Miracle-dz/UniFAR-FTUs huggingface dataset:
Chamber formation and morphogenesis in the developing mammalian heart.

In this study we challenge the generally accepted view that cardiac chambers form from an array of segmental primordia arranged along the anteroposterior axis of the linear and looping heart tube. We traced the spatial pattern of expression of genes encoding atrial natriuretic factor, sarcoplasmic reticulum calcium ATPase, Chisel, Irx5, Irx4, myosin light chain 2v, and beta-myosin heavy chain and related these to morphogenesis. Based on the patterns we propose a two-step model for chamber formation in the embryonic heart. First, a linear heart forms, which is composed of "primary" myocardium that nonetheless shows polarity in phenotype and gene expression along its anteroposterior and dorsoventral axes. Second, specialized ventricular chamber myocardium is specified at the ventral surface of the linear heart tube, while distinct left and right atrial myocardium forms more caudally on laterodorsal surfaces. The process of looping aligns these primordial chambers such that they face the outer curvature. Myocardium of the inner curvature, as well as that of inflow tract, atrioventricular canal, and outflow tract, retains the molecular signature originally found in linear heart tube myocardium. Evidence for distinct transcriptional programs which govern compartmentalization in the forming heart is seen in the patterns of expression of Hand1 for the dorsoventral axis, Irx4 and Tbx5 for the anteroposterior axis, and Irx5 for the distinction between primary and chamber myocardium.
Simulation approach on step speed control of Induction Motor using Lab View

This paper gives an overview on Simulation approaches for the Induction Motor using Lab VIEW. Lab View is a Simulation software used for monitoring and control process. Lab VIEW software's can be used in Real Time process applications also for continuous monitoring. Today's Industrial Control Applications are done by Remote Process only. Lab VIEW Software plays major role in Industrial Monitoring and control systems. It is One of the most common applications required in remote control and monitoring. Drive control system has various types of controller, in order to perform some actions such as control the speed, forward and reverse turning direction of the motor. Lab VIEW is a human machine interfaces design software that is user friendly. It can be easily communicate with different hardware.
Mutation of the c-fos gene dyad symmetry element inhibits serum inducibility of transcription in vivo and the nuclear regulatory factor binding in vitro

In vitro mutagenesis of a 61-base-pair DNA sequence element that is necessary for induction of the c-fos proto-oncogene by growth factors revealed that a small region of dyad symmetry within the sequence element is critical for c-fos transcriptional activation. The same c-fos dyad symmetry element was found to bind a nuclear protein in vitro, causing a specific mobility shift of this c-fos regulatory sequence. An analysis of insertion and deletion mutants established a strict correlation between the ability of the dyad symmetry element to promote serum activation of c-fos transcription and in vitro nuclear protein binding. These experiments suggest that the DNA mobility shift assay detects a nuclear protein that mediates growth factor stimulation of c-fos expression. In vitro competition experiments indicate that the c-fos regulatory factor also binds to sequences within another growth factor-inducible gene, the beta-actin gene.
Intact hemisphere and corpus callosum compensate for visuomotor functions after early visual cortex damage

Significance The brain is resilient to injury and the possibility to promote recovery rests with our ability to understand the nature of postlesional plasticity. After damage to the visual cortex some patients with clinical blindness still react to unseen stimuli with appropriate motor responses, a phenomenon known as “blindsight. ” Our findings in one patient with early primary visual cortex damage suggest that this nonconscious visuomotor ability depends partly on the compensatory activity of the intact hemisphere, which can be dynamically recruited through the corpus callosum. Functional interactions between the damaged and intact hemisphere are subserved by changes in the underlying anatomical connections. These observations provide a framework for future investigations of functional recovery after brain damage and on mechanisms that mediate nonconscious abilities. Unilateral damage to the primary visual cortex (V1) leads to clinical blindness in the opposite visual hemifield, yet nonconscious ability to transform unseen visual input into motor output can be retained, a condition known as “blindsight. ” Here we combined psychophysics, functional magnetic resonance imaging, and tractography to investigate the functional and structural properties that enable the developing brain to partly overcome the effects of early V1 lesion in one blindsight patient. Visual stimuli appeared in either the intact or blind hemifield and simple responses were given with either the left or right hand, thereby creating conditions where visual input and motor output involve the same or opposite hemisphere. When the V1-damaged hemisphere was challenged by incoming visual stimuli, or controlled manual responses to these unseen stimuli, the corpus callosum (CC) dynamically recruited areas in the visual dorsal stream and premotor cortex of the intact hemisphere to compensate for altered visuomotor functions. These compensatory changes in functional brain activity were paralleled by increased connections in posterior regions of the CC, where fibers connecting homologous areas of the parietal cortex course.
DNA-binding properties of a herpes simplex virus immediate early protein

