gebhart/patrepeval huggingface dataset:
Fast binding site mapping using GPUs and CUDA (2010)

Binding site mapping refers to the computational prediction of the regions on a protein surface that are likely to bind a small molecule with high affinity. The process involves flexibly docking a variety of small molecule probes and finding a consensus site that binds most of those probes. Due to the computational complexity of flexible docking, the process is often split into two steps: the first performs rigid docking between the protein and the probe; the second models the side chain flexibility by energy-minimizing the (few thousand) top scoring protein-probe complexes generated by the first step. Both these steps are computationally very expensive, requiring many hours of runtime per probe on a serial CPU. In the current article, we accelerate a production mapping software program using NVIDIA GPUs. We accelerate both the rigid-docking and the energy minimization steps of the program. The result is a 30× speedup on rigid docking and 12× on energy minimization, resulting in a 13× overall speedup over the current single core implementation.
Study on the synthesis–microstructure-performance relationship of layered Li-excess nickel–manganese oxide as a Li-ion battery cathode prepared by high-temperature calcination (2013)

Spherical composite oxide Li1.5Ni0.25Mn0.75O2.5 (or 0.5Li2MnO3·0.5LiNi0.5Mn0.5O2) powder as a Li-ion battery cathode has been synthesized by high-temperature calcination of a mixture containing Li2CO3 and (Ni0.25Mn0.75)CO3, which is synthesized by a continuous co-precipitation method. The evolution in the microstructure of the oxide during calcination is studied mainly by transmission X-ray microscopy (TXM), complemented by X-ray diffraction and thermogravimetry, and it can be divided into three major stages. The first stage takes place below 400 °C, and is characterized by the decomposition of the transition metal carbonates to form amorphous oxides, leading to the formation of internal cracks due to extensive densification. The second stage occurs between 400 and 800 °C, and involves complete Li1.5Ni0.25Mn0.75O2.5 formation and the development of a unique radially-distributed pore structure. The third stage takes place above 800 °C and during prolonged heating at 900 °C, and is characterized by grain growth and change into a randomly distributed tortuous pore structure. TXM 3D-elemental analysis gives statistical evidence showing heterogeneity in the distributions of Ni and Mn, which causes capacity loss and might be a common problem encountered in the two-step precipitation–calcination process. The electrochemical performance of the resulting Li1.5Ni0.25Mn0.75O2.5 powder exhibits complex dependence on the microstructure. The radially distributed pore pattern and small grain size produced by moderate heating favor the rate performance of the composite oxide cathode by reducing charge-transfer resistance and enhancing apparent Li ion solid-state diffusivity. A large grain size resulting from prolonged heating, on the other hand, reduces the formation of the spinel MnO2 domain upon de-lithiation of the Li2MnO3 component of the composite oxide.
Spatio-Temporal Spectrum Sensing in Cognitive Radio Networks Using Beamformer-Aided SVM Algorithms (2018)

This paper addresses the problem of spectrum sensing in multi-antenna cognitive radio system using the support vector machine (SVM) algorithms. First, we formulated the spectrum sensing problem under multiple primary users scenarios as a multiple state signal detection problem. Next, we propose a novel beamformer-aided feature realization strategy for enhancing the capability of the SVM for signal classification under both single and multiple primary users conditions. Then, we investigate the error correcting output codes-based multi-class SVM algorithms and provide a multiple independent model alternative for solving the multiple state spectrum sensing problem. The performance of the proposed detectors is quantified in terms of probability of detection, probability of false alarm, receiver operating characteristics (ROC), area under ROC curves, and overall classification accuracy. Simulation results show that the proposed detectors are robust to both temporal and joint spatio-temporal detection of spectrum holes in cognitive radio networks.
Laboratory Evaluation of Crumb Rubber Modified Asphalt Mixes (2004)

The paper presents the details of various investigations conducted for the laboratory evaluation of the performance of crumb–rubber modified asphalt mixes. Crumb rubber (CR) obtained from discarded truck and bus tires was used to modify 80/100 penetration grade asphalt cement. Fatigue and permanent deformation characteristics, temperature and moisture susceptibility, and oxidative aging are some of the performance indicators of mixes evaluated. A static indentation test was adopted for assessing the relative permanent deformation characteristics of different mixes. Three aggregate gradations: (1) superpave; (2) gradation specified by the Ministry of Surface Transport, India for asphalt concrete; and (3) one gap gradation, were considered in the investigation. Compared to normal mixes, CR modified mixes were found to have improved fatigue and permanent deformation characteristics. They also showed lower temperature susceptibility and greater resistance to moisture damage compared to normal mixes. Superpave mixes gave better overall performance compared to the mixes having other aggregate gradations.
Analysis of Materials by Electron-Excited Auger Electrons (1968)

