gebhart/patrepeval huggingface dataset:
Identification of common polymorphisms in the coding sequence of the human MSH receptor (MCIR) with possible biological effects (1997)

The extension locus has been identified in many mammalian species as a gene that determines the relative amounts of eumelanin and phaeomelanin pigments in hair and skin. In at least three species, this locus has been demonstrated to encode the melanocyte-stimulating hormone receptor (MC1-R), and functionally variant alleles have been demonstrated to cause a broad range of pigmentation phenotypes. To test for MC1-R allelic variation in man, genomic DNA was extracted from skin samples collected from patients with different skin types (I-VI), and eye and hair color. A PCR-based approach was used to amplify the full-length coding sequence of the MC1-R and the resulting products were sequenced. Two polymorphic alleles were identified with single point mutations in the coding sequence: a valine-to-methionine substitution at position 92 (V92M), and an aspartic acid-to-glutamic acid substitution at position 84 (D84E). RFLP analysis demonstrated the presence of the V92M allele in 4 out of 60 (6.6%) of individuals examined, predominantly those with blue eyes and blond hair. This polymorphism was found in both heterozygous and homozygous states in individuals with type I skin. The D84E allele was found in one individual with skin type I; this person also has the V92 M allele and thus is a compound heterozygote.
Bankruptcy Prediction Using Multiple Classifier System with Mutual Information Feature Grouping (2006)

The prediction of bankruptcy helps an organization to choose its business partners and banks to approve or reject loan requests. So, it is essential to predict the bankruptcy of an organization. In this work, a multiple classifier system which combines decision from several different base classifiers trained using different samples with different input features is proposed for the bankruptcy prediction. The input features for each base classifier are selected using its mutual information with respect to the output. Experimental results of the proposed method using a real bankruptcy dataset from Compustat Global Dataset are promising.
Movement analysis of Parkinsonians (2002)

Neurologists need a rating scale for their patients that help in setting the medication and treatment. In the daily routine neurologists evaluate the movement of Parkinsonians. Different devices aid the objective evaluation. The authors tested 13 Parkinsonians, 36 young healthy and 13 senior healthy subjects using marker-based motion analysis. The reproducibility of the movement test is varying, even healthy subjects exhibit substantial differences while performing movement patterns. However, for most tested persons it is possible to define a subset of movement patterns so that the related parameters were relatively stable for that person. The "personalisation" of the test is in harmony with the fact that the manifestation of the disease is unique for each patient.
Molecular homology among members of the <i>R</i> gene family in maize (1993)

The R gene family determines the timing, distribution and amount of anthocyanin pigmentation in maize. This family comprises a set of regulatory genes, consisting of a cluster of several elements at the R locus, on chromosome 10, the Lc and Sn gene lying about two units R distal and B on chromosome 2. Each gene determines a tissue-specific pigmentation of different parts of the seed and plant. The proposed duplicated function of R, Sn, Lc and B loci is reflected in cDNA sequence similarity. In this paper an extensive analysis of the predicted proteins of the R, Sn, Lc and B genes together with a search for putative sites of post-translational modification is reported. A comparison with the prosite database discloses several N-glycosylation and phosphorylation sites, as well as the basic Helix-Loop-Helix (HLH) domain of transcriptional activators. Sn, Lc, and R-S show a high conservation of these sites, while B is more divergent. Analysis of the 5' leader of mRNA sequences discloses the presence of five ATG triplets with two upstream open reading frames (uORFs) of 38 and 15 amino acids and a loop structure indicating a possible mechanism of control at the translational level. It is conceivable that possible mechanisms acting at the translational and post-translational level could modulate the expression and the activation of these transcription factors. Northern analysis of various tissues of different R alleles highlights a strict correlation between pigment accumulation in different tissues and the expression of the regulatory and structural genes suggesting that the pattern of pigmentation relies on a mechanism of differential expression of the members of the R family. Analysis of the Sn promoter discloses the presence of several sequences resembling binding sites of known transcription factors (as GAGA and GT) that might be responsible for the spatial and light-induced expression of this gene. Two regions include a short sequence homologous to the consensus binding site of the B-HLH domain suggesting a self-regulatory control of the Sn gene.
A novel method for medical implant in-body localization (2012)

