gebhart/patrepeval huggingface dataset:
Active: A Unified Platform for Building Intelligent Web Interaction Assistants (2006)

Computer systems keep growing in complexity, processing power and Web connectivity. To leverage this rich environment and to better assist users, a new type of intelligent assistant software is required. Building intelligent assistants is a difficult task that requires expertise in many AI and engineering related fields. We believe that providing a unified tool and a set of associated methodologies to create end-to-end intelligent software will bring many benefits to this area of research. Our solution, the Active framework, introduces the original concept of active ontologies to model and implement intelligent applications in a single and coherent software environment. As an example, this paper illustrates how Active has been used to create an intelligent assistant to help mobile users retrieve online information using a multimodal dialog approach
Reg protein is overexpressed in gastric cancer cells, where it activates a signal transduction pathway that converges on ERK1/2 to stimulate growth (2002)

Reg is a growth factor with mitogenic effects on pancreatic beta cells and gastric stem cells. To date, there has been no information available on Reg-mediated intracellular signal transduction pathways. The role of Reg in the gastric carcinogenesis is also unknown. In the current study, the Reg signaling pathway in gastric cancer cell was examined. Reg treatment of MKN45 gastric cancer cells resulted in tyrosyl-phoshorylation of several cellular proteins and subsequent activation of classical MAPK, ERK1/2. Reg also stimulated thymidine incorporation in MKN45 and AGS gastric cancer cells in a dose-dependent manner. Finally, Reg was shown to be highly expressed in a large number of gastric cancers in vivo. Taken together, these data suggest that gastric cancer cells have gained the ability to overexpress Reg protein, which confer upon themselves added proliferative capacities, resulting in a considerable growth advantage.
Structure and surface exposure of protein IIs of Neisseria gonorrhoeae JS3 (1985)

Colonies of Neisseria gonorrhoeae JS3, each bearing a predominate protein II (PII) type, were derived from a progenitor transparent colony. Five distinct PIIs were identified and isolated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The PII bands were excised from gels of unlabeled whole cells and from gels containing lysates of surface-radioiodinated bacteria. These were subjected to alpha-chymotrypsin digestion and two-dimensional peptide mapping, which allowed for a comparison of both the primary structures of the PIIs and the identification of surface-exposed regions of the molecules. The results demonstrated that PIIs are unrelated to either Protein I or Protein III in structure but are closely related to one another, sharing about two-thirds of the peptides generated by alpha-chymotrypsin. The remaining third of the peptides varied with each PII, resulting in unique portions of the molecule being exposed on the bacterial surface. However, the variable peptides were not always among the exposed peptides, suggesting that the structural differences in the PIIs occur at a discrete site (or sites) of the PII molecule and not randomly throughout the protein. Such alterations can result in the exposure of distant, nonvariant portions of the molecule to the surface, perhaps by conformational changes. These bacteria can thus present a variety of new immunodeterminant sites to the host during the course of disease.
The Utility of Carbohydrate Microarrays in Glycomics (2006)

Carbohydrate microarrays are powerful tools in glycomics. Interactions of different carbohydrate structures with a wide variety of biological targets, including proteins, RNA, viruses, and whole cells, have been investigated using this technique. Binding preferences and specificities, inhibition of interactions, enzymatic activities, and structure-function relationships have been determined. Screening and characterization of antibodies have been conducted using microarrays. Binding of whole cells to the arrays has been exploited to search for novel binding proteins and to detect bacteria in blood. Here, we review the different techniques for carbohydrate microarray production and application. To illustrate the utility of arrays for glycomics research, some select experiments are discussed in greater detail.
Characteristic Recognition of N-Acetylgalactosamine by an Invertebrate C-type Lectin, CEL-I, Revealed by X-ray Crystallographic Analysis (2004)

