Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of the Human Immunodeficiency Virus Type 1 Long Terminal Repeat Promoter by Conversion of an NF-κB Enhancer Element into a GABP Binding Site

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) transcription is regulated by the viral Tat protein and cellular factors, of which the concentration and activity may depend on the cell type. Viral long terminal repeat (LTR) promoter sequences are therefore optimized to suit the specific nuclear environment of the target host cell. In long-term cultures of a Tat-defective, poorly replicating HIV-1 mutant, we selected for a faster-replicating virus with a 1-nucleotide deletion in the upstream copy of two highly conserved NF-κB binding sites. The variant enhancer sequence demonstrated a severe loss of NF-κB binding in protein binding assays. Interestingly, we observed a new binding activity that is specific for the variant NF-κB sequence and is present in the nuclear extract of unstimulated cells that lack NF-κB. These results suggest that inactivation of the NF-κB site coincides with binding of another transcription factor. Fine mapping of the sequence requirements for binding of this factor revealed a core sequence similar to that of Ets binding sites, and supershift assays with antibodies demonstrated the involvement of the GABP transcription factor. Transient transfection experiments with LTR-chloramphenicol acetyltransferase constructs indicated that the variant LTR promoter is specifically inhibited by GABP in the absence of Tat, but this promoter was dramatically more responsive to Tat than the wild-type LTR. Introduction of this GABP site into the LAI virus yielded a specific gain of fitness in SupT1 cells, which contain little NF-κB protein. These results suggest that GABP potentiates Tat-mediated activation of LTR transcription and viral replication in some cell types. Conversion of an NF-κB into a GABP binding site is likely to have occurred also during the worldwide spread of HIV-1, as we noticed the same LTR modification in subtype E isolates from Thailand. This typical LTR promoter configuration may provide these viruses with unique biological properties.
Topology Identification Based on Multiple Source Network Tomography

Without the cooperation of internal nodes, the traceroute-based approaches and the SNMP-based approaches will fail to identify the topology of the work. Meanwhile, network tomography techniques can infer the logical topology of network without the cooperation of nodes. This paper focuses on the multiple source, multiple destination network tomography problem. The main contributions are as follows. First, A new measurement method is proposed to evaluate the link utilization of the shared path of the 2-by-1 component in the M-by-N network. Second, with the novel methodology, we firstly resolve the key problem of logical topology identification by multiple source network tomography. Additionally, The accuracy and efficiency of methodology is validated by the simulation results.
Data-driven Affective Enhancement of Images

With the current trend of digital camera revolution, it is increasingly important and desirable to generate high-impact photography that can have a lasting influence on the viewer. Recently, there is an increasing interest of computational/data-driven methodologies for more sophisticated controls such as aesthetics and emotions. Professionals usually rely on experience and intuition to choose appropriate color compositions which makes this process tedious and labor-intensive. Our goal in this paper is to learn implicit adjustment rules associated with the emotional properties of images from a set of training examples. Given a pair of image before and after adjustments, we discover the underlying mathematical relationships optimally connecting the color-contrast properties between them. As a first step we collect ground-truth data and construct a training database consisting of sample images and their different enhanced versions, and ask a set of human participants to mark their preferences. We employ machine learning techniques to understand the implicit relationship between an original image and its adjusted version, and derive statistical solutions to develop an enhancement function in a mathematical form. We conduct user studies to evaluate the effectiveness of our approach.
Lie on the Fly: Iterative Voting Center with Manipulative Voters

Manipulation can be performed when intermediate voting results are known; voters might attempt to vote strategically and try and manipulate the results during an iterative voting process. When only partial voting preferences are available, preference elicitation is necessary. In this paper, we combine two approaches of iterative processes: iterative preference elicitation and iterative voting and study the outcome and performance of a setting where manipulative voters submit partial preferences. We provide practical algorithms for manipulation under the Borda voting rule and evaluate those using different voting centers: the Careful voting center that tries to avoid manipulation and the Naive voting center. We show that in practice, manipulation happens in a low percentage of the settings and has a low impact on the final outcome. The Careful voting center reduces manipulation even further.
Risks and Safeguards for the Requirements Engineering Process in Global Software Development

