Miracle-dz/UniFAR-FTUs huggingface dataset:
-Regulated Genes in Low-GC-Content Gram-Positive Bacteria †

Identification of the B Regulon of Bacillus cereus and Conservation of -Regulated Genes in Low-GC-Content Gram-Positive Bacteria † Willem van Schaik,‡ Menno van der Voort, Douwe Molenaar, Roy Moezelaar, Willem M. de Vos, and Tjakko Abee* Wageningen Centre for Food Sciences, P.O. Box 557, 6700AN Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University and Research Centre, P.O. Box 8129, 6700EV Wageningen, The Netherlands; NIZO Food Research, P.O. Box 20, 6710BA Ede, The Netherlands; and Food Technology Centre, Wageningen University and Research Centre, P.O. Box 17, 6700AA Wageningen, The Netherlands
The First Structures of T Cell Receptors

he structure of the MHC class I molecule HLA-A2 reported in 1987 by Bjorkman et al. (1) had revealed how peptide Ags are presented to T cells: peptides are buried in the long and deep groove of the MHC molecule, ﬂanked on each side by a long a helix. The structure immediately suggested that TCRs recognize the compound surface formed by the MHC helices and the embedded peptide (2), and a number of groups started to work on the extremely challenging problem of crystallizing a complex of peptide– MHC bound to a TCR. This quest was driven by several conceptually important problems. Among these, the most important question was how T cells recognize MHC despite the vast diversity within the T cell repertoire. Would there be a general binding mode of TCR on the MHC helices that explained MHC restriction, or would TCRs be able to bind to MHC proteins in many different ways? If a general binding mode indeed existed, how could it accommodate the vast repertoire of TCR sequences and the polymorphic nature of MHC molecules? In addition, would MHC class I and class II proteins be recognized in a similar manner? Thus, the goal of this effort was to provide a deﬁnitive molecular understanding for the concept of “MHC restriction”, revealed by the elegant functional experiments of Zinkernagel and Doherty (3), for which both received the Nobel Prize in Physiology or Med-icine in the same year these two structures were published.
Theory of multirate signal processing with application to signal and image reconstruction

Abstract : Signal processing methods for signals sampled at different rates are investigated and applied to the problem of signal and image reconstruction or super-resolution reconstruction. The problem is approached from the viewpoint of linear mean-square estimation theory and multirate signal processing for one- and two-dimensional signals. A new look is taken at multirate system theory in one and two dimensions which provides the framework for these methodologies. A careful analysis of linear optimal filtering for problems involving different input and output sampling rates is conducted. This results in the development of index mapping techniques that simplify the formulation of Wiener-Hopf equations whose solution determine the optimal filters. The required filters exhibit periodicity in both one and two dimensions, due to the difference in sampling rates. The reconstruction algorithms developed are applied to one- and two-dimensional reconstruction problems.
Numerical simulations of thermal instabilities in stratified gases

L'evolution de l'instabilite thermique d'un plasma non-magnetise en equilibre hydrostatique dans un champ gravitationnel uniforme est analysee avec une approximation un fluide. Il est montre que les effets de flottabilite changent substantiellement la nature de l'instabilite thermique et qu'une perturbation isobare en forme de bulle subit des instabilites de Rayleigh-Taylor et d'ecoulement cisaille.
[hal-00577273, v1] GLRT-Based Framework for the Multidimensional Statistical Resolution Limit

Recently, a criterion for Multidimensional Statistical Resolution Limit (MSRL) evaluation, which is defined as the minimal separation to resolve two closely spaced signals depending on several parameters, was empirically proposed in [1] but without a statistical analysis. In this paper, we fill this lack by demonstrating that this MSRL criterion is asymptotically equivalent (upon to a translator factor) to a UMP (Uniformly Most Powerful) test among all invariant statistical tests. This result is an extension of a previous work on mono-dimensional SRL ( i.e.,when the signals only depend on one parameter). As an illustrative example, the 3-D harmonic retrieval case for wireless channel sounding is treated to show the good agreement of the proposed result.
Establishment of a Method to Extract UX Related to Car Accessories, and its Data Analysis: Aiming

