Miracle-dz/UniFAR-FTUs huggingface dataset:
Different Pathways Regulate Expression of the Skeletal Myosin Heavy Chain Genes*

Mammalian skeletal muscles are a mosaic of different fiber types largely defined by differential myosin heavy chain (MyHC) expression. Little is known about the molecular mechanisms regulating expression of the MyHC gene family members in different fiber types. In this work, we identified several cis- andtrans-elements that regulate expression of the three adult fast MyHC genes. Despite multiple DNA-binding motifs for well characterized muscle transcription factors upstream of all three fast MyHC genes, expression of MyoD/Myf-5, calcineurin, or NFAT3 had different effects on the three promoters. MyoD or Myf-5 overexpression preferentially activated the IIb promoter, whereas NFAT or activated calcineurin overexpression preferentially activated the IIa promoter. Calcineurin had a 50–100-fold stimulatory effect on the IIa promoter, and the known downstream effectors of calcineurin (myocyte enhancer factor-2 and NFAT) cannot completely account for this activation. Finally, we identified two elements critical for regulating MyHC-IId/x expression: a 130-base pair enhancer element and a CArG-like element that inhibited IId/x promoter activity in vitro. Thus, we have found specific regulatory pathways that are distinct for the three adult fast MyHC genes. These elements are logical candidates for fiber-specific control of skeletal muscle gene expression in vivo.
Extending multi-tenant architectures: a database model for a multi-target support in SaaS applications

Multi-tenant architectures (MTAs) are considered a cornerstone in the success of Software as a Service as a new application distribution formula. Multi-tenancy allows multiple customers (i.e. tenants) to be consolidated into the same operational system. This way, tenants run and share the same application instance as well as costs, which are significantly reduced. Functional needs vary from one tenant to another; either companies from different sectors run different types of applications or, although deploying the same functionality, they do differ in the extent of their complexity. In any case, MTA leaves one major concern regarding the companies’ data, their privacy and security, which requires special attention to the data layer. In this article, we propose an extended data model that enhances traditional MTAs in respect of this concern. This extension – called multi-target – allows MT applications to host, manage and serve multiple functionalities within the same multi-tenant (MT) environment. The practical deployment of this approach will allow SaaS vendors to target multiple markets or address different levels of functional complexity and yet commercialise just one single MT application. The applicability of the approach is demonstrated via a case study of a real multi-tenancy multi-target (MT2) implementation, called Globalgest.
Mesial Temporal Lobe Epilepsy: What Have We Learned?

Mesial temporal lobe epilepsy is the most common form of human epilepsy, and its pathophysiological substrate is usually hippocampal sclerosis, the most common epileptogenic lesion encountered in patients with epilepsy. The disabling seizures associated with mesial temporal lobe epilepsy are typically resistant to antiepileptic drugs but can be abolished in most patients by surgical treatment. Anteromesial temporal resection, therefore, is the most common surgical procedure performed to treat epilepsy, and stereo-tactically implanted intracerebral electrodes are required in some patients to localize the epileptogenic region. This clinical setting provides a large number of patients for invasive in vivo research with microelectrode and microdialysis techniques and in vitro research following surgical resection on a single epileptic disorder. Consequently, much has now been learned about the fundamental neuronal mechanisms underlying the epileptogenic properties of the human hippocampus in mesial temporal lobe epilepsy. Parallel reiterative studies in patients and animal models of this disorder indicate that enhanced inhibition, in addition to enhanced excitation, underlies the appearance of hypersynchronous neuronal discharges responsible for generating spontaneous seizures. Recent studies have elucidated what may be unique electrophysiological markers of epileptogenicity, which could have valuable diagnostic utility. Although basic research on mesial temporal lobe epilepsy may ultimately suggest novel approaches to treatment and prevention, attention must also be given to maximizing the application of available effective treatments. In particular, the safety and efficacy of surgical therapy has greatly improved in recent years, yet this alternative treatment remains seriously underutilized worldwide. An appropriate increase in referral of patients with this surgically remediable syndrome to epilepsy centers will not only relieve a great many patients of their disabling seizures and reduce the burden of epilepsy but will also provide increased opportunities for invasive research that could ultimately result in even more effective therapies or cures.
The influence of fluorinated SiNx gate insulator in a-InGaZnO thin film transistors

