Miracle-dz/UniFAR-FTUs huggingface dataset:
Assisted reproductive technology and major structural birth defects in the United States.

BACKGROUND With >1% of US births occurring following use of assisted reproductive technology (ART), it is critical to examine whether ART is associated with birth defects. METHODS We analyzed data from the National Birth Defects Prevention Study, a population-based, multicenter, case-control study of birth defects. We included mothers of fetuses or live-born infants with a major birth defect (case infants) and mothers who had live-born infants who did not have a major birth defect (control infants), delivered during the period October 1997-December 2003. We compared mothers who reported ART use (IVF or ICSI) with those who had unassisted conceptions. Multiple logistic regression was used to adjust for the following confounders: maternal race/ethnicity, maternal age, smoking and parity; we stratified by plurality. RESULTS ART was reported by 1.1% of all control mothers, and by 4.5% of control mothers 35 years or older. Among singleton births, ART was associated with septal heart defects (adjusted odds ratio [aOR] = 2.1, 95% confidence intervals [CI] 1.1-4.0), cleft lip with or without cleft palate (aOR = 2.4, 95% CI 1.2-5.1), esophageal atresia (aOR = 4.5, 95% CI 1.9-10.5) and anorectal atresia (aOR = 3.7, 95% CI 1.5-9.1). Among multiple births, ART was not significantly associated with any of the birth defects studied. CONCLUSIONS These findings suggest that some birth defects occur more often among infants conceived with ART. Although the mechanism is not clear, couples considering ART should be informed of all potential risks and benefits.
Crohn Disease: mural attenuation and thickness at contrast-enhanced CT Enterography--correlation with endoscopic and histologic findings of inflammation.

PURPOSE To determine retrospectively if quantitative measures of small-bowel mural attenuation and thickness at computed tomographic (CT) enterography correlate with endoscopic and histologic findings of small-bowel inflammation and to estimate the performance of these measures in predicting inflammatory Crohn disease. MATERIALS AND METHODS The institutional review board approved this HIPAA-compliant retrospective study, which was conducted with patient informed consent. CT enterography data in 96 patients (31 male patients and 65 female patients) who underwent ileoscopy with or without biopsy were examined for CT signs of active Crohn disease. The most highly enhancing segment of terminal ileum and a normal-appearing ileal loop were identified. After it was confirmed that semiautomated software could accurately measure mural attenuation and thickness, the selected terminal ileal and normal-appearing (control) ileal loops were examined (20 automated measurements at each location) to quantify mural attenuation and wall thickness. Results were compared with endoscopy and histology reports by using logistic regression analysis and receiver operating characteristic curves. RESULTS Quantitative measures of terminal ileal mural attenuation and wall thickness correlated significantly with active Crohn disease (P < .001). Small-bowel wall thickness was not a significant factor after attenuation was taken into account. A threshold attenuation value with a sensitivity of 90% (18 of 20) for definite Crohn disease (compared with a sensitivity of 80% [16 of 20] for radiologist assessment) was selected. In patients who underwent ileal biopsy, threshold attenuation had a sensitivity identical to that of ileoscopy (81% [26 of 32]; 95% confidence interval: 64%, 93%) in predicting histologic inflammation. CONCLUSION Quantitative measures of mural attenuation and wall thickness at CT enterography correlate highly with ileoscopic and histologic findings of inflammatory Crohn disease. Quantitative measures of mural attenuation are sensitive markers of small bowel inflammation.
Two clinical phenotypes in polycythemia vera.

