gebhart/patrepeval huggingface dataset:
Search for contact interactions and large extra dimensions in the dilepton channel using proton–proton collisions at √s = 8 TeV with the ATLAS detector (2014)

A search is conducted for non-resonant new phenomena in dielectron and dimuon final states, originating from either contact interactions or large extra spatial dimensions. The LHC 2012 proton–proton collision dataset recorded by the ATLAS detector is used, corresponding to 20 fb−1 at √s = 8 TeV. The dilepton invariant mass spectrum is a discriminating variable in both searches, with the contact interaction search additionally utilizing the dilepton forward-backward asymmetry. No significant deviations from the Standard Model expectation are observed. Lower limits are set on the llqq contact interaction scale between 15.4 TeV and 26.3 TeV, at the 95 % credibility level. For large extra spatial dimensions, lower limits are set on the string scale MS between 3.2 TeV to 5.0 TeV
Interaction between the pili of Pseudomonas aeruginosa PAK and its carbohydrate receptor β-D-GalNAc(1->4) β-D-Gal analogs (1998)

Pseudomonas aeruginosa employs pili to mediate adherence to epithelial cell surface receptors. Previously, it has been shown that the pilus adhesin of P. aeruginosa PAK binds to the ganglioside asialo-GM 1 . In particular, it was found that the carbohydrate sequence β-D-GalNAc(1-&gt;4) β-D-Gal is the minimal carbohydrate receptor sequence of asialo-GM 1 . To study the binding specificity of P. aeruginosa, O-modified and N-modified sugar analogs, where each hydroxyl group was substituted either by O-methyl or O-propyl and the acetamido group was changed to a propionamido group, were synthesized. The sugar analogs were evaluated as inhibitors in a competitive solid phase binding assay. The results demonstrate that the pili of P. aeruginosa PAK accepts a variety of sugar analogs possessing the sequence β-D-GalNAc(1-&gt;4) β-D-Gal. Most sugar analogs bind with a similar order of magnitude (50% inhibitory concentration (IC 50 ) = 60-130 μM) except for the 2-O-propyl derivative 7 (IC 50 = 8 ± 4 μM) compared with an IC 50 of 79 ± 18 μM for the native compound. The significant increase in binding affinity of 2-O-propyl derivative 7 suggests that improved inhibitors of adhesion may be prepared by introducing a hydrophobic side chain at the 2-position of galactose.Key words: Pseudomonas aeruginosa, pili, adhesion, carbohydrate.
ASCVac-1, a Multi-Peptide Chimeric Vaccine, Protects Mice Against Ascaris suum Infection (2021)

Control of human ascariasis, the most prevalent neglected tropical disease globally affecting 450 million people, mostly relies on mass drug administration of anthelmintics. However, chemotherapy alone is not efficient due to the high re-infection rate for people who live in the endemic area. The development of a vaccine that reduces the intensity of infection and maintains lower morbidity should be the primary target for infection control. Previously, our group demonstrated that immunization with crude <i>Ascaris</i> antigens in mice induced an IgG-mediated protective response with significant worm reduction. Here, we aimed to develop a multipeptide chimera vaccine based on conserved B-cell epitopes predicted from 17 common helminth proteomes using a bioinformatics algorithm. More than 480 B-cell epitopes were identified that are conserved in all 17 helminths. The <i>Ascaris</i>-specific epitopes were selected based on their reactivity to the pooled sera of mice immunized with <i>Ascaris</i> crude antigens or infected three times with <i>A. suum</i> infective eggs. The top 35 peptides with the strongest reactivity to <i>Ascaris</i> immune serum were selected to construct a chimeric antigen connected in sequence based on conformation. This chimera, called ASCVac-1, was produced as a soluble recombinant protein in an <i>Escherichia coli</i> expression system and, formulated with MPLA, was used to immunize mice. Mice immunized with ASCVac-1/MPLA showed around 50% reduced larvae production in the lungs after being challenged with <i>A. suum</i> infective eggs, along with significantly reduced inflammation and lung tissue/function damage. The reduced parasite count and pathology in infected lungs were associated with strong Th2 immune responses characterized by the high titers of antigen-specific IgG and its subclasses (IgG1, IgG2a, and IgG3) in the sera and significantly increased IL-4, IL-5, IL-13 levels in lung tissues. The reduced IL-33 titers and stimulated eosinophils were also observed in lung tissues and may also contribute to the ASCVac-1-induced protection. Taken together, the preclinical trial with ASCVac-1 chimera in a mouse model demonstrated its significant vaccine efficacy associated with strong IgG-based Th2 responses, without IgE induction, thus reducing the risk of an allergic response. All results suggest that the multiepitope-based ASCVac-1 chimera is a promising vaccine candidate against <i>Ascaris</i> sp. infections.
Genetic and Functional Analysis of Polymorphisms in the Human Dopamine Receptor and Transporter Genes in Small Cell Lung Cancer (2015)

