gebhart/patrepeval huggingface dataset:
Biomarkers for epithelial-mesenchymal transitions (2009)

Somatic cells that change from one mature phenotype to another exhibit the property of plasticity. It is increasingly clear that epithelial and endothelial cells enjoy some of this plasticity, which is easily demonstrated by studying the process of epithelial-mesenchymal transition (EMT). Published reports from the literature typically rely on ad hoc criteria for determining EMT events; consequently, there is some uncertainty as to whether the same process occurs under different experimental conditions. As we discuss in this Personal Perspective, we believe that context and various changes in plasticity biomarkers can help identify at least three types of EMT and that using a collection of criteria for EMT increases the likelihood that everyone is studying the same phenomenon - namely, the transition of epithelial and endothelial cells to a motile phenotype.
Towards real-time guidewire detection and tracking in the field of neuroradiology (2009)

Two-dimensional roadmapping is considered state-of-the-art in guidewire navigation during endovascular interventions. This paper presents a methodology for extracting the guidewire from a sequence of 2-D roadmap images in almost real time. The detected guidewire can be used to improve its visibility on noisy fluoroscopic images or to do a back projection of the guidewire into a registered 3-D vessel tree. A lineness filter based on the Hessian matrix is used to detect only those line structures in the image that lie within the vessel tree. Loose wire fragments are properly linked by a novel connection method fulfilling clinical processing requirements. We show that Dijkstra's algorithm can be applied to efficiently compute the optimal connection path. The entire guidewire is finally approximated by a B-spline curve in a least-squares manner. The proposed method is both integrated into a commercial clinical prototype and evaluated on five different patient data sets containing up to 249 frames per image series.
Different somatic and germline HPRT1 mutations promote use of a common, cryptic intron 1 splice site Communicated by: Daniel F. Schorderet Online Citation: Human Mutation, Mutation in Brief #246 (1999) Online http://journals.wiley.com/1059-7794/pdf/mutation/246.pdf (1999)

Aberrant hypoxanthine phosphoribosyltransferase (HUGO-approved gene symbol HPRT1; MIM# 308000) mRNA splicing, promoted by splice site mutation or loss, is a common mechanism for loss of the purine salvage enzyme HPRT1 from human cells. We report here two in vivo somatic HPRT1 mutations in human kidney tubular epithelial cells that disrupt HPRT1 intron 1 splicing and lead to the inclusion of intron 1 sequence. We propose an explanation for the use of a common, cryptic intron 1 splice donor site by these two mutations, and by 14 additional human HPRT1 mutations that lead to aberrant splicing with the incorporation of intron 1 sequence into mRNA. Hum Mutat 13:504–505, 1999. © 1999 Wiley-Liss, Inc.
Improving Spatial Perception for Augmented Reality X-Ray Vision (2009)

Augmented reality x-ray vision allows users to see through walls and view real occluded objects and locations. We present an augmented reality x-ray vision system that employs multiple view modes to support new visualizations that provide depth cues and spatial awareness to users. The edge overlay visualization provides depth cues to make hidden objects appear to be behind walls, rather than floating in front of them. Utilizing this edge overlay, the tunnel cut-out visualization provides details about occluding layers between the user and remote location. Inherent limitations of these visualizations are addressed by our addition of view modes allowing the user to obtain additional detail by zooming in, or an overview of the environment via an overhead exocentric view.
Sputum Biomarkers of Inflammation and Lung Function Decline in Children with Cystic Fibrosis (2012)

In children with CF, a single determination of sputum biomarkers, particularly neutrophil elastase, has predictive value for subsequent lung function decline, and longitudinal changes in sputum inflammatory biomarkers are related to lung function changes. Based on our results, sputum neutrophil elastase was the most informative biomarker to monitor disease activity.
Circulating Megakaryocytes and Platelet Release in the Lung (1965)