The rise of new development paradigms such as Global Software Development (GSD) forces Requirements Engineering (RE) to face up to new challenges and risks not common in traditional development models. When an organization first embarks upon a GSD project it exposes itself to plenty of risks. Many of these risks appear as a result of the lack of experience of the development team on GSD projects. A Systematic Literature Review (SLR) has led to the compilation of a repository which gathers the risks that concern RE when developed in a distributed software development environment, as well as a set of safeguards, which help overcoming such risks. This repository, open to progressive enrichment, provides a novel basis to assist in RE activities for GSD projects. It could be especially useful when the developers have little experience in distributed projects and cannot prevent communication, distance, cultural, or organizational risks. Although the repository collects the main contributions from published work in the field, it has not been validated on real GSD projects yet.
A RANDOMIZED CONTROLLED TRIAL OF CBT-I AND CPAP FOR COMORBID INSOMNIA AND OSA: INITIAL FINDINGS FROM THE MATRICS STUDY

which insomnia subjects are instructed to stop taking study medication after 6 months of nightly use. Methods: DSM-V diagnosed insomnia subjects, 23-61 yrs, (n=25, 21 females), with disturbed sleep (i.e. polysomnographic sleep efficiency of ≤85%), no other sleep disorder, unstable medical or psychiatric disorder or drug dependency completed the trial. Participants were randomized to zolpidem XR (12.5 mg), eszopiclone (3 mg) or placebo nightly for 6 months (groups A: n=10, B: n=6, C: n=9). After 6 months of nighty use, over a 2-week choice period, they were instructed to discontinue hypnotic use, but if necessary, to take either 1, 2, or 3 capsules of medication (zolpidem XR 6.25 mg, 6.25 mg, placebo; eszopiclone 2 mg, 1 mg, placebo 1, 2 and 3 respectively; or 3 placebos). Results: The number of capsules taken declined from week 1 to 2 (p< .01). Over 2 weeks 13 participants took 0 (48%), 8 ≤ 6 (32%) and 4 ≥10 capsules (1 each took 42, 19, 13, and 10). Among those taking capsules most took one capsule per night and 9 took > 1 capsule. Those 4 taking ≥ 10 were younger (p<.05), but did not differ in screening sleep efficiency or blinded treatment group. Importantly 1 subject took every capsule available. Conclusion: The majority (80%) of the participants discontinued 6-month nightly hypnotic use (i.e. took < 6 total capsules over 2 weeks) and among those taking capsules the rate declined from week 1 to 2. Age may help identify the few with difficulty discontinuing. Support (If Any): NIDA, grant#: R01DA038177 awarded to Dr. Roehrs
The Relation between Evenness and Diversity

Contrary to common belief, decomposition of diversity into independent richness and evenness components is mathematically impossible. However, richness can be decomposed into independent diversity and evenness or inequality components. The evenness or inequality component derived in this way is connected to most of the common measures of evenness and inequality in ecology and economics. This perspective justifies the derivation of measures of relative evenness, which give the amount of evenness relative to the maximum and minimum possible for a given richness. Pielou’s [1] evenness measure J is shown to be such a measure.
Specific inhibitory synapses shift the balance from feedforward to feedback inhibition of hippocampal CA1 pyramidal cells