The regulatory role of dopamine (DA) in endocrine, cardiovascular and renal functions has been extensively studied and used for clinical purposes. More recently DA has been indicated as a regulatory molecule for immune cells and malignant cell proliferation. We assessed the expression and the functional role DA, DA receptors, and transporters in primary small cell lung cancer (SCLC). By HPLC DA plasma levels were more elevated in SCLC patients in comparison with NSCLC patients and healthy controls. SCLC cell expressed DA D1- and D2-like receptors and membrane and vesicular transporters at protein and mRNA levels. We also investigated the effects of independent D1- or D2-like receptor stimulation on SCLC cell cultures. DA D1 receptor agonist SKF38393 induced the increase of cAMP levels and DARPP-32 protein expression without affecting SCLC growth rate. Cell treatment with the DA D1 receptor antagonist SCH23390 inhibited SKF38393 effects. In contrast, the DA D2 receptor agonist quinpirole (10 μM) counteracted, in a dose and time dependent way, SCLC cell proliferation, it did not affect cAMP levels and decreased phosphorylated AKT that was induced by DA D2 receptor antagonist sulpiride. However, in only one SCLC line, stimulation of DA D2 receptor failed to inhibit cell proliferation in vitro. This effect was associated to the existence of rs6275 and rs6277 polymorphisms in the D2 gene. These results gave more insight into DA control of lung cancer cell behavior and suggested the existence of different SCLC phenotypes.
Effects of transforming growth factor‐β1 on extracellular matrix gene expression by human fibroblasts from a laryngeal stenotic lesion (1996)

Transforming growth factor-beta1 appears to play important roles in normal wound healing by increasing synthesis of extracellular matrix components. However, the role of transforming growth factor-beta1 in the production of excessive scar tissue by fibroblasts from stenotic lesions of the larynx has not been evaluated. We examined the effect of transforming growth factor-beta1 on the steady-state messenger RNA levels of elastin, alpha2(l) procollagen, and lysyl oxidase (the enzyme that cross-links both of these structural proteins) in cell cultures of diploid human fibroblasts established from fetal skin, newborn foreskin, and an adult laryngeal stenotic lesion. Time-course and dose-response experiments demonstrated that treatment with 500 pmol/L transforming growth factor-beta1 for 20 hours induced maximal levels of mRNA for elastin (7- to 59-fold) and alpha2(l) procollagen (1.7- to 2.4-fold) in all three cultures of fibroblasts. Transforming growth factor-beta1 also increased levels of lysyl oxidase mRNA in fibroblasts cultured from newborn foreskin (2.4-fold) and a stenotic lesion (10-fold) but had minimal effects on the fibroblasts cultured from fetal skin (1.1-fold), which constitutively expressed high levels of lysyl oxidase mRNA. Furthermore, the fibroblast culture established from a laryngeal stenotic lesion responded with the highest fold-induction for all three mRNAs. Inhibition of mRNA synthesis by actinomycin D showed that transcription was required for transforming growth factor-beta1 induction of elastin, alpha2(l) procollagen, and lysyl oxidase mRNA in all three cultures of fibroblasts. Inhibition of protein synthesis by cycloheximide showed that translation was required for maximal induction by transforming growth factor-beta1 of elastin mRNA but had no observable effect on alpha2(l) procollagen mRNA in all three cultures of fibroblasts. In addition, translation was required for maximal induction of the lysyl oxidase mRNA by transforming growth factor-beta1 in the fibroblasts cultured from a stenotic lesion but not for fibroblast cultures established from fetal and adult skin. These results show that transforming growth factor-beta1 coordinately increases mRNA levels for the structural extracellular matrix proteins collagen and elastin, as well as for the cross-linking enzyme, lysyl oxidase. These data also support the hypothesis that transforming growth factor-beta1 may contribute to the formation of laryngeal stenotic lesions.
SET-NUP214 is a recurrent γδ lineage-specific fusion transcript associated with corticosteroid/chemotherapy resistance in adult T-ALL (2014)

