gebhart/patrepeval huggingface dataset:
Antisense transcripts and protein binding motifs within the Wilms tumour (WT1) locus. (1994)

Transcription of the WT1 locus is restricted, both temporally and spatially, to a subset of epithelial cells in mammalian kidneys and gonads. WT1, one of the two divergent transcripts mapping to this locus encodes a zinc finger protein that is likely a transcriptional regulator. The other transcript, WIT1, encodes a product of unknown function that is subject to alternate splicing in the region immediately 5' of the WT1 gene. Analysis of the 5' end of this locus further revealed the presence of multiple transcriptional start sites for both genes, such that some of the WIT1 transcripts are encoded by the antisense strand of the first exon of WT1. The genomic region surrounding the transcriptional start sites appears to constitute part of a bi-directional promoter based on the ability of a DNA fragment derived from this region to direct expression of a chimeric CAT gene construct in transient transfection assays. Discrete sequences within the region are capable of interaction in vitro with nuclear extracts derived from a variety of rat and mouse tissues. Interestingly, recombinant WT1, representing the product of zinc finger region of the most abundant of the four alternatively spliced transcripts, is also capable of binding to sequences within this region.
Artificial Neural Networks in Medical Images for Diagnosis Heart Valve Diseases (2013)

Neural networks are currently a hot research area in medicine. Medical image recognition algorithms have been widely applied to help with the diagnosis of various diseases more accurately. This paper presents an image processing-based artificial neural network for the diagnosis of heart valve diseases. The goal of the paper is to implement image processing techniques by extracting texture features from medical echocardiography images, combining intensity histogram features and Gray Level Cooccurrence Matrix (GLCM) features, then developing an artificial neural network for automatic classification based on back-propagation algorithm to classify heart valve diseases more accurately. The proposed method performance was evaluated in terms of precision, recall and accuracy. The experimental results confirm the efficiency of the proposed method that provides good classification efficiency.
Demonstration of All-Optical Divider Circuit Using SOA-MZI-Type xor Gate and Feedback Loop for Forward Error Detection (2011)

We investigated the feasibility of using an optical divider circuit with a semiconductor optical amplifier Mach-Zehnder interferometer (SOA-MZI)-based exclusive or (XOR) gate for an all-optical forward error detection and correction scheme with a cyclic code. We employed a conventional cyclic code scheme: the same divider circuit acts as both encoder and decoder with a given generator polynomial. The divider circuit consists of cascaded XOR circuits and feedback lines. Therefore, the performance of the XOR circuit is one of the key factors for realizing an all-optical scheme. We numerically investigated the operation performance of the SOA-MZI-based all-optical XOR gate. Dynamic operation was simulated using rate equations via the transfer matrix method. The XOR function was also investigated experimentally. The eye diagram obtained from the simulation at a bit rate of 10 Gb/s showed good qualitative agreement with experimental results. Additionally, we confirmed that the optimal condition for a high quality factor (Q-factor) is obtained with equal power for each signal. Next, we demonstrated all-optical divider processing with the SOA-MZI-based XOR circuit and a feedback line that forms the generator polynomial <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</i> + 1. The preliminary results for division operation could be verified.
Electrostatics and electrical transport in semiconductor nanowire Schottky diodes (2012)

The electrostatics and electrical transport characteristics in semiconductor nanowire Schottky diodes are studied using three-dimensional finite-element simulations. From the simulations, the dependences of the depletion region width on the bias and the doping level are found to deviate significantly from the relations in the bulk Schottky model, indicating different electrostatic properties in nanowire Schottky junctions. Furthermore, simulations of the current-voltage relation, which is corroborated by experimental measurements, demonstrate that the standard analytical model is not sufficient to describe current-voltage characteristics in nanowire Schottky diodes. An important implication is that the commonly used analytical model is not valid for extracting the ideality factor and the Schottky barrier height. These findings suggest that numerical simulations are critical to evaluating nanoscale device performance and guiding device development efforts.
Synthetic approaches to versatile hemoprotein model compounds built from porphyrins and peptides (1982)

