gebhart/patrepeval huggingface dataset:
IMMUNOGENETICS OF CELL SURFACE ANTIGENS OF MOUSE LEUKEMIA (1977)

INTRODUCTION . . . . . . . .... .... . . . . . . . . . . . . . . . . . ..... . .... . . . . ... ... ... . . . .. . . . . . ... . ....... 1 28 TECHNIQUES FOR THE IN VITRO ANALYSIS OF SURFACE ANTIGENS OF LEUKEMIA CELLS .... ... ....... ... . .... . . .. ... ........ 1 29 Antibody Detection Systems ...... . . . . . . . . . . . . . . . . . . . . 1 29 Preparation of A ntisera . . . . ......... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 29 Qualitative and Quantitative A bsorption Analysis In Vitro ........ . ... . . ... ... ........ 132 Standard Test Cells . . . . . . ........ 132 Other Techniques for Analyzing Cell Surface Antigens ........ . . . . . . . . .. . . . . . . ... . ...... 134
Adenovirus-mediated human prostasin gene delivery is linked to increased aldosterone production and hypertension in rats (2003)

Prostasin has been demonstrated to be an activator of epithelial sodium channels in cultured renal and bronchial epithelial cells. In this study, we evaluated the effects of adenovirus-mediated gene transfer of human prostasin on blood pressure regulation and sodium reabsorption in Wistar rats. Expression of human prostasin mRNA was identified in rat adrenal gland, liver, kidney, heart, lung, and aorta, and immunoreactive human prostasin was detected in the circulation and urine of rats receiving prostasin gene transfer. A single injection of adenovirus carrying the prostasin gene caused prolonged increases in blood pressure for 3-4 wk. Blood pressure increase was accompanied by elevated plasma aldosterone levels and reduced plasma renin activity. The increase in blood pressure and plasma aldosterone levels as well as the reduction of plasma renin activity correlated with the expression of human prostasin transgene. Elevated plasma aldosterone levels were detected at 3 days after gene transfer before the development of hypertension, indicating that stimulation of mineralocorticoid production is the primary target of prostasin. Prostasin gene transfer significantly reduced urinary K(+) excretion but increased urinary Na(+) and kallikrein excretion. Elevated renal kallikrein levels promote natriuresis, which may lead to sodium escape and prevent further increases of blood pressure after prostasin gene transfer. In summary, these results suggest that prostasin participates in blood pressure and electrolyte homeostasis by regulating the renin-angiotensin-aldosterone and kallikrein-kinin systems.
Evaluating the Therapeutic Potential of a Non-Natural Nucleotide That Inhibits Human Ribonucleotide Reductase (2012)

Abstract Human ribonucleotide reductase (hRR) is the key enzyme involved in de novo dNTP synthesis and thus represents an important therapeutic target against hyperproliferative diseases, most notably cancer. The purpose of this study was to evaluate the ability of non-natural indolyl-2′-deoxynucleoside triphosphates to inhibit the activity of hRR. The structural similarities of these analogues with dATP predicted that they would inhibit hRR activity by binding to its allosteric sites. In silico analysis and in vitro characterization identified one particular analogue designated as 5-nitro-indolyl-2′-deoxyribose triphosphate (5-NITP) that inhibits hRR. 5-NITP binding to hRR was determined by isothermal titration calorimetry. X-ray crystal structure of 5-NITP bound to RR1 was determined. Cell-based studies showed the anti-cancer effects of the corresponding non-natural nucleoside against leukemia cells. 5-NITP binds to hRR with micromolar affinity. Binding does not induce hexamerization of hRR1 like dATP, the native allosteric inhibitor of hRR that binds with high affinity to the A-site. The X-ray crystal structure of Saccharomyces cerevisiae RR1-5-NITP (ScRR1-5-NITP) complex determined to 2.3 Å resolution shows that 5-NITP does not bind to the A-site but rather at the S-site. Regardless, 5-nitro-indolyl-2′-deoxynucleoside (5-NIdR) produces cytostatic and cytotoxic effects against human leukemia cells by altering cell-cycle progression. Our studies provide useful insights toward developing new inhibitors with improved potency and efficacy against hRR. Mol Cancer Ther; 11(10); 2077–86. ©2012 AACR.
DIFFERENTIAL REGULATION OF ACTIVATION-ASSOCIATED RECEPTOR EXPRESSION ON CD4− AND CD8-POSITIVE T LYMPHOCYTES BY ALLOSENSITIZED SUPPRESSOR T CELLS (1989)

