Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlation between effects of 24 different cytochalasins on cellular structures and cellular events and those on actin in vitro

To compare the effects of cytochalasins on the cellular level with those on the molecular level, 24 cytochalasins, 20 natural compounds and 4 derivatives, were used. The following effects were tested for each of 24 cytochalasins; (a) four high dose (2-20 muM) effects on the cellular level: rounding up of fibroblastic cells, contraction of actin cables, formation of hairy filaments containing actin, and inhibition of lymphocyte capping; (b) a low dose (0.2-2 muM) effect: inhibition of membrane ruffling; and (c) two in vitro effects: an inhibition of actin filament elongation (the high affinity effect [low dose effect] in vitro) and an effect on viscosity of actin filaments(the low affinity effect [high dose effect] in vitro). These results indicated that there are almost the same hierarchic orders of relative effectiveness of different cytochalasins between low and high dose effects and between cellular and molecular effects. From the data obtained with the 24 cytochalasins, we have calculated correlation coefficients of 0.87 and 0.79 between an effect in vivo, inhibition of capping, and an effect in vitro, inhibition of actin filament elongation, as well as between inhibition of capping and another effect in vitro, effect on viscosity of actin filaments, respectively. Furthermore, a correlation coefficient between the high affinity effect and the low affinity effect determined in vitro was calculated to be 0.90 from the data obtained in this study. The strong positive correlation among low and high dose effects in vivo and those in vitro suggests that most of the effects caused by a cytochalasin, irrespective of doses or affected phenomena, might be attributed to the interaction between the drug and the common target protein, actin. In the course of the immunofluorescence microscope study on cytochalasin-treated cells using actin antibody, we have found that aspochalasin D, a 10-isopropylcytochalasin, strongly induced the formation of rodlets containing actin in the cytoplasm of the treated fibroblasts. In contrast, the other cytochalasins, including cytochalasin B, cytochalasin C, cytochalasin D, and cytochalasin H, were found to induce the formation of nuclear rodlets. Both cytoplasmic and nuclear rodlets found in the cytochalasin-treated cells were similar in ultrastructures to those induced by 5 to 10 percent (vol/vol) dimethyl sulfoxide in the same type of cells.
Endurance Training Attenuates Catabolic Signals Induced by TNF-α in Muscle of Mice.

PURPOSE To determine whether endurance training attenuates the negative effects induced by an acute injection of tumor necrosis factor-α (TNF-α) in skeletal muscle of mice. METHODS Trained (6 wk of endurance training at 60% of maximal velocity) and untrained mice were injected with TNF-α or vehicle and killed 6 h after. Tibialis anterior muscles were analyzed using Western blot and qRT-PCR for markers of inflammation and protein synthesis/degradation. RESULTS Independently of training, TNF-α increased the mRNA of cytokines and downregulated signals linked to protein synthesis. The phosphorylation of IKKα/β and IκBα induced by TNF-α was blunted in trained mice, suggesting altered NF-κB activation. This was associated with lower induction of several markers of protein degradation (FoxO1, MURF1, MAFbx, myostatin, Gabarapl1, and LC3BII/LC3BI ratio). CONCLUSIONS Endurance training protects skeletal muscle against the activation of protein degradation signaling pathways induced by TNF-α.
Non-rigid point set registration for Chinese characters using structure-guided coherent point drift

This paper proposes a non-rigid point set registration method called Structure-Guided Coherent Point Drift (SGCPD). The key idea of our method is to utilize structural information and combine the global and local point registrations together to improve the original Coherent Point Drift (CPD) algorithm. Specifically, given two point sets, we first align them using the CPD method with Localized Operator (CPDLO). Then we divide the target point set into several subsets and apply CPDLO to each subset. Finally, we implement the above two procedures until convergence. In this manner, more detailed information can be well exploited and thus higher registration accuracy can be achieved. Experimental results demonstrate that our method outperforms the original CPD approach on both point registration accuracy and skeleton decomposition accuracy for Chinese characters.
Formation shape control based on bearing rigidity

Distance measurements are not the only geometric quantities that can be used for multi-agent formation shape control. Bearing measurements can be used in conjunction with distances. This article employs bearing rigidity for mobile formations, which was developed for robot and sensor network localisation, so that bearings can be used for shape control in mobile formations. The first part of this article examines graph theoretical models for formation network analysis and control law design that are needed to maintain the shape of a formation in two-dimensional space, while the formation moves as a cohesive whole. Bearing-based shape control for a formation of mobile agents involves the design of distributed control laws that ensure the formation moves, so that bearing constraints maintain some desired values. The second part of this article focuses on the design of a distributed control scheme for nonholonomic agents to solve the bearing-based formation shape control problem. In particular, a control law using feedback linearisation is proposed based on shape variables. We simulate the shape control behaviour on differential drive agents for an exemplary bearing rigid formation using the results obtained in the first and second parts of this article.
RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model