Feedforward and feedback inhibition are two fundamental modes of operation widespread in the nervous system. We have functionally identified synaptic connections between rat CA1 hippocampal interneurons of the stratum oriens (SO) and interneurons of the stratum lacunosum moleculare (SLM), which can act as feedback and feedforward interneurons, respectively. The unitary inhibitory postsynaptic currents (uIPSCs) detected with K‐gluconate‐based patch solution at −50 mV had an amplitude of 20.0 ± 2.0 pA, rise time 2.2 ± 0.2 ms, decay time 25 ± 2.2 ms, jitter 1.4 ± 0.2 ms (average ± SEM, n = 39), and were abolished by the γ‐aminobutyric acid (GABA)A receptor antagonist 2‐(3‐carboxypropyl)‐3‐amino‐6‐methoxyphenyl‐pyridazinium bromide (SR 95531). Post hoc anatomical characterization revealed that all but one of the identified presynaptic neurons were oriens‐lacunosum moleculare (O‐LM) cells, whereas the postsynaptic neurons were highly heterogeneous, including neurogliaform (n = 4), basket (n = 4), Schaffer collateral‐associated (n = 10) and perforant path‐associated (n = 9) cells. We investigated the short‐term plasticity expressed at these synapses, and found that stimulation at 10–40 Hz resulted in short‐term depression of uIPSCs. This short‐term plasticity was determined by presynaptic factors and was not target‐cell specific. We found that the feedforward inhibition elicited by the direct cortical input including the perforant path onto CA1 pyramidal cells was modulated through the inhibitory synapses we have characterized. Our data show that the inhibitory synapses between interneurons of the SO and SLM shift the balance between feedback and feedforward inhibition onto CA1 pyramidal neurons.
Generating test cases for real-time systems from logic specifications

We address the problem of automated derivation of functional test cases for real-time systems, by introducing techniques for generating test cases from formal specifications written in TRIO, a language that extends classical temporal logic to deal explicitly with time measures. We describe an interactive tool that has been built to implement these techniques, based on interpretation algorithms of the TRIO language. Several heuristic criteria are suggested to reduce drastically the size of the test cases that are generated. Experience in the use of the tool on real-life cases is reported.
Spatial pyramid mining for logo detection in natural scenes

This work introduces a novel data mining scheme, spatial pyramid mining, to discover association rules at multiple resolutions in order to identify frequent spatial configurations of local features that correspond to classes of logos appearing in real world scenes. By indexing representative examples by the mined rules we can efficiently detect a variety of different lettering or design marks associated with a brand. Features in an image are marked by matching rules to representative examples selected via a weighted cosine similarity measure. Logos are localized in an image via density-based clustering of matched features. Precision vs. recall curves are presented for experiments on a dataset of web images of nearly 1,000 images containing seven popular logo types.
Outcome of Stroke With Mild or Rapidly Improving Symptoms

Background and Purpose— Acute ischemic stroke with mild or rapidly improving symptoms is expected to result in good functional outcome, whether treated or not. Therefore, thrombolysis with its potential risks does not seem to be justified in such patients. However, recent studies indicate that the outcome is not invariably benign. Methods— We analyzed clinical and radiological data of patients with stroke who presented within 6 hours of stroke onset and did not receive thrombolysis because of mild or rapidly improving symptoms. Univariate and logistic regression analyses were performed to define predictors of clinical outcome. Results— One hundred sixty-two consecutive patients (110 men and 52 women) aged 63±13 years were included. The median National Institutes of Health Stroke Scale score on admission was 2 (range, 1 to 14). All patients presented within 6 hours of symptom onset. After 3 months, modified Rankin Scale score was ≤1 in 122 patients (75%), indicating a favorable outcome. Thirty-eight patients (23.5%) had an unfavorable outcome (modified Rankin Scale 2 to 5) and 2 patients (1.3%) had died. Baseline National Institutes of Health Stroke Scale score ≥10 points increased the odds of unfavorable outcome or death 16.9-fold (95% CI: 1.8 to 159.5; P<0.013), and proximal vessel occlusion increased the odds 7.13-fold (95% CI: 1.1 to 45.5; P<0.038). Conclusions— Seventy-five percent of patients with mild or rapidly improving symptoms will have a favorable outcome after 3 months. Therefore, a decision against thrombolysis seems to be justified in the majority of patients. However, selected patients, especially those with proximal vessel occlusions and baseline National Institutes of Health Stroke Scale scores ≥10 points, might derive a benefit from thrombolysis.
“Utter Failure” or Unity out of Diversity? Debating and Evaluating Policies of Multiculturalism 1

