gebhart/patrepeval huggingface dataset:
Integrin-mediated Signaling Events in Human Endothelial Cells (1998)

Vascular endothelial cells are important in a variety of physiological and pathophysiological processes. The growth and functions of vascular endothelial cells are regulated both by soluble mitogenic and differentiation factors and by interactions with the extracellular matrix; however, relatively little is known about the role of the matrix. In the present study, we investigate whether integrin-mediated anchorage to a substratum coated with the extracellular matrix protein fibronectin regulates growth factor signaling events in human endothelial cells. We show that cell adhesion to fibronectin and growth factor stimulation trigger distinct initial tyrosine phosphorylation events in endothelial cells. Thus, integrin-dependent adhesion of endothelial cells leads to tyrosine phosphorylation of both focal adhesion kinase and paxillin, but not of several growth factor receptors. Conversely, EGF stimulation causes receptor autophosphorylation, with no effect on focal adhesion kinase or paxillin tyrosine phosphorylation. Adhesion to fibronectin, in the absence of growth factors, leads to activation of MAPK. In addition, adhesion to fibronectin also potentiates growth factor signaling to MAPK. Thus, polypeptide growth factor activation of MAPK in anchored cells is far more effective than in cells maintained in suspension. Other agonists known to activate MAPK were also examined for their ability to activate MAPK in an anchorage-dependent manner. The neuropeptide bombesin, the bioactive lipid lysophosphatidic acid (LPA), and the cytokine tumor necrosis factor alpha, which signal through diverse mechanisms, were all able to activate MAPK to a much greater degree in fibronectin-adherent cells than in suspended cells. In addition, tumor necrosis factor alpha activation of c-Jun kinase (JNK) was also much more robust in anchored cells. Together, these data suggest a cooperation between integrins and soluble mitogens in efficient propagation of signals to downstream kinases. This cooperation may contribute to anchorage dependence of mitogenic cell cycle progression.
Spoken-language research at Carnegie Mellon (1992)

The goal of speech research at Carnegie Mellon continues to be the development of spoken language systems that effectively integrate speech processing into the human-computer interface in a way that facilitates the use of computers in the performance of practical tasks. Research in spoken language is currently focussed in the following areas:• Improved speech recognition technologies: Extending the useful vocabulary of of SPHINX-II by use of better phonetic models and better search techniques, providing for rapid configuration for new tasks.• Fluent human/machine interfaces: Developing an understanding of how people interact by voice with computer systems, in the context of Office Management and other domains.• Understanding spontaneous spoken language: Developing flexible parsing strategies to cope with phenomena peculiar to the lexical and grammatical structure of spoken language. Development of automatic training procedures for these grammars.• Dialog modeling: Applying constraints based on dialog, semantic, and pragmatic knowledge to identify and correct inaccurate portions of recognized utterances.• Acoustical and environmental robustness: Developing procedures to enable good recognition in office environments with desktop microphones and a useful level of recognition in more severe environments.
Improving modal choice and transport efficiency with the virtual ridesharing agency (2005)

While the road capacity is limited and less and less space on the road is left, a large number of seats in cars are currently not occupied. The promotion of carpooling is a very challenging but, at the same time, a very efficient task. With WIGeoPOOL an exchange service for carpools is been developed, that makes carpooling as easy as possible. With the integration of the arrangement of carpools in a multimodal traffic and traveller information system, WIGeoPOOL is a major innovation. The GIS-based, intelligent searching algorithm presents the various travelling possibilities as well as the arrangement of carpools to the user in an easy way, and what is more, it compares the single modes in an objective way. Through the open architecture of the system and interfaces it's possible to use all types of mobile devices in addition to the traditional Internet PC. Even the integration into navigational systems is possible. Under the frame of the R&D-programme 12, intelligent infrastructure, of the Austrian ministry of Transport, Innovation and Technology, WIGeoPOOL is being developed and will be presented to the public in September 2005. Moreover, the integration with the Offboard navigation will be demonstrated at the beginning of 2006. Multimodal traffic and traveller information systems clearly have a positive influence on the traveller's behaviour and mode choice. Transport modes, which are environmentally friendly and more efficient, profit the most.
Histone deacetylase inhibitors induce cell death in supratentorial primitive neuroectodermal tumor cells (2006)

