Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the Role of Candida albicans Agglutinin-Like Sequence (Als) Proteins in Human Oral Epithelial Cell Interactions

The fungus C. albicans uses adhesins to interact with human epithelial surfaces in the processes of colonization and pathogenesis. The C. albicans ALS (agglutinin-like sequence) gene family encodes eight large cell-surface glycoproteins (Als1-Als7 and Als9) that have adhesive function. This study utilized C. albicans Δals mutant strains to investigate the role of the Als family in oral epithelial cell adhesion and damage, cytokine induction and activation of a MAPK-based (MKP1/c-Fos) signaling pathway that discriminates between yeast and hyphae. Of the eight Δals mutants tested, only the Δals3 strain showed significant reductions in oral epithelial cell adhesion and damage, and cytokine production. High fungal:epithelial cell multiplicities of infection were able to rescue the cell damage and cytokine production phenotypes, demonstrating the importance of fungal burden in mucosal infections. Despite its adhesion, damage and cytokine induction phenotypes, the Δals3 strain induced MKP1 phosphorylation and c-Fos production to a similar extent as control cells. Our data demonstrate that Als3 is involved directly in epithelial adhesion but indirectly in cell damage and cytokine induction, and is not the factor targeted by oral epithelial cells to discriminate between the yeast and hyphal form of C. albicans.
Transforming Timing Diagrams into KAOS

Requirements engineering is an important part of developing programs. It is an essential stage of the software development process that defines what a product or system should to achieve. The UML Timing diagram and Knowledge Acquisition in Automated Specification (KAOS) model are requirements engineering techniques. KAOS is a goal-oriented requirements approach while the Timing diagram is a graphical notation used for explaining software timing requirements. KAOS uses linear temporal logic (LTL) to describe time constraints in goal and operation models. Similarly, the Timing diagram can describe some temporal operators such as X (next), U (until) and R (release) over some period of time. Thus, our aim is to use the Timing diagram to generate parts of a KAOS model. In this paper we demonstrate techniques for creating a KAOS goal model from a Timing diagram. The Timing diagram which is used in this paper is adapted from the UML 2.0 Timing diagram and includes features to support translation into KAOS. We use a case study of a Lift system as an example to explain the translation processes described
A Comparison of the Salivary Gland Chromosomes of Drosophila Melanogaster and D. Simulans.

HE general problem of chromosomes and speciation has interested T cytologists and geneticists for a long time. The earlier studies on animals dealt with comparisons of the metaphase chromosomes, and evidence for homologies in related species was restricted to a similarity in chromosome number and to the appearance of the individual elements. Following MULLER’S X-ray work and the discovery of numerous chromosome rearrangements, the judging of homologies by comparing metaphase elements appeared hazardous because it became clear that very extensive gene realignments may occur without one’s being able to detect them in the condensed chromosomes. In addition to this, the presence of inert chromatin (MULLER and PAINTER 1932) could make such comparisons very misleading. PAINTER’S discovery and development of the salivary gland method for the study of chromosomes, opened a new era for the cytologist. He pointed out in his first paper (1933) that homologous chromosomes undergo somatic synapsis, and due to this phenomenon it is possible to compare in the most exact way the “active” or euchromatic areas in salivary gland chromosomes. In closely related species which can be hybridized one should be able to detect any chromosome rearrangements which might have occurred since the related forms originated from a common ancestor. The salivary gland chromosome method has been employed thus far in the study of three species crosses. The first of these is the Drosophila melanogaster and D . simulans cross reported by PATAU in 1935. He found that with a few exceptions there is usually close synapsis in hybrids in the euchromatic areas. The distal ends of some of the chromosomes do not conjugate. There are two extra lines in the X chromosome of D . simularts which are not seen in D. melanogaster, and in the right arm of the third chromosome there is a long inversion, reported earlier by STURTEVANT (1929) who based his conclusion on genetic data. PATAU also noted that a part of the non-inverted proximal end of the right arm of the third chromosome failed to synapse and that the fourth chromosomes were entirely different and would not conjugate in hybrids.
Kalman Filter in a Network of Linear Dynamical Systems