Abstract 1. Megakaryocytes were demonstrated in central venous blood of each of 23 patients who underwent cardiac catheterization. Cell counts ranged from 0.7 to 5.9 megakaryocytes per ml. of blood; the equivalent of one-third of these cells were considered to contain a full complement of cytoplasm. It has become evident that megakaryocytes are normal constituents of blood. 2. In an attempt to quantify megakaryocyte migration from the bone marrow it was calculated that from 20-50 per cent of the mature megakaryocyte population enters the blood and ultimately reaches the lungs. The possibility that all megakaryocytes migrate from the marrow is not precluded with certainty by these studies. 3. It was estimated that from 7-17 per cent of the body’s platelets are released in the pulmonary capillaries. If all megakaryocytes migrate from the bone marrow, then as much as 33 per cent of the platelet population is delivered to the blood in the lungs.
Age-related changes in oxidized proteins. (1987)

We have previously described the oxidative inactivation of several key metabolic enzymes by a variety of mixed function oxidation systems. Because many of the enzymes which are inactivated have been shown by others to accumulate as inactive or less active forms during cellular aging, we have examined the levels of oxidatively modified proteins in two model systems used for studies on aging. The results show that levels of oxidatively modified proteins increase with age in circulating erythrocytes, and this change is correlated with the loss of marker enzyme activity. Our studies also show that in cultured fibroblasts from normal donors the levels of oxidatively modified proteins increase only after the age of 60. However, the levels of oxidatively modified proteins in fibroblasts from individuals with progeria or Werner's syndrome are significantly higher than age-matched controls. Moreover, treatment of glucose-6-phosphate dehydrogenase with a mixed function oxidation system leads to oxidative modification and increased heat lability of the enzyme. Taken together these results suggest that loss of functional enzyme activity and increased heat lability of enzymes during aging may be due in part to oxidative modification by mixed function oxidation systems.
Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures (1992)

The three-dimensional solution structure of the recombinant B domain (FB) of staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G, was determined by NMR spectroscopy and hybrid distance geometry-dynamical simulated annealing calculations. On the basis of 692 experimental constraints including 587 distance constraints obtained from the nuclear Overhauser effect (NOE), 57 torsion angle (phi, chi 1) constraints, and 48 constraints associated with 24 hydrogen bonds, a total of 10 converged structures of FB were obtained. The atomic root mean square difference among the 10 converged structures is 0.52 +/- 0.10 A for the backbone atoms and 0.98 +/- 0.08 A for all heavy atoms (excluding the N-terminal segment from Thr1 to Glu9 and the C-terminal segment from Gln56 to Ala60, which are partially disordered). FB is composed of a bundle of three alpha-helices, i.e., helix I (Gln10-His19), helix II (Glu25-Asp37), and helix III (Ser42-Ala55). Helix II and helix III are antiparallel to each other, whereas the long axis of helix I is tilted at an angle of about 30 degrees with respect to those of helix II and helix III. Most of the hydrophobic residues of FB are buried in the interior of the bundle of the three helices. It is suggested that the buried hydrophobic residues form a hydrophobic core, contributing to the stability of FB.(ABSTRACT TRUNCATED AT 250 WORDS)
Characterizing Facial Skin Ageing in Humans: Disentangling Extrinsic from Intrinsic Biological Phenomena (2015)

Facial skin ageing is caused by intrinsic and extrinsic mechanisms. Intrinsic ageing is highly related to chronological age. Age related skin changes can be measured using clinical and biophysical methods. The aim of this study was to evaluate whether and how clinical characteristics and biophysical parameters are associated with each other with and without adjustment for chronological age. Twenty-four female subjects of three age groups were enrolled. Clinical assessments (global facial skin ageing, wrinkling, and sagging), and biophysical measurements (roughness, colour, skin elasticity, and barrier function) were conducted at both upper cheeks. Pearson's correlations and linear regression models adjusted for age were calculated. Most of the measured parameters were correlated with chronological age (e.g., association with wrinkle score, r = 0.901) and with each other (e.g., residual skin deformation and wrinkle score, r = 0.606). After statistical adjustment for age, only few associations remained (e.g., mean roughness (R z ) and luminance (L (*)), β = -0.507, R (2) = 0.377). Chronological age as surrogate marker for intrinsic ageing has the most important influence on most facial skin ageing signs. Changes in skin elasticity, wrinkling, sagging, and yellowness seem to be caused by additional extrinsic ageing.
Occurrence of CNS demyelinating disease in patients with myasthenia gravis (2006)

