gebhart/patrepeval huggingface dataset:
On the performance of high-rate TPC/SPC codes and LDPC codes over partial response channels (2002)

This paper evaluates two-dimensional turbo product codes based on single-parity check codes (TPC/SPC) and low-density parity check (LDPC) codes for use in digital magnetic recording systems. It is first shown that the combination of a TPC/SPC code and a precoded partial response (PR) channel results in a good distance spectrum due to the interleaving gain. Then, density evolution is used to compute the thresholds for TPC/SPC codes and LDPC codes over PR channels. Analysis shows that TPC/SPC codes have a performance close to that of LDPC codes for large codeword lengths. Simulation results for practical block lengths show that TPC/SPC codes perform as well as LDPC codes in terms of bit error rate, but possess better burst error statistics which is important in the presence of an outer Reed-Solomon code. Further, the encoding complexity of TPC/SPC codes is only linear in the codeword length and the generator matrix does not have to be stored explicitly. Based on. the results in the paper and these advantages, TPC/SPC codes seem like a viable alternative to LDPC codes.
Designing CMOS/molecular memories while considering device parameter variations (2007)

In recent years, many advances have been made in the development of molecular scale devices. Experimental data shows that these devices have potential for use in both memory and logic. This article describes the challenges faced in building crossbar array-based molecular memory and develops a methodology to optimize molecular scale architectures based on experimental device data taken at room temperature. In particular, issues in reading and writing such as memory using CMOS are discussed, and a solution is introduced for easily reading device conductivity states (typically characterized by very small currents). Additionally, a metric is derived to determine the voltages for writing to the crossbar array. The proposed memory design is also simulated with consideration to device parameter variations. Thus, the results presented here shed light on important design choices to be made at multiple abstraction levels, from devices to architectures. Simulation results, incorporating experimental device data, are presented using Cadence Spectre.
Spin Transfer Torque driven dynamics of the synthetic antiferromagnetic reference layer of perpendicular MRAM devices (2017)

Spin Transfer Torque Magnetic Random Access Memories (STT-MRAM) are based on Magnetic Tunnel Junctions (MTJs) made out of two ferromagnetic electrodes separated by a MgO tunnel barrier. Here we report experimental data of the STT-induced dynamics of a SAF RL in perpendicularly magnetized STT-MRAM devices. We show evidence of different RL dynamical modes depending on the SAF properties. We also develop an analytical model based on a 3-layer macrospin model, which allows us to reproduce the main feature of the experimental data and to derive a phase diagram of the RL dynamics. Experimental data of RL dynamics are obtained using time-resolved resistance measurements of individual MRAM devices.
Glutamic acid-141: a heme ‘bodyguard’ in anionic tobacco peroxidase (2007)

The role of the conserved glutamic acid residue in anionic plant peroxidases with regard to substrate specificity and stability was examined. A Glu141Phe substitution was generated in tobacco anionic peroxidase (TOP) to mimic neutral plant peroxidases such as horseradish peroxidase C (HRP C). The newly constructed enzyme was compared to wild-type recombinant TOP and HRP C expressed in E. coli. The Glu141Phe substitution supports heme entrapment during the refolding procedure and increases the reactivation yield to 30% compared to 7% for wild-type TOP. The mutation reduces the activity towards ABTS, o-phenylenediamine, guaiacol and ferrocyanide to 50% of the wild-type activity. No changes are observed with respect to activity for the lignin precursor substrates, coumaric and ferulic acid. The Glu141Phe mutation destabilizes the enzyme upon storage and against radical inactivation, mimicking inactivation in the reaction course. Structural alignment shows that Glu141 in TOP is likely to be hydrogen-bonded to Gln149, similar to the Glu143-Lys151 bond in Arabidopsis A2 peroxidase. Supposedly, the Glu141-Gln149 bond provides TOP with two different modes of stabilization: (1) it prevents heme dissociation, i.e., it 'guards' heme inside the active center; and (2) it constitutes a shield to protect the active center from solvent-derived radicals.
Solution conformations of some azetidine cyclic peptides (1978)

