gebhart/patrepeval huggingface dataset:
Mycobacterium bovis BCG-Mediated Protection against W-Beijing Strains of Mycobacterium tuberculosis Is Diminished Concomitant with the Emergence of Regulatory T Cells (2011)

Despite issues relating to variable efficacy in the past, the Mycobacterium bovis BCG vaccine remains the basis for new-generation recombinant vaccines currently in clinical trials. To date, vaccines have been tested mostly against laboratory strains and not against the newly emerging clinical strains. In this study, we evaluated the ability of BCG Pasteur to protect mice from aerosol infections with two highly virulent W-Beijing clinical strains, HN878 and SA161. In a conventional 30-day protection assay, BCG was highly protective against both strains, but by day 60 of the assay, this protection was diminished. Histological examination of the lungs of vaccinated animals showed reduced lung consolidation and smaller and more-organized granulomas in the vaccinated mice after 30 days, but in both cases, these tissues demonstrated worsening pathology over time. Effector T cell responses were increased in the vaccinated mice infected with HN878, but these diminished in number after day 30 of the infections concomitant with increased CD4(+) Foxp3(+) T cells in the lungs, draining lymph nodes, and the spleen. Given the concomitant decrease in effector immunity and continued expansion of regulatory Foxp3(+) cells observed here, it is reasonable to hypothesize that downregulation of effector immunity by these cells may be a serious impediment to the efficacy of BCG-based vaccines.
Phase I/II trial of intravenous OV001 oncolytic virus in resistant glioblastoma multiforme (GBM) (2004)

1515 Background: OV001 (NDV HUJ) is an oncolytic, non-engineered, lentogenic strain of Newcastle Disease Virus (NDV). Following preclinical repetitive dosing toxicity studies, a Phase I/II trial was initiated in GBM determining safety and imaging response. Methods: Patients (11–58yrs, KPS 50–90%) with primary glioblastoma were enrolled 17–49 wks following diagnosis and failure of previous therapy. The first part of the study used an intra-patient dose escalation method with one cycle dosage steps of 0.1, 0.5, 1, 5 and 10 BIU units of OV001 (1 BIU = 1x109 EID50, 50% egg infectious dose). One cycle consisted of 15 min IV infusions on each of 5 consecutive days over a period of 7 d (<1BIU) or 14 d (>=1BIU). Patient reaching 10 BIU received 3 additional cycles of 50 BIU. Patients enrolled in the second part received three cycles of 10 BIU. Patients without progressive disease were maintained with 2 doses of 10 BIU IV weekly. Results: In Phase I, 4/6 patients completed all 3 cycles of 50 BIU of OV001; in the Phase II part, as of Dec 01, 2003, 3/4 patients in Phase II part completed all 3 cycles of 10 BIU. Grade I/II constitutional fever was seen in 5 patients and was the only adverse event related to OV001 administration. MTD was not reached. Patients that did not complete dosing were withdrawn due to disease progression. All tested patients developed anti-NDV hemagglutinin antibodies after 7–14 days. NDV was recovered from one tumor biopsy. One patient has a continuing near complete response 30 weeks after start of dosing. A second patient maintained stable disease between 16–26 weeks. Conclusions: Intravenous OV001 is well tolerated and most excitingly a near complete response provides proof of concept of its therapeutic potential. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration OVCure (Israel) Ltd. OVCure (Israel) Ltd. OVCure, Inc. OVCure (Israel) Ltd.
Probing Crystallization of Calcium Oxalate Monohydrate and the Role of Macromolecule Additives with in Situ Atomic Force Microscopy (2004)