The SET-NUP214 (TAF1/CAN) fusion gene is a rare genetic event in T-cell acute lymphoblastic leukemia (T-ALL). Eleven (6%) of 196 T-ALL patients enrolled in the French Group for Research on Adult Acute Lymphoblastic Leukemia (GRAALL) 2003 and 2005 trials harbored a SET-NUP214 transcript. SET-NUP214-positive patients were predominantly (10 [91%] of 11) T-cell receptor (TCR)-negative and strikingly associated with TCRγδ lineage T-ALLs, as defined by expression of TCRγδ, TCRδ and/or TCRγ rearrangements but no complete TCRβ variable diversity joining rearrangement in surface CD3/TCR-negative cases. When compared with SET-NUP214-negative patients, SET-NUP214-positive patients showed a significantly higher rate of corticosteroid resistance (91% vs 44%; P = .003) and chemotherapy resistance (100% vs 44%; P = .0001). All SET-NUP214-positive patients but one achieved complete remission, and 9 were allografted. Despite the poor early-treatment sensitivity, the outcome of SET-NUP214-positive patients was similar to that of SET-NUP214-negative patients.
Supplementary Figure S4 from Preclinical Antitumor Efficacy of BAY 1129980—a Novel Auristatin-Based Anti-C4.4A (LYPD3) Antibody–Drug Conjugate for the Treatment of Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Internalization and cytotoxicity of C4.4A-Ab.&lt;/p&gt;
Statistical Inference for Data Adaptive Target Parameters (2016)

Consider one observes n i.i.d. copies of a random variable with a probability distribution that is known to be an element of a particular statistical model. In order to define our statistical target we partition the sample in V equal size sub-samples, and use this partitioning to define V splits in an estimation sample (one of the V subsamples) and corresponding complementary parameter-generating sample. For each of the V parameter-generating samples, we apply an algorithm that maps the sample to a statistical target parameter. We define our sample-split data adaptive statistical target parameter as the average of these V-sample specific target parameters. We present an estimator (and corresponding central limit theorem) of this type of data adaptive target parameter. This general methodology for generating data adaptive target parameters is demonstrated with a number of practical examples that highlight new opportunities for statistical learning from data. This new framework provides a rigorous statistical methodology for both exploratory and confirmatory analysis within the same data. Given that more research is becoming "data-driven", the theory developed within this paper provides a new impetus for a greater involvement of statistical inference into problems that are being increasingly addressed by clever, yet ad hoc pattern finding methods. To suggest such potential, and to verify the predictions of the theory, extensive simulation studies, along with a data analysis based on adaptively determined intervention rules are shown and give insight into how to structure such an approach. The results show that the data adaptive target parameter approach provides a general framework and resulting methodology for data-driven science.
Fas Ligand mRNA Levels of Circulating Leukocytes Reflect Endothelial Dysfunction in Hyperlipidemic but Not in Non-Hyperlipidemic Patients (2006)

To find a novel marker for identifying patients at high-risk for endothelial dysfunction among patients with atherosclerosis, we examined the correlation between mRNA levels of Fas ligand (FasL), an apoptosis-inducing factor, in circulating leukocytes and clinical parameters in these patients. FasL mRNA levels of circulating leukocytes were measured with the TaqMan-PCR method. A negative correlation was observed between brachial artery flow-mediated dilatation (%FMD) and FasL mRNA levels of leukocytes in hyperlipidemic but not in non-hyperlipidemic patients. %FMD was more impaired in patients with a high level of FasL mRNA than in those with a low level of FasL mRNA. Interestingly, the improvement of %FMD by treatment with a 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor (simvastatin) was greater in the group showing a decrease in FasL mRNA than in the group with no such decrease. Additionally, simvastatin suppressed the FasL mRNA expression in leukocytes and decreased plasma oxidized low-density lipoprotein (OxLDL) levels. Furthermore, the supernatant of cultured leukocytes from hyperlipidemic patients induced cell death in Jurkat T cells, which was neutralized by an antibody against FasL. These findings suggest that high FasL mRNA expression in circulating leukocytes may be a marker of high-risk for endothelial dysfunction in hyperlipidemic but not in non-hyperlipidemic patients. This information may provide a novel basis for targeting of statin therapy in patients with vulnerable plaques.
CRITERIA FOR HIGH DESIGN SPEED FACILITIES (2007)

