gebhart/patrepeval huggingface dataset:
Sequence to structure alignment in comparative modeling using PrISM (1999)

PrISM (Protein Informatics System for Modeling) is a protein analysis and modeling system in which informatics, alignment, modeling, and assessment modules are integrated in a computational environment where protein analysis and modeling protocols can be designed and assessed interactively. It can then be used automatically and repetitively in response to a variety of protein analysis and modeling problems. PrISM was used to predict a single model for each of the 43 targets in the CASP3 experiment. In this paper, we present results for 13 target sequences, which we consider to be comparative modeling targets with clearly related structural templates. We emphasize the problem of aligning a target sequence to a template structure with various alignment methods. When more than one alignment method and/or parameter set are applied, the final alignment is chosen on the basis of a model ranking system also used in PrISM's fold recognition module. Advanced sequence-template alignment procedures in PrISM are useful in some cases when standard pairwise dynamic programming algorithm fail to make any reasonable global alignment. The same procedures, however, failed in other cases, corresponding to remotely related query-template pairs that involved extensive insertions and deletions.
Analysis and improvement of the consistency of extended Kalman filter based SLAM (2008)

In this work, we study the inconsistency of EKF-based SLAM from the perspective of observability. We analytically prove that when the Jacobians of the state and measurement models are evaluated at the latest state estimates during every time step, the linearized error-state system model of the EKF-based SLAM has observable subspace of dimension higher than that of the actual, nonlinear, SLAM system. As a result, the covariance estimates of the EKF undergo reduction in directions of the state space where no information is available, which is a primary cause of inconsistency. To address this issue, a new “First Estimates Jacobian” (FEJ) EKF is proposed, which is shown to perform better in terms of consistency. In the FEJ-EKF, the filter Jacobians are calculated using the first-ever available estimates for each state variable, which insures that the observable subspace of the error-state system model is of the same dimension as that of the underlying nonlinear SLAM system. The theoretical analysis is validated through extensive simulations.
Bromide-dependent toxicity of eosinophil peroxidase for endothelium and isolated working rat hearts: a model for eosinophilic endocarditis. (1991)

Eosinophilic endocarditis is a potentially lethal complication of chronic peripheral blood hypereosinophilia. We hypothesized that eosinophil peroxidase (EPO), an abundant eosinophil (EO) cationic granule protein, promotes eosinophilic endocarditis by binding to negatively charged endocardium, and there generating cytotoxic oxidants. Using an immunocytochemical technique, we demonstrated endocardial deposition of EPO in the heart of a patient with hypereosinophilic heart disease. Because EPO preferentially oxidizes Br- to hypobromous acid (HOBr) rather than Cl- to hypochlorous acid (HOCl) at physiologic halide concentrations, we characterized the Br(-)-dependent toxicity of both activated EOs and purified human EPO towards several types of endothelial cells and isolated working rat hearts. In RPMI supplemented with 100 microM Br-, phorbol myristate acetate-activated EOs, but not polymorphonuclear leukocytes, caused 1.8-3.6 times as much 51Cr release from four types of endothelial cell monolayers as in RPMI alone. H2O2 and purified human EPO, especially when bound to cell surfaces, mediated extraordinarily potent, completely Br(-)-dependent cytolysis of endothelial cells that was reversed by peroxidase inhibitors, HOBr scavengers, and competitive substrates. We further modeled eosinophilic endocarditis by instilling EPO into the left ventricles of isolated rat hearts, flushing unbound EPO, then perfusing them with a buffer containing 100 microM Br- and 1 microM H2O2. Acute congestive heart failure (evidenced by a precipitous decrement in rate pressure product, stroke volume work, aortic output, and MVO2 to 0-33% of control values) ensued over 20 min, which deletion of EPO, Br-, or H2O2 completely abrogated. These findings raise the possibility that EPO bound to endocardial cells might utilize H2O2 generated either by overlying phagocytes or endogenous cardiac metabolism along with the virtually inexhaustible supply of Br- from flowing blood to fuel HOBr-mediated cell damage. By this mechanism, EPO may play an important role in the pathogenesis of eosinophilic endocarditis.
An efficient partitioning algorithm for distributed virtual environment systems (2002)