Histone deacetylase inhibitors (HDIs) are a promising new class of antineoplastic agents with the capacity to induce differentiation and/or apoptosis of cancer cells. The objective of this study was to evaluate the activity of HDIs against supratentorial primitive neuroectodermal tumor (sPNET) cells. We show that the HDIs, suberoylanilide hydroxamic acid, sodium butyrate, and trichostatin A, induced cell death, and activated caspase-3 and -9 in a sPNET cell line, PFSK. The poly-caspase inhibitor z-VAD-fmk partially prevented the action of HDIs, as judged by determining the mitochondrial membrane potential and by quantifying internucleosomal DNA fragmentation. In conclusion, the HDIs explored possess potent activity against sPNET cells, suggesting that HDIs may be effective in the treatment of sPNET.
Spectral excitation coding of speech at 2.4 kb/s (2002)

We present spectral excitation coding (SEC), a speech codec based on a sinusoidal model applied to the excitation signal. A phase dispersion algorithm allows the same model to be used for voiced as well as unvoiced and transitional sounds. The phase dispersion algorithm significantly improves the perceived quality resulting in more natural reconstructed speech. A new technique for variable dimension vector quantization called nonsquare transform vector quantization (NSTVQ) is used for quantization of the harmonic magnitudes. The SEC system at 2.45 kb/s achieved an MOS score 0.8 points higher than the 2.4 kb/s ZPC-10 standard. A preliminary 1.85 kb/s SEC system which uses zero-bit magnitude quantization is also presented. Informal listening tests indicate that the quality of the 1.85 kb/s system exceeds that of the LPC-10 standard.
Autologous Peptides Constitutively Occupy the Antigen Binding Site on Ia (1988)

Low molecular weight material associated with affinity-purified class II major histocompatibility complex (MHC) molecules of mouse (Ia) had the expected properties of peptides bound to the antigen binding site of Ia. Thus, the low molecular weight material derived from the I-Ad isotype was efficient in inhibiting the binding of 125I-labeled I-Ad-specific peptide to I-Ad, but did not significantly inhibit the binding of an I-Ed-specific peptide to I-Ed; the reciprocal isotype-specific inhibition was demonstrated with low molecular weight material derived from I-Ed. The inhibitory material was predominantly peptide in nature, as shown by its susceptibility to protease digestion. It was heterogeneous as measured by gel filtration (mean molecular weight approximately 3000), and when characterized by high-performance liquid chromatography, it eluted over a wide concentration of solvent. Such self peptide-MHC complexes may have broad significance in the biology of T cell responses, including generation of the T cell repertoire, the specificity of mixed lymphocyte responses, and the immune surveillance of self and nonself antigens in peripheral lymphoid tissues.
Endometriosis: Oestrogen and progesterone receptors in endometriotic tissue and endometrium: comparison of different cycle phases and ages* (1993)

The levels of oestrogen and progesterone receptors were analysed in 62 endometriotic tissue samples obtained at laparotomy of 58 women and in samples of endometrium obtained simultaneously from 49 of the women. Both ligand techniques and enzyme immunoassays were used for the assays. The steroid receptor levels were significantly lower in endometriotic tissue than in endometrium, both in cytosol and nuclear fractions. The differences were most pronounced in follicular phase. In endometrium the oestrogen and progesterone receptor levels varied during the menstrual cycle, being highest in follicular phase. In endometriotic tissue, the oestrogen receptor level remained low throughout the cycle. The progesterone receptor level, determined by immunoassay, increased during the menstrual cycle, being higher in luteal than in follicular phase. This cycle phase pattern was found neither in the nuclear progesterone receptor level nor when the cytosol was assayed with the ligand technique. In contrast to endometrium, there were no correlations between patients' age and steroid receptor levels in endometriotic tissue. The results show that oestrogen and progesterone receptors in endometriotic tissue have a different pattern during the menstrual cycle than endometrium and that the progesterone receptors synthesized are not all biologically active. These results strengthen previous data indicating differences in the hormonal regulation of the two tissue types.
Energetics of Substrate Binding and Catalysis by Class 1 (Glycosylhydrolase Family 47) α-Mannosidases Involved in N-Glycan Processing and Endoplasmic Reticulum Quality Control (2005)

