Miracle-dz/UniFAR-FTUs huggingface dataset:
HoxA13 Regulates Phenotype Regionalization of Human Pregnant Myometrium.

CONTEXT Bipedalism separates humans from most other animal species, but results in significant physiologic challenges, particularly with respect to the maintenance of pregnancy and induction of parturition. A contracted lower uterine segment (LUS) and a relaxed uterine fundal myometrium (FUN) during pregnancy are required to prevent pressure on the cervix from the fetal head due to gravity. With the onset of labor, this regionalization of myometrial function must be reversed, allowing descent of the fetus, dilation of the cervix, and expulsion of the fetus through the birth canal. However, the molecular mechanisms remain unclear. OBJECTIVE AND DESIGN This study sought to identify phenotypic regionalization of LUS and FUN during pregnancy, RNA sequencing was performed to analyze the human myometrial transcriptome. Real-time PCR and immunoblotting were applied to validate sequencing results. Cell contraction/adhesion assays and gene microarrays were used to study the cellular functions of the identified genes. RESULTS Homeobox A13 (HoxA13), prostacyclin synthase (PTGIS), and periostin (POSTN) genes are more highly expressed in LUS than FUN of nonlaboring, but not laboring, myometrial cells at term. HoxA13 up-regulates transcription of PTGIS and POSTN genes. Elevated HoxA13 expression enhances myometrial cell contractility and cell-cell adhesion. Gene microarray studies show that HoxA13-regulated genes are associated with immune response, gap junction/cell adhesion, and pregnancy. CONCLUSION The LUS expresses higher levels of HoxA13, PTGIS, and POSTN, and is more contractile than the FUN at term prior to labor. This pregnancy-maintaining regionalization of myometrial function may be mediated by HoxA13.
Requirement of Heat Shock Protein 90 for Human Hepatitis B Virus Reverse Transcriptase Function

ABSTRACT The initiation of reverse transcription and nucleocapsid assembly in hepatitis B virus (HBV) depends on the specific recognition of an RNA signal (the packaging signal, ε) on the pregenomic RNA (pgRNA) by the viral reverse transcriptase (RT). RT-ε interaction in the duck hepatitis B virus (DHBV) was recently shown to require the molecular chaperone complex, the heat shock protein 90 (Hsp90). However, the requirement for RT-ε interaction in the human HBV has remained unknown due to the inability to obtain a purified RT protein active in specific ε binding. We now report that Hsp90 is also required for HBV RT-ε interaction. Inhibition of Hsp90 led to diminished HBV pgRNA packaging into nucleocapsids in cells, which depends on RT-ε interaction. Furthermore, using truncated HBV RT proteins purified from bacteria and five purified Hsp90 chaperone factors, we have developed an in vitro RT-ε binding assay. Our results demonstrate that Hsp90, in a dynamic process that was dependent on ATP hydrolysis, facilitated RT-ε interaction in HBV, as in DHBV. Specific ε binding required sequences from both the amino-terminal terminal protein and the carboxy-terminal RT domain. Only the cognate HBV ε, but not the DHBV ε, could bind the HBV RT proteins. Furthermore, the internal bulge, but not the apical loop, of ε was required for RT binding. The establishment of a defined in vitro reconstitution system has now paved the way for future biochemical and structural studies to elucidate the mechanisms of RT-ε interaction and chaperone activation.
Adapting Models of Visual Aesthetics for Personalized Content Creation

This paper introduces a search-based approach to personalized content generation with respect to visual aesthetics. The approach is based on a two-step adaptation procedure where: 1) the evaluation function that characterizes the content is adjusted to match the visual aesthetics of users; and 2) the content itself is optimized based on the personalized evaluation function. To test the efficacy of the approach, we design fitness functions based on universal properties of visual perception, inspired by psychological and neurobiological research. Using these visual properties, we generate aesthetically pleasing 2-D game spaceships via neuroevolutionary constrained optimization and evaluate the impact of the designed visual properties on the generated spaceships. The offline generated spaceships are used as the initial population of an interactive evolution experiment in which players are asked to choose spaceships according to their visual taste: the impact of the various visual properties is adjusted based on player preferences and new content is generated online based on the updated computational model of visual aesthetics of the player. Results are presented that show the potential of the approach in generating content which is based on subjective criteria of visual aesthetics.
A Convex Formulation for Mixed Regression with Two Components: Minimax Optimal Rates

