Miracle-dz/UniFAR-FTUs huggingface dataset:
Nuclear Factor YY1 Inhibits Transforming Growth Factor β- and Bone Morphogenetic Protein-Induced Cell Differentiation

ABSTRACT Smad proteins transduce transforming growth factor β (TGF-β) and bone morphogenetic protein (BMP) signals that regulate cell growth and differentiation. We have identified YY1, a transcription factor that positively or negatively regulates transcription of many genes, as a novel Smad-interacting protein. YY1 represses the induction of immediate-early genes to TGF-β and BMP, such as the plasminogen activator inhibitor 1 gene (PAI-1) and the inhibitor of differentiation/inhibitor of DNA binding 1 gene (Id-1). YY1 inhibits binding of Smads to their cognate DNA elements in vitro and blocks Smad recruitment to the Smad-binding element-rich region of the PAI-1 promoter in vivo. YY1 interacts with the conserved N-terminal Mad homology 1 domain of Smad4 and to a lesser extent with Smad1, Smad2, and Smad3. The YY1 zinc finger domain mediates the association with Smads and is necessary for the repressive effect of YY1 on Smad transcriptional activity. Moreover, downregulation of endogenous YY1 by antisense and small interfering RNA strategies results in enhanced transcriptional responses to TGF-β or BMP. Ectopic expression of YY1 inhibits, while knockdown of endogenous YY1 enhances, TGF-β- and BMP-induced cell differentiation. In contrast, overexpression or knockdown of YY1 does not affect growth inhibition induced by TGF-β or BMP. Accordingly, YY1 does not interfere with the regulation of immediate-early genes involved in the TGF-β growth-inhibitory response, the cell cycle inhibitors p15 and p21, and the proto-oncogene c-myc. In conclusion, YY1 represses Smad transcriptional activities in a gene-specific manner and thus regulates cell differentiation induced by TGF-β superfamily pathways.
Comparative study of seeding methods for three-dimensional polymeric scaffolds

Development of tissue-engineered devices may be enhanced by combining cells with porous absorbable polymeric scaffolds before implantation. The cells are seeded throughout the scaffolds and allowed to proliferate in vitro for a predetermined amount of time. The distribution of cells throughout the porous material is one critical component determining success or failure of the tissue-engineered device. This can influence both the successful integration of the device with the host tissue as well as the development of a vascularized network throughout the entire scaffold volume. This research sought to compare different seeding and proliferation methods to select an ideal method for a polyglycolide/aortic endothelial cell system. Two seeding environments, static and dynamic, and three proliferation environments, static, dynamic, and bioreactor, were analyzed, for a total of six possible methods. The six seeding and proliferation combinations were analyzed following a 1-week total culture time. It was determined that for this specific system, dynamic seeding followed by a dynamic proliferation phase is the least promising method and dynamic seeding followed by a bioreactor proliferation phase is the most promising.
Impedance design of quasi-Z source network to limit double fundamental frequency voltage and current ripples in single-phase quasi-Z source inverter

This paper proposes an analytic model to calculate the double fundamental frequency (2ω) voltage and current ripples for single-phase quasi-Z-source inverter (qZSI). The model enables the exact calculation of the 2 Ω components of the inductor current and the capacitor voltage, which is crucial for designing a single-phase qZSI system. A guideline for selecting the capacitance and inductance in quasi-Z-source (qZS) network to limit both the dc-link voltage and input current 2ω ripples within a tolerable range is presented. Three cases are tested to verify the proposed analytic model and the design method by using simulation and experimental results. The identical analytic calculation result, the simulation result, and the experimental result validate the analytic model and the design method.
High-performance patch antennas based on NonPeriodic artificial planes

