gebhart/patrepeval huggingface dataset:
Fibrogenesis II. Metalloproteinases and their inhibitors in liver fibrosis (2000)

Liver fibrosis is characterized by activation of hepatic stellate cells, which are then involved in synthesis of matrix proteins and in regulating matrix degradation. In the acute phases of liver injury and as liver fibrosis progresses, there is increased expression of matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs). Among the changes described, striking features include increased expression of gelatinase A (MMP-2) and membrane type 1-MMP (MT(1)-MMP; MMP-14) as well as TIMP-1 and TIMP-2. These molecules and other family members are involved in regulating degradation of both normal and fibrotic liver matrix. This article outlines recent progress in this field and discusses the mechanisms by which MMPs and TIMPs may contribute to the progression and regression of liver fibrosis. Recently described properties of MMPs and TIMPs of relevance to the pathogenesis of liver fibrosis are outlined. The proposal that regression of liver fibrosis is mediated by decreased expression of TIMPs and involves degradation of fibrillar collagens by a combination of MT(1)-MMP and gelatinase A, in addition to interstitial collagenase, is explored.
Synthesis of bufadienolides. Synthesis of bufalin and resibufogenin (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of bufadienolides. Synthesis of bufalin and resibufogeninFranz Sondheimer, W. McCrae, and W. G. SalmondCite this: J. Am. Chem. Soc. 1969, 91, 5, 1228–1230Publication Date (Print):February 1, 1969Publication History Published online1 May 2002Published inissue 1 February 1969https://pubs.acs.org/doi/10.1021/ja01033a039https://doi.org/10.1021/ja01033a039research-articleACS PublicationsRequest reuse permissionsArticle Views410Altmetric-Citations41LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Quinquethiophene light-emitting diodes with molecular dimensions (1997)

Light-emitting diodes using Langmuir-Blodgett films of quinquethiophene as the emitting layer have been fabricated, and electrically and optically characterized. By utilizing additional layers of electron-transporting materials, the emitting material thickness has been reduced down to a single monolayer without serious decrease in the quantum efficiency. These electronic devices are valuable tools for studying carrier injection and transport, exciton formation, and quenching on a real molecular scale.
Dual-release formulation, a novel principle in <scp>l</scp> -dopa treatment of Parkinson’s disease (2001)

A single morning dose of dual-release formulation was compared with a slow-release formulation of L-dopa plus benserazide in a randomized, double-blind, cross-over study in 16 fluctuating patients with PD. The mean time to "on" was shorter with the dual-release formulation (43 +/- 31 minutes) than with the slow-release formulation (81 +/- 39 minutes) (p < 0.001), whereas the mean time to relapse to "off" was similar for both formulations. The dual-release formulation had a significantly shorter time to reach peak concentration (t(max)) and greater maximum concentration (C(max)) and area under the plasma concentration time curve (AUC(0--5 h)) than the slow-release formulation, whereas apparent elimination half-life (t(1/2)) was similar for both formulations.
Visualizing queries in a distributed digital library system (2002)

A general user interface paradigm is presented which is capable of modelling iterative query refinement and embedding several common and advanced query techniques. A prototype implementation of this user interface called AQUA has been applied to the NCSTRL (Networked Computer Science Technical Reports Library) distributed digital library.
A qualitative study to explore the concept of fatigue/tiredness in cancer patients and in healthy individuals (1996)

Interest in fatigue research has grown since the finding that fatigue/tiredness is the most frequently reported symptom of cancer and its treatment. But even though several authors have tried to conceptualize fatigue (Piper & Rieger, 1989; Cimprich, 1992; Gibson & Edwards, 1985; Winningham, 1994; Irvine et al. 1994; Grandjean, 1970; et al.), its mechanisms are still poorly understood. The aim of this study was two-fold: i) to explore fatigue in cancer patients, inductively, and ii) to compare fatigue/tiredness experiences of healthy individuals with those of cancer patients to identify cancer-specific fatigue/tiredness and related concepts. A qualitative research strategy was adopted using a grounded-theory approach. The prospective study took place in the Oncology Department of the Kantonsspital St Gallen (Switzerland) with samples of 20 cancer patients and 20 healthy individuals. Unstructured, tape-recorded interviews were conducted to collect data. Transcripts of the interviews were analysed using content analysis and constant comparison. Although different themes emerged between the two groups, both fitted a classification system that categorized expression of fatigue/tiredness as physical, affective or cognitive. Physical signs were more frequent than affective and cognitive signs in both groups. For the cancer patients, fatigue involved decreased physical performance, extreme, unusual tiredness, weakness and an unusual need for rest, which was distinctly different for healthy persons. Affective and cognitive distress were also more prominent in cancer patients. Interestingly, the concept of malaise was not identified by either sample and not understood as an expression of fatigue by this German-speaking population. Linguistic differences in the description of fatigue/tiredness between healthy and ill individuals revealed different perceptions of the phenomenon. A step-like theory, involving nociception, perception and expression of tiredness, was put forward tentatively to explain the production of fatigue/tiredness. The emerging concepts break tiredness/fatigue into expressions of physical, affective and cognitive tiredness/fatigue. The experience is different between healthy individuals and cancer patients. The generalization of data needs precaution but the results of the study identify and clarify ideas that might form an important basis for further, controlled studies.
Stochastic inference with deterministic spiking neurons (2013)