Abstract The 1 H‐nmr spectra (270 MHz) of cyclic di‐ and tri‐ L ‐azatidine‐2‐carboxylic acid [cy‐clo( L ‐Aze) 2 and cyclo( L ‐Aze) 3 ] were determined in CDCl 3 and D 2 O and computer simulated. The spectral results were compared with those obtained with cyclo ( L ‐Pro) 2 and cyclo ( L, ‐Pro) 3 . In CDCl 3 and D 2 O solution, the four membered ring of cyclo ( L ‐Aze) 2 is puckered with the α‐proton in a pseudo‐axial position, and the ϕ angle is smaller in absolute value than −60°, as found for cyclo ( L ‐Pro) 2, . The puckering of the four‐membered ring of cyclo( L, ‐Aze) 3 in CDCl 3 has the α‐proton in a pseudo–equatorial position and ϕ angle larger in absolute value than −60°, in agreement with cyclo( L ‐Pro) 3 . In D 2 O, cyclo( L ‐Aze) 3 was found to interconvert rapidly between different conformers. In the azetidine cyclic peptides studied, the range of values found for the ϕ angles was smaller than in the related proline cyclic peptides, indicating greater rigidity in the four‐membered ring.
Calculation of the Hydroplaning of a Deformable Smooth‐Shaped and Longitudinally‐Grooved Tire (1997)

Abstract The dynamic hydroplaning of a deformable automobile tire is calculated. The three‐dimensional flow around the tire is described by an efficient free surface model and the Navier‐Stokes equations. The effects of turbulence are modeled by the well‐known k,ε‐model . The deformation of the tire is calculated using a noncommercial finite element program, in which all components of the three‐dimensional tire are taken into account with their own mechanical and constitutive behavior. The deformation of the tire during stationary hydroplaning is found by an iterative solution procedure. The result of the calculation is the pressure distribution and the velocity field. The integration of the pressure distribution acting on the tire surface yields the lift and drag forces as well as lift and drag coefficients. The calculations are performed for a smooth‐shaped tire at speeds of 30, 60, and 90 km/h driving speed and an 8 mm high water film. The results are compared with those of the undeformable tire. The calculated pressure distribution on the pavement shows very good agreement with experimentally obtained data. At 90 km/h the model predicts that the water penetrates the contact area of the tire whereas the tire still has contact with the road in the shoulder area. This is also found in experiments. Further, calculations are performed for a deformable tire with three circumferential grooves. Here the influence of different water depths at a speed of 90 km/h is investigated. The groove depth of the tire is 8 mm whereas the water depth varies between 4, 8, and 12 mm. The calculations show the intrusion of a water wedge into the contact area. As in previous studies it is found that the tire deformation has a very strong influence on the resulting lift forces.
Mining Feature Models from Functional Requirements (2016)

Feature models (FMs) are widely used to describe software product lines (SPL). They specify common and variation points in the domain of the SPL. Because of their wide domain coverage, FM development requires extensive domain analysis and important domain expertise that is often hard to acquire. These development requirements motivated us to propose, in this paper, a top-down method that extracts automatically an FM from functional requirements of product variants. Besides its automation, its novelty stems from the use of semantic information mined through natural language processing techniques to extract potential features from each product variant. To account for name variations, our method harmonizes the names of the features extracted from the product variants by using a classification technique to group similar features. In addition, to determine the feature type, it uses the formal concept analysis technique to distinguish mandatory from optional features. Furthermore, to structure the FM, it uses a set of semantic criteria to determine the constraints among the features. The paper reports on a quantitative and a comparative evaluation of the method on existing FMs, and it examines the conformity of the generated FMs to the input functional requirements, based on experts' feedbacks.
Enhanced efflux of [3H]vinblastine from Chinese hamster ovary cells transfected with a full-length complementary DNA clone for the mdr1 gene. (1989)

