gebhart/patrepeval huggingface dataset:
Two‐dimensional RPLC‐RPLC system with different pH in two dimensions for separation of alkaloids from Corydalis yanhusuo W. T. Wang (2009)

An effective method utilizing the same RP chromatographic column with different pH in first and second LC dimensions has been developed for separation of the basic compounds from traditional Chinese medicines (TCMs). In this work, the alkaloids in Corydalis yanhusuo which is an important TCM were selected as a model to develop the method. The additives and pH values of the mobile phase were optimized in this work. To investigate the feasibility of this method, off-line mode separation was performed in the experiments. According to the UV-absorption intensity, there were eight fractions collected in acidic conditions. All the fractions were analyzed in basic conditions. The results showed that the chromatographic selectivities were significantly different in the separations performed with acidic and alkaline elution systems. Complementary separation was achieved in this work. It is demonstrated that this method would be an effective tool for alkaloids research. Based on the different pH of the mobile phase in this method, it could also be suitable to analyze compounds which were sensible to the pH of the solution.
Phase unwrapping in the three-point Dixon method for fat suppression MR imaging. (1994)

This method of 3PD data reconstruction appears to be promising for routine application of fat suppression MR imaging in a clinical setting.
Accuracy of Atrial Tachyarrhythmia Detection in Implantable Devices with Arrhythmia Therapies (2004)

The clinical application of atrial tachyarrhythmia (AT) episode data stored by implantable devices is presently limited by the high proportion of inappropriate detection. We quantified the percentage of inappropriate AT detection in two implantable devices with AT diagnostics and therapies via meta-analysis of stored AT episodes from a number of clinical trials. The AT500 and GEM III AT, contain dual chamber logic to discriminate AT from ventricular tachycardia and far-field R wave (FFRW) oversensing using dual chamber bipolar electrograms. A subset of data from four clinical trials of 1,142 patients was considered. Manual analysis was performed on 21,553 stored episodes with atrial EGM and marker channel from 409 patients with stored episodes and the market-released device detection configuration. The percentage of episodes with inappropriate detection and termination was evaluated and compared between septal and nonseptal lead locations. The percentage of inappropriately detected episodes receiving ATP therapy was also determined. The percentage of episodes appropriately detected and the percentage of net episode duration (i.e., burden) recorded by the device were also determined from a separate analysis of 24-hour Holter recordings from a subset of 40 patients from one trial. Adjusted estimates of the percentage of appropriate [corrected] detection were 95.3% (93.5-96.7; 95% CI) for AT500 and 95.7% (84.3-98.9) for GEM III AT. Inappropriate detection was primarily due to FFRW oversensing or brief runs of premature atrial contractions (PACs). The device detected 100% of the sustained atrial arrhythmia episodes and 95.3% (range 76.1-99.9) of the net AT duration observed on the Holter recordings. AT detection was not influenced by atrial lead location. Appropriate detection of normal sinus rhythm at episode termination was 83.7% (80.7-86.3) for AT500 and 92.1% (84.5-96.2) for GEM III AT. Accurate detection and discrimination of FFRWs validates the reliability of AT diagnostic data and decreases the risk of inappropriate device therapy.
Arthritis induced in rats by cloned T lymphocytes responsive to mycobacteria but not to collagen type II. (1984)

We have been studying the pathogenesis of adjuvant arthritis in rats using a long-term cell line of T lymphocytes, the A2 line, which can induce polyarthritis and can also be used to vaccinate rats against adjuvant arthritis. Although line A2 was selected for its proliferative response to mycobacteria, it also responded to collagen type II. To elucidate its role of responsiveness to collagen type II and the relationship between arthritogenicity and vaccination, we cloned A2 and selected a subline A2b. We now report that subline A2b, which bore a marker of helper/delayed hypersensitivity T lymphocytes, was strongly arthritogenic, but could not vaccinate against arthritis. Moreover, A2b showed no response to collagen type II. Therefore, reactivity to collagen type II is not a requisite for arthritogenicity, and mediation of arthritis and vaccination can be distinct properties of different populations of T lymphocytes.
Crystal Structure and Function of a DARPin Neutralizing Inhibitor of Lactococcal Phage TP901-1 (2009)