Several strategies for the preparation of mono- and bi-functional porphyrins (amino and carboxylate) to which oligopeptides can be attached have been investigated. A porphyrinyl amino-acid derivative has been synthesised by coupling a porphyrin monopropionate with phenylalanine methyl ester. Routes to pyrroles bearing butoxycarbonylaminoethyl side-chains via Curtius-type degradations, are described, and their potential for elaboration into porphyrins is discussed. The most promising bifunctional porphyrin with differentially protected amino and carboxylate side-chains was found to be the butoxycarbonylhydrazido methyl ester derivative of mesoporphyrin-II.
Connecting mirror neurons and forward models (2003)

Two recent developments in motor neuroscience are promising the extension of theoretical concepts from motor control towards cognitive processes, including human social interactions and understanding the intentions of others. The first of these is the discovery of what are now called mirror neurons, which code for both observed and executed actions. The second is the concept of internal models, and in particular recent proposals that forward and inverse models operate in paired modules. These two ideas will be briefly introduced, and a recent suggestion linking between the two processes of mirroring and modelling will be described which may underlie our abilities for imitating actions, for cooperation between two actors, and possibly for communication via gesture and language.
Autophagy Is Pro-Senescence When Seen in Close-Up, but Anti-Senescence in Long-Shot (2017)

When mammalian cells and animals face a variety of internal or external stresses, they need to make homeostatic changes so as to cope with various stresses. To this end, mammalian cells are equipped with two critical stress responses, autophagy and cellular senescence. Autophagy and cellular senescence share a number of stimuli including telomere shortening, DNA damage, oncogenic stress and oxidative stress, suggesting their intimate relationship. Autophagy is originally thought to suppress cellular senescence by removing damaged macromolecules or organelles, yet recent studies also indicated that autophagy promotes cellular senescence by facilitating the synthesis of senescence-associated secretory proteins. These seemingly opposite roles of autophagy may reflect a complex picture of autophagic regulation on cellular senescence, including different types of autophagy or a unique spatiotemporal activation of autophagy. Thus, a better understanding of autophagy process will lead us to not only elucidate the conundrum how autophagy plays dual roles in the regulation of cellular senescence but also helps the development of new therapeutic strategies for many human diseases associated with cellular senescence. We address the pro-senescence and anti-senescence roles of autophagy while focusing on the potential mechanistic aspects of this complex relationship between autophagy and cellular senescence.
Acetaminophen‐induced acute liver failure (2005)

Severe acetaminophen hepatotoxicity frequently leads to acute liver failure (ALF). We determined the incidence, risk factors, and outcomes of acetaminophen-induced ALF at 22 tertiary care centers in the United States. Detailed prospective data were gathered on 662 consecutive patients over a 6-year period fulfilling standard criteria for ALF (coagulopathy and encephalopathy), from which 275 (42%) were determined to result from acetaminophen liver injury. The annual percentage of acetaminophen-related ALF rose during the study from 28% in 1998 to 51% in 2003. Median dose ingested was 24 g (equivalent to 48 extra-strength tablets). Unintentional overdoses accounted for 131 (48%) cases, intentional (suicide attempts) 122 (44%), and 22 (8%) were of unknown intent. In the unintentional group, 38% took two or more acetaminophen preparations simultaneously, and 63% used narcotic-containing compounds. Eighty-one percent of unintentional patients reported taking acetaminophen and/or other analgesics for acute or chronic pain syndromes. Overall, 178 subjects (65%) survived, 74 (27%) died without transplantation, and 23 subjects (8%) underwent liver transplantation; 71% were alive at 3 weeks. Transplant-free survival rate and rate of liver transplantation were similar between intentional and unintentional groups. In conclusion, acetaminophen hepatotoxicity far exceeds other causes of acute liver failure in the United States. Susceptible patients have concomitant depression, chronic pain, alcohol or narcotic use, and/or take several preparations simultaneously. Education of patients, physicians, and pharmacies to limit high-risk use settings is recommended.
Intraputaminal Infusion of Nerve Growth Factor to Support Adrenal Medullary Autografts in Parkinson's Disease (1991)