Several novel high-performance patch antennas based on non-periodic artificial planes composed by specific artificial magnetic conductor (AMC) or electric band gap (EBG) structures are proposed. Firstly, aiming at improving current uniformity for high gain, a stub-loaded artificial magnetic conductor (SLAMC) structure is proposed as the ground plane of a patch antenna to achieve a gain enhancement of 1.73dB compared with ordinary square AMC plane. For further enhancement, a novel cylindrically-projected artificial plane composed by non-periodic rectangle AMC (RAMC) structure is presented, and it can be similarly equivalent to a cylindrical metal reflector for strongly focusing electromagnetic waves to realize an extremely directive antenna with high aperture efficiency of over 90%. On the basis, a novel spherically-projected RAMC plane is applied in dual-polarized patch antennas to realize very high aperture efficiency of over 100% and very high polarization-isolation of over 55dB. In addition, a new off-center EBG structure is also used as a unit cell of nonperiodic artificial plane, which introduce additional adjustable method in uniform period for performance improvement.
Further Developments of the Fisher Information Matrix in Nonlinear Mixed Effects Models with Evaluation in Population Pharmacokinetics

We extend the development of the expression of the Fisher information matrix in nonlinear mixed effects models for designs evaluation. We consider the dependence of the marginal variance of the observations with the mean parameters and assume an heteroscedastic variance error model. Complex models with interoccasions variability and parameters quantifying the influence of covariates are introduced. Two methods using a Taylor expansion of the model around the expectation of the random effects or a simulated value, using then Monte Carlo integration, are proposed and compared. Relevance of the resulting standard errors is investigated in a simulation study with NONMEM.
Case Study: Application of Isometric Progressive Resistance Oropharyngeal Therapy Using the Madison Oral Strengthening Therapeutic Device

Abstract Purpose: Isometric progressive resistance oropharyngeal (I-PRO) therapy improves swallowing function; however, current devices utilize a single sensor that provides limited information or are prohibitively expensive. This single-subject study presents results of I-PRO therapy, detraining, and maintenance using the 5-sensor Madison Oral Strengthening Therapeutic (MOST) device combined with upper esophageal sphincter (UES) dilatation. Methods: A 56-year-old female nurse who was 27 months post stroke and subsequent to traditional behavioral interventions and UES dilatations presented limited to gastrostomy tube intake only and expectorating all saliva. She completed 8 weeks of I-PRO therapy, 5 weeks of detraining, and 9 weeks of I-PRO maintenance (reduced frequency) followed by a third UES dilatation post intervention. Data included diet inventory, lingual pressures (MOST), lingual volume (magnetic resonance imaging), postswallow residue (videofluoroscopy), UES and pharyngeal pressures (high-resolution manometry), and quality of life (QOL). Results: Findings after 8 weeks of I-PRO therapy were progression to general oral diet, 15 lb weight gain, increased isometric pressures (Δ >16 kPa) with transference to swallowing pressures, increased lingual volume (8.3%), reduced pharyngeal wall residue (P = .03), increased pharyngeal pressures (Δ > 43 mm Hg) and increased UES opening (nadir) pressures (Δ > 9 mm Hg) with improved temporopressure coordination across the pharynx, and improved QOL. After detraining, decreased isometric pressures and reduced UES opening were noted. After I-PRO maintenance, isometric anterior lingual pressures returned to levels noted after the 8 weeks of intervention. Conclusion: I-PRO therapy, facilitated by the MOST device combined with instrumental UES dilatation, improved swallow safety, increased oropharyngeal intake, and facilitated UES opening while enriching QOL.
Hypercapnic acidosis attenuates the pulmonary innate immune response in ventilated healthy mice*