We consider the mixed regression problem with two components, under adversarial and stochastic noise. We give a convex optimization formulation that provably recovers the true solution, and provide upper bounds on the recovery errors for both arbitrary noise and stochastic noise settings. We also give matching minimax lower bounds (up to log factors), showing that under certain assumptions, our algorithm is information-theoretically optimal. Our results represent the first tractable algorithm guaranteeing successful recovery with tight bounds on recovery errors and sample complexity.
Pressure‐Dependent Elastic and Transport Properties of Porous and Permeable Rocks: Microstructural Control

Although several studies aimed at linking electrical and hydraulic transport properties in rocks, the existing models remain at most incomplete. Based on this observation, in addition to the transport properties, this contribution investigates the pressure dependence of P wave velocities and porosity for three porous rocks. Apart from hydraulic conductivity, all physical properties show an important dependence to the confining pressure. In particular, electrical resistivity reaches an asymptote at low confining pressures. Using the measured P wave velocities and effective medium theories, the microcrack density (ρ) and its evolution with confining pressure are estimated. For the three rocks, the microcrack density at which electrical resistivity reaches a plateau is of ρ ~0.13. This value corresponds to the threshold for crack percolation in media containing microcracks exclusively. This suggests that in porous and microcracked rocks, electrical resistivity is controlled by two independent hydraulic pathways of tubes and cracks acting in parallel. In contrast, this percolation threshold is not observed in the permeability data. A simple conceptual model is finally introduced that explains the fundamental differences between transport properties.
Side effects of fast-acting dynamic range compression that affect intelligibility in a competing speech task.

Using a cochlear implant simulator, Stone and Moore [J. Acoust. Soc. Am. 114, 1023-1034 (2003)] reported that wideband fast-acting compression led to poorer intelligibility than slow-acting compression in a competing speech task. Compression speed was varied by using different pairs of attack and release times. In the first experiment reported here, it is shown that attack times less than about 2 ms in a wideband compressor are deleterious to intelligibility. In experiment 2, fast wideband compression was applied to the target and background either before or after mixing. The former reduced the modulation depth of each signal but maintained the independence between the two signals, while the latter introduced "comodulation. " Using simulations with 6 and 11 channels, intelligibility was higher when compression was applied before mixing. In experiment 3, wideband compression was compared with multichannel compression; the latter led to reduced comodulation effects. For 6 channels, the position of the compressor, either wideband or within each channel, had no effect on intelligibility. For 11 channels, channel compression severely degraded intelligibility compared to wideband compression, presumably because of the greater reduction of across-channel contrasts. Overall, caution appears necessary in the use of fast-acting compression in cochlear implants, so as to preserve intelligibility.
Glycyrrhetinic Acid inhibits cell growth and induces apoptosis in ovarian cancer a2780 cells.

PURPOSE Accumulating evidence indicates that glycyrrhizin (GZ) and its hydrolyzed metabolite 18-β glycyrrhetinic acid (GA) exhibit anti-inflammatory and anticancer activities. The objective of this study was to examine the in vitro cytotoxic activity of GA on human ovarian cancer A2780 cells. METHODS A2780 cells were cultured in RPMI1640 containing 10% fetal bovine serum. Cells were treated with different doses of GA and cell viability and proliferation were detected by dye exclusion and 3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) assays. Apoptosis induction and expression of Fas and Fas ligand (FasL) were analyzed by flow cytometry. RESULTS We observed that GA decreases cell viability and suppressed cells proliferation in a dose-dependent manner as detected by dye-exclusion and XTT assayes. In addition, our flow cytometry data show that GA not only induces apoptosis in A2780 cells but also upregulates both Fas and FasL on these cells in a dose-dependent manner. CONCLUSION we demonstrate that GA causes cell death in A2780 cells by inducing apoptosis.
A simplified audiovisual fusion model with application to large-vocabulary recognition of French Canadian speech