The herpes simplex virus alpha, or immediate early, protein ICP4 has been shown to be central to the control of the early stages of virus replication. The detailed mechanism of this control is unknown. In this communication we show that purified ICP4 was unable to bind to DNA even though the protein was capable of such activity in a crude extract. Addition of either infected- or uninfected-cell extracts to the purified protein restored its DNA-binding activity. These results suggest that ICP4 binds to DNA only via a component of uninfected cells.
Step timing adjustment: A step toward generating robust gaits

Step adjustment for humanoid robots has been shown to improve robustness in gaits. However, step duration adaptation is often neglected in control strategies. In this paper, we propose an approach that combines both step location and timing adjustment for generating robust gaits. In this approach, step location and step timing are decided, based on feedback from the current state of the robot. The proposed approach is comprised of two stages. In the first stage, the nominal step location and step duration for the next step or a previewed number of steps are specified. In this stage which is done at the start of each step, the main goal is to specify the best step length and step duration for a desired walking speed. The second stage deals with finding the best landing point and landing time of the swing foot at each control cycle. In this stage, stability of the gaits is preserved by specifying a desired offset between the swing foot landing point and the Divergent Component of Motion (DCM) at the end of current step. After specifying the landing point of the swing foot at a desired time, the swing foot trajectory is regenerated at each control cycle to realize desired landing properties. Simulation on different scenarios shows the robustness of the generated gaits from our proposed approach compared to the case where no timing adjustment is employed.
Improving Chinese Semantic Role Labeling with Rich Syntactic Features

Developing features has been shown crucial to advancing the state-of-the-art in Semantic Role Labeling (SRL). To improve Chinese SRL, we propose a set of additional features, some of which are designed to better capture structural information. Our system achieves 93.49 Fmeasure, a significant improvement over the best reported performance 92.0. We are further concerned with the effect of parsing in Chinese SRL. We empirically analyze the two-fold effect, grouping words into constituents and providing syntactic information. We also give some preliminary linguistic explanations.
Transcriptional derepression of the murine Cyp1a‐1 gene by mevinolin

