Miracle-dz/UniFAR-FTUs huggingface dataset:
A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference

Vaccinia virus (VACV) is a large, cytoplasmic, double-stranded DNA virus that requires complex interactions with host proteins in order to replicate. To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. The experimental design incorporated a low multiplicity of infection, thereby enhancing detection of cellular proteins involved in cell-to-cell spread of VACV. The screen revealed 153 pro- and 149 anti-viral HFs that strongly influenced VACV replication. These HFs were investigated further by comparisons with transcriptional profiling data sets and HFs identified in RNAi screens of other viruses. In addition, functional and pathway analysis of the entire screen was carried out to highlight cellular mechanisms involved in VACV replication. This revealed, as anticipated, that many pro-viral HFs are involved in translation of mRNA and, unexpectedly, suggested that a range of proteins involved in cellular transcriptional processes and several DNA repair pathways possess anti-viral activity. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. This advancement in our understanding of the VACV life cycle provides a reliable knowledge base for the improvement of poxvirus-based vaccine vectors and development of anti-viral theraputics.
Development of Real-Time Driver's Health Detection System by Using Smart Handle

The number of vehicle accidents due to driver's drowsiness continues to increase. Therefore, prompt and effective detection for driver's health during driving is crucial to improvement of traffic safety. A set of real-time healthdetection system built-in a smart handle for driver is proposed in the research. By monitoring driver’s biological signals, including respiration, hand gripping force, photoplethysmogram (PPG), and electrocardiogram (ECG), driver's health condition (drowsiness) is able to be detected via the developed algorithm. Meanwhile the driver's state of arrhythmia can be diagnosed too. The test results indicate that the developed real-time driver’s health detection system can effectively monitor not only the state of vigilance but also the state of arrhythmia of a driver.
Innovative Design as Systematic Search

We present a new algorithm, SIE, for designing lumped parameter models from first principles. Like the IBIS system of Williams [1989, 1990], SIE uses a qualitative representation of parameter interactions to guide its search and speed the test for working designs. But SIE's interaction set representation is considerably simpler than IBIS's space of potential and existing interactions. Furthermore, SIE is both complete and systematic - it explores the space of possible designs in an nonredundant manner.
The effect of anticipated and experienced regret and pride on investors' future selling decisions

This paper investigates the effect of anticipated/experienced regret and pride on individual investors' decisions to hold or sell a winning or losing investment, in the form of the disposition effect. As expected the results suggest that in the loss domain, low anticipated regret predicts a greater probability of selling a losing investment. While in the gain domain, high anticipated pride indicates a greater probability of selling a winning investment. The effects of high experienced regret/pride on the selling probability are found as well. An unexpected finding is that regret (pride) seems to be not only relevant for the loss (gain) domain, but also for the gain (loss) domain. In addition, this paper presents evidence of interconnectedness between anticipated and experienced emotions. The authors discuss the implications of these findings and possible avenues for further research.
Gaze movements and spatial working memory in collision avoidance: a traffic intersection task

Street crossing under traffic is an everyday activity including collision detection as well as avoidance of objects in the path of motion. Such tasks demand extraction and representation of spatio-temporal information about relevant obstacles in an optimized format. Relevant task information is extracted visually by the use of gaze movements and represented in spatial working memory. In a virtual reality traffic intersection task, subjects are confronted with a two-lane intersection where cars are appearing with different frequencies, corresponding to high and low traffic densities. Under free observation and exploration of the scenery (using unrestricted eye and head movements) the overall task for the subjects was to predict the potential-of-collision (POC) of the cars or to adjust an adequate driving speed in order to cross the intersection without collision (i.e., to find the free space for crossing). In a series of experiments, gaze movement parameters, task performance, and the representation of car positions within working memory at distinct time points were assessed in normal subjects as well as in neurological patients suffering from homonymous hemianopia. In the following, we review the findings of these experiments together with other studies and provide a new perspective of the role of gaze behavior and spatial memory in collision detection and avoidance, focusing on the following questions: (1) which sensory variables can be identified supporting adequate collision detection? (2) How do gaze movements and working memory contribute to collision avoidance when multiple moving objects are present and (3) how do they correlate with task performance? (4) How do patients with homonymous visual field defects (HVFDs) use gaze movements and working memory to compensate for visual field loss? In conclusion, we extend the theory of collision detection and avoidance in the case of multiple moving objects and provide a new perspective on the combined operation of external (bottom-up) and internal (top-down) cues in a traffic intersection task.
Telepsychiatry in the assessment and treatment of schizophrenia.