The seemingly stochastic transient dynamics of neocortical circuits observed in vivo have been hypothesized to represent a signature of ongoing stochastic inference. In vitro neurons, on the other hand, exhibit a highly deterministic response to various types of stimulation. We show that an ensemble of deterministic leaky integrate-and-fire neurons embedded in a spiking noisy environment can attain the correct firing statistics in order to sample from a well-defined target distribution. We provide an analytical derivation of the activation function on the single cell level; for recurrent networks, we examine convergence towards stationarity in computer simulations and demonstrate sample-based Bayesian inference in a mixed graphical model. This establishes a rigorous link between deterministic neuron models and functional stochastic dynamics on the network level.
The Identification and Characterization of Collagen Receptors Involved in HeLa Cell-Substratum Adhesion (1989)

Four proteins of molecular mass 102, 87, 45, and 38 kDa were isolated from plasma membrane preparations by affinity chromatography. The 102-, 87-, and 38-kDa proteins were shown to be collagen receptors involved in the adhesion of HeLa cells to a gelatin substratum. All four proteins were eluted by high salt from affinity columns made of either types I or IV collagen or type I gelatin. Generally, a total of six major proteins were found in the high salt eluates, although the relative amounts of each varied among experiments. Immunoprecipitation, immunoblotting, and limited peptide mapping indicated that the 102-kDa protein was most sensitive to proteolysis leading to the formation of proteins of molecular mass 58 and 54 kDa. Even in the presence of a mixture of protease inhibitors the 58-kDa fragment was usually the more abundant species. Lectin binding indicated that the 102-, 87-, and 38-kDa proteins contain carbohydrate. Phase-partitioning with Triton X-114 and the need to solubilize the proteins in Triton X-100 indicated that the 102-, 87-, 45-, and 38-kDa proteins have a hydrophobic domain. The 87-kDa protein partitioned exclusively with the detergent-rich phase, suggesting that it is the most hydrophobic. Cell surface labeling with 125I indicated that the four proteins have an extracellular domain. Four criteria were used to determine which of the four proteins are collagen receptors mediating cell-substrate adhesion: 1) during HeLa cell adhesion, proteins with Mr values similar to all four proteins or their peptide fragments were cross-linked to a gelatin substratum derivatized with a photoactivatable probe; 2) a pentapeptide containing the Arg-Gly-Asp cell recognition sequence eluted the same four proteins as those found by high salt elution of collagen affinity columns; 3) monospecific antibodies to the 102-, 87-, and 38-kDa proteins, but not the 45-kDa protein, inhibited the spreading of HeLa cells on a gelatin substratum; 4) monospecific antibodies to the 102-, 87-, and 38-kDa proteins, but not the 45-kDa protein, bound to culture dishes substituted for gelatin in mediating the spreading of HeLa cells. Taken together, the data suggest that the 102-, 87-, and 38-kDa proteins are collagen receptors involved in HeLa cell adhesion. Although the 45-kDa protein has two of the characteristics of a collagen receptor defined here, it does not fit the criteria for one involved in cell-substratum adhesion.
Optical rotation at the free surface of a nematic liquid crystal (1989)

Abstract When a small droplet of a nematic liquid crystal is placed on a horizontal glass plate in the presence of a magnetic field, the plane of polarization of light transmitted upward through the liquid crystal can be rotated. A defect usually forms preferring a direction perpendicular to the magnetic field and forming a diagonal of the droplet. This defect divides the free surface into regions giving rise to optical rotations that are clockwise and counterclockwise. It is suggested that the defect may be similar to a Helfrich splay-bend wall and the optical rotation in the regions near the defect may be explained by surface effects at the free surface of a liquid crystal.
Two-Dimensional Structure of Disulfides and Thiols on Gold(111) (1998)