Distributed virtual environment (DVE) systems model and simulate the activities of thousands of entities interacting in a virtual world over a wide area network. Possible applications for DVE systems are multiplayer video games, military and industrial trainings, and collaborative engineering. In general, a DVE system is composed of many servers and each server is responsible to manage multiple clients who want to participate in the virtual world. Each server receives updates from different clients (such as the current position and orientation of each client) and then delivers this information to other clients in the virtual world. The server also needs to perform other tasks, such as object collision detection and synchronization control. A large scale DVE system needs to support many clients and this imposes a heavy requirement on networking resources and computational resources. Therefore, how to meet the growing requirement of bandwidth and computational resources is one of the major challenges in designing a scalable and cost-effective DVE system. In this paper, we propose an efficient partitioning algorithm that addresses the scalability issue of designing a large scale DVE system. The main idea is to dynamically divide the virtual world into different partitions and then efficiently assign these partitions to different servers. This way, each server will process approximately the same amount of workload. Another objective of the partitioning algorithm is to reduce the server-to-server communication overhead. The theoretical foundation of our dynamic partitioning algorithm is based on the linear optimization principle. We also illustrate how one can parallelize the proposed partitioning algorithm so that it can efficiently partition a very large scale DVE system. Lastly, experiments are carried out to illustrate the effectiveness of the proposed partitioning algorithm under various settings of the virtual world.
Fast full search block motion estimation for H.264/AVC with multilevel successive elimination algorithm (2005)

We modify the multilevel successive elimination algorithm (MSEA) to make it compatible with the motion estimation required for the H.264/AVC video coding standard. The algorithm must be changed to support the multiple block sizes and the criterion to be minimized has to be rate-distortion-based to allow efficient encoding. We use MSEA for eliminating the smallest 4/spl times/4 -pixel blocks and either derive lower bound or exact criterion for larger blocks based on the small block bounds or criterions, correspondingly. The resulting algorithm needs 60%-70% less time than the original motion estimation in the reference encoder but it still yields a practically equivalent video quality and bit rate.
Expression of CD94 and NKG2 molecules on human CD4+ T cells in response to CD3-mediated stimulation (2001)

We investigated the ability of human peripheral CD4(+) cells to express CD94 and NKG2 molecules as a consequence of CD3-mediated activation. Using highly purified peripheral CD4(+) T cells, we found expression of both CD94 and NKG2A 15 days after CD3-mediated stimulation of cells. We also determined by reverse transcriptase-PCR that all gene members of NKG2 family-namely, NKG2A, -C, -D, and -E-are sequentially expressed on CD4(+) cells. We found that this expression is tightly regulated by cytokines, and we identified transforming growth factor-beta1 and interleukin-10 as the main factors that, on CD3-dependent stimulation, positively contribute to the expression of CD94 and NKG2A on CD4(+) cells. We also investigated the functional role of NKG2A and found that coligation of CD3 and NKG2A by specific monoclonal antibodies results in significant inhibition of interferon gamma and tumor necrosis factor alpha production by stimulated CD4(+) cells. The presence and function of these receptors on CD4(+) lymphocytes support a more general role for NKG2 molecules, whose functions were originally thought to be confined to cytotoxic cells, in the immune system.
The SCRIPPS trial--catheter-based radiotherapy to inhibit coronary restenosis. (2000)

The SCRIPPS trial is a randomized, double-blind, placebo-controlled trial evaluating the impact of gamma radiation to inhibit in-stent restenosis. Fifty-five patients were enrolled; twenty-six were assigned to receive catheter-based radiation with Ir-192 and 29 were treated with placebo. Angiographic restenosis in the Ir-192-treated patients was significantly reduced at six months (17% vs. 54%; p = 0.01), with the results sustained at 3-year follow-up (33.3% vs. 63. 6%; p<0.05). Likewise, the composite clinical endpoint of death, myocardial infarction or target lesion revascularization was also commensurately lower in the treated group as compared to the placebo group (23.1% vs. 55.2%; p = 0.01). Late angiography revealed no perforation, aneurysm or pseudoaneurysm or special safety issues unique to radiotherapy.
Optimization of solid supports for combinatorial chemical synthesis (1999)