This paper is concerned with the problem of distributed Kalman filtering in a network of interconnected subsystems with distributed control protocols. We consider networks, which can be either homogeneous or heterogeneous, of linear time-invariant subsystems, given in the state-space form. We propose a distributed Kalman filtering scheme for this setup. The proposed method provides, at each node, an estimation of the state parameter, only based on locally available measurements and those from the neighbor nodes. The special feature of this method is that it exploits the particular structure of the considered network to obtain an estimate using only one prediction/update step at each time step. We show that the estimate produced by the proposed method asymptotically approaches that of the centralized Kalman filter, i.e., the optimal one with global knowledge of all network parameters, and we are able to bound the convergence rate. Moreover, if the initial states of all subsystems are mutually uncorrelated, the estimates of these two schemes are identical at each time step.
The connection of socio-demographic factors and child-parent relationships to the psychological aspects of children’s development

The connection of socio-demographic factors and child-parent relationships to the psychological aspects of children’s development Vladimir S. Sobkina,b* , Aleksandr N. Veraksab, Darya A. Bukhalenkovab, Aleksandra V. Fedotovaa, Ulia A. Khalutinaa, Vera A. Yakupovab a Institute for the Management of Education of the Russian Academy of Education, Moscow, Russia b Faculty of Psychology, Lomonosov Moscow State University, Moscow, Russia
PKCε Phosphorylates and Mediates the Cell Membrane Localization of RhoA

Protein kinase Cε (PKCε) signals through RhoA to modulate cell invasion and motility. In this study, the multifaceted interaction between PKCε and RhoA was defined. Phosphopeptide mapping revealed that PKCε phosphorylates RhoA at T127 and S188. Recombinant PKCε bound to recombinant RhoA in the absence of ATP indicating that the association between PKCε and RhoA does not require an active ATP-docked PKCε conformation. Activation of PKCε resulted in a dramatic coordinated translocation of PKCε and RhoA from the cytoplasm to the cell membrane using time-lapse fluorescence microscopy. Stoichiometric FRET analysis revealed that the molecular interaction between PKCε and RhoA is a biphasic event, an initial peak at the cytoplasm and a gradual prolonged increase at the cell membrane for the entire time-course (12.5 minutes). These results suggest that the PKCε-RhoA complex is assembled in the cytoplasm and subsequently recruited to the cell membrane. Kinase inactive (K437R) PKCε is able to recruit RhoA to the cell membrane indicating that the association between PKCε and RhoA is proximal to the active catalytic site and perhaps independent of a PKCε-RhoA phosphorylation event. This work demonstrates, for the first time, that PKCε phosphorylates and modulates the cell membrane translocation of RhoA.
Mammary gland factor (MGF) is a novel member of the cytokine regulated transcription factor gene family and confers the prolactin response.

