Miracle-dz/UniFAR-FTUs huggingface dataset:
A Study of Molecular Signals Deregulating Mismatch Repair Genes in Prostate Cancer Compared to Benign Prostatic Hyperplasia

Prostate cancer is one of the leading causes of mortality among aging males. There is an unmet requirement of clinically useful biomarkers for early detection of prostate cancer to reduce the liabilities of overtreatment and accompanying morbidity. The present population-based study investigates the factors disrupting expression of multiple functionally related genes of DNA mismatch repair pathway in prostate cancer patients to identify molecular attributes distinguishing adenocarcinoma from benign hyperplasia of prostate. Gene expression was compared between tissue samples from prostate cancer and benign prostatic hyperplasia using real-time-PCR, western blot and immunohistochemistry. Assessment of genotypes of seven single-nucleotide-polymorphisms of three MMR genes was conducted using PCR-coupled RFLP and sequencing. Promoter methylation was interrogated by methylation-specific-PCR and bisulfite-sequencing. Interaction between microRNAs and MMR genes was verified by 3'UTR-based dual luciferase assays. Concurrent reduction of three MMR genes namely hMLH1, hMSH6 and hMSH2 (34-85%, P<0.05) was observed in prostate cancer tissues. hMSH6 polymorphism rs1800932(Pro92Pro) conferred a borderline protection in cancer patients (OR = 0.33, 95% CI = 0.15-0.75). Relative transcript level of hMLH1 was inversely related (r = -0.59, P<0.05) with methylation quotient of its promoter which showed a significantly higher methylation density (P = 0.008, Z = -2.649) in cancer patients. hsa-miR-155, hsa-miR-141 and hsa-miR-21 gene expressions were significantly elevated (66-85%, P<0.05) in tumor specimens and negatively correlated (r = -0.602 to -0.527, P<0.05) with that of MMR genes. hsa-miR-155 & hsa-miR-141 and hsa-miR-155 & hsa-miR-21 were demonstrated to bind to their putative seed sequences in hMLH1 and hMSH6 3’UTRs respectively. Relatively higher expression of DNA methyl-transferases (DNMT1 and DNMT3b) and HIF-1α genes (34-50%, P<0.05) were also detected in tumor tissues. This study provides statistical evidence that MMR deficiency is correlated with hypermethylation of hMLH1 promoter and upregulation of hsa-miR-155, hsa-miR-141 and hsa-miR-21 in prostate cancer. This comparative study reflects that microRNA expression level, particularly hsa-miR-155, exhibits predictive signature of prostate adenocarcinoma.
Hide and seek: Detecting sensors in P2P botnets

Many cyber-crimes, such as Denial of Service (DoS) attacks and banking frauds, originate from botnets. To prevent botnets from being taken down easily, botmasters have adopted peer-to-peer (P2P) mechanisms to prevent any single point of failure. However, sensor nodes that are often used for both, monitoring and executing sinkholing attacks, are threatening such botnets. In this paper, we introduce a novel mechanism to detect sensor nodes in P2P botnets using the clustering coefficient as a metric. We evaluated our mechanism on the real-world botnet Sality over the course of a week and were able to detect an average of 25 sensors per day with a false positive rate of 20%.
Design of a novel covert SSVEP-based BCI

Brain computer interfaces (BCI) employing steady-state visually evoked potential (SSVEP) modulations have been investigated increasingly in the last years because of their high signalto-noise ratio and information transfer rate. However, independent SSVEP BCI based on covert attention show a drop in robustness which makes it difficult to use on patients with impaired or nonexistent ocular motor control. In the present paper, offline analysis is aimed at investigating the influence of three important parameters on the performance of covert SSVEP BCI : feature extraction algorithms, window length and number of harmonics. We also proposed a new ”checkerboard” pattern and compared its performance with lines pattern. We have shown that the use of this pattern and only one harmonic yielded an average accuracy of approximately 79% across five subjects (with four subjects at more than 81%) with 6s-window length and feature extraction algorithm based on canonical correlation analysis or lock-in analyzer system. The short 5 or 6s-concentration time, the absence of training due to the use of only one harmonic, the robustness make this method very well suited for detecting command following and testing communication in unresponsive post-comatose patients.
“Slow Activity Transients” in Infant Rat Visual Cortex:A Spreading Synchronous Oscillation Patterned by Retinal Waves