CEL-I is a C-type lectin, purified from the sea cucumber Cucumaria echinata, that shows a high specificity for N-acetylgalactosamine (GalNAc). We determined the crystal structures of CEL-I and its complex with GalNAc at 2.0 and 1.7 A resolution, respectively. CEL-I forms a disulfide-linked homodimer and contains two intramolecular disulfide bonds, although it lacks one intramolecular disulfide bond that is widely conserved among various C-type carbohydrate recognition domains (CRDs). Although the sequence similarity of CEL-I with other C-type CRDs is low, the overall folding of CEL-I was quite similar to those of other C-type CRDs. The structure of the complex with GalNAc revealed that the basic recognition mode of GalNAc was very similar to that for the GalNAc-binding mutant of the mannose-binding protein. However, the acetamido group of GalNAc appeared to be recognized more strongly by the combination of hydrogen bonds to Arg115 and van der Waals interaction with Gln70. Mutational analyses, in which Gln70 and/or Arg115 were replaced by alanine, confirmed that these residues contributed to GalNAc recognition in a cooperative manner.
High-Voltage and High-Temperature Applications of DTMOS With Reverse Schottky Barrier on Substrate Contacts (2004)

In this letter, for the first time, application of dynamic threshold voltage MOSFET (DTMOS) with reverse Schottky barrier on substrate contacts (RSBSCs) for high voltage and high temperature is presented. By this RSBSC, DTMOS can be operated at high voltage (>0.7 V), and exhibits excellent performance at high temperature in terms of ideal subthreshold slope, low threshold voltage and high driving current.
A multimeric MR-optical contrast agent for multimodal imaging (2014)

We describe the design, synthesis and in vitro evaluation of a multimodal and multimeric contrast agent. The agent consists of three macrocyclic Gd(III) chelates conjugated to a fluorophore and possesses high relaxivity, water solubility, and is nontoxic. The modular synthesis is amenable for the incorporation of a variety of fluorophores to generate molecular constructs for a number of applications.
Extraction of vocal-tract system characteristics from speech signals (1998)

We propose methods to track natural variations in the characteristics of the vocal-tract system from speech signals. We are especially interested in the cases where these characteristics vary over time, as happens in dynamic sounds such as consonant-vowel transitions. We show that the selection of appropriate analysis segments is crucial in these methods, and we propose a selection based on estimated instants of significant excitation. These instants are obtained by a method based on the average group-delay property of minimum-phase signals. In voiced speech, they correspond to the instants of glottal closure. The vocal-tract system is characterized by its formant parameters, which are extracted from the analysis segments. Because the segments are always at the same relative position in each pitch period, in voiced speech the extracted formants are consistent across successive pitch periods. We demonstrate the results of the analysis for several difficult cases of speech signals.
Extraction of Cholesterol with Methyl-β-Cyclodextrin Perturbs Formation of Clathrin-coated Endocytic Vesicles (1999)

The importance of cholesterol for endocytosis has been investigated in HEp-2 and other cell lines by using methyl-beta-cyclodextrin (MbetaCD) to selectively extract cholesterol from the plasma membrane. MbetaCD treatment strongly inhibited endocytosis of transferrin and EGF, whereas endocytosis of ricin was less affected. The inhibition of transferrin endocytosis was completely reversible. On removal of MbetaCD it was restored by continued incubation of the cells even in serum-free medium. The recovery in serum-free medium was inhibited by addition of lovastatin, which prevents cholesterol synthesis, but endocytosis recovered when a water-soluble form of cholesterol was added together with lovastatin. Electron microscopical studies of MbetaCD-treated HEp-2 cells revealed that typical invaginated caveolae were no longer present. Moreover, the invagination of clathrin-coated pits was strongly inhibited, resulting in accumulation of shallow coated pits. Quantitative immunogold labeling showed that transferrin receptors were concentrated in coated pits to the same degree (approximately sevenfold) after MbetaCD treatment as in control cells. Our results therefore indicate that although clathrin-independent (and caveolae-independent) endocytosis still operates after removal of cholesterol, cholesterol is essential for the formation of clathrin-coated endocytic vesicles.
Variable structure systems with sliding modes (1977)

Variable structure systems consist of a set of continuous subsystems together with suitable switching logic. Advantageous properties result from changing structures according to this switching logic. Design and analysis for this class of systems are surveyed in this paper.
Isolation of two novel myb‐like genes from Arabidopsis and studies on the DNA‐binding properties of their products (1995)