Motivation: Regulatory, non-coding RNAs often function by forming a duplex with other RNAs. It is therefore of interest to predict putative RNA–RNA duplexes in silico on a genome-wide scale. Current computational methods for predicting these interactions range from fast complementary-based searches to those that take intramolecular binding into account. Together these methods constitute a trade-off between speed and accuracy, while leaving room for improvement within the context of genome-wide screens. A fast pre-filtering of putative duplexes would therefore be desirable. Results: We present RIsearch, an implementation of a simplified Turner energy model for fast computation of hybridization, which significantly reduces runtime while maintaining accuracy. Its time complexity for sequences of lengths m and n is with a much smaller pre-factor than other tools. We show that this energy model is an accurate approximation of the full energy model for near-complementary RNA–RNA duplexes. RIsearch uses a Smith–Waterman-like algorithm using a dinucleotide scoring matrix which approximates the Turner nearest-neighbor energies. We show in benchmarks that we achieve a speed improvement of at least 2.4× compared with RNAplex, the currently fastest method for searching near-complementary regions. RIsearch shows a prediction accuracy similar to RNAplex on two datasets of known bacterial short RNA (sRNA)–messenger RNA (mRNA) and eukaryotic microRNA (miRNA)–mRNA interactions. Using RIsearch as a pre-filter in genome-wide screens reduces the number of binding site candidates reported by miRNA target prediction programs, such as TargetScanS and miRanda, by up to 70%. Likewise, substantial filtering was performed on bacterial RNA–RNA interaction data. Availability: The source code for RIsearch is available at: http://rth.dk/resources/risearch. Contact: gorodkin@rth.dk Supplementary information: Supplementary data are available at Bioinformatics online.
Hardware evaluation of the stream cipher-based hash functions RadioGatún and irRUPT

In the next years, new hash function candidates will replace the old MD5 and SHA-1 standards and the current SHA-2 family. The hash algorithms RadioGatún and irRUPT are potential successors based on a stream structure, which allows the achievement of high throughputs (particularly with long input messages) with minimal area occupation. In this paper, several hardware architectures of the two above mentioned hash algorithms have been investigated. The implementation on ASIC of RadioGatún with a word length of 64 bits shows a complexity of 46 k gate equivalents (GE) and reaches 5.7 Gbps throughput with a 3 · 64-bit input message. The same design approaches 120 Gbps on ASIC with long input messages (63.4 Gbps on a Virtex-4 FPGA with 2.9 kSlices). On the other hand, the irRUPT core turns out to be the most compact circuit (only 5.8 kGE on ASIC, and 370 Slices on FPGA) achieving 2.4 Gbps (with long input messages) on ASIC, and 1.1 Gbps on FPGA.
Thermal challenges to building reliable embedded systems

More and more embedded systems are used in safety-critical areas such as automotive electronics and medical applications. These safety-critical applications impose stringent requirements on reliability, performance, low-power and testability of the underlying VLSI circuits. With silicon technology scaling, however, VLSI circuits operate very often at high temperature, which has negative impact on reliability, performance, power-efficiency and testability. This paper discusses several thermal impacts on VLSI circuits and their related challenges. It presents also a few emerging techniques that take temperature into account in the design and test processes.
Indirect 2D Touch Panning: How Does It Affect Spatial Memory and Navigation Performance?

We present experimental work which explores the effect of touch indirectness on spatial memory and navigation performance in a 2D panning task. In this regard and based on the theory of embodied cognition, prior work has observed performance increases for direct touch input over indirect mouse input. As indirect touch systems gain in importance, we designed an experiment to systematically investigate the effect of spatial indirectness while maintaining the proprioceptive and kinesthetic cues provided by touch input. In an abstract search task, participants of our study navigated a 2D space and were asked to reproduce spatial item configurations in a recall task. Our results indicate that spatial memory performance is not decreased by a spatial separation of touch input gestures and visual display. Further, our results suggest that decreasing the size of the input surface in the indirect condition increases the navigation efficiency.
Efficient Solving of the Satisfiability Modulo Bit-Vectors Problem and Some Extensions to SMT

Decision procedures for expressive logics such as linear arithmetic, bit-vectors, uninterpreted functions, arrays or combinations of theories are becoming increasingly important in various areas of hardware and software development and verification such as test pattern generation, equivalence checking, assertion based verification and model checking. In particular, the need for bit-precise reasoning is an important target for research into decision procedures. In this thesis we will describe work on creating an efficient decision procedure for Satisfiability Modulo the Theory of fixed-width bit-vectors, and how such a solver can be used in a real-world application. We will also introduce some extensions of the basic decision procedure allowing for optimisation, and compact representation of constraints in a SMT solver, showing how these can be succinctly and elegantly described as a theory allowing for the extension with minimal changes to SMT solvers.
Interactive system for dynamic scene lighting using captured video environment maps