We fabricated highly reliable amorphous In-Ga-Zn-O thin-film transistors (a-IGZO TFTs) with fluorinated silicon nitride (SiN<sub>x</sub>) as a gate insulator. The SiN<sub>x</sub> layer was formed with utilizing SiF<sub>4</sub>/N<sub>2</sub> as source gases at a temperature as low as 150°C. We studied the influence of hydrogen and fluorine on the electrical characteristics.
The Use of the Finasteride-Adjusted Prostate Cancer Prevention Trial Prostate Cancer Risk Calculator in a Mexican Referral Population: A Validation Study

Objectives: To perform the first validation study of the finasteride-adjusted Prostate Cancer Prevention Trial Prostate Cancer Risk Calculator (finPCPTRC) in a contemporary referral population in Mexico. Methods: 837 patients referred to the Instituto Nacional de Cancerología, Mexico City, Mexico, between 2005 and 2009 were used to validate the finPCPTRC by examining various measures of discrimination and calibration. Net benefit curve analysis was used to gain insight into the use of the finPCPTRC for clinical decisions. Results: Prostate cancer (PCa) incidence (72.8%) was high in this Mexican referral cohort and 45.7% of men who were diagnosed with PCa had high-grade lesions (HGPCa, Gleason score >6). 1.3% of the patients were taking finasteride. The finPCPTRC was a superior diagnostic tool compared to prostate-specific antigen alone when discriminating patients with PCa from those without PCa (AUC = 0.784 vs. AUC = 0.687, p < 0.001) and when discriminating patients with HGPCa from those without HGPCa (AUC = 0.768 vs. AUC = 0.739, p < 0.001). The finPCPTRC underestimated the risk of PCa but overestimated the risk of HGPCa (both p < 0.001). Compared with other strategies to opt for biopsy, the net benefit would be larger with utilization of the finPCPTRC for patients accepting higher risks of HGPCa. Conclusions: Rates of biopsy-detectable PCa and HGPCa were high and 1.3% of this referral cohort in Mexico was taking finasteride. The risks of PCa or HGPCa calculated by the finPCPTRC were not well calibrated for this referral Mexican population and new clinical diagnostic tools are needed.
A convenient cell fusion assay for the study of SARS‐CoV entry and inhibition

SARS‐CoV spike (S) protein‐mediated cell fusion is important for the viral entry mechanism and identification of SARS‐CoV entry inhibitors. In order to avoid the high risks involved in handling SARS‐CoV and to facilitate the study of viral fusion mechanism, we established the cell lines: SR‐COS7 cells that stably express both SARS‐CoV S protein and red fluorescence protein, R‐COS7 cells that stably express red fluorescence protein, and AG‐COS7 cells that stably express both ACE2 and green fluorescence protein, respectively. When SR‐COS7 cells or R‐COS7 cells were cocultured with AG‐COS7 cells, syncytia with yellow fluorescence were conveniently observed after 12 h in SR‐COS7 cells plus AG‐COS7 cells, but not in R‐COS7 cells plus AG‐COS7 cells. The cell‐to‐cell fusion efficiency was simply determined for quantitative analysis based on the number of syncytium detected by flow cytometry. Such new cell‐to‐cell fusion model was further assessed by the potent HR2 peptide inhibitor, which led to the obvious decrease of the cell‐to‐cell fusion efficiency. The successful fusion and inhibition of cell‐based binding assay shows that it can be well used for the study of SARS‐CoV entry and inhibition. iubmb Life, 58: 480 ‐ 486, 2006
A retrospective study on surgical management of chronic pancreatitis in Chinese children