An increased incidence of multiple sclerosis (MS) has been reported in patients with myasthenia gravis (MG). We reviewed records of 214 patients with MG. CNS demyelinating disease (CNSDD) occurred in five patients (2.3%). CNSDD always occurred after the diagnosis of MG. Myelitis (including recurrent myelitis) was the most common CNS manifestation. All patients had antinuclear antibodies. CNSDD occurs more frequently in patients with MG and may be related to immune-modulating treatments including thymectomy.
Immunostimulating Complexes Incorporating Eimeria tenella Antigens and Plant Saponins as Effective Delivery System for Coccidia Vaccine Immunization (2008)

Immunostimulating complexes (ISCOMs) are unique, multimolecular structures formed by encapsulating antigens, lipids, and triterpene saponins of plant origin, and are an effective delivery system for various kinds of antigens. The uses of ISCOMs formulated with saponins from plants collected in Kazakhstan, with antigens from the poultry coccidian parasite Eimeria tenella, were evaluated for their potential use in developing a vaccine for control of avian coccidiosis. Saponins isolated from the plants Aesculus hippocastanum and Glycyrrhiza glabra were partially purified by HPLC. The saponin fractions obtained from HPLC were evaluated for toxicity in chickens and chicken embryos. The HPLC saponin fractions with the least toxicity, compared to a commercial saponin Quil A, were used to assemble ISCOMs. When chicks were immunized with ISCOMs prepared with saponins from Kazakhstan plants and E. tenella antigens, and then challenged with E. tenella oocysts, significant protection was conveyed compared to immunization with antigen alone. The results of this study indicate that ISCOMs formulated with saponins isolated from plants indigenous to Kazakhstan are an effective antigen delivery system which may be successfully used, with low toxicity, for preparation of highly immunogenic coccidia vaccine.
Precise localization of several covalent RNA‐RNA cross‐link in Escherichia coli 16S RNA (1983)

The RNA-RNA cross-linking reagent N-acetyl-N'-(p-glyoxylyl-benzoyl)cystamine, which reacts via its glyoxal residue with guanines not involved in G X C base pairs, has been used to introduce reversible RNA-RNA cross-links into Escherichia coli 16S rRNA. A two-dimensional gel method has been devised for the separation of the cross-linked oligonucleotides, and the precise location of guanines involved in four of these cross-links has been determined by sequencing the oligonucleotides. One cross-link involves guanosines 1315 and 1360 situated in two hairpin end loops of domain III. The other cross-links involves pairs of guanosine situated within the same hairpin end loops.
Growth of Vertical GaAs Nanowires on an Amorphous Substrate via a Fiber-Textured Si Platform (2013)

We demonstrate the vertical self-catalyzed molecular beam epitaxy (MBE) growth of GaAs nanowires on an amorphous SiO2 substrate by using a smooth [111] fiber-textured silicon thin film with very large grains, fabricated by aluminum-induced crystallization. This generic platform paves the way to the use of inexpensive substrates for the fabrication of dense ensembles of vertically standing nanowires (NWs) with promising perspectives for the integration of NWs in devices.
Pyridone-carboxylic acids as antibacterial agents. I. Synthesis and antibacterial activity of 1-alkyl-1,4-dihydro-4-oxo-1,8- and 1,6-naphthyridine-3-carboxylic acids. (1982)

Condensation of 2-amino-6-chloropyridine (1) with diethyl ethoxymethylenemalonate gave the aminomethylenemalonate 2, which upon thermal cyclization (Gould-Jacobs reaction) afforded ethyl 7-chloro-1, 4-dihydro-4-oxo-1, 8-naphthyridine-3-carboxylate (3). Alkylation of 3 produced the 1-alkyl derivative 4. Substitution of 4 with a cyclic amine gave ethyl 7-substituted 1-alkyl-1, 4-dihydro-4-oxo-1, 8-naphthyridine-3-carboxylate (5). The ester 5 was hydrolyzed to the corresponding carboxylic acid 6. 7-Substituted 1-alkyl-1, 4-dihydro-4-oxo-1, 6-naphthyridine-3-carboxylic acids (20) were also synthesized from 4-amino-2-chloropyridine (13) in a similar manner. The in vitro antibacterial activity was enhanced by the presence of a cyclic amine at position 7 on 6 and 20. In general, the 1, 8-naphthyridine 6 was more active than the 1, 6-naphthyrdine counterpart 20. 1-Ethyl-1, 4-dihydro-4-oxo-7-(1-piperazinyl)-1, 8-naphthyridine-3-carboxylic acid (6e) (an analog of both pipemidic acid and nalidixic acid) was comparable to pipemidic acid but superior to nalidixic acid in terms of activity in vitro against Pseudomonas aeruginosa.
Hierarchical model of gene regulation by transforming growth factor β (2003)