Background:Mechanical ventilation with small tidal volumes reduces the development of ventilator-induced lung injury and mortality, but may increase Paco2. It is not clear whether the beneficial effect of a lung-protective strategy results from reduced ventilation pressures/tidal volumes or is mediated by the effects of hypercapnic acidosis on the inflammatory response involved in the pathogenesis of ventilator-induced lung injury. Objective:To analyze whether hypercapnic acidosis affects lung tissue cytokine levels and leukocyte influx in healthy ventilated mice. Study Design:Analysis of lung tissue and plasma concentrations of interleukin (IL)-1&bgr;, tumor necrosis factor (TNF)-&agr;, IL-6, IL-10, and keratocyte-derived chemokine after 2 hrs of mechanical ventilation (Vt 8 mL/kg, positive end-expiratory pressure 4 cm H2O) with 0.06% CO2 (room air), 2% CO2, or 4% CO2. Subjects:Healthy C57BL6 mice (n = 40). Measurements/Results:Paco2 and pH were within normal range when ventilated with 0.06% CO2 and significantly changed with 2% and 4% CO2: (mean ± sd) pH 7.23 ± 0.06 and 7.15 ± 0.04, Paco2 7.9 ± 1.4 and 10.8 ± 0.7 kPa, respectively (p < 0.005). Blood pressure remained within normal limits in all animals. Quantitative microscopic analysis showed a 4.7 ± 3.7-fold increase (p < 0.01) in pulmonary leukocyte influx in normocapnic ventilated animals and a significant reduction in leukocyte influx of 57 ± 32% (p < 0.01) and 67 ± 22% (p < 0.01) when ventilated with 2% and 4% CO2, respectively. Normocapnic ventilation induced a significant elevation of lung tissue IL-1&bgr; (1516 ± 119 ng/mL), TNF-&agr; (344 ± 88 ng/mL), IL-6 (6310 ± 807 ng/mL), IL-10 (995 ± 152 ng/mL), and keratocyte-derived chemokine (36,966 ± 15,294 ng/mL) (all p-values <0.01). Hypercapnic acidosis with 2% respectively 4% CO2 significantly attenuated this increase with 25 ± 32% and 54 ± 32% (IL-1&bgr;, p < 0.01); 17 ± 36% and 58 ± 33% (TNF-&agr;, p < 0.02); 22 ± 34% and 89 ± 6% (IL-6, p < 0.01); 20 ± 31% and 67 ± 17% (IL-10, p < 0.01) and 16 ± 44% and 45 ± 30% (keratocyte-derived chemokine, p = 0.07). Conclusion:Hypercapnic acidosis attenuates the mechanical ventilation-induced immune response independent from reduced tidal volumes/pressures and may protect the lung from ventilator induced lung injury.
Teaching Stats for Data Science

ABSTRACT “Data science” is a useful catchword for methods and concepts original to the field of statistics, but typically being applied to large, multivariate, observational records. Such datasets call for techniques not often part of an introduction to statistics: modeling, consideration of covariates, sophisticated visualization, and causal reasoning. This article re-imagines introductory statistics as an introduction to data science and proposes a sequence of 10 blocks that together compose a suitable course for extracting information from contemporary data. Recent extensions to the mosaic packages for R together with tools from the “tidyverse” provide a concise and readable notation for wrangling, visualization, model-building, and model interpretation: the fundamental computational tasks of data science.
Single-channel music/speech separation using non-linear masks

In this paper, we address the problem of monaural music and speech separation, based on soft mask filtering. Likewise other well-known techniques, the estimation of statistical model of the sources are needed. Hence, we employ Vector quantization (VQ) for synthesis stage which results in more accurate codebook entries for each source in contrast to the commonly used GMM (Gaussian Mixture Model) approach. In separation stage we compare the non linear mask proposed in this work with other well-known techniques in terms of undesirable signal to interference ratio (SIR) effects. It is demonstrated that the proposed semi soft mask results in the best performance in terms of both SIR and subjective measures.
The First Room‐Temperature Ferroelectric Sn Insulator and Its Polarization Switching Kinetics

Sr3 Sn2 O7 is the first room-temperature ferroelectric Sn insulator with switchable electric polarization. The ferroelastic twin domains are observed using a polarized optical microscope. The polarization hysteresis loop clearly demonstrates the ferroelectric property. Intriguing polarization switching kinetics are observed through an in situ poling process using a dark-field transmission electron microscopy technique.
Affective State and Voice: Reproducibility and Sensitivity of Speech Parameters

