Miracle-dz/UniFAR-FTUs huggingface dataset:
Dual-function transcription factors and their entourage

Much of what we, as plant molecular biologists studying gene regulation, know comes from paradigms characterized or developed in mammalian systems. Although plants, animals, and fungi have been diverging for a very long time, a great deal of the machineries and components discovered in yeast and mammals seem to have been maintained in plants. Nevertheless, despite this apparent conservation, evolutionary pressures on the mechanisms of gene regulation are likely to be different between these kingdoms, given their different environmental constraints. As such, it is imperative for plant molecular biologists to develop their own paradigms, even on seemingly conserved systems. It is with this intent that we compare and contrast the regulation of two pathogenesis-related genes, the arabidopsis PR-1 and potato PR-10a genes. The transcription factors regulating these genes present prime paradigms for the study of plant signal- and context-dependent dual-function transcription factors.
Recent Developments in Skin Deformation for Character Animation

Achieving realistic skin deformation efficiently is a very important task for character animation. With the development of skin deformation, the efficiency and effectiveness of character modelling and animation have been obviously enhanced. In this paper, we survey the recent literature on skin deformation according to three types of approaches: purely geometric, physics-based, and data driven. Especially we focus on the work since 2009. We review the problems they primarily tackles, the methodologies they applies, and the advantages and disadvantages they have. At last, we discuss directions for future research.
Serotonin Clearance In Vivo Is Altered to a Greater Extent by Antidepressant-Induced Downregulation of the Serotonin Transporter than by Acute Blockade of this Transporter

Serotonin uptake, mediated by the serotonin transporter (SERT), is blocked acutely by antidepressants such as the selective serotonin reuptake inhibitors (SSRIs), but such blockade does not correlate temporally with the onset of therapeutic improvement. Treatment with SSRIs for 21 d induced downregulation of the SERT (Benmansour et al., 1999). The time course of SERT downregulation as well as the time course for its recovery after cessation of treatment with the SSRI sertraline were investigated using tritiated cyanoimipramine to measure SERT binding sites. To determine if there was a temporal correlation between the time when sertraline induced downregulation of the SERT and when marked alteration in SERT function occurred, clearance of locally applied 5-HT into the CA3 region of hippocampus was achieved using in vivo electrochemistry. After 4 or 10 d treatment with sertraline, SERT binding sites decreased very little (15–30%), and the chronoamperometric signals for serotonin in sertraline-treated rats were comparable with ones obtained in control animals. By contrast, after 15 d of treatment, when SERT binding sites were markedly reduced by 80%, there was robust decrease in the clearance of 5-HT. Moreover, the functional consequences of SERT downregulation as measured by chronoamperometry were significantly greater than those seen after acute blockade of the SERT by SSRIs. SERT binding sites decreases are not a consequence of reduced SERT gene expression, as revealed by in situhybridization measurements. SSRI-induced downregulation of the SERT may be a key component for the clinical response to SSRIs.
MAPPING THE DENSE SCOTOMA AND ITS ENLARGEMENT IN STARGARDT DISEASE

Purpose: To describe the enlargement of the dense scotoma over time in Stargardt disease and to highlight methodologic issues in tracking enlargement. Methods: Retrospective study of patients with full mapping of the border of the dense scotoma using the MP-1 for at least two visits. Results: 14 eyes of 7 patients met this criterion. Patients had median of 3 visits (range 2–5), with median total follow-up of 4.5 years (range 1.5–8). Mean baseline visual acuity was 20/56 (range 20/25–20/200), mean baseline dense scotoma area was 2.23 mm2 (range 0.41–5.48), and mean dense scotoma enlargement rate was 1.36 mm2/year (range 0.22–2.91). The younger patients tended to have more rapid loss of visual acuity, which tended to plateau when the visual acuity was 20/100 or worse. The patients who developed Stargardt before age 20 years, and the single patient who developed Stargardt disease after age 40 years, had more rapid enlargement rates, with preservation of central vision in the oldest patient. The ability to precisely define the dense scotoma area was dependent on the density location of the points tested; this led to significant variability in the assessment of the scotoma enlargement rate in three of the seven patients. The dense scotoma was not described adequately by the extent of the homogeneous dark area on fundus autofluorescence imaging. Conclusion: Microperimetry is necessary for mapping the scotoma in patients with Stargardt disease, because current imaging is not adequate. Standardized grid testing, plus a standardized procedure for refining the border of the dense scotoma, should allow more precise testing and longitudinal assessment of enlargement rates.
Structural similarity indices for high dynamic range imaging

