Miracle-dz/UniFAR-FTUs huggingface dataset:
Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins

Two different strategies for stabilizing proteins are (i) positive design in which the native state is stabilized and (ii) negative design in which competing non-native conformations are destabilized. Here, the circumstances under which one strategy might be favored over the other are explored in the case of lattice models of proteins and then generalized and discussed with regard to real proteins. The balance between positive and negative design of proteins is found to be determined by their average “contact-frequency”, a property that corresponds to the fraction of states in the conformational ensemble of the sequence in which a pair of residues is in contact. Lattice model proteins with a high average contact-frequency are found to use negative design more than model proteins with a low average contact-frequency. A mathematical derivation of this result indicates that it is general and likely to hold also for real proteins. Comparison of the results of correlated mutation analysis for real proteins with typical contact-frequencies to those of proteins likely to have high contact-frequencies (such as disordered proteins and proteins that are dependent on chaperonins for their folding) indicates that the latter tend to have stronger interactions between residues that are not in contact in their native conformation. Hence, our work indicates that negative design is employed when insufficient stabilization is achieved via positive design owing to high contact-frequencies.
A robust joint face model for human emotion recognition

Having computers recognise emotions has benefits for human-computer interaction, psychology, and behavioural analysis. Unfortunately it is a very difficult problem, partly because humans can, to some extent, control the appearance of an emotion on their faces. In this paper we show that building statistical shape models of different parts of the face and combining them can give more successful results than using only a model of the whole face.
Motion parallax in cluttered scenes : frequency domain PCA

When an observer moves through a rigid 3D cluttered scene suc h as a forest, the set of image velocities in each local image region is constrained to lie near a line in ve locity space. Estimating the directions of such lines in different regions is useful for computing the observer’s 3D motion, in particular, since each of these lines points towards the observer’s heading direction. Recently we intr oduced a frequency domain method for estimating the motion parallax line of a local region. The method was based o n a bowtie distribution of the 3D power spectrum. Here we introduce a simpler method which is based on a 2D princ i al omponents analysis of the sum of squared normalized power spectrum. The new method avoids motion com pensation, which is typically used to subtract out the average velocity in the local region. The new method thus demonstrates that the computational problem of estimating the average velocity in a local region can be trea ted independently of the problem of estimating the direction of motion parallax in the region. Index Terms (EDICS) Motion detection and estimation: Optical flow, Tran sform based approaches, parametric models
Evolved stars suggest an external origin of the enhanced metallicity in planet-hosting stars

Aims. Exo-planets are preferentially found around high metallicity main sequence stars. We aim at investigating whether evolved stars share this property, and what this tells about planet formation. Methods. Statistical tools and the basic concepts of stellar evolution theory are applied to published results as well as our own radial velocity and chemical analyses of evolved stars. Results. We show that the metal distributions of planet-hosting (P-H) dwarfs and giants are different, and that the latter do not favor metal-rich systems. Rather, these stars follow the same age-metalicity relation as the giants without planets in our sample. The straightforward explanation is to attribute the difference between dwarfs and giants to the much larger masses of giants’ convective envelopes. If the metal excess on the main sequence is due to pollution, the effects of dilution naturally explains why it is not observed among evolved stars. Conclusions. Although we cannot exclude other explanations, the lack of any preference for metal-rich systems among P-H giants could be a strong indication of the accretion of metal-rich material. We discuss further tests, as well as some predictions and consequences of this hypothesis.
The Domain Ontology and Domain Rules Based Requirements Model Checking

Many ontology-based methods have been proposed and applied in order to elicit system requirements correctly and unambiguously. However, most of ontologies in these methods are purely conceptual models. Furthermore, the domain knowledge base only captures domain concepts and neglects domain-restricted rules. If the requirements model violate these rules or contradict the usual business behavior, they become unreasonable. This paper suggests a formal approach to precisely describe ontology using description logic at first, and then model the integrity rules and derivation rules which restrict the business behavior. All the rules are represented in three aspects: syntax, semantics and visualization. Finally, the requirements model checking framework is provided combining domain ontology and domain rules, which makes the requirements elicitation process both guided by domain ontology and restricted by domain rules. Therefore, the acquired requirements would comply with both business needs and domain knowledge.
Respiratory Virus Pneumonia after Hematopoietic Cell Transplantation (HCT): Associations between Viral Load in Bronchoalveolar Lavage Samples, Viral RNA Detection in Serum Samples, and Clinical Outcomes of HCT