In mouse hepatoma Hepa‐1c1c7 cultures, polycyclic aromatic compounds such as benzol[a]pyrene and 2,3,7,8‐tetrachlorodibenzo‐p‐dioxin (TCDD; dioxin) activate the Cyp1a‐1 (cytochrome P1450) and Nmo‐1[NAD(P)H:menadione oxidoreductase] genes, two members of the aromatic hydrocarbon (Ah)‐responsive gene battery. Mevinolin is known to inhibit 3‐hydroxy‐3‐methylglutaryl CoA (HMG‐CoA) reductase (EC 1.1.1.34), the rate‐limiting step in cholesterol biosynthesis. We show here that in the absence of TCDD, mevinolin markedly increases Cyp1a‐1 transcription, CYP1A1 mRNA and protein levels and enzyme activity, and NMO1 mRNA concentrations. Addition of mevalonate, the product of HMG‐CoA reductase activity, fails to reverse the effects of mevinolin. In fact, when used at high concentrations, mevalonate activates Cyp1a‐1 transcription. Mevinolin‐induced Cyp1a‐1 gene activation: (1) occurs independently of the lipid content of the growth medium, (2) is not suppressed by adding 25‐hydroxycholesterol, which blocks MHG‐CoA reductase activity, and (3) requires a functional Ah receptor and unimpaired nuclear translocation of the receptor. It is possible that an unknown metabolite (or metabolites) of mevinolin activates Cyp1a‐1 expression and that high concentrations of mevalonate act via the same mechanism. Using chimaeric plasmids that contain different lengths of Cyp1a‐1 5′ flanking regions fused to the bacterial neomycin (neo) gene, we find that the mevinolin effect on Cyp1a‐1 induction requires the 5′ flanking sequences between ‐1647 and ‐824, which are also needed for TCDD induction. Mevinolin, however, is not a ligand for the Ah receptor. Gel mobility shift assays revealed that Cyp1a‐1 activation caused by mevinolin does not involve the ligand‐dependent formation of a functional Ah receptor‐dependent DNA‐binding complex, but instead appears to be correlated with release of a putative repressor from its cognate DNA site. Our results suggest that the basel level of Cyp1a‐1 transcription is maintained by an unknown negative regulatory factor. We propose that Cyp1a‐1 transcriptional activation can result not only from induction by polycyclic aromatic compounds but also from derepression by mevinolin, independent of HMG‐CoA reductase inhibition. —Puga, A. ; Ray‐Chaudhuri, B. ; Nebert, D. W. Transcriptional derepression of the murine Cyp1a‐1 gene by mevinolin. FASEB J. 6: 777‐785; 1992.
Spectrum Allocation for Frequency-Agile Radio Networks under Physical Interference Models

Spectrum frequency allocation problems are fundamental problems in wireless spectrum auctions and wireless LAN management. Due to their complexity, most existing proposals simplify the allocation problems by reducing physical interference to a graph-based interference model. In this paper, we propose LIGHTHOUSE, a new line of efficient approximation algorithms that operate directly on physical interference models and perform within a constant bound from the optimum under geometric signal propagation. Our design is motivated by the fact that conventional greedy methods become brittle under physical interference models although they perform well under graph interference models. We overcome such brittleness by building a new globalized optimization path, first reducing the optimization constraints into linear constraints to produce a starting solution and then applying iterative improvements to approach the global optimum. To our best knowledge, our solution is the first to achieve a constant approximation bound. It also has low complexity and supports a wide-range of optimization goals. Experiments show that our solution outperforms existing solutions by 50 + % in utilization, and is within 10% gap from the optimal solution.
Cloning and characterization of T-cell-reactive protein antigens from Listeria monocytogenes

To explore the molecular basis of the T-cell-mediated immune response to Listeria monocytogenes, we cloned and expressed listerial antigens in Escherichia coli using the lambda-ZAP bacteriophage and Bluescript plasmid vectors. A two-stage screening strategy was implemented to identify T-cell-reactive antigens; the first stage involved antibodies or oligonucleotide probes and the second stage was based on assays for T-cell activation. A library of genomic DNA from L. monocytogenes was generated in lambda-ZAP, and then antigens, were detected in infected cells with a polyclonal rabbit anti-L. monocytogenes antiserum and an L. monocytogenes-specific monoclonal antibody. Also, synthetic oligonucleotide probes corresponding to the structural gene for listeriolysin O (LLO) were used to screen the recombinant DNA library. In each case, positive isolates were evaluated for T-cell antigenicity by measuring antigen-induced interleukin-2 production by polyclonal T cells taken from L. monocytogenes-immune mice. Phage clones were subcloned and expressed in the Bluescript plasmid and tested further for antigenic activity and LLO expression. Using this screening strategy, we successfully identified bacterial clones producing recombinant listerial antigens which activate L. monocytogenes-immune T cells in vitro. Antigens operative in the T-cell response during infection with L. monocytogenes include LLO, 62- and 39-kilodalton proteins, and other poorly defined bacterial surface components. We also found that high concentrations of recombinant LLO inhibited macrophage-mediated antigen presentation. These results are discussed in terms of the multiple functions of LLO as a virulence factor, inhibitor of antigen presentation, and potent antigen in the T-cell response to L. monocytogenes. These studies represent the first step toward a genetic definition of the antigens recognized in immune defense to L. monocytogenes.
An intrusion-tolerant password authentication system