The energy spectra of Auger electrons emitted from many elements and alloys have been observed. Differentiation of the secondary electron-energy distribution by perturbation and synchronous detection techniques, and suppression of the effects of low-energy secondaries, were used to obtain well-defined spectra. The Auger lines afford a sensitive indicator for light elements, though spectra for elements as heavy as gold have been obtained. Because the method examines only a superficial layer of the sample, it is useful for detecting contamination, surface migration, or segregation, and for diffusion studies. Cleaning of the surfaces is critical for useful analysis. Quantitative analysis is hindered by noise and the lack of known surface conditions for calibration.
Pathogenicity and immune response against porcine circovirus type 3 infection in caesarean-derived, colostrum-deprived pigs (2020)

Recently, a novel PCV species (PCV3) has been detected in cases associated with sow mortality, lesions consistent with porcine dermatitis and nephropathy syndrome, reproductive failure and multisystemic inflammation. The pathogenesis and clinical significance of PCV3 is still unclear. In this study, we investigated the immunopathogenesis of PCV3 in CD/CD pigs. Four treatment groups, PCV3 (<i>n</i>=6), PCV3-KLH (<i>n</i>=6), control (<i>n</i>=3) and control-KLH (<i>n</i>=3), were included with PCV3-positive tissue homogenate (gc=3.38×10<sup>12</sup> ml<sup>-1</sup> and gc=1.04×10<sup>11</sup> ml<sup>-1</sup>), confirmed by quantitative PCR (qPCR) and next-generation sequencing. Clinical signs, viremia, viral shedding, systemic cytokines, humoral (IgG) and T-cellular response were evaluated for 42 days. At necropsy, tissues were collected for histological evaluation and PCV3 detection by qPCR and <i>in situ</i> hybridization. No significant clinical signs were observed through the study. Viremia was detected in both PCV3-inoculated groups from 3 days post-inoculation (p.i.) until the end of the study. Nasal shedding was detected from 3 to 28 days p.i. and faecal shedding was transient. PCV3 induced an early (7 days p.i.) and sustained (42 days p.i.) IgG response. No significant T-cell response was observed. Histological evaluation demonstrated lesions consistent with multisystemic inflammation and perivasculitis. All tissues evaluated were positive by qPCR and virus replication was confirmed by positive <i>in situ</i> hybridization. This study demonstrated the potential role of PCV3 in subclinical infection, producing a mild, multisystemic inflammatory response, prolonged viremia detectable for 42 days p.i., presence of IgG humoral response and viral shedding in nasal secretions. More research is required to understand and elucidate potential co-factors necessary in the manifestation and severity of clinical disease.
A cellist with arm pain: thermal asymmetry in scalenus anticus syndrome. (1991)

We report on a cellist with pain and coldness of the upper extremity. Abnormal thermographic studies were instrumental in uncovering intermittent compression of the subclavian artery, and this prompted us to study the effects of cello playing on skin temperature asymmetry. Temperature asymmetry was defined as the temperature difference (delta-T) from one hand to the other. In 57 controls, mean delta-T at rest was .309 +/- .254C. Exercising the upper extremities by prolonged elbow flexion or by movements mimicking cello playing in controls did not significantly affect delta-T. In our patient, delta-T was ten times control (3.6C). Angiography showed extrinsic compression of the subclavian artery occurring only after cello playing; sympathetic ganglion block relieved the pain. Our patient's abnormal skin temperature may have reflected sympathetic vasomotor hyperactivity. Intermittent neurovascular compression and sympathetic hyperactivity appear to be factors in scalenus anticus syndrome.
An asymptotically optimal algorithm for job shop scheduling (2003)