BACKGROUND Polycythemia vera is the ultimate phenotypic consequence of the V617F mutation in Janus kinase 2 (encoded by JAK2), but the extent to which this mutation influences the behavior of the involved CD34+ hematopoietic stem cells is unknown. METHODS We analyzed gene expression in CD34+ peripheral-blood cells from 19 patients with polycythemia vera, using oligonucleotide microarray technology after correcting for potential confounding by sex, since the phenotypic features of the disease differ between men and women. RESULTS Men with polycythemia vera had twice as many up-regulated or down-regulated genes as women with polycythemia vera, in a comparison of gene expression in the patients and in healthy persons of the same sex, but there were 102 genes with differential regulation that was concordant in men and women. When these genes were used for class discovery by means of unsupervised hierarchical clustering, the 19 patients could be divided into two groups that did not differ significantly with respect to age, neutrophil JAK2 V617F allele burden, white-cell count, platelet count, or clonal dominance. However, they did differ significantly with respect to disease duration; hemoglobin level; frequency of thromboembolic events, palpable splenomegaly, and splenectomy; chemotherapy exposure; leukemic transformation; and survival. The unsupervised clustering was confirmed by a supervised approach with the use of a top-scoring-pair classifier that segregated the 19 patients into the same two phenotypic groups with 100% accuracy. CONCLUSIONS Removing sex as a potential confounder, we identified an accurate molecular method for classifying patients with polycythemia vera according to disease behavior, independently of their JAK2 V617F allele burden, and identified previously unrecognized molecular pathways in polycythemia vera outside the canonical JAK2 pathway that may be amenable to targeted therapy. (Funded by the Department of Defense and the National Institutes of Health.).
Two CDC42 paralogues modulate Cryptococcus neoformans thermotolerance and morphogenesis under host physiological conditions

The precise regulation of morphogenesis is a key mechanism by which cells respond to a variety of stresses, including those encountered by microbial pathogens in the host. The polarity protein Cdc42 regulates cellular morphogenesis throughout eukaryotes, and we explore the role of Cdc42 proteins in the host survival of the human fungal pathogen Cryptococcus neoformans. Uniquely, C. neoformans has two functional Cdc42 paralogues, Cdc42 and Cdc420. Here we investigate the contribution of each paralogue to resistance to host stress. In contrast to non‐pathogenic model organisms, C. neoformans Cdc42 proteins are not required for viability under non‐stress conditions but are required for resistance to high temperature. The paralogues play differential roles in actin and septin organization and act downstream of C. neoformans Ras1 to regulate its morphogenesis sub‐pathway, but not its effects on mating. Cdc42, and not Cdc420, is upregulated in response to temperature stress and is required for virulence in a murine model of cryptococcosis. The C. neoformans Cdc42 proteins likely perform complementary functions with other Rho‐like GTPases to control cell polarity, septin organization and hyphal transitions that allow survival in the environment and in the host.
Creep modeling and creep life estimation of Gr.91

Abstract The creep behavior and deciding factors for creep life have been investigated for Gr.91 in the temperature range between 450 and 725°C. The longest time to rupture was 68755 h. The creep life is inversely proportional to the minimum creep rate multiplied by the increase in creep rate by strain in the acceleration region for a wide range of test temperature and duration. The minimum creep rate depends on both the time to minimum creep rate and the strain to minimum creep rate. The strain to minimum creep rate decreases with decreasing stress, suggesting that the creep deformation in the transient region is significantly inhomogeneous at low stresses. The creep life is correlated with the creep deformation parameters in the transient region so that we can predict the creep life from a short-term creep test for up to the end of transient region, corresponding to less than 30% of the creep life, without any stress extrapolation.
Notes on the quantum tetrahedron

This is a set of notes describing several aspects of the space of paths on ADE Dynkin diagrams, with a particular attention paid to the graph E 6 . Many results originally due to A. Ocneanu are here described in a very elementary way (manipulation of square or rectangular matrices). We recall the concept of essential matrices (intertwiners) for a graph and describe their module properties with respect to right and left actions of fusion algebras. In the case of the graph E 6 , essential matrices build up a right module with respect to its own fusion algebra but a left module with respect to the fusion algebra of A 11 . We present two original results: 1) Our ﬁrst contribution is to show how to recover the Ocneanu graph of quantum symmetries of the Dynkin diagram E 6 from the natural multiplication deﬁned in the tensor square of its fusion algebra (the tensor product should be taken over a particular subalgebra); this is the Cayley graph for the two generators of the twelve dimensional algebra E 6 ⊗ A 3 E 6 (here A 3 and E 6 refer to the commutative fusion algebras of the corresponding graphs). 2) To every point of the graph of quantum symmetries one can associate a particular matrix describing the “ torus structure” of the chosen Dynkin diagram; following Ocneanu, one obtains in this way, in the case of E 6 , twelve such matrices of dimension 11 × 11, one of them is a modular invariant and encodes the partition function of the corresponding conformal ﬁeld theory. Our own next contribution is to provide a simple algorithm for the determination of these matrices. bigebra.
Optical and Structural Characterization of Diffuse Reflectance Standards

