Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

Motivation: The identification of transcription factor (TF) binding sites and the regulatory circuitry that they define is currently an area of intense research. Data from whole-genome chromatin immunoprecipitation (ChIP–chip), whole-genome expression microarrays, and sequencing of multiple closely related genomes have all proven useful. By and large, existing methods treat the interpretation of functional data as a classification problem (between bound and unbound DNA), and the analysis of comparative data as a problem of local alignment (to recover phylogenetic footprints of presumably functional elements). Both of these approaches suffer from the inability to model and detect low-affinity binding sites, which have recently been shown to be abundant and functional. Results: We have developed a method that discovers functional regulatory targets of TFs by predicting the total affinity of each promoter for those factors and then comparing that affinity across orthologous promoters in closely related species. At each promoter, we consider the minimum affinity among orthologs to be the fraction of the affinity that is functional. Because we calculate the affinity of the entire promoter, our method is independent of local alignment. By comparing with functional annotation information and gene expression data in Saccharomyces cerevisiae, we have validated that this biophysically motivated use of evolutionary conservation gives rise to dramatic improvement in prediction of regulatory connectivity and factor–factor interactions compared to the use of a single genome. We propose novel biological functions for several yeast TFs, including the factors Snt2 and Stb4, for which no function has been reported. Our affinity-based approach towards comparative genomics may allow a more quantitative analysis of the principles governing the evolution of non-coding DNA. Availability: The MatrixREDUCE software package is available from http://www.bussemakerlab. org/software/MatrixREDUCE Contact: Harmen.Bussemaker@columbia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Carbon-based nanostructured materials and their composites as supercapacitor electrodes

This critical review provides an overview of current research on carbon-based nanostructured materials and their composites for use as supercapacitor electrodes. Particular emphasis has been directed towards basic principles of supercapacitors and various factors affecting their performance. The focus of the review is the detailed discussion regarding the performance and stability of carbon-based materials and their composites. Pseudo-active species, such as, conducting polymer/metal oxide have been found to exhibit pseudo-capacitive behavior and carbon-based materials demonstrate electrical double layer capacitance. Carbon-based materials, such as, graphene, carbon nanotubes, and carbon nanofibers, provide high surface area for the deposition of conducting polymer/metal oxide that facilitates the efficient ion diffusion phenomenon and contribute towards higher specific capacitance of the carbon based composite materials with excellent cyclic stability. However, further scope of research still exists from the view point of developing high energy supercapacitor devices in a cost effective and simple way. This review will be of value to researchers and emerging scientists dealing with or interested in carbon chemistry.
Using Existing Systems to Supplement Small Amounts of Annotated Grammatical Relations Training Data

Grammatical relationships (GRs) form an important level of natural language processing, but different sets of GRs are useful for different purposes. Therefore, one may often only have time to obtain a small training corpus with the desired GR annotations. To boost the performance from using such a small training corpus on a transformation rule learner, we use existing systems that find related types of annotations.
Advanced antistatic/anticorrosion coatings prepared from polystyrene composites incorporating dodecylbenzenesulfonic acid‐doped SiO2@polyaniline core–shell microspheres

We present the preparation of advanced antistatic and anticorrosion coatings of polystyrene (PS) incorporating a suitable amount of dodecylbenzenesulfonic acid (DBSA)-doped SiO2@polyaniline (SP) core – shell microspheres. First, aniline-anchored SiO2 (AS) microspheres that were about 850 nm in diameter were synthesized using the conventional base-catalyzed sol – gel process with tetraethyl orthosilicate in the presence of N-[3-(trimethoxysilyl)propyl]aniline. SP core – shell microspheres were then synthesized by chemical oxidative polymerization of aniline monomers with ammonium persulfate as an oxidizing agent in the presence of the AS microspheres. The polyaniline shell thickness of the as-prepared core – shell microspheres was estimated to be about 120 nm. The AS and SP microspheres were further characterized using Fourier transform infrared spectroscopy, scanning electron microscopy (SEM) and transmission electron microscopy. The as-synthesized DBSA-doped SP core – shell microspheres were then blended into PS using N-methyl-2-pyrrolidone as solvent and then cast onto a cold – rolled steel (CRS) electrode to obtain antistatic and anticorrosion coatings with a thickness of about 10 µm. The corrosion protection efficiency of the as-prepared coating materials on the CRS electrode was investigated using a series of systematic electrochemical measurements under saline conditions. The enhanced corrosion protection ability of the PS/SP composite coatings may be attributed to the formation of a dense passive metal oxide layer induced by the redox catalytic effect of the polyaniline shell of the as-synthesized core – shell microspheres, as evidenced by electron spectroscopy for chemical analysis and SEM observations. Moreover, the PS composite coating containing 10 wt% of the SP core – shell microspheres showed an electrical resistance of about 3.65 × 10 9 � cm −2 , which meets the requirements for antistatic applications. c � 2012 Society of Chemical Industry
A dual-mode highly efficient 60 GHz power amplifier in 65 nm CMOS