In this paper, a structural similarity index is first proposed for two images with possibly different dynamic ranges and intensities as well as possibly small rotation and translation. The proposed index is then extended by dividing two images into local windows, and the similarity is detected by checking all pairs of local windows. It is shown by experimental results that the proposed indices are more robust to large intensity and dynamic range changes of two images from the same scene than the structural similarity (SSIM) index in [4].
Modelling Cochlear Mechanics

The cochlea plays a crucial role in mammal hearing. The basic function of the cochlea is to map sounds of different frequencies onto corresponding characteristic positions on the basilar membrane (BM). Sounds enter the fluid-filled cochlea and cause deflection of the BM due to pressure differences between the cochlear fluid chambers. These deflections travel along the cochlea, increasing in amplitude, until a frequency-dependent characteristic position and then decay away rapidly. The hair cells can detect these deflections and encode them as neural signals. Modelling the mechanics of the cochlea is of help in interpreting experimental observations and also can provide predictions of the results of experiments that cannot currently be performed due to technical limitations. This paper focuses on reviewing the numerical modelling of the mechanical and electrical processes in the cochlea, which include fluid coupling, micromechanics, the cochlear amplifier, nonlinearity, and electrical coupling.
Biochemical Characterization of Ochratoxin A-Producing Strains of the Genus Penicillium

ABSTRACT In order to explore the biochemical scope of ochratoxin A-producing penicillia, we screened 48 Penicillium verrucosumisolates for the production of secondary metabolites. Fungal metabolites were analyzed by high-pressure liquid or gas chromatography coupled to diode array detection or mass spectrometry. The following metabolites were identified: ochratoxins A and B, citrinin, verrucolones, verrucines, anacines, sclerotigenin, lumpidin, fumiquinazolines, alantrypinones, daldinin D, dipodazine, penigequinolines A and B, 2-pentanone, and 2-methyl-isoborneol. By use of average linking clustering based on binary (nonvolatile) metabolite data, the 48 isolates could be grouped into two large and clearly separated groups and a small outlying group of four non-ochratoxin-producing isolates. The largest group, containing 24 isolates, mainly originating from plant sources, included the type culture of P. verrucosum. These isolates produced ochratoxin A, verrucolones, citrinin, and verrucines and had a characteristic dark brown reverse color on yeast extract-sucrose agar medium. Almost all of a group of 20 isolates mainly originating from cheese and meat products had a pale cream reverse color on yeast extract-sucrose agar medium and produced ochratoxin A, verrucolones, anacines, and sclerotigenin. This group included the former type culture of P. nordicum. We also found that P. verrucosum isolates and threeP. nordicum isolates incorporated phenylalanine into verrucine and lumpidin metabolites, a finding which could explain why those isolates produced relatively lower levels of ochratoxins than did most isolates of P. nordicum.
Dr. Jekyll and Mr. Hyde: The Two Faces of the FUS/EWS/TAF15 Protein Family

FUS, EWS, and TAF15 form the FET family of RNA-binding proteins whose genes are found rearranged with various transcription factor genes predominantly in sarcomas and in rare hematopoietic and epithelial cancers. The resulting fusion gene products have attracted considerable interest as diagnostic and promising therapeutic targets. So far, oncogenic FET fusion proteins have been regarded as strong transcription factors that aberrantly activate or repress target genes of their DNA-binding fusion partners. However, the role of the transactivating domain in the context of the normal FET proteins is poorly defined, and, therefore, our knowledge on how FET aberrations impact on tumor biology is incomplete. Since we believe that a full understanding of aberrant FET protein function can only arise from looking at both sides of the coin, the good and the evil, this paper summarizes evidence for the central function of FET proteins in bridging RNA transcription, processing, transport, and DNA repair.
Intimate Partner Violence and Women’s Help-seeking Behaviour: Evidence from India

