Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism of benefit of negative inotropes in obstructive hypertrophic cardiomyopathy.

BACKGROUND Drugs with negative inotropic effect are widely used to decrease obstruction in hypertrophic cardiomyopathy (HCM). However, the mechanism of therapeutic benefit has not been studied. METHODS AND RESULTS We used M-mode, two-dimensional, and pulsed Doppler echocardiography to study 11 patients with obstructive HCM before and after medical elimination of left ventricular outflow tract obstruction. We measured 148 digitized pulsed Doppler tracings recorded in the left ventricular cavity 2.5 cm apical of the mitral valve. Successful treatment slowed average acceleration of left ventricular ejection by 34% (P=.001). Mean time to peak velocity in the left ventricle was prolonged 31% (P=.001). Mean time to an ejection velocity of 60 cm/s was prolonged 91% (P=.001). Before treatment, left ventricular ejection velocity peaked in the first half of systole; after successful treatment, it peaked in the second half (P=.001). In contrast, after treatment, we found no change in peak left ventricular ejection velocity. We also found no change in the distance between the mitral coaptation point and the septum, as measured in two planes, indicating no treatment-induced alteration of this anatomic relationship. CONCLUSIONS Medical treatment eliminates mitral-septal contact and obstruction by decreasing left ventricular ejection acceleration. By slowing acceleration, treatment reduces the hydrodynamic force on the protruding mitral leaflet and delays mitral-septal contact. This, in turn, results in a lower final pressure gradient.
Impact of the Adenoviral E4 Orf3 Protein on the Activity and Posttranslational Modification of p53

ABSTRACT Our previous studies have established that the p53 populations that accumulate in normal human cells exposed to etoposide or infected by an E1B 55-kDa protein-null mutant of human adenovirus type 5 carry a large number of posttranslational modifications at numerous residues (C. J. DeHart, J. S. Chahal, S. J. Flint, and D. H. Perlman, Mol Cell Proteomics 13:1–17, 2014, http://dx.doi.org/10.1074/mcp.M113.030254). In the absence of this E1B protein, the p53 transcriptional program is not induced, and it has been reported that the viral E4 Orf3 protein inactivates p53 (C. Soria, F. E. Estermann, K. C. Espantman, and C. C. O'Shea, Nature 466:1076–1081, 2010, http://dx.doi.org/10.1038/nature09307). As the latter protein disrupts nuclear Pml bodies, sites at which p53 is modified, we used mass spectrometry to catalogue the posttranscriptional modifications of the p53 population that accumulates when neither the E1B 55-kDa nor the E4 Orf3 protein is made in infected cells. Eighty-five residues carrying 163 modifications were identified. The overall patterns of posttranslational modification of this population and p53 present in cells infected by an E1B 55-kDa-null mutant were similar. The efficiencies with which the two forms of p53 bound to a consensus DNA recognition sequence could not be distinguished and were lower than that of transcriptionally active p53. The absence of the E4 Orf3 protein increased expression of several p53-responsive genes when the E1B protein was also absent from infected cells. However, expression of these genes did not attain the levels observed when p53 was activated in response to etoposide treatment and remained lower than those measured in mock-infected cells. IMPORTANCE The tumor suppressor p53, a master regulator of cellular responses to stress, is inactivated and destroyed in cells infected by species C human adenoviruses, such as type 5. It is targeted for proteasomal degradation by the action of a virus-specific E3 ubiquitin ligase that contains the viral E1B 55-kDa and E4 Orf6 proteins, while the E4 Orf3 protein has been reported to block its ability to stimulate expression of p53-dependent genes. The comparisons reported here of the posttranslational modifications and activities of p53 populations that accumulate in infected normal human cells in the absence of both mechanisms of inactivation or of only the E3 ligase revealed little impact of the E4 Orf3 protein. These observations indicate that E4 Orf3-dependent disruption of Pml bodies does not have a major effect on the pattern of p53 posttranslational modifications in adenovirus-infected cells. Furthermore, they suggest that one or more additional viral proteins contribute to blocking p53 activation and the consequences that are deleterious for viral reproduction, such as apoptosis or cell cycle arrest.
How can low-pressure channels and deforming tills coexist subglacially?