Kidney stones are crystal aggregates, most commonly containing calcium oxalate monohydrate (COM) microcrystals as the primary constituent. Macromolecules, specifically proteins rich with anionic side chains, are thought to play an important role in the regulation of COM growth, aggregation, and attachment to cells, all key processes in kidney stone formation. The microscopic events associated with crystal growth on the [010], [121], and [100] faces have been examined with in situ atomic force microscopy (AFM). Lattice images of each face reveal two-dimensional unit cells consistent with the COM crystal structure. Each face exhibits hillocks with step sites that can be assigned to specific crystal planes, enabling direct determination of growth rates along specific crystallographic directions. The rates of growth are found to depend on the degree of supersaturation of calcium oxalate in the growth medium, and the growth rates are very sensitive to the manner in which the growth solutions are prepared and introduced to the AFM cell. The addition of macromolecules with anionic side chains, specifically poly(acrylic acid), poly(aspartic acid), and poly(glutamic acid), results in inhibition of growth on the hillock step planes. The magnitude of this effect depends on the macromolecule structure, macromolecule concentration, and the identity of the step site. Poly(acrylic acid) was the most effective inhibitor of growth. Whereas poly(aspartic acid) inhibited growth on the (021) step planes of the (100) hillocks more than poly(glutamic acid), the opposite was found for the same step planes on the (010) hillocks. This suggests that growth inhibition is due to macromolecule binding to both planes of the step site or pinning of the steps due to binding to the (100) and (010) faces alone. The different profiles observed for these three macromolecules argue that local binding of anionic side chains to crystal surface sites governs growth inhibition rather than any secondary polymer structure. Growth inhibition by cationic macromolecules is negligible, further supporting an important role for proteins rich in anionic side chains in the regulation of kidney stone formation.
Is the Intrinsic Thermoelectric Power of Carbon Nanotubes Positive? (2000)

The thermoelectric power (TEP) of single-walled carbon nanotubes (SWNTs) is extremely sensitive to gas exposure history. Samples exposed to air or oxygen have an always positive TEP, suggestive of holelike carriers. However, at fixed temperature the TEP crosses zero and becomes progressively more negative as the SWNTs are stripped of oxygen. The time constant for oxygen adsorption/desorption is strongly temperature dependent and ranges from seconds to many days, leading to apparently "variable" TEP for a given sample at a given temperature. The saturated TEP can be accounted for within a model of strong oxygen doping of the semiconducting nanotubes.
The action-state diagram: a compact finite state machine representation for user interface and small embedded reactive systems (1991)

The authors describe the use of action-state diagrams in the software development of small embedded reactive systems. The proposed method allows specification, design, and coding phases to be combined with a formal notation. Direct mapping from design to code is also presented. It is also shown that this method covers all the functionality of the classical state transition diagram. The suitability of this method for user interface problems is also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characteristics of calves produced with sperm sexed by flow cytometry/cell sorting1 (2004)

The objectives of this study were to determine whether calves produced by sexed sperm differed from controls and to what extent the sex ratio of calves was altered by the sexing procedure. Data were collected from 1,169 calves produced from sperm sexed by flow cytometry/cell sorting after staining with Hoechst 33342, and 793 calves produced from control sperm during breeding trials between 1997 and 2001. Least squares ANOVA were completed using factors of treatment (sexed vs. control sperm), 19 management groups from 13 field trials, and calf sex. Responses analyzed include gestation length, birth weight, calving ease, calf vigor, weaning weight, abortion rate, and death rates (neonatal and through weaning). No significant difference was observed for any response due to treatment or treatment interactions (P > 0.10). Therefore, calves produced from sexed sperm grew and developed normally both pre- and postnatally. A neurological disorder was observed in four control calves and one sexed calf from one farm. No gross anatomical abnormalities were reported for any calves in the study. Differences were observed for all responses among management groups (P < 0.03 for abortions and P < 0.01 for all other responses). Heifer and bull calves differed (P < 0.001) in gestation length (278.4 and 279.6 d), birth weight (32.8 and 35.2 kg), calving ease (1.15 and 1.30), and weaning weight (233 and 247 kg). Gestation length did not affect characteristics of calves. The sex ratio at birth of calves from unsexed control sperm was 49.2% male. Sexing accuracy of X-sorted sperm was 87.8% female calves, and Y-sorted sperm produced 92.1% male calves. Flow cytometry/cell sorting can be used to preselect sex of calves safely with approximately 90% accuracy.
Deep semantic analysis of text (2008)