A primary feature of the preterm infant electroencephalogram is the presence of large infra-slow potentials containing rapid oscillations called slow activity transients (SATs). Such activity has not been described in animal models, and their generative mechanisms are unknown. Here we use direct-current and multisite extracellular, as well as whole-cell, recording in vivo to demonstrate the existence of regularly repeating SATs in the visual cortex of infant rats before eye opening. Present only in absence of anesthesia, SATs at postnatal day 10–11 were identifiable as a separate group of long-duration (∼10 s) events that consisted of large (>1 mV) negative local-field potentials produced by the summation of multiple bursts of rapid oscillatory activity (15–30 Hz). SATs synchronized the vast majority of neuronal activity (87%) in the visual cortex before eye opening. Enucleation eliminated SATs, and their duration, interevent interval, and sub-burst structure matched those of phase III retinal waves recorded in vitro. Retinal waves, however, lacked rapid oscillations, suggesting that they arise centrally. Multielectrode recordings showed that SATs spread horizontally in cortex and synchronize activity at coactive locales via the rapid oscillations. SATs were clearly different from ongoing cortical activity, which was observable as a separate class of short bursts from postnatal day 9. Together, our data suggest that, in vivo, early cortical activity is primarily determined by peripheral inputs—retinal waves in visual cortex—that provide excitatory input, and by thalamocortical circuitry, which transforms this input to beta oscillations. We propose that the synchronous oscillations of SATs participate in the formation of visual circuitry.
Adaptive prefetching for device-independent file I/O

Device independent I/O has been a holy grail to operating system designers since the early days of UNIX. Unfortunately, existing operating systems fall short of this goal for multimedia applications. Techniques such as caching and sequential read-ahead can help mask I/O latency in some cases, but in others they increase latency and add substantial jitter. Multimedia applications, such as video players, are sensitive to vagaries in performance since I/O latency and jitter affect the quality of presentation. Our solution uses adaptive prefetching to reduce both latency and jitter. Applications submit file access plans to the prefetcher, which then generates I/O requests to the operating system and manages the buffer cache to isolate the application from variations in device performance. Our experiments show device independence can be achieved: an MPEG video player sees the same latency when reading from a local disk or an NFS server. Moreover, our approach reduces jitter substantially.
Studies on Various Performance, Combustion & Emission Characteristics of An IDI CI Engine With Multi-Hole Injector At Different Injection Pressures And Using SVO-Diesel Blend As Fuel

This paper includes various experimental tests and analysis carried out on an IDI CI Engine using SVO (Straight Vegetable Oil)-Jatropha & Diesel blend in 40:60 proportions. For this test the Conventional Single-hole Injector was replaced by newly fabricated & customized Multi-hole injector with four-hole nozzle. The engine was run at constant rated speed (1000 rpm) and various performance, combustion and emission characteristics were measured at different engine load(10% to 100%) using an eddy current dynamometer as loading unit. The combustion characteristics (i.e, P-Ɵ curve, differential heat release rate and integral heat release rate) were measured with the help of Advanced Combustion Analyzer unit. The performance characteristics (i.e, brake specific energy consumption and thermal efficiency) were calculated using mathematical relations. The emission characteristics (i.e, smoke opacity, HC, NOx, O2, CO2 and CO) were measured with the help of Smoke meter and 5-Gas Analyzer set-up The same methodology was adopted with different injection pressures (210, 250 & 270 bar).
Body size stigmatization: an examination of attitudes of african american preschool-age children attending head start.