Abstract Background. Few data exist on respiratory virus quantitation in lower respiratory samples and detection in serum from hematopoietic cell transplant (HCT) recipients with respiratory virus-associated pneumonia. Methods. We retrospectively identified HCT recipients with respiratory syncytial virus (RSV), parainfluenza virus, influenza virus, metapneumovirus (MPV), and coronavirus (CoV) detected in bronchoalveolar lavage (BAL) samples, and we tested stored BAL and/or serum samples by quantitative polymerase chain reaction. Results. In 85 BAL samples from 82 patients, median viral loads were as follows: for RSV (n=35), 2.6×106 copies/mL; for parainfluenza virus (n=35), 4.9×107 copies/mL; for influenza virus (n=9), 6.8×105 copies/mL; for MPV (n=7), 3.9×107 copies/mL; and for CoV (n=4), 1.8×105 copies/mL. Quantitative viral load was not associated with mechanical ventilation or death. Viral RNA was detected in serum samples from 6 of 66 patients: 4 of 41 with RSV pneumonia, 1 with influenza B, and 1 with MPV/influenza A virus/CoV coinfection (influenza A virus and MPV RNA detected). RSV detection in serum was associated with high viral load in BAL samples (P=.05), and viral RNA detection in serum was significantly associated with death (adjusted rate ratio, 1.8; P=.02). Conclusion. Quantitative polymerase chain reaction detects high viral loads in BAL samples from HCT recipients with respiratory virus pneumonia. Viral RNA is also detectable in the serum of patients with RSV, influenza, and MPV pneumonia and may correlate with the severity of disease.
Path Cost Distribution Estimation Using Trajectory Data

With the growing volumes of vehicle trajectory data, it becomes increasingly possible to capture time-varying and uncertain travel costs in a road network, including travel time and fuel consumption. The current paradigm represents a road network as a weighted graph; it blasts trajectories into small fragments that fit the under-lying edges to assign weights to edges; and it then applies a routing algorithm to the resulting graph. We propose a new paradigm, the hybrid graph , that targets more accurate and more efficient path cost distribution estimation. The new paradigm avoids blasting trajectories into small fragments and instead assigns weights to paths rather than simply to the edges. We show how to compute path weights using trajectory data while taking into account the travel cost dependencies among the edges in the paths. Given a departure time and a query path, we show how to select an optimal set of weights with associated paths that cover the query path and such that the weights enable the most accurate joint cost distribution estimation for the query path. The cost distribution of the query path is then computed accurately using the joint distribution. Finally, we show how the resulting method for computing cost distributions of paths can be integrated into existing routing algorithms. Empirical studies with substantial trajectory data from two different cities offer insight into the design properties of the proposed method and confirm that the method is effective in real-world settings.
Claudin interactions in and out of the tight junction

Claudins form the paracellular tight junction seal in epithelial tissues. Although there is still limited information on how these proteins are organized at the junction, a number of recent studies have provided useful insights both into claudin-claudin interactions and into interactions between claudins and other proteins. The focus of this review is to summarize recent information about claudin interactions and to identify critical unanswered questions about claudin organization and tight junction structure which will be required to understand claudin function.
Defective Flux of Thrombospondin-4 through the Secretory Pathway Impairs Cardiomyocyte Membrane Stability and Causes Cardiomyopathy

Thrombospondins are stress-inducible secreted glycoproteins with critical functions in tissue injury and healing. Thrombospondin-4 (Thbs4) is protective in cardiac and skeletal muscle, where it activates an adaptive endoplasmic reticulum (ER) stress response, induces expansion of the ER, and enhances sarcolemmal stability. ABSTRACT Thrombospondins are stress-inducible secreted glycoproteins with critical functions in tissue injury and healing. Thrombospondin-4 (Thbs4) is protective in cardiac and skeletal muscle, where it activates an adaptive endoplasmic reticulum (ER) stress response, induces expansion of the ER, and enhances sarcolemmal stability. However, it is unclear if Thbs4 has these protective functions from within the cell, from the extracellular matrix, or from the secretion process itself. In this study, we generated transgenic mice with cardiac cell-specific overexpression of a secretion-defective mutant of Thbs4 to evaluate its exclusive intracellular and secretion-dependent functions. Like wild-type Thbs4, the secretion-defective mutant upregulates the adaptive ER stress response and expands the ER and intracellular vesicles in cardiomyocytes. However, only the secretion-defective Thbs4 mutant produces cardiomyopathy with sarcolemmal weakness and rupture that is associated with reduced adhesion-forming glycoproteins in the membrane. Similarly, deletion of Thbs4 in the mdx mouse model of Duchenne muscular dystrophy enhances cardiomyocyte membrane instability and cardiomyopathy. Finally, overexpression of the secretion-defective Thbs4 mutant in Drosophila, but not wild-type Thbs4, impaired muscle function and sarcomere alignment. These results suggest that transit through the secretory pathway is required for Thbs4 to augment sarcolemmal stability, while ER stress induction and vesicular expansion mediated by Thbs4 are exclusively intracellular processes.
Assessment of a high-resolution central scheme for the solution of the relativistic hydrodynamics equations