BACKGROUND Telehealth technology has become more available to providers as a means of treating chronic diseases. Consideration of the applicability of telehealth technology in the treatment of schizophrenia calls for a review of the evidence base in light of the special needs and challenges in the treatment of this population. Our aims are to assess the types and nature of distant interventions for patients with schizophrenia, either telephone-based, internet-based or video-based telehealth systems. METHODS The following databases--MEDLINE, PsycINFO, CINAHL, the Cochrane Library, the Cochrane Database of Systematic Reviews, the Database of Abstracts of Reviews of Effects, and EMBASE--were searched for the following terms alone or in combination with schizophrenia: telepsychiatry or telemedicine or telepsychology or satellite communication or remote communication. Inclusion criteria were: 1) articles dealing with telephone-, internet- or video-based interventions and 2) studies emphasizing development of an intervention, feasibility or clinical trials. Exclusions included were: 1) single case reports and 2) papers not written in English. With our search terms, we retrieved a total of 390 articles, of which 18 unique articles were relevant. RESULTS Based on the limited data available, the use of modalities involving the telephone, internet and videoconferencing appears to be feasible in patients with schizophrenia. In addition, preliminary evidence suggests these modalities appear to improve patient outcomes. DISCUSSION More research is needed. Investigators need to improve existing telehealth systems. In addition, researchers need to focus on developing newer interventions and determining whether these approaches can improve patient outcomes.
Re-architecting DRAM with Monolithically Integrated Silicon Photonics

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission. Future manycore computing systems will only deliver increased performance if memory bandwidth improves also. Projected scaling of electrical DRAM architectures appears unlikely to suffice, being constrained by pin count and pin bandwidth, and by total chip power, including off-chip signaling, cross-chip interconnect, and bank access energy. In this work, we redesign the main memory system using a proposed monolithically integrated silicon photonics technology and show that it provides a promising solution to all of these issues. Photonics can provide high aggregate pin-bandwidth density through dense wavelength-division multiplexing (DWDM). Photonic signaling also provides energy-efficient long-range communication, which we exploit to not only reduce chip-chip link power but also extend on to the DRAMs to reduce cross-chip interconnect power. To balance these large improvements in interconnect bandwidth and power, we must also improve the energy efficiency of the DRAM banks themselves, as we now require many concurrently accessed banks to support the available bandwidth. We explore decreasing the number of bits activated per bank to increase the banks' energy efficiency. Since DRAM chips are a very cost-sensitive commodity, we weigh these efficiency gains against any area overhead. Due to the immature nature of photonics technology, we explore a large design space to capture plausible designs for a range of different technology assumptions. Our most promising design point yields approximately a 10× improvement in power for the same throughput as a projected future electrical-only DRAM, with slightly reduced area. Finally, we propose a new form of optical power guiding which increases the scalability of our memory architecture and allows for a single chip design to be used in both high capacity or high bandwidth memory configurations.
Changes in neurofilament transport coincide temporally with alterations in the caliber of axons in regenerating motor fibers

The delivery of neurofilaments via axonal transport has been proposed as an important mechanism for regulating axonal caliber. If this hypothesis is correct, alterations in axonal caliber should appear coincident with changes in the delivery of neurofilaments to the axon. The purpose of this study was to determine whether alterations in the caliber of axons in the proximal stumps of transected motor fibers precede, coincide with, or occur substantially later than changes in the delivery of neurofilaments via axonal transport. Between 3 d and 12 wk after crushing the sciatic nerves of 7-wk-old rats, lumbar motor neurons were labeled by the intraspinal injection of [35S]methionine. In neurons labeled between 3 d and 6 wk after axotomy, the relative amount of neurofilament protein in the slow component, as reflected by the ratio of the radioactivities of the 145-kD neurofilament protein to tubulin, was reduced to 30-40% of the control value. Moreover, as determined by immunoreactivity on blots, the amounts of neurofilament protein and tubulin in these nerve fibers were reduced fourfold and twofold, respectively. Thus, changes in the ratio of labeled neurofilament protein to tubulin correlated with comparable changes in the quantities of these proteins in nerve fibers. This decrease in the quantity of neurofilament proteins delivered to axons coincided temporally with reductions in axonal caliber. After regeneration occurred, the delivery of neurofilament proteins returned to pre- axotomy levels (i.e., 8 wk after axotomy), and caliber was restored with resumption of normal age-related radial growth of these axons. Thus, changes in axonal caliber coincided temporally with alterations in the delivery of neurofilament proteins. These results suggest that the majority of neurofilaments in these motor fibers continuously move in the anterograde direction as part of the slow component of axonal transport and that the transport of neurofilaments plays an important role in regulating the caliber of these axons.
The HuRef Browser: a web resource for individual human genomics

