the group leader/clinician in managing identity negotiation in aphasia therapy.
A decoupling calibration method based on genetic algorithm for three dimensional electric field sensor

The accuracy of three dimensional (3D) electric field measurements is seriously affected by coupling interferences. In order to obtain precise measurements, this paper proposes a decoupling calibration method based on genetic algorithm (GA) for 3D electric field sensors. Compared with previous methods based on the matrix inversion technology, this method utilizes GA to obtain an optimal calibration matrix directly, which avoids the calculation errors in the matrix inversion. Comparison experiments with matrix inversion technology and this method are conducted. Experimental results show that the proposed calibration method can effectively eliminate coupling interferences, improve the calibration precision and realize accurate measurements.
Inhibition of TPA‐induced NF‐κB nuclear translocation and production of NO and PGE2 by the anti‐rheumatic gold compounds

Auranofin, aurothioglucose and aurothiomalate (10 μM each) inhibited 12‐O‐tetradecanoylphorbol 13‐acetate (TPA, 16.2 nM)‐induced nuclear translocation of nuclear factor‐kappa B (NF‐κB), and production of nitric oxide (NO) and prostaglandin E2 (PGE2) in rat peritoneal macrophages when the cells were pre‐incubated with each gold compound for 20h. Without pre‐incubation for 20h, aurothioglucose and aurothiomalate, but not auranofin, failed to inhibit the TPA‐induced NF‐κB nuclear translocation and production of NO and PGE2. Auranofin, aurothioglucose and aurothiomalate did not affect the direct binding of NF‐κB to the DNA probe. It was suggested that these gold compounds inhibit the TPA‐induced production of NO and PGE2 by inhibiting the NF‐κB nuclear translocation.
Identical twins and Bayes' theorem in the 21st century

In an article in Science on "Bayes' Theorem in the 21st Century", Bradley Efron uses Bayes' theorem to calculate the probability that twins are identical given that the sonogram shows twin boys. He concludes that Bayesian calculations cannot be uncritically accepted when using uninformative priors. While we agree that the choice of the prior is essential, we argue that the calculations on identical twins give a biased impression of the influence of uninformative priors in Bayesian data analyses.
Adaptive Immunity Restricts Replication of Novel Murine Astroviruses

ABSTRACT The mechanisms of astrovirus pathogenesis are largely unknown, in part due to a lack of a small-animal model of disease. Using shotgun sequencing and a custom analysis pipeline, we identified two novel astroviruses capable of infecting research mice, murine astrovirus (MuAstV) STL1 and STL2. Subsequent analysis revealed the presence of at least two additional viruses (MuAstV STL3 and STL4), suggestive of a diverse population of murine astroviruses in research mice. Complete genomic characterization and subsequent phylogenetic analysis showed that MuAstV STL1 to STL4 are members of the mamastrovirus genus and are likely members of a new mamastrovirus genogroup. Using Rag1 −/− mice deficient in B and T cells, we demonstrate that adaptive immunity is required to control MuAstV infection. Furthermore, using Stat1 −/− mice deficient in innate signaling, we demonstrate a role for the innate immune response in the control of MuAstV replication. Our results demonstrate that MuAstV STL permits the study of the mechanisms of astrovirus infection and host-pathogen interactions in a genetically manipulable small-animal model. Finally, we detected MuAstV in commercially available mice, suggesting that these viruses may be present in academic and commercial research mouse facilities, with possible implications for interpretation of data generated in current mouse models of disease.
Extraction of pulmonary vessels from MDCT thorax scans

This paper considers problem of pulmonary vessels identification in MDCT thorax scans. Specifically, the method for vessels segmentation is proposed. The introduced method is 3D region growing approach were growth of the region is guided and constrained by results of random walk segmentation applied to consecutive CT slices. The main steps of the proposed approach are described. Results of vessel segmentation from exemplary MDCT datasets provided by the introduced method are presented and discussed.
Band selection for hyperspectral images based on impurity function

Band selection for hyperspectral images is an effective technique to mitigate the curse of dimensionality. A variety of band selection methods have been suggested in the past. This paper presents a novel band prioritization based on impurity function (IF) for the band selection of hyperspectral images. The proposed IF band selection (IFBS) is incorporated with particle swarm optimization (PSO) band selection which has been developed to effectively group highly correlated bands of hyperspectral images into high corrected modules. It uses a particle swarm optimization scheme, which is a well-known method to solve the optimization problems, to develop an effective feature extraction algorithm for hyperspectral imagery. After PSO method is applied to the band reduction of hyperspectral images, the proposed IFBS is applied to enhance the efficiency of band selection. The propose method is evaluated by MODIS/ASTER airborne simulator (MASTER) for land cover classification during the Pacrim II campaign. The performance of IFBS is validated by the supervised k-nearest neighbor (KNN) classifier. Experimental results demonstrate that the proposed IFBS approach is an effective method for dimensionality reduction and feature extraction. Compared to other band selection methods, IFBS can effectively select the most significant bands for the image classification of hyperspectral images.
A UML-extended Approach for Mining OLAP Data Cubes in Complex Knowledge Discovery Environments

