Miracle-dz/UniFAR-FTUs huggingface dataset:
Convergence of Molecular, Modeling, and Systems Approaches for an Understanding of the Escherichia coli Heat Shock Response

SUMMARY The heat shock response (HSR) is a homeostatic response that maintains the proper protein-folding environment in the cell. This response is universal, and many of its components are well conserved from bacteria to humans. In this review, we focus on the regulation of one of the most well-characterized HSRs, that of Escherichia coli. We show that even for this simple model organism, we still do not fully understand the central component of heat shock regulation, a chaperone-mediated negative feedback loop. In addition, we review other components that contribute to the regulation of the HSR in E. coli and discuss how these additional components contribute to regulation. Finally, we discuss recent genomic experiments that reveal additional functional aspects of the HSR.
SE362 Lecture 25: Leadership

To secure accurate control over rapid diffusion such as the diffusion of zinc into gallium arsenide, the source and slices to be processed are isolated from one another during an initial warm-up period. This is done using one vessel for the crystal slice and a second vessel for the source. The source vessel initially blocks an opening in the slice vessel while the source and slice are brought to the desired diffusion temperature. The source vessel is then slid through the opening to a diffusing position in which a trailing part of the source vessel again plugs the opening in the slice vessel and in which an open part of the source vessel is now in the interior of the slice vessel. Use of this arrangement avoids the uncontrolled diffusion which occurs in current diffusion capsules during initial heating of the capsule.
Plant extinctions and introductions lead to phylogenetic and taxonomic homogenization of the European flora

Human activities have altered the composition of biotas through two fundamental processes: native extinctions and alien introductions. Both processes affect the taxonomic (i.e., species identity) and phylogenetic (i.e., species evolutionary history) structure of species assemblages. However, it is not known what the relative magnitude of these effects is at large spatial scales. Here we analyze the large-scale effects of plant extinctions and introductions on taxonomic and phylogenetic diversity of floras across Europe, using data from 23 regions. Considering both native losses and alien additions in concert reveals that plant invasions since AD 1500 exceeded extinctions, resulting in (i) increased taxonomic diversity (i.e., species richness) but decreased phylogenetic diversity within European regions, and (ii) increased taxonomic and phylogenetic similarity among European regions. Those extinct species were phylogenetically and taxonomically unique and typical of individual regions, and extinctions usually were not continent-wide and therefore led to differentiation. By contrast, because introduced alien species tended to be closely related to native species, the floristic differentiation due to species extinction was lessened by taxonomic and phylogenetic homogenization effects. This was especially due to species that are alien to a region but native to other parts of Europe. As a result, floras of many European regions have partly lost and will continue to lose their uniqueness. The results suggest that biodiversity needs to be assessed in terms of both species taxonomic and phylogenetic identity, but the latter is rarely used as a metric of the biodiversity dynamics.
Extracting Protein-Reaction Information from Tables of Unpredictable Format and Content in the Molecular Biology Literature

Tables in technical papers often provide much useful information that is not present in text. This paper focuses on the specific problem of automated table reading (ATR): automating the interpretation and extraction of information from proteinreaction information (PRI) tables in the molecular biology literature (MBL), in the context of a general knowledge-based approach to automating table reading.We report on the results of our system evaluation, which demonstrated a precision of greater than . 9 in identifying relevant tables and . 8 in mapping tables to correct relational schema.
Likelihood of Treatment in a Coronary Care Unit for a First-Time Myocardial Infarction in Relation to Sex, Country of Birth and Socioeconomic Position in Sweden

Objective To examine the relationship between sex, country of birth, level of education as an indicator of socioeconomic position, and the likelihood of treatment in a coronary care unit (CCU) for a first-time myocardial infarction. Design Nationwide register based study. Setting Sweden. Patients 199 906 patients (114 387 men and 85,519 women) of all ages who were admitted to hospital for first-time myocardial infarction between 2001 and 2009. Main outcome measures Admission to a coronary care unit due to myocardial infarction. Results Despite the observed increasing access to coronary care units over time, the proportion of women treated in a coronary care unit was 13% less than for men. As compared with men, the multivariable adjusted odds ratio among women was 0.80 (95% confidence interval 0.77 to 0.82). This lower proportion of women treated in a CCU varied by age and year of diagnosis and country of birth. Overall, there was no evidence of a difference in likelihood of treatment in a coronary care unit between Sweden-born and foreign-born patients. As compared with patients with high education, the adjusted odds ratio among patients with a low level of education was 0.93 (95% confidence interval 0.89 to 0.96). Conclusions Foreign-born and Sweden-born first-time myocardial infarction patients had equal opportunity of being treated in a coronary care unit in Sweden; this is in contrast to the situation in many other countries with large immigrant populations. However, the apparent lower rate of coronary care unit admission after first-time myocardial infarction among women and patients with low socioeconomic position warrants further investigation.
TCP Skudai: A High Performance TCP Variant for Collaborative Virtual Environment Systems