The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef. The browser provides a comparative view between the NCBI human reference sequence and the HuRef assembly, and it enables the navigation of the HuRef genome in the context of HuRef, NCBI and Ensembl annotations. Single nucleotide polymorphisms, indels, inversions, structural and copy-number variations are shown in the context of existing functional annotations on either genome in the comparative view. Demonstrated here are some potential uses of the browser to enable a better understanding of individual human genetic variation. The browser provides full access to the underlying reads with sequence and quality information, the genome assembly and the evidence supporting the identification of DNA polymorphisms. The HuRef Browser is a unique and versatile tool for browsing genome assemblies and studying individual human sequence variation in a diploid context. The browser is available online at http://huref.jcvi. org.
Higher dimensional recombination of intersecting D-branes

We study recombinations of D-brane systems intersecting at more than one angle using super Yang-Mills theory. We find the condensation of an off-diagonal tachyon mode relates to the recombination, as was clarified for branes at one angle in [5]. For branes at two angles, after the tachyon mode between two D2-branes condensed, D2-brane charge is distributed in the bulk near the intersection point. We also find that, when two intersection angles are equal, the off-diagonal lowest mode is massless, and a new stable non-abelian configuration, which is supersymmetric up to a quadratic order in the fluctuations, is obtained by the deformation by this mode.
A reverse engineering approach to support software maintenance: version control knowledge extraction

Most traditional reverse engineering tools focus on abstraction and analysis of source code, presenting a visual representation of the software architecture. This approach can be both helpful and cost effective in software maintenance tasks. However, where large software teams are concerned, with moderate levels of employee turnover, traditional reverse engineering tools can be inadequate. To address this issue, we examine the use of software process data, such as software artifact change history and developer activities. We propose the application of this data confers additional information developers need to better understand, maintain and develop software in large team settings. To explore this hypothesis, we evaluate the use of a tool, Xia, in the navigation of both software artifacts and their version history. This work introduces Xia, reveals the results of our evaluation and proposes directions for future research in this area.
Hirshfeld atom refinement

The new automated iterative Hirshfeld atom refinement method is explained and validated through comparison of structural models of Gly–l-Ala obtained from synchrotron X-ray and neutron diffraction data at 12, 50, 150 and 295 K. Structural parameters involving hydrogen atoms are determined with comparable precision from both experiments and agree mostly to within two combined standard uncertainties.
Pirfenidone inhibits migration, differentiation, and proliferation of human retinal pigment epithelial cells in vitro

Purpose To investigate the effects of pirfenidone (PFD) on the migration, differentiation, and proliferation of retinal pigment epithelial (RPE) cells and demonstrate whether the drug induces cytotoxicity. Methods Human RPE cells (line D407) were treated with various concentrations of PFD. Cell migration was measured with scratch assay. The protein levels of fibronectin (FN), connective tissue growth factor (CTGF), α-smooth muscle actin (α-SMA), transforming growth factor beta (TGFβS), and Smads were assessed with western blot analyses. Levels of mRNA of TGFβS, FN, and Snail1 were analyzed using reverse transcriptase–polymerase chain reaction. Cell apoptosis was detected with flow cytometry using the Annexin V/PI apoptosis kit, and the percentages of cells labeled in different apoptotic stage were compared. A Trypan Blue assay was used to assess cell viability. Results PFD inhibited RPE cell migration. Western blot analyses showed that PFD inhibited the expression of FN, α-SMA, CTGF, TGFβ1, TGFβ2, Smad2/3, and Smad4. Similarly, PFD also downregulated mRNA levels of Snail1, FN, TGFβ1, and TGFβ2. No significant differences in cell apoptosis or viability were observed between the control and PFD-treated groups. Conclusions PFD inhibited RPE cell migration, differentiation, and proliferation in vitro and caused no significant cytotoxicity.
The history of control: from idea to technology

has been almost six years since the last special issue of the Magazine on the history of control. The June 1996 issue, titled “On the History of Control Research” and organized by guest editor Linda Bushnell, provided an overview of the development of control system technology and highlighted the contributions of individual researchers. We are pleased to present a new collection of articles that significantly expands on the earlier issue. Before describing the contents of this exciting issue, it is important to acknowledge the ongoing efforts of the IEEE CSS History Committee, chaired by Daniel Abramovitch. He has been active in directing the activities of the commit-
The Fezf 2 – Ctip 2 genetic pathway regulates the fate choice of subcortical projection neurons in the developing cerebral cortex