Nascent glycoproteins are subject to quality control in the lumen of the endoplasmic reticulum (ER) where they can either be effectively folded with the aid of a collection of ER chaperones or they can be targeted for disposal in a process known as ER-associated degradation. Initiation of the ER disposal process involves selective trimming of N-glycans by ER alpha-mannosidase I and subsequent recognition by the ER degradation-enhancing alpha-mannosidase-like protein family of lectins, both members of glycosylhydrolase family 47. The kinetics and energetics of substrate binding and catalysis by members of this family were investigated here by the analysis of wild type and mutant forms of human ER alpha-mannosidase I. The contributions of several amino acid residues and an enzyme-associated Ca(2+) ion to substrate binding and catalysis were demonstrated by a combination of surface plasmon resonance and enzyme kinetic analyses. One mutant, E330Q, shown previously to alter general acid function within the catalytic site, resulted in an enzyme that possessed increased glycan binding affinity but compromised glycan hydrolysis. This mutant protein was used in a series of glycan binding studies with a library of mannose-containing ligands to examine the energetics of Man(9)GlcNAc(2) substrate interactions. These studies provide a framework for understanding the nature of the unusual substrate interactions within the family 47 mannosidases involved in glycan maturation and ER-associated glycoprotein degradation.
Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens (2009)

The G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of cellular processes.
Animal Models of Osteoarthritis (2008)

The complex pathobiologic changes of human joint disease, particularly osteoarthritis (OA), normally take several decades to develop and may be influenced by a multitude of genetic and environmental factors. The need to clarify the molecular events that occur in joint tissues at the onset and during the progression of OA has necessitated the use of models, which, although imperfect, can exhibit many of the pathologic features that characterize the human disease. In vitro studies have proven invaluable in defining specific molecular and cellular events in degradation of joint tissues such as cartilage. However, to fully understand the complex inter-relationship between the different disease mechanisms, joint tissues and body systems, studying OA in animal models is necessary. Models of inflammatory arthropathies have proven predictive of clinical efficacy, with therapies that are beneficial in animals having significant benefit in treatment of rheumatoid arthritis in humans. While none of the available animal models of OA can truly be said to be predictive, as no anti-OA therapies have yet proven to be disease modifying in human trials, this approach represents a cornerstone for discovery of new anti-OA therapeutic targets and drugs. In this paper the available species and models of OA are reviewed and their potential utility discussed. Keywords: osteoarthritis (OA), genetic and environmental factors, cartilage, inflammatory arthropathies, Rheumatoid arthritis (RA), anti-OA drug, mouse models
Examination of ammonia–poly(pyrrole) interactions by piezoelectric and conductivity measurements (1991)

The conducting polymer poly(pyrrole), electrochemically prepared and doped with anions, has been found to be a responsive coating for a piezoelectric gas detection system. Polymers doped with bromide, nitrate and sulphate ions were tested. It was found that samples of ammonia gas cause a measurable frequency decrease, interpreted as adsorption by the polymer coating of the quartz crystal; the linear range was 0.05–1% for mixtures of the gas in nitrogen. These signals were found to correspond to simultaneous conductivity changes of a similarly prepared poly(pyrrole) sample, showing analogies in the two sensing mechanisms. The duality of the poly(pyrrole) response increases the possibilities of using it as a gas sensor.
Using an Artificial Neural Bypass to Restore Cortical Control of Rhythmic Movements in a Human with Quadriplegia (2016)