In order to find factors which determine the two-dimensional structure of self-assembled monolayers (SAMs), several classes of thiols and disulfides on gold (111) have been investigated by atomic force microscopy (AFM). SAMs were formed from a series of symmetrical and asymmetrical diethylalkanoate disulfides, -hydroxy- and -carboxyalkanethiols, diacetylene disulfides, and different anthracene terminated thiols and disulfides. In all the cases, two-dimensional crystalline structures could be resolved; even for an asymmetrical diethylalkanoate disulfide that had a chain length difference of five methylene units. The lattices were analyzed quantitatively. Two distinctly different types of crystalline structures were observed, namely, a hexagonal and a centered rectangular lattice. For the diethylalkanoate disulfides with short alkyl chains (n <- 10) both structural phases were observed, domains with a hexagonal lattice existing simultaneously with centered rectangular domains. The length of the alkyl chain determined the probability of finding disulfides in the hexagonal structure. This dependence on the shape of the molecules as well as the clear contrast of SAMs of asymmetric disulfides suggest that the AFM tip penetrates into the SAMs and probes, at least partially, the interior of the layers. With the atomic force microscope no difference was observed between SAMs formed from thiols and those from disulfides.
Integral spectrophotometric analysis of 5‐aminolaevulinic acid‐induced fluorescence cytology of the urinary bladder (2006)

Spectrofluorometric analysis of lavage sample sediments can be used to detect tumour-associated red fluorescence of PPIX in TCCB. Immediate significant and objective measurements are possible, which could be further automated for the rapid diagnosis of TCCB.
Long-Term Form and Function of Neoesophagus After Experimental Replacement of Thoracic Esophagus With Nitinol Composite Artificial Esophagus (2010)

Attempts were made to observe long-term form and function of neoesophagus with three pigs that survived for more than 42 months after Nitinol composite artificial esophagus replacement. The neoesophagus was shorter in length than resected esophagus (shorten rate 13.9 +/- 3.1) and thinner than normal esophagus (thickness rate 53.8 +/- 5.5). Esophagography and endoscopic findings indicated that the neoesophagus was dilatation of cystic form, and there was not autonomic peristalsis or constrictive motion. Microscopical findings showed that the wall of the neoesophagus consisted of fibrous connective tissue and esophageal mucosa.These results suggest that the long-term neoesophagus is a stratified squamous epithelium cover scar tissue tube. Although it does not have peristaltic function, experimental pigs can survive long-term with the neoesophagus.
Cell Therapy-Processing Economics: Small-Scale Microfactories as a Stepping Stone Toward Large-Scale Macrofactories (2018)

This research outlines the feasibility of cell microfactories but highlighted that there is a strong pressure to automate processes and split the quality control cost-burden over larger production batches. The study explores one potential paradigm of cell-based therapy provisioning as a potential exemplar on which to base manufacturing strategy.
Designing tangible programming languages for classroom use (2007)

This paper describes a new technique for implementing educational programming languages using tangible interface technology. It emphasizes the use of inexpensive and durable parts with no embedded electronics or power supplies. Students create programs in offline settings---on their desks or on the floor---and use a portable scanning station to compile their code. We argue that languages created with this approach offer an appealing and practical alternative to text-based and visual languages for classroom use. In this paper we discuss the motivations for our project and describe the design and implementation of two tangible programming languages. We also describe an initial case study with children and outline future research goals.
Translational and Rotational Motion of Probes in Supercooled 1,3,5-Tris(naphthyl)benzene (1996)

Measurements of the rotational and translational motion of several probe molecules in supercooled 1,3-bis(1-naphthyl)-5-(2-naphthyl)benzene (ααβ-TNB) are reported. Rotational correlation times from 10-10 to 103 s were measured in the temperature range from 341 to 515 K (Tg = 343.5 K). Translational diffusion coefficients ranged from 10-6 to 10-15 cm2/s over a similar temperature range. The rotational correlation times of all probes have essentially the same temperature dependence as the viscosity of TNB. In contrast, the translational diffusion of the smallest probe, tetracene, is observed to have a significantly weaker temperature dependence. At Tg, the translational diffusion coefficient of tetracene is 300 times larger than expected based on its rotational correlation time. Similar enhancements of translational diffusion near Tg have recently been observed in other glass-forming liquids. These observations suggest that dynamics in TNB and other supercooled liquids are spatially heterogeneous. The probes used in this study were tetracene, rubrene, 9,10-diphenylanthracene, and 9,10-bis(phenylethynyl)anthracene.
Structural and Functional Analysis of the Complex between Citrate and the Zinc Peptidase Carboxypeptidase A (2011)

A high-resolution carboxypeptidase-Zn(2+)-citrate complex was studied by X-ray diffraction and enzyme kinetics for the first time. The citrate molecule acts as a competitive inhibitor of this benchmark zinc-dependent peptidase, chelating the catalytic zinc ion in the active site of the enzyme and inducing a conformational change such that carboxypeptidase adopts the conformation expected to occur by substrate binding. Citrate adopts an extended conformation with half of the molecule facing the zinc ion, while the other half is docked in the S1' hydrophobic specificity pocket of the enzyme, in contrast with the binding mode expected for a substrate like phenylalanine or a peptidomimetic inhibitor like benzylsuccinic acid. Combined structural and enzymatic analysis describes the characteristics of the binding of this ligand that, acting against physiologically relevant zinc-dependent proteases, may serve as a general model in the design of new drug-protecting molecules for the oral delivery of drugs of peptide origin.
Word spotting: a new approach to indexing handwriting (1996)