Two novel myb-like genes (atmyb6 and atmyb7) were isolated from an Arabidopsis thaliana cDNA library. The entire proteins or the Myb domains encoded by the genes were expressed as fusion proteins in Escherichia coli. The DNA-binding domain of the murine c-Myb was also expressed in the same way for use in comparative studies. The fusion proteins were examined for their DNA-binding activity using the animal c-Myb DNA-binding site (MBS) and the binding site of the maize P gene product (PBS). The Myb domain of Atmyb6 bound to PBS more efficiently than to MBS. Complete Atmyb6 and Atmyb7 proteins preferentially bound to PBS but not MBS. This suggests that the in vitro binding consensus sequences for both Atmyb6 and Atmyb7 are similar to PBS. The binding of the Myb domain of Atmyb6 to both PBS and MBS raises the possibility that the protein recognizes multiple sequences in vivo. The third alpha-helix and three adjacent amino acids in the third repeat (R3) of c-Myb was replaced with the analogous sequence of Atmyb6 to create a chimeric Myb protein. This chimeric protein bound to PBS with a low affinity but failed to bind to MBS. Thus the binding pattern of the chimeric Myb protein is similar to that of the Atmyb6. This result suggests that the last 20 amino acids in the R3 repeat of Atmyb6 play a major role in DNA-binding.
Efficacy of a five-drug combination including ritonavir, saquinavir and efavirenz in patients who failed on a conventional triple-drug regimen: phenotypic resistance to protease inhibitors predicts outcome of therapy (1999)

Our results indicate that the combination of ritonavir, saquinavir and efavirenz is safe and effective at 24 weeks in over two-thirds of patients who previously failed on highly active antiretroviral therapy, and that the determination of phenotypic resistance may be of greater value than the detection of resistance mutations to predict the outcome of salvage therapy in this setting.
Structural diversity of self-cleaving ribozymes (2000)

In vitro selection was used to isolate Mg(2+)-dependent self-cleaving ribozymes from random sequence. Characterization of representative clones revealed the emergence of at least 12 classes of ribozymes that adopt distinct secondary structure motifs. Only one class corresponds to a previously known structural motif, that of the naturally occurring hammerhead ribozyme. Each ribozyme promotes self-cleavage via an internal phosphoester transfer reaction involving the adjacent 2'-hydroxyl group with a chemical rate enhancement of between 10(3)- and 10(6)-fold greater than the corresponding uncatalyzed rate. These findings indicate that RNA can form a multitude of secondary and tertiary structures that promote cleavage by internal phosphoester transfer. Upon further in vitro selection, a class I ribozyme that adopts an "X motif" structure dominates over all other ribozymes in the population. Thus, self-cleaving RNAs isolated by in vitro selection from random-sequence populations can rival the catalytic efficiency of natural ribozymes.
Patterning colloidal monolayer films using microcontact particle stripping (2007)

We combined the basic component of microcontact printing (μCP), the use of an elastomeric stamp to transfer a pattern, with colloidal lithography, a parallel technique to obtain arrays of nanostructures at surfaces. This novel method, entitled microcontact particle stripping (μCPS), uses a stamp to selectively remove the pre-adsorbed particles located in the contact regions, leaving the particles in the non-contact regions unaffected. The particles, in the nanopatterned regions, can further be used as a lithographic mask.
The Parker Flex-Tip Tube versus a Standard Tube for Fiberoptic Orotracheal Intubation (2003)

During oral fiberoptic intubation, the use of the Parker Flex-Tip tube is associated with greater incidence of initial success of passage of the tube into trachea when compared to a standard endotracheal tube.
Hormone replacement therapy. Current controversies. (2003)

Hormone replacement therapy has had a controversial history since its introduction for medical use several decades ago. Current evidence indicates that users of hormone replacement therapy have an increased risk of venous thromboembolism, stroke, and coronary heart disease compared to non-users. Among users, the risk of breast cancer is modestly increased. This effect becomes apparent after 4 to 5 years use and primarily with use of combination estrogen plus progestin products. The risk of colorectal cancer is decreased with use of hormone replacement therapy. In addition, the risk of osteopenia and osteoporosis is decreased as is the risk of osteoporotic fracture.
IMT-2000: service provider's perspective (1997)