This study examines the role of socio-economic characteristics that influence a battered woman in India to either remain silent or approach someone for help in response to domestic violence. We investigate the influence of socio-economic factors on choosing between formal and informal sources of seeking help. The dataset used for the analysis is a nationally representative, community-based survey database—the National Family Health Survey-3 (NFHS-3). A logistic regression framework was used to analyze the data. The results suggest that education and economic empowerment play a crucial role in deciding whether to seek help to stop domestic violence. Women exposed to violence attempts utilize both formal and informal sources of help; however, informal sources of help are more popular compared with formal sources in India. JEL: J12
Rational development of antimicrobial peptides for therapeutic use: design and production of highly active compounds

NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12-56127 Pisa, Italy * corresponding author: mariagrazia.diluca@sns.it The emergence of drug-resistant pathogenic microbial strains has created an urgent need for new anti-infective molecule development. In order to avoid the spread of bacterial resistance, there is pressing demand to design a novel class of antibiotics having different mechanism of action in comparison to existing drugs. Natural antimicrobial peptides (AMPs) represent a novel class of molecules with a broad spectrum of activity and a low rate in inducing bacterial resistance. However, until now, many AMPs have failed in clinical trials because of several drawbacks that strongly limit their applicability such as degradation, cytotoxicity and high production cost. Thus, to overcome the limitations of native peptides, a rational
An 18 kDa Scaffold Protein Is Critical for Staphylococcus epidermidis Biofilm Formation

Virulence of the nosocomial pathogen Staphylococcus epidermidis is crucially linked to formation of adherent biofilms on artificial surfaces. Biofilm assembly is significantly fostered by production of a bacteria derived extracellular matrix. However, the matrix composition, spatial organization, and relevance of specific molecular interactions for integration of bacterial cells into the multilayered biofilm community are not fully understood. Here we report on the function of novel 18 kDa Small basic protein (Sbp) that was isolated from S. epidermidis biofilm matrix preparations by an affinity chromatographic approach. Sbp accumulates within the biofilm matrix, being preferentially deposited at the biofilm–substratum interface. Analysis of Sbp-negative S. epidermidis mutants demonstrated the importance of Sbp for sustained colonization of abiotic surfaces, but also epithelial cells. In addition, Sbp promotes assembly of S. epidermidis cell aggregates and establishment of multilayered biofilms by influencing polysaccharide intercellular-adhesin (PIA) and accumulation associated protein (Aap) mediated intercellular aggregation. While inactivation of Sbp indirectly resulted in reduced PIA-synthesis and biofilm formation, Sbp serves as an essential ligand during Aap domain-B mediated biofilm accumulation. Our data support the conclusion that Sbp serves as an S. epidermidis biofilm scaffold protein that significantly contributes to key steps of surface colonization. Sbp-negative S. epidermidis mutants showed no attenuated virulence in a mouse catheter infection model. Nevertheless, the high prevalence of sbp in commensal and invasive S. epidermidis populations suggests that Sbp plays a significant role as a co-factor during both multi-factorial commensal colonization and infection of artificial surfaces.
HMM-based Human Action Recognition Using Multiview Image Sequences

In this paper, we present a novel method for human action recognition from any arbitrary view image sequence that uses the Cartesian component of optical flow velocity and human body silhouette feature vector information. We use principal component analysis (PCA) to reduce the higher dimensional silhouette feature space into lower dimensional feature space. The action region in an image frame represents Q-dimensional optical flow feature vector and R-dimensional silhouette feature vector. We represent each action using a set of hidden Markov models and we model each action for any viewing direction by using the combined (Q + R) -dimensional features at any instant of time. We perform experiments of the proposed method by using KU gesture database and manually captured data. Experimental results of different actions from any viewing direction are correctly classified by our method, which indicate the robustness of our view-independent method
Protection against ischemic injury by nonvasoactive concentrations of nitric oxide synthase inhibitors in the perfused rabbit heart.