Multidrug-resistant Chinese hamster ovary cell clones stably transfected with, and overexpressing, the mouse mdr1 complementary DNA clone along with drug-sensitive Chinese hamster ovary control cells were characterized for their capacities to accumulate and retain [3H]vinblastine. Multidrug-resistant mdr1 transfectants show a 3-4-fold decrease in [3H]vinblastine accumulation, compared to their drug-sensitive counterparts. After ATP depletion, this difference in [3H]vinblastine accumulation between mdr1 transfectants and control cells effectively disappears. This ATP-dependent decreased drug accumulation is paralleled in mdr1 transfectants by an enhanced capacity of these cells to extrude the drug in an ATP-dependent manner. In medium containing glucose and glutamine, the mdr1 transfectants release preloaded drug at a rate five times that of control, drug-sensitive cells. In ATP-depleted control and mdr1-transfected cells, there is little difference in the rate or extent of [3H]vinblastine release. The observation that the mdr1 transfectants show a decreased [3H]vinblastine accumulation and an increased vinblastine release, both of which are abolished when cellular ATP levels are reduced, provides a direct demonstration that the product of the transfected mdr1 gene is responsible for a mechanism controlling cellular drug levels in an ATP-dependent manner. However, attempts to establish competition for [3H]vinblastine transport by vincristine, daunomycin, and actinomycin D were only partly successful in mdr1 transfectants.
Neutrophil Maturity in Cancer (2019)

Neutrophils are implicated in almost every stage of oncogenesis and paradoxically display anti- and pro-tumor properties. Accumulating evidence indicates that neutrophils display diversity in their phenotype resulting from functional plasticity and/or changes to granulopoiesis. In cancer, neutrophils at a range of maturation stages can be identified in the blood and tissues (i.e., outside of their developmental niche). The functional capacity of neutrophils at different states of maturation is poorly understood resulting from challenges in their isolation, identification, and investigation. Thus, the impact of neutrophil maturity on cancer progression and therapy remains enigmatic. In this review, we discuss the identification, prevalence, and function of immature and mature neutrophils in cancer and the potential impact of this on tumor progression and cancer therapy.
Summary of Modeling and Simulation for NIST RoboCrane? Applications (1997)

The Intelligent Systems Division (ISD) at the National Institute of Standards and Technology has been using modeling and simulation and software for conceptual design and prototyping of advanced robotic cranes. RoboCrane ® concepts have been developed for various applications, such as military ISO-container handlers on land and sea, large-scale welding and gripping, and nuclear waste remediation. The capability to develop our models in an advanced solid modeler and convert them into moving, controlled designs is critical to achieve the level of confidence that is required before building a full-scale prototype. Although we do have scaledprototypes of some of our designs, the computer model, controlled with simulation programming and developed from imported solid models, offers a good way for sponsors to see the concepts and capabilities of the RoboCrane ® systems. This overview paper summarizes the efforts of ISD in developing the RoboCrane ® simulations and the important role simulation and modeling tools have within our projects. Keywords: simulation, computer-aided-design, solid modeling, graphic programming, conceptual design, robotic cranes, RoboCrane®, operator interface
Successful Stem Cell Therapy Using Umbilical Cord Blood-Derived Multipotent Stem Cells for Buerger's Disease and Ischemic Limb Disease Animal Model (2006)

Buerger's disease, also known as thromboangiitis obliterans, is a nonatherosclerotic, inflammatory, vasoocclusive disease. It is characterized pathologically as a panangiitis of medium and small blood vessels, including both arteries and adjacent veins, especially the distal extremities (the feet and the hands). There is no curative medication or surgery for this disease. In the present study, we transplanted human leukocyte antigen-matched human umbilical cord blood (UCB)-derived mesenchymal stem cells (MSCs) into four men with Buerger's disease who had already received medical treatment and surgical therapies. After the stem cell transplantation, ischemic rest pain suddenly disappeared from their affected extremities. The necrotic skin lesions were healed within 4 weeks. In the follow-up angiography, digital capillaries were increased in number and size. In addition, vascular resistance in the affected extremities, compared with the preoperative examination, was markedly decreased due to improvement of the peripheral circulation. Because an animal model of Buerger's disease is absent and also to understand human results, we transplanted human UCB-derived MSCs to athymic nude mice with hind limb ischemia by femoral artery ligation. Up to 60% of the hind limbs were salvaged in the femoral artery-ligated animals. By in situ hybridization, the human UCB-derived MSCs were detected in the arterial walls of the ischemic hind limb in the treated group. Therefore, it is suggested that human UCB-derived MSC transplantation may be a new and useful therapeutic armament for Buerger's disease and similar ischemic diseases.
Low‐dose ranitidine for the relief of heartburn (1999)