We describe a graphical logical form as a semantic representation for text understanding. This representation was designed to bridge the gap between highly expressive "deep" representations of logical forms and more shallow semantic encodings such as word senses and semantic relations. It preserves rich semantic content while allowing for compact ambiguity encoding and viable partial representations. We describe our system for semantic text processing, which has the TRIPS parser at the core, augmented with statistical preprocessing techniques and online lexical lookup. We also present an evaluation metric for the representation and use it to evaluate the performance of the TRIPS parser on the common task paragraphs.
The resurfacing of adult rabbit articular cartilage by multiple perforations through the subchondral bone (1976)

The repair of articular cartilage removed from the femora of adult rabbits at the knee was studied. When multiple perforations were made through the subchondral bone a cartilaginous material, staining heavily with safranin O, first filled the holes. This material resembled hyaline cartilage, and by twelve months there was complete resurfacing of the joint, although the material lost its hyaline appearance after eight months and at one year it resembled dense collagenous tissue.
Protein Tyrosine Phosphatase Substrate Specificity: Size and Phosphotyrosine Positioning Requirements in Peptide Substrates (1994)

The structural requirements of substrates for two recombinant protein tyrosine phosphatases (PTPases) are probed using various-sized synthetic phosphotyrosine (pY)-containing peptides corresponding to the autophosphorylation site in EGF receptor (EGFR) at Y992. The peptide EGFR988-998 (DADEpYLIPQQG) is chosen as a template due to its favorable kinetic constants. The contribution of individual amino acids on both sides of pY to binding and catalysis was assessed by kinetic analysis using a continuous, spectrophotometric assay. For both Yersinia PTPase and a soluble recombinant mammalian PTPase of 323 amino acid residues (rat PTP1), efficient binding and catalysis required six amino acids including the pY residue, i.e., four residues N-terminal to pY and one residue C-terminal to pY. Thus, PTPase substrate specificity is primarily dictated by residues to the N-terminal side of pY. The pY moiety and the rest of the peptide interact with PTPases in a cooperative manner. The presence of pY in the peptide substrate is necessary but not sufficient for high-affinity binding, since phosphotyrosine and other simple aryl phosphates exhibit weak binding, and dephosphorylated peptides do not bind to PTPases. Two variations on the pY moiety are also examined in order to assess their utility in PTPase inhibitor design. It is demonstrated that the thiophosphoryl analog in which one of the phosphate oxygens is replaced by sulfur can be hydrolyzed by PTPases, whereas the phosphonomethylphenylalanine analog in which the tyrosyl oxygen is replaced by a CH2 group is a competitive and nonhydrolyzable inhibitor, with Ki values of 18.6 and 10.2 microM, respectively, for the Yersinia PTPase and the rat PTP1.
Purification to homogeneity and partial characterization of cytotoxic lymphocyte maturation factor from human B-lymphoblastoid cells. (1990)

A cytokine that can synergize with interleukin 2 to activate cytotoxic lymphocytes was purified to homogeneity. The protein, provisionally called cytotoxic lymphocyte maturation factor (CLMF), was isolated from a human B-lymphoblastoid cell line that was induced to secrete lymphokines by culture with phorbol ester and calcium ionophore. The purification method, utilizing classical and high-performance liquid chromatographic techniques, yielded protein with a specific activity of 8.5 x 10(7) units/mg in a T-cell growth factor assay. Analysis of the purified protein by sodium dodecyl sulfate/polyacrylamide gel electrophoresis demonstrated that CLMF is a 75-kDa heterodimer composed of disulfide-bonded 40-kDa and 35-kDa subunits. Determination of the N-terminal amino acid sequences of the two subunits revealed that both subunits are not related to any previously identified cytokine. Purified CLMF stimulated the proliferation of human phytohemagglutinin-activated lymphoblasts by itself and exerted additive effects when used in combination with suboptimal amounts of interleukin 2. Furthermore, the purified protein was shown to synergize with low concentrations of interleukin 2 in causing the induction of lymphokine-activated killer cells.
The cytotoxicity of chemotherapy drugs varies in cervical cancer cells depending on the p53 status (2004)