In Collaborative Virtual Environment (CVE) systems, one of the main research topics in is how to efficiently transmit message to minimized delay, provide scalability and reliability, and also the choice of transport protocol. TCP is the most widely used protocol in the design of CVE systems, and its throughput deteriorates in the network with large delay due to it conservative congestion control. TCP removes network congestion by adjusting sending rate according to available bandwidth. Researchers have shown that TCP underutilizes bandwidth in a high-speed network and in a long distance network. With the increasing number of concurrent distant collaborators in CVE systems, TCP may not provide the level of consistency and scalability required in the systems. Many researchers have proposed different modifications of TCP, but rarely addressed the issues in CVE systems. In this paper, we proposed a novel TCP variant conceptual model called TCP Skudai, aimed at achieving a high performance congestion control algorithm for CVE systems. The methods used in the conceptualizations lies within adding constraints to the phases of transmission: slow start, congestion avoidance, fast retransmit, and fast recovery based on principle of packet conservation.
Irradiance governs exploitation of fungi: fine-tuning of carbon gain by two partially myco-heterotrophic orchids

While all members of the Orchidaceae are fully dependent on mycorrhizal fungi during their achlorophyllous juvenile stages, mature plants may remain fully myco-heterotrophic, become fully autotrophic or develop a nutritional mode where the carbon gain through photosynthesis is complemented by organic carbon from fungal partners. This so-called partial myco-heterotrophy is intriguingly complex. Current knowledge indicates a large range in the proportion of fungus-derived carbon between and within partially myco-heterotrophic plant species. However, the driving factors for this variation are so far mostly unknown. Here we show for two green species of the orchid genus Cephalanthera that light availability is the major determinant of the degree of myco-heterotrophy. Using leaf stable isotope natural abundance analysis together with time-integrated microscale light climate monitoring we could demonstrate that there is a sensitive reaction to varying light availability within forests. Low light levels result in strong myco-heterotrophy while higher irradiances successively drive the orchids towards autotrophy. Our results demonstrate that partial myco-heterotrophy in these species is not a static nutritional mode but a flexible mechanism driven by light availability which allows a balanced usage of carbon resources available in nature.
Identification of a Short Region on Chromosome 6 Affecting Direct Calving Ease in Piedmontese Cattle Breed

Calving in cattle is affected by calf morphology and by dam characteristics. It is described by two different traits: maternal calving ease, which is the ability to generate dams with good physiological predisposition to calving, and direct calving ease, which is the ability to generate calves that are easily born. The aim of this study was to identify regions of cattle genome harboring genes possibly affecting direct calving ease in the Piedmontese cattle breed. A population of 323 bulls scored for direct calving ease (EBV) was analyzed by a medium-density SNP marker panel (54,001 SNPs) to perform a genome-wide scan. The strongest signal was detected on chromosome 6 between 37.8 and 38.7 Mb where 13 SNPs associated to direct calving ease were found. Three genes are located in this region: LAP3, encoding for a leucine aminopeptidase involved in the oxytocin hydrolysis; NCAPG, encoding for a non-SMC condensin I complex, which has been associated in cattle with fetal growth and carcass size; and LCORL, which has been associated to height in humans and cattle. To further confirm the results of the genome-wide scan we genotyped additional SNPs within these genes and analyzed their association with direct calving ease. The results of this additional analysis fully confirmed the findings of the GWAS and particularly indicated LAP3 as the most probable gene involved. Linkage Disequilibrium (LD) analysis showed high correlation between SNPs located within LAP3 and LCORL indicating a possible selection signature due either to increased fitness or breeders’ selection for the trait.
A Novel Computational Method for Inferring Dynamic Genetic Regulatory Trajectories

