gebhart/patrepeval huggingface dataset:
Developmental changes in heparan sulfate expression: in situ detection with mAbs. (1992)

Two mAbs that are specific for heparan sulfate-related epitopes have been raised and used to analyze the cellular and tissular distribution of this glycosaminoglycan during development. mAb 10E4 reacts with an epitope that occurs in native heparan sulfate chains and that is destroyed by N-desulfation of the glycosaminoglycan. The antibody does not react with hyaluronate, chondroitin sulfate, or DNA, and reacts only poorly with heparin. The reactivity of proteoglycan extracts or tissue sections with the 10E4 antibody is completely abolished by heparitinase, but is only partially affected by heparinase. mAb 3G10, in contrast, reacts only with heparitinase-treated heparan sulfate chains, proteoglycans, or tissue sections. The 3G10 epitope is destroyed by treatment with mercuric acetate, which indicates that the desaturated uronate generated by the lyase is essential for the reactivity of the antibody. The 3G10 epitope is not generated by treating heparan sulfate proteoglycans with heparinase or chondroitin sulfate proteoglycans with chondroitin sulfate lyases, which indicates that the 3G10 antibody recognizes desaturated uronates that occur in specific structural contexts. The antibody 10E4 and, after heparitinase treatment, the antibody 3G10 decorate the surfaces of many cell types and the extracellular matrix in proximity of the cells, in particular, the basement membranes. The analysis of embryonic and adult tissues reveals important temporal and regional differences in the abundance of the 10E4 and 3G10 epitopes at these sites. Moreover, the staining pattern of the two antibodies is not always superimposable, which is indicative of regional differences in the exposure or structure of the tissular heparan sulfates. As a whole the results suggest that heparan sulfate abounds at sites of active morphogenesis and that the expression of this glycosaminoglycan is developmentally regulated.
A simple microassay for erythropoietin based on 3H-thymidine incorporation into spleen cells from phenylhydrazine treated mice. (1983)

Spleens taken from B6C3F1 mice on the third day following the second of 2 daily injections of phenylhydrazine HCl (60 mg/kg) contain approximately 10 times the number of cells (i.e., 10(9) cells) found in spleens from normal mice. More than 90% of these spleen cells are recognizable erythroid and form the basis of a new in vitro microassay for erythropoietin (Ep) which uses 3H-thymidine incorporation as an endpoint. This assay takes 24 h and can be carried out in the presence of either 20% FCS or a well-defined serum substitute. Under the conditions used, Ep levels from 30 mU/well down to as little as 0.2 mU/well can be accurately measured with a corresponding variation in counts of 50-100-fold. One spleen is sufficient for 1000 triplicate Ep determinations, and the use of this microassay procedure requires only very small (1-60) microliters) samples for evaluation. Preliminary studies with human plasma suggest that this assay may be more specific for Ep than established in vitro 59Fe bioassay methods.
Calcium Channels, Stores, and Oscillations (1990)

MULTIPLE CaH ENTRY MECHANISMS ... . . . . . . . . 716 Diversity of Voltage-gated Ca2+ Channels (VOCs) 7 17 Common Features of Voltage-gated CaN Channels .. . . 72 1 Subunit Composition of DHP-sensitive CaN Channels 722 Structural Properties of DHP-resistant CaN Channels ........ . . . . .... . . . . . . . . . . . . . . . . . . . . . . . . . . . . 725 Receptor-operated CaN Channels (ROCs) 725 Second Messenger-operated CaN Channels (SMOCs) 726 Mechanically Operated CaN Channels (MOCs) 727 Tonically Active (background) Ca2+ Channels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 727 Gap Junction Channels ......... 727
Spin-transfer torque for continuously variable magnetization (2006)

We report quantum and semiclassical calculations of spin current and spin-transfer torque in a free-electron Stoner model for systems where the magnetization varies continuously in one dimension. Analytic results are obtained for an infinite spin spiral and numerical results are obtained for realistic domain wall profiles. The adiabatic limit describes conduction electron spins that follow the sum of the exchange field and an effective, velocity-dependent field produced by the gradient of the magnetization in the wall. Nonadiabatic effects arise for short domain walls but their magnitude decreases exponentially as the wall width increases. Our results cast doubt on the existence of a recently proposed nonadiabatic contribution to the spin-transfer torque due to spin-flip scattering.
Modulation of food intake by peripherally administered amylin (1994)

