Miracle-dz/UniFAR-FTUs huggingface dataset:
STAMP: a web tool for exploring DNA-binding motif similarities

STAMP is a newly developed web server that is designed to support the study of DNA-binding motifs. STAMP may be used to query motifs against databases of known motifs; the software aligns input motifs against the chosen database (or alternatively against a user-provided dataset), and lists of the highest-scoring matches are returned. Such similarity-search functionality is expected to facilitate the identification of transcription factors that potentially interact with newly discovered motifs. STAMP also automatically builds multiple alignments, familial binding profiles and similarity trees when more than one motif is inputted. These functions are expected to enable evolutionary studies on sets of related motifs and fixed-order regulatory modules, as well as illustrating similarities and redundancies within the input motif collection. STAMP is a highly flexible alignment platform, allowing users to ‘mix-and-match’ between various implemented comparison metrics, alignment methods (local or global, gapped or ungapped), multiple alignment strategies and tree-building methods. Motifs may be inputted as frequency matrices (in many of the commonly used formats), consensus sequences, or alignments of known binding sites. STAMP also directly accepts the output files from 12 supported motif-finders, enabling quick interpretation of motif-discovery analyses. STAMP is available at http://www.benoslab. pitt.edu/stamp
Subjective Probabilities in Choice Experiments' Design: Three Essays

This dissertation which consists of three essays investigates the influence of subjective probabilities on decision making processes under conditions of risk. In particular, it examines whether subjects adjust new risk information on their prior subjective estimates, and, to what extent this adjustment affects their choices. In the first essay, by using an artefactual field experiment, I examine the potential correlation between incentive compatibility and validity of subjective probabilities elicited via the Exchangeability Method, an innovative elicitation mechanism which consists of several chained questions. Here, validity is investigated using de Finettiâs notion of coherence under which subjective probabilities are coherent if and only if they obey all axioms and theorems of probability theory. Experimental results suggest that subjects provided with monetary incentives and randomized questions more likely express valid subjective probabilities than others because they are not aware of the chaining which undermines the incentive compatibility of the Exchangeability Method. In the second essay, by using the same experimental data, I show that valid subjective probabilities do not significantly diverge from invalid ones, indicative of little effect of internal validity on the actual magnitude of subjective probabilities. In the third essay, by using a field Choice Experiment, I investigate to what extent subjects adjust risk information given in the status quo alternative on their subjective probability estimates. An innovative two-stage approach that incorporates subjective probabilities into Choice Experimentsâ design is developed to investigate this phenomenon, known as the scenario adjustment. In the first stage, subjective probabilities that given outcomes will occur are elicited using the Exchangeability Method. In the second stage, two treatment groups are designed: in the first group, each subject is presented with a status quo alternative which incorporates her/his subjective probabilities, and, hence, no adjustment is required; in the second group, each subject faces a status quo alternative where the presented risk is not consistent with her/his probability estimates, and, hence, a mental adjustment to the scenario might take place. By comparing willingness to pay across the treatment groups, my results suggest that, when subjects are provided with SQ alternatives in which the risk is lower than the perceived one, the mental adjustment takes place, but, when subjects are provided with SQ alternatives in which the risk is higher than their own estimates, these subjects appear to make irrational choices.
Detecting Antigen-Specific T Cell Responses: From Bulk Populations to Single Cells

A new generation of sensitive T cell-based assays facilitates the direct quantitation and characterization of antigen-specific T cell responses. Single-cell analyses have focused on measuring the quality and breadth of a response. Accumulating data from these studies demonstrate that there is considerable, previously-unrecognized, heterogeneity. Standard assays, such as the ICS, are often insufficient for characterization of rare subsets of cells. Enhanced flow cytometry with imaging capabilities enables the determination of cell morphology, as well as the spatial localization of the protein molecules within a single cell. Advances in both microfluidics and digital PCR have improved the efficiency of single-cell sorting and allowed multiplexed gene detection at the single-cell level. Delving further into the transcriptome of single-cells using RNA-seq is likely to reveal the fine-specificity of cellular events such as alternative splicing (i.e., splice variants) and allele-specific expression, and will also define the roles of new genes. Finally, detailed analysis of clonally related antigen-specific T cells using single-cell TCR RNA-seq will provide information on pathways of differentiation of memory T cells. With these state of the art technologies the transcriptomics and genomics of Ag-specific T cells can be more definitively elucidated.
Chronopharmacology for deoxyspergualin: toxicity and efficacy in the rat.