Milk protein gene expression in mammary epithelial cells is regulated by the action of the lactogenic hormones insulin, glucocorticoids and prolactin. The mammary gland factor, MGF, has been shown to be a central mediator in the lactogenic hormone response. The DNA binding activity of MGF is hormonally regulated and essential for beta‐casein promoter activity. We have used Red A Sepharose‐ and sequence‐specific DNA affinity chromatography to purify MGF from mammary gland tissue of lactating sheep. Proteins of 84 and 92 kDa were obtained, proteolytically digested and the resulting peptides separated by reverse phase high pressure liquid chromatography. The 84 and 92 kDa proteins yielded very similar peptide patterns. The amino acid sequence of two peptides was determined. The sequence information was used to derive oligonucleotide probes. A cDNA library from the mRNA of mammary gland tissue of lactating sheep was screened and a molecular clone encoding MGF was isolated. MGF consists of 734 amino acids and has sequence homology with the 113 (Stat113) and 91 kDa (Stat91) components of ISGF3, transcription factors which are signal transducers of IFN‐alpha/beta and IFN‐gamma. Two species of MGF mRNA of 6.5 and 4.5 kb were detected in mammary gland tissue of lactating sheep. Lower mRNA expression was found in ovary, thymus, spleen, kidney, lung, muscle and the adrenal gland. MGF cDNA was incorporated into a eukaryotic expression vector and cotransfected with a vector encoding the long form of the prolactin receptor into COS cells. A strong MGF‐specific bandshift was obtained with nuclear extracts of COS cells induced with prolactin. Treatment of activated MGF with a tyrosine‐specific protein phosphatase resulted in the loss of DNA binding activity. Prolactin‐dependent transactivation of a beta‐casein promoter‐luciferase reporter gene construct was observed in transfected cells.
Curvature scale space corner detector with adaptive threshold and dynamic region of support

Corners play an important role in object identification methods used in machine vision and image processing systems. Single-scale feature detection finds it hard to detect both fine and coarse features at the same time. On the other hand, multi-scale feature detection is inherently able to solve this problem. This paper proposes an improved multi-scale corner detector with dynamic region of support, which is based on curvature scale space (CSS) technique. The proposed detector first uses an adaptive local curvature threshold instead of a single global threshold as in the original and enhanced CSS methods. Second, the angles of corner candidates are checked in a dynamic region of support for eliminating falsely detected corners. The proposed method has been evaluated over a number of images and compared with some popular corner detectors. The results showed that the proposed method offers a robust and effective solution to images containing widely different size features.
Reference Genes for Expression Studies in Hypoxia and Hyperglycemia Models in Human Umbilical Vein Endothelial Cells

Human umbilical vein endothelial cell (HUVEC)-based gene expression studies performed under hypoxia and/or hyperglycemia show huge potential for modeling endothelial cell response in cardiovascular disease and diabetes. However, such studies require reference genes that are stable across the whole range of experimental conditions. These reference genes have not been comprehensively defined to date. We applied human genome-wide microarrays and quantitative real-time PCR (qRT-PCR) on RNA obtained from primary HUVEC cultures that were incubated for 24 hr either in euglycemic or in hyperglycemic conditions and then subjected to short-term CoCl2-induced hypoxia for 1, 3, or 12 hr. Using whole-transcript arrays, we selected 10 commonly used reference genes with no significant expression variation across eight different conditions. These genes were ranked using NormFinder software according to their stability values. Consequently, five genes were selected for validation by qRT-PCR. These were ribosomal protein large P0 (RPLP0), transferrin receptor (TFRC), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-glucuronidase (GUSB), and β-actin (ACTB). All five genes displayed stable expression under hyperglycemia. However, only RPLP0 and TFRC genes were stable under hypoxia up to 12 hr. Under hyperglycemia combined with hypoxia up to 12 hr, the expression of RPLP0, TFRC, GUSB, and ACTB genes remained unchanged. Our findings strongly confirm that RPLP0 and TFRC are the most suitable reference genes for HUVEC gene expression experiments subjected to hypoxia and/or hyperglycemia for the given experimental conditions. We provide further evidence that even commonly known references genes require experimental validation for all conditions involved.
BGP convergence in virtual private networks

Multi-protocol label switching (MPLS) virtual private networks (VPNs) have had significant and growing commercial deployments. In this paper we present the first systematic study of BGP convergence in MPLS VPNs using data collected from a large tier-1 ISP. We combine several data sources to produce a methodology to accurately estimate routing convergence delays. We discovered an iBGP version of BGP path exploration, and show that the route invisibility problem occurs frequently and is one of the most significant contributing factors to BGP convergence delay in the VPNs we studied. We therefore propose and evaluate several configuration changes that can be employed to greatly improve the routing convergence time and minimize the connectivity disruption in the face of network changes.
Short N-secure fingerprinting code for image