Pancreatic diseases in the children include a wide spectrum such as acute pancreatitis, acute recurrent pancreatitis, chronic pancreatitis (CP) and pancreatic disease without pancreatitis, and the management of these diseases are quite different from those in the adults. In this study we retrospectively analyzed the pathogenesis and management of CP in 12 Chinese children (7 male and 5 female, aged 6 to 12 years old). Laboratory examinations showed that serum levels of amylase and lipase increased in all patients. Radiological examinations showed that 2 children had pancreatic duct stricture, 3 children had pancreatic atrophy, 3 children had pancreatic duct dilation with pancreaticobiliary malunion, and 4 children had pancreatic duct dilation with stones. For surgical treatment, 5 patients received longitudinal pancreaticojejunostomy and 7 patients received distal pancreatectomy with Roux-en-Y pancreaticojejunostomy. All patients had good outcomes without postoperative complications. The follow-up ranged from 1.5 year to 4.5 years, and all patients had no recurrent abdominal pain. Our study suggests that individualized management for CP in the children is necessary and effective.
Taking Quinazoline as a General Support‐Nog to Design Potent and Selective Kinase Inhibitors: Application to FMS‐like Tyrosine Kinase 3

The dramatic success of the first approved protein kinase inhibitor imatinib (Gleevec) for the treatment of chronic myelogenous leukemia has fueled an explosion in kinase inhibitor research in both the pharmaceutical industry and academia. However, due to the large size of the protein kinase superfamily and the fact that most kinase inhibitors bind in the highly conserved ATP binding pocket, it is extremely difficult to impart selectivity to kinase inhibitors. This has been the most challenging problem in the discovery and development of drugs that target protein kinases. Over the past decade, significant efforts have been devoted to address this problem. Even so, a very limited number of specific kinase inhibitors have been identified at present. Herein we report a very simple and efficient strategy to design selective kinase inhibitors. This strategy is then applied to the design of FMS-like tyrosine kinase 3 (FLT3) inhibitors. The basic idea of this strategy originates from an observation of chemical structures and binding modes of some known kinase inhibitors. Currently there are nine kinase inhibitors approved as marketed drugs by the US Food and Drug Administration (FDA; see figure S1 in the Supporting Information). Three of them are 4-anilinoquinazoline derivatives, namely gefitinib (Iressa), erlotinib (Tarceva), and lapatinib (Tykerb). These inhibitors adopt very similar binding modes in the active sites of their respective target kinases: the quinazoline ring is located at the front of the ATP binding pocket, where it is sandwiched between two loops in the Nand C-lobes of the catalytic domain. Furthermore, it is consistently oriented with its N1 atom hydrogen bonded to an amide group in the so-called “hinge” region of the kinase, which connects the Nand Clobes. 4-Aniline substituents, at various angles with respect to the quinazoline ring plane, match the hydrophobic pocket at the back of the ATP binding cleft. The 6and 7-substituents of the quinazoline ring extend into the solvent and are generally poorly ordered; these positions are often modified for the purpose of improving the pharmacokinetic properties of the inhibitors. To examine whether this binding mode of 4-anilinoquinazoline-type kinase inhibitors is universally adopted in other kinases, we collected all the 4-anilinoquinazoline-type inhibitor– kinase complex structures available from the Protein Data Bank (PDB; see figure S2 in the Supporting Information). Figure 1 a shows an aligned superposition of these crystal structures,
Robustness study of a new iterative Soft Bit Rate estimation

Performance of communications systems receivers is generally estimated by the bit error rate (BER) which is computed using the Monte Carlo (MC) simulation (Bit Error Counting). In a previous paper, an alternative new method based on an estimation in an iterative and nonparametric way, of the probability density function (pdf) of the soft decision of the received bit, was suggested. It was shown that the hard decision is not needed to compute the BER and the total number of transmitted data needed is very small compared to the classical MC simulation. In this paper, it is proposed to study the robustness of this method. Simulation results of the suggested BER are given using a simple synchronous CDMA system.
Heterogeneous Regional Endocardial Repolarization is Associated with Increased Risk for Ischemia‐Dependent Ventricular Fibrillation after Myocardial Infarction

Introduction: The aim of this study was to investigate whether the characteristics of endocardial ventricular repolarization are associated with differential risk for sudden death. Prolonged surface QT interval is associated with increased arrhythmic risk after myocardial infarction (MI), but the underlying mechanism of QT prolongation and its relation to lethal arrhythmias are unclear.
Technical pitfalls potentially affecting diagnoses in immunohistochemistry