Wireless communication medical implants are gaining an important role in healthcare systems by controlling and transmitting the vital information of the patients. Recently, Wireless Capsule Endoscopy (WCE) has become a popular method to visualize and diagnose the human gastrointestinal (GI) tract. Estimating the exact location of the capsule when each image is taken is a very critical issue in capsule endoscopy. Most of the common capsule localization methods are based on estimating one or more location-dependent signal parameters like TOA or RSS. However, some unique challenges exist for in-body localization due to the complex nature within the human body. In this paper, we propose a novel one-stage localization method based on spatial sparsity in 3D space. In this method, we directly estimate the location of the capsule (as the emitter) without going through the intermediate stage of TOA or signal strength estimation. We evaluate the performance of the proposed method using Monte Carlo simulation with an RF signal following the allowable power and bandwidth ranges according to the standards. The results show that the proposed method is very effective and accurate even in massive multipath and shadowing conditions.
Cast Shadow Removal Using Time and Exposure Varying Images (2009)

Shadows are the natural accomplice of objects. As such, they have affected various algorithms dealing with image segmentation, object tracking and recognition. A lot of research has been focused on removing shadows from images while preserving the information available in the shadow region. In this paper, we present a simple yet robust algorithm for cast shadow removal utilizing images taken at different times with different exposures. While different exposures allow good recovery of shadow regions, the time-varying feature is used to suppress the shadow edges.
Molecular Anatomy of Tyrosinase and its Related Proteins: Beyond the Histidine‐Bound Metal Catalytic Center (2002)

The structure of tyrosinase (Tyr) is reviewed from a double point of view. On the one hand, by comparison of all Tyr found throughout nature, from prokaryotic organisms to mammals and on the other, by comparison with the tyrosinase related proteins (Tyrps) that appeared late in evolution, and are only found in higher animals. Their structures are reviewed as a whole rather than focused on the histidine (His)-bound metal active site, which is the part of the molecule common to all these proteins. The availability of crystallographic data of hemocyanins and recently of sweet potato catechol oxidase has improved the model of the three-dimensional structure of the Tyr family. Accordingly, Tyr has a higher structural disorder than hemocyanins, particularly at the CuA site. The active site seems to be characterized by the formation of a hydrophobic pocket with a number of conserved aromatic residues sited close to the well-known His. Other regions specific of the mammalian enzymes, such as the cytosolic C-terminal tail, the cysteine clusters, and the N-glycosylation sequons, are also discussed. The complete understanding of the Tyr copper-binding domain and the characterization of the residues determinant of the relative substrate affinities of the Tyrps will improve the design of targeted mutagenesis experiments to understand the different catalytic capabilities of Tyr and Tyrps. This may assist future aims, from the design of more efficient bacterial Tyr for biotechnological applications to the design of inhibitors of undesirable fruit browning in vegetables or of color skin modulators in animals.
Cognitive control of fixation duration in visual search: The role of extrafoveal processing (2014)

Participants' eye movements were monitored in two visual search experiments that manipulated target-distractor similarity (high vs. low) as well as the availability of distractors for extrafoveal processing (Free-Viewing vs. No-Preview). The influence of the target-distractor similarity by preview manipulation on the distributions of first fixation and second fixation duration was examined by using a survival analysis technique which provided precise estimates of the timing of the first discernible influence of target-distractor similarity on fixation duration. We found a significant influence of target-distractor similarity on first fixation duration in normal visual search (Free Viewing) as early as 26–28 ms from the start of fixation. In contrast, the influence of target-distractor similarity occurred much later (199–233 ms) in the No-Preview condition. The present study also documented robust and fast acting extrafoveal and foveal preview effects. Implications for models of eye-movement control and visual search are discussed.
Real-time detection of central carbon metabolism in living<i>Escherichia coli</i>and its response to perturbations (2011)

The direct tracking of cellular reactions in vivo has been facilitated with recent technologies that strongly enhance NMR signals in substrates of interest. This methodology can be used to assay intracellular reactions that occur within seconds to few minutes, as the NMR signal enhancement typically fades on this time scale. Here, we show that the enhancement of (13)C nuclear spin polarization in deuterated glucose allows to directly follow the flux of glucose signal through rather extended reaction networks of central carbon metabolism in living Escherichia coli. Alterations in central carbon metabolism depending on the growth phase or upon chemical perturbations are visualized with minimal data processing by instantaneous observation of cellular reactions.
Transmission characteristics of a coaxial optical fiber line (1993)

A coaxial optical fiber line is proposed and studied as a long-distance transmission medium. The radial structure consists of a core surrounded by two clads. The inner clad has higher refractive index than the core and the outer clad. Guided modes are thus characterized by a concentrated field in the inner clad and evanescent fields in both the core and the outer clad. Using a rigorous modal analysis, characteristic curves for a monomode coaxial fiber line are presented. It is shown that the zero-dispersion wavelength can be placed at any desired value by proper choice of the refractive index contrast and the fiber dimensions. The proposed coaxial line compares well with the known W-profiled line with respect to ease of manufacture and dispersion characteristics.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Obituary: A Life Of Dedication A.G.Brighton (1900-1988) and The Sedgwick Museum, Cambridge (1989)