Ranitidine 75 mg provides prompt relief of heartburn that lasts for up to 12 h and has a safety profile comparable to that of placebo.
Detection and Characterization of Human Group C Rotaviruses in Bangladesh (2005)

Group C rotaviruses were detected by reverse transcription-PCR in 14 (2.3%) of 611 group A rotavirus-negative stool specimens from the patients admitted to the International Centre for Diarrhoeal Disease Research, Bangladesh hospital, Dhaka, Bangladesh, during July to December 2003. The low rate of detection suggested that infection with group C rotaviruses was an uncommon cause of hospitalization due to gastroenteritis. In addition, coinfections with pathogenic enteric bacteria were frequently observed in group C rotavirus-infected patients. Nucleotide sequence comparison of the VP4, VP6, and VP7 genes revealed that the Bangladeshi group C rotaviruses were most similar to Nigerian group C rotavirus strains. Phylogenetic analysis suggested that all human group C rotaviruses, including the strains isolated in our study, clustered in a monophyletic branch, which was distantly related to the branch comprised of animal group C rotaviruses.
Osmium‐Mediated Transformation of 4‐Thiouridine to Cytidine as Key To Study RNA Dynamics by Sequencing (2017)

Abstract To understand the functional roles of RNA in the cell, it is essential to elucidate the dynamics of their production, processing and decay. A recent method for assessing mRNA dynamics is metabolic labeling with 4‐thiouridine (4sU), followed by thio‐selective attachment of affinity tags. Detection of labeled transcripts by affinity purification and hybridization to microarrays or by deep sequencing then reveals RNA expression levels. Here, we present a novel sequencing method (TUC‐seq) that eliminates affinity purification and allows for direct assessment of 4sU‐labeled RNA. It employs an OsO 4 ‐mediated transformation to convert 4sU into cytosine. We exemplify the utility of the new method for verification of endogenous 4sU in tRNAs and for the detection of pulse‐labeled mRNA of seven selected genes in mammalian cells to determine the relative abundance of the new transcripts. The results prove TUC‐seq as a straight‐forward and highly versatile method for studies of cellular RNA dynamics.
The P450 Gene Superfamily: Recommended Nomenclature (1987)

A nomenclature for the P450 gene superfamily is proposed based on evolution. Recommendations include Roman numerals for distinct gene families, capital letters for subfamilies, and Arabic numerals for individual genes. An updating of this list, which presently includes 65 entries, will be required every 1-2 years. Assignment of orthologous genes is presently uncertain in some cases--between widely diverged species and especially in the P450II family due to the large number of genes. As more is known, it might become necessary to change some gene assignments that are based on our present knowledge.
Invariant Pattern Recognition Using Fourieir-Mellin Descriptors Of Images Spectra (1987)

Geometrical moments are attractive for image-distortion invariant pattern recognition. Orientation scale and position of the image are readily determined by its moments. Rotation-, scale- and shift-invariant features can also be extracted using moment invariants. Some optical methods for generating image moments have been proposed and a single-chip VLSI implementation for generating real-time 2-dimensional image moments has recently been achieved. The applications of the moment method will be further expanded.
Composite bolometers for submillimeter wavelengths (1978)

The fabrication and optimization of composite submillimeter wave bolometers with metal film absorbing elements and doped Ge thermometers are described. Performance characteristics are given for 4 x 4-mm bolometers designed for operation at both (4)He and (3)He temperatures. The performance expected from such bolometers when they are optimized for various values of background loading is calculated. Current dependent noise, which can arise from any of several sources, is included in the analysis. This can make it impossible to reach the background fluctuation noise limit. Feed structures for these bolometers which employ Winston light concentrators are described.
Properties of Opiate-Receptor Binding in Rat Brain (1973)