Abstract Deforming till and low-pressure water channels are observed to coexist subglacially, but till also is observed to creep rapidly into low-pressure subglacial regions. A simple model shows that these observations are not contradictory. Creep of a thin till to a low-pressure region can occur from a narrow zone only, and will lead to isolation of channels from till farther away.
Reducing Hospital Expenditures With the COPE (Creating Opportunities for Parent Empowerment) Program for Parents and Premature Infants: An Analysis of Direct Healthcare Neonatal Intensive Care Unit Costs and Savings

More than 500,000 premature infants are born in the United States every year. Preterm birth results in a multitude of negative adverse outcomes for children, including extended stays in the neonatal intensive care unit (NICU), developmental delays, physical and mental health/behavioral problems, increased medical utilization, and poor academic performance. In addition, parents of preterms experience a higher incidence of depression and anxiety disorders along with altered parent-infant interactions and overprotective parenting, which negatively impact their children. The costs associated with preterm birth are exorbitant. In 2005, it is estimated that preterm birth cost the United States $26.2 billion. The purpose of this study was to perform a cost analysis of the Creating Opportunities for Parent Empowerment (COPE) program for parents of premature infants, a manualized educational-behavioral intervention program comprising audiotaped information and an activity workbook that is administered to parents in 4 phases, the first phase commencing 2 to 4 days after admission to the NICU. Findings indicated that the COPE program resulted in cost savings of at least $4864 per infant. In addition to improving parent and child outcomes, routine implementation of COPE in NICUs across the United States could save the healthcare system more than $2 billion per year.
SEGMENTATION AND CONTENT-BASED WATERMARKING FOR IMAGE INDEXING

In this paper, a novel approach to image indexing using content-based watermarking is presented. The proposed system uses color image segmentation and watermarking in order to facilitate content-based indexing, retrieval and manipulation of digital images and image regions. A novel segmentation algorithm is applied on reduced images and the resulting segmentation mask is embedded in the image using watermarking techniques. In each region of the image, indexing information is additionally embedded. In this way, the proposed system is endowed with content-based access and indexing capabilities which can be easily exploited via a simple watermark detection process. Several experiments have shown the potential of this approach.
Time-dependent systems of generalized Young measures

In this paper some new tools for the study of evolution problems in the framework of Young measures are introduced. A suitable notion of time-dependent system of generalized Young measures is defined, which allows us to extend the classical notions of total variation and absolute continuity with respect to time, as well as the notion of time derivative. The main results are a Helly type theorem for sequences of systems of generalized Young measures and a theorem about the existence of the time derivative for systems with bounded variation with respect to time.
Authoring Hierarchical Road Networks

We present a procedural method for generating hierarchical road networks connecting cities, towns and villages over large terrains. Our approach relies on an original geometric graph generation algorithm based on a non‐Euclidean metric combined with a path merging algorithm that creates junctions between the different types of roads. Unlike previous work, our method allows high level user control by manipulating the density and the pattern of the network. The geometry of the highways, primary and secondary roads as well as the interchanges and intersections are automatically created from the graph structure by instantiating generic parameterized models.
Performance Evaluation of NIPT in Detection of Chromosomal Copy Number Variants Using Low-Coverage Whole-Genome Sequencing of Plasma DNA