This paper presents a 60 GHz power amplifier utilizing a novel technique to achieve high efficiency at high output power levels. The proposed topology provides the capability of dual mode operation. The output power of a conventional class A power amplifier will be combined with the power provided by an amplifier operating at a different class to achieve higher efficiency at higher output levels. Driver stages to provide high power gain consist of an enhanced cascode stage followed by a common source amplifier with transformer-coupled impedance matching networks. Fabricated in 65 nm CMOS process, the measured gain of the 0.32 mm2 power amplifier is 17.7 dB at 60 GHz with a wide 3dB band width of 12 GHz while consuming 378 mW from a 1.2V supply. A maximum saturated output power of 16.8 dBm is measured with the 14.5% peak power added efficiency at 60 GHz.
VenPro: A Morphological Analyzer for Venetan

This document reports the process of extending MorphoPro for Venetan, a lesser-used language spoken in the Nort-Eastern part of Italy. MorphoPro is the morphological component of TextPro, a suite of tools oriented towards a number of NLP tasks. In order to extend this component to Venetan, we developed a declarative representation of the morphological knowledge necessary to analyze and synthesize Venetan words. This task was challenging for several reasons, which are common to a number of lesser-used languages: although Venetan is widely used as an oral language in everyday life, its written usage is very limited; efforts for defining a standard orthography and grammar are very recent and not well established; despite recent attempts to propose a unified orthography, no Venetan standard is widely used. Besides, there are different geographical varieties and it is strongly influenced by Italian.
Working with(out) a net: improvisational theater and enhanced well-being

Improvisational theater (improv) fits well into an academic definition of improvisation: “the process and product of creativity occurring simultaneously” (Lewis and Lovatt, 2013). The simultaneity in improv comes from the lack of scripting: players appear on stage, ask the audience for a suggestion, for example, “any object smaller than a breadbox,” and begin a frolic of their own that often lasts about 30 min. This article highlights several parallels between practices in improv and practices in several domains of applied psychology: body awareness and mindfulness, positive psychology interventions, and person-centered psychotherapy. What accounts for these parallels? Here I conclude that both improv and applied psychology practices aim to increase personal awareness, interpersonal attentiveness, and trust among members of the ensemble. The metaphor of “working without a net” certainly seems to apply to improv. For example, a respected improv manual says, “True improvisation is getting on-stage and performing without any preparation or planning… Strictly speaking, improvisation is making it up as you go along” (Halpern et al., 1994). Nervous anticipation of performing without a memorized script is the felt sense of working without a net. But there is more to the story than that; we return to a reversal of the metaphor at the end of the article. Spontaneity, like luck, favors the well-prepared. The virtuoso pianist who improvises brilliantly may be one who practiced more than 10,000 h as a youngster, on fire with a “rage to master” (Ericsson et al., 1993; Winner, 1996). Or perhaps not; there is dispute about the relationship between talent and practice at the high-end of performance skill in some fields (Epstein, 2013). Nevertheless, all forms of improvisation and competitive performance require basics to be learned and practiced until they become “second nature. ” Improv actors practice their form repeatedly but don't repeat or rehearse the content of their scenes. The concept of spontaneity needs to be considered in this context: spontaneous creative content is grounded in improv fundamentals that are practiced repeatedly. It is form, not content, that is rehearsed. Many of these practices, also called “games,” are also used by actors training for scripted theater (e.g., Stanislavski, 1989). Our inquiry is whether there is a positive relationship between improv practice and well-being in other life domains. There is a good reason to think so: important theatrical skills are represented, with different names, in the methods of body awareness and other meditations, applied positive psychology, and psychotherapy. If particular practices in these domains are psychologically healthy, then practicing them through improv might also increase well-being. Finally, because improv is unavoidably social, performers are always embedded in the social milieux of improv communities. There are transitions from classroom and small stage to what is after all “but a stage”: life itself.
Educational attainment, labour market position and mental ill health as pathways from adversities in adolescence to disability pension in early adulthood: A Finnish cohort study using register data