In this paper, we describe the optical properties of Labsphere diffuse reflectance standards of different nominal reflectance. Specifically, we analyze their properties of hemispherical total reflectance and angular distribution of scattered light intensity, as function of the angle of incidence and wavelength of a laser beam. Our main objective is to find the difference between the optical behavior of a real diffuser of given average reflectance and that of an ideal Lambertian diffuser. The optical characterizations were carried out by using original methods and apparatus, and were followed by SEM-EDS analysis with the aim to relate the optical properties with the morphological and structural characteristics. The optical characterizations demonstrate that the standards with high nominal total reflectance approach better the Lambertian behavior. This result is confirmed by SEM analysis, showing, for these samples, the most rugged surfaces and a porous material.
Fatigue of Quasi-Isotropic Composite Cylinders under Tension-Tension Loading

Life prediction techniques for structural composites are based on test data obtained from coupon specimens. A tension fatigue life prediction methodology based on a through-thickness damage accumulation model is used to predict the fatigue failure of composite coupon specimens. Its applicability to thin-walled cylindrical specimens is in vestigated by comparing the fatigue behavior of composite coupon specimens to that of composite thin-walled cylindrical specimens. AS4/3501-6 graphite-epoxy coupon speci mens and thin-walled cylinder specimens with the same layup sequence of [0/ ± 45/90] s were tested under static and fatigue loading conditions. Reasonably good agreement is found between the measured and predicted lives of the coupon specimens. Although the ultimate stresses of coupon and cylindrical specimens are different, it is observed that their fatigue lives at the same percentage of ultimate stress are nearly identical, independent of the coupon edge effect. It is concluded that the fatigue life prediction methodology for coupon specimens could be extended to estimate the fatigue life of the thin-walled graphite/epoxy composite cylinders used in this study.
The Facultative Intracellular Pathogen Candida glabrata Subverts Macrophage Cytokine Production and Phagolysosome Maturation

Although Candida glabrata is an important human pathogenic yeast, its pathogenicity mechanisms are largely unknown. Immune evasion strategies seem to play key roles during infection, since very little inflammation is observed in mouse models. Furthermore, C. glabrata multiplies intracellularly after engulfment by macrophages. In this study, we sought to identify the strategies that enable C. glabrata to survive phagosome biogenesis and antimicrobial activities within human monocyte-derived macrophages. We show that, despite significant intracellular proliferation, macrophage damage or apoptosis was not apparent, and production of reactive oxygen species was inhibited. Additionally, with the exception of GM-CSF, levels of pro- and anti-inflammatory cytokines were only marginally increased. We demonstrate that adhesion to and internalization by macrophages occur within minutes, and recruitment of endosomal early endosomal Ag 1 and lysosomal-associated membrane protein 1 indicates phagosome maturation. However, phagosomes containing viable C. glabrata, but not heat-killed yeasts, failed to recruit cathepsin D and were only weakly acidified. This inhibition of acidification did not require fungal viability, but it had a heat-sensitive surface attribute. Therefore, C. glabrata modifies the phagosome into a nonacidified environment and multiplies until the host cells finally lyse and release the fungi. Our results suggest persistence of C. glabrata within macrophages as a possible immune evasion strategy.
Effects of Early Life Stress on [11C]DASB Positron Emission Tomography Imaging of Serotonin Transporters in Adolescent Peer- and Mother-Reared Rhesus Monkeys

