Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of network-topology to propagation on networks

We study the effect of the network topology to propagation phenomena on networks in this article. We do not assume any propagation model such as the contact process or SIR model[1] because the study is only the consideratons of the purely topological effect, especially the effect of cycles of a network. To uncover universal properties independent of explicit propagation models is expected due to it. First of all, we introduce some indeces for propagation phenomena of a network. Second we introduce a concept of cycles with a little differences to usal cycles, which is called “STOC” in the body of this article. We find some analytic relations between thesm, STOC and some indeces. Moreover we can find the total number of STOCs in a network, analytically. This consideration leads to an extension of the celebrated “Euler's polyhedron formula”, which is only applicable to planar graphs. This extended formula is applicable to any graphs. Last we estimate numerically the indeces and the number of STOCs based on the theoretical considerations for some complex networks and make some discussion on the effects of cycles in networks to propagation.
RAG-Heptamer Interaction in the Synaptic Complex Is a Crucial Biochemical Checkpoint for the 12/23 Recombination Rule*

In V(D)J recombination, the RAG1 and RAG2 protein complex cleaves the recombination signal sequences (RSSs), generating a hairpin structure at the coding end. The cleavage occurs only between two RSSs with different spacer lengths of 12 and 23 bp. Here we report that in the synaptic complex, recombination-activating gene (RAG) proteins interact with the 7-mer and unstack the adjacent base in the coding region. We generated a RAG1 mutant that exhibits reduced RAG-7-mer interaction, unstacking of the coding base, and hairpin formation. Mutation of the 23-RSS at the first position of the 7-mer, which has been reported to impair the cleavage of the partner 12-RSS, demonstrated phenotypes similar to those of the RAG1 mutant; the RAG interaction and base unstacking in the partner 12-RSS are reduced. We propose that the RAG-7-mer interaction is a critical step for coding DNA distortion and hairpin formation in the context of the 12/23 rule.
Remote sensing is a viable tool for mapping soil salinity in agricultural lands

Soil salinity negatively impacts the productivity and profitability of western San Joaquin Valley (WSJV) farmland. Many factors, including drought, climate change, reduced water allocations, and land-use changes could worsen salinity conditions there, and in other agricultural lands in the state. Mapping soil salinity at regional and state levels is essential for identifying drivers and trends in agricultural soil salinity, and for developing mitigation strategies, but traditional soil sampling for salinity does not allow for accurate large-scale mapping. We tested remote-sensing modeling to map root zone soil salinity for farmland in the WSJV. According to our map, 0.78 million acres are salt affected (i.e., ECe > 4 dS/m), which represents 45% of the mapped farmland; 30% of that acreage is strongly or extremely saline. Independent validations of the remote-sensing estimations indicated acceptable to excellent correspondences, except in areas of low salinity and high soil heterogeneity. Remote sensing is a viable tool for helping landowners make decisions about land use and also for helping water districts and state agencies develop salinity mitigation strategies.
Students, Courses and Colleges:: The Situation, Consequences and Actions Needed

Higher education is the main source of executive manpower and professional technology for businesses, yet it is only in the last few months of the education system that firms make contact with the education elite. When a graduate is recruited, a firm obtains two things — the individual and the training. Many firms concentrate on the individual when selecting potential executives, although if a company is seeking technologists, a student's course is more important. Businesses dedicate much effort to obtaining the best of the output of the education system and spend generously on management training, but pay little attention to the mechanism that brings together the two raw materials — sixth formers and courses in higher education. In the long‐run, a business is only as good as the people it employs and the failure to manage the process that ensures a flow of the right people into business is reflected in the failure of British businesses to be competitive.
Genetic Variation at the MHC in a Population of Introduced Wild Turkeys

Genetic variation in the major histocompatibility complex (MHC) is known to affect disease resistance in many species. Investigations of MHC diversity in populations of wild species have focused on the antigen presenting class IIβ molecules due to the known polymorphic nature of these genes and the role these molecules play in pathogen recognition. Studies of MHC haplotype variation in the turkey (Meleagris gallopavo) are limited. This study was designed to examine MHC diversity in a group of Eastern wild turkeys (Meleagris gallopavo silvestris) collected during population expansion following reintroduction of the species in southern Wisconsin, USA. Southern blotting with BG and class IIβ probes and single nucleotide polymorphism (SNP) genotyping was used to measure MHC variation. SNP analysis focused on single copy MHC genes flanking the highly polymorphic class IIβ genes. Southern blotting identified 27 class IIβ phenotypes, whereas SNP analysis identified 13 SNP haplotypes occurring in 28 combined genotypes. Results show that genetic diversity estimates based on RFLP (Southern blot) analysis underestimate the level of variation detected by SNP analysis. Sequence analysis of the mitochondrial D-loop identified 7 mitochondrial haplotypes (mitotypes) in the sampled birds. Results show that wild turkeys located in southern Wisconsin have a genetically diverse MHC and originate from several maternal lineages.
"Being With" Bipolar Disorder