Combinatorial libraries of designed ankyrin repeat proteins (DARPins) have been proven to be a valuable source of specific binding proteins, as they can be expressed at very high levels and are very stable. We report here the selection of DARPins directed against a macromolecular multiprotein complex, the baseplate BppUxBppL complex of the lactococcal phage TP901-1. Using ribosome display, we selected several DARPins that bound specifically to the tip of the receptor-binding protein (RBP, the BppL trimer). The three selected DARPins display high specificity and affinity in the low nanomolar range and bind with a stoichiometry of one DARPin per BppL trimer. The crystal structure of a DARPin complexed with the RBP was solved at 2.1 A resolution. The DARPinxRBP interface is of the concave (DARPin)-convex (RBP) type, typical of other DARPin protein complexes and different from what is observed with a camelid VHH domain, which penetrates the phage p2 RBP inter-monomer interface. Finally, phage infection assays demonstrated that TP901-1 infection of Lactococcus lactis cells was inhibited by each of the three selected DARPins. This study provides proof of concept for the possible use of DARPins to circumvent viral infection. It also provides support for the use of DARPins in co-crystallization, due to their rigidity and their ability to provide multiple crystal contacts.
The CCR6/CCL20 Axis Mediates Th17 Cell Migration to the Ocular Surface in Dry Eye Disease (2013)

Local neutralization of CCL20 decreases Th17 cell infiltration of the ocular surface in DED, leading to improvement in clinical signs of disease. This suggests that CCR6/CCL20 interactions direct Th17 cell migration in DED and that disruption of this axis may be a novel therapeutic approach to this condition.
A first prospective study of the individual straight line velocity of the spermatozoon and its influences on the fertilization rate after intracytoplasmic sperm injection (1998)

The straight line velocity of 500 individual spermatozoa was measured immediately before their direct injection into the cytoplasm of 500 metaphase II oocytes. The straight line velocity (VSL) did not have a normal distribution (P < 0.01) and ranged between 0 and 35 microm/s. The fertilization rate (84%) was significantly (P < 0.008) higher in the quartile of the sperm population with the highest VSL compared to the fertilization rate (68%) in the quartile with the lowest VSL. Embryo cleavage and embryo quality were not different in the quartiles of the sperm population used for injection.
Enhanced Detection of Human Immunodeficiency Virus Type 1-Specific T-Cell Responses to Highly Variable Regions by Using Peptides Based on Autologous Virus Sequences (2003)

The antigenic diversity of human immunodeficiency virus type 1 (HIV-1) represents a significant challenge for vaccine design as well as the comprehensive assessment of HIV-1-specific immune responses in infected persons. In this study we assessed the impact of antigen variability on the characterization of HIV-1-specific T-cell responses by using an HIV-1 database to determine the sequence variability at each position in all expressed HIV-1 proteins and a comprehensive data set of CD8 T-cell responses to a reference strain of HIV-1 in infected persons. Gamma interferon Elispot analysis of HIV-1 clade B-specific T-cell responses to 504 overlapping peptides spanning the entire expressed HIV-1 genome derived from 57 infected subjects demonstrated that the average amino acid variability within a peptide (entropy) was inversely correlated to the measured frequency at which the peptide was recognized (P = 6 x 10(-7)). Subsequent studies in six persons to assess T-cell responses against p24 Gag, Tat, and Vpr peptides based on autologous virus sequences demonstrated that 29% (12 of 42) of targeted peptides were only detected with peptides representing the autologous virus strain compared to the HIV-1 clade B consensus sequence. The use of autologous peptides also allowed the detection of significantly stronger HIV-1-specific T-cell responses in the more variable regulatory and accessory HIV-1 proteins Tat and Vpr (P = 0.007). Taken together, these data indicate that accurate assessment of T-cell responses directed against the more variable regulatory and accessory HIV-1 proteins requires reagents based on autologous virus sequences. They also demonstrate that CD8 T-cell responses to the variable HIV-1 proteins are more common than previously reported.
A 500:1 SCALE MODEL OF WARLA A WIDE APERTURE RADIO LOCATION ARRAY, (1963)