[(3)H]Naloxone, a potent opiate antagonist, binds stereospecifically to opiate-receptor sites in rat-brain tissue. The binding is time, temperature, and pH dependent and saturable with respect to [(3)H]naloxone and tissue concentration. The [(3)H]naloxone-receptor complex formation is bimolecular with a dissociation constant of 20 nM. 15 Opiate agonists and antagonists compete for the same receptors, whose density is 30 pmol/g. Potencies of opiates and their antagonists in displacing [(3)H]naloxone binding parallel their pharmacological potencies.
DEM Generation and Building Detection from Lidar Data (2005)

This article explains the technique of DEM generation and building detection from Lidar (Light Detection and Ranging) data. Compared with traditional photogrammetry, lidar has advantages in measuring surface in terms of accuracy and density, automation, and fast delivery time. The author presents lidar as a companion technology for traditional photogrammetry. The direct product that can be derived from lidar data is the DSM (Digital Surface Model), which depicts the topography of the earth’s surface, including objects above the terrain. Further processing can be carried out to generate DEM (Digital Terrain Model) and object models like buildings, which is very useful information in telecommunication, city planning, flood control, and tourism. The author proposes a new method to extract ground points for DEM generation and to detect points belonging to buildings; a further strategy for boundary regularization is also proposed. The author concludes that these new methods for DEM generation and building detection are very efficient and effective, particularly in urban and suburban areas.
Stem cells as biological heart pacemakers (2005)

Abnormalities in the pacemaker function of the heart or in cardiac impulse conduction may result in the appearance of a slow heart rate, traditionally requiring the implantation of a permanent electronic pacemaker. In recent years, a number of experimental approaches have been developed in an attempt to generate biological alternatives to implantable electronic devices. These strategies include, initially, a number of gene therapy approaches (aiming to manipulate the expression of ionic currents or their modulators and thereby convert quiescent cardiomyocytes into pacemaking cells) and, more recently, the use of cell therapy and tissue engineering. The latter approach explored the possibility of grafting pacemaking cells, either derived directly during the differentiation of human embryonic stem cells or engineered from mesenchymal stem cells, into the myocardium. This review will describe each of these approaches, focusing mainly on the stem cell strategies, their possible advantages and shortcomings, as well as the avenues required to make biological pacemaking a clinical reality.
Clinical implementation of dose-volume histogram predictions for organs-at-risk in IMRT planning (2014)

True quality control (QC) of the planning process requires quantitative assessments of treatment plan quality itself, and QC in IMRT has been stymied by intra-patient anatomical variability and inherently complex three-dimensional dose distributions. In this work we describe the development of an automated system to reduce clinical IMRT planning variability and improve plan quality using mathematical models that predict achievable OAR DVHs based on individual patient anatomy. These models rely on the correlation of expected dose to the minimum distance from a voxel to the PTV surface, whereby a three-parameter probability distribution function (PDF) was used to model iso-distance OAR subvolume dose distributions. DVH models were obtained by fitting the evolution of the PDF with distance. Initial validation on clinical cohorts of 40 prostate and 24 head-and-neck plans demonstrated highly accurate model-based predictions for achievable DVHs in rectum, bladder, and parotid glands. By quantifying the integrated difference between candidate DVHs and predicted DVHs, the models correctly identified plans with under-spared OARs, validated by replanning all cases and correlating any realized improvements against the predicted gains. Clinical implementation of these predictive models was demonstrated in the PINNACLE treatment planning system by use of existing margin expansion utilities and the scripting functionality inherent to the system. To maintain independence from specific planning software, a system was developed in MATLAB to directly process DICOM-RT data. Both model training and patient-specific analyses were demonstrated with significant computational accelerations from parallelization.
Treatment of Cystic Acne with Gamma Globulin (1961)

Gamma globulin seems to offer a valuable adjunct in the treatment of stubborn instances of cystic acne.