Background: We investigated whether social adversities (parents’ receipt of income support and care placement) in adolescence were associated with the receipt of work disability pension (DP) in early adulthood. A further aim was to examine whether and to what extent individual educational attainment, labour market position and mental disorders during the period of transition to adulthood operate as underlying mechanisms in this relationship. Methods: This was a nationwide cohort study of a 60% representative sample of Finnish young adults born between 1983 and 1985 with no prior DP at entry to the study (N=116,788). Data from several nationwide registers were used with a follow-up time from 2004 to 2010. The age range of the cohort was 19–21 years at the beginning of the follow-up period. Hazards ratios (HRs) with 95% confidence intervals (CIs) were calculated using a Cox regression. Mediation analyses for educational attainment, labour market position and purchases of psychotropic drugs were performed. Results: A total of 1597 (1.37%) people were granted a DP during the follow-up period of 687,429 years at risk. After adjustment for mediators, the HR (95% CI) of DP for those whose parents had received income support was 1.36 (1.21–1.53) for men and 1.21 (1.07–1.36) for women. The corresponding figures for those with a history of care placement were 1.23 (1.00–1.51) and 1.58 (1.29–1.92), respectively. Conclusions: Social adversities in adolescence increase the risk of DP in early adulthood. The intergenerational social determination of disability could be addressed through interventions promoting mental health and improving educational and employment opportunities for young people.
Transgenic anopheline mosquitoes impaired in transmission of a malaria parasite

We thank the patients for contributing to this study; Y. Terado for discussions on immunohistochemistry, K. Tachampa and J. Y. Kim for help in characterization of URAT1; A. Toki, M. Takahashi and M. Ikeda for technical assistance; and Merck Research Laboratories for providing losartan and EXP-3174. The anti-URAT1 polyclonal antibody was supplied by Trans Genic Inc. (formerly Kumamoto Immunochemical Laboratory). This work was supported in part by grants from the Japanese Ministry of Education, Science, Sports, Culture and Technology, Grants-in-Aid for Scientific Research, andHighTech Research Center, the Science Research Promotion Fund of the Japan Private School Promotion Foundation.
Least restrictive and minimally deviating supervisor for Safe semi-autonomous driving at an intersection: An MIQP approach

Although significant progress has been made in the last few years towards cooperative and autonomous driving, the transition from human-driven to fully automated vehicles is expected to happen slowly. The question of semi-autonomous driving, where Advanced Driver Assistance Systems assist human drivers in their decisions, will therefore become increasingly important. In this paper, we consider the problem of safe intersection crossing for semi-autonomous vehicles with communication capacities. We design an intersection supervisor based on a mixed-integer quadratic programming approach which monitors the control inputs of each vehicle, and overrides those controls when necessary to ensure that all vehicles can navigate safely. Moreover, the solution control deviates minimally from the vehicles target inputs: overriding only occurs when it is strictly necessary, in which case the control is chosen as close as possible to the driver's intent. We theoretically prove that the supervisor needs only consider a finite future time horizon to ensure safety and deadlock avoidance over an infinite time horizon, and we demonstrate through simulation that this algorithm can work in real time. Additionally, unlike previous work, our formulation is suitable for complex intersection geometries with a high number of vehicles.
Number, distribution, and morphology of retinal ganglion cells with axons regenerated into peripheral nerve graft in adult cats

The optic nerve of adult cats was transected and an autologous peripheral nerve was transplanted to the stump. Two months later retinal ganglion cells (RGCs) that had regenerated their axons were retrogradely labeled with fluorescent dye injected into the graft. The more than 4000 labeled cells, which were 3.0–4.3% of total ganglion cell number in the intact retina, were distributed in a high-density area elongating horizontally, in a pattern similar to that observed in the intact retina. The dendritic morphology of RGCs with regenerated axons was examined after intracellular injections of HRP or Lucifer yellow in vitro. The morphology of alpha- and gamma-cells appeared comparable to normal, whereas the dendrites of some beta-cells seemed to degenerate. Some “unclassified” cells could not be identified as alpha-, beta-, or gamma-cells. The main dendrites of most unclassified cells were thin and less ramified than alpha- and beta-cells. Some unclassified cells had a vacant area in their dendritic fields, suggesting degenerative change in dendrites. The distal dendrites of some unclassified and gamma-cells had many fine processes that probably regrew during axonal regeneration. The proportion of alpha-, beta-, and other cells including gamma- and unclassified cells in the regenerating cell population was evaluated by examining all of the Lucifer yellow- injected cells in local patches. The average proportion of alpha-cells was 23.9%, about six times higher than in intact retinas. The average proportion of beta-cells was 50.3%, slightly higher than in intact retinas. The remaining cells (25.7%) could not be categorized as alpha or beta; this proportion is about half that found in intact retinas. These findings suggest that alpha-cells have the highest capacity to regenerate their axons into nerve grafts, rather than all types equally regenerating their axons.
Code-on-Demand and Code Adaptation for Mobile Computing