Transforming growth factor betas (TGF-betas) regulate key aspects of embryonic development and major human diseases. Although Smad2, Smad3, and extracellular signal-regulated kinase (ERK) mitogen-activated protein kinases (MAPKs) have been proposed as key mediators in TGF-beta signaling, their functional specificities and interactivity in controlling transcriptional programs in different cell types and (patho)physiological contexts are not known. We investigated expression profiles of genes controlled by TGF-beta in fibroblasts with ablations of Smad2, Smad3, and ERK MAPK. Our results suggest that Smad3 is the essential mediator of TGF-beta signaling and directly activates genes encoding regulators of transcription and signal transducers through Smad3/Smad4 DNA-binding motif repeats that are characteristic for immediate-early target genes of TGF-beta but absent in intermediate target genes. In contrast, Smad2 and ERK predominantly transmodulated regulation of both immediate-early and intermediate genes by TGF-beta/Smad3. These results suggest a previously uncharacterized hierarchical model of gene regulation by TGF-beta in which TGF-beta causes direct activation by Smad3 of cascades of regulators of transcription and signaling that are transmodulated by Smad2 and/or ERK.
Isolation of cDNA sequences coding for a part of human tissue plasminogen activator. (1983)

We have isolated a cDNA sequence coding for a part of human tissue plasminogen activator. mRNA coding for tissue plasminogen activator was partially purified, copied into double-stranded cDNA, and cloned into Escherichia coli. Two sets of partially overlapping oligodeoxynucleotide mixtures corresponding to all possible coding sequences for a known portion of the tissue plasminogen activator gene were prepared. One set was used as a probe to screen cDNA containing bacterial clones and both were used as probes in hybridization against purified plasmid DNA. Of 4,200 bacterial clones examined, 1 carried a plasmid that hybridized to both sets of oligonucleotides. This plasmid contained a 370-base-pair cDNA insert, which was shown by nucleotide sequence analysis to code for the cleavage site region in the one-chain form of the human tissue plasminogen activator.
Developmentally regulated alternative splicing generates a complex array of Drosophila para sodium channel isoforms (1994)

The para locus encodes the predominant class of sodium channels expressed in Drosophila neurons. Previous sequence analysis of para cDNAs indicated the occurrence of alternative splicing at several sites within the open reading frame. Here we report a detailed analysis of this alternative splicing and its regulation during development. We have used a combination of RNA-PCR and sequence analysis to examine a 1.7 kilobase region of the para mRNA that encompasses the previously reported sites of alternative splicing. Five sites of alternative splicing were identified; 48 different splice variants could be generated by the differential exon usage observed. The number of splice forms and their relative frequency in vivo were characterized in RNA samples of both embryos and adults. The range of splice types was found to be much more diverse in adults than in embryos; of a total of 19 different combinations of alternative exons, 11 splice types were found in embryos and 18 in adults. Usage of some individual alternative exons changed during development; a newly identified exon, which is found in one of two forms either 24 or 30 base pairs long, was present in about 85% of para transcripts from embryos but only 7% of those in adults. These data suggest that a wide variety of subtly distinct Na channel isoforms are present in Drosophila, and that these may provide a range of voltage-gated sodium channel functions. Although multiple sodium channel genes have already been described in both Drosophila and mammalian systems, this study provides a clear indication that sodium channel variability may be much greater than previously thought.
Spatial Distribution Measurement of Ions Surrounding an Alpha Source using a New Micro-ionization Chamber (2005)