Result of the immunohistochemical reactions routinely used in diagnostic surgical pathology should be properly interpreted, since false results, related to technical and interpretative pitfalls may lead to incorrect diagnosis. The main sources of such pitfalls are reviewed, analytically described and related to different steps (fixation, tissue processing and embedding, decalcification, antigen retrieval) which may affect the accuracy of immunohistochemistry. In addition, the presence of endogenous enzyme activity, improper binding of avidin to endogenous biotin, incorrect use of antibodies, chromogen and detection systems, as well as incorrect interpretation may produce unreliable data. The high frequency and extension of such pitfalls make mandatory the use of internal and external controls and adoption of cross-validation programmes. The present study, supported by an extensive review of the related literature, is intended as a guideline leading to proper interpretation of immunohistochemical data, an essential component of the diagnostic process. Experience on the antigen retrieval procedures for different antigens is also presented.
AML1/ETO inhibits AML1/CCAAT-enhancer binding protein-alpha mediated activation of the CD11c promoter and represses CD11c expression in HL60 cells.

The translocation t(8;21)(q22;q22) creates the AML1/ETO-protein that interferes with normal myeloid differentiation. CD11c, a myeloid differentiation marker, was identified as new target for AML1/ETO-dependent gene repression. The C-terminus of ETO may mediate this effect by recruitment of histone deacetylases and/or direct interaction with other transcription factors, e.g. AML1 and C/EBPα.
Prognostic significance of Ep‐CAM AND Her‐2/neu overexpression in invasive breast cancer

To assess the frequency and prognostic impact of Ep‐CAM and Her‐2/neu overexpression in patients with breast cancer and to determine its relationship with other prognostic markers, 205 breast cancer patients with a median follow‐up of 10.8 years were enrolled in this retrospective study. Overexpression of Ep‐CAM and Her‐2/neu in tumor tissue samples was assessed by immunohistochemistry. Tumors presenting a Her‐2/neu 2+ staining were additionally analyzed by FISH to exclude false positive results. Ep‐CAM and Her‐2/neu overexpression was found in 35.6% and 19.5% of the tumor samples, respectively. Both Ep‐CAM and Her‐2/neu overexpression were predictive for poor disease‐free (DFS) and disease‐related overall survival (DROS). Concurrent Ep‐CAM and Her‐2/neu overexpression was present in 13.2% of tumor specimens and had an additive negative impact on DFS and DROS. This minority of patients had a median time to relapse of only 34 months, whereas the median time to relapse was not reached in the patient population without Her‐2/neu and Ep‐CAM overexpression. By multivariate analysis Ep‐CAM overexpression proved to be an indicator of poor prognosis, independent of tumor size, histologic grade, hormone receptor expression and Her‐2/neu overexpression. In conclusion, overexpression of Ep‐CAM and Her‐2/neu complement each other as predictors for poor prognosis in patients with invasive breast cancer. Determination of these tumor markers should help in assigning breast cancer patients to 1 of 3 distinct risk categories. © 2002 Wiley‐Liss, Inc.
Human immunodeficiency virus type 1 drug susceptibility determination by using recombinant viruses generated from patient sera tested in a cell-killing assay

A simple approach for the determination of drug susceptibilities by using human immunodeficiency virus type 1 (HIV-1) RNA from the sera of patients is described. HIV-1 RNA was extracted from patient sera, and the 5' part of the reverse transcriptase (RT) gene was transcribed into DNA and amplified in a nested PCR. The amplified fragment covers the 3' part of the protease gene and amino acids 1 to 304 of the RT gene. This fragment can be introduced through homologous recombination, as described previously, into a novel HIV-1 reference strain (pHXB2 delta 2-261RT) from which amino acids 2 to 261 of RT have been deleted. The resulting recombinant virus expresses all properties of the HXB2 reference strain except for those encoded by the introduced part of the patient RT gene. Recombinant viruses were subsequently tested for drug susceptibility in a microtiter format killing assay [3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide assay] as well as in the standard HeLa CD4+ plaque reduction assay. Similar susceptibility profiles were obtained by each assay with recombinant viruses derived from patients receiving alternating nevirapine and zidovudine treatment or lamivudine-zidovudine combination therapy. In conclusion, this approach enables high-through-put determination of the drug susceptibilities of serum RNA-derived RT genes, independent of the patient's viral background, and generates the possibility of relating changes in susceptibility to changes in viral genotypes.
Diabetes Self-Care and the Older Adult