Summary In 1986, we started an extensive investigation into the nonverbal information transmitted in human speech. As part of this investigation, we had designed a study of healthy subjects -stratified according to sex, age and education - in order to gain valuable insights into the “typical” nonverbal activities of a speaker. The specific design of this study with 3 different types of texts and 2 repeated measurements at an interval of 14 days was used to test the stability of speech parameters over time as well as their sensitivity to form and content of text. In a first approach, we directed our efforts towards a set of major scalar quantities which earlier investigators had described as playing a key role in modelling affect in terms of directly measurable speech parameters. Based on a sample of 97 persons and with the help of a fully computerized digital approach to speech processing, we found that the four major speech parameters “mean vocal pitch”, “time duration of pauses”, “time duration of utterances”, and “energy” are sufficiently reproducible under constant experimental conditions, whereas some significant differences showed up with regard to the sensitivity of these parameters to form and content of the spoken text. No substantial impact originated from the external factors sex, age and education, except for the tonal shift of one octave between males and females. On the other hand, the overwhelming variety of individual voice patterns obviously excludes any simple model (which applies in general) of the nonverbal component of human speech. However, our analyses offered some important clues as to how appropriate models may be derived by means of adaptive procedures.
Consideration of reactivity to acute fish toxicity of α,β-unsaturated carbonyl ketones and aldehydes

To understand the key factor for fish toxicity of 11 α,β-unsaturated carbonyl aldehydes and ketones, we used quantum chemical calculations to investigate their Michael reactions with methanethiol or glutathione. We used two reaction schemes, with and without an explicit water molecule (Scheme-1wat and Scheme-0wat, respectively), to account for the effects of a catalytic water molecule on the reaction pathway. We determined the energies of the reactants, transition states (TS), and products, as well as the activation energies of the reactions. The acute fish toxicities of nine of the carbonyl compounds were evaluated to correlate with their hydrophobicities; no correlation was observed for acrolein and crotonaldehyde. The most toxic compound, acrolein, had the lowest activation energy. The activation energy of the reaction could be estimated with Scheme-1wat but not with Scheme-0wat. The complexity of the reaction pathways of the compounds was reflected in the difficulty of the TS structure searches when Scheme-1wat was used with the polarizable continuum model. The theoretical estimations of activation energies of α,β-unsaturated carbonyl compounds with catalytic molecules or groups including hydrogen-bond networks may complement traditional tools for predicting the acute aquatic toxicities of compounds that cannot be easily obtained experimentally.
Dopamine receptor properties in Parkinson's disease and Huntington's chorea evaluated by positron emission tomography using 11C‐N‐methyl‐spiperone

ABSTRACT— Dopaminergic receptor properties in the striatum of patients with Parkinson s disease (PD) and Huntington's chorea (HD) were studied by positron emission tomography (PET), using 11C‐N‐methyl‐spiperone as a dopamine D2 receptor ligand. The time‐dependent regional radioactive uptake in the caudate nucleus and the putamen was measured and fitted to a 3‐compartment pharmacokinetic model. The rate constant k3 for specific binding to the receptor compartment in the striatum was determined in relation to the binding in regions with a low density of specific binding sites, such as the cerebellum and the frontal cortex–k3, which is a measure of the receptor density, was reduced in one patient with HD but less affected in PD in comparison with healthy controls. The pattern of k3 values calculated from the 6 PD patients is discussed in relation to any side‐to‐side differences in dopamine receptor densities in hemiparkinsonism and to possible “hypersensitivity” of dopamine receptors in the early stage of the disease and down‐regulation in more advanced disease.
Instructions for use Title Rule-based Approach to Extracting Location , Creator and Membership-related Information fromWikipedia-based Information-rich Taxonomy for ConceptNet Expansion

In this paper we present a method for extracting IsA assertions (hyponymy relations), AtLocation assertions (informing of the location of an object or place), LocatedNear assertions (informing of neighboring locations), CreatedBy assertions (informing of the creator of an object) and MemberOf assertions (informing of group membership) automatically from Japanese Wikipedia XML dump files. These assertions would be suitable for introduction to the Japanese part of the ConceptNet common sense knowledge ontology. We use the Hyponymy extraction tool v1.0, which analyzes definition, category and hierarchy structures of Wikipedia articles to extract IsA assertions and produce an information-rich taxonomy. From this taxonomy we extract additional information, in this case AtLocation, LocatedNear, CreatedBy and MemberOf types of assertions, using our original method. The presented experiments prove that we achieved our research goal on a large scale: both methods produce satisfactory results, and we were able to acquire 5,866,680 IsA assertions with 96.0% reliability, 131,760 AtLocation assertion pairs with 93.5% reliability, 6,217 LocatedNear assertion pairs with 98.5% reliability, 270,230 CreatedBy assertion pairs with 78.5% reliability and 21,053 MemberOf assertions with 87.0% reliability. Our method surpassed the baseline system in terms of both precision and the number of acquired assertions.
Information Provision Modules to Support Creation of Slides with Easily Understandable Presentation