Recently, a new alpha radioactivity measurement technique was proposed, which directly measures ions surrounding alpha radioactivity. In order to implement this technique, a better understanding of ion's behavior is required. We have developed a micro-ionization chamber with multi-channel charge-integrating ASICs (Application Specific Integrated Circuit). In this study, we will introduce the design of the micro-ionization chamber and show first results from ion measurements using an 241 Am alpha source. When we increase the electric field, the spatial distribution of ions exhibited two different components. Simulation calculations were also performed to account for these components.
Role of Tetrodotoxin-Resistant Na+Current Slow Inactivation in Adaptation of Action Potential Firing in Small-Diameter Dorsal Root Ganglion Neurons (2003)

When acutely dissociated small-diameter dorsal root ganglion (DRG) neurons were stimulated with repeated current injections or prolonged application of capsaicin, their action potential firing quickly adapted. Because TTX-resistant (TTX-R) sodium current in these presumptive nociceptors generates a large fraction of depolarizing current during the action potential, we examined the possible role of inactivation of TTX-R sodium channels in producing adaptation. Under voltage clamp, TTX-R current elicited by short depolarizations showed strong use dependence at frequencies as low as 1 Hz, although recovery from fast inactivation was complete in approximately 10-30 msec. This use-dependent reduction was the result of the entry of TTX-R sodium channels into slow inactivated states. Slow inactivation was more effectively produced by steady depolarization than by cycling channels through open states. Slow inactivation was steeply voltage dependent, with a Boltzmann slope factor of 5 mV, a midpoint near -45 mV (5 sec conditioning pulses), and completeness of approximately 93% positive to -20 mV. The time constant for entry (approximately 200 msec) was independent of voltage from -20 mV to +60 mV, whereas recovery kinetics were moderately voltage dependent (time constant, approximately 1.5 sec at -60 mV and approximately 0.5 sec at -100 mV). Using a prerecorded current-clamp response to capsaicin as a voltage-clamp command waveform, we found that adaptation of firing occurred with a time course similar to that of development of slow inactivation. Thus, slow inactivation of the TTX-R sodium current limits the duration of small DRG cell firing in response to maintained stimuli and may contribute to cross desensitization between chemical and electrical stimuli.
Towards Fish Lipid Nutrigenomics: Current State and Prospects for Fin-Fish Aquaculture (2008)

Lipids are the predominant source of energy for fish. The mechanisms by which fish allocate energy from lipids for metabolism, development, growth, and reproduction are critical for understanding key life-history strategies and transitions. Currently, the major lipid component in aquaculture diets is fish oil (FO), derived from wild capture fisheries that are exploited at their maximum sustainable limit. The increasing demand from aquaculture for FO will soon exceed supply and threaten the viability of aquaculture. Thus, it is essential to minimize FO use in aquaculture diets. This might be achieved by a greater understanding of lipid storage and muscle growth, or the identification of alternatives to FO in feeds. This review focuses on recent research applying molecular and genomic techniques to the study of fin-fish lipid metabolism from an aquaculture perspective. Accordingly, particular emphasis will be given to fatty acid metabolism and to highly unsaturated fatty acid (HUFA) biosynthesis and to the transcriptional mechanisms and endocrine factors that regulate these processes in fish. Comparative studies of gene function and distribution are described, which, when integrated with recent fish genome sequence information, provide insights into lipid homeostasis and the outcomes associated with the replacement of FO in fish diets.
ABS and active suspension control via high order sliding modes and linear geometric methods for disturbance rejection (2011)

In this work, high order sliding mode techniques are used to control an Anti-lock Brake System (ABS) which is assisted with an active suspension. The main objective is to modify the slip rate of a vehicle and ensure a shorter stopping distance in the braking process. The control system is designed in independent way for the ABS and the suspension subsystem. For the ABS subsystem a second order sliding mode controller is used. On the other hand, for the active suspension subsystem the supertwisting algorithm combined with regular form and linear geometric techniques is proposed. The use of sliding mode controllers allows that both closed-loop subsystems are robust against a class of external perturbations and system uncertainties, furthermore the chattering effect is reduced and higher tracking accuracy is obtained. The effectiveness of the proposed control strategy is confirmed via simulations.