BACKGROUND Deoxyspergualin (DSG), a potent immunosuppressive drug, has been clinically used as a rescue therapy for acute graft rejection. However, DSG has severe adverse effects that limits its use. Here, we examined the optimized therapeutic protocol for DSG using chronopharmacological profiles of it. METHODS First, a dosing time-dependent difference in the toxicity and efficacy of DSG was determined using a heterotopic heart transplantation model. Second, chronokinetics of DSG were examined to reveal the mechanism for dosing time-dependent differences in the effect. RESULTS In rats treated with DSG at the active period, bone marrow suppression and damage of small intestine were significantly severe. However, no significant difference was found in cardiac allograft survival and pharmacokinetics according to the timing of drug administration. CONCLUSIONS The toxicity of DSG varied with the dosing time, whereas its efficacy did not. The chronopharmacological approach may provide merits for immunosuppressive therapy with DSG in clinical organ transplantation.
Software Requirements Elicitation Tools for Service Oriented Architecture : Comparative Analysis

Software requirements are specification of what should be implemented; they are descriptions of how the system should behave, a system property or attribute, or they may be a constraint on the development process of the system [1]. Requirements are specifications of the services that the system should provide, the constraints on the system and the background information that is necessary to developing the system [2]. Finally, a requirement is a singular documented need of what a particular product or service should perform [3]. The latter definition is applicable in system engineering and software engineering. One can notice that the previous definitions are defining software requirements as specifications that cover system’s behaviour, attribute, capability, characteristic, or quality of a system for a user to utilize and benefit from, satisfying planned or expected objectives.
New Hippocampal Neurons Mature Rapidly in Response to Ketamine But Are Not Required for Its Acute Antidepressant Effects on Neophagia in Rats123

Abstract Virtually all antidepressant agents increase the birth of granule neurons in the adult dentate gyrus in rodents, providing a key basis for the neurogenesis hypothesis of antidepressant action. The novel antidepressant ketamine, however, shows antidepressant activity in humans within hours, far too rapid for a mechanism involving neuronal birth. Ketamine could potentially act more rapidly by enhancing maturation of new neurons born weeks earlier. To test this possibility, we assessed the effects of S-ketamine (S-(+)-ketamine hydrochloride) injection on maturation, as well as birth and survival, of new dentate gyrus granule neurons in rats, using the immediate-early gene zif268, proliferating cell nuclear antigen, and BrdU, respectively. We show that S-ketamine has rapid effects on new neurons, increasing the proportion of functionally mature young granule neurons within 2 h. A single injection of S-ketamine also increased cell proliferation and functional maturation, and decreased depressive-like behavior, for at least 4 weeks in rats treated with long-term corticosterone administration (a depression model) and controls. However, the behavioral effects of S-ketamine on neophagia were unaffected by elimination of adult neurogenesis. Together, these results indicate that ketamine has surprisingly rapid and long-lasting effects on the recruitment of young neurons into hippocampal networks, but that ketamine has antidepressant-like effects that are independent of adult neurogenesis.
Performance level modulates adult age differences in brain activation during spatial working memory

Working memory (WM) shows pronounced age-related decline. Functional magnetic resonance imaging (fMRI) studies have revealed age differences in task-related brain activation. Evidence based primarily on episodic memory studies suggests that brain activation patterns can be modulated by task difficulty in both younger and older adults. In most fMRI aging studies on WM, however, performance level has not been considered, so that age differences in activation patterns are confounded with age differences in performance level. Here, we address this issue by comparing younger and older low and high performers in an event-related fMRI study. Thirty younger (20–30 years) and 30 older (60–70 years) healthy adults were tested with a spatial WM task with three load levels. A region-of-interest analysis revealed marked differences in the activation patterns between high and low performers in both age groups. Critically, among the older adults, a more “youth-like” load-dependent modulation of the blood oxygen level-dependent signal was associated with higher levels of spatial WM performance. These findings underscore the need of taking performance level into account when studying changes in functional brain activation patterns from early to late adulthood.
The impact of work-family factors in the relationships between organizational and occupational characteristics and intention to stay

In this study work-family factors were examined as mediating variables on the relationships between organizational and occupational characteristics as the independent variables and intention to stay as the dependent variable. Self-administered research questionnaire was utilized for data collection and data was collected from 240 middle age single mother employees in Klang Valley, Malaysia. Samples were determined through simple random sampling method from six single mother associations. Descriptive statistical analysis was conducted to describe the respondents. Pearson Product Moment Correlation was used to determine the relationships among variables and Structural Equation Modeling using AMOS version 16.0 was utilized for model testing and to verify the presence of mediation effects. Further, the Soble’s z-test was used to test whether the mediators carry the effect of the independent variables on the dependent variable. The findings indicated that there were positive and negative relationships among variables. The results also established the presence of mediation effects between the independent and dependent variables. Organizations may utilize work-family factors as mechanism to promote longer retention among employees.
Activation of nestin‐positive duct stem (NPDS) cells in pancreas upon neogenic motivation and possible cytodifferentiation into insulin‐secreting cells from NPDS cells