Until recently, resins were used primarily for peptide and oligonucleotide synthesis. Recent advances in combinatorial chemistry have fostered increased acceptance of resins as supports for the synthesis of small molecule libraries. The methodology for selecting a resin bead that is ideal for the solid phase synthesis of small molecules is described in this review. The process of manufacturing a typical resin, the UniSphere-200, is also explained. Furthermore, a new approach is proposed for the solid phase synthesis of analogs which are traditionally done in solution phase. This new procedure involves the use of building blocks attached to an activated resin. These building blocks are displaced by a functional group on the scaffold around which the analogs are built. Use of an excess of resin-linked building blocks drives the reaction to completion. Additionally, a newly developed, grafted surface solid support, is described. This support, the MicroTube, can be used for the synthesis of large numbers of discrete molecules by a patented directed sorting method.
Using GVF Snake to Segment Liver from CT Images (2006)

Liver segmentation on computed tomography (CT) images is a challenging task because the images are often corrupted by noise and sampling artifacts. Thus we choose GVF snake to perform the task. Unfortunately, GVF snake use Gaussian function to generate the edge map. We find that this often cause new problems such as blur the liver boundary. To avoid this, a Canny edge detector is a good choice. Another problem during the segmentation is that GVF snake cannot works well with bad initialization, especially when encounter deep concavities. Fortunately we find that if the initial contour can cross the "bottleneck" of the deep concave, it can easily reach the boundary of liver. Thus an algorithm was developed to generate the initial contour automatically. We introduce a new "maximum force angle map" to evaluate the direction variability of the GVF forces. This map can mark up the "bottleneck " and give a trace to run through it. There may be other trace we do not need in the map. With the help of transcendental knowledge about the liver, such as the position, the shape and the Hounsfield unit range of the liver, the correct trace can be found. The contour of this trace is suitable for using as initial contour for GVF snake. By this means we finally segment the liver slice by slice correctly.
Anti-Mycobacterium tuberculosis activity of antituberculosis drugs and amoxicillin/clavulanate combination (2015)

We report the in vitro drugs interaction by the resazurin drugs combination microtiter assay (REDCA) of amoxicillin (AMO)/clavulanate (CLAV) with isoniazid (INH), ethambutol (EMB), and rifampicin (RIF) against susceptible and resistant Mycobacterium tuberculosis isolates. The addition of AMO/CLAV to classical antituberculosis drugs should be explored as a promising alternative for the treatment of resistant tuberculosis (TB).
Monte Carlo method for computing density of states and quench probability of potential energy and enthalpy landscapes (2007)

The thermodynamics and kinetics of a many-body system can be described in terms of a potential energy landscape in multidimensional configuration space. The partition function of such a landscape can be written in terms of a density of states, which can be computed using a variety of Monte Carlo techniques. In this paper, a new self-consistent Monte Carlo method for computing density of states is described that uses importance sampling and a multiplicative update factor to achieve rapid convergence. The technique is then applied to compute the equilibrium quench probability of the various inherent structures (minima) in the landscape. The quench probability depends on both the potential energy of the inherent structure and the volume of its corresponding basin in configuration space. Finally, the methodology is extended to the isothermal-isobaric ensemble in order to compute inherent structure quench probabilities in an enthalpy landscape.
Dependence of anomalous Nernst effect on crystal orientation in highly ordered γ′-Fe<sub>4</sub>N films with anti-perovskite structure (2017)

The anomalous Nernst effect (ANE) in highly ordered Fe4N films was examined in the measurement configuration with an in-plane temperature gradient (∇Tx). The anomalous Nernst coefficient (Qs) in the case of ∇Tx ∥ Fe4N[110] was clearly larger than that in the case of ∇Tx ∥ Fe4N[100]. Note here that no reports on the Qs in Fe4N films have been presented. This anisotropic Qs (Qani) was also observed in a different configuration with an out-of-plane temperature gradient. Unlike Fe4N, pure Fe and A2-FeAl systems showed a negligible Qani. This Qani might be attributed to the specific hybridization effects between the 3d orbitals of Fe and the 2p orbitals of N.
Characterization of CdSe-nanocrystals used in semiconductors for aerospace applications: Production and optical properties (2014)