In this paper, I explore the impact of bipolar disorder on the experiences of two groups of postsecondary students. I theorize that Bourdieu’s (1986) theory of forms of capital provides a lens for understanding how these students negotiate social, cultural, institutional, and symbolic forms of capital in their daily academic lives. I analyze the studies using a constant comparative method often used in research employing ethnographic techniques. The findings examine students’ concerns around learning and achievement within university settings and the debilitating effects of stigma on individuals identified with bipolar disorder. In doing so, the findings reinforce Bourdieu’s theory of capital, because students require relevant support to increase their access to capital in terms of educational certification, employment, finances, and membership in valued groups. However, Bourdieu’s theory has significant limitations. For the bipolar students in these studies, a form of intrapersonal capital, or personal power, was needed to take responsibility for their education and lives, and to positively influence those around them. The implications suggest that instructors in higher education need to accept students with bipolar disorders, while students with bipolar disorders need to reach out to instructors and share their needs. Keywords: bi-polar disorders; post secondary students; higher education
Approche hybride de segmentation de page à base d'un descripteur de traits

In this paper we present a new hybrid page segmentation approach based on connected component and region analysis. We first describe our stroke descriptor that detects text and line component candidates using the skeleton of the binarized document image. Then, the active contour Chan and Vese model is applied to segment the rest of the image into photo and background regions. This classification is verified by studying the variation of each detected region. Finally, we cluster the text candidates using mean-shift analysis technique according to their corresponding sizes and we present our multiscale projection profile approach to gather separately horizontal and vertical text regions. We evaluate the performances of our approach by comparing it to the existing methods that participated in ICDAR page segmentation competition. MOTS-CLÉS : Descripteur de traits; Segmentation de page; Mean-shift.
On computation with 'probabilities' modulo k

We propose a framework to study models of computation of indeterministic data, represented by abstract "distributions". In these distributions, probabilities are replaced by "amplitudes" drawn from a fixed semi-ring $S$, of which the non-negative reals, the complex numbers, finite fields $\mathbb F_{p^r}$, and cyclic rings $\mathbb Z_k$ are examples. Varying $S$ yields different models of computation, which we may investigate to better understand the (likely) difference in power between randomised and quantum computation. The "modal quantum states" of Schumacher and Westmoreland [arXiv:1010.2929] are examples of such distributions, for $S$ a finite field. For $S = \mathbb F_2$, Willcock and Sabry [arXiv:1102.3587] show that UNIQUE-SAT is solvable by polynomial-time uniform circuit families consisting of invertible gates. We characterize the decision problems solvable by polynomial uniform circuit families, using either invertible or "unitary" transformations over cyclic rings $S = \mathbb Z_k$, or (in the case that $k$ is a prime power) finite fields $S = \mathbb F_k$. In particular, for $k$ a prime power, these are precisely the problems in the class $\mathsf{Mod}_k\mathsf P$.
Feature Selection for Malware Classification

In applying machine learning to malware identification, different types of features have proven to be successful. These features have also been tested with different kinds of classification methodologies and have had varying degrees of success. Every time a new machine learning methodology is introduced for classifying malware, there is the potential for increasing the overall quality of malware classification in the field. Even new classifiers with the same accuracy as those used previously can be combined using one of a few different ensemble techniques sharpen the classification and raise the accuracy to new heights. For our purposes, we have attempted to create a coalition of classifiers which each use different features. These classifiers when trained, provide multiple angles to the same problem and can be used to test ensemble techniques. Eventually, such an ensemble of individual malware classifiers could create a highly precise means of picking out malware from other software. Specifically, we have created a convolutional neural network which processes byte data as an image, and a deep feed forward neural network which utilizes opcode N-gram features. Both of these classifiers, while not perfect, provide a significant level of classification. They achieve this independently of one another, and when combined, they each contribute enough to improve the final accuracy. The majority of the effort in this research was placed on gathering the N-gram features, a time and resource intensive process. Tinkering with the parameters or structure of classifiers could provide further improvements to the system.
Magnetic resonance imaging investigations of directed influence in the brain: methodological contributions and application to task switching studies

• A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers.
Realizing Emotional Autonomous Virtual Agents in a Multi-user Virtual Environment