Experimental studies in rodents show that beta-nerve growth factor can increase the survival, neurite outgrowth, and functional effect of grafts of adrenal chromaffin cells to the basal ganglia. We, therefore, have begun to investigate whether treatment with nerve growth factor might also increase the functional effect of autografts of adrenal medullary tissue in patients with Parkinson's disease. Previous studies have shown that stereotactic implantation of adrenal tissue pieces produces a transient functional improvement that lasts for a few months. This report describes a trial of grafting of adrenal chromaffin tissue into the putamen, supported by infusion of nerve growth factor. The patient is a 63-year-old woman with a 19-year history of Parkinson's disease, now complicated by on-off phenomena and drug-induced hyperkinesia, despite optimized medical management. The left adrenal gland was removed, and the medulla was dissected into 1- to 2-mm3 pieces in a solution containing nerve growth factor purified from mouse submandibular gland. Pieces were implanted in six tracts 3 to 4 mm from a previously placed cannula in the left putamen. Through the cannula, nerve growth factor was infused for 23 days for a total dose of 3.3 mg. Clinical assessment consisted of global ratings for rigidity and/or hypokinesia and for drug-induced hyperkinesia. Measures of gait and fine-motor control were also made. The motor readiness potential and auditory evoked potentials were recorded.(ABSTRACT TRUNCATED AT 250 WORDS)
Fast Multiresolution Extraction of Multiple Transparent Isosurfaces (2001)

In this paper, we present a multiresolution algorithm which is capable to render multiple transparent isosurfaces under realtime constraints. To this end, the underlying 3D data set is covered with a hierarchical tetrahedral grid. The multiresolution extraction algorithm is then based on an adaptive traversal of the tetrahedral grid with the help of error indicators. The display of transparent isosurfaces using alpha blending requires a backtofront rendering of the isosurface triangles. This is achieved by a hierarchical sorting procedure of the tetrahedra and the hierarchical computation of data gradients. We will also comment on the automated selection of suitable isovalues for visualization applications.
Physiotherapy and Weaning From Prolonged Mechanical Ventilation (2018)

Our data support the inclusion of physiotherapy in the management of patients requiring prolonged mechanical ventilation.
Isolation of an Encapsulated Strain of <i>Staphylococcus epidermidis</i> (1979)

An encapsulated strain of Staphylococcus epidermidis isolated from a human clinical specimen was demonstrated by electron microscopy. The outermost layer of the cell wall of these organisms probably consists mostly of polysaccharide.
(Invited) CIGS-Based Solar Cells Prepared from Electrodeposited Precursor Films (2012)

Abstract not Available.
Manitest: Are classifiers really invariant? (2015)

Invariance to geometric transformations is a highly desirable property of automatic classifiers in many image recognition tasks. Nevertheless, it is unclear to which extent state-of-the-art classifiers are invariant to basic transformations such as rotations and translations. This is mainly due to the lack of general methods that properly measure such an invariance. In this paper, we propose a rigorous and systematic approach for quantifying the invariance to geometric transformations of any classifier. Our key idea is to cast the problem of assessing a classifier's invariance as the computation of geodesics along the manifold of transformed images. We propose the Manitest method, built on the efficient Fast Marching algorithm to compute the invariance of classifiers. Our new method quantifies in particular the importance of data augmentation for learning invariance from data, and the increased invariance of convolutional neural networks with depth. We foresee that the proposed generic tool for measuring invariance to a large class of geometric transformations and arbitrary classifiers will have many applications for evaluating and comparing classifiers based on their invariance, and help improving the invariance of existing classifiers.
Compact MOS Modelling for Analogue Circuit Simulation (1994)