This article provides an overview of the important issues for the development of the next generation of wireless access systems from the service provider's perspective. The specifications for this future global wireless access system (IMT-2000) are currently being developed within the International Telecommunication Union (ITU).
B-raf, a new member of the raf family, is activated by DNA rearrangement. (1988)

Complementary DNA clones of a putative transforming gene were isolated from NIH 3T3 cells transformed with human Ewing sarcoma DNA. The gene was termed B-raf because it is related to but distinct from c-raf and A-raf. It appears that substitution in the amino-terminal portion of the normal B-raf protein confers transforming activity to the gene.
Electrical Stimulation Accelerates Axonal and Functional Peripheral Nerve Regeneration across Long Gaps (2011)

Short-term low-frequency electrical stimulation (ESTIM) of proximal peripheral nerve stumps prior to end-to-end coaptation or tubular bridging of small distances has been reported to increase preferential motor reinnervation and functional motor recovery in animal models and human patients undergoing carpal tunnel release surgery. We investigated the effects of ESTIM on regeneration across rat sciatic nerve gaps, which exceed distances that allow spontaneous regeneration. Three different reconstruction approaches were combined with ESTIM in the experimental groups. Nerve gaps (13 mm) were bridged using (I) nerve autotransplantation, (II) transplantation of differentially filled silicone tubes, or (III) transplantation of tubular grafts containing fibroblast growth factor-2 overexpressing Schwann cells (SCs) for gene therapy. The regeneration outcome was followed for up to 8 weeks, and functionally as well as histomorphometrically analyzed in comparison to non-stimulated control groups. Combining ESTIM with nerve autotransplantation significantly increased the nerve fiber density in the regenerated nerve, and the grade of functional recovery as detected by electrodiagnostic recordings from the gastrocnemius muscle. The combination of ESTIM with transplantation of naïve SCs increased the regeneration of gap-bridging nerve tissue. Although macroscopic tissue regeneration was not further improved after combining ESTIM with FGF-2(21/23-kD) gene therapy, the latter resulted in a high rate of regenerated nerves that functionally reconnected to the target muscle. Based on our results, brief ESTIM shows high potential to accelerate axonal as well as functional (motor and sensory) outcomes in the clinical setting of peripheral nerve gap reconstruction in human patients.
Phasor approach to fluorescence lifetime microscopy distinguishes different metabolic states of germ cells in a live tissue (2011)

We describe a label-free imaging method to monitor stem-cell metabolism that discriminates different states of stem cells as they differentiate in living tissues. In this method we use intrinsic fluorescence biomarkers and the phasor approach to fluorescence lifetime imaging microscopy in conjunction with image segmentation, which we use to introduce the concept of the cell phasor. In live tissues we are able to identify intrinsic fluorophores, such as collagen, retinol, retinoic acid, porphyrin, flavins, and free and bound NADH. We have exploited the cell phasor approach to detect a trend in metabolite concentrations along the main axis of the Caenorhabditis elegans germ line. This trend is consistent with known changes in metabolic states during differentiation. The cell phasor approach to lifetime imaging provides a label-free, fit-free, and sensitive method to identify different metabolic states of cells during differentiation, to sense small changes in the redox state of cells, and may identify symmetric and asymmetric divisions and predict cell fate. Our method is a promising noninvasive optical tool for monitoring metabolic pathways during differentiation or disease progression, and for cell sorting in unlabeled tissues.
Tunable diode laser based spectroscopic system for ammonia detection in human respiration (1987)

A high-resolution infrared optical absorption spectroscopy system based on lead-salt tunable diode lasers as light sources has been developed for detection and monitoring of trace gases by resolving their narrow-width absorption bands. The system is a double beam setup, where a reference cell containing the monitored gas is used for tuning and locking the laser light frequency to that of a desired absorption line and a measurement cell where the examined gas flows continuously at a reduced pressure. Frequency modulation of the laser light is achieved by square waveform modulation of its current source and both the frequency locking and signal analysis devices are based on sample-and-hold techniques. The system capability is demonstrated by the monitoring of ammonia traces in human breath. Gas trace monitoring in respiration may prove to be an effective medical diagnostic method.
Fumaric acid production by fermentation (2008)