We propose asymptotically optimal algorithms for job shop scheduling. We propose a fluid relaxation for the job shop scheduling problem, in which we replace discrete jobs with the flow of a continuous fluid. We compute an optimal solution of the fluid relaxation in closed form, obtain a lower bound C/sub max/ to the job shop scheduling problem, and construct a feasible schedule from the fluid relaxation with objective value at most C/sub max/+O(/spl radic/C/sub max/), where the constant in the O(/spl middot/) notation is independent of the number of jobs. However, it depends on the processing times of the jobs, thus producing an asymptotically optimal schedule as the total number of jobs tends to infinity. If the initially present jobs increase proportionally, then our algorithm produces a schedule with value at most C/sub max/+O(1). In computational experiments our algorithms produce schedules which are within 1% of optimality even for moderately sized problems.
Repeated Platelet Concentrate Injections Enhance Reparative Response of Microfractures in the Treatment of Chondral Defects of the Knee: An Experimental Study in an Animal Model (2012)

Periodical intra-articular injections of platelet concentrate after microfractures may improve cartilage repair and prevent further degenerative changes.
Nitrogen/Palladium-Codoped TiO<sub>2</sub>for Efficient Visible Light Photocatalytic Dye Degradation (2011)

Elimination of toxic organic compounds from wastewater is currently one of the most important subjects in water pollution control. Eosin Yellow, an anionic xanthene fluorescent dye, known to be carcinogenic, originates mainly from textile industrial processes and is resistant to conventional chemical or biological water treatment methods. Photocatalysis using non metal/platinum group metal-codoped TiO2 may provide effective means of removing such dyes from contaminated water. In this study, nitrogen/palladium-codoped TiO2 photocatalysts were prepared by calcination of the hydrolysis product of titanium isopropoxide, Ti(OC3H7)4, with aqueous ammonia. Samples were characterized by Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, thermogravimetric analysis (TGA), diffuse reflectance UV–vis spectrophotometry, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Anatase phase particles of size range 10–20 nm were confirmed by XRD, Raman, TEM, and SEM analysis. Codoping imparted a red shift in the absorption edges of the materials. Codoped TiO2 showed greater photocatalytic Eosin Yellow degradation efficiency compared to singly doped N–TiO2 or Pd–TiO2 under visible light irradiation. The highest initial reaction rate of 2.238 × 10–2 min–1 was observed for N/Pd–TiO2 (0.8% Pd). The results demonstrated that the N/Pd-codoped TiO2 (0.6% Pd) sample could completely degrade the dye in 3 h, while the commercial TiO2, (Degussa P25) showed the lowest dye degradation efficiency.
Digital tomosynthesis mammography: intra- and interplane artifact reduction for high-contrast objects on reconstructed slices using a priori 3D geometrical information (2007)

We are developing a computerized technique to reduce intra- and interplane ghosting artifacts caused by high-contrast objects such as dense microcalcifications (MCs) or metal markers on the reconstructed slices of digital tomosynthesis mammography (DTM). In this study, we designed a constrained iterative artifact reduction method based on <i>a priori </i>3D information of individual MCs. We first segmented individual MCs on projection views (PVs) using an automated MC detection system. The centroid and the contrast profile of the individual MCs in the 3D breast volume were estimated from the backprojection of the segmented individual MCs on high-resolution (0.1 mm isotropic voxel size) reconstructed DTM slices. An isolated volume of interest (VOI) containing one or a few MCs is then modeled as a high-contrast object embedded in a local homogeneous background. A shift-variant 3D impulse response matrix (IRM) of the projection-reconstruction (PR) system for the extracted VOI was calculated using the DTM geometry and the reconstruction algorithm. The PR system for this VOI is characterized by a system of linear equations. A constrained iterative method was used to solve these equations for the effective linear attenuation coefficients (eLACs) within the isolated VOI. Spatial constraint and positivity constraint were used in this method. Finally, the intra- and interplane artifacts on the whole breast volume resulting from the MC were calculated using the corresponding impulse responses and subsequently subtracted from the original reconstructed slices. The performance of our artifact-reduction method was evaluated using a computer-simulated MC phantom, as well as phantom images and patient DTMs obtained with IRB approval. A GE prototype DTM system that acquires 21 PVs in 3º increments over a ±30º range was used for image acquisition in this study. For the computer-simulated MC phantom, the eLACs can be estimated accurately, thus the interplane artifacts were effectively removed. For MCs in phantom and patient DTMs, our method reduced the artifacts but also created small over-corrected areas in some cases. Potential reasons for this may include: the simplified mathematical modeling of the forward projection process, and the amplified noise in the solution of the system of linear equations.
Secretion, processing and activation of bacterial extracellular proteases (1989)