Neuroprosthetic technology has been used to restore cortical control of discrete (non-rhythmic) hand movements in a paralyzed person. However, cortical control of rhythmic movements which originate in the brain but are coordinated by Central Pattern Generator (CPG) neural networks in the spinal cord has not been demonstrated previously. Here we show a demonstration of an artificial neural bypass technology that decodes cortical activity and emulates spinal cord CPG function allowing volitional rhythmic hand movement. The technology uses a combination of signals recorded from the brain, machine-learning algorithms to decode the signals, a numerical model of CPG network, and a neuromuscular electrical stimulation system to evoke rhythmic movements. Using the neural bypass, a quadriplegic participant was able to initiate, sustain, and switch between rhythmic and discrete finger movements, using his thoughts alone. These results have implications in advancing neuroprosthetic technology to restore complex movements in people living with paralysis.
Decreased motor inhibition in Tourette's disorder: evidence from transcranial magnetic stimulation (1997)

Findings are consistent with the hypothesis that tics in Tourette's disorder originate either from a primarily subcortical disorder affecting the motor cortex through disinhibited afferent signals or from impaired inhibition directly at the level of the motor cortex or both.
A specific 31-nucleotide domain of U1 RNA directly interacts with the 70K small nuclear ribonucleoprotein component. (1989)

We have defined the nucleotide sequence of a protein-binding domain within U1 RNA that specifically recognizes and binds both to a U1 small nuclear ribonucleoprotein component (the 70K protein) and to the previously defined RNA-binding domain of the 70K protein. We have investigated direct interactions between purified U1 RNA and 70K protein by reconstitution in vitro. Thirty-one nucleotides of U1 RNA, corresponding to stem-loop I, were required for this interaction. Nucleotides at the 5' end of U1 RNA that are involved in base pairing with the 5' splice site of pre-mRNA were not required for binding. In contrast to other reports, these findings demonstrate that a specific domain of U1 RNA can bind directly to the 70K protein independently of any other snRNP-associated proteins.
Practical Aerobic Oxidations of Alcohols and Amines with Homogeneous Copper/TEMPO and Related Catalyst Systems (2014)

Oxidations of alcohols and amines are common reactions in the synthesis of organic molecules in the laboratory and industry. Aerobic oxidation methods have long been sought for these transformations, but few practical methods exist that offer advantages over traditional oxidation methods. Recently developed homogeneous Cu/TEMPO (TEMPO = 2,2,6,6-tetramethylpiperidinyl-N-oxyl) and related catalyst systems appear to fill this void. The reactions exhibit high levels of chemoselectivity and broad functional-group tolerance, and they often operate efficiently at room temperature with ambient air as the oxidant. These advances, together with their historical context and recent applications, are highlighted in this Minireview.
Involvement of ABC transporters in melanogenesis and the development of multidrug resistance of melanoma (2009)

Because melanomas are intrinsically resistant to conventional radiotherapy and chemotherapy, many alternative treatment approaches have been developed such as biochemotherapy and immunotherapy. The most common cause of multidrug resistance (MDR) in human cancers is the expression and function of one or more ATP-binding cassette (ABC) transporters that efflux anticancer drugs from cells. Melanoma cells express a group of ABC transporters (such as ABCA9, ABCB1, ABCB5, ABCB8, ABCC1, ABCC2, and ABCD1) that may be associated with the resistance of melanoma cells to a broad range of anticancer drugs and/or of melanocytes to toxic melanin intermediates and metabolites. In this review, we propose a model (termed the ABC-M model) in which the intrinsic MDR of melanoma cells is at least in part because of the transporter systems that may also play a critical role in reducing the cytotoxicity of the melanogenic pathway in melanocytes. The ABC-M model suggests molecular strategies to reverse MDR function in the context of the melanogenic pathway, which could open therapeutic avenues towards the ultimate goal of circumventing clinical MDR in patients with melanoma.
Chromosomal Mosaicism in Human Feto-Placental Development: Implications for Prenatal Diagnosis (2014)