Semiconductor nanocrystals (NC's) are the materials with dimensions less than 10 nm. When the dimensions of nanocrystals are reduced the bulk bohr diameter, the photo generated electron-hole pair becomes confined and nanocrystal exhibits size dependent upon optical properties. This work is focused on the studying of CdSe semiconductor nanocrystals. These nanocrystals are considered as one of the most widely studies semiconductors because of their size – tunable optical properties from the visible spectrum. CdSe-nanocrystals are produced and obtained throughout the experimental setup initiated at Nano-NRIAG Unit (NNU), which has been constructed and assembled at NRIAG institute. This unit has a specific characterization for preparing chemical compositions, which may be used for solar cell fabrications and space science technology. The materials prepared included cadmium oxide and selinid have sizes ranging between 2.27 nm and 3.75 nm. CdSe-nanocrystals are synthesized in "TOP/TOPO (tri–octyl phosphine/tri–octyl phosphine oxide). Diagnostic tools, include UV analysis, TEM microscope, and X-ray diffraction, which are considered for the analytical studies of the obtained materials. The results show that, in this size regime, the generated particles have unique optical properties, which is achieved from the UV analysis. Also, the TEM image analysis shows the size and shape of the produced particles. These studies are carried out to optimize the photoluminescent efficiency of these nanoparticles. Moreover, the data revealed that, the grain size of nanocrystals is dependent upon the growth time in turn, it leads to a change in the energy gap. Some applications of this class of materials are outlined.
An error control system with multiple-stage forward error corrections (1990)

A robust error control coding system is presented. This system is a cascaded FEC (forward error control) scheme supported by parity retransmissions for further error correction in the erroneous data words. The error performance and throughput efficiency of the system are analyzed. Two specific examples of the error control system are studied. The first example does not use an inner code, and the outer code, which is not interleaved, is a shortened code of the NASA standard RS code over GF(2/sup 8/). The second example, as proposed for NASA uses the same shortened RS code as the base outer code C/sub 2/, except that it is interleaved to a depth of 2. It is shown that both examples provide high reliability and throughput efficiency even for high channel bit-error rates in the range of 10/sup -2/.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Apoptosis and autophagy have opposite roles on imatinib-induced K562 leukemia cell senescence (2012)

Imatinib, the anti-Abl tyrosine kinase inhibitor used as first-line therapy in chronic myeloid leukemia (CML), eliminates CML cells mainly by apoptosis and induces autophagy. Analysis of imatinib-treated K562 cells reveals a cell population with cell cycle arrest, p27 increase and senescence-associated beta galactosidase (SA-β-Gal) staining. Preventing apoptosis by caspase inhibition decreases annexin V-positive cells, caspase-3 cleavage and increases the SA-β-Gal-positive cell population. In addition, a concomitant increase of the cell cycle inhibitors p21 and p27 is detected emphasizing the senescent phenotype. Inhibition of apoptosis by targeting Bim expression or overexpression of Bcl2 potentiates senescence. The inhibition of autophagy by silencing the expression of the proteins ATG7 or Beclin-1 prevents the increase of SA-β-Gal staining in response to imatinib plus Z-Vad. In contrast, in apoptotic-deficient cells (Bim expression or overexpression of Bcl2), the inhibition of autophagy did not significantly modify the SA-β-Gal-positive cell population. Surprisingly, targeting autophagy by inhibiting ATG5 is accompanied by a strong SA-β-Gal staining, suggesting a specific inhibitory role on senescence. These results demonstrate that in addition to apoptosis and autophagy, imatinib induced senescence in K562 CML cells. Moreover, apoptosis is limiting the senescent response to imatinib, whereas autophagy seems to have an opposite role.
A floating-point library for integer processors (2004)