Many different bacteria secrete proteases into the culture medium. Extracellular proteases produced by Gram-positive bacteria are secreted by a signal-peptide-dependent pathway and have a propeptide located between the signal peptide and the mature protein. Many extracellular proteases synthesized by Gram-negative bacteria are also produced as precursors with a signal peptide. However, at least two species of Gram-negative bacteria secrete one or more proteases via a novel signal-peptide-independent route. Most proteases secreted by Gram-negative bacteria also have a propeptide whose length and location vary according to the protease. Specific features of protease secretion pathways and the mechanisms of protease activation are discussed with particular reference to some of the best-characterized extracellular proteases produced by Gram-positive and Gram-negative bacteria.
Uses of the Internet: Rural Special Education Materials for Teachers and Parents (1999)

The Internet offers important educational and resource information and interactive opportunities for teachers and parents of children with disabilities in rural areas. In this paper, Internet locations for teachers are highlighted and include multipurpose sites, sites for special education teachers, general disability sites, and sites related to specific disabilities. Parental education sites related to learning about disabilities, home coping strategies, finding special education information and organizations, legal issues and IEP processes are provided. Rural special educators can use the Internet information and interactive opportunities to further their knowledge as well as to assist parents of children with disabilities in learning more about disabilities, organizations, and resources for families. It is hoped that rural special educators can empower parents to use Internet services themselves to better understand their child's disability and the resources available.
Silver nanowires in poly(methyl methacrylate) as a conductive nanocomposite for microfabrication (2016)

A novel nanocomposite resist is presented based on AgNWs dispersed in poly(methyl methacrylate). It is shown that this nanocomposite resist displays sheet resistances below 10 Ω sq−1 for concentrations of AgNWs higher than and can be used for a wide range of microfabrication techniques. The resist can act as a conductive ink that cures at room temperature, form thin films with low sheet resistances, and be used in fast replication methods derived from soft lithography. Furthermore, it can be applied for nano-scale fabrication via electron beam lithography (EBL) on different substrates, including flexible and insulating materials, providing a straightforward method to avoid charging effects. This, being the first report about a nanocomposite resist based on AgNWs for EBL, describes a simple procedure to account for suspended nanowires, forming bridges, nanocantilevers and more complex nanostructures. A wide range of opportunities opens for the single-step fabrication of electronic components in the nano and micro scale.
A Novel Low-Latency V2V Resource Allocation Scheme Based on Cellular V2X Communications (2018)

In vehicular ad hoc networks (VANETs), cellular vehicle-to-everything (C-V2X) is an emerging technology for communications between vehicle-to-infrastructure, vehicle-to-pedestrian, and vehicle-to-network which improves traffic efficiency, road safety, and the availability of infotainment services. Herein, a novel V2V-enabled resource allocation scheme based on C-V2X technology is proposed to improve the reliability and latency of VANETs. The key idea is that V2V communications based on cellular-V2X technology among vehicles remove the contention latency and can assist for longer distance communications. Particularly, we propose a hybrid architecture, where the V2V links are controlled by the cellular eNodeB in the overlay scheme. In this scheme, every vehicle periodically checks its packet lifetime and requests the cellular eNodeB to determine V2V links. The optimum resource allocation problem at the cellular eNodeB is to choose optimum receiver vehicles to determine V2V links and allocate suitable channels to minimize the total latency. This problem is equivalent to the maximum weighted independent set problem (MWIS-AW) with associated weights, which is NP-hard. In order to compute the weights, an analytical approach is developed to model the expected latency and packet delivery ratio. Moreover, a greedy cellular-based V2V link selection algorithm is proposed to solve MWIS-AW problem and develop a theoretical performance lower bound. Simulation results show that the proposed scheme significantly outperforms the existing schemes in terms of latency, throughput, and packet delivery ratio.
한국여성의 정치참여와 여성복지정책 변화 -남녀고용평등법의 제,개정을 중심으로- (2004)