Pyramidal neurons in the deep layers of the cerebral cortex can be classified into two major classes: callosal projection neurons and long-range subcortical neurons. We and others have shown that a gene expressed specifically by subcortical projection neurons, Fezf2, is required for the formation of axonal projections to the spinal cord, tectum, and pons. Here, we report that Fezf2 regulates a decision between subcortical vs. callosal projection neuron fates. Fezf2 / neurons adopt the fate of callosal projection neurons as assessed by their axonal projections, electrophysiological properties, and acquisition of Satb2 expression. Ctip2 is a major downstream effector of Fezf2 in regulating the extension of axons toward subcortical targets and can rescue the axonal phenotype of Fezf2 mutants. When ectopically expressed, either Fezf2 or Ctip2 can alter the axonal targeting of corticocortical projection neurons and cause them to project to subcortical targets, although Fezf2 can promote a subcortical projection neuron fate in the absence of Ctip2 expression.
Efficiency of the UV/H2O2 process for the disinfection of humic surface waters

The efficiency of the UV/H2O2 process for the disinfection of total coliforms and the prevention of bacterial regrowth in humic surface waters were investigated. Inactivation of total coliforms was determined in water samples containing various concentrations ranging from 0–10 mg/L dissolved organic carbon (DOC) of fulvic acid, which were exposed to various doses (68–681 mWs/cm2) of UV radiation in the presence of 0.125 mg/L and 3.000 mg/L of hydrogen peroxide. Disinfection efficiencies of the UV radiation and the UV/H2O2 processes were compared. The results of bacterial inactivation experiments showed that the performances of the UV and the UV/H2O2 (0.125) were comparable whereas the UV/H2O2 (3.000) process showed significant improvement in performance, especially, in highly humic waters. Inactivation coefficient appeared to be almost doubled by the addition of 3.000 mg/L hydrogen peroxide during the treatment of highly humic waters. In contradiction to significant regrowth which occurred in the single UV radiation treatment, residual bacteria following the UV/H2O2 (0.125) and the UV/H2O2 (3.000) treatments were completely inactivated during dark incubation indicating the elimination of possible bacterial regrowth.
ASPECTOS DA LEGISLAÇÃO AMBIENTAL PARA A REVEGETAÇÃO DE MATAS CILIARES NO ESTADO DO PARANÁ

Este trabalho de revisao tem como objetivo discutir aspectos importantes sobre a preservacao de areas de mata ciliar, assim como dos problemas causados pela presenca de especies arboreas exoticas, abordar sobre a legislacao brasileira e do estado do Parana na protecao as matas ciliares e na proibicao das especies exoticas invasoras e, relacionar especies lenhosas nativas na revegetacao de matas ciliares no estado. Como caracteristica do tipo de pesquisa, focou-se nas peculiaridades da legislacao existente, entre o nivel federal e estadual, que confere o regulamento e especificacoes para tratar do assunto. Verificou-se que a legislacao brasileira abriu interpretacoes que possibilitaram a introducao de especies exoticas invasoras, como Pinus spp. e Eucalyptus spp . Somente em 2011, a legislacao brasileira tomou medidas para tentar reverter esta situacao ao criar a Resolucao no 429 que estabeleceu metodologias para recuperacao de areas degradadas sem o uso de especies exoticas. O estado do Parana se encontrava em alerta com tal situacao desde 2009, e por meio da Portaria no 125 do Instituto Ambiental do Parana (IAP), reconheceu uma lista de especies exoticas invasoras, permitindo a criacao ou o cultivo somente em determinados casos, incorporando, tambem, uma lista de especies arboreas nativas recomendadas na revegetacao de mata ciliares a qual distribui as especies nas divisoes bioclimaticas, considerando a melhor adaptacao de cada uma em cada regiao, viabilizando o processo de restauracao das matas ciliares.
Compatibility and Reparation of Web Service Processes

When two Web services work together, they exchange messages in a predefined interface process. Two interface processes should be compatible when they can work properly. Our idea to fix incompatibility problem in service processes is to change an incompatible process so that the new process can simulate a compatible process. We consider not only the control flow but also the data flow in modeling the processes into FSMs. We present a technique that not only detects the incompatibility, but also provides resolution strategies to generate the new process.
Algebra of inference in graphical models revisited

Graphical Models use the intuitive and well-studied methods of graph theory to implicitly represent dependencies between variables in large systems and model the global behaviour of a complex system by specifying only local factors. The variational perspective poses inference as optimization and provides a rich framework to study inference when the object of interest is a (log) probability. However, graphical models can operate on a much wider set of algebraic structures. This paper builds on the work of Aji and McEliece (2000), to formally and broadly express what constitutes an inference problem in a graphical model. We then study the computational complexity of inference and show that inference in any commutative semiring is NP-hard under randomized reduction. By confining inference to four basic operations of min, max, sum and product, we introduce the inference hierarchy with an eye on computational complexity and establish the limits of message passing using distributive law in solving the problems in this hierarchy.