OBJECTIVE To assess body size stigmatization attitudes (BSSA), their effect on friendship selection, and controllability beliefs in a sample of African American preschool-age children of low socioeconomic status. METHODS Participants included 76 children attending Head Start. Children completed an adjective task, a friendship selection task, and a controllability task. RESULTS On the adjective task, the Overweight figure received significantly more negative mean ratings than the Underweight figure; however, there were no significant differences between the mean ratings for the Overweight and Average figures or the Average and Underweight figures. On the friendship selection task, children preferred the Average or Underweight figures as playmates and friends. On the controllability task, greater control was associated with the Overweight figure than the Underweight figure. CONCLUSION Results suggest that BSSA may be present in a sample of African American preschool-age children of low socioeconomic status. These attitudes may influence friendship selection and controllability beliefs.
AAV Vector-Mediated Overexpression of CB1 Cannabinoid Receptor in Pyramidal Neurons of the Hippocampus Protects against Seizure-Induced Excitoxicity

The CB1 cannabinoid receptor is the most abundant G-protein coupled receptor in the brain and a key regulator of neuronal excitability. There is strong evidence that CB1 receptor on glutamatergic hippocampal neurons is beneficial to alleviate epileptiform seizures in mouse and man. Therefore, we hypothesized that experimentally increased CB1 gene dosage in principal neurons would have therapeutic effects in kainic acid (KA)-induced hippocampal pathogenesis. Here, we show that virus-mediated conditional overexpression of CB1 receptor in pyramidal and mossy cells of the hippocampus is neuroprotective and moderates convulsions in the acute KA seizure model in mice. We introduce a recombinant adeno-associated virus (AAV) genome with a short stop element flanked by loxP sites, for highly efficient attenuation of transgene expression on the transcriptional level. The presence of Cre-recombinase is strictly necessary for expression of reporter proteins or CB1 receptor in vitro and in vivo. Transgenic CB1 receptor immunoreactivity is targeted to glutamatergic neurons after stereotaxic delivery of AAV to the dorsal hippocampus of the driver mice NEX-cre. Increased CB1 receptor protein levels in hippocampal lysates of AAV-treated Cre-mice is paralleled by enhanced cannabinoid-induced G-protein activation. KA-induced seizure severity and mortality is reduced in CB1 receptor overexpressors compared with AAV-treated control animals. Neuronal damage in the hippocampal CA3 field is specifically absent from AAV-treated Cre-transgenics, but evident throughout cortical areas of both treatment groups. Our data provide further evidence for a role of increased CB1 signaling in pyramidal hippocampal neurons as a safeguard against the adverse effects of excessive excitatory network activity.
Metrics for the design of visual displays of information

In product development, designers are often faced with the daunting tasks of interpreting, filtering, and managing enormous amounts of information. Examples include marketing data, product specification data, and project scheduling data. Although potentially useful information is buried in mountains of data, few tools exist to help users extract relevant information from these databases. Product developers need this pertinent information for more informed and therefore, more effective decision-making. This thesis explores the use of visualization techniques to reveal the inter-relational information hidden in databases. Visual displays enable designers to make decisions based on the overall relations in a database rather than the individual pieces of data. Information visualization has recently become a topic of significant interest especially with the availability of graphically agile computers, increased computational power, and advanced communication capabilities. It is a relatively new field of research where several point designs of new visualization techniques and tools have been proposed and developed. The premise of this thesis is that visual displays of information take advantage of the visual processing capabilities of humans, which leads to the identification of trends and patterns in data. Unfortunately, little is known about how to measure the effectiveness of visualizations. Based on a representational framework, a task-dependent approach, and a measure of information content, this thesis establishes metrics for the design of visual displays of information. To investigate the efficacy of these techniques, visualization tools were developed for exploring the patent database, a publication database, and the product development process. Empirical testing of the patent database visual tool demonstrated an increase in the capabilities of the designers using the visualization tool. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Answering without answering: Shifting as an evasive rhetorical strategy

In the context of political press conferences, the authors explore a particular category of subtle evasions they term shifting. When shifting, the interviewee seemingly accepts to answer the journalist’s question. However, in providing the answer, the interviewee refocuses the question replacing its critical aspect with a more favorable one. Guided by classical rhetoric, the authors unfold the underlying logic of a shift. Analyzing 14 press conferences held by the Danish Prime Minister, Lars Løkke Rasmussen, they identify three subcategories of shifting: shift in time, shift of agent, and shift of level. Ideally, knowledge of the different shifting strategies can enable journalists to detect a shift and promptly react when interviewees shift the focus of a question.
Parvovirus b19 infection in fetal deaths.