We assess the suitability of a recent high-resolution central scheme developed by Kurganov & Tadmor (2000) for the solution of the relativistic hydrodynamic equations. The novelty of this approach relies on the absence of Riemann solvers in the solution procedure. The computations we present are performed in one and two spatial dimensions in Minkowski spacetime. Standard numerical experiments such as shock tubes and the relativistic flat-faced step test are performed. As an astrophysical application the article includes two-dimensional simulations of the propagation of relativistic jets using both Cartesian and cylindrical coordinates. The simulations reported clearly show the capabilities of the numerical scheme of yielding satisfactory results, with an accuracy comparable to that obtained by the so-called high-resolution shock-capturing schemes based upon Riemann solvers (Godunov-type schemes), even well inside the ultrarelativistic regime. Such a central scheme can be straight- forwardly applied to hyperbolic systems of conservation laws for which the characteristic structure is not explicitly known, or in cases where a numerical computation of the exact solution of the Riemann problem is prohibitively expensive. Finally, we present comparisons with results obtained using various Godunov-type schemes as well as with those obtained using other high-resolution central schemes which have recently been reported in the literature.
Towards a MR image-guided SMA-actuated neurosurgical robot

We present our work towards the development of a MR image-guided SMA-actuated neurosurgical robot. We used two antagonistic SMA wires as actuators for each joint in the robot, so that each joint can be actuated independently. We also modeled and tested the force behaviour of SMA wires in the bent configuration, which can be used as a guideline for SMA actuator selection. Due to the size scale of the robot, it is impossible to have individual position sensors at each joint and hence we rely primarily on vision feedback to control the joint motion of the robot. The images used to control the robot in this paper were obtained from a camera with the goal of eventually using MR images to control the end-effector motion. We then developed a control strategy and a switching circuit to control multiple links simultaneously and independently using only one power supply. Experimental results from our current prototype of a 3-DOF robot showed that we can actuate the robot and hence observe joint motion in a gelatin slab. We also did a series of experiments inside the MRI to show that the robot is fully MRI-compatible and creates no significant image distortion in the MR images.
Rapid Prototyping, Materials for RP and Applications of RP

Vikram Singh Master of technology 4 Sem. Roll. No. I 118 May 2013 Green Hills Engineering College Solan (Himachal Pradesh Technical University Hamirpur (H.P.) --------------------------------------------------------------------------------------------------------------------ABSTRACTION This paper present an assessment of the “state of the art” in respect to rapid prototyping processes. Based on a variety of reference materials on latest developments of modern RP techniques and the applications of the modern RP techniques. It also to identifying the reasons why these processes have developed and identifying the key features of the process.
Iterative Most-Likely Point Registration (IMLP): A Robust Algorithm for Computing Optimal Shape Alignment

We present a probabilistic registration algorithm that robustly solves the problem of rigid-body alignment between two shapes with high accuracy, by aptly modeling measurement noise in each shape, whether isotropic or anisotropic. For point-cloud shapes, the probabilistic framework additionally enables modeling locally-linear surface regions in the vicinity of each point to further improve registration accuracy. The proposed Iterative Most-Likely Point (IMLP) algorithm is formed as a variant of the popular Iterative Closest Point (ICP) algorithm, which iterates between point-correspondence and point-registration steps. IMLP’s probabilistic framework is used to incorporate a generalized noise model into both the correspondence and the registration phases of the algorithm, hence its name as a most-likely point method rather than a closest-point method. To efficiently compute the most-likely correspondences, we devise a novel search strategy based on a principal direction (PD)-tree search. We also propose a new approach to solve the generalized total-least-squares (GTLS) sub-problem of the registration phase, wherein the point correspondences are registered under a generalized noise model. Our GTLS approach has improved accuracy, efficiency, and stability compared to prior methods presented for this problem and offers a straightforward implementation using standard least squares. We evaluate the performance of IMLP relative to a large number of prior algorithms including ICP, a robust variant on ICP, Generalized ICP (GICP), and Coherent Point Drift (CPD), as well as drawing close comparison with the prior anisotropic registration methods of GTLS-ICP and A-ICP. The performance of IMLP is shown to be superior with respect to these algorithms over a wide range of noise conditions, outliers, and misalignments using both mesh and point-cloud representations of various shapes.
Management of newly diagnosed high‐risk and intermediate‐risk follicular lymphoma with 90Y ibritumomab tiuxetan in a phase II study