A. G. Brighton, curator of the Sedgwick Museum from 1931 to 1968, died on 9 April 1988 at the age of 87. A short obituary appeared in The Times on 12 April. In vie-w of the decisive part played by Brighton in the development of one of our major geological museums and his role in the evolution of modern standards of specimen documentation, it seems important to give a fuller account of his life's work. For this, nowhere is more appropriate than the Geological Curator because Brighton was the epitome of the dedicated, professional, geological curator.
Correlation-based query relaxation for example-based dialog modeling (2009)

Query relaxation refers to the process of reducing the number of constraints on a query if it returns no result when searching a database. This is an important process to enable extraction of an appropriate number of query results because queries that are too strictly constrained may return no result, whereas queries that are too loosely constrained may return too many results. This paper proposes an automated method of correlation-based query relaxation (CBQR) to select an appropriate constraint subset. The example-based dialog modeling framework was used to validate our algorithm. Preliminary results show that the proposed method facilitates the automation of query relaxation. We believe that the CBQR algorithm effectively relaxes constraints on failed queries to return more dialog examples.
Composite flexural-mode resonator with controllable turnover temperature (2007)

This paper presents the design and characterization of a flexural mode composite resonator whose inherent frequency sensitivity to temperature changes is reduced. The resonator is an encapsulated single anchor, double ended tuning fork (DETF) composed of single crystal silicon with a silicon dioxide coating. The frequency variation with temperature of the composite resonator exhibits a turnover temperature at which the frequency does not change with temperature. The turnover temperature can be controlled by varying the thickness of the silicon dioxide. This useful characteristic could be combined with active temperature compensation for more precise timing applications. The fabricated devices show a temperature sensitivity that is comparable to a quartz crystal tuning fork resonator.
Cellular Pathology of Atherosclerosis (2005)

Although platelets do not ordinarily bind to endothelial cells (EC), pathological interactions between platelets and arterial EC may contribute to the propagation of atheroma. Previously, in an in vitro model of atherogenesis, where leukocyte adhesion to EC cocultured with smooth muscle cells was greatly enhanced, we also observed attachment of platelets to the EC layer. Developing this system to specifically model platelet adhesion, we show that EC cocultured with smooth muscle cells can bind platelets in a process that is dependent on EC activation by tumor necrosis factor (TNF)-alpha and transforming growth factor (TGF)-beta1. Recapitulating the model using EC alone, we found that a combination of TGF-beta1 and TNF-alpha promoted high levels of platelet adhesion compared with either agent used in isolation. Platelet adhesion was inhibited by antibodies against GPIb-IX-V or alpha(IIb)beta3 integrin, indicating that both receptors are required for stable adhesion. Platelet activation during interaction with the EC was also essential, as treatment with prostacyclin or theophylline abolished stable adhesion. Confocal microscopy of the surface of EC activated with TNF-alpha and TGF-beta1 revealed an extensive matrix of von Willebrand factor that was able to support the adhesion of flowing platelets at wall shear rates below 400 s(-1). Thus, we have demonstrated a novel route of EC activation which is relevant to the atherosclerotic microenvironment. EC activated in this manner would therefore be capable of recruiting platelets in the low-shear environments that commonly exist at points of atheroma formation.
Application of Rapid Isothermal Annealing to Shallow p‐n Junctions via  BF 2 Implants (1985)

Results of rapid isothermal annealing (RIA) experiments are reported. Wafer warpage, temperature homogeneity, slip lines, and reproducibility of temperature cycles have been investigated. Sheet resistance measurements were carried out for RIA (1000°C, 10s) and for conventional furnace annealing for 30 and 50 keV implants, the ion dose varying between . Spreading resistance measurements revealed that, in the case of RIA, junctions as shallow as 0.17, 0.19, and 0.21 μm have been obtained, respectively, for ion doses of at a energy of 50 keV. Junction depths obtained through RIA are a factor of 3–4 lower than those obtained by conventional annealing; dopant redistribution is negligible. Boron and fluorine atom concentration profiles have been equally investigated by secondary ion mass spectrometry (SIMS).
Improved method for the routine identification of toxigenic Escherichia coli by DNA amplification of a conserved region of the heat-labile toxin A subunit (1991)