The potential of fumaric acid as a raw material in the polymer industry and the increment of cost of petroleum-based fumaric acid raises interest in fermentation processes for production of this compound from renewable resources. Although the chemical process yields 112% w/w fumaric acid from maleic anhydride and the fermentation process yields only 85% w/w from glucose, the latter raw material is three times cheaper. Besides, the fermentation fixes CO2. Production of fumaric acid by Rhizopus species and the involved metabolic pathways are reviewed. Submerged fermentation systems coupled with product recovery techniques seem to have achieved economically attractive yields and productivities. Future prospects for improvement of fumaric acid production include metabolic engineering approaches to achieve low pH fermentations.
Tau consists of a set of proteins with repeated C-terminal microtubule-binding domains and variable N-terminal domains. (1989)

Tau proteins consist of a family of proteins, heterogeneous in size, which associate with microtubules in vivo and are induced during neurite outgrowth. In humans, tau is one of the major components of the pathognomonic neurofibrillary tangles in Alzheimer's disease brain. Screening of a cDNA library prepared from bovine brain led to the isolation of several cDNA clones encoding tau proteins with different N termini and differing by insertions or deletions, suggesting differential splicing of the tau transcripts. One of the N-terminal domains and the repeated C-terminal domain of the encoded tau proteins are recognized by polyclonal antibodies to bovine tau. The bovine tau proteins are highly homologous to murine and human tau, especially within the repeated C-terminal domain. Compared with murine and human tau, bovine tau contains the insertion of three longer segments, one of which is an additional characteristic repeat. Portions of tau proteins generated by in vitro translation were used to show that these repeats represent tubulin-binding domains, two of which are sufficient to bind to microtubules assembled from purified tubulin in the presence of taxol.
Visual Recognition and Efficient Isolation of Apoptotic Cells with Fluorescent-Magnetic-Biotargeting Multifunctional Nanospheres (2007)

Our results show that fluorescent-magnetic-biotargeting trifunctional nanospheres can be a powerful tool for rapidly recognizing, magnetically enriching and sorting, and simultaneously identifying different kinds of cells.
Postoperative Impairment of Cognitive Function in Rats (2007)

These results suggest that splenectomy performed during neuroleptic anesthesia triggers a cognitive decline that is associated with a hippocampal inflammatory response that seems to be due to proinflammatory cytokine-dependent activation of glial cells.
Human calcitonin gene related peptide: a potent endogenous vasodilator in man (1986)

In addition to calcitonin and katacalcin, it is now known that the human calcitonin gene encodes a novel peptide called calcitonin gene related peptide (CGRP). In experimental animals, CGRP produces vasodilatation and complex changes in plasma calcium. We have now assessed its biological activity in man by infusing human CGRP (hCGRP) into six normal volunteers. hCGRP (545 pmol/min) caused the diastolic pressure to fall from 64 +/- 5 to 55 +/- 7 mmHg (P less than 0.05), the heart rate to increase from 61 +/- 7 to 87 +/- 5 beats/min (P less than 0.05) and the skin temperature to increase from 33.7 +/- 0.9 to 34.9 +/- 0.5 degrees C. Plasma noradrenaline increased from 481 +/- 126 to 835 +/- 65 pg/ml (P less than 0.05) and plasma adrenaline from 57 +/- 17 to 82 +/- 12 pg/ml (P less than 0.05). There were no significant changes in the albumin-corrected plasma calcium. hCGRP is thus a potent endogenous vasodilator in man and is in fact more potent than any other known vasodilator. Together with the observations that CGRP circulates in normal subjects at relatively high concentration (approximately 25 pmol/l) and that CGRP is present in perivascular nerves, this study suggests a possible role for CGRP in controlling peripheral vascular tone in man.