Amylin has been demonstrated to produce anorexia in rodents. Its mechanism of action is unknown. We have studied the effect of amylin on food intake in mice in a variety of paradigms to determine whether it inhibits food intake by a peripheral mechanism of action. In addition, we determined its effect in genetically obese mice models and whether its effects differed in aged mice. Cholecystokinin is the prototypic satiety agent. The effects of amylin on reducing food intake were not attenuated by the cholecystokinin antagonist L-364718, suggesting that it does not produce its effect through the release of cholecystokinin. A number of gastrointestinal peptides produce anorexia by stimulating ascending vagal fibers. For this reason, we studied the effect of truncal vagotomy on the suppression of feeding induced by amylin. Vagotomy did not prevent amylin from inhibiting food intake. Amylin was equally effective at reducing food intake in genetically obese (ob/ob) and lean (ob/c) mice and in diabetic (db/db) and lean (db/c) mice. Amylin effectively suppressed food intake in mice over the age of 4-22 mo. These studies further support the role of the pancreatic hormone amylin as a peripherally acting satiety agent.
The Chemical Versatility of Natural-Product Assembly Lines (2007)

Microbial natural products of both polyketide and nonribosomal peptide origin have been and continue to be important therapeutic agents as antibiotics, immunosupressants, and antitumor drugs. Because the biosynthetic genes for these metabolites are clustered for coordinate regulation, the sequencing of bacterial genomes continues to reveal unanticipated biosynthetic capacity for novel natural products. The re-engineering of pathways for such secondary metabolites to make novel molecular variants will be enabled by understanding of the chemical logic and protein machinery in the producer microbes. This Account analyzes the chemical principles and molecular logic that allows simple primary metabolite building blocks to be converted to complex architectural scaffolds of polyketides (PK), nonribosomal peptides (NRP), and NRP-PK hybrids. The first guiding principle is that PK and NRP chains are assembled as thioseters tethered to phosphopantetheinyl arms of carrier proteins that serve as thiotemplates for chain elongation. The second principle is that gate keeper protein domains select distinct monomers to be activated and incorporated with positional specificity into the growing natural product chains. Chain growth is via thioclaisen condensations for PK and via amide bond formation for elongating NRP chains. Release of the full length acyl/peptidyl chains is mediated by thioesterases, some of which catalyze hydrolysis while others catalyze regiospecific macrocyclization to build in conformational constraints. Tailoring of PK and NRP chains, by acylation, alkylation, glycosylation, and oxidoreduction, occurs both during tethered chain growth and after thioesterase-mediated release. Analysis of the types of protein domains that carry out chain initiation, elongation, tailoring, and termination steps gives insight into how NRP and PK biosynthetic assembly lines can be redirected to make novel molecules.
Rapid purification of synthetic oligonucleotides: a convenient alternative to high-performance liquid chromatography and polyacrylamide gel electrophoresis. (1990)

A new method has been developed to purify and detritylate milligram amounts of synthetic oligonucleotides. Dimethoxytrityl oligonucleotides from 15 to 100 nucleotides in length are applied in triethylammonium acetate or concentrated ammonium hydroxide to a disposable chromatographic cartridge, the NENSORB PREP Nucleic Acid Purification Cartridge. Salts, failure sequences and synthetic by-products are washed away while the desired, full-length, dimethoxytrityl oligonucleotide remains bound to the cartridge. The trityl group is hydrolyzed from the 5'-end of the oligonucleotide with an acid wash and then the purified oligonucleotide is eluted with 35% methanol. Oligonucleotides are recovered salt-free with purities greater than 95%. NENSORB PREP-purified primers provide superior sequence data compared to similar primers used without purification and equivalent data to primers purified by polyacrylamide gel electrophoresis when used in manual radiometric Sanger sequencing.
Adenosine: electrophysiologic effects and therapeutic use for terminating paroxysmal supraventricular tachycardia. (1983)