Objectives The aim of this study was to assess the performance of noninvasively prenatal testing (NIPT) for fetal copy number variants (CNVs) in clinical samples, using a whole-genome sequencing method. Method A total of 919 archived maternal plasma samples with karyotyping/microarray results, including 33 CNVs samples and 886 normal samples from September 1, 2011 to May 31, 2013, were enrolled in this study. The samples were randomly rearranged and blindly sequenced by low-coverage (about 7M reads) whole-genome sequencing of plasma DNA. Fetal CNVs were detected by Fetal Copy-number Analysis through Maternal Plasma Sequencing (FCAPS) to compare to the karyotyping/microarray results. Sensitivity, specificity and were evaluated. Results 33 samples with deletions/duplications ranging from 1 to 129 Mb were detected with the consistent CNV size and location to karyotyping/microarray results in the study. Ten false positive results and two false negative results were obtained. The sensitivity and specificity of detection deletions/duplications were 84.21% and 98.42%, respectively. Conclusion Whole-genome sequencing-based NIPT has high performance in detecting genome-wide CNVs, in particular >10Mb CNVs using the current FCAPS algorithm. It is possible to implement the current method in NIPT to prenatally screening for fetal CNVs.
Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual–based approach

Changes in agricultural practices and forest fragmentation can have a dramatic effect on landscape connectivity and the dispersal of animals, potentially reducing gene flow within populations. In this study, we assessed the influence of woodland connectivity on gene flow in a traditionally forest‐dwelling species — the European roe deer — in a fragmented landscape. From a sample of 648 roe deer spatially referenced within a study area of 55 × 40 km, interindividual genetic distances were calculated from genotypes at 12 polymorphic microsatellite loci. We calculated two geographical distances between each pair of individuals: the Euclidean distance (straight line) and the ‘least cost distance’ (the trajectory that maximizes the use of wooded corridors). We tested the correlation between genetic pairwise distances and the two types of geographical pairwise distance using Mantel tests. The correlation was better using the least cost distance, which takes into account the distribution of wooded patches, especially for females (the correlation was stronger but not significant for males). These results suggest that in a fragmented woodland area roe deer dispersal is strongly linked to wooded structures and hence that gene flow within the roe deer population is influenced by the connectivity of the landscape.
Enhancing an Embedded Processor Core for Efficient and Isolated Execution of Cryptographic Algorithms

We propose enhancing a reconfigurable and extensible embedded RISC processor core with a protected zone for isolated execution of cryptographic algorithms. The protected zone is a collection of processor subsystems such as functional units optimized for high-speed execution of integer operations, a small amount of local memory for storing sensitive data during cryptographic computations, and special-purpose and cryptographic registers to execute instructions securely. We outline the principles for secure software implementations of cryptographic algorithms in a processor equipped with the proposed protected zone. We demonstrate the efficiency and effectiveness of our proposed zone by implementing the most-commonly used cryptographic algorithms in the protected zone; namely RSA, elliptic curve cryptography, pairing-based cryptography, AES block cipher, and SHA-1 and SHA-256 cryptographic hash functions. In terms of time efficiency, our software implementations of cryptographic algorithms running on the enhanced core compare favorably with equivalent software implementations on similar processors reported in the literature. The protected zone is designed in such a modular fashion that it can easily be integrated into any RISC processor. The proposed enhancements for the protected zone are realized on an FPGA device. The implementation results on the FPGA confirm that its area overhead is relatively moderate in the sense that it can be used in many embedded processors. Finally, the protected zone is useful against cold-boot and micro-architectural side-channel attacks such as cache-based and branch prediction attacks.
University of Glasgow at TREC 2010: Experiments with Terrier in Blog and Web Tracks

In TREC 2010, we continue to build upon the Voting Model and experiment with our novel xQuAD framework within the auspices of the Terrier IR Platform. In particular, our focus is the development of novel applications for data-driven learning in the Blog and Web tracks, with experimentation spanning hundreds of features. In the Blog track, we propose novel feature sets for the ranking of blogs, news stories and blog posts. In the Web track, we propose novel selective approaches for adhoc and diversity search.
Comparative study of various PV technologies in terms of energy yield and annual degradation