In this paper, we propose theoretical assertions and practical instances of an innovative UML-extended approach for mining OLAP data cubes in complex knowledge discovery environments. This analytical contribution is further extended by means of a comprehensive set of case studies that clearly demonstrate the feasibility and the benefits of the proposed approach in the context of next generation DataWarehousing/Data-Mining platforms.
The effect of heat addition on slightly compressible flow: The example of vortex pair motion

The effect of a point heat source on the two‐dimensional irrotational flow of a slightly compressible nonviscous and nondiffusive fluid is studied. Heat is added at a constant rate and with a prescribed spatial distribution. The Mach number M is assumed small and the governing equations are solved to order M2 by a generalization of the Rayleigh–Janzen expansion. The interaction between entropy variations produced by the heat source and the pressure field generates a wake consisting of a vortex sheet and a dipole sheet extending downstream of the heat source, and this in turn perturbs the flow at order M2. A general result is that if heat is added where the gas is compressed by the flow, the impulse directed against the free stream is increased and vice versa. Cross‐stream impulse is produced if the heat source is not on the axis of symmetry (if any) of the flow. This would result in a lifting force if a cylinder is providing the perturbation to the free stream. When heat is added on the downstream dividin.
Factors Predictive of Postoperative Morbidity and Cost in Patients With Endometrial Cancer

OBJECTIVE: To identify patient characteristics and perioperative factors predictive of 30-day morbidity and cost in patients with endometrial carcinoma. METHODS: Data of consecutive patients treated with hysterectomy for endometrial carcinoma between 1999 and 2008 were collected prospectively. Thirty predictors were chosen from more than 130 collected based on anticipated clinical relevance and prevalence (more than 3%). Complications were graded per the Accordion Classification. Multivariable models were developed using stepwise and backward variable selection methods. Thirty-day cost analyses were expressed in 2010 Medicare dollars. RESULTS: Of 1,369 patients, significant predictors (P<.01) of grade 2 and higher morbidity included American Society of Anesthesiologists physical status classification system class higher than 2 (odds ratio [OR] 2.1), preoperative white blood count (OR 2.1 per doubling), history of deep vein thrombosis (OR 2.1), pelvic and para-aortic lymphadenectomy (OR 2.3 compared with no lymphadenectomy), laparotomy (OR 2.8 compared with minimally invasive surgery), myometrial invasion more than 50% (OR 2.4), operating time (OR 1.9 per doubling), and grade 4 surgical complexity (OR 2.7 compared with grade 1). After controlling for patient factors in a multivariable model, laparotomy, pelvic, and para-aortic lymphadenectomy were associated with significant increases in cost compared with the use of minimally invasive surgery or hysterectomy alone. CONCLUSION: This analysis identifies patient and perioperative care factors predictive of 30-day morbidity and cost. These data are useful for preoperative counseling, for defining equitable reimbursement and factors critical for risk-adjustment when comparing outcomes, and for identifying areas for quality improvement in patients with endometrial carcinoma. Given the marked increases in morbidity and cost associated with laparotomy and lymphadenectomy, minimally invasive surgery and selective lymphadenectomy should be standard treatment for patients with endometrial carcinoma. LEVEL OF EVIDENCE: II
The Copenhagen School Health Records Register

Introduction: The Copenhagen School Health Records Register is an electronic register of health examination information on 372,636 children who attended school in Copenhagen, Denmark from 1936 to 2005. Content: The register contains serial measurements of height and weight as well as birth weight from 1942 onwards. Through unique personal identification numbers, linkages are possible to national registers and population studies. Validity and coverage: Measurements were recorded in the health records with precision. Virtually every schoolchild is included in the register. Conclusion: The unique qualities of the size, population-based nature and linkage possibilities of the cohort make it an invaluable resource for research.
A Phylogenetic Study of Cuphea (Lythraceae) Based on Morphology and Nuclear Rdna ITS Sequences