Thi report describes the design, construction, and testing of a microwave scale model of a circular array of broadband antennas. The ultimate goal of this work is the construction of a high gain direction finding array using frequency independent antennas which would permit efficient operation over the 2-32 Mc range. The scale model is an attempt to experimentally verify certain theoretical results which were obtained from calculations performed on a computer. Restructions imposed on the array by the necessity of keeping inter-element phase center spacings less than approximately .75 wavelengths have forced the use of three sets of log-periodic elements - one set being added for each higher frequency band. The model discussed here represents only the lowest frequency band of the full array. A scaled frequency range of 1000 to 2500 Mc (array diamter of 29 in.) which corresponded to the 2-5 Mc range (array diameter of 1210 ft.) was employed as the model frequency limits. Typical radiation patterns of the model are presented and their relation to computed patterns are discussed. (Author)
MPLS Generic Associated Channel (G-ACh) Advertisement Protocol (2014)

The MPLS Generic Associated Channel (G-ACh) provides an auxiliary
logical data channel associated with a Label Switched Path (LSP), a
pseudowire, or a section (link) over which a variety of protocols may
flow. These protocols are commonly used to provide Operations,
Administration, and Maintenance (OAM) mechanisms associated with the
primary data channel. This document specifies simple procedures by
which an endpoint of an LSP, pseudowire, or section may inform the
other endpoints of its capabilities and configuration parameters, or
other application-specific information. This information may then be
used by the receiver to validate or adjust its local configuration,
and by the network operator for diagnostic purposes.
Double-Blind, Placebo-Controlled Trial of a Herpes Simplex Virus Type 2 Glycoprotein Vaccine in Persons at High Risk for Genital Herpes Infection (1990)

To determine the efficacy of a herpes simplex virus type 2 (HSV-2) glycoprotein subunit vaccine, vaccine (50 micrograms) or placebo was administered intramuscularly at weeks 0, 4, and 22 to 161 persons who lacked HSV-2 antibodies and were sex partners of persons with recurrent genital herpes. The annual rate of acquisition of HSV infection was similar among vaccine and placebo recipients (10.7% and 8%, respectively) but was higher in initially seronegative subjects (15.5%) than in those with HSV-1 at entry (5.9%). Eleven (79%) of the 14 HSV infections acquired during follow-up were symptomatic. Vaccination elicited ELISA antibody titers to glycoproteins gD2 and gB2 that were only 10% and 5%, respectively, of titers found in persons with recurrent genital HSV-2 infection. This vaccine failed to provide protection from acquisition of genital HSV infection. The lack of efficacy appears to be related, in part, to the poor immunogenicity of the vaccine.
Receptor‐binding domain of human α2‐macroglobulin Expression, folding and biochemical characterization of a high‐affinity recombinant derivative (1994)

A recombinant version of the receptor binding domain (RBDv) of human alpha 2-macroglobulin (alpha 2M) has been expressed in E. coli and refolded using a novel iterative procedure. RBDv (Val1299-Ala1451) is extended by 15 residues at the N-terminal side of the Lys1313-Glu papain cleavage site in human alpha 2M. RBDv contains the intra-chain bridge Cys1329-Cys1444 and is soluble and monomeric. Competition experiments with 125I-labelled methylamine-treated alpha 2M reveal that RBDv binds to the placental receptor for transformed alpha 2M with a Kd of 8 nM, i.e. the binding affinity of RBDv is of the same order of magnitude as the intrinsic affinity for binding of one domain in transformed alpha 2M to one receptor molecule.
YKL-40 Expression is Associated with Poorer Response to Radiation and Shorter Overall Survival in Glioblastoma (2005)

The findings implicate YKL-40 as an important marker of therapeutic response and genetic subtype in glioblastomas and suggest that it may play an oncogenic role in these tumors.
The function of sphingolipids in the nervous system: lessons learnt from mouse models of specific sphingolipid activator protein deficiencies (2007)