BACKGROUND Parvovirus B19 infection during pregnancy can lead to nonimmune fetal hydrops, miscarriage, and intrauterine fetal death (IUFD). Some studies have suggested that parvovirus B19 infection may surprisingly often result in nonhydropic fetal death during the third trimester, in the absence of maternal serological evidence of acute infection. This study was conducted to investigate the prevalence of parvovirus B19 DNA among fetuses from miscarriages and IUFDs. METHODS We retrospectively studied 535 unborn fetuses, including 120 fetuses from miscarriages and 169 from IUFDs. The control fetuses were 246 fetuses from induced abortions. All fetuses were autopsied from July 1992 through December 1995 and from January 2003 through December 2005 in Helsinki, Finland. The period included a major epidemic of parvovirus B19 infection in 1993. Formalin-fixed, paraffin-embedded fetal tissues were studied with use of a highly sensitive and specific PCR that was capable of detecting all 3 parvovirus B19 genotypes and by histologic examination. In addition, maternal parvovirus B19 serological status was determined. RESULTS Parvovirus B19 DNA was detected in 5 fetuses with gestational ages of 14, 22, 23, 30, and 39 weeks; these included fetuses from 4 (2.4%) of the 169 IUFDs and 1 (0.8%) of the 120 miscarriages. During the epidemic year 1993, the prevalence of parvovirus B19 DNA-positive fetal deaths was 6 times the prevalence during nonepidemic years. All 5 mothers of the parvovirus B19 DNA-positive fetuses had serological signs of acute parvovirus B19 infection close to the time of fetal death. The only nonhydropic fetus was full-term. CONCLUSIONS Our findings indicate that the prevalence of parvovirus B19 infection among fetuses from IUFDs is low. In particular, our findings did not verify the claimed high prevalence of third-trimester nonhydropic IUFDs associated with parvovirus B19.
Investigating the Relation between Empathy and Prosocial Behavior: An Emotion Regulation Framework

Little is known about the complex processes leading to prosocial behavior. However, theories suggests that empathy, empathic responding, and emotion regulation abilities, may all contribute to the presence or absence of prosocial behavior. While theoretical papers demonstrate relationships between these constructs, researchers to date have only focused on small aspects of this complex relationship (e.g., the relationship between sympathy and emotion regulation, the relationship between empathy and prosocial behavior). This study proposed a complex model whereby empathy was both directly related to prosocial behavior and indirectly related to prosocial behavior via sympathy or personal distress. Furthermore, this study proposed an emotion regulation framework for understanding the relation between empathy and prosocial behavior, suggesting that one’s emotion regulation abilities would cause a differential presentation of empathic responses, leading to a potential increase or decrease in prosocial behavior. An adult sample was recruited. Analyses were completed using Structural Equation Modeling (SEM). Results indicate that hypothesized model adequately fit the data. All hypothesized associations between variables were significant. However, contrary to the hypothesis, emotion regulation ability did not alter the associations between study constructs. Strengths, limitations, and implications will be discussed.
Collaboration and Teamwork on a MOOC Platform: A Toolset