Stem cells in adult pancreas and their specific marker are poorly characterized. We hypothesized that pancreatic stem cells could evolve from the duct system in response to neogenic stimulation and may transiently express nestin during tissue regeneration. After partial pancreatectomy (Px), we found extensive formation of ductules consisting of nestin‐positive epithelial cells with higher replicating ability in the neogenic foci, particularly at day 3 after Px. Nestin was highly expressed in the earlier stages of ductule morphogenesis and then regressed as the cells evolved toward differentiated pancreatic cell types. The neogenic ductules were isolated for the culture of nestin‐positive duct stem cells. These nestin‐positive duct cells were numerous and displayed extensive self‐replication in the duct cell explants after 2–3 days of culture, thus depicted as nestin‐positive duct stem (NPDS) cells. As seen in the tissue of neogenic foci, NPDS cells were negative for cytokeratin‐20 and vimentin, the marker for duct epithelial and mesenchymal cells, respectively. Endocrine cells, mostly insulin cells, were present in the explants at day 2 as single cells or as small clusters adjacent to the NPDS cells, and formed islet‐like masses at day 3 of culture, suggesting islet cell differentiation from NPDS cells. In addition, insulin secretion from these beta cells responded to glucose stimulation. We found transient up‐regulation of PDX‐1 expression by reverse transcriptase‐polymerase chain reaction at day 3 after Px in pancreatic tissue. Higher expression of PDX‐1 was seen in the culture of neogenic ductules than that of ducts isolated from the sham‐operated pancreas. In particular, a subpopulation of nestin‐positive cells in the duct cell explants formed from the neogenic ductules expressed PDX‐1 in their nuclei. Taken together, this information suggests that NPDS cells could be generated from adult pancreas by neogenic motivations and they may differentiate into insulin‐secreting cells. Developmental Dynamics 230:1–11, 2004. © 2004 Wiley‐Liss, Inc.
An efficient algorithm for isomorphism-aware custom instruction identification for extensible processors

Extensible processors have been widely used to achieve the conflicting demands for performance improvement, low power consumption, and flexibility. As extensible processors have become more popular, several algorithms have been proposed for automatically identifying instruction-set extensions in order to reduce the effort of manual design and verification. However, most of them focus on finding large and complex instructions that are used only once, rather than repeatedly used ones. Moreover, some other approaches that consider recurrence are limited to finding small instructions. This paper proposes a novel algorithm that considers the instruction reusability as well as I/O serialization. In order to overcome high complexity of the problem, we develop a canonical form construction algorithm for fast isomorphism detection on directed acyclic graphs and an incremental template generation algorithm that identifies the best custom instruction with a user-defined fitness function. Moreover, our algorithm serializes I/O operations so that the numbers of inputs and outputs of custom instructions are not limited by the microarchitecture. Experimental results show that our algorithm achieves significant improvement over previous approaches in terms of algorithm runtime as well as performance gain obtained by the custom instructions.
Success/Failure Prediction of Noninvasive Mechanical Ventilation in Intensive Care Units

Summary Objectives: This paper addresses the problem of decision-making in relation to the administration of noninvasive mechanical ventila tion (NIMV) in intensive care units. Methods: Data mining methods were employed to find out the factors influencing the success/failure of NIMV and to predict its results in future patients. These artificial intelligence-based methods have not been applied in this field in spite of the good results obtained in other medical areas. Results: Feature selection methods provided the most influential variables in the success/ failure of NIMV, such as NIMV hours, PaCO2 at the start, PaO2 / FiO2 ratio at the start, hematocrit at the start or PaO2 / FiO2 ratio after two hours. These methods were also used in the preprocessing step with the aim of improving the results of the classifiers. The algorithms provided the best results when the dataset used as input was the one containing the attributes selected with the CFS method. Conclusions: Data mining methods can be successfully applied to determine the most influential factors in the success/failure of NIMV and also to predict NIMV results in future patients. The results provided by classifiers can be improved by preprocessing the data with feature selection techniques.
WebShield: Enabling Various Web Defense Techniques without Client Side Modifications