We present an interactive system for fully dynamic scene lighting using captured high dynamic range (HDR) video environment maps. The key component of our system is an algorithm for efficient decomposition of HDR video environment map captured over hemisphere into a set of representative directional light sources, which can be used for the direct lighting computation with shadows using graphics hardware. The resulting lights exhibit good temporal coherence and their number can be adaptively changed to keep a constant framerate while good spatial distribution (stratification) properties are maintained. We can handle a large number of light sources with shadows using a novel technique which reduces the cost of BRDF-based shading and visibility computations. We demonstrate the use of our system in a mixed reality application in which real and synthetic objects are illuminated by consistent lighting at interactive framerates.
Work or Learning Implications of Classroom Metaphors

The workplace metaphor has often been used to drive research as well as teaching models. Conceptualizing the classroom as a work setting, however, neglects the unique qualities of the classroom that create a “learning setting. ” After some of the benefits and limitations of using the workplace metaphor in classroom research are noted, some characteristics that differentiate learning settings from work and recreational settings are described. Suggestions for the development of a model of the classroom as a learning setting based on cognitive approaches to learning and on classroom research are outlined. Implications of this model are presented.
Viscoelastic stress relaxation in human skeletal muscle.

Viscoelastic stress relaxation refers to the decrease in tensile stress over time that occurs when a body under tensile stress is held at a fixed length. The purpose of this study was to demonstrate viscoelastic stress relaxation in human skeletal muscle. Resistance to stretch (tensile force), hip flexion range of motion (ROM), and reflex contractile activity (IEMG) of the hamstring muscle group were measured during a passive straight leg raise. The testing protocol involved a first stretch to the maximum tolerated ROM with the lower extremity held at that point for 45 s (test 1). All 15 subjects tested (9 men, 6 women) had a stretch induced EMG response. The onset of a sustained EMG response occurred at a specific hip flexion angle in 10 subjects. These 10 subjects (6 men, 4 women) underwent a second straight leg raise stretch (test 2) to a ROM 5 degrees below the ROM at which the onset of EMG activity occurred in test 1. The stretch was held at this hip flexion angle for 45 s. There was a significant decrease in force at final ROM during the 45 s in test 1 (11.35 +/- 1.75 N, P < 0.0001) and in test 2 (4.2 +/- 1.55 N, P < 0.05). The percent decrease from the force at the respective final ROM was not significantly different between the tests (14.4 +/- 2.2% in test 1 and 13 +/- 2.3% in test 2). In test 1 there was a significant decrease over time in IEMG of 59.71 +/- 16.01 microV.s (P < 0.01) which was not significantly correlated to the decrease in force. (ABSTRACT TRUNCATED AT 250 WORDS)
Semantic Interoperability of Sensor Data with Volunteered Geographic Information: A Unified Model

Abstract: The increasing availability of sensor devices has resulted in important volumes of sensor data, which has raised the issue of making these data fully discoverable and interpretable by applications and end-users. The idea of OGC Sensor Web Enablement (SWE) has addressed this issue by proposing a set of standards to enable accessibility of sensor data over the Web. Similarly, there is a growing interest in volunteered geographic information (VGI). Considering that several researchers have highlighted the potential of this new type of information as a complement to existing, “traditional” data, it becomes important to develop frameworks to support the integration of VGI from several sources and with other types of data. In this paper, we make a first step in this direction by proposing a framework for the semantic interoperability of sensor data and VGI. After having performed an investigation of the types of VGI applications, we have developed a conceptual model of VGI aligned with relevant ISO standards for describing geospatial features. The purpose of this model is to support the generation of common descriptions for VGI applications, which will act as interfaces to higher-level services, such as discovery and reasoning services, in order to be exploited in conjunction with sensor data by client applications. This process is described through architecture for semantic interoperability of sensor data and VGI that we have developed and that we intend to use to set guidelines for future research on integration of VGI in sensor data cyberinfrastructures. We illustrate the
Tobit model estimation and sliced inverse regression

It is not unusual for the response variable in a regression model to be subject to censoring or truncation. Tobit regression models are specific examples of such a situation, where for some observations the observed response is not the actual response, but the censoring value (often zero), and an indicator that censoring (from below) has occurred. It is well-known that the maximum likelihood estimator for such a linear model assuming Gaussian errors is not consistent if the error term is not homoscedastic and normally distributed. In this paper, we consider estimation in the Tobit regression context when homoscedasticity and normality of errors do not hold, as well as when the true response is an unspecified nonlinear function of linear terms, using sliced inverse regression (SIR). The properties of SIR estimation for Tobit models are explored both theoretically and based on extensive Monte Carlo simulations.We show that the SIR estimator is a strong competitor to other Tobit regression estimators, in that it has good properties when the usual linear model assumptions hold, and can be much more effective than other Tobit model estimators when those assumptions break down. An example related to household charitable donations demonstrates the usefulness of the SIR estimator.
Dynamic Sustainability