Most of the Multi-user Virtual Environment Systems (MVE) today do not allow computer-controlled virtual agents to interact with real users in an emotional manner. In this paper, we aim to design autonomous virtual agents that can generate emotional behaviors through textual dialogs, route selection, and body gestures when interacting with other avatars controlled by real users or by the computer. These behaviors are expressed via interaction events delivered through the network. The interaction events are generated according to the mental state of the agent based on a psychological model including emotion, memory, and personal traits. We have also designed an update mechanism to interpret an interaction event and update the mental state of the virtual agent accordingly. This model has been implemented and tested in an experimental MVE platform based on VRML/X3D to evaluate the effectiveness of the design. With the mechanism of autonomous virtual agent proposed in this paper, we hope to enhance MVE with virtual agents possessing emotional behaviors that can be easily authored by regular users.
Cytotoxic T cells clear virus but augment lung pathology in mice infected with respiratory syncytial virus

We have examined the function of class I MHC-restricted cytotoxic T cells in experimental respiratory syncytial virus (RSV) infection of BALB/c mice by transfer of T cell line MJC-A2 and CTL clone E8a into RSV-infected mice. The T cell line cleared pulmonary RSV infection within 5 d in persistently infected gamma-irradiated mice, but caused acute respiratory disease. This was only seen in infected mice and was often lethal after transfer of greater than 3 x 10(6) CTL. Lower numbers of CTL produced less severe disease but still cleared lung RSV, albeit over a longer time course (up to 10 d). Clearance of lung RSV in immunocompetent mice by the T cell line and CTL clone was again accompanied by acute and sometimes lethal respiratory disease. Bronchoalveolar lavage showed severe lung hemorrhage and frequent neutrophil efflux in mice with CTL-augmented disease.
Adolescent Stress Induced by Family Structures and its Effect on Adult Health : A Longitudinal Assessment

This study strives to explain the decrease in health among children and young adults in the United States in recent decades by examining the relationship between adolescent family environments and health measures of the individuals as adults. The study utilizes the National Longitudinal Study of Adolescent Health (Add Health) dataset Waves I and IV to analyze health measures commonly used to rate the wear and tear on the body such as high blood pressure BMI (Body Mass Index) diabetes high cholesterol and poor purported health. Findings suggest that family structure during adolescence is an important predictor of adult health outcomes. Yet it also underscores that family structure is complicated and cannot be simplified into a traditional versus nontraditional family dichotomy. Results from Logistic Regression models indicate when disaggregating the many different forms of "alternative family forms" that the two biological parent home is not necessarily less stressful than all alternative family forms. Siblings also play a very integral part in the relationship between family structure and health as an adult. Multivariate models suggest that siblings have a positive effect in the family. In particular being an only child is associated with higher levels of obesity and high blood pressure. Finding presented here underscore the importance of siblings to long term health. Yet they also provide some preliminary support for the perspective that different types of siblings may have different impacts. Indeed it appears that variations in sibling structure may explain some of the association between guardian structure and long term health. This study confirms the conclusions of other researchers that health among young people in this country is on the decline.
A gaze prediction technique for open signed video content using a track before detect algorithm

This paper proposes a gaze prediction model for open signed video content. A face detection algorithm is used to locate faces across each frame in both profile and frontal orientations. A grid-based likelihood ratio track before detect routine is used to predict the orientation of the signer's head, which allows the gaze location to be localised to either the signer or the inset. The face detections are then used to narrow down the gaze prediction further. The gaze predictor is able to predict the results of an eye tracking study with up to 95% accuracy, and an average accuracy of over 80%.
BACOM2: a Java tool for detecting normal cell contamination of copy number in heterogeneous tumor

We develop a cross-platform open-source Java application (BACOM2) with graphic user interface (GUI), and users also can use a XML file to set the parameters of algorithm model, file paths and the dataset of paired samples. BACOM2 implements the new entire pipeline of copy number change analysis for heterogeneous cancer tissues, including extraction of raw copy number signals from CEL files of paired samples, attenuation correction, identification of balanced AB-genotype loci, copy number detection and segmentation, global baseline calculation and absolute normalization, differentiation of deletion types, estimation of the normal tissue fraction and correction of normal tissue contamination. BACOM2 focuses on the common tools for data preparation and absolute normalization for copy number analysis of heterogeneous cancer tissues. The software provides an additional choice for scientists who require a user-friendly, high-speed processing, cross-platform computing environment for large copy number data analysis.
Numerical Simulation of Turbulent Flows with Sheet Cavitation

A pressure-based algorithm is developed and applied to compute turbulent sheet cavitating flows. Single-fluid Navier-Stokes equations, cast in their conservative form, along with a volume fraction transport equation are employed. The flow is computed in both phases with the vapor pressure recovered inside the cavity via a mass transfer model. A pressure-velocity-density coupling scheme along with an upwinded density interpolation is developed to handle the large density ratio associated with cavitation. The method is assessed through simulations of cavitating flows over a cylindrical object and an airfoil. The results show satisfactory agreement with experimental data in pressure distribution. In addition, information such as wall shear stress distributions and related velocity and turbulence fields is highlighted for both axisymmetric projectile and NACA airfoil.
Inhibition of bone resrption by selctive inactivators of cysteine proteinases

