Miracle-dz/UniFAR-FTUs huggingface dataset:
An examination of the efficiency of the sequential parallel design in psychiatric clinical trials

Background Psychiatric clinical trials have a high failure rate, even among agents which are known to be effective. Because of this high failure rate, a novel clinical trial design has been proposed which incorporates a second phase in which non-responders to placebo are randomly reassigned to drug or placebo. Purpose The purpose of this research is to examine the efficiency of this new design compared to the conventional two arm clinical trial. We consider both binary and continuous endpoints. Methods The limiting distribution of a class of weighted average test statistics is obtained for the binary case which allows analytic calculation of the power for a given set of parameters. For the continuous case, we examine the efficiency of seemingly unrelated regression and a weighted average statistic via simulation. Results The novel design reduces the sample size 20—25% compared to the standard design under a wide range of parameters. Limitations There are no actual trials with the novel design therefore assumptions of the effect size across two periods for actual psychiatric agents is unknown. Conclusions The new design reduces sample size which in turn should reduce the cost of clinical trials. Further refinements of the design are possible including alternative test statistics and incorporation of additional data from placebo responders. Clinical Trials 2007; 4: 309—317. http://ctj.sagepub. com
Endogenous emergence of institutions to sustain cooperation

Formal and informal institutions, such as laws and social norms, are pervasive in daily life. They help maintain cooperation by coordinating and constraining individuals’ behaviors. However, our understanding of the comparative benets and the endogenous emergence of institutions remains limited. Here, we study the emergence and performance of sanctioning institutions in a public goods context when individuals are free to migrate between dierent institutions. We show experimentally that ecient peer and centralized sanctioning emerge as dominant institutions that immediately generate and maintain high levels of cooperation without much need for costly punishment. The quick establishment of high cooperation is due to both the self-selection of prosocial individuals into these institutions and the institutions’ intrinsically benecial properties. In addition, voluntary migration into the centralized sanctioning institution leads to the selection of stable prosocial leaders who refrain from antisocial punishment, while remnants of antisocial punishment still exist under peer punishment.
Fission Yeast Swi5-Sfr1 Protein Complex, an Activator of Rad51 Recombinase, Forms an Extremely Elongated Dogleg-shaped Structure

Background: The Swi5-Sfr1 protein complex is an activator of Rad51 recombinase, which mediates DNA strand exchange in homologous recombination. Results: Swi5 and Sfr1 form a 1:1 complex, which exhibits an extremely elongated dogleg-shaped structure in solution. Conclusion: The Swi5-Sfr1 structure is suitable for binding within the helical groove of the Rad51 filament. Significance: A structural model will advance our understanding of the molecular mechanism of homologous recombination. In eukaryotes, DNA strand exchange is the central reaction of homologous recombination, which is promoted by Rad51 recombinases forming a right-handed nucleoprotein filament on single-stranded DNA, also known as a presynaptic filament. Accessory proteins known as recombination mediators are required for the formation of the active presynaptic filament. One such mediator in the fission yeast Schizosaccharomyces pombe is the Swi5-Sfr1 complex, which has been identified as an activator of Rad51 that assists in presynaptic filament formation and stimulates its strand exchange reaction. Here, we determined the 1:1 binding stoichiometry between the two subunits of the Swi5-Sfr1 complex using analytical ultracentrifugation and electrospray ionization mass spectrometry. Small-angle x-ray scattering experiments revealed that the Swi5-Sfr1 complex displays an extremely elongated dogleg-shaped structure in solution, which is consistent with its exceptionally high frictional ratio (f/f0) of 2.0 ± 0.2 obtained by analytical ultracentrifugation. Furthermore, we determined a rough topology of the complex by comparing the small-angle x-ray scattering-based structures of the Swi5-Sfr1 complex and four Swi5-Sfr1-Fab complexes, in which the Fab fragments of monoclonal antibodies were specifically bound to experimentally determined sites of Sfr1. We propose a model for how the Swi5-Sfr1 complex binds to the Rad51 filament, in which the Swi5-Sfr1 complex fits into the groove of the Rad51 filament, leading to an active and stable presynaptic filament.
Calcineurin-Binding Protein Cbp1 Directs the Specificity of Calcineurin-Dependent Hyphal Elongation during Mating in Cryptococcus neoformans