In a password-based authentication system, to authenticate a user, a server typically stores password verification data (PVD), which is a value derived from the user's password using publicly known functions. For those users whose passwords fall within an attacker's dictionary, their PVDs, if stolen (for example, through server compromise), allows the attacker to mount off-line dictionary attacks. We describe a password authentication system that can tolerate server compromises. The described system uses multiple (say n) servers to share password verification data and never reconstructs the shared PVD during user authentications. Only a threshold number (say t, t/spl les/n) of these servers are required for a user authentication and compromising up to (t-1) of these servers will not allow an attacker to mount off-line dictionary attacks, even if a user's password falls within the attacker's dictionary. The described system can still function if some of the servers are unavailable. We give the system architecture and implementation details. Our experimental results show that the described system works well. The given system can be used to build intrusion-tolerant applications.
LARGE‐SCALE PREDICTOR VALIDATION IN PROJECT A: DATA COLLECTION PROCEDURES AND DATA BASE PREPARATION

The data base for the Army Selection and Classification Project (Project A) contains two major samples referred to as the concurrent validation sample and the longitudinal validation sample. The former was drawn from a cohort that joined the Army in 1983/84, and the latter from a cohort that entered in 1986/87. This paper describes the data base resulting from the concurrent sample. The sampling procedure, the distribution of sample sizes over jobs, the total array of variables, and the data collection procedures are described. Also discussed are the extensive data editing procedures that were used to deal with missing data.
Characterization of the genes of the 2,3-butanediol operons from Klebsiella terrigena and Enterobacter aerogenes

The genes involved in the 2,3-butanediol pathway coding for alpha-acetolactate decarboxylase, alpha-acetolactate synthase (alpha-ALS), and acetoin (diacetyl) reductase were isolated from Klebsiella terrigena and shown to be located in one operon. This operon was also shown to exist in Enterobacter aerogenes. The budA gene, coding for alpha-acetolactate decarboxylase, gives in both organisms a protein of 259 amino acids. The amino acid similarity between these proteins is 87%. The K. terrigena genes budB and budC, coding for alpha-ALS and acetoin reductase, respectively, were sequenced. The 559-amino-acid-long alpha-ALS enzyme shows similarities to the large subunits of the Escherichia coli anabolic alpha-ALS enzymes encoded by the genes ilvB, ilvG, and ilvI. The K. terrigena alpha-ALS is also shown to complement an anabolic alpha-ALS-deficient E. coli strain for valine synthesis. The 243-amino-acid-long acetoin reductase has the consensus amino acid sequence for the insect-type alcohol dehydrogenase/ribitol dehydrogenase family and has extensive similarities with the N-terminal and internal regions of three known dehydrogenases and one oxidoreductase.
Estimating effects from randomized trials with discontinuations: the need for intent-to-treat design and G-estimation

Background Randomized trials provide pivotal evidence for evaluation and approval of therapies. Nonetheless, such trials are often plagued by noncompliance, especially in the form of premature discontinuation of treatment. While intent-to-treat (ITT) analysis can provide valid tests of no-effect hypotheses, some trials may make ITT analysis impossible by ceasing follow-up when patients go off assigned treatment. Furthermore, estimates based on ITT, on-treatment, or per-protocol comparisons can seriously understate harm or benefit. Purpose To show how g-estimation based on randomization status is a natural generalization of ITT null testing to estimating efficacy from trials with important discontinuation or noncompliance. Methods We contrast with an analysis of the effect of a tiotropium inhaler on the occurrence of chronic obstructive pulmonary disease (COPD) events in a six-month double-blind placebo-controlled trial of 1829 patients with good but imperfect compliance. Results The covariate-adjusted point estimates, 95% confidence limits (CL), and null P-values comparing expected COPD event times in placebo versus tiotropium patients were: ITT, 1.21, CL = 1.02, 1.43, P = 0.027; on-treatment, 1.27, CL = 1.06, 1.52, P = 0.009; per-protocol, 1.36, CL = 1.13, 1.63, P = 0.001; and g-estimation, 1.31, CL = 1.03,1.72, P = 0.027. Thus g-estimation preserved the ITT test of the null, but exhibited more uncertainty about the size of the tiotropium effect than the other methods. In particular, it allowed for a much larger potential effect than did ITT analysis, but produced a much larger null P than exhibited by per-protocol analysis. Limitations Like ITT analysis, g-estimation requires all patients be followed to the end of the trial protocol, regardless of whether they comply with the protocol. Like on-treatment and per-protocol analyses, it also requires accurate compliance information be recorded. Conclusion G-estimation should become a standard procedure for the analysis of trials with noncompliance. Software to do so is available in major packages, and the procedure is easily coded for other packages. Clinical Trials 2008; 5: 5—13. http://ctj.sagepub. com
Droid Analytics: A Signature Based Analytic System to Collect, Extract, Analyze and Associate Android Malware