The prevalence of diabetes is highest in older adults, a population that is increasing. Diabetes self-care is complex with important recommendations for nutrition, physical activity, checking glucose levels, and taking medication. Older adults with diabetes have unique issues that impact self-care. As people age, their health status, support systems, physical and mental abilities, and nutritional requirements change. Furthermore, comorbidities, complications, and polypharmacy complicate diabetes self-care. Depression is also more common among the elderly and may lead to deterioration in self-care behaviors. Because of concerns about cognitive deficits and multiple comorbidities, adults older than 65 years are often excluded from research trials. Thus, little clinical evidence is available and the most appropriate treatment approaches and how to best support older patients’ self-care efforts are unclear. This review summarizes the current literature, research findings, and expert and consensus recommendations with their rationales.
Requirements-based testing: an overview

The article provides an overview of the requirements based testing (RBT) process and an overview of CaliberRBT, the tool that supports the RBT process. The intended audience for the paper is project managers, development managers, developers, test managers and test practitioners who are interested in understanding requirements based testing and how it can be applied to their organization.
Indonesian news auto summarization in infrastructure development topic using 5W+1H consideration

With an average reading speed of 200–500 words per minute, at least human takes 2 to 3 minutes to read and understand one news in online media. The number of news updates on an online media in a few minutes can be a lot and it's time-consuming if a reader has to read the contents of all the news. Reading a summary that represents the main idea of the news can be a solution to save time. This study considers the 5W + 1H element in generating news summaries because this element is important in a news. The single news from online media pages is taken by scanning and grabbing process which is further will be sanitized, then segmentation and tokenizing to break the news into sentences and words. Each sentence classified into multi-label whether it contains 5W + 1H (What, Who, Where, When, Why and/or How) or nothing else by using training data that has been built. Sentences containing 5W + 1H will be selected as summary sentences. Testing of summary results shows the average precision 91%, recall 67% and f-measure 76%.
Transporte aéreo no Brasil: a crise da aviação comercial

O artigo analisa os principais aspectos economicos e atuais do transporte aereo no Brasil, destacando a crise recente da aviacao comercial, incluindo-se nesta as aviacoes regional, economica e executiva, os impactos da crise sobre os segmentos de manutencao de aeronaves e de carga aerea e sobre o sistema aeroportuario brasileiro. O artigo conclui que a fusao da TAM com a Varig e um passo essencial para a reestruturacao da aviacao comercial brasileira.
Solving Private Systems of Linear Equations with Garbled Circuits

The advent of the big data revolution has made it possible to analyse ever more complex datasets for scientific and social insights. At the same time, a widespread concern for the use given to these datasets has spurred an interest in privacypreserving data analysis. The goal of this line of research is to build frameworks allowing individuals to contribute their personal data for aggregate analysis without compromising their privacy. Secure multi-party computation (MPC) provides fundamental tools for the design of such frameworks, specially since MPC implementations published in recent years have showcased the practical feasibility of theoretical constructions pioneered by Yao [1]. However, generic approaches to MPC rarely scale to problem sizes commonly found in real-world applications of privacy-preserving data analysis involving massive datasets. The search for practical alternatives has lead to the design of hybrid approaches that carefully combine several MPC techniques. Identifying building blocks common to these solutions is an important endeavor if we hope to make progress in the design of robust and scalable tools for privacy-preserving data analysis. In this work we initiate a systematic study of methods for solving private systems of linear equations in a setting commonly found in private linear regression [2] and collaborative filtering [3] protocols. Methods for solving private systems of linear equations have been considered before, but no thorough comparison between different approaches can be found in the literature. Our goal is to provide such comparison and derive guidelines for practitioners that can lead to more efficient implementations tailored for privacy-preserving data analysis.