ABSTRACT Mating and virulence of the human fungal pathogen Cryptococcus neoformans are controlled by calcineurin, a serine-threonine-specific calcium-activated phosphatase that is the target of the immunosuppressive drugs cyclosporine A and FK506. In previous studies, a calcineurin binding protein (Cbp1, Rcn1, Dscr1/Csp1-3/MCIP1-3) that is conserved from yeasts to humans has been identified, but whether this protein functions to regulate calcineurin activity or facilitate calcineurin function as a signaling effector has been unclear. Here we show that, like calcineurin, Cbp1 is required for mating in C. neoformans. By contrast, Cbp1 plays no role in promoting calcineurin-dependent growth at 37°C and is not essential for haploid fruiting. Site-directed mutagenesis studies provide evidence that tandem phosphorylation and dephosphorylation of two serine residues in the conserved SP repeat motif are critical for Cbp1 function. Epistasis analysis supports models in which Cbp1 functions coordinately with calcineurin to direct hyphal elongation during mating. Taken together, these findings provide insights into the roles of Cbp1 as an accessory subunit or effector of calcineurin-specific signaling pathways, which may be features conserved among the calcipressins to govern calcineurin signaling in immune cells, cardiomyocytes, and neurons of multicellular eukaryotes.
Left‐handedness in asthmatic children

Left‐handedness has been associated with asthma and allergic disorders. The Geschwind–Behan–Galaburda (GBG) hypothesis could explain this association. In view of previous findings, we investigated the distribution of laterality scores among asthmatic children and controls aged 4–8 years old. Seventy families with asthmatic children were administered the International Study of Asthma and Allergy in Childhood (ISAAC) questionnaire and the Edinburgh Left‐handedness Inventory. A sample of 70 families with non‐asthmatic, healthy children was used as controls. The majority of children had mild asthma. Ambidexterity was the main feature in the asthmatic children. A statistically significant difference in the laterality quotient (LQ) distribution was found in the group of asthmatic children with allergic rhinitis (LQ mean value in the asthmatic children with allergic rhinitis: 42.85 vs. 79.50 in the rest of the asthmatic children). These results suggest that there is a tendency towards left‐handedness in asthmatic children and lend support to the GBG hypothesis.
Antiviral Effect and Virus-Host Interactions in Response to Alpha Interferon, Gamma Interferon, Poly(I)-Poly(C), Tumor Necrosis Factor Alpha, and Ribavirin in Hepatitis C Virus Subgenomic Replicons

ABSTRACT The recently developed hepatitis C virus (HCV) subgenomic replicon system was utilized to evaluate the efficacy of several known antiviral agents. Cell lines that persistently maintained a genotype 1b replicon were selected. The replicon resident in each cell line had acquired adaptive mutations in the NS5A region that increased colony-forming efficiency, and some replicons had acquired NS3 mutations that alone did not enhance colony-forming efficiency but were synergistic with NS5A mutations. A replicon constructed from the infectious clone of the HCV-1 strain (genotype 1a) was not capable of inducing colony formation even after the introduction of adaptive mutations identified in the genotype 1b replicon. Alpha interferon (IFN-α), IFN-γ, and ribavirin exhibited antiviral activity, while double-stranded RNA (dsRNA) and tumor necrosis factor alpha did not. Analysis of transcript levels for a series of genes stimulated by IFN (ISGs) or dsRNA following treatment with IFN-α, IFN-γ, and dsRNA revealed that both IFNs increased ISG transcript levels, but that some aspect of the dsRNA response pathway was defective in Huh7 cells and replicon cell lines in comparison to primary chimpanzee and tamarin hepatocytes. The colony-forming efficiency of the replicon was reduced or eliminated following replication in the presence of ribavirin, implicating the induction of error-prone replication. The potential role of error-prone replication in the synergy observed between IFN-α and ribavirin in attaining sustained viral clearance is discussed. These studies reveal characteristics of Huh7 cells that may contribute to their unique capacity to support HCV RNA synthesis and demonstrate the utility of the replicon system for mechanistic studies on antiviral agents.
Toward faster algorithms for dynamic traffic assignment. I. Parametric quickest‐path trees