Peer-reared (PR) rhesus monkeys with early maternal separation later exhibit aggressiveness, impaired impulse control, alcohol abuse, and low CSF 5-hydroxyindoleacetic acid. This study compared regional brain serotonin transporter (SERT) binding between nine PR and seven mother-reared rhesus monkeys with [11C]DASB positron emission tomography (PET) imaging. Parametric images of binding potential (BP) (which is proportional to Bmax/KD, in which Bmax is transporter density and KD is dissociation constant) and relative blood flow (R1) were generated by the two-parameter multilinear reference tissue model. R1 images were used for coregistration and normalization of PET parametric data to the magnetic resonance imaging template space. Group BP differences were analyzed voxelwise by Student's t test in SPM2. Region of interest-based parameter values were also calculated to obtain the magnitude of regional BP differences between the two groups. For the PR group, SERT BP was decreased by 10–23% across a range of brain areas consisting of the raphe, thalamus, hypothalamus, caudate and putamen, globus pallidum, anterior cingulate gyrus, and medial temporal regions, including amygdala and hippocampus (cluster-level corrected p = 0.002). For the latter three regions, BP was decreased in the right hemisphere. These results agree with the hypothesis that early maternal deprivation affects the development of the serotonergic system and suggest that decreased serotonergic innervations in the critical brain regions may explain some of the behavioral and biochemical abnormalities in PR monkeys.
Comment on “Number-space mapping in the newborn chick resembles humans’ mental number line”

Rugani et al. (Reports, 30 January 3015, p. 534) tested 3-day-old domestic chicks using an innovative experimental setup and demonstrate the presence of the mental number line. We raise concerns regarding this conclusion by highlighting the possible loopholes in the experimental design and the data analysis procedures. We further suggest auxiliary experiments that can substantiate the authors’ claim.
Iodinated Contrast Media Increased the Risk of Thyroid Dysfunction: A 6-Year Retrospective Cohort Study.

CONTEXT The risks of thyroid dysfunction after iodinated contrast media (ICM) exposure are largely unknown, especially in Asian populations. OBJECTIVE The objective was to determine whether ICM exposure in patients with normal thyroid would increase the risk of thyroid dysfunction, including hyperthyroidism or hypothyroidism. DESIGN This was a retrospective cohort study including a random selection of 1 million people in 2005. SETTING General population of Taiwan was studied. PATIENTS Patients with ICM exposure were identified as cases, whereas patients without any ICM exposure were selected as controls. INTERVENTION Interventions included ICM exposure or nonexposure in normal thyroid function patients. MAIN OUTCOME The primary endpoint was the composite risk of thyroid dysfunction associated with ICM exposure. RESULTS A total of 19 642 cases and 78 568 matched controls were recruited in this study. The mean ages of ICM exposure and nonexposure were 53.9 and 53.6 years, respectively, and mean follow-up durations were 4.1 and 5.6 years, respectively. After adjustment, patients with ICM exposure had a significantly higher risk of thyroid dysfunction (hazard ratio, 1.46; 95% confidence interval [CI], 1.29-1.66). In the subgroup analysis, the adjusted hazard ratios of hyperthyroidism and hypothyroidism compared with controls were 1.22 (95% CI, 1.04-1.44) and 2.00 (95% CI, 1.65-2.44), respectively. CONCLUSIONS ICM exposure was associated with higher risk of thyroid dysfunction, including hyperthyroidism and hypothyroidism.
Heregulin-dependent Activation of Phosphoinositide 3-Kinase and Akt via the ErbB2/ErbB3 Co-receptor*