BACKGROUND The functional and metabolic effects of inhibitors of nitric oxide (NO) synthase on ischemic hearts have not been investigated. This work was designed to perform such a study in isolated perfused rabbit hearts submitted to low-flow ischemia. METHODS AND RESULTS After a 30-minute equilibration period, the hearts were submitted to low-flow ischemia for 60 minutes followed by reperfusion for 30 minutes. Functional and metabolic parameters were followed in hearts perfused with or without inhibitors of NO synthase or NO precursors, which were added 15 minutes before ischemia but were absent during reperfusion. Ischemic contracture was delayed and reduced in hearts perfused with 1 mumol/L L-N-monomethylarginine (L-NMMA) or 1 mumol/L L-N-arginine methylester, two inhibitors of NO synthase, but not with D-N-monomethylarginine, the inactive enantiomer of L-NMMA. The protection was suppressed by addition to the perfusate containing L-NMMA of 1 mmol/L L-arginine or 0.1 mmol/L sodium nitroprusside but not by addition of 10 mumol/L 8-bromo cGMP, a cGMP analogue. The functional protection by 1 mumol/L L-NMMA was related to a stimulation of glycolysis from exogenous glucose and a preservation of the glycogen stores. This resulted in a better maintenance of high-energy phosphates and a lower acidosis as measured by 31P nuclear magnetic resonance spectroscopy. During reperfusion, functional recovery was more than doubled, and enzyme release was halved in L-NMMA-treated hearts compared with controls. The functional and metabolic protection was maximal at 1 nmol/L to 1 mumol/L L-NMMA, ie, below the vasoactive concentrations of the inhibitor. CONCLUSIONS Nonvasoactive concentrations of NO synthase inhibitors protect the heart against ischemic damage; this relates to a stimulation of glycolysis from exogenous glucose.
Optimization of uncertainty load restoration strategy based on assessment of Conditional Value-at-Risk

With the increasing of thermostatically controlled load proportion and the accessing of renewable energy, problems caused by the uncertainty of load becoming non-negligible for load restoration. In this paper, we focus on deal with uncertainty problems of load restoration during the last stage of network reconfiguration. Primarily, Conditional Value-at-Risk (CVaR) is introduced to describe load randomness and Analytic hierarchy process (AHP) to deal with fuzzy information for load comprehensive weight evaluation. In order to determine restoration strategy, Particle Swarm Optimization (PSO) is employed to obtain the solution of the multi-constraint optimization model, the objective of which is to restore maximal outage loads in deterministic confidence level. Particularly, transient process is considered when load pick up. Furthermore, taking risk assessment into account, the value function is proposed by which can find the proper confidence level following a system uncertainty reserve for load uncertainty though evaluating strategy's comprehensive value of profit and risk. Ultimately, we can find the best strategy with a suggested system uncertainty reserve to offer advice for dispatcher. An example is provided to demonstrate the effectiveness of the method by the use of PSS/E and Python.
Heart Rate Variability Biofeedback and Executive Functioning in Individuals with Chronic Traumatic Brain Injury

Heart Rate Variability Biofeedback and Executive Functioning in Individuals with Chronic Traumatic Brain Injury By Sonya Kim This study sought to determine if individuals with neurological damage can be trained to regulate their emotions through psychophysiological processes and thereby can learn to improve executive functioning and enhance clear thinking. Participants were drawn from AHRC, a community-based structured day program in New York City that provides long-term rehabilitation services for individuals with severe brain injuries who are past the post-acute phase of rehabilitation. Contrary to commonly held beliefs that further rehabilitation or recovery is impossible for such a population, one key premise of this study is that given appropriate training, people with chronic brain injury can continue to make substantial improvements in their functioning. This study used a non-randomized experimental design with repeated measures at 3-time-points. The primary training tool was HeartMath Institute’s heart rate variability (HRV) PCemWave. This study provides one of the first empirical demonstrations of psychophysiological self-regulation training applied to individuals with severe brain injuries who were on the average 24 years post-injury. Because this study provides empirical evidence that the brain and emotions are connected in the body – as opposed to operating in the separate domains created by the traditional mind/body divide – it also presents the possibility that this connection could be used to train individuals with brain injury to better self-regulate their behavior and thereby control disinhibition and impulsivity. Evidence is also presented that even individuals who sustained severe brain injuries and are long past the post-acute phase of rehabilitation can learn new techniques, respond to biofeedback, and greatly increase coherence in heart rate
100-Year Return Value Estimates for Ocean Wind Speed and Significant Wave Height from the ERA-40 Data