Being first in a three‐part series promising a practical solution to the user‐equilibrium dynamic traffic assignment problem, this paper devises a parametric quickest‐path tree algorithm, whose model makes three practical assumptions: (i) the traversal time of an arc i → j is a piecewise linear function of the arrival time at its i‐node; (ii) the traversal time of a path is the sum of its arcs' traversal times; and (iii) the FIFO constraint holds, that is, later departure implies later arrival. The algorithm finds a quickest path, and its associated earliest arrival time, to every node for every desired departure time from the origin. Its parametric approach transforms a min‐path tree for one departure‐time interval into another for the next adjacent interval, whose shared boundary the algorithm determines on the fly. By building relatively few trees, it provides the topology explicitly and the arrival times implicitly of all min‐path trees. Tests show the algorithm running upward of 10 times faster than the conventional brute‐force approach, which explicitly builds a min‐path tree for every departure time. Besides dynamic traffic assignment, other applications for which these findings have utility include traffic control planning, vehicle routing and scheduling, real‐time highway route guidance, etc. © 2002 Wiley Periodicals, Inc.
Pulmonary Edema Assessed by Ultrasound: Impact in Cardiology and Intensive Care Practice

Pulmonary edema is a frequent condition found in adult patients hospitalized in cardiology wards and intensive care units. Ultrasonography is a diagnostic modality with a high sensitivity for the detection of extravascular lung water, visualized as B lines, and usually caused by cardiogenic or noncardiogenic pulmonary edema. This paper highlights a simple method for the assessment of patients with pulmonary edema, which allows for a differential diagnosis of its possible mechanism and contributes to therapeutic intervention guiding and monitoring.
The Function of the p190 Rho GTPase-activating Protein Is Controlled by Its N-terminal GTP Binding Domain*

p190 is a GTPase-activating protein (GAP) for the Rho family of GTPases. The GAP domain of p190 is at the C terminus of the protein. At its N terminus, p190 contains a GTP binding domain of unknown significance. We have introduced a mutation (Ser36 → Asn) into this domain of p190 that decreased its ability to bind guanine nucleotide when expressed as a hemagglutinin (HA)-tagged protein in COS cells. In vitro,both the wild type and S36N mutant HA-p190 proteins showed similar GAP activities toward RhoA, but when expressed in NIH 3T3 fibroblasts only wild type p190 appeared able to function as a RhoGAP. Wild type HA-p190 induced a phenotype of rounded cells with long, beaded extensions similar to that seen when Rho function is disrupted by ADP-ribosylation. HA-p190(S36N), although expressed at a similar level to the wild type protein, had no discernible effect on the cells. The beaded extension phenotype induced by wild type HA-p190 required GAP function. A GAP-defective mutant, p190(R1283A), had no effect on cell morphology. Moreover, the beaded extension phenotype could be suppressed by co-expression of a gain-of-function Rho mutant, RhoA(G14V), or Rac mutant, Rac1(G12V). Activation of the Jun kinase (JNK) via muscarinic receptors was inhibited by wild type HA-p190, but JNK activity was enhanced by the S36N mutant. Co-expression of HA-p190 with a fragment containing only the mutated GTP binding domain partially inhibited the beaded extension phenotype, suggesting that it may sequester a factor required for p190 function. Taken together these data demonstrate that within the cell, the Rho/Rac GAP activity of p190 can be regulated by the N-terminal GTP binding domain.
Preventing Illegal Usage of Mobile Phone Software