- Today, cars and PCs are prevalent in our daily lives and have reached high levels of function, performance, and accessibility. In addition to the product itself, user experience (UX) has become important. However, the methods to assess UX in real applications and effectively use UX to develop new products are not established. Therefore, this study aimed to establish and verify a design planning process based on UX using a wireless car key as the model application. Particularly, this paper focuses on a method to extract UX. First, we surveyed how users interact with cars and determined the types of positive experiences users have in daily life, especially related to wireless keys. We first divided the car driving experience into six steps from the user’s departure to their arrival at the destination. We let the users describe their actions, positive feelings, and emotions at each step. From 84 users, we collected 397 UX data as sets of actions, positive feelings, and emotions (scores). These UX data were arranged by the KJ method, and 25 categories were formed based on the type of experience. We also established a method to perform the above UX data collection more effectively through a mobile application, and put it to practical use.
QRM: a Case for Convergence: a Reminder that Quality Risk Management Must Work With Other Risk Management Systems

This article reflects that Quality Risk Management (QRM) is operating in a different technological environment since the ICH Q9: Quality Risk Management [1] guidance was first published in 2005. This paper explores the array of risk management systems that influence operations in a typical modern high-tech manufacturing facility. These ‘other’ risk management systems, either directly or indirectly, inform both the risk assessments and the control strategies developed by QRM. Convergence is another word for coming together. In order to assure that QRM can fully align and converge within operations, it must also ensure that it can align with these allied risk management systems. Introduction 2005 was a very different technological landscape than today. The only available tablet was medicinal. Wi-Fi in the home was unheard off – no internet, no Netflix. While the I-Pod was newly available, it was 2007 before the I-phone was launched, and with it the ability to both surf the internet and photograph our surfing all with one pocket size device. Windows XP was the operating system on our desktops, and it could only access Facebook if located on a college campus. CDs were used to back up data. Clouds caused rain showers. In 2005, the pharmaceutical industry began its journey with Quality Risk Management (QRM) with the publication of a guidance by the International Council for Harmonisation (ICH). This body, formed to enhance convergence across global regulatory requirements, published ICH Q9: Quality Risk Management. [1] The objective was to establish the principles and tools to enable the application of QRM in a Pharmaceutical Quality System (PQS). The two primary principles of ICH Q9 are that: • The evaluation of the risk to quality should be based on scientific knowledge and ultimately link to the protection of the patient; and
Effects of Tanezumab on Osteoarthritis of the Knee: A Systematic Review and Meta- Analysis

Background: Tanezumab is known as a new medical treatment for patients with osteoarthritis (OA) of the knee. We performed this meta-analysis to investigate the efficacy and safety of Tanezumab for treatment of patients with knee OA. Methods: We systematically searched randomized controlled trials from MEDLINE, Scopus, EMBASE, EBSCO, and the Cochrane Central Register of Controlled Trials (CENTRAL). The selected primary outcomes for this study were mean change in the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) pain, the WOMAC physical function and patient's global assessment (PGA). Outcomes were reported using the standard mean difference (SMD) or odds ratio (OR) with 95% confidence interval (CI). We evaluated the pooled data using a random and fixed effects models. Results: Of the studies that were found during systematic search, five studies were eligible and were included in this meta-analysis. Compared with the placebo groups, tanezumab showed a significant more reduction in mean of the WOMAC pain (SMD = -0.92, 95% CI -1.47 to -0.37, P=0.001), the WOMAC physical function (SMD = -0.59, 95% CI -0.79 to -0.39, P<0.01), and PGA (SMD = -0.36, 95% CI -0.45 to -0.27, P<0.01). There was no significant difference in serious adverse events (OR = 1.38, 95% CI 0.59 to 3.21, P = 0.48) between the tanezumab and placebo groups. Placebo significantly decreased discontinuations due to adverse events (OR = 0.37, 95% CI 0.21 to 0.64, P = 0.001), abnormal peripheral sensations (OR = 0.32, 95% CI 0.21 to 0.50, P<0.01), and peripheral neuropathy (OR = 0.25, 95% CI 0.13 to 0.48, P<0.01). Conclusion: This meta-analysis showed that Tanezumab can decrease pain and improve function for patients with OA of the knee. However, due to the limited number of studies, this conclusion should be interpreted cautiously and further clinical randomized controlled trials will be required to approve the efficacy and safety of tanezumab for OA of the knee.
Insight from Nigerian Banking Customers Discussions: A Study of Contextual Semantic Search and Twitter Sentiment Analysis