Current accelerated tests of photovoltaic (PV) modules mostly prevent infant mortality but do not fully duplicate changes occurring in the field nor can predict useful lifetime. Therefore, monitoring of field-deployed thin film PV modules was undertaken at FSEC with goals to assess their performance in hot and humid climate under high voltage operation and to correlate the PV performance with the meteorological parameters. This paper presents performance analysis of a-Si:H and CIGS PV modules that were field deployed in the hot and humid climate over a period of approximately 30 months. The modules were connected in series so as to build maximum open circuit voltage of less than ±600 V with respect to ground and maintained at near maximum power point conditions. Statistical data analysis of PV parameters along with meteorological parameters that were continuously monitored is carried out on regular basis with PVUSA type regression analysis. Current-voltage (I–V) characteristic of module arrays that are obtained periodically complement the continuous data monitoring. The annual energy yield was calculated for both the PV technologies based on the data averaged over every fifteen minutes. Moreover, comparison of the two technologies was carried out based on the estimated annual degradation.
A Qualitative Study Comparing the Assay Performance Characteristics Between the 2007 and the 2013 American Society for Clinical Oncology and College of American Pathologists HER2 Scoring Methods in Mucinous Epithelial Ovarian Cancer

AbstractThe remarkable success of trastuzumab and other newly developed anti-HER2 (human epidermal growth factor receptor 2) therapies in breast, gastric, or gastroesophageal junction cancer patients has supported us to investigate the HER2 status and its possible therapeutic implication in mucinous epithelial ovarian cancer (EOC). However, there is currently no standardization of HER2 scoring criteria in mucinous EOC. In this study, we aimed to compare both the assay performance characteristics of the 2007 and the 2013 American Society for Clinical Oncology and College of American Pathologists scoring methods. Forty-nine tissue microarray samples of mucinous EOC from Asian women were analyzed by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) tests using the 2007 and the 2013 criteria, respectively. The overall concordance between IHC and FISH by the 2007 criteria was 97.92 % (kappa = 0.921), and that by the 2013 criteria was 100% (kappa = 1.000). The percentage of Her2 FISH-amplified cases showed an increasing trend significantly through their corresponding HER2 IHC ordinals by the 2007 and the 2013 criteria, respectively (P < 0.001, P < 0.001). After excluding equivocal cases, the specificity (100%) and positive predictive value (100%) were unchanged under either the 2007 or the 2013 criteria. The sensitivity (100%), negative predictive value (NPV) (100%), and accuracy (100%) of HER2 IHC were higher under the 2013 criteria than those (sensitivity 87.5%, NPV 97.6%, and accuracy 97.9%) under the 2007 criteria. Of the total 49 cases, the number (n = 4) of HER2 IHC equivocal results under the 2013 criteria was 4-fold higher than that (n = 1) under the 2007 criteria (8.16% vs 2.04%). Conclusively, if first tested by IHC, the 2013 criteria caused more equivocal HER2 IHC cases to be referred to Her2 FISH testing than the 2007 criteria. That decreased the false-negative rate of HER2 status and increased the detection rates of HER2 positivity in mucinous EOC.
Learning to Transfer

Transfer learning borrows knowledge from a source domain to facilitate learning in a target domain. Two primary issues to be addressed in transfer learning are what and how to transfer. For a pair of domains, adopting different transfer learning algorithms results in different knowledge transferred between them. To discover the optimal transfer learning algorithm that maximally improves the learning performance in the target domain, researchers have to exhaustively explore all existing transfer learning algorithms, which is computationally intractable. As a trade-off, a sub-optimal algorithm is selected, which requires considerable expertise in an ad-hoc way. Meanwhile, it is widely accepted in educational psychology that human beings improve transfer learning skills of deciding what to transfer through meta-cognitive reflection on inductive transfer learning practices. Motivated by this, we propose a novel transfer learning framework known as Learning to Transfer (L2T) to automatically determine what and how to transfer are the best by leveraging previous transfer learning experiences. We establish the L2T framework in two stages: 1) we first learn a reflection function encrypting transfer learning skills from experiences; and 2) we infer what and how to transfer for a newly arrived pair of domains by optimizing the reflection function. Extensive experiments demonstrate the L2T's superiority over several state-of-the-art transfer learning algorithms and its effectiveness on discovering more transferable knowledge.
Syntactic and Semantic Kernels for Short Text Pair Categorization