We have generated specific saposin A and D deficient mouse mutants by the gene targeting technology. Saposin A deficient mice showed the clinical, biochemical and pathological phenotype of a chronic form of globoid cell leukodystrophy (Krabbe disease) establishing that saposin A is essential for in vivo degradation of galactosylceramide. Saposin D deficient mice showed an accumulation of ceramides containing alpha-hydroxy fatty acids (HFA/d18:1) in the brain and kidney and showed renal tubular degeneration and cerebellar Purkinje cell loss. Here we review the current information which we have learnt from these mouse models of specific sphingolipid activator protein deficiencies. Collectively, the information provides support for the potential importance of sphingolipids in the function of the nervous system.
Cell cycle regulated transcription of heterochromatin in mammals vs. fission yeast: Functional conservation or coincidence? (2008)

Although it is tempting to speculate that the transcription-dependent heterochromatin assembly pathway found in fission yeast may operate in higher mammals, transcription of heterochromatin has been difficult to substantiate in mammalian cells. We recently demonstrated that transcription from the mouse pericentric heterochromatin major (gamma) satellite repeats is under cell cycle control, being sharply downregulated at the metaphase to anaphase transition and resuming in late G(1)-phase dependent upon passage through the restriction point. The highest rates of transcription were in early S-phase and again in mitosis with different RNA products detected at each of these times.(1) Importantly, differences in the percentage of cells in G(1)-phase can account for past discrepancies in the detection of major satellite transcripts and suggest that pericentric heterochromatin transcription takes place in all proliferating mammalian cells. A similar cell cycle regulation of heterochromatin transcription has now been shown in fission yeast,(2,3) providing further support for a conserved mechanism. However, there are still fundamental differences between these two systems that preclude the identification of a functional or mechanistic link.
Defect microchemistry in SiO2/Si structures (1990)

The chemical behavior of defects in SiO2/Si structures is a key to the success of Si field effect transistor (FET) technology. By exercising a high degree of control over the processing environment, it has been possible to elucidate microchemical behavior intrinsic to the SiO2/Si interface, particularly the oxide decomposition reaction Si + SiO2→2 SiO and its microstructural and electrical consequences. Initiation of this reaction is shown to occur at existing defect sites, leading to lateral growth of voids in the oxide. At earlier stages of reaction, electrically active defects are generated, following a process that can be reversed by the presence of oxygen; the detailed chemistry indicates competition between decomposition and reoxidation reactions at the defect site, i.e., the defect microchemistry emulates known macroscopic chemical reactions. These results have significance both for defect identification and control in processing. Finally, positron annihilation studies have shown strong evidence for the presence of microvoids in as-grown thermal oxide, similar to the early stages of oxide void growth under inert annealing conditions; these microvoids could be yet another manifestation of the oxide decomposition reaction, here competing with direct Si oxidation.
Oct-1 and Oct-2 potentiate functional interactions of a transcription factor with the proximal sequence element of small nuclear RNA genes. (1992)

The promoters of both RNA polymerase II- and RNA polymerase III-transcribed small nuclear RNA (snRNA) genes contain an essential and highly conserved proximal sequence element (PSE) approximately 55 bp upstream from the transcription start site. In addition, the upstream enhancers of all snRNA genes contain binding sites for octamer-binding transcription factors (Octs), and functional studies have indicated that the PSE and octamer elements work cooperatively. The present study has identified and characterized a novel transcription factor (designated PTF) which specifically binds to the PSE sequence of both RNA polymerase II- and RNA polymerase III-transcribed snRNA genes. PTF binding is markedly potentiated by Oct binding to an adjacent octamer site. This potentiation is effected by Oct-1, Oct-2, or the conserved POU domain of these factors. In agreement with these results and despite the independent binding of Octs to the promoter, PTF and Oct-1 enhance transcription from the 7SK promoter in an interdependent manner. Moreover, the POU domain of Oct-1 is sufficient for significant in vitro activity in the presence of PTF. These results suggest that essential activation domains reside in PTF and that the potentiation of PTF binding by Octs plays a key role in the function of octamer-containing snRNA gene enhancers.
Staging of Neurofibrillary Pathology in Alzheimer's Disease: A Study of the BrainNet Europe Consortium (2008)