There are many historical manuscripts written in a single hand which it would be useful to index. Examples include the W.B. DuBois collection at the University of Massachusetts and the early Presidential libraries at the Library of Congress. Since Optical Character Recognition (OCR) does not work well on handwriting, an alternative scheme based on matching the images of the words is proposed for indexing such texts. The current paper deals with the matching aspects of this process. Two different techniques for matching words are discussed. The first method matches words assuming that the transformation between the words may be modelled by a translation (shift). The second method matches words assuming that the transformation between the words may be modelled by an affine transform. Experiments are shown demonstrating the feasibility of the approach for indexing handwriting. The method should also be applicable to retrieving previously stored material from personal digital assistants (PDAs).
Photoelectrophoretic Transport and Hybridization of DNA Oligonucleotides on Unpatterned Silicon Substrates (2000)

We describe a platform for photoelectrophoretic transport and electronic hybridization of fluorescence-labeled DNA oligonucleotides in a low conductivity electrolyte. At the core of the platform is a chemically stabilized semiconductor photodiode or photoconductor surface coated with a streptavidin−agarose permeation layer. Micro-illumination of this surface generates photoelectrochemical currents that are used to electrophoretically transport and attach biotinylated DNA capture strands to arbitrarily selected locations. The same process is then used to transport and electronically hybridize fluorescence-labeled DNA target strands to the previously attached capture strands. Signal detection is accomplished either by a fluorescence scanner or a CCD camera. This represents a flexible electronic DNA assay platform that does not rely on pre-patterned microelectronic arrays.
Immunocytochemical Localization of Acrosin on Both Acrosomal Membranes and in the Acrosomal Matrix of Porcine Spermatozoa (1983)

Immunocytochemical techniques were employed to determine, at the ultrastructural level, the location of acrosin in porcine spermatozoa. Antisera to highly purified porcine acrosin was produced in rabbits. The (Fab')2 fragments of the immunoglobulins were purified and conjugated with horseradish peroxidase (HRP). Washed, formaldehyde-fixed spermatozoa were reacted with the labeled antiacrosin immunoglobulins, utilizing a direct staining technique. Electron microscopy revealed that the peroxidase reaction product of HRP-antiporcine acrosin was distributed evenly over the outer acrosomal membrane of spermatozoa with intact acrosomes. The labeled antibody was also distributed evenly over the inner acrosomal membrane of cells when the overlying acrosomal structures were absent. In some spermatozoa, labeling was noted throughout the acrosomal matrix. No significant labeling was observed in control specimens when spermatozoa were exposed to HRP-antiporcine acrosin immunoglobulins that had been adsorbed previously with excess purified acrosin or exposed to HRP-conjugated rabbit antiporcine immunoglobulins. This pattern of labeling is consistent with the hypothesis that acrosin may function as a zona lysin. The observation that the outer acrosomal membrane and acrosomal matrix are labeled suggests that acrosin is not exclusively located on the inner acrosomal membrane and, thus, could participate in physiologic events other than zona penetration.
Complete Genome Sequence of Channel Catfish Gastrointestinal Septicemia Isolate Edwardsiella tarda C07-087 (2013)

Edwardsiella tarda is a Gram-negative facultative anaerobe causing disease in animals and humans. Here, we announce the complete genome sequence of the channel catfish isolate E. tarda strain C07-87, which was isolated from an outbreak of gastrointestinal septicemia on a commercial catfish farm.
MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data (2017)

Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. However, the repeat nature of the tRNA templates and the idiosyncrasies of tRNA sequences necessitate the development and use of methodologies that differ markedly from those used to analyze RNA-seq data when studying microRNAs (miRNAs) or messenger RNAs (mRNAs). Here we present MINTmap (for MItochondrial and Nuclear TRF mapping), a method and a software package that was developed specifically for the quick, deterministic and exhaustive identification of tRFs in short RNA-seq datasets. In addition to identifying them, MINTmap is able to unambiguously calculate and report both raw and normalized abundances for the discovered tRFs. Furthermore, to ensure specificity, MINTmap identifies the subset of discovered tRFs that could be originating outside of tRNA space and flags them as candidate false positives. Our comparative analysis shows that MINTmap exhibits superior sensitivity and specificity to other available methods while also being exceptionally fast. The MINTmap codes are available through https://github.com/TJU-CMC-Org/MINTmap/ under an open source GNU GPL v3.0 license.