Mobile software industry is suffering from the illegal usage of the software. PKI will not be a solution for small software distribution. We introduce a lightweight but safe method to prevent illegal usage of mobile phone software, by instrumentation on binary for device-identity check. The method is now being implemented on a presumable code on demand (COD) server for WIPI (Wireless Internet Platform for Interoperability).
Investigating the Neural Correlates of Schemas: Ventromedial Prefrontal Cortex Is Necessary for Normal Schematic Influence on Memory

Schemas, as memory representations of typical contexts, allow for generalization from previous experiences while often improving memory organization and accuracy. However, these advantageous characteristics of schematic memory may come at the cost of episode-specific information. In the human brain, this tradeoff between general and specific knowledge has been linked to differential contributions of the medial temporal lobes (MTL) to episode-specific memory and the ventromedial prefrontal cortex (vmPFC) to generalized, schematic memory. Here, we used a neuropsychological approach to test whether participants with focal vmPFC damage (n = 6) would show a reduced influence of schematic memory relative to healthy normal comparison participants (n = 12) in a recognition task that presented schematically congruent or incongruent contexts at study. As predicted, normal comparison participants were more likely to identify items as old after studying them in congruent contexts, and this effect was reflected in increased true and false recognition. These effects of prior context on recognition were not observed in the vmPFC group, suggesting that vmPFC damage reduced the influence of schematic memory. These findings are consistent with the proposition that the vmPFC plays an important role in integrating previous experience into ongoing memory processes while acting as part of a larger memory network. SIGNIFICANCE STATEMENT In the human brain, new memories are strongly influenced by existing knowledge of relevant context (sometimes called “schemas”). Schemas can benefit memory by expediting learning and increasing capacity in familiar contexts, but these benefits may simultaneously reduce episode-specific memory. Here we show that damage to the human ventromedial prefrontal cortex (vmPFC) reduced the influence of existing knowledge on new memories. Our findings suggest that the vmPFC plays a key role in schematic memory processes by integrating previous experiences and contextual information to influence memory. These findings provide novel insight into the brain regions necessary for normal schematic memory and enhance our understanding of the brain networks supporting memory processes.
Development of a palpable carotid pulse pressure sensor using electromagnetic induction

This paper proposes a novel non-invasive palpable sensor for measuring carotid pulse pressure. The unit consists of a sensing plastic chip, a pair of coil printed circuit boards, a pair of springs attached between the circuit board and the plastic chip. The distance between the boards is monitored from the displacement of the springs, and the information is converted into a voltage signal based on electromagnetic induction. In this study, the optimal forces externally applied to the proposed sensor were first examined to allow accurate measurement of carotid pulse wave amplitude variations, and it was found that the force applied when the measured maximum amplitudes of the sensor were obtained yielded the best performance. Next, carotid pulse waves were measured using the sensor with these optimal forces, and the results were compared with carotid pulse pressure values measured using a commercial pulse wave transducer. The coefficients of correlation between the two were 0.9 or more. It was therefore concluded that the proposed sensor enables noninvasive measurement of carotid pulse waves.
Appearance Modelling for 4D Representations

Capturing spatio-temporal models (4D modelling) from real world imagery has received a growing interest during the last years urged by the increasing demands of real-world applications and the tremendous amount of easily accessible image data. The general objective is to produce realistic representations of the world from captured video sequences. Although geometric modelling has already reached a high level of maturity, the appearance aspect has not been fully explored. The current thesis addresses the problem of appearance modelling for realistic spatio-temporal representations. We propose a view-independent, high resolution appearance representation that successfully encodes the high visual variability of objects under various movements.First, we introduce a common appearance space to express all the available visual information from the captured images. In this space we define the representation of the global appearance of the subject. We then introduce a linear image formation model to simulate the capturing process and to express the multi-camera observations as different realizations of the common appearance. Identifying that the principle of Super-Resolution technique governs also our multi-view scenario, we extend the image generative model to accommodate it. In our work, we use Bayesian inference to solve for the super-resolved common appearance.Second, we propose a temporally coherent appearance representation. We extend the image formation model to generateimages of the subject captured in a small time interval. Our starting point is the observation thatthe appearance of the subject does not change dramatically in a predefined small time interval and the visual information from each view and each frame corresponds to the same appearance representation.We use Bayesian inference to exploit the visual redundant as well as the hidden non-redundant information across time, in order to obtain an appearance representation with fine details.Third, we leverage the interdependency of geometry and photometry and use it toestimate appearance and geometry in a joint manner. We show that by jointly estimating both, we are able to enhance the geometry globally that in turn leads to a significant appearance improvement.Finally, to further encode the dynamic appearance variability of objects that undergo several movements, we cast the appearance modelling as a dimensionality reduction problem. We propose a view-independent representation which builds on PCA and decomposesthe underlying appearance variability into Eigen textures and Eigen warps. The proposed framework is shown to accurately reproduce appearances with compact representations and to resolve appearance interpolation and completion tasks.
Computing Optic Flow with ArduEye Vision Sensor