Five‐year overall survival for high‐risk Follicular Lymphoma International Prognostic Index follicular lymphoma is only approximately 50% compared with 90% for low risk. To evaluate an approach to improve upon this poor outcome, we completed an exploratory phase II trial of intensified treatment for patients with intermediate and high‐risk follicular lymphoma. Front‐line treatment with chemo‐immunotherapy consisting of rituximab, cyclophosphamide, vincristine, doxorubicin, and prednisone was followed by radio‐ immunotherapy with 90‐Yttrium ibritumomab tiuxetan consolidation, and 2 years of rituximab maintenance. The 5‐year overall survival for intermediate and high‐risk patients was 88% and 83%, respectively. Of 33 enrolled patients, 3 were off study before receiving radio‐immunotherapy. Three months post radio‐immunotherapy, 28/33 (85%) patients had achieved complete response including 6 patients who had only a partial response to chemo‐immunotherapy and converted to complete response after radio‐immunotherapy. The 5‐year progression‐free survival for intermediate and high risk was 79% and 58%, respectively. Nine of 19 patients with molecular markers patients remain in molecular and clinical complete remission with a median follow‐up of 48 months (range 3‐84 months). Post radio‐immunotherapy, hematologic toxicities were mostly grade 1 and 2. However, asymptomatic grade 3 or 4 thrombocytopenia and neutropenia occurred in 11%‐36% and 10%‐24% of patients, respectively. Myelodysplastic syndrome occurred in 1 patient 4 years post treatment. Whereas many patients had prolonged B‐cell reduction and low immunoglobulin levels post treatment, previous immunities to rubella were maintained. More aggressive upfront approaches such as this may benefit higher risk follicular lymphoma, but confirmatory trials are required. http://www.clinicaltrials. gov: NCT01446562.
Single image 3D object detection and pose estimation for grasping

We present a novel approach for detecting objects and estimating their 3D pose in single images of cluttered scenes. Objects are given in terms of 3D models without accompanying texture cues. A deformable parts-based model is trained on clusters of silhouettes of similar poses and produces hypotheses about possible object locations at test time. Objects are simultaneously segmented and verified inside each hypothesis bounding region by selecting the set of superpixels whose collective shape matches the model silhouette. A final iteration on the 6-DOF object pose minimizes the distance between the selected image contours and the actual projection of the 3D model. We demonstrate successful grasps using our detection and pose estimate with a PR2 robot. Extensive evaluation with a novel ground truth dataset shows the considerable benefit of using shape-driven cues for detecting objects in heavily cluttered scenes.
Revisiting Serial Arithmetic: A Performance and Tradeoff Analysis for Parallel Applications on Modern FPGAs

Serial arithmetic cores reduce area compared to bit-parallel alternatives, but are generally assumed to be inappropriate for high-performance FPGA applications due to a significant reduction in throughput. In this paper, we perform a performance and tradeoff analysis of Xilinx 7-series specialized architectures for a novel serial adder tree and multiplier. We show that these serial arithmetic architectures significantly improve functional density due to an average 2x clock speedup compared to bit-parallel alternatives, which provides attractive tradeoffs for different usage scenarios. We also show that serial arithmetic can surprisingly provide better performance than bit-parallel alternatives when replication is solely limited by an area constraint and not application parallelism or input bandwidth. We evaluate this performance improvement on several highly parallel sliding-window applications, showing average speedups of 4.8x and 4.4x compared to bit-parallel implementations over a variety of area constraints.
Managing the computer resource

Based on the study of expenditures for data processing, a descriptive stage hypothesis is presented. It is suggested that the planning, organizing, and controlling activities associated with managing the computer resource will change in character over a period of time, and will evolve in patterns roughly correlated to four stages of the computer budget: Stage I (computer acquisition), Stage II (intense system development), Stage III (proliferation of controls), and Stage IV (user/service orientation). Each stage is described and related to individual tasks for managing the computer resource.
To be in between: The meaning of PIS-divorce groups for children from divorced families

The aim of this study was to gain increased understanding about lived experiences of teenagers participating in PIS-divorce groups (programme for implementation of divorce groups in school). From the perspective of caring science and based on an ontological assumption of human interdependence, as well as earlier research that showed lack of consensus on the effect of divorce on children, the question that we felt needed to be asked was how teenagers experienced PIS-divorce groups, and the meaning of this experience in the time after. The methodological approach was phenomenological-hermeneutical. The sample is based on interviews with five teenagers. The analysis uncovered two themes: To be in between and To be there for each other. Teenagers viewed the offer of support as important. PIS-divorce groups enabled them to increase their understanding of their life situation. The caring science concepts of suffering, love, and interdependence have contributed to give new and deeper understanding to teenagers’ lived experience.