A new, simple and practical way of fusing audio and visual information to enhance audiovisual automatic speech recognition within the framework of an application of large-vocabulary speech recognition of French Canadian speech is presented, and the experimental methodology is described in detail. The visual information about mouth shape is extracted off-line using a cascade of weak classifiers and a Kalman filter, and is combined with the large-vocabulary speech recognition system of the Centre de Recherche Informatique de Montreal. The visual classification is performed by a pair-wise kernel-based linear discriminant analysis (KLDA) applied on a principal component analysis (PCA) subspace, followed by a binary combination and voting algorithm on 35 French phonetic classes. Three fusion approaches are compared: (1) standard low-level feature-based fusion, (2) decision-based fusion within the framework of the transferable belief model (an interpretation of the Dempster-Shafer evidential theory), and (3) a combination of (1) and (2). For decision-based fusion, the audio information is considered to be a precise Bayesian source, while the visual information is considered an imprecise evidential source. This treatment ensures that the visual information does not significantly degrade the audio information in situations where the audio performs well (e.g., a controlled noise-free environment). Results show significant improvement in the word error rate to a level comparable to that of more sophisticated systems. To the authors' knowledge, this work is the first to address large-vocabulary audiovisual recognition of French Canadian speech and decision-based audiovisual fusion within the transferable belief model.
Usage and Perceived Side Effects of Personal Protective Measures against Mosquitoes among Current Users in Delhi

Background. Mosquito-borne diseases constitute an important cause of morbidity and mortality. The use of personal protective measures (PPM) like mats, bednets, screening, repellents, liquid vaporizers, mosquito coils, and so forth has been advocated as an effective tool in control of mosquito-borne diseases, but data about the safety profile of personal protective measures is still scarce. Objective. To study the usage and side effects of personal protective measures against mosquitoes among current users in Delhi. Materials and Methods. A community-based cross-sectional study among 350 adult individuals selected by systematic sampling method. Data was collected using pretested semistructured questionnaire after taking written informed consent. Data was analysed using SPSS version 17. Chi-square/Fisher's Exact test was used for qualitative variables to find association and P value <0.05 was considered significant. Results. Out of 350 families selected, 210 belonged to rural area and 140 to urban area. Personal protective measures were used by 219 (62.5%) subjects. Liquid vaporizer was the most preferred method (41.4%). Most common perceived side effect of personal protective measures was headache (7.7%). Other perceived side effects were cough (3.2%), sore throat (2.7%), allergy (1.3%), and eye irritation (0.9%) predominantly among coil users. Conclusion. There is a need to have a close watch for side effects of personal protective measures among users. Further research is also needed to develop safe and effective personal protective measures against mosquitoes.
Inference on the Instrumental Quantile Regression Process for Structural and Treatment Effect Models

We introduce a class of instrumental quantile regression methods for heterogeneous treatment effect models and simultaneous equations models with nonadditive errors and offer computable methods for estimation and inference. These methods can be used to evaluate the impact of endogenous variables or treatments on the entire distribution of outcomes. We describe an estimator of the instrumental variable quantile regression process and the set of inference procedures derived from it. We focus our discussion of inference on tests of distributional equality, constancy of effects, conditional dominance, and exogeneity. We apply the procedures to characterize the returns to schooling in the U.S. JEL Classification: C10, C11, C13, C15
In Depth Analysis of the Helicobacter pylori cag Pathogenicity Island Transcriptional Responses