We present a novel method called Time Series Affinity Propagation (TSAP) for inferring regulatory states and trajectories from time series genomic data. This method builds on the Affinity Propagation method of Frey and Dueck [10]. TSAP incorporates temporal constraints to more accurately model the dynamic nature of underlying biological mechanisms. We first apply TSAP to synthetic data and demonstrate its ability to recover underlying structure that is obscured by noise. We then apply TSAP to real data and demonstrate that it provides insight into the relationship between gene expression and histone posttranslational modifications during motor neuron development. In particular, the trajectories taken by the Hox genes through the space of regulatory states are characterized. Understanding the dynamics of Hox regulation is important because the Hox genes play a fundamental role in the establishment of motor neuron sub-type identity during development [6]. Thesis Supervisor: David K. Gifford Title: Professor of Electrical Engineering and Computer Science
The Economics of Geographical Indications: Towards a Conceptual Framework for Geographical Indication Research in Developing Countries

Over the past two decades, agrifood systems have experienced a significant move towards market differentiation and product proliferation in many parts of the world. This product proliferation and differentiation is associated with what Allaire (2003) described as “the immaterialization of food and the institutionalization of quality”, which is translating into an increasing complexity of quality and new quality conventions. These institutions go beyond the neo-classical model of market pricing and quality signaling through price mechanisms, to instances where institutions that define and enforce quality standards and norms become key to the performance of market mechanisms. As stated by Sauvee and Valceschini (2003): “In the current competitive universe, the definition of quality and the information on qualities are from now on at the heart of the competitive strategies of economic actors”.
Measuring Equity Share Related Risk Perception of Investors in Economically Backward Regions

Risk perception is an idiosyncratic process of interpretation. It is a highly personal process of making a decision based on an individual’s frame of reference that has evolved over time. The purpose of this paper is to find out the risk perception level of equity investors and to identify the factors influencing their risk perception. The study was conducted using a stratified random sampling design of 358 investors. It was found that the overall risk perception level of equity investors is moderate and that the main factors affecting their risk perception are information screening, investment education, fear psychosis, fundamental expertise, technical expertise, familiarity bias, information asymmetry, understanding of the market, etc. Considering the above findings, efforts should be made to bring people with a high risk perception to the low risk perception category by providing them with training to handle or manage high-risk scenarios which will help in promoting an equity-investment culture.
What can history tell us?: towards different models of interaction with document histories

The current Web is a dynamic collection where little effort is made to version pages or to enable users to access historical data. As a consequence, they generally do not have sufficient temporal support when browsing the Web. However, we think that there are many benefits to be obtained from integrating documents with their histories. For example, a document's history can enable us to travel back through time to establish its trustworthiness. This paper discusses the possible types of interactions that users could have with document histories and it presents several examples of systems that we have implemented for utilizing this historical data. To support our view, we present the results of an online survey conducted with the objective of investigating user needs for temporal support on the Web. Although the results indicated quite low use of Web archives by users, they simultaneously emphasized their considerable interest in page histories.
Standing of nucleic acid testing strategies in veterinary diagnosis laboratories to uncover Mycobacterium tuberculosis complex members

Nucleic acid testing (NAT) designate any molecular approach used for the detection, identification, and characterization of pathogenic microorganisms, enabling the rapid, specific, and sensitive diagnostic of infectious diseases, such as tuberculosis. These assays have been widely used since the 90s of the last century in human clinical laboratories and, subsequently, also in veterinary diagnostics. Most NAT strategies are based in the polymerase chain reaction (PCR) and its several enhancements and variations. From the conventional PCR, real-time PCR and its combinations, isothermal DNA amplification, to the nanotechnologies, here we review how the NAT assays have been applied to decipher if and which member of the Mycobacterium tuberculosis complex is present in a clinical sample. Recent advances in DNA sequencing also brought new challenges and have made possible to generate rapidly and at a low cost, large amounts of sequence data. This revolution with the high-throughput sequencing (HTS) technologies makes whole genome sequencing (WGS) and metagenomics the trendiest NAT strategies, today. The ranking of NAT techniques in the field of clinical diagnostics is rising, and we provide a SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis with our view of the use of molecular diagnostics for detecting tuberculosis in veterinary laboratories, notwithstanding the gold standard being still the classical culture of the agent. The complementary use of both classical and molecular diagnostics approaches is recommended to speed the diagnostic, enabling a fast decision by competent authorities and rapid tackling of the disease.
A zero-knowledge protocol based on a new product of durations

Whenever we need to conduct a privacy assessment, Zero-knowledge protocol is the one that we can consider. It is used in consulting for privacy and security solutions. In this protocol, there are often two parties: one party has to prove to the other that a statement is true, without revealing anything accepting the veracity. They have an agreement on the way of asking question and answering. Some people use one-time checking method, some use an interactive method. In this paper, we introduce an algebraic structure of durations and its application to design a Zero-knowledge protocol with high reliability. The complexity for cracking this protocol is O(2n x n! ) and for implementing is O(n) where n is the length of the key.
Architecture of Collaborative Design Based on Grid