Adenosine was administered intravenously to 17 patients undergoing intracardiac electrophysiologic studies. At a mean dose of 179 +/- 88 micrograms/kg (+/- SD), adenosine suppressed sinus node automaticity and depressed atrioventricular (AV) nodal conduction. These effects were less than 20 sec in duration and were not influenced by muscarinic blockade with atropine (0.02 to 0.03 mg/kg). Adenosine at this dose had no effect on antegrade conduction over accessory pathways in patients with Wolff-Parkinson-White syndrome. No independent hemodynamic effects were observed. In six patients, adenosine was administered intravenously during stimulation-induced paroxysmal supraventricular tachycardia. In the five patients in whom the reentry loop of their tachycardia included the AV node, adenosine at a mean dose of 83 +/- 35 micrograms/kg (+/- SD) terminated their tachycardia within 20 sec after peripheral intravenous injection. The dose of adenosine required to terminate these tachycardias did not produce manifest sinus node suppression, and sinus rhythm promptly resumed in all patients. Adenosine did not terminate either supraventricular tachycardia due to intra-atrial reentry or atrial flutter, but did produce transient AV block during these arrhythmias. Our findings demonstrate that the human sinus and AV nodes are sensitive to physiologic doses of adenosine and that adenosine may be used safely and effectively to terminate acute episodes of supraventricular tachycardia that involve the AV node in the reentry pathway.
EEG Recorded from the Ear: Characterizing the Ear-EEG Method (2015)

Highlights Auditory middle and late latency responses can be recorded reliably from ear-EEG.For sources close to the ear, ear-EEG has the same signal-to-noise-ratio as scalp.Ear-EEG is an excellent match for power spectrum-based analysis. A method for measuring electroencephalograms (EEG) from the outer ear, so-called ear-EEG, has recently been proposed. The method could potentially enable robust recording of EEG in natural environments. The objective of this study was to substantiate the ear-EEG method by using a larger population of subjects and several paradigms. For rigor, we considered simultaneous scalp and ear-EEG recordings with common reference. More precisely, 32 conventional scalp electrodes and 12 ear electrodes allowed a thorough comparison between conventional and ear electrodes, testing several different placements of references. The paradigms probed auditory onset response, mismatch negativity, auditory steady-state response and alpha power attenuation. By comparing event related potential (ERP) waveforms from the mismatch response paradigm, the signal measured from the ear electrodes was found to reflect the same cortical activity as that from nearby scalp electrodes. It was also found that referencing the ear-EEG electrodes to another within-ear electrode affects the time-domain recorded waveform (relative to scalp recordings), but not the timing of individual components. It was furthermore found that auditory steady-state responses and alpha-band modulation were measured reliably with the ear-EEG modality. Finally, our findings showed that the auditory mismatch response was difficult to monitor with the ear-EEG. We conclude that ear-EEG yields similar performance as conventional EEG for spectrogram-based analysis, similar timing of ERP components, and equal signal strength for sources close to the ear. Ear-EEG can reliably measure activity from regions of the cortex which are located close to the ears, especially in paradigms employing frequency-domain analyses.
Essential Amino Acids for Substrate Binding and Catalysis of Human Flap Endonuclease 1 (1996)

Human flap endonuclease 1 (FEN-1) is a member of the structure-specific endonuclease family and is involved in DNA repair. Eight restrictively conserved amino acids in FEN-1 have been converted individually to an alanine to elucidate their roles in specific DNA substrate binding and catalysis. Flap endonuclease activity of the wild type and mutant enzymes was measured by kinetic flow cytometry. Mutants D34A, D86A, and D181A lost their cleavage activity completely but retained substrate binding ability, as measured by their ability to inhibit the wild type enzyme in a competition assay. This indicates that these amino acids contribute to integrity of the enzyme active site. Loss of both binding and cleavage competency for the flap substrate by mutants E156A, G231A, and D233A suggests that these amino acids are involved in substrate binding. Mutants R103A and D179A retained wild type-like enzyme activity.
OpenNMT: Open-Source Toolkit for Neural Machine Translation (2017)

We describe an open-source toolkit for neural machine translation (NMT). The toolkit prioritizes efficiency, modularity, and extensibility with the goal of supporting NMT research into model architectures, feature representations, and source modalities, while maintaining competitive performance and reasonable training requirements. The toolkit consists of modeling and translation support, as well as detailed pedagogical documentation about the underlying techniques.
Accumulation of trimethylamine and trimethylamine-N-oxide in end-stage renal disease patients undergoing haemodialysis (2006)