Fingerprinting is one of many copyright protection methods and an extended technique of watermarking. In fingerprinting the identity of customer is embedded into the content in a way that is difficult to erase. The main difference between watermarking and fingerprinting is that different copies for each customer can be produced. Attackers compare several fingerprinting copies and find the location of the embedded information and destroy it by altering the values in those places where a difference was detected. In this paper, we propose a short fingerprinting code which is robust to the collusion attack of N customers, in the proposed fingerprinting scheme, two kinds of code are used. The first code has the same value for all customers and is embedded at the same location like watermark. The second code is designed unique for each customer. We apply this scheme to the digital image and show that it has some robustness against collusion attacks.
LIVING IN POVERTY: IMPLICATIONS FOR WORK ATTITUDES AND BEHAVIORS

Poverty is a powerful context that can affect individuals psychologically and socially, as well as financially. My work aims to introduce a discussion of poverty into the work domain, specifically examining how it can be defined at work, and how it affects work attitudes and behaviors. I present two papers that propose and test a theory of poverty's multifaceted effects on work outcomes (e.g., discretionary behaviors, job attachment, and career development) through a set of mediating mechanisms (e.g., self-efficacy, negative affectivity, and the diversity of social resources).
toxFlow v.0.1 Tutorial

toxFlow is an application of web tools for Gene Set Variation Analysis (GSVA) and toxicity prediction using read across technique and it is released under GNU General Public License. The application consists of three main parts, in three different tabs (as can be seen in Fig.1). The first two parts can be used independently, while the third part depends on model training, thus it cannot be performed prior to the second part:
Multi-consistency Data Replication

Replication is a technique widely used in parallel and distributed systems to provide qualities such as performance, scalability, reliability and availability to their clients. These qualities comprise the non-functional requirements of the system. But the functional requirement consistency may also get affected as a side-effect of replication. Different replica control protocols provide different levels of consistency from the system. In this paper we present the middleware based McRep replication protocol that supports multiple consistency model in a distributed system with replicated data. Both correctness criteria and divergence aspects of a consistency model can be specified in the McRep configuration. Supported correctness criteria include linearizability, sequential consistency, serializability, snapshot isolation and causal consistency. Bounds on divergence can be specified in either version metric or delay metric. Our approach allows the same middleware to be used for applications requiring different consistency guarantees, eliminating the need for mastering a new replication middleware or framework for every application. We carried out experiments to compare the performance of various consistency requirements in terms of response time, concurrency conflict and bandwidth overhead. We demonstrate that in McRep workloads only pay for the consistency guarantees they actually need.
Parasitic Manipulation of Host Behaviour: Baculovirus SeMNPV EGT Facilitates Tree-Top Disease in Spodoptera exigua Larvae by Extending the Time to Death

Many parasites enhance their dispersal and transmission by manipulating host behaviour. One intriguing example concerns baculoviruses that induce hyperactivity and tree-top disease (i.e., climbing to elevated positions prior to death) in their caterpillar hosts. Little is known about the underlying mechanisms of such parasite-induced behavioural changes. Here, we studied the role of the ecdysteroid UDP-glucosyltransferase (egt) gene of Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) in tree-top disease in S. exigua larvae. Larvae infected with a mutant virus lacking the egt gene exhibited a shorter time to death and died before the induction of tree-top disease. Moreover, deletion of either the open reading frame or the ATG start codon of the egt gene prevented tree-top disease, indicating that the EGT protein is involved in this process. We hypothesize that SeMNPV EGT facilitates tree-top disease in S. exigua larvae by prolonging the larval time to death. Additionally, we discuss the role of egt in baculovirus-induced tree-top disease.
The Power of Metaphor: Examining Its Influence on Social Life