The ErbB2/ErbB3 heregulin co-receptor has been shown to couple to phosphoinositide (PI) 3-kinase in a heregulin-dependent manner. The recruitment and activation of PI 3-kinase by this co-receptor is presumed to occur via its interaction with phosphorylated Tyr-Xaa-Xaa-Met (YXXM) motifs occurring in the ErbB3 C terminus. In this study, mutant ErbB3 receptor proteins expressed in COS7 cells were used to investigate PI 3-kinase-dependent signaling pathways activated by the ErbB2/ErbB3 co-receptor. We observed that a mutant ErbB3 protein with each of its six YXXM motifs containing a Tyr → Phe substitution was unable to bind either the p85 regulatory or p110 catalytic subunit of PI 3-kinase. However, restoration of a single YXXM motif was sufficient to mediate association with the PI 3-kinase holoenzyme, although at a lower level than wild-type ErbB3. When ErbB3 YXXM motifs were restored in pairs, evidence for cooperativity between two, those incorporating Tyr-1273 and Tyr-1286, was observed. Interestingly, we have shown that an apparent association of PI 3-kinase activity with ErbB2/Neu was due to the residual presence of ErbB3 in ErbB2 immunoprecipitates. The necessity of ErbB3 association with PI 3-kinase for downstream signaling to the effector kinase Akt was also investigated. Here, the heregulin-dependent translocation of Akt to the plasma membrane and its subsequent activation was observed in intact NIH-3T3 fibroblasts. Recruitment of PI 3-kinase to ErbB3 was required for both activities, and it appeared that ErbB2 activation alone was not sufficient to activate PI 3-kinase signaling in these cells.
Super-resolution Using Constrained Deep Texture Synthesis

Hallucinating high frequency image details in single image super-resolution is a challenging task. Traditional super-resolution methods tend to produce oversmoothed output images due to the ambiguity in mapping between low and high resolution patches. We build on recent success in deep learning based texture synthesis and show that this rich feature space can facilitate successful transfer and synthesis of high frequency image details to improve the visual quality of super-resolution results on a wide variety of natural textures and images.
Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees

Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. The drivers of this variation are not well understood. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to contribute to explaining the variation. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics; closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species. Our results suggest that phylogenetically correlated intrinsic factors, namely traits of the genera themselves, shape among lineage variation in range size, abundance and species richness. We postulate that tree stature may be one particularly relevant trait. However, other traits may also be relevant, and our study reinforces the need for ambitious compilations of trait data for Amazonian trees. In the meantime, our study shows how large-scale phylogenies can help to elucidate, and contribute to explaining, macroecological and macroevolutionary patterns in hyperdiverse, yet poorly understood regions like the Amazon Basin.
Studies of InGaN LEDs degradation

Light-emitting diodes (LEDs) degradation during 10 000 hours and the influence of ultrasonic action on the InGaN LEDs were investigated. The model of LED degradation is suggested and based on 1) common LED is the combination of parallel Small-LEDs (S-LED) which correspond to the areas with different concentration of In atoms; 2) redistribution of In atoms in quantum-dimensional active region of blue InGaN LED under strong piezoelectric effect and spontaneous polarization induced by ultrasonics; 3) the ultrasonics which is used in creating LEDs can make defects in heterostructures and they (during LEDs work) are heated by current or ultrasonic, can be increased and that's why nonradiation recombination decreases LEDs efficiency. It can be said that great current density flows through areas with low In concentration and therefore S-LEDs are "burned out" and irradiate less. At the areas with average In concentration the densities decrease. That is why electroluminescence spectrum, radiation power, luminous intensity characteristics are shifted to the long wave region. All that also exactly corresponds with our experimental results of LEDs degradation investigation during 10 000 hours.
Software defect prediction using static code metrics underestimates defect-proneness

Many studies have been carried out to predict the presence of software code defects using static code metrics. Such studies typically report how a classifier performs with real world data, but usually no analysis of the predictions is carried out. An analysis of this kind may be worthwhile as it can illuminate the motivation behind the predictions and the severity of the misclassifications. This investigation involves a manual analysis of the predictions made by Support Vector Machine classifiers using data from the NASA Metrics Data Program repository. The findings show that the predictions are generally well motivated and that the classifiers were, on average, more “confident” in the predictions they made which were correct.