The Philips compact MOS model, MOS MODEL 9, has been developed for the simulation of analogue circuits. With only 18 parameters mos MODEL 9 describes accurately the characteristics in the operating regions most important for analogue design [1,2]. Recently the capabilities of the model in describing various processes, with minimum channel lengths as low as 0.35 ?m, have been presented [1]. MOS MODEL 9 has now become public domain [2]. This paper discusses the physical background of the model. Special emphasis is placed on the description of the subthreshold behaviour, which is of paramount importance in low voltage applications, and on the geometric scaling of the relevant model parameters.
1550-nm High-Speed Short-Cavity VCSELs (2011)

The latest advances in 1550-nm high-speed short-cavity vertical-cavity surface-emitting lasers (VCSELs) are presented. The electrical, optical, and thermal design of these devices is discussed with respect to their high-speed modulation behavior. The implemented design improvements allow high output powers for ambient temperatures up to 90°C, high differential quantum efficiencies up to 40%, temperature-stable single-mode emission, low thermal resistances down to 1.6 K/mW, small-signal modulation bandwidths in excess of 17 GHz, and error-free data transmission at room temperature at data rates of 35 Gb/s in back-to-back configuration and up to 25 Gb/s over 4.2 km of single-mode fiber.
Stable Control of Haptics (2007)

Introduction Humans interact with their surrounding environment through five sensory channels, popularly labeled &quot;sight,&quot; &quot;sound,&quot; &quot;taste,&quot; &quot;smell,&quot; and &quot;touch.&quot; It is our sense of touch which provides us with much of the information necessary to modify and manipulate the world around us. The word haptic refers to something &quot;of or relating to the sense of touch&quot;[1] : conveying information on physical properties such as inertia, friction, compliance, temperature, and roughness. This sense can be divided into two categories: the kinesthetic sense, through which we sense movement or force in muscles and joints; and the tactile sense, through which we sense shapes and textures. This chapter will focus on the stable control of devices and systems which support haptic interaction, especially relating to the use of kinesthetic sense in virtual environments. 1.1 History of Haptics Haptics research grew rapidly in the 1990&apos;s as researchers and corporations discovered more uses for force feed
Early Stages of Intergranular Stress Corrosion Cracking (1997)

Abstract Environment-induced crack growth generally progresses through several stages prior to component failure. Early stages of localized corrosion (crack initiation), and short crack growth are early stages in crack development that are summarized in this paper. The implications of these stages on component reliability derive from the extended time that the crack exists in the early stages because crack velocity is low. The duration of the early stages provides a greater opportunity for corrective action if short cracks can be detected. Several important reasons for understanding short crack behavior are: 1) component life prediction requires a knowledge of the total life cycle of the crack including the early stages, 2) greater reliability is possible if the transition between short and long crack behavior is known since component life after this transition is short and 3) remedial actions are often more effective for short than long cracks.
Identification of Genetic Markers for Differentiation of Shiga Toxin-Producing, Enteropathogenic, and Avirulent Strains of<i>Escherichia coli</i>O26 (2011)