Across immigrant-receiving democracies, “multiculturalism” has come under assault by political decision-makers and commentators. The academic debate, while less fiery, is also heated. We start by outlining the multiple meanings of “multiculturalism”: a term for demographic diversity; a political philosophy of equality or justice; a set of policies to recognize and accommodate ethno-racial and religious diversity; or a public discourse recognizing and valorizing pluralism. We then review the existing empirical literature and offer some new statistical analyses to assess what we know about the harm or benefits of multicultural policies, focusing on sociopolitical outcomes. We conclude that multicultural policies appear to have some modest positive effects on sociopolitical integration for first-generation immigrants and likely little direct effect, positive or negative, on those in the second generation. On the question of majority backlash, the limited scholarship is mixed; we speculate that multiculturalism works best in places where both minorities and majority residents see it as part of a common national project. We end by considering the conditions under which this happens and whether there are distinctions between “Anglo-settler” and other countries.
Towards Effective Emotional Support for Community First Responders Experiencing Stress

Community First Responders are often the first on the scene in rural medical emergencies, and experience situations where stress is inherent. One way of reducing this stress is through the use of an Empathic Conversational Agent which can provide Emotional Support, and be applied to systems designed for the pre-hospital care domain. This paper outlines the groundwork for this goal by describing the development of stories which describe a particular stressor, and validated Emotional Support categories and statements. These will be used when developing an algorithm for adapting Emotional Support to different stressful situations. We identified 5 categories of Emotional Support, and a set of 52 statements which were validated as belonging to these categories. We then present a preliminary analysis of the patterns of usage of Emotional Support categories for each of the stressors.
Towards the introduction of human perception in a natural scene classification system

In this paper we develop a method to optimize a machine-based semantic categorization of natural images according to human perception. First, the categories are determined through a psychophysical experiment. The similarity matrices obtained from human responses are analyzed by a multidimensional scaling technique called Curvilinear Component Analysis (CCA). The same is done with an automatic image indexing system based on similarities between the outputs of Gabor filters applied to the images. Then we show that, by using the human categorization to balance the filter outputs, the system’s performance may be significantly improved.
Colorado's Prospects for Interstate Commerce in Renewable Power

Colorado has more renewable energy potential than it is ever likely to need for its own in-state electricity consumption. Such abundance may suggest an opportunity for the state to sell renewable power elsewhere, but Colorado faces considerable competition from other western states that may have better resources and easier access to key markets on the West Coast. This report examines factors that will be important to the development of interstate commerce for electricity generated from renewable resources. It examines market fundamentals in a regional context, and then looks at the implications for Colorado.
Incremental creation of a 3D map with a stereocamera

This paper describes a concept for the creation of a 3D model of the environment by a mobile robot. This technique is called SLAM — Simultaneous Localization and Mapping. In this case we use stereocamera to find the significant features by the SURF detector. The SURF detector will also serve for the matching of the correspondent points in the both images. These points will then be connected to the triangular mesh and displayed.
Postural force fields of the human arm and their role in generating multijoint movements