TMA and TMNO accumulate between haemodialysis sessions in ESRD patients, but are efficiently removed during a single haemodialysis session.
THz imaging of skin tissue &#x2014; Exploiting the strong reflectivity of liquid water (2010)

We present a novel system for imaging burns and other lesions of human skin tissue utilizing the acute sensitivity of THz radiation to water concentration. It is a THz impulse radar that carries out reflective, 2D imaging with a photoconductive-switch wideband illuminator, a Schottky-rectifying gated receiver, and mechanical scanning. It has been used to image burns with ~2 mm spatial resolution in ≈5 min over 1 KPixel and 1 sq inch.
Nonsense codons can reduce the abundance of nuclear mRNA without affecting the abundance of pre-mRNA or the half-life of cytoplasmic mRNA. (1993)

The abundance of the mRNA for human triosephosphate isomerase (TPI) is decreased to approximately 20% of normal by frameshift and nonsense mutations that cause translation to terminate at a nonsense codon within the first three-fourths of the reading frame. Results of previous studies inhibiting RNA synthesis with actinomycin D suggested that the decrease is not attributable to an increased rate of cytoplasmic mRNA decay. However, the step in TPI RNA metabolism that is altered was not defined, and the use of actinomycin D, in affecting all polymerase II-transcribed genes, could result in artifactual conclusions. In data presented here, the nonsense codon-mediated reduction in the level of TPI mRNA is shown to be characteristic of both nuclear and cytoplasmic fractions of the cell, indicating that the altered metabolic step is nucleus associated. Neither aberrancies in gene transcription nor aberrancies in RNA splicing appear to contribute to the reduction since there were no accompanying changes in the amount of nuclear run-on transcription, the level of any of the six introns in TPI pre-mRNA, or the size of processed mRNA in the nucleus. Deletion of all splice sites that reside downstream of a nonsense codon does not abrogate the reduction, indicating that the reduction takes place independently of the splicing of a downstream intron. Experiments that placed TPI gene expression under the control of the human c-fos promoter, which can be transiently activated by the addition of serum to serum-deprived cells, verified that there is no detectable effect of a nonsense codon on the turnover of cytoplasmic mRNA.
Changes in microRNA expression levels correlate with clinicopathological features and prognoses in endometrial serous adenocarcinomas (2009)

This study aimed to determine the expression profiles of microRNAs (miRNAs) in endometrial serous adenocarcinoma and to examine the association between miRNA expression and clinical outcomes. Twenty-one patients diagnosed with endometrial serous adenocarcinoma between January 2001 and December 2006 were enrolled. miRNA expression profiles were examined using miRNA microarray and qRT-PCR. miRNA expression levels were correlated with clinicopathological variables and survival rates. A total of 120 miRNAs were differentially expressed in endometrial serous adenocarcinoma compared to normal endometria. Of these, 54 miRNAs were down-regulated (>2-fold), including miR-101, miR-10b*, miR-152, and miR-29b, and the remainder were up-regulated (>2-fold), including miR-200a, miR-200b, and miR-205. Decreased expression of miR-10b*, miR-29b, and miR-455-5p was correlated with vascular invasion (P = 0.048, P = 0.013, and P = 0.032, respectively). Univariate analysis revealed that lower expression of miR-101, miR-10b*, miR-139-5p, miR-152, miR-29b, and miR-455-5p was significantly correlated with poor overall survival (P < 0.05), and reduced expression of miR-152, miR-29b, and miR-455-5p was significantly correlated with poor disease-free survival (P < 0.05). Multivariate analysis demonstrated that decreased expression of miR-152 (P = 0.021) was a statistically independent risk factor for overall survival, and decreased expression levels of miR-101 (P = 0.016) and miR-152 (P = 0.010) were statistically independent risk factors for disease-free survival. In addition, transfection of miR-101 or miR-152 precursors into an endometrial serous carcinoma cell line inhibited cell growth (P < 0.0001 and P = 0.01, respectively). Moreover, strong positive immunoreactivity of cyclooxygenase-2 (COX-2) was significantly correlated with down-regulation of miR-101 (P = 0.035). These findings suggest that the dysregulation of miRNAs is associated with the poor prognosis in endometrial serous adenocarcinoma patients.
Cognitive Enhancers as Adjuncts to Psychotherapy (2004)