The severity of symptoms elicited by the widespread human pathogen Helicobacter pylori is strongly influenced by the genetic diversity of the infecting strain. Among the most important pathogen factors that carry an increased risk for gastric cancer are specific genotypes of the cag pathogenicity island (cag-PAI), encoding a type IV secretion system (T4SS) responsible for the translocation of the CagA effector oncoprotein. To date, little is known about the regulatory events important for the expression of a functional cag-T4SS. Here we demonstrate that the cag-PAI cistrons are subjected to a complex network of direct and indirect transcriptional regulations. We show that promoters of cag operons encoding structural T4SS components display homogeneous transcript levels, while promoters of cag operons encoding accessory factors vary considerably in their basal transcription levels and responses. Most cag promoters are transcriptionally responsive to growth-phase, pH and other stress-factors, although in many cases in a pleiotropic fashion. Interestingly, transcription from the Pcagζ promoter controlling the expression of transglycolase and T4SS stabilizing factors, is triggered by co-culture with a gastric cell line, providing an explanation for the increased formation of the secretion system observed upon bacterial contact with host cells. Finally, we demonstrate that the highly transcribed cagA oncogene is repressed by iron limitation through a direct apo-Fur regulation mechanism. Together the results shed light on regulatory aspects of the cag-PAI, which may be involved in relevant molecular and etiological aspects of H. pylori pathogenesis.
Harris Infant Neuromotor Test: Comparison of US and Canadian Normative Data and Examination of Concurrent Validity With the Ages and Stages Questionnaire

Background: The Harris Infant Neuromotor Test (HINT) was developed as a screening tool for potential motor and cognitive developmental disorders in infants. Scoring on the HINT has been shown to be reliable, and several studies have supported the validity of the HINT. Normative values for the tool have been developed using Canadian infants. Objective: The aims of this study were (1) to further evaluate the validity of the HINT by comparing data obtained on US infants who were developing typically with data previously acquired on Canadian infants and (2) to determine the concurrent validity of the HINT with the Ages and Stages Questionnaire (ASQ). Secondary analyses of HINT scores for US white and nonwhite infants and for US infants who had parents with lower levels of education and US infants who had parents with higher levels of education (as a proxy for socioeconomic status [SES]) were conducted. Design: Cross-sectional exploratory and quasi-experimental comparative research designs were used to evaluate the validity of the HINT. Methods: Sixty-seven infants from the United States who were developing typically and who were aged 2.5 to 12.5 months were recruited via convenience sampling. Sixty-four of these infants were compared with Canadian infants matched for age, sex, ethnicity or race, and parental education. The HINT was administered by raters who had been trained to attain acceptable levels of interrater reliability, and parents completed the ASQ. The HINT scores for US white versus nonwhite infants (n=46) and infants who had parents with lower SES versus a higher SES (n=52) were compared. Results: There were no significant differences between HINT total scores for US and Canadian infants or for US racial or ethnic groups and SES groups. There were high correlations (r=−.82 to −.84) between HINT and ASQ scores. Limitations: The study used a small US sample with limited geographical diversity. Small sample numbers also did not allow for comparisons of specific racial or ethnic groups. The SES groups were created primarily using parental education as a proxy for SES. Conclusions: The results suggest that HINT screening in the United States is supported on the basis of Canadian norms and the validity of the HINT in screening for motor and cognitive delays. Although there is preliminary support for the HINT as an appropriate screening tool for US infants who are nonwhite or who have parents with a lower SES, more research is warranted.
Sulfotransferases of Two Specificities Function in the Reconstitution of High Endothelial Cell Ligands for L-selectin

L-selectin, a lectin-like receptor, mediates rolling of lymphocytes on high endothelial venules (HEVs) in secondary lymphoid organs by interacting with HEV ligands. These ligands consist of a complex of sialomucins, candidates for which are glycosylation- dependent cell adhesion molecule 1 (GlyCAM-1), CD34, and podocalyxin. The ligands must be sialylated, fucosylated, and sulfated for optimal recognition by L-selectin. Our previous structural characterization of GlyCAM-1 has demonstrated two sulfation modifications, Gal-6-sulfate and GlcNAc-6-sulfate in the context of sialyl Lewis x. We now report the cloning of a Gal-6-sulfotransferase and a GlcNAc-6-sulfotransferase, which can modify GlyCAM-1 and CD34. The Gal-6-sulfotransferase shows a wide tissue distribution. In contrast, the GlcNAc-6-sulfotransferase is highly restricted to HEVs, as revealed by Northern analysis and in situ hybridization. Expression of either enzyme in Chinese hamster ovary cells, along with CD34 and fucosyltransferase VII, results in ligand activity, as detected by binding of an L-selectin/IgM chimera. When coexpressed, the two sulfotransferases synergize to produce strongly enhanced chimera binding.
Automatic ulcer detection scheme using gray scale histogram from wireless capsule endoscopy