It has been recognized that molecular classifications will form the basis for neuropathological diagnostic work in the future. Consequently, in order to reach a diagnosis of Alzheimer's disease (AD), the presence of hyperphosphorylated tau (HP-tau) and beta-amyloid protein in brain tissue must be unequivocal. In addition, the stepwise progression of pathology needs to be assessed. This paper deals exclusively with the regional assessment of AD-related HP-tau pathology. The objective was to provide straightforward instructions to aid in the assessment of AD-related immunohistochemically (IHC) detected HP-tau pathology and to test the concordance of assessments made by 25 independent evaluators. The assessment of progression in 7-microm-thick sections was based on assessment of IHC labeled HP-tau immunoreactive neuropil threads (NTs). Our results indicate that good agreement can be reached when the lesions are substantial, i.e., the lesions have reached isocortical structures (stage V-VI absolute agreement 91%), whereas when only mild subtle lesions were present the agreement was poorer (I-II absolute agreement 50%). Thus, in a research setting when the extent of lesions is mild, it is strongly recommended that the assessment of lesions should be carried out by at least two independent observers.
Regulation of Phospho-2-keto-3-deoxy-heptonate Aldolase (DAHP Synthase) and Anthranilate Synthase of Pseudomonas aureofaciens (1980)

Phospho-2-keto-3-deoxy-heptonate aldolase (DAHP synthase) of Pseudomonas aureofaciens ATCC 15926 was inhibited by L-tyrosine. The inhibition was competitive with erythrose 4-phosphate as the varied substrate but non-competitive with respect to phosphoenolpyruvate. Anthranilate synthase was inhibited by L-tryptophan. The inhibition was competitive with respect to chorismate but non-competitive with L-glutamine or NH4+ as the varied substrate. DAHP synthase and anthranilate synthase were not repressed when aromatic amino acids were included in the growth medium. In bacteria grown in the presence of L-phenylalanine, the anthranilate synthase activity was enhanced about threefold compared with the control. Similar results were obtained with the mutant strain P. aureofaciens ACN, which produces increased amounts of pyrrolnitrin.
Recognition of prokaryotic transcription terminators by spinach chloroplast RNA polymerase (1988)

To determine whether chloroplast RNA polymerase will accurately terminate transcription in vitro, we have fused the spinach chloroplast rbcL promoter to the 3' end of the rbcL gene as well as to various factor independent transcription terminators from E. coli. Transcription of the rbcL minigene did not result in production of the expected 265 nucleotide RNA. However, the spinach chloroplast RNA polymerase did terminate transcription with varying efficiency at the thra, rrnB, rrnC and gene 32 terminators. The most efficient transcription termination was observed for the threonine attenuator. For each of the prokaryotic terminators, the chloroplast enzyme ceased transcription at essentially the same position as the E. coli RNA polymerase. These data indicate that the transcription termination process in chloroplasts has some features in common with the mechanism used in prokaryotes.
A 100-kV ion probe microfabrication system with a tetrode gun (1981)

In the design of probe-forming systems incorporating liquid-metal ion sources, it is necessary to maximize the current into a probe of controlled diameter and to employ a configuration that is compatible with the incorporation of a filter for the selection of ion species. A variable-magnification two-lens system has been adopted as the basis of a microfabrication machine for direct selective ion implantation of wafers, and a 100-kV system has been designed. Its tetrode gun acts as the first lens and is followed by an einzel lens as the probe-forming objective. The system has been analyzed and operating characteristics have been computed, predicting a current of 0.1 nA in a 0.1 μm diameter probe and 10 nA into 1 μm diam.
Latent Regression Forest: Structured Estimation of 3D Articulated Hand Posture (2014)

In this paper we present the Latent Regression Forest (LRF), a novel framework for real-time, 3D hand pose estimation from a single depth image. In contrast to prior forest-based methods, which take dense pixels as input, classify them independently and then estimate joint positions afterwards, our method can be considered as a structured coarse-to-fine search, starting from the centre of mass of a point cloud until locating all the skeletal joints. The searching process is guided by a learnt Latent Tree Model which reflects the hierarchical topology of the hand. Our main contributions can be summarised as follows: (i) Learning the topology of the hand in an unsupervised, data-driven manner. (ii) A new forest-based, discriminative framework for structured search in images, as well as an error regression step to avoid error accumulation. (iii) A new multi-view hand pose dataset containing 180K annotated images from 10 different subjects. Our experiments show that the LRF out-performs state-of-the-art methods in both accuracy and efficiency.