Chromosomal mosaicism is one of the primary interpretative issues in prenatal diagnosis. In this review, the mechanisms underlying feto-placental chromosomal mosaicism are presented. Based on the substantial retrospective diagnostic experience with chorionic villi samples (CVS) of a prenatal diagnosis laboratory the following items are discussed: (i) The frequency of the different types of mosaicism (confined placental, CPM, and true fetal mosaicisms, TFM); (ii) The risk of fetal confirmation after the detection of a mosaic in CVS stratified by chromosome abnormality and placental tissue involvement; (iii) The frequency of uniparental disomy for imprinted chromosomes associated with CPM; (iv) The incidence of false-positive and false-negative results in CVS samples analyzed by only (semi-)direct preparation or long term culture; and (v) The implications of the presence of a feto-placental mosaicism for microarray analysis of CVS and non-invasive prenatal screening (NIPS).
Antisense oligonucleotides: basic concepts and mechanisms. (2002)

Conceptual simplicity, the possibility of rational design, relatively inexpensive cost, and developments in the sequencing of human genome have led to the use of short fragments of nucleic acid, commonly called oligonucleotides, either as therapeutic agents or as tools to study gene function.
Chromosomal abnormalities and novel disease‐related regions in progression from Barrett's esophagus to esophageal adenocarcinoma (2009)

Barrett's esophagus (BE) is a metaplastic condition caused by chronic gastroesophageal reflux which represents an early step in the development of esophageal adenocarcinoma (EAC). Single-nucleotide polymorphism microarray (SNP-chip) analysis is a novel, precise, high-throughput approach to examine genomic alterations in neoplasia. Using 250K SNP-chips, we examined the neoplastic progression of BE to EAC, studying 11 matched sample sets: 6 sets of normal esophagus (NE), BE and EAC, 4 of NE and BE and 1 of NE and EAC. Six (60%) of 10 total BE samples and 4 (57%) of 7 total EAC samples exhibited 1 or more genomic abnormalities comprising deletions, duplications, amplifications and copy-number-neutral loss of heterozygosity (CNN-LOH). Several shared abnormalities were identified, including chromosome 9p CNN-LOH [2 BE samples (20%)], deletion of CDKN2A [4 BE samples (40%)] and amplification of 17q12-21.2 involving the ERBB2, RARA and TOP2A genes [3.1 Mb, 2 EAC (29%)]. Interestingly, 1 BE sample contained a homozygous deletion spanning 9p22.3-p22.2 (1.2 Mb): this region harbors only 1 known gene, basonuclin 2 (BNC2). Real-time PCR analysis confirmed the deletion of this gene and decreased the expression of BNC2 mRNA in the BE sample. Furthermore, transfection and stable expression of BNC2 caused growth arrest of OE33 EAC cells, suggesting that BNC2 functions as a tumor suppressor gene in the esophagus and that deletion of this gene occurs during the development of EAC. Thus, this SNP-chip analysis has identified several early cytogenetic events and novel candidate cancer-related genes that are potentially involved in the evolution of BE to EAC.
Smartphone-Based Point-of-Care Urinalysis Under Variable Illumination (2017)

Urine tests are performed by using an off-the-shelf reference sheet to compare the color of test strips. However, the tabular representation is difficult to use and more prone to visual errors, especially when the reference color-swatches to be compared are spatially apart. Thus, making it is difficult to distinguish between the subtle differences of shades on the reagent pads. This manuscript represents a new arrangement of reference arrays for urine test strips (urinalysis). Reference color swatches are grouped in a doughnut chart, surrounding each reagent pad on the strip. The urine test can be evaluated using naked eye by referring to the strip with no additional sheet necessary. Along with this new strip, an algorithm for smartphone based application is also proposed as an alternative to deliver diagnostic results. The proposed colorimetric detection method evaluates the captured image of the strip, under various color spaces and evaluates ten different tests for urine. Thus, the proposed system can deliver results on the spot using both naked eye and smartphone. The proposed scheme delivered accurate results under various environmental illumination conditions without any calibration requirements, exhibiting performances suitable for real-life applications and an ease for a common user.