Today, web attacks are increasing in frequency, severity and sophistication. Existing solutions are either hostbased which suffer deployment problems or middlebox approaches that can only accommodate certain security protection mechanisms with limited protection. In this paper, we propose four design principles for general middlebox frameworks of web protection, and apply these principles to design WebShield, which can enable various host-based security mechanisms. In particular, we run all the JavaScript from remote web servers only at shadow browser instances inside the middlebox, and only run our trusted JavaScript rendering agent at client browsers. The trusted rendering agent turns browsers into a thin web terminal by reconstructing the encoded DOM of a webpage. We implement a prototype of WebShield. Evaluation demonstrates that a general JavaScript rendering agent can render webpages precisely and be just slightly slower than direct access. We further demonstrate that our design can work well with interactive web applications such as JavaScript games. WebShield can detect attacks deeply embedded in dynamic HTML pages including the ones in complex Web 2.0 applications, and can also detect both known and unknown vulnerabilities. We further show that WebShield is scalable for deployment.
The mummified brain of a pleistocene woolly mammoth (Mammuthus primigenius) compared with the brain of the extant African elephant (Loxodonta africana)

This study presents the results of an examination of the mummified brain of a pleistocene woolly mammoth (Mammuthus primigenius) recovered from the Yakutian permafrost in Siberia, Russia. This unique specimen (from 39,440–38,850 years BP) provides the rare opportunity to compare the brain morphology of this extinct species with a related extant species, the African elephant (Loxodonta africana). An anatomical description of the preserved brain of the woolly mammoth is provided, along with a series of quantitative analyses of various brain structures. These descriptions are based on visual inspection of the actual specimen as well as qualitative and quantitative comparison of computed tomography imaging data obtained for the woolly mammoth in comparison with magnetic resonance imaging data from three African elephant brains. In general, the brain of the woolly mammoth specimen examined, estimated to weigh between 4,230 and 4,340 g, showed the typical shape, size, and gross structures observed in extant elephants. Quantitative comparative analyses of various features of the brain, such as the amygdala, corpus callosum, cerebellum, and gyrnecephalic index, all indicate that the brain of the woolly mammoth specimen examined has many similarities with that of modern African elephants. The analysis provided here indicates that a specific brain type representative of the Elephantidae is likely to be a feature of this mammalian family. In addition, the extensive similarities between the woolly mammoth brain and the African elephant brain indicate that the specializations observed in the extant elephant brain are likely to have been present in the woolly mammoth. J. Comp. Neurol. 523:2326–2343, 2015. © 2015 Wiley Periodicals, Inc.
Isothermal seed germination of Adenanthera pavonina

This work reports aspects of seed germination at different temperatures of Adenanthera pavonina L. , a woody Southeast Asian Leguminosae. Germination was studied by measuring the final percentages, the rate, the rate variance and the synchronisation of the individual seeds calculated by the minimal informational entropy of frequencies distribution of seed germination. Overlapping the germinability range with the range for the highest values of germination rates and the minimal informational entropy of frequencies distribution of seed germination, we found that the best temperature for the germination of A. pavonina seeds is 35 oC. The slope µ of the Arrhenius plot of the germination rates is positive for T 35 oC. The activation enthalpies, estimated from closely-spaced points, shows that |ΔH-| < 12 Cal mol-1 occur for temperatures in the range between 25 oC and 40 oC. The ecological implication of these results are that this species may germinate very fast in tropical areas during the summer season. This may be an advantage to the establishment of this species under the climatic conditions in those areas.
Quantitative analysis of cadherin-catenin-actin reorganization during development of cell-cell adhesion

Epithelial cell-cell adhesion requires interactions between opposing extracellular domains of E-cadherin, and among the cytoplasmic domain of E-cadherin, catenins, and actin cytoskeleton. Little is known about how the cadherin-catenin-actin complex is assembled upon cell-cell contact, or how these complexes initiate and strengthen adhesion. We have used time-lapse differential interference contrast (DIC) imaging to observe the development of cell-cell contacts, and quantitative retrospective immunocytochemistry to measure recruitment of proteins to those contacts. We show that E-cadherin, alpha-catenin, and beta- catenin, but not plakoglobin, coassemble into Triton X-100 insoluble (TX-insoluble) structures at cell-cell contacts with kinetics similar to those for strengthening of E-cadherin-mediated cell adhesion (Angres, B., A. Barth, and W.J. Nelson. 1996. J. Cell Biol. 134:549- 557). TX-insoluble E-cadherin, alpha-catenin, and beta-catenin colocalize along cell-cell contacts in spatially discrete micro-domains which we designate "puncta," and the relative amounts of each protein in each punctum increase proportionally. As the length of the contact increases, the number of puncta increases proportionally along the contact and each punctum is associated with a bundle of actin filaments. These results indicate that localized clustering of E- cadherin/catenin complexes into puncta and their association with actin is involved in initiating cell contacts. Subsequently, the spatial ordering of additional puncta along the contact may be involved in zippering membranes together, resulting in rapid strengthening of adhesion.