Metastatic cervical cancer remains a clinical problem. The development of more efficient treatment modalities and the optimal use of chemo- and radiotherapy require better understanding of their impact on regulation of cell survival and apoptosis, but the issue is insufficiently explored. Human papillomavirus (HPV) E6 protein is present in nearly all cervical cancers, targeting the p53 tumor suppressor protein for degradation. We studied the role of p53 in mediating the cytotoxic effects of 31 chemotherapy compounds. SiHa cervical cancer cells, carrying wild type (wt) p53 and HPV16 genome, were stably transfected with dominant negative p53 (DDp53) or ectopic HPV16 E6 in order to inhibit p53 function. The effects of chemotherapy drugs in these cells were compared to the effects in cells retaining endogenous residual p53 activity. Twenty-ight out of 31 drugs reduced the amount of E6 mRNA, but only some induced marked p53 activation. In clonogenic cell survival experiments, the presence of DDp53 and ectopic E6 either increased or decreased cytotoxicity, depending on the drug. The decrease of E6 mRNA was necessary, but not sufficient event in the p53 activation by chemotherapy. The impact of p53 on clonogenic cell survival varied between 0-60%, indicating that p53 plays an important, but not crucial role in response to chemotherapy. The finding that chemosensitivity varies depending on the p53 status may have clinical implications, since early stage cervical cancer cells usually carry wt p53, whereas p53 mutations are frequently found in advanced disease.
Using Corneal Height Maps and Polynomial Decomposition to Determine Corneal Aberrations (1997)

Videokeratoscopic height data are useful for analyzing and quantifying corneal deformity arising from disease or refractive surgery and they provide a sophisticated alternative or complement to dioptric power maps.
Differential Regulation of Glucose Transport and Transporters by Glucose in Vascular Endothelial and Smooth Muscle Cells (1993)

Hyperglycemia has been implicated in the pathogenesis of both micro- and macrovascular complications in diabetes. Little is known, however, about glucose transporters and their regulation in the vascular system. In this study, the regulation of glucose transporters by glucose was examined in cultured BAECs and BSMCs, and in human arterial smooth muscle cells. Both BAECs and BSMCs transported glucose via the facilitated diffusion transport system. Glucose-transport activity in vascular smooth muscle cells was inversely and reversibly regulated by glucose. Exposure of BSMCs and HSMCs to high glucose decreased Vmax for 2DG and 3-O-MG uptake, whereas Km remained unchanged. The hexose-transport system of BAECs exhibited lower 2DG and 3-O-MG uptake compared with BSMCs and showed little or no adaptation to changes in ambient glucose. Northern blot analysis demonstrated that GLUT1 mRNA levels in BAECs and BSMCs were unaffected by the concentration of glucose in the medium. GLUT2-5 mRNA could not be detected by Northern blot analysis. GLUT1 protein, quantified by Western blot analysis, was more abundant in BSMCs than in BAECs and was decreased by approximately 50% when medium glucose was elevated from 1.2 to 22 mM for 24 h. The alterations in the level of GLUT1 protein correlated with the changes observed in transport activity. These observations suggest differential regulation of glucose transporter in response to glucose between smooth muscle and endothelial cells. The sites of autoregulation may involve translational control and/or the stability of the protein in the smooth muscle cells.(ABSTRACT TRUNCATED AT 250 WORDS)
Ionization energy of the shallow nitrogen acceptor in zinc selenide (1983)