This book explores the possibility that people understand abstract social concepts using metaphor, which from this perspective is not simply a matter of words. Rather, it is a cognitive tool that people routinely use to understand abstract concepts (such as morality) in terms of superficially dissimilar concepts that are relatively easier to comprehend (such as cleanliness). Although observations on metaphor's cognitive significance date back to Aristotle, the development of a formal theoretical framework, labeled conceptual metaphor theory, has stimulated systematic empirical study on metaphor's role in social psychological phenomena primarily over the past decade.
Rare Variants in Calcium Homeostasis Modulator 1 (CALHM1) Found in Early Onset Alzheimer’s Disease Patients Alter Calcium Homeostasis

Calcium signaling in the brain is fundamental to the learning and memory process and there is evidence to suggest that its dysfunction is involved in the pathological pathways underlying Alzheimer’s disease (AD). Recently, the calcium hypothesis of AD has received support with the identification of the non-selective Ca2+-permeable channel CALHM1. A genetic polymorphism (p. P86L) in CALHM1 reduces plasma membrane Ca2+ permeability and is associated with an earlier age-at-onset of AD. To investigate the role of CALHM1 variants in early-onset AD (EOAD), we sequenced all CALHM1 coding regions in three independent series comprising 284 EOAD patients and 326 controls. Two missense mutations in patients (p.G330D and p.R154H) and one (p.A213T) in a control individual were identified. Calcium imaging analyses revealed that while the mutation found in a control (p.A213T) behaved as wild-type CALHM1 (CALHM1-WT), a complete abolishment of the Ca2+ influx was associated with the mutations found in EOAD patients (p.G330D and p.R154H). Notably, the previously reported p. P86L mutation was associated with an intermediate Ca2+ influx between the CALHM1-WT and the p.G330D and p.R154H mutations. Since neither expression of wild-type nor mutant CALHM1 affected amyloid ß-peptide (Aß) production or Aß-mediated cellular toxicity, we conclude that rare genetic variants in CALHM1 lead to Ca2+ dysregulation and may contribute to the risk of EOAD through a mechanism independent from the classical Aß cascade.
Stress and Coping as a Function of Experience Level in Collegiate Flight Students

Aviation as an industry requires a high degree of precision at all times. Large amounts of stress have been known to decrease performance to undesirable levels. While stress reactions and the coping skills used after encountering stressful situations differ from person to person, generalities can be made by comparing differences between groups. A large number of pilot applicants receive initial training within a university flight program each year. In order to better understand the perceived stress level and the coping skills used by these students, the current research project administered a perceived stress test and a coping skills inventory to two groups of collegiate pilots: a first-year group (n 5 50) and a junior/senior group (n 5 32). Differences were found between the stress levels and coping skills used by this sample population. High risk industries such as aviation require consistently high levels of performance from employees, regardless of environmental pressures. This is especially the case in flight training, where flight students must adapt to the risks and hazards of the flight environment while learning a new, complex skill set. This can easily leave aviation students feeling overwhelmed. While individual differences play a large role in determining how students respond when placed in stressful situations, generalities can be made using larger groups of students. The current research study measured perceived stress levels and coping skills utilized by two groups of collegiate aviation students drawn from a large Midwestern university.
A novel method to manage very large raster data on distributed key-value storage system

With the rapid development of information technologies and GIS techniques, raster data amount is growing on an unprecedented scale. Existing WebGIS based on local file systems and RDBMS cannot manage very large raster data efficiently because of limited storage capacity of single node. Although expensive storage devices are used to enlarge capacity, WebGIS is still vulnerable to suffer from single point of failure for its poor scalability. We propose a novel method to manage very large raster data, it has three characteristics. Firstly, raster data management system is built upon distributed key-value storage system instead of local file system and RDBMS, it has good scalability and high availability. Secondly, revised quadtree-based raster index is built in system to improve access efficiency. Thirdly, our prototype is transparent to WebGIS applications, and hence can integrate with existing applications seamlessly. The experimental results show that our method outperforms existing methods.