Teamwork is an an important topic in education. It fosters deep learning and allows educators to assign interesting tasks, which would be too complex to be solved by single participants due to the time restrictions defined by the context of a course.Furthermore, today's jobs require an increasing amount of team skills. On the other hand, teamwork comes with a variety of issues of its own. Particularly in large scale settings, such as MOOCs, teamwork is challenging. Courses often end with dysfunctional teams due to drop-outs or insufficient matching. The paper at hand presents a set of three tools that we have recently added to our system to enable teamwork in our courses. This toolset consists of the TeamBuilder, a tool to match successful teams based on a variable set of parameters, CollabSpaces, providing teams with a secluded area to communicate and collaborate within the course context, and a TeamPeerAssessment tool, which allows to provide teams with complex tasks and which allows assessment that suffiiently scales for the MOOC context. The presented tools are evaluated in terms of success rates of the created teams and workload reduction for the courses' teaching teams.
Video Games Exposure and Sexism in a Representative Sample of Adolescents

Research has indicated that many video games are saturated with stereotypes of women and that these contents may cultivate sexism. The purpose of this study was to assess the relationship between video game exposure and sexism for the first time in a large and representative sample. Our aim was also to measure the strength of this association when two other significant and well-studied sources of sexism, television exposure and religiosity, were also included in a multivariate model. A representative sample of 13520 French youth aged 11–19 years completed a survey measuring weekly video game and television exposure, religiosity, and sexist attitudes toward women. Controlling for gender and socioeconomic level, results showed that video game exposure and religiosity were both related to sexism. Implications of these results for future research on sexism in video games are discussed.
Analytic Functions, Singularities and Edges: A New Formalism

Methods for detecting edges, be they multidimensional or multiresolution, ultimately reduce to finding extremal points, first derivatives or zeros of second derivatives. However, problems such as missing edges, weak edges due to thresholding, derivatives not existing and false edge generation, are some of the consequences. We adopt a new formalism: edges are singularities of the mathematically smoothest function possible - the complex analytic function. We embed a real image into the real part of an analytic function. After solving the conjugate harmonic problem, edges in discrete images are identified from the imaginary part. The analytic function model is inherently two-dimensional and an invariant measure. Comparisons are made with other standard edge detection methods. We outline issues that need to be considered for establishing analytic functions for edge detection
Rushes Video Parsing Using Video Sequence Alignment

In this paper, we propose a novel method inspired by the bio-informatics domain to parse a rushes video into scenes and takes. The Smith-Waterman algorithm provides an efficient way to compare sequences by comparing segments of all possible lengths and optimizing the similarity measure. We propose to adapt this method in order to detect repetitive sequences in rushes video. Based on the alignments found, we can parse the video into scenes and takes. By comparing takes together, we can select the most complete take in each scene. This method is evaluated on several rushes videos from the TRECVID BBC Rushes Summarization campaign.
The Value-Added Nature of Service-Learning

This research explores the benefits of service-learning among a group of Midwestern college students. Students enrolled in a section of a Juvenile Delinquency course served as volunteers at a juvenile detention facility and were studied using a pre-test/post-test survey design. This pilot project also included a comparison group of students in a section of the course which did not involve service-learning. The study compared service-learning to non-service-learning students in terms of attitudes regarding juvenile delinquency, punishment, and attributions of criminal behavior. We also examined any possible effects of service-learning on student academic skills, career goals, and comfort level with delinquents. Overall, we found that the service-learning project was a valuable educational tool having a positive impact on a number of student outcomes. We discuss the implications of these findings for service-learning research and practice.
Finding Decision Rules with Genetic Algorithms

Many decisions involve conflicting objectives that cannot be optimized simultaneously. For example, in choosing an apartment, none of the available options typically has the best commute, is in the nicest neighborhood, and rents for the lowest price; in making a decision of this sort, we examine tradeoffs. How these tradeoffs are made depends on the decision process and preferences of the decision maker.
The assessment of depth of anaesthesia in animals and man

The assessment of the depth of anaesthesia in man has received much attention in recent years, following a number of reports of people being aware during surgery. A range of different measures have been suggested for determining the adequacy of anaesthesia in man, but such a critical assessment is rarely applied to laboratory animals. This article describes the methods used to assess anaesthetic depth in both man and animals, and compares the relative states of knowledge about anaesthetic depth in animals and man.