—Abstract—Globally, the bank is a signiﬁcant ﬁnan-cial institution that engages customers in millions daily. This ﬁnancial institution helps its customers in saving their money, with withdrawals, and money transfer electronically. Despite the inevitability of these ﬁnancial institutions, they are still struggling to improve their customer’s satisfaction index scores. The intervention of the Central Bank and Federal Competition and Consumer Protection Commission are yielding positive results whenever the local bank failed, but the response time to the customer grievances is quite challenging. The literature reviewed for this study indicates the cruciality of the sentiment analysis technique. This study utilized Twitter Crawler API called the Twitter Scraper for data collection and Textblob, Vader and SentiStrength for the data analyses. The result shows the sentiments in the International Authorization Banking group as against the National Authorization group and a slight difference between the polarities of their customer’s tweets. This study gives new insights internationally and nationally to banking managers and proposes future research directions.
Nutrient Delivery Systems: The Future Strategy for Chronic Diseases

Thus far, a variety of delivery systems have been investigated and successfully evaluated for nutrient delivery applications [1], including colloidal nanoparticles [2,3], nanoemulsions [4,5], nanofibers [6], hydrogels [7,8], solid lipid nanoparticles [9], etc. The type of delivery systems mainly depends upon the nutrient to be encapsulated and its delivery site in the body. Various nutrients have been studied in the development of delivery systems, including vitamins [10,11], polyphenols [12,13], essential oils [4,14], bioactive indoles [15] and peptides [16], etc. Different technologies, including spray drying, electrospinning, electrospray, freeze drying, emulsification, coacervation, ionic gelation, etc., have all been tested for their feasibility and applications in the field of food science [17].
Numerical Simulation of Heat Transfer and Pressure Drop of Pseudo-Plastic Fluid in a Pipe Heat Exchanger Equipped with a Modified Twisted Tape

The present paper, heat transfer and flow of shear-thinning non-Newtonian fluids in a circular tube under constant heat flux with a modified twisted tape, have been numerically studied in a laminar, steady state and three-dimensional regime. The finite volume method was used to numerically solve the governing equations, modified power law model be used to describe the dependence between the stresses and shear rates. The physical model is a circular tube with a standard twisted tape with decreasing its width, also a hollow tape in circular tube with increase in the central cavity of the tape. The heat transfer and the overall performance are unfavorable by cutting off the tape edge. Instead decrease tape width ratio, hollow tape with different removal ratio was used to improve thermal efficiency. the numerical results show that the removal ratio (hollow width of the tape divided by the initial width) equal to 0.3 in the fluids with behavioral indexes 0.86, 0.55 and 0.41 can cause 17.95%, 18.49% and 19.69% increases thermal performance compared to the best thermal performance mode, respectively. Therefore, the hollow twisted tape is a promising technique for laminar convective heat transfer enhancement.
Research on Teaching Practice of Literature Review Writing for Higher Vocational Undergraduates

This paper is a teaching summary of the literature review writing course which is integrated into the literature review course framework and oriented to higher vocational undergraduates.The basic steps of literature review writing are introduced through example teaching, and the structure and organization characteristics of different literature reviews and writing details such as common traps to avoid and commonly used beautiful words and sentences are shown.Special emphasis is placed on the use of appropriate scaffolding in the teaching process to help students with different ability levels master the writing skills of literature review . According to the feedback after class, most students have mastered the essentials of literature review writing and realized the significance of literature review writing, whether it is short-term academic research or work.Individual students can consciously find problems in work and seek help from others to complete improvement.The results showed that the students understood and mastered the writing skills of literature review, which laid a good foundation for further study and work.
Comparative Study of Data Mining Based Classification Algorithms