Incativators of cystein proteinases (CPs) were tested as inhibitors of bone resorption in vitro and in vivo. The following four CP inactivators were tested: Ep453, the membrane‐permeant produrg of Ep475, a compound with low membrane pereability which inhibits cathepsins B, L, S, H, and calpain; Ep453, the membrane‐permeant prodrug of Ep475; CA074, a compound with low membrane permeability which selectivly inactives cathepsin B; and CA07Me, the membrane‐permanent prodrug of CA074. The test systems consisted of (1) monitoring the release of radioisotope from prelabelled mousecalvarial explants and (2) assessing the extene of bone resorption in and isolated osteoclast assay using confocal laser microscopy. Ep453, Ep475, and CA074Me inhebited both stimulated and basal bone resorption in vitro while CA074 WASA without effect; The inhibition was reversible and dose dependent. None of the inhibitors affected protein synthesis, DNA synthesis, the PTH‐enhanced secretion of β‐glucuronised, and N‐acetyle‐β‐glucosaminidase, or the spontaneous release of lactate dehyrogenese. Ep453, Ep475, and CA074Me does‐dependently inhibited the resorption activity of isolated areat osteoclassts cultured on bone slices with a maximal effect at 50 μM. The munber of resorption pits and their mean volume was reduced, whilest the mean administration subcutaneously at a dose of 60 μg/g body weight inhibited bone resorption in vivo as measured by an in vivo/in vitro assay, by about 20%. This study demonestration that cathepsins B,L, and/or S are involved in bone resorpotion in vitro and in vivo. Whilest cathepsin L and/or S act extracellularly, and possibly intractually, cathepsin B mediate its effects intracellularly perpheps through the activation of other proteinases involved in subsosteoclastic collagen degradition.
Imagining the impossible before breakfast: the relation between creativity, dissociation, and sleep

Dissociative symptoms have been related to higher rapid eye movement sleep density, a sleep phase during which hyperassociativity may occur. This may enhance artistic creativity during the day. To test this hypothesis, we conducted a creative photo contest to explore the relation between dissociation, sleep, and creativity. During the contest, participants (N = 72) took one photo per day for five consecutive days, based on specific daily themes (consisting of single words) and the instruction to take as creative a photo as possible each day. Furthermore, they completed daily measures of state dissociation and a short sleep diary. The photos and their captions were ranked by two professional photographers and two clinical psychologists based on creativity, originality, bizarreness, and quality. We expected that dissociative people would rank higher in the contest compared with low-dissociative participants, and that the most original photos would be taken on days when the participants scored highest on acute dissociation. We found that acute dissociation predicted a higher ranking on creativity. Poorer sleep quality and fewer hours of sleep predicted more bizarreness in the photos and captions. None of the trait measures could predict creativity. In sum, acute dissociation related to enhanced creativity. These findings contribute to our understanding of dissociative symptomatology.
Sleep quality but not sleep quantity effects on cortisol responses to acute psychosocial stress

Abstract Given the well-documented deleterious health effects, poor sleep has become a serious public health concern and increasing efforts are directed toward understanding underlying pathways. One potential mechanism may be stress and its biological correlates; however, studies investigating the effects of poor sleep on a body’s capacity to deal with challenges are lacking. The current study thus aimed at testing the effects of sleep quality and quantity on cortisol responses to acute psychosocial stress. A total of 73 college-aged adults (44 females) were investigated. Self-reported sleep behavior was assessed via the Pittsburgh Sleep Quality Index and salivary cortisol responses to the Trier Social Stress Test were measured. In terms of sleep quality, we found a significant three-way interaction, such that relative to bad sleep quality, men who reported fairly good or very good sleep quality showed blunted or exaggerated cortisol responses, respectively, while women’s stress responses were less dependent on their self-reported sleep quality. Contrarily, average sleep duration did not appear to impact cortisol stress responses. Lastly, participants who reported daytime dysfunctions (i.e. having trouble staying awake or keeping up enthusiasm) also showed a trend to blunted cortisol stress responses compared to participants who did not experience these types of daytime dysfunctions. Overall, the current study suggests gender-specific stress reactivity dysfunctions as one mechanism linking poor sleep with detrimental physical health outcomes. Furthermore, the observed differential sleep effects may indicate that while the body may be unable to maintain normal hypothalamic-pituitary-adrenal functioning in an acute psychosocial stress situation after falling prey to low sleep quality, it may retain capacities to deal with challenges during extended times of sleep deprivation.