The Texas Department of Transportation (TxDOT) is embarking on a multi-decade effort to expand the state’s transportation system. To accomplish this expansion, TxDOT has expressed an interest in using higher design speeds [above 80 mph (130 km/h)] to promote faster and more efficient travel within the state. Current state and national roadway design guidance does not provide criteria for design speeds above 80 mph (130 km/h), so design values are not available. The purpose of TxDOT Project 0-5544, Development of High Speed Design Criteria and Evaluation of Roadside Safety Features, was to expand upon existing design guidance and identify new criteria for design speeds up to 100 mph (160 km/h). Determination of preliminary criteria required extrapolation of existing equations along with the use of engineering judgment. A Roundtable Discussion Group was assembled to obtain practicing engineers’ opinions and views on the methodology used to determine the criteria and on the specific values of the criteria. The technical report developed as part of this project presents issues and concerns and shows potential values generated for design speeds of 85 to 100 mph (140 to 160 km/h) for: stopping sight distance, grades, vertical alignment, lane width, shoulder width, cross slope, horizontal alignment and superelevation, ramp design speed, ramp grades and profiles, ramp cross section and cross slope, distance between successive ramps, ramp lane and shoulder widths, ramp acceleration and deceleration lengths, roadside clear zones, median width, roadside slopes and ditches, crash testing, and roadside safety devices. The criteria developed in the project were provided to TxDOT. TxDOT incorporated project findings in the new TxDOT Roadway Design Manual Chapter 8: Mobility Corridor (5R) Design Criteria.
Standard Treatments Induce Antigen-Specific Immune Responses in Prostate Cancer (2007)

We show for the first time that standard treatments induce antigen-specific immune responses in prostate cancer patients. Thus, immunologic mechanisms may contribute to clinical outcomes after hormone and radiation therapy, an effect that could potentially be exploited as a practical, personalized form of immunotherapy.
A DFT study of the role of water in the rhodium-catalyzed hydrogenation of acetone (2016)

The positive effect of the addition of water to acetone hydrogenation by [RhH₂(PR₃)₂S₂]⁺ catalysts has been studied by DFT calculations. The studied energetic profiles reveal that the more favourable mechanistic path involves a hydride migration to the ketone followed by a reductive elimination that is assisted by two water molecules.
523 Design of tailor made implants using VCAD system (2006)

Making of tailor made implants that is adaptive for each patients is needed. We are developing VCAD system that is integrating CAT, CAD, CAM, CAE. In this paper, we report exploratory experiments of the development of tailor made artificial capital femur system. We made capital femur models based on X-Ray CT images, and modeled shape of implants that reflects real capital femur shape. This models have VCAD native format that can dynamic simulation include FEM analysis, and can manufacture implants.
Cibacron Blue-induced modification of neutral proteinase from horse blood leukocytes. (1982)

The proteolytic activity of the elastase-like proteinase from granules of horse blood leukocytes is retained on a column of Cibacron Blue-Sepharose and can be eluted with 0.5 M KSCN. During this procedure its mol. wt. is reduced from 49000 to 30000 and isoelectric point is shifted towards higher pH. The inactive protein not adsorbed on Cibacron Blue-Sepharose is strongly acidic and shows a mol. wt. of 20000. Upon mixing this protein with the modified enzyme the native proteinase is reconstituted as shown by polyacrylamide gel electrophoresis at pH 8.3 and isoelectric focusing in a sucrose gradient.
Ribozymes as therapeutic agents and genetic tools (2002)

INTRODUCTION Ribozymes are RNA molecules capable of acting as enzymes even in the complete absence of proteins. They have the catalytic activity of breaking and/or forming covalent bonds with extraordinary specificity, accelerating the rate of these catalytic reactions. The ability of RNA to serve as a catalyst was first shown for the self-splicing Group I intron of Tetrahymena and the RNA moiety of RNAse P (Cech, 1990; GuerrierTakada et al., 1983; Kruger et al., 1982). Group I introns, which range in size from 200 to 1500 nucleotides, are classified by phylogenetically conserved secondary structures, as well as by certain functional characteristics. These introns possess many of the attributes of protein enzymes, including sub-strate and cofactor binding domains. The well studied Tetrahymena intron has been shown to harbor important tertiary interactions with the substrate molecule and to undergo conformational shifts. It can also be engineered to bind, cleave and release multiple substrates. RNAse P is a ubiquitous enzyme that cleaves the 5′ precursor segment from pre-transfer RNA molecules. The holoenzyme is comprised of at least one protein and one RNA subunit (ranging in size from 140 to 490 nucleotides, depending on the organism) (Kurz and Fierke, 2000). The RNA of the bacterial enzyme alone, under the appropriate salt and ionic conditions, can site specifically cleave the 5′ leader segment from precursor t-RNAs (Guerrier-Takada et al., 1983).
Figure S5 from An AIB1 Isoform Alters Enhancer Access and Enables Progression of Early-Stage Triple-Negative Breast Cancer (2023)