Smartphones and mobile devices are rapidly becoming indispensable devices for many users. Unfortunately, they also become fertile grounds for hackers to deploy malware. There is an urgent need to have a "security analytic & forensic system" which can facilitate analysts to examine, dissect, associate and correlate large number of mobile applications. An effective analytic system needs to address the following questions: How to automatically collect and manage a high volume of mobile malware? How to analyze a zero-day suspicious application, and compare or associate it with existing malware families in the database? How to reveal similar malicious logic in various malware, and to quickly identify the new malicious code segment? In this paper, we present the design and implementation of DroidAnalytics, a signature based analytic system to automatically collect, manage, analyze and extract android malware. The system facilitates analysts to retrieve, associate and reveal malicious logics at the "opcode level". We demonstrate the efficacy of DroidAnalytics using 150, 368 Android applications, and successfully determine 2, 475 Android malware from 102 different families, with 327 of them being zero-day malware samples from six different families. To the best of our knowledge, this is the first reported case in showing such a large Android malware analysis/detection. The evaluation shows the DroidAnalytics is a valuable tool and is effective in analyzing malware repackaging and mutations.
Does induction of plastic change in motor cortex improve leg function after stroke?

Combined peripheral nerve and brain stimulation (“dual stimulation”) induces changes in the excitability of normal motor cortex. The authors sought to establish whether dual stimulation would also induce motor cortex plasticity and associated functional improvements in nine stroke patients with chronic stable hemiparesis. Following 4 weeks of daily dual stimulation, improvements were seen in some neurophysiological and functional measures. This technique may offer therapeutic opportunities in some stroke patients.
Performance on nonlinguistic visual tasks by children with language impairment

ABSTRACT The performance of 8- to 13-year-old monolingual English-speaking children with language impairment (LI) on seven nonlinguistic tasks was compared with two groups of typically developing children, monolingual English-speaking children, and proficient Spanish–English sequential bilingual children. Group differences were apparent, with a key finding that the LI group was observably slower than both typical groups in mental rotation and arithmetic, and also slower than the typical monolingual group in odd man out, pattern matching, and form completion. Overall, the response time (RT) increased equivalently across groups as task difficulty increased. Chronological age and perceptual–motor speed contributed to task performance, especially for the shorter tasks. RT trajectories across the 6-year age span showed that task RT decreased with age, but with greater variability for longer tasks that may also be more vulnerable to the effect of experience.
Generalized Agreement for Bidirectional Word Alignment

While agreement-based joint training has proven to deliver state-of-the-art alignment accuracy, the produced word alignments are usually restricted to one-toone mappings because of the hard constraint on agreement. We propose a general framework to allow for arbitrary loss functions that measure the disagreement between asymmetric alignments. The loss functions can not only be defined between asymmetric alignments but also between alignments and other latent structures such as phrase segmentations. We use a Viterbi EM algorithm to train the joint model since the inference is intractable. Experiments on ChineseEnglish translation show that joint training with generalized agreement achieves significant improvements over two state-ofthe-art alignment methods.