These pilot data provide initial support for the use of acute dosing of DCS as an adjunct to exposure-based psychotherapy to accelerate the associative learning processes that contribute to correcting psychopathology.
<title>HelpMate autonomous mobile robot navigation system</title> (1991)

HelpMate is a mobile robotic materials transport system that performs fetch and carry tasks at Danbury Hospital. It autonomously navigates along the main arteries of the hospital crossing between buildings via interconnecting hallways and uses radio to communicate with the elevator. HelpMate uses sensor information to follow straight paths down hallways and to successfully reach its destination. Also HelpMate has the ability to sense obstacles in its path and plot a course around them. A two part vision system is employed on HelpMate to aid in navigation and obstacle avoidance. One part determines the vehicle''s orientation and position in the hallway by looking at the ceiling lights. The other part uses structured light projecting forward into the immediate path of the robot to detect obstacles.
Reducing the peak-to-average power ratio in OFDM radio transmission systems (2002)

An important difficulty which has to be solved in OFDM transmission systems is the large peak-to-average power ratio of the OFDM signal. Without any measures, the signal is limited by the power amplifier in the transmitter which causes interference both of the signal itself and in adjacent frequency bands. A method is proposed which considerably reduces the peak-to-average power ratio of the OFDM signal by means of signal processing.
Mucosal Adjuvanticity and Immunogenicity of LTR72, a Novel Mutant of Escherichia coli Heat-labile Enterotoxin with Partial Knockout of ADP-ribosyltransferase Activity (1998)

Heat-labile Escherichia coli enterotoxin (LT) has the innate property of being a strong mucosal immunogen and adjuvant. In the attempt to reduce toxicity and maintain the useful immunological properties, several LT mutants have been produced. Some of these are promising mucosal adjuvants. However, so far, only those that were still toxic maintained full adjuvanticity. In this paper we describe a novel LT mutant with greatly reduced toxicity that maintains most of the adjuvanticity. The new mutant (LTR72), that contains a substitution Ala --> Arg in position 72 of the A subunit, showed only 0.6% of the LT enzymatic activity, was 100,000-fold less toxic than wild-type LT in Y1 cells in vitro, and was at least 20 times less effective than wild-type LT in the rabbit ileal loop assay in vivo. At a dose of 1 microg, LTR72 exhibited a mucosal adjuvanticity, similar to that observed with wild-type LT, better than that induced by the nontoxic, enzymatically inactive LTK63 mutant, and much greater than that of the recombinant B subunit. This trend was consistent for both the amounts and kinetics of the antibody induced, and priming of antigen-specific T lymphocytes. The data suggest that the innate high adjuvanticity of LT derives from the independent contribution of the nontoxic AB complex and the enzymatic activity. LTR72 optimizes the use of both properties: the enzymatic activity for which traces are enough, and the nontoxic AB complex, the effect of which is dose dependent. In fact, in dose-response experiments in mice, 20 microg of LTR72 were a stronger mucosal adjuvant than wild-type LT. This suggests that LTR72 may be an excellent candidate to be tested in clinical trials.
Beyond Lambert: reconstructing surfaces with arbitrary BRDFs (2002)

We address an open and hitherto neglected problem in computer vision, how to reconstruct the geometry of objects with arbitrary and possibly anisotropic bidirectional reflectance distribution functions (BRDFs). Present reconstruction techniques, whether stereo vision, structure from motion, laser range finding, etc. make explicit or implicit assumptions about the BRDF. Here, we introduce two methods that were developed by re-examining the underlying image formation process; the methods make no assumptions about the object's shape, the presence or absence of shadowing, or the nature of the BRDF which may vary over the surface. The first method takes advantage of Helmholtz reciprocity, while the second method exploits the fact that the radiance along a ray of light is constant. In particular, the first method uses stereo pairs of images in which point light sources are co-located at the centers of projection of the stereo cameras. The second method is based on double covering a scene's incident light field; the depths of surface points are estimated using a large collection of images in which the viewpoint remains fixed and a point light source illuminates the object. Results from our implementations lend empirical support to both techniques.