Wireless capsule endoscopy (WCE) is one of the most recent and effective video technologies to diagnose gastrointestinal (GI) diseases, such as ulcer in GI tract. Because of long duration of WCE videos, it is a burden for the physicians to analyze large number of image frames. This time consuming process often leads to human error. Hence, an automatic scheme for ulcer image detection in WCE video has great demand. In this paper, an automatic scheme based on image histogram is proposed to detect ulcer frames in WCE video. In order to compute the histograms from pixel values, instead of using conventional RGB color plane, gray scale is used, which offers the scope of utilizing brightness of color. Based on extensive experimentation, it is found that histogram patterns, obtained from ulcer and non-ulcer images in gray scale, exhibit significant differences. Cumulative pixel number of the pixel values in gray scale over an optimum threshold is chosen as feature through histogram analysis. Moreover, this 1-D feature offers computational advantage and ease of implementation. For the purpose of classification, the support vector machine (SVM) supervised classifier is used. Also, performance of the proposed method obtained from several other classifiers is compared. The performance of the proposed method is tested on several WCE images taken from publicly available WCE video database and it is found that, the proposed method offers superior classification performance, in comparison to that obtained by some existing methods, in terms of accuracy, specificity, and sensitivity.
Treatment simulation approaches for the estimation of the distributions of treatment quality parameters generated by geometrical uncertainties

Geometric uncertainties arise during treatment planning and treatment and mean that dose-dependent parameters such as EUD are random variables with a patient specific probability distribution. Treatment planning with highly conformal treatment techniques such as intensity modulated radiation therapy requires new evaluation tools which allow us to estimate this influence of geometrical uncertainties on the probable treatment dose for a planned dose distribution. Monte Carlo simulations of treatment courses with recalculation of the dose according to the daily geometric errors are a gold standard for such an evaluation. Distribution histograms which show the relative frequency of a treatment quality parameter in the treatment simulations can be used to evaluate the potential risks and chances of a planned dose distribution. As treatment simulations with dose recalculation are very time consuming for sufficient statistical accuracy, it is proposed to do treatment simulations in the dose parameter space where the result is mainly determined by the systematic and random component of the geometrical uncertainties. Comparison of the parameter space simulation method with the gold standard for prostate cases and a head and neck case shows good agreement as long as the number of fractions is high enough and the influence of tissue inhomogeneities and surface curvature on the dose is small.
Structure of Shiga Toxin Type 2 (Stx2) from Escherichia coli O157:H7*

Several serotypes of Escherichia coli produce protein toxins closely related to Shiga toxin (Stx) from Shigella dysenteriae serotype 1. These Stx-producing E. coli cause outbreaks of hemorrhagic colitis and hemolytic uremic syndrome in humans, with the latter being more likely if the E. coli produce Stx2 than if they only produce Stx1. To investigate the differences among the Stxs, which are all AB5 toxins, the crystal structure of Stx2 from E. coli O157:H7 was determined at 1.8-Å resolution and compared with the known structure of Stx. Our major finding was that, in contrast to Stx, the active site of the A-subunit of Stx2 is accessible in the holotoxin, and a molecule of formic acid and a water molecule mimic the binding of the adenine base of the substrate. Further, the A-subunit adopts a different orientation with respect to the B-subunits in Stx2 than in Stx, due to interactions between the carboxyl termini of the B-subunits and neighboring regions of the A-subunit. Of the three types of receptor-binding sites in the B-pentamer, one has a different conformation in Stx2 than in Stx, and the carboxyl terminus of the A-subunit binds at another. Any of these structural differences might result in different mechanisms of action of the two toxins and the development of hemolytic uremic syndrome upon exposure to Stx2.