Abstract Cuphea is an endemic genus of the New World and the most speciose member of the Lythraceae with ca. 260 species classified in two subgenera and 13 sections. As a first attempt to construct a phylogenetic framework for the genus, data from morphology and nuclear ITS sequences for 53 species and four outgroup taxa were analyzed. Independent results employing morphological and molecular datasets confirmed Cuphea as monophyletic with Pleurophora as sister. The morphological strict consensus tree was substantially unresolved. The ITS parsimony and maximum likelihood phylogenies indicated South America as the initial center of diversification and identified a deep trichotomy, one branch of which was equivalent to subg. Cuphea. The ITS analyses also recognized seven well-supported clades, each composed of members from two to four taxonomic sections. Species of section Melvilla appear in five of the seven clades, supporting the hypothesis that the large, intensely-colored, bird-pollinated floral tubes that define the section are convergent, having evolved from smaller, more promiscuously-pollinated, green-tubed flowers. Sixteen endemic North American species have a single South American origin and form the core of a secondary center of Cuphea diversification in Mexico. The ITS analyses provide initial phylogenetic hypotheses for the genus that clarify relationships previously obscured by the highly homoplastic nature of the morphological taxonomic characters.
A simple method to retrospectively estimate patient dose-area product for chest tomosynthesis examinations performed using VolumeRAD.

PURPOSE The purpose of the present work was to develop and validate a method of retrospectively estimating the dose-area product (DAP) of a chest tomosynthesis examination performed using the VolumeRAD system (GE Healthcare, Chalfont St. Giles, UK) from digital imaging and communications in medicine (DICOM) data available in the scout image. METHODS DICOM data were retrieved for 20 patients undergoing chest tomosynthesis using VolumeRAD. Using information about how the exposure parameters for the tomosynthesis examination are determined by the scout image, a correction factor for the adjustment in field size with projection angle was determined. The correction factor was used to estimate the DAP for 20 additional chest tomosynthesis examinations from DICOM data available in the scout images, which was compared with the actual DAP registered for the projection radiographs acquired during the tomosynthesis examination. RESULTS A field size correction factor of 0.935 was determined. Applying the developed method using this factor, the average difference between the estimated DAP and the actual DAP was 0.2%, with a standard deviation of 0.8%. However, the difference was not normally distributed and the maximum error was only 1.0%. The validity and reliability of the presented method were thus very high. CONCLUSIONS A method to estimate the DAP of a chest tomosynthesis examination performed using the VolumeRAD system from DICOM data in the scout image was developed and validated. As the scout image normally is the only image connected to the tomosynthesis examination stored in the picture archiving and communication system (PACS) containing dose data, the method may be of value for retrospectively estimating patient dose in clinical use of chest tomosynthesis.
Soft error reliability improvements for implantable medical devices

As the expectations of physicians and patients have matured, the desire to utilize advanced CMOS technologies to provide increasingly sophisticated therapeutic and diagnostic capabilities has grown. This has pushed the high reliability implantable device business into the use of processes that are much more susceptible to soft error events than in the past. This paper discusses experimental and modeling results of logic upsets in a 0.25 mum CMOS IC process.
So Fair a House

Archaeologists have proposed that quite a number of structures dating to the Pre-Pottery Neolithic A and B in southwest Asia were nondomestic ritual buildings, sometimes described specifically as temples or shrines, and these figure large in some interpretations of social change in the Near Eastern Neolithic. Yet the evidence supporting the identification of cult buildings is often equivocal or depends on ethnocentric distinctions between sacred and profane spaces. This paper explores the case of Göbekli Tepe, a large Pre-Pottery Neolithic site in Turkey that its excavator claims consisted only of temples, to illustrate weaknesses in some kinds of claims about Neolithic sacred spaces and to explore some of the problems of identifying prehistoric ritual. Consideration of the evidence suggests the alternative hypothesis that the buildings at Göbekli Tepe may actually be houses, albeit ones that are rich in symbolic content.
Ischemic Preconditioning: Triggering Role of Nitric Oxide-Derived Oxidants in Isolated Hearts

There is evidence that oxidants generated during ischemic preconditioning (IPC) trigger or mediate cardioprotection. We examined whether a causal relationship exists between oxidant formation during ischemic preconditioning and cardioprotection. We monitored formation of dityrosine in crystalloid-perfused guinea pig isolated hearts after a preconditioning protocol and after prolonged ischemia. Superoxide dismutase, catalase, and glutathione (SCG), or the l-arginine analogue NGnitro l-arginine methyl ester (l-NAME) were given during preconditioning. Dityrosine was observed in the coronary effluent immediately after both stimuli, but not after bracketing with SCG or l-NAME. After prolonged ischemia, dityrosine was significantly lower in the IPC group than in other groups. IPC was evidenced by improved mechanical and metabolic function on reperfusion, and by reduced infarction. These effects were abrogated by either SCG or l-NAME. These data support the hypothesis that the formation of nitric oxide-derived oxidants during ischemic preconditioning is causally related to myocardial adaptation to reperfusion injury.