80년대 이후 우리나라 여성운동은 민주화운동과 함께 전통적 여성단체와는 성격을 달리하는 성차별에 대한 근본적인 원인 및 해결을 추구하는 페미니즘을 기반으로 한 진보적 여성운동으로 질적 전환을 하게 되었다. 여성운동은 다양한 여성문제를 사회적 문제로 부상시키고 문제에 대한 정치적 해결을 요구하며 나아가 이를 정치적 논점으로 이슈화함으로써 정책형성 및 입법화에 이르도록 하였다. 이 과정에서 여성과 여성문제에 대한 정치적 가시성은 점차 높아졌으며 정책의제는 여성주의적 사고와 활동에 의해 정치화된 쟁점을 분명하게 거론하며 여성분야의 정책을 수행하한 제도적 장치가 마련되기도 하였다. 그런데 정책형성 및 결정은 특정욕구에 대한 요구(demends) 및 이슈화 그리고 정치적 의제, 결정 등의 일련의 과정을 거치게 된다. 여기서 여성복지문제나 이슈는 정치적으로나 경제적으로 힘이 약한 사람들의 문제로 가부장적 세력의 저항을 받게 되기에 법제정이 어렵게 되거나 된다고 해도 한계점을 지니게 된다. 우리나라의 경우 1980년대 후반에 들어와서 민주화와 함께 여성운동세력이 정책과정에 어느 정도 개입할 수 있게 되었으며 유권자로서 여성의 정치참여 증가는 각 정당으로 하여금 여성관련 정책을 공약화하는 계기가 되었다. 정책결정자로서의 여성 국회의원은 소수이지만 여성정책의 결정과정에 영향을 미치게 되었다. 이런 점에서 여성유권자의 역할, 정책결정자로서의 여성의원의 역할, 그리고 여성문제를 이슈화하고 쟁점화 하는 여성단체 그리고 이들간의 상호관계는 여성복지정책의 향방에 중요한 요인이라는 점을 알 수 있다. 본 연구는 여성의 정치참여가 여성복지정책의 형성 및 결정과정에 어떠한 영향을 미쳤는가에 연구목적을 두고 위로부터의 정책이 아닌 아래로부터의 요구에 기반을 두고 진행된 여성복지정책을 분석하였다. 분석대상은 여성복지정책중 1987년 제정된 이래 2001년 현재 4차례에 걸쳐 제ㆍ개정과정을 중심으로 여성의 정치참여와 가부장적 세력의 대응, 국내외 상황 및 법의 성격변화 등으로 하였다.
Modeling and Performance Limits of Switched-Capacitor DC–DC Converters Capable of Resonant Operation With a Single Inductor (2017)

This paper explores generalized output impedance models and develops a new performance-limit figure of merit (FOM) for switched-capacitor (SC) dc-dc converters that can be resonated or soft-charged with a single inductor. Compared to past work, the output impedance model is greatly simplified through a two-port charge multiplier treatment, yet it maintains accuracy across conversion ratios and is valid in both slow- and fast-switching operation. Building on previous analytical treatments of SC and ReSC converters, the model is expanded to derive optimizations that include both conduction and switching losses. The process is used to identify a new FOM for hybrid-resonant SC converters that can be used to identify the most suitable architectures for a given conversion ratio and relevant (energy or area) constraints on flying capacitors. This is used to highlight the active-device and capacitance utilizations of common topologies, as well as which are most favorable for hybrid-resonant operation.
Antagonism between retinoic acid receptors and AP-1: implications for tumor promotion and inflammation. (1991)

Retinoids such as retinoic acid (RA) are potent anti-arthritic and anti-neoplastic agents. We investigated the mechanism by which RA inhibits induction of collagenase gene transcription by inflammatory mediators, tumor promoters, and proto-oncogenes. We found that the RA receptors (RARs) are potent inhibitors of AP-1 activity generated either by cJun homodimers or cJun/cFos heterodimers. In addition, both cJun and cFos can inhibit RAR activity. In vitro experiments suggested that this inhibition is due to an interaction between RAR and AP-1 proteins that results in mutual loss of DNA-binding activity. The RARs need not bind to the AP-1 site, neither does AP-1 bind to RA response elements. An understanding of this antagonism between the RAR and AP-1 might help to elucidate the anti-neoplastic and anti-arthritic effects of RA as well as its effects on cell differentiation and proliferation.
A Theoretical Analysis of a New Polarimetric Optical Scheme for Glucose Sensing in the Human Eye (2002)

The challenging task of in vivo polarimetric glucose sensing is the identification and selection of a scheme to optically access the aqueous humor of the human eye. In this short communication an earlier approach of Cote et al. is theoretically compared with our new optical scheme. Simulations of the new scheme using the eye model of Navarro, suggest that the new optical geometry can overcome the limitations of the previous approach for in vivo measurements of glucose in a human eye.