Automatic detection of general relations between short texts is a complex task that cannot be carried out only relying on language models and bag-of-words. Therefore, learning methods to exploit syntax and semantics are required. In this paper, we present a new kernel for the representation of shallow semantic information along with a comprehensive study on kernel methods for the exploitation of syntactic/semantic structures for short text pair categorization. Our experiments with Support Vector Machines on question/answer classification show that our kernels can be used to greatly improve system accuracy.
Coordinated control of a series-parallel hybrid electric bus during EV/HEV mode transition

Hybrid electric buses have been a promising technology to improve fuel economy and vehicle drivability. Due to the distinct transient response characteristics between different power sources and the discontinuity of the transmitted clutch torque, the output torque fluctuations of hybrid powertrains and the resulting vehicle jerks may occur during mode transitions, especially for the transition from the EV (electric vehicle) mode to the HEV (hybrid electric vehicle) mode. Aiming at achieving a smooth transition from the EV mode to the HEV mode for a series-parallel hybrid electric bus, this paper proposes a transient control strategy to coordinate the diesel engine and the motors during the transition process. The EV/HEV mode-transition control strategy is developed according to the operating status of the clutch, and the engine throttle is restricted during the transition process. In this control strategy, a fuzzy adaptive inference system is developed to estimate the difference between the actual and target engine torques. Then, the estimated torque difference is incorporated with a sliding mode controller to regulate the output torques of the integrated starter generator (ISG)and the traction motor (TM) to reduce the torque fluctuations in the powertrain. A simulation is performed using a forward-facing HEV model to validate the effectiveness of the proposed control strategy, and the results show significant reductions in torque fluctuations and vehicle jerks during the EV/HEV mode transition. Key-words: series-parallel hybrid electric bus; EV/HEV mode transition; transient response; fuzzy adaptive sliding mode control; coordinated control
Accurate Measurement-Based WCET Analysis in the Absence of Source and Binary Code

Estimating the worst-case execution time (WCET) of real-time embedded systems is compulsory for the verification of their correct functioning. Traditionally, the WCET of a program is estimated assuming availability of the program's binary which is disassembled to reconstruct the program, and in some cases its source code to derive useful high-level execution information. However, in certain scenarios the program's owner requires that the binary of the program not be reverse-engineered to protect intellectual property, and in extreme situations, the program's binary is not available for the analysis, in which case it is substituted by program-execution traces. In this paper we show that we can obtain WCET estimates for programs based on runtime-generated or owner-provided time-stamped execution traces and without the need to access the source code or reverse-engineer the binaries of the programs. We show that we can provide very accurate WCET estimations using both integer linear programming (ILP) and constraint logic programming (CLP). Our method generates safe and tight WCET estimations for all the benchmarks used in the evaluation.
Fast Two-scale Methods for Eikonal Equations

Fast Marching and Fast Sweeping are the two most commonly used methods for solving the eikonal equation. Each of these methods performs best on a different set of problems. Fast Sweeping, for example, will outperform Fast Marching on problems where the characteristics are largely straight lines. Fast Marching, on the other hand, is usually more efficient than Fast Sweeping on problems where characteristics frequently change their directions and on domains with complicated geometry. In this paper we explore the possibility of combining the best features of both approaches by using Marching on a coarser scale and sweeping on a finer scale. We present three new hybrid methods based on this idea and illustrate their properties in several numerical examples with continuous and piecewise-constant speed functions in $R^2$.