To solve the resource sharing and real-time interactive problems in collaborative design, we present a prototype system named grid-based collaborative design system (GCDS) integrating both computer supported collaborative design(CSCD) and grid technology which not only maintains data consistency across globally-distributed locations seamlessly, but also allows members of collaborative work team to access the storage system and computing resources such as HPC transparently and security. A three-tier communication framework is also proposed to realize GCDS by use high performance computers(HPC) conveniently.
Constructing Orthogonal Reenable Function Vectors with Prescribed Approximation Order and Smoothness

We review and announce results from 6] and 7] and demonstrate their utility in constructing orthogonal reenable function vectors with prescribed approximation order and smoothness. In the case of local dimension 3 and approximation order 2, our approach naturally produces the family of orthogonal multiwavelets originally found in 2] as well as Daubechies' well known scaling function 2. In Section 5 we use our techniques to construct an orthogonal reenable function vector with two entries, one supported on 0;2] and one supported on 0;3], that is continuously diierential and provides approximation order 3.
Pettit National Ice Center Public Skate Participation Survey

PETTIT NATIONAL ICE CENTER PUBLIC SKATE PARTICIPATION SURVEY Andrew Christopher Brown, B.A. Marquette University, 2014 This research project seeks to identify areas that the Pettit National Ice Center can address in order to increase customer satisfaction, thereby transforming infrequent users into repeat clientele. One hundred-fifty individuals were surveyed utilizing a mixed methods approach which produced qualitative and quantitative results for analysis. Key recommendations for the Pettit National Ice Center include providing improved customer service, improving the appearance and quality of equipment inside the facility, increasing its online presence, and identifying potential revenue generators. PETTIT NATIONAL ICE CENTER i ACKNOWLEDGMENTS Andrew Christopher Brown, B.A. I honestly do not know which is tougher – writing a professional project or finding the words to thank those that made it all possible. There are so many people I need to thank but I fear that list may be longer than this project. I have tried to find the words to express everything I wish to convey, but after some reflection, I found that others have said it better than I ever could. “You can’t live a perfect day without doing something for someone who will never be able to repay you. ” John Wooden To Dr. Jay Caulfield and Dr. Paul McInerny – Thank you for providing me with this opportunity. I may never be able to repay you for the experience you gave me, but please know that it is people like you that make Marquette truly special. “I’ve learned that people will forget what you said, people will forget what you did, but people will never forget how you made them feel. ” Maya Angelou To my family and friends – Without whom none of my success would be possible. You have loved me for everything I am and everything I not, but always made me feel worthy of your love. “The greatest gift anyone can give another person: believing in them. ” Jim Valvano To Michaela – Thank you for never giving up on me. Your constant belief in me gives me the confidence I always seemed to lack before you. I am truly humbled by your presence in my life. “All our dreams can come true.if we have the courage to pursue them. ” Walt Disney PETTIT NATIONAL ICE CENTER ii
The Correlation of Perceived Social Support and Emotional Schemes With Students’ Social Anxiety

Materials and Methods: The current correlational analytic study was conducted on all undergraduate students of Islamic Azad University, Rasht Branch in the academic year of 2015-2016 that was 3986 people. In the current study, 351 students with social anxiety were selected using the convenient sampling method and Morgan table. The study tools included the Zimet perceived social support scale, the Leahy emotional Schemas scale, and Jerabek social anxiety questionnaire. The collected data were analyzed using descriptive statistics and Pearson correlation coefficient test.
CP-673451, a platelet-derived growth-factor receptor inhibitor, suppresses lung cancer cell proliferation and migration

Lung cancer is the leading cause of cancer mortality in the world. Although some advances in lung cancer therapy have been made, patient survival is still poor. The platelet-derived growth factor receptors (PDGFRs) and their ligands play critical roles in the regulation of many cancer cell processes, including cell survival and cell motility. Herein, we investigate the anticancer activities of CP-673451, a potent selective inhibitor of PDGFR kinase, in non-small-cell lung cancer (NSCLC) therapy. We found that CP-673451 is effective at suppressing cell viability, inducing cell apoptosis, and inhibiting cell migration and invasion by suppressing the PDGFR downstream signaling pathway in NSCLC cells. Furthermore, CP-673451 is effective at suppressing NSCLC tumor growth in vivo. In summary, our studies suggest that CP-673451 might be a promising therapeutic compound for NSCLC.