When a perturbation displaces the human hand from equilibrium, arm muscles respond by producing restoring forces. When a set of displacements are given at various directions from the same equilibrium position, the resulting restoring forces form a “postural force field. ” It is not known whether these postural forces are related to those generated when a reaching movement is executed. However, if a movement is a consequence of a shift of the equilibrium position of the hand toward the target, then, from the postural force field, predictions can be made regarding the nature of the elastic forces acting on the hand during the movement. We have taken the first steps in testing this hypothesis by measuring the postural force field of a subject's arm over relatively large distances, and comparing these forces with the static forces generated at the hand while the subject attempted a reaching movement. Using a robot manipulandum, the hand was displaced at various directions from an equilibrium position. The measured restoring forces were fitted to a nonlinear model to define a postural force field for that equilibrium position. This field was used to predict elastic forces generated when the subject attempted to move the manipulandum from a point on the circumference of a circle to a target at its center--the center corresponded to the equilibrium position at which the postural field was measured. In some of the movement trials, the manipulandum was locked during approximately the first 120 msec of the program for motion and the resulting static “evoked” forces measured. We found that (1) the evoked forces did not point to the target, but were a function of the configuration of the arm and rotated with the shoulder joint, and (2) the magnitude of the evoked forces varied systematically, even though the movements were of the same magnitude. These patterns were remarkably similar to those observed in the postural forces. Our results provide experimental evidence linking maintenance of posture in a multijoint system to that of generating a movement. The evidence is consistent with the hypothesis that the CNS programs a reaching movement by shifting the equilibrium position of the hand toward the target.
Cyberinfrastructure on Tumor Gene Expresstion Data Processing

Malignant tumor or cancer is one of serious diseases threatening human health. It is a challenging issue on how to diagnose the malignant tumor earlier and more accurately. A feasible way on cancer diagnosis is efficiently to share and analyze tumor related data. We work on a cyberinfrastructure which presents data sharing and data analysis solutions to reveal the relationship between tumor and gene.
Characterization of class 1 integrons and antibiotic resistance genes in multidrug-resistant Salmonella enterica isolates from foodstuff and related sources

In recent years, an increase in the occurrence of antimicrobial resistance among Salmonella enterica has been observed in several countries, which is worrisome because S. enterica is one of the most common causes of human gastroenteritis worldwide. The aim of this study was to characterize class 1 integrons and antibiotic resistance genotypes in Salmonella enterica isolates recovered from foodstuff and related sources. Nineteen multidrug-resistant (MDR) Salmonella enterica isolates were recovered. Higher resistance rates to tetracycline (90%), streptomycin (80%), sulfamethoxazole-trimethoprim (80%), ampicillin (60%) and nalidixic acid (70%) were related to the presence of the tetA, aadA, sul1/sul2, blaTEM-1 genes, and a codon mutation at position 83 of the gyrA gene, respectively. Class 1 integrons harboring aadA, blaTEM-1, sul1 or dhfr1 genes were detected in nine (45%) Salmonella enterica strains belonging to serotypes Brandenburg, Panama, Agona, Mbandaka and Alachua. Finally, clonal dissemination of S. Panama, S. Derby and S. Mbandaka was confirmed by PFGE. Detection of clonally related MDR Salmonella enterica suggests that endemic serotypes can be supported by class 1 integron-borne gene cassettes and/or mutations in drug targets. Emergence and dissemination of multidrug-resistant Salmonella enterica can have a major public health impact in an environment where large-scale suppliers ship their products.
Renewable energy systems for generating electric power: A review

This paper reviews various schemes utilized for generating electric power from renewable energy resources, which are suitable for interconnecting with a power grid as well as for using as an isolated system. As all the renewable energy resources except geothermal energy, being climate dependent, the power generated from them is of varying magnitude-even sometimes no power is generated at all. The other drawbacks are the poor power quality and the high cost of generation, which are the big challenges for meeting the target of ever increasing demand of electric power by renewable energy systems in an efficient and effective way. The various schemes described in the literature for improving the power quality as well as the overall performance of the system by using developed technologies involving power electronics, are reviewed in the paper. In order to achieve the continuous power of constant magnitude up to the satisfactory level, the hybrid schemes using two or more renewable energy sources or any conventional system with some energy storage methods for backup are also discussed. Despite this technological development, still an urgent need to further investigate some other renewable energy source or scheme to provide continuous energy of constant magnitude at low cost is earnestly observed in the paper.