Most commercial software packages present the user with a monolithic software program bundling many functions and features. The user pays for the unneeded features, and mobile devices have insufficient resources to cope. We introduce Sparkle, a proof-of-concept, mobile middleware for code adaptation using the code-on-demand design paradigm. To allow as many useful applications as possible to run on a mobile device, we propose changing the software development paradigm from monolithic chunks to small functionalities which can be dynamically downloaded on demand to the mobile device, and be disposed of afterward. An application could have unlimited functionalities which are selected on-the-fly based on the context.
User Flexibility Aware Price Policy Synthesis for Smart Grids

In order to optimally manage a modern electricity distribution network, peaks in residential users demand should be avoided, as this can reduce energy and network asset management costs. Furthermore, this must be done without compressing residential users demand. To this aim, in a demand response setting, residential users are given a price policy, which economically motivates them to shift their loads in order to achieve this goal. However, if the price policy for all users is similar, this demand response may result in simply shifting the demand peaks (peak rebound), leaving the problem unsolved. In this paper we propose a novel methodology which i) for each network substation s, automatically computes the desired power profile to be kept in order to optimally manage the network itself, ii) for each network substation s, automatically synthesizes individualized price policies for residential users connected to s, so that s is kept at the desired profile. Note that price policies individualization avoids the peak rebound problem, as different users have different low tariff areas. Furthermore, our methodology measures the flexibility of a residential user as the capacity needed by a home energy storage system (e.g., a battery) to always follow the given price policy, thus mitigating residential users discomfort. We show the feasibility of our approach on a realistic scenario taken from an existing medium voltage Danish distribution network.
FZR2/CCS52A1 Expression Is a Determinant of Endoreduplication and Cell Expansion in Arabidopsis1[W][OA]

Endoreduplication, a modified cell cycle that allows cells to increase ploidy without subsequent cell division, is a key component of plant growth and development. In this work, we show that some, but not all, of the endoreduplication of Arabidopsis (Arabidopsis thaliana) is mediated by the expression of a WD40 gene, FIZZY-RELATED2 (FZR2). Loss-of-function alleles show reduced endoreduplication and reduced expansion in trichomes and other leaf cells. Misexpression of FZR2 is sufficient to drive ectopic or extra endoreduplication in leaves, roots, and flowers, leading to alteration of cell sizes and, sometimes, organ size and shape. Our data, which suggest that reduced cell size can be compensated by increased cell proliferation to allow normal leaf morphology, are discussed with respect to the so-called compensation mechanism of plant development.
Spanners: a formal framework for information extraction

An intrinsic part of information extraction is the creation and manipulation of relations extracted from text. In this paper, we develop a foundational framework where the central construct is what we call a spanner. A spanner maps an input string into relations over the spans (intervals specified by bounding indices) of the string. The focus of this paper is on the representation of spanners. Conceptually, there are two kinds of such representations. Spanners defined in a primitive representation extract relations directly from the input string; those defined in an algebra apply algebraic operations to the primitively represented spanners. This framework is driven by SystemT, an IBM commercial product for text analysis, where the primitive representation is that of regular expressions with capture variables. We define additional types of primitive spanner representations by means of two kinds of automata that assign spans to variables. We prove that the first kind has the same expressive power as regular expressions with capture variables; the second kind expresses precisely the algebra of the regular spanners---the closure of the first kind under standard relational operators. The core spanners extend the regular ones by string-equality selection (an extension used in SystemT). We give some fundamental results on the expressiveness of regular and core spanners. As an example, we prove that regular spanners are closed under difference (and complement), but core spanners are not. Finally, we establish connections with related notions in the literature.
Hormone phage: An enrichment method for variant proteins with altered binding properties

Human growth hormone (hGH), a 191 residue protein containing two disulfide bonds, was fused to the carboxyl‐terminal domain of the gene III protein, a minor coat protein exposed at one end of the filamentous phage M13. The gene fusion was cloned into a plasmid containing origins of replication for Escherichia coli and filamentous phage and was packaged into phagemid particles upon infection by an M13KO7 helper phage. Transcription of the hGH‐gene III fusion was controlled so that usually no more than one copy of the fusion protein was displayed along with the four copies of the wild‐type gene III protein. The hGH‐gene III fusion protein was properly folded, as judged by reactivity with six hGH monoclonal antibodies whose epitopes are sensitive to the folded conformation of hGH. Moreover, the hGH–gene III phagemid particles were enriched over 5000‐fold from non‐hGH phage, and 8‐fold from a mutant hGH phagemid following a single hGH‐specific elution step from hGH receptor‐coated beads. The hGH phagemid should be useful for isolating new receptor binding mutants of hGH. More generally, this expression system may allow other large proteins with discontinuous binding epitopes to be displayed, and binding selections applied to their mutated gene III fusions on filamentous phage.