Including visual information in slides is one of the important factors for enabling the audience to easily understand the content of a slide presentation. However, it's difficult for an inexperienced preparer to improve the presentation of slides without adequate experience and awareness of the requirements of a good slide. The authors developed Presentation Gadgets, which consists of modules that can be used to support the creation of slides that represent information in an audience friendly manner. Presentation Gadgets provide information on web-based slides, web pages, web news, and web images, thus supporting replacement of content on slides with visual representations and illustrations of key points, and insertion of common topics and it helps identifying slides that need improvement. To construct the previously mentioned modules, the authors developed a novel slide search method and slide ranking method and to allow easy access to information, Presentation Gadgets has a user interface that automatically creates queries from the selected slide text or speech text that is recognized by a speech recognition engine. By using Presentation Gadgets, an inexperienced slide preparer can effectively create slides that are easily understandable because he/she can interactively refer to various information resources relating to the slide content based on the situation.
A method determining parameters of SVR model based on Probability and Statistics

To get over the difficulties in adopting conventional leaving-one cross validation method to decide the parameters of support vector regression (SVR) forecasting model for small sample with noise or errors, an advanced method was developed based on the theories of probability and statistics. The proposed method considered that the true parameters of the model should have much higher probability to gain better forecasting results than that of others. Living examples show that the SVR forecasting model with the parameters calculated by the method presented here has better results than that of other parameters
Dr. Josef Steiner Cancer Research Prize Lecture: The role of physiological cell death in neoplastic transformation and in anti‐cancer therapy

Cell death is a physiological process which is required for normal development and existence of multi‐cellular organisms. Physiological cell death, or apoptosis, is controlled by an evolutionarily conserved mechanism. Abnormalities in this process are implicated as a cause or contributing factor in a variety of diseases. Inhibition of apoptosis can promote neoplastic transformation, particularly in combination with dysregulated cell‐cycle control, and can influence the response of tumour cells to anti‐cancer therapy. Molecular biological and biochemical approaches are used to find missing cell‐death regulators and to define signalling cascades, while experiments in genetically modified mice will identify the essential function of these molecules. Discoveries from cell death research should provide clues for designing therapies for a variety of diseases, including degenerative disorders, auto‐immunity and cancer. Int. J. Cancer 81:505–511, 1999. © 1999 Wiley‐Liss, Inc.
Acoustic and HF Detection of Defects on Porcelain Pin Insulators

A review of the condition assessment methods of porcelain insulators shows that there is motivation for further improvements particularly regarding applications in distribution systems. Acoustic and high frequency (HF) methods are quite attractive mainly due to better immunity to noise and the relative easiness with which they can be adapted to in-service monitoring applications. These methods have therefore attracted considerable attention in recent research work. A laboratory experiment was set up to study electrical discharges on artificial defects made on porcelain insulators. A standard partial discharge detection method was used simultaneously with acoustic and high frequency techniques. Comparisons and contrasts of the signals were done. All the techniques gave discharge signals that had distinct features for each defect. This opens up opportunities for defect recognition through discharge signal processing.
A multi-RRT based hierarchical path planning method

The Rapidly-Exploring Random Tree (RRT) algorithm is an efficient approach to solve the path planning problem with nonholonomic constraint of wheeled mobile robot. However, the efficiency of the RRT algorithm will be reduced dramatically when a large amount of obstacles scatter in the environment. On the other hand, the RRT path planner is not optimized, which becomes the bottleneck of the traditional RRT algorithm. In this paper, a two-leveled hierarchical path planning method is presented to overcome the difficulties mentioned above. On the top level of the method, a multi-RRT framework is created by artificial-guided points to exploit and generate traversable area through RRT local exploration and merge function; on the bottom level, a heuristic search algorithm is adopted to effectively search for a feasible trajectory in the traversable area. The experimental results verify the effectiveness of the proposed method in solving the problem of wheeled robot path planning in complex environments.