: lassification is an important data mining technique based on machine learning with broad applications. It classifies various kinds of data and used in nearly every field of our life. Classification is used to classify each item in a set of data into one of predefined set of classes or groups. This paper describes the performance analysis of Naïve Bayes and J48 classification algorithm based on the correct and incorrect instances of data classification. Naive Bayes algorithm is based on probability and j48 algorithm is based on decision tree. In this paper we compare and perform evaluation of classifiers NAIVE BAYES and J48 in the context of mushroom dataset in UCI repository to maximize true positive rate and minimize false positive rate of defaulters rather than achieving only higher classification accuracy using WEKA tool. The experiments results shown in this paper are about true positive rate, false positive rate, classification accuracy and cost analysis. The results in the paper on mushroom dataset in UCI repository also show that the efficiency and accuracy of J48 and Naive Bayes is good.
Madurasinghe, Vichithranie W. and Eldridge, Sandra and Forbes, Gordon (2016) Guidelines for reporting

Background: Recruitment to clinical trials is difficult with many trials failing to recruit to target and within time. Embedding trials of recruitment interventions within host trials may provide a successful way to improve this. There are no guidelines for reporting such embedded methodology trials. As part of the Medical Research Council funded Systematic Techniques for Assisting Recruitment to Trials (MRC START) programme designed to test interventions to improve recruitment to trials, we developed guidelines for reporting embedded trials. Methods: We followed a three-phase guideline development process: (1) pre-meeting literature review to generate items for the reporting guidelines; (2) face-to-face consensus meetings to draft the reporting guidelines; and (3) post-meeting feedback review, and pilot testing, followed by finalisation of the reporting guidelines. Results: We developed a reporting checklist based on the Consolidated Standards for Reporting Trials (CONSORT) statement 2010. Embedded trials evaluating recruitment interventions should follow the CONSORT statement 2010 and report all items listed as essential. We used a number of examples to illustrate key issues that arise in embedded trials and how best to report them, including (a) how to deal with description of the host trial; (b) the importance of describing items that may differ in the host and embedded trials (such as the setting and the eligible population); and (c) the importance of identifying clearly the point at which the recruitment interventions were embedded in the host trial. Conclusions: Implementation of these guidelines will improve the quality of reports of embedded recruitment trials while advancing the science, design and conduct of embedded trials as a whole.
Austin Biomarkers & Diagnosis Implication of miRNAs in the Pathogenesis of Gallbladder Cancer

MicroRNAs (miRNAs) are small non-coding RNAs which regulate key cellular processes through a negative post-transcriptional regulation of their target mRNAs. They can act either as oncogenes or as tumor suppressors or as both, depending on the specific tissue expression. Oncogenic miRNAs act directly on mRNAs from genes with pro-apoptotic or anti-proliferative roles. Conversely, tumor-suppressor miRNAs repress the expression of genes with oncogenic functions. Deregulation of many of these miRNAs has been associated with tumorigenesis in various cancers and recent studies have shown evidences of abnormal miRNA expression in gallbladder cancer. Here, we review our current understanding of the expression changes in tumor-suppressor miRNAs (miR-1, miR-145, miR-135a-5p, miR-26a, miR-34a, miR-335, miR-130a and miR-218-5p) and oncogenic miRNAs (miR-155, miR-20a and miR-182) and its implication in the pathogenesis of gallbladder cancer and their potential as diagnostic and prognostic markers.
Biochemical and Genetic Studies of the Initiation of Human Rhinovirus 2 RNA Replication: Identification of a cis-Replicating Element in the Coding Sequence of 2A