This paper presents a C library for the software support of single precision floating-point (FP) arithmetic on processors without FP hardware units such as VLIW or DSP processor cores for embedded applications. This library provides several levels of compliance to the IEEE 754 FP standard. The complete specifications of the standard can be used or just some relaxed characteristics such as restricted rounding modes or computations without denormal numbers. This library is evaluated on the ST200 VLIW processors from STMicroelectronics.
SALSA: analyzing logs as state machines (2008)

SALSA examines system logs to derive state-machine views of the sytem’s execution, along with controlflow, data-flow models and related statistics. Exploiting SALSA’s derived views and statistics, we can effectively construct higher-level useful analyses. We demonstrate SALSA’s approach by analyzing system logs generated in a Hadoop cluster, and then illustrate SALSA’s value by developing visualization and failure-diagnosis techniques, for three different Hadoop workloads, based on our derived state-machine views and statistics. 1
Growth Factor<i>erv1</i>-like Modulates Drp1 to Preserve Mitochondrial Dynamics and Function in Mouse Embryonic Stem Cells (2010)

Mitochondria, the dynamic energy powerhouses of the cell, have vital roles in a multitude of cellular processes including differentiation and cell survival. Tight regulation of mitochondrial dynamics, integrity and function is indispensible for preservation of homeostasis in all cells, including pluripotent stem cells. The ability to proliferate and self-renew indefinitely bestows the pluripotent embryonic stem cells (ESCs) with immense curative potential. Mechanisms that preserve mitochondrial well-being, and therefore maintain "stemness," are vital in realizing the full potential of ESCs in therapeutic regenerative medicine. However, virtually nothing is known regarding the regulation of mitochondrial dynamics and function and the relationship thereof to overall cell fate and function in pluripotent ESCs or other somatic stem cells. Using loss- and gain-of-function approaches, we show that growth factor erv1-like (Gfer) plays an essential pro-survival role in the maintenance of murine ESC pluripotency by preserving the structural and functional integrity of their mitochondria, through modulation of the key mitochondrial fission factor Drp1.
[Study on the mitochondrial DNA mutations in patients with early-onset diabetes mellitus]. (2005)

The above findings suggest that mtDNA mutation may be implicated in the pathogenesis of the examined diabetes.
Ultra-thin enhanced-absorption long-wave infrared detectors (2018)

We propose an architecture for enhanced absorption in ultra-thin strained layer superlattice detectors utilizing a hybrid optical cavity design. Our detector architecture utilizes a designer-metal doped semiconductor ground plane beneath the ultra-subwavelength thickness long-wavelength infrared absorber material, upon which we pattern metallic antenna structures. We demonstrate the potential for near 50% detector absorption in absorber layers with thicknesses of approximately λ0/50, using realistic material parameters. We investigate detector absorption as a function of wavelength and incidence angle, as well as detector geometry. The proposed device architecture offers the potential for high efficiency detectors with minimal growth costs and relaxed design parameters.
Study of Sources and Distribution Characteristics of Polychlorinated Naphthalenes (2009)

Polychlorinated naphthalenes (PCNs) are ubiquitous contaminants in the global environment. Due to their potential for toxicity, bioaccumulation and persistence similar to polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), PCNs have been listed as Additional POPs Candidates to the Stockholm Convention by some countries and international organizations. PCNs were in use as dielectric (insulating) fluids in electrical equipments and as heat-transfer fluids and plasticisers. Stockpiles may still exist. Putting these chemicals under global control could help to ensure their proper disposal. PCNs can be also formed as unintentional produced persistent organic pollutants. PCNs release to the environment from stack gas and solid waste in thermal processes. The character of PCNs, the source identification, analytical methods, environment level, environment transportation and sink are reviewed in this paper. Primary studies on PCNs in China are also mentioned. The trends of research and environmet management countermeasure on PCNs are also discussed.
Contact electrode method for fabricatingbulk periodically poled LiNbO <sub>3</sub> (1998)

The authors demonstrate the contact electrode method, in which a structured electrode is pressed into contact with the crystals. Bulk periodically poled lithium niobate (PPLN) with 6.58 µm period, 0.3 mm thickness, and an effective interaction length of 3 mm is fabricated. A second-harmonic power of 62.5 mW with 3.2 W of CW fundamental is achieved using an Nd:YAG laser.