&lt;p&gt;A) Principal component analyses of RNA-Seq from MCFDCIS and MCF10A cell lines and the AIB1Î"4 corresponding clones. B) Relapse free survival and overall survival KM-plots in patients with ER-negative breast tumors separated by AIB1Î"4 top regulated genes in MCFDCIS cells. AIB1Î"4 signature gene list used to generate the KM-plots is in Supplementary table S3. C) Volcano plots illustrating differentially expressed genes (DEGs) regulated by AIB1Î"4 in MCF10A cell clones (|log2(FC)|&gt;1.5 and -log(adj p-val)&gt;1.3). Full list of DEGs in Supplementary table S1. D) Significantly enriched hallmark pathways from gene set enrichment analyses (GSEA) associated with AIB1Î"4 expression in MCF10A cells. Full list of enriched pathways in Supplementary table S2. E) Top canonical pathways altered in MCF10A-Î"4 compared to control MCF10A cells identified by Ingenuity Pathway Analysis (IPA). |z-score|&gt;1, p-val &lt;0.05. F) Relapse free survival KM-plots in patients with ER-negative breast tumors separated by AIB1Î"4 top regulated genes in MCF10A cells. AIB1Î"4 signature gene list used to generate the KM-plots in Supplementary table S3. G) Western blot of EMT markers of DCIS cells induced by DCIS-Î"4 for the indicated times. Actin is used as a loading control. Band quantification is indicated in red. H) A volcano plot illustrating differentially expressed genes (DEGs) in MCFDCIS-Î"4 when co-cultured with MCFDCIS compared to MCFDCIS-Î"4 alone. Mixed cells were then separated by flow cytometry prior to RNA-seq analysis. (|log2(FC)|&gt;1.5 and -log(adj p-val)&gt;1.3). Full list of DEGs in Supplementary table S1.&lt;/p&gt;
A leakage-tolerant low-leakage register file with conditional sleep transistor (2004)

This paper describes a 256/spl times/64b 3-read, 3-write ported leakage tolerant low leakage register file. The local bitline shares a sleep transistor for aggressive bitline leakage reduction/tolerance to enable high fanin bitlines and uses low V/sub th/ transistors. The sleep transistor is turned on while accessing the local bitline and conditionally turned off, if the dynamic node should remain high. Simulation results shows that proposed technique achieves 9% improvement in performance with 14/spl times/ reduction in local bitline leakage (97/spl times/ reduction as compared to any previously proposed low V/sub th/, leakage tolerant register file) enabling 70% reduction in keeper size, while keeping the same noise robustness as optimized high performance conventional high V/sub th/ implementation.
Accurate description of the optical response of a multilayered spherical system in the long wavelength approximation (2010)

The optical response of a multilayered spherical system of unlimited number of layers (a ``matryoshka'') in the long wavelength limit can be accounted for from the knowledge of the static multipole polarizability of the system to first-order accuracy. However, for systems of ultrasmall dimensions or systems with sizes not-too-small compared to the wavelength, this ordinary quasistatic long wavelength approximation (LWA) becomes inaccurate. Here we introduce two significant modifications of the LWA for such a nanomatryoshka in each of the two limits: the nonlocal optical response for ultrasmall systems $(&lt;10\text{ }\text{nm})$, and the ``finite-wavelength corrections'' for systems $\ensuremath{\sim}100\text{ }\text{nm}$. This is accomplished by employing the previous work for a single-layer shell, in combination with a certain effective-medium approach formulated recently in the literature. Numerical calculations for the extinction cross sections for such a system of different dimensions are provided as illustrations for these effects. This formulation thus provides significant improvements on the ordinary LWA, yielding enough accuracy for the description of the optical response of these nanoshell systems over an appreciable range of sizes, without resorting to more involved quantum mechanical or fully electrodynamic calculations.