Abstract In this article global estimates of 100-yr return values of wind speed and significant wave height are presented. These estimates are based on the ECMWF 40-yr Re-Analysis (ERA-40) data and are linearly corrected using estimates based on buoy data. This correction is supported by global Topographic Ocean Experiment (TOPEX) altimeter data estimates. The calculation of return values is based on the peaks-over-threshold method. The large amount of data used in this study provides evidence that the distributions of significant wave height and wind speed data belong to the domain of attraction of the exponential. Further, the effect of the space and time variability of significant wave height and wind speed on the prediction of their extreme values is assessed. This is done by performing detailed global extreme value analyses using different decadal subperiods of the 45-yr-long ERA-40 dataset.
Optimized Silicon QPSK Modulator With 64-Gb/s Modulation Speed

We demonstrate a compact silicon quadrature phase-shift keying (QPSK) modulator consisting of two nested Mach-Zehnder interferometers with a size of 4.5-mm<sup>2</sup>. The V<sub>11</sub> · L of the modulator is 1.4 V · cm with an insertion loss of 8 dB. In addition, 64-Gb/s QPSK modulation is achieved with an error vector magnitude (EVM) of 24.4% and bit error rate (BER) of 2.1 × 10<sup>-5</sup> at the received optical power of -10 dBm after the device and an EVM of 31.7% and BER of 8.4 × 10<sup>-4</sup> at the received optical power of 0 dBm after 10-km single-mode fiber transmission. The estimated power consumption is 7.1 pJ/bit for the 64-Gb/s QPSK modulation.
Can API-RCP achieve max-min fair bandwidth allocation in a multi-bottleneck network?

Theoretical analysis and experiments have shown that TCP can become oscillatory and prone to instability in high bandwidth-delay-product networks. XCP was proposed to overcome these shortcomings by advertising an explicit window adjustment from the routers to the sources. However, XCP may under-utilize the bandwidth in a multi-bottleneck network and cause some flows to receive an arbitrarily small fraction of their max-min fair rates. Using solid control theoretical analysis and design, API-RCP has solved this potential problem of XCP successfully. Why API-RCP can achieve max-min fair bandwidth allocation and full link utilization in steady state in multi-bottleneck networks? To address this question, we made a simple theoretical analysis and then verify it by OPNET® simulations. We also propose a controller design scheme to optimize the system performance with minimum control errors. We demonstrate the improved performance through comparison between API-RCP and TCP/RED in a multi-bottleneck network.
Crowd-based urban characterization: extracting crowd behavioral patterns in urban areas from Twitter

The advent of location-based social networking sites provides an open sharing space of crowd-sourced lifelogs that can be regarded as a novel source to monitor massive crowds' lifestyles in the real world. In this paper, we challenge to analyze urban characteristics in terms of crowd behavior by utilizing the crowd lifelogs in urban area. In order to collect crowd behavioral data, we utilize Twitter where enormous numbers of geo-tagged crowd's micro lifelogs can be easily acquired. We model the crowd behavior on the social network sites as a feature, which will be used to derive crowd-based urban characteristics. Based on this crowd behavior feature, we analyze significant crowd behavioral patterns for extracting urban characteristics. In the experiment, we actually conduct the urban characterization over the crowd behavioral patterns using a large number of geo-tagged tweets found in Japan from Twitter and report a comparison result with map-based observation of cities as an evaluation.