Abstract : Flight control of micro aerial vehicles (MAVs) is challenging due to the size of small-scale robotics platforms, which places size, weight, and power limitations on onboard sensors, as well as restricts the data processing algorithms that can be implemented on the platforms. We focus on computing optic flow in order to control a MAV using small vision chips as opposed to a complex camera system in order to cut down on the size and weight of the sensors as well as the processing power needed. We propose using an externally produced vision sensor by Centeye, ArduEye, to develop an algorithm for computing optic flow, from existing algorithms tailored to the sensor, to be used to control a quadrotor. Such efforts will benefit the various MAV research thrusts by providing a successful optic flow sensor and data processing algorithm that can be applied to the flight control of other robotic platforms.
Measurements and analysis of a 4×4 vehicle-to-ground MIMO channel using SAGE

The widely used broadband wireless technology enables a novel application of providing high-quality communications between vehicles and traffic control centers, which is collectively referred to as vehicle-to-ground communications. Channel modeling is in rapidly increasing demand to design and optimize the vehicle-to-ground communication systems. And practical channel models are only available when accurate estimations of the channel parameters are feasible. By adopting quadrature encoding and spectrum spreading, a novel and low-cost measurement method is proposed in this paper. The method can be implemented to achieve channel matrix accurately and furthermore determinate the parameters of a MIMO channel by using the space-alternating generalized expectation-maximization (SAGE) algorithm. Then the method was carried out in a measurement of a vehicle-mounted 4×4 MIMO system. Both large-scale and small-scale fading are investigated and analyzed. A path loss (PL) model and characteristics of channel parameters including PDP, K-factor, angle of arrival (AOA), angle of departure (AOD) and spatial correlation matrixes for V2G channel modeling are given based on the estimations. These results offer a valuable reference for future studies.
PIXE analysis in different stages of psoriatic skin.

Elemental distribution in psoriatic skin varies with the functional state of the keratinocytes, e.g., electrolytes influence cell metabolism and cell proliferation, and trace elements play a crucial role in a great number of enzymes. Elemental distribution in pinpoint lesions, old plaques, and uninvolved skin of 5 psoriatic patients and 4 healthy controls was studied by means of PIXE (proton-induced x-ray emission) analysis. This technique allows the simultaneous detection of elements with an atomic number greater than or equal to 14 along the epidermis and dermis in freeze-dried skin biopsies. Trace elements such as Fe, Cu, and Zn were determined down to a level of 1 ppm. In comparison with uninvolved skin, concentrations of P and K were elevated in psoriatic epidermis. In addition, increased levels of K were correlated with the stage of the psoriatic lesion. Zinc concentrations were significantly elevated in pinpoint lesions. The Zn concentration profiles within the epidermis and upper dermis showed high correlation to the P concentration profiles. Iron levels were decreased in old psoriatic plaques, whereas Cu concentrations varied considerably. In comparison to the controls, Cl concentrations were markedly decreased in the dermis of involved and uninvolved psoriatic skin, whereas epidermal Cl levels were unaffected. As high K levels prevent the Ca-induced differentiation of keratinocytes, high K levels may be the cause of the high cell differentiation in psoriatic skin. Elevated DNA- and RNA-polymerases might be the cause of elevated Zn levels in pinpoint lesions.