Objectives: Although Housing First (HF) is a popular evidence-based intervention for persons experiencing homelessness and mental illness, research exploring its sustainability over time is scant. This mixed methods study captures practitioners' perspectives on key shifts in implementation of Housing First in a large urban center, and factors affecting fidelity to the model over time. Methods: This study uses fidelity assessments, at baseline and 18-months later, completed as part of the largest field trial of Housing First to date, and qualitative data from 28 front-line service providers and their managers. Results: Our findings reveal how the shifting landscape of implementation morphed some early troublespots into persistent challenges and exposed key factors facilitating fidelity to the model in a dynamic context. Conclusions: This study supports the importance of gathering provider perspectives over time to optimize the fit between the model and its changing local contexts and ensure maximal benefit of the intervention.
RFID indoor positioning system based on read rate measurement information

In this paper we present a brief description of the developed radio frequency identification system for indoor objects positioning. The possibility of using measurement information of integral read rate types is described. It is experimentally determined that localization accuracy obtained using mean read rate measurement information is comparable to one obtained using received signal strength measurement information. This result allows us to eliminate measurement of signals power characteristics which leads to possibility of using structurally simpler readers.
Suppressed expression of RETROGRADE-REGULATED MALE STERILITY restores pollen fertility in cytoplasmic male sterile rice plants

Conflict/reconciliation between mitochondria and nuclei in plants is manifested by the fate of pollen (viable or nonviable) in the cytoplasmic male sterility (CMS)/fertility restoration (Rf) system. Through positional cloning, we identified a nuclear candidate gene, RETROGRADE-REGULATED MALE STERILITY (RMS) for Rf17, a fertility restorer gene for Chinese wild rice (CW)-type CMS in rice (Oryza sativa L.). RNA interference-mediated gene silencing of RMS restored fertility to a CMS plant, whereas its overexpression in the fertility restorer line induced pollen abortion. The mRNA expression level of RMS in mature anthers depended on cytoplasmic genotype, suggesting that RMS is a candidate gene to be regulated via retrograde signaling. We found that a reduced-expression allele of the RMS gene restored fertility in haploid pollen, whereas a normal-expression allele caused pollen to die in the CW-type CMS. RMS encodes a mitochondrial protein, 178 aa in length, of unknown function, unlike the majority of other Rf genes cloned thus far, which encode pentatricopeptide repeat proteins. The unique features of RMS provide novel insights into retrograde signaling and CMS.
Ultrasonographic Estimation of Endotracheal Tube Size in Paediatric Patients and its Comparison with Physical Indices Based Formulae: A Prospective Study.

INTRODUCTION Choosing the correct Endotracheal Tube (ETT) size is important in paediatric anaesthesia. The subglottic diameter being the narrowest diameter of the paediatric upper airway plays an important role in appropriate ETT size selection. AIM This study was planned to determine the accuracy of Ultrasonography (USG) to assess the appropriate ETT size and compare it with physical indices based formulae. The secondary outcome was to assess the number of times the tube was changed based on air leak test for USG estimated tube size. MATERIALS AND METHODS After ethical committee approval, a prospective clinical observational study for a period of one year was conducted on 75 children (power of study 80%, confidence interval 95%) aged one to 14 years of American Society of Anaesthesiologists Physical Status (ASA) I and II undergoing elective surgery under general anaesthesia with orotracheal intubation. Parental consent was obtained. Pre-anaesthetic ultrasonography was performed on every patient at the subglottic region. The tracheal subglottic diameter was estimated to select the ETT size for cuffed and uncuffed tubes. The size estimated by USG and that based on age and height based formulae were compared with clinically used appropriate tube size. Data analysis was done using IBM Statistical Package for the Social Sciences (SPSS) version 20.0; One-way Analysis of Variance (ANOVA) and t-test for comparison were used. RESULTS USG predicted the appropriate ETT size (p<0.05) better than physical indices based formulae for cuffed and uncuffed tubes. The age based formula predicted the clinically used ETT size well (p=0.58) and the height based formula did not correlate with clinically used tube size (p=0.0002 - a statistically significant value). Eight patients required change of tube once. CONCLUSION Ultrasonographic estimation of subglottic diameter is useful for optimal paediatric ETT size selection. USG is effective in estimating the appropriate sized ETT both for cuffed and uncuffed tubes.