Shiga toxin-producing Escherichia coli (STEC) O26 is one of the top five enterohemorrhagic E. coli (EHEC) O groups most often associated with hemorrhagic colitis and hemolytic uremic syndrome (HUS) worldwide. STEC O26 is considered to have evolved from enteropathogenic (EPEC) O26 strains through the acquisition of Shiga toxin (Stx)-encoding genes. Our PCR data identified several STEC-like strains expressing all features of STEC except Stx production and carrying remnants of Stx phages that were probably derivatives of EHEC O26. EHEC and EPEC O26 strains phenotypically resemble O26 EHEC-like and apathogenic E. coli O26 strains and are therefore undistinguishable by cultural methods. A clear discrimination between the different O26 groups is required for diagnostics in patients and for control of food safety. To develop an assay for specific detection of EHEC and EHEC-like O26 strains, we used a high-throughput PCR approach for selection of discriminative genetic markers among 33 tested genes mostly encoding type III secretion system effector proteins. The genes ECs1822, nleH1-2, nleA, nleC, nleH1-1, nleG, nleG2, nleG6-1, nleG6-2, espJ, espM2, nleG8-2, espG, ent (or espL2), nleB, nleE, efa1, and espB were detected at different frequencies in O26 EHEC, EHEC-like, and EPEC strains, indicating the possible role of these genes in virulence of human pathogenic O26 strains. The espK and espN genes were detected only in EHEC and EHEC-like O26 strains. espK was present in 99.14% of EHEC and 91.14% of EHEC-like O26 strains and was hence the best candidate as a genetic marker for characterizing these pathogroups. These data were corroborated by a genotyping real-time PCR test based on allelic discrimination of the arcA (aerobic respiratory control protein A) gene. The results indicate that a combination of molecular detection tools for O26 wzx (wzx(O26)), eae-beta, stx, espK, and arcA genotyping is highly discriminative for clear identification of EHEC and EHEC-like E. coli O26 strains. This simple diagnostic test might be applicable in hospital service laboratories or public health laboratories to test strains isolated from stools of patients suffering from diarrhea.
Immunoblotting in the clinical laboratory. (1989)

Since its introduction in 1979 protein blotting has become a routine tool in research laboratories. In the clinical laboratory its potential is becoming recognised for applications in fields such as infectious and autoimmune diseases, allergy and others. In this article we would like to outline the basic principles of protein blotting, to illustrate these with some examples related to clinical applications and to point out differences between these and classical methods.
Dynamic data allocation with replication in distributed systems (2011)

The goal of fragment allocation in distributed database systems is to place data fragments at sites so as to minimize the overall data transmission cost incurred to answer queries. We consider the problem of fragment allocation in lazily replicated systems and address both placement and replication issues in an integrated approach. While replication can improve performance via increased locality, excessive replication can incur extra overhead cost to maintain replicas. A comprehensive model that takes into account network topology, fragment correlation, and data access patterns is presented. Based on this model, we propose an algorithm to find near-optimal dynamic allocation solutions. Experimental results show the efficacy of the proposed solution.
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes (2006)

TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to their specific molecular functions. Most TIGRFAMs models describe 'equivalog' families, where both orthology and lateral gene transfer may be part of the evolutionary history, but where a single molecular function has been conserved. The Genome Properties system contains a queriable set of metabolic reconstructions, genome metrics and extractions of information from the scientific literature. Its genome-by-genome assertions of whether or not specific structures, pathways or systems are present provide high-level conceptual descriptions of genomic content. These assertions enable comparative genomics, provide a meaningful biological context to aid in manual annotation, support assignments of Gene Ontology (GO) biological process terms and help validate HMM-based predictions of protein function. The Genome Properties system is particularly useful as a generator of phylogenetic profiles, through which new protein family functions may be discovered. The TIGRFAMs and Genome Properties systems can be accessed at http://www.tigr.org/TIGRFAMs and http://www.tigr.org/Genome_Properties.
An automatic construction of a person's face model from the person's two orthogonal views (2003)

A new approach to the construction of a person's three-dimensional face model from the person's two orthogonal views is presented. This approach is a no hair-style interference method, which constructs the person's face model and hair model independently. The person's fine facial structures, i.e., eyes, nose, and lips, as well as the person's outline in two orthogonal views are obtained. A feature-based generic three-dimensional bald head model is then used to adjust its predefined features to fit the person's fine structures and outline morphologically in two respective views. The independently obtained three-dimensional hair model is put on the morphed bald head model to be the person's three-dimensional geometrical face model. The person's realistic face model is finally obtained by using the texture mapping of the person's image in two orthogonal views onto the person's three-dimensional face model. This paper shows the detail process of the construction of a person's face model from the person's two orthogonal views.