This report describes a DNA amplification procedure for routine identification of heat-labile-toxin-producing Escherichia coli. Two oligonucleotide primers were used in a polymerase chain reaction procedure to amplify a highly conserved region of the A subunit of the heat-labile enterotoxin gene. Amplifications were done directly on E. coli colonies from plates when Salmonella, Shigella, or parasite infections were excluded as agents of the severe diarrhea in the patients. The conditions for the polymerase chain reaction method were empirically determined, and the procedure is inexpensive, sensitive, and specific. Positive results can be obtained over a wide variation in bacterial numbers, with no inhibition of Thermus aquaticus DNA polymerase. Detection of the amplified product can be done by agarose gel electrophoresis, which is specific and sensitive enough for routine diagnosis of this pathogen in clinical isolates. If greater sensitivity and specificity are required, hybridization with 32P- or alkaline phosphatase-labeled oligonucleotide probes can be used. Our results suggest that heat-labile-toxin-producing E. coli is responsible for about 9% of nondiagnosed diarrhea cases in Tygerberg Hospital, Tygerberg, Republic of South Africa.
Visual place recognition for persistent robot navigation in changing environments (2014)

This thesis demonstrates that robots can learn about how the world changes, and can use this information to recognise where they are, even when the appearance of the environment has changed a great deal. The ability to localise in highly dynamic environments using vision only is a key tool for achieving long-term, autonomous navigation in unstructured outdoor environments. The proposed learning algorithms are designed to be unsupervised, and can be generated by the robot online in response to its observations of the world, without requiring information from a human operator or other external source.
Thiazolium-dependent catalytic antibodies produced using a covalent modification strategy† (1999)

A thiazolium cofactor was introduced at a unique active site residue within antibodies that were generated by reactive immunization; the modified antibodies catalyzed a new cofactor-dependent reaction.
RADAR Dose Estimate Report: A Compendium of Radiopharmaceutical Dose Estimates Based on OLINDA/EXM Version 2.0 (2017)

A compendium of about 100 radiopharmaceuticals, based on the OLINDA/EXM version 2.0 software, is presented. A new generation of voxel-based, realistic human computational phantoms developed by the RADAR committee of the Society of Nuclear Medicine and Molecular Imaging, based on 2007 recommendations of the International Commission on Radiological Protection, was used to develop the dose estimates, and the most recent biokinetic models were used as well. These estimates will be made available in electronic form and can be modified and updated as models are changed and as new radiopharmaceuticals are added.
Nonlinear Chemical Dynamics:  Oscillations, Patterns, and Chaos (1996)

Chemical reactions with nonlinear kinetic behavior can give rise to a remarkable set of spatiotemporal phenomena. These include periodic and chaotic changes in concentration, traveling waves of chemical reactivity, and stationary spatial (Turing) patterns. Although chemists were initially skeptical of the existence and the relevance of these phenomena, much progress has been made in the past two decades in characterizing, designing, modeling, and understanding them. Several nonlinear dynamical phenomena in chemical systems provide simpler analogues of behaviors found in biological systems.
Asymmetric Syntheses of the Homalium Alkaloids (−)-(<i>S</i>,<i>S</i>)-Homaline and (−)-(<i>R</i>,<i>R</i>)-Hopromine (2012)

The highly diastereoselective conjugate additions of the novel lithium amide reagents lithium (R)-N-(3-chloropropyl)-N-(α-methylbenzyl)amide and lithium (R)-N-(3-chloropropyl)-N-(α-methyl-p-methoxybenzyl)amide to α,β-unsaturated esters were used as the key steps in syntheses of the homalium alkaloids (-)-(S,S)-homaline and (-)-(R,R)-hopromine. The asymmetric synthesis of (-)-(S,S)-homaline was achieved in 8 steps and 18% overall yield, and the asymmetric synthesis of (-)-(R,R)-hopromine was achieved in 9 steps and 23% overall yield, from commercially available starting materials in each case. These syntheses therefore represent by far the most efficient total asymmetric syntheses of these alkaloids reported to date. A sample of the (4'R,4''S)-epimer of hopromine was also produced using this approach, which provided the first unambiguous confirmation of its absolute configuration and therefore that of natural (-)-(R,R)-hopromine.
Pattern-Affinitive Propagation across Depth, Surface Normal and Semantic Segmentation (2019)

In this paper, we propose a novel Pattern-Affinitive Propagation (PAP) framework to jointly predict depth, surface normal and semantic segmentation. The motivation behind it comes from the statistic observation that pattern-affinitive pairs recur much frequently across different tasks as well as within a task. Thus, we can conduct two types of propagations, cross-task propagation and task-specific propagation, to adaptively diffuse those similar patterns. The former integrates cross-task affinity patterns to adapt to each task therein through the calculation on non-local relationships. Next the latter performs an iterative diffusion in the feature space so that the cross-task affinity patterns can be widely-spread within the task. Accordingly, the learning of each task can be regularized and boosted by the complementary task-level affinities. Extensive experiments demonstrate the effectiveness and the superiority of our method on the joint three tasks. Meanwhile, we achieve the state-of-the-art or competitive results on the three related datasets, NYUD-v2, SUN-RGBD and KITTI.