We have previously shown that the RNA polymerase 3D of human rhinovirus 2 (HRV2) catalyzes the covalent linkage of UMP to the terminal protein (VPg) using poly(A) as a template (K. Gerber, E. Wimmer, and A. V. Paul, J. Virol. 75:10969–10978, 2001). The products of this in vitro reaction are VPgpU, VPgpUpU, and VPg-poly(U), the 5 end of minus-strand RNA. In the present study we used an assay system developed for poliovirus 3D (A. V. Paul, E. Rieder, D. W. Kim, J. H. van Boom, and E. Wimmer, J. Virol. 74: 10359–10370, 2000) to search for a viral sequence or structure in HRV2 RNA that would provide specificity to this reaction. We now show that a small hairpin in HRV2 RNA [cre(2A)], located in the coding sequence of 2A, serves as the primary template for HRV2 3D in the uridylylation of HRV2 VPg, yielding VPgpU and VPgpUpU. The in vitro reaction is strongly stimulated by the addition of purified HRV2 3CD. Our analyses suggest that HRV2 3D uses a “slide-back” mechanism during synthesis of the VPg-linked precursors. The corresponding cisreplicating RNA elements in the 2C coding region of poliovirus type 1 Mahoney (I. Goodfellow, Y. Chaudhry, A. Richardson, J. Meredith, J. W. Almond, W. Barclay, and D. J. Evans, J. Virol. 74:4590–4600, 2000) and VP1 of HRV14 (K. L. McKnight and S. M. Lemon, RNA 4:1569–1584, 1998) can be functionally exchanged in the assay with cre(2A) of HRV2. Mutations of either the first or the second A in the conserved A1A2A3CA sequence in the loop of HRV2 cre(2A) abolished both viral growth and the RNA’s ability to serve as a template in the in vitro VPg uridylylation reaction.
Identifi cation of specifi c histidines as pH sensors in fl avivirus membrane fusion

The Rockefeller University Press $30.00 J. Cell Biol. Vol. 183 No. 2 353–361 www.jcb. org/cgi/doi/10.1083/jcb.200806081 JCB 353 Correspondence to Karin Stiasny: karin.stiasny@meduniwien.ac. at Abbreviations used in this paper: DI, domain I; FP, fusion peptide; RSP, recombinant subviral particle; sE, soluble E; TBEV, tick-borne encephalitis virus; WT, wild type. The online version of this article contains supplemental material. Introduction
RRU_A_299801 155..165

Department of Urology, Nara Medical University, Kashihara, Nara, 634-8522, Japan Purpose: Reports suggest that partial nephrectomy provides no significant benefit in terms of cancer-specific and overall survival (OS) compared to radical nephrectomy. Here, we focused on survival in terms of life expectancy and investigated the significance of partial nephrectomy for localized renal cell carcinoma (RCC) patients. Patients and Methods: Our retrospective study included 937 patients (median age 63 years) with localized RCC who underwent partial nephrectomy or radical nephrectomy. Various predictive factors were explored, and the association between actual OS and life expectancy was analyzed. Results: Performance status (PS) ≥1 and tumor size ≥40 mm were identified as independent poor prognostic factors for cancer-specific survival. Age ≥60, male sex, PS ≥1, C-reactive protein elevation, pT1b stage, and radical nephrectomy were identified as independent poor prognostic factors for OS. OS and life expectancy did not differ in the partial nephrectomy group (P=0.11). OS was significantly shorter than life expectancy in the radical nephrectomy group (P<0.0001). In PS0 or pT1a patients, there was a significant difference between actual OS and life expectancy in the radical nephrectomy group (P<0.0001), but not in the partial nephrectomy group (P=0.15). In patients with a life expectancy ≥10 years, PS0, and pTa, OS and life expectancy differed in the radical nephrectomy group, but not in the partial nephrectomy group. Conclusion: Partial nephrectomy can improve actual OS, and notably, PS and tumor size are crucial factors that determine the choice of surgical procedure. Further research is needed to establish appropriate treatment strategies and criteria for clinical practice.