Evidence on the presence and binding energy of the shallow N acceptor is obtained for growth-doped liquid-phase-epitaxial (LPE) and organometallic chemical-vapor-deposited (OMCVD) ZnSe thin single-crystal layers. The small increase in N-acceptor bound-exciton (BE) binding energy ${E}_{\mathrm{BX}}$ relative to the Li acceptor, 0.3 meV, is clearly established from intercomparison of spectral features and use of tunable dye-laser spectroscopy. The LPE crystals contain a new unidentified donor ${E}_{D}=26.8$ meV, as well as In and Al minor donors, while the dominant donor in these OMCVD crystals is Ga. Selectively excited donor-acceptor-pair (DAP) luminescence spectra contain a satellite structure which provides an estimate of ${({E}_{A})}_{\mathrm{N}}=111\ifmmode\pm\else\textpm\fi{}1$ meV, distinctly 2.2\ifmmode\pm\else\textpm\fi{}0.5 meV shallower than the Li acceptor but \ensuremath{\sim}21 meV deeper than some previous estimates from LPE ZnSe:N. This estimate is confirmed by ${A}^{0}$,$X$ BE "two-hole" satellites observed under strong optical pumping. The effective-mass value of ${E}_{A}$ is placed close to 110 meV. The dependence of displacement energy of this structure on DAP separation is very significant in the comparison of Li and N acceptors. The relationship of ${E}_{\mathrm{BX}}$ and ${E}_{A}$ is retrograde for the shallowest acceptors N, Li, and Na so far identified in ZnSe. Sharp differences between the excitation spectra of BE photoluminescence between $n$-type ZnSe and $p$-type ZnTe doped to comparable concentrations are discussed. It is concluded that the best N-doped OMCVD ZnSe yet available is still $n$ type due to residual donors.
Dynamic Anchor Feature Selection for Single-Shot Object Detection (2019)

The design of anchors is critical to the performance of one-stage detectors. Recently, the anchor refinement module (ARM) has been proposed to adjust the initialization of default anchors, providing the detector a better anchor reference. However, this module brings another problem: all pixels at a feature map have the same receptive field while the anchors associated with each pixel have different positions and sizes. This discordance may lead to a less effective detector. In this paper, we present a dynamic feature selection operation to select new pixels in a feature map for each refined anchor received from the ARM. The pixels are selected based on the new anchor position and size so that the receptive filed of these pixels can fit the anchor areas well, which makes the detector, especially the regression part, much easier to optimize. Furthermore, to enhance the representation ability of selected feature pixels, we design a bidirectional feature fusion module by combining features from early and deep layers. Extensive experiments on both PASCAL VOC and COCO demonstrate the effectiveness of our dynamic anchor feature selection (DAFS) operation. For the case of high IoU threshold, our DAFS can improve the mAP by a large margin.
Japanese morning glory dusky mutants displaying reddish‐brown or purplish‐gray flowers are deficient in a novel glycosylation enzyme for anthocyanin biosynthesis, UDP‐glucose:anthocyanidin 3‐O‐glucoside‐2′′‐O‐glucosyltransferase, due to 4‐bp insertions in the gene (2005)

Bright blue or red flowers in the Japanese morning glory (Ipomoea nil) contain anthocyanidin 3-O-sophoroside derivatives, whereas the reddish-brown or purplish-gray petals in its dusky mutants accumulate anthocyanidin 3-O-glucoside derivatives. The Dusky gene was found to encode a novel glucosyltransferase, UDP-glucose:anthocyanidin 3-O-glucoside-2''-O-glucosyltransferase (3GGT), which mediates the glucosylation of anthocyanidin 3-O-glucosides to yield anthocyanidin 3-O-sophorosides. Ipomoea nil carries one copy of the 3GGT gene that contains no intron and produces 1.6-kbp transcripts mainly in the petals and tubes of flower buds at around 24 h before flower opening. The gene products of both In3GGT in I. nil and Ip3GGT in the common morning glory (Ipomoea purpurea) comprise 459 amino acids and showed a close relationship to the petunia UDP-rhamnose:anthocyanidin 3-O-glucoside-6''-O-rhamnosyltransferase (3RT), which controls the addition of a rhamnose molecule to anthocyanidin 3-O-glucosides for conversion into anthocyanidin 3-O-rutinosides. All of the 30 dusky mutants tested were found to carry the 4-bp insertion mutations GGAT or CGAT at an identical position near the 3' end of the gene, and the insertions caused frameshift mutations. The expected 3GGT enzymatic activities were found in the crude extracts of Escherichia coli, in which the 3GGT cDNA of I. nil or I. purpurea was expressed, while no such activity was detected in the extracts expressed with the dusky mutant cDNAs containing 4-bp insertions. Moreover, the introduced Ip3GGT cDNA efficiently produced 3GGT that converted cyanidin 3-O-glucoside into cyanidin 3-O-sophoroside in transgenic petunia plants.