We have demonstrated by two-color flow cytometry that allosensitized human suppressor T cells thwart progression of alloactivated T cells into the G1B stage of the cell cycle, and consequently prevent the expression of transferrin receptors on the majority of alloreactive MLR responder cells (P less than 0.005). Suppressor cells inhibit transferrin as well as interleukin-2 receptor expression on both CD4- and CD8-positive responder cells. The addition of 20 U/ml of recombinant interleukin-2 at the initiation of suppressor coculture bioassays completely neutralizes the suppressive effect of suppressor T cells exerted on CD8-positive responder T cells, but does not restore expression of transferrin and interleukin-2 receptors on CD4-positive T cells. Hence, CD4-positive T cells are the direct target of the suppressor cells, while inhibition of transferrin and interleukin-2 receptor expression on CD8-positive T cells results from reduced levels of interleukin-2 in suppressor cell-regulated cultures. In suppressor cell modified mixed lymphocyte reactions supplemented with exogenous interleukin-2 CD8+/CD28- responder cells proliferate preferentially. It is apparent that mixed lymphocyte reactions supplemented with allosensitized suppressor cells cultured in an interleukin-2-rich environment create a milieu that permits the preferential expansion of T cells with suppressor effector phenotype. This in vitro system provides a convenient model in which to cultivate activated CD8+/CD28- T cells.
High wall-plug efficiency blue III-nitride LEDs designed for low current density operation (2017)

Commercial LEDs for solid-state lighting are often designed for operation at current densities in the droop regime (~35 A/cm<sup>2</sup>) to minimize costly chip area; however, many benefits can be realized by operating at low current density (J ≈1 - 5 A/cm<sup>2</sup>). Along with mitigation of droop losses and reduction of the operating voltage, low J operation of LEDs opens the design space for high light extraction efficiency (LEE). This work presents detailed ray tracing simulations of an LED design for low J operation with LEE ≈94%. The design is realized experimentally resulting in a peak wall-plug efficiency of 78.1% occurring at 3.45 A/cm<sup>2</sup> and producing an output power of 7.2 mW for a 0.1 mm<sup>2</sup> emitting area. At this operation point, the photon voltage V<sub>p</sub>=hνq exceeds the forward voltage (V), corresponding to a Vp/V = 103%.
Beyond-CMOS vanadium dioxide devices and oscillators for brain-like information processing (2021)

International audience
Data from Spliced Peptides and Cytokine-Driven Changes in the Immunopeptidome of Melanoma (2023)

&lt;div&gt;Abstract&lt;p&gt;Antigen recognition by CD8&lt;sup&gt;+&lt;/sup&gt; T cells is governed by the pool of peptide antigens presented on the cell surface in the context of HLA class I complexes. Studies have shown not only a high degree of plasticity in the immunopeptidome, but also that a considerable fraction of all presented peptides is generated through proteasome-mediated splicing of noncontiguous regions of proteins to form novel peptide antigens. Here, we used high-resolution mass spectrometry combined with new bioinformatic approaches to characterize the immunopeptidome of melanoma cells in the presence or absence of IFNγ. In total, we identified more than 60,000 peptides from a single patient-derived cell line (LM-MEL-44) and demonstrated that IFNγ induced changes in the peptidome, with an overlap of only approximately 50% between basal and treated cells. Around 6% to 8% of the peptides were identified as &lt;i&gt;cis&lt;/i&gt;-spliced peptides, and 2,213 peptides (1,827 linear and 386 &lt;i&gt;cis&lt;/i&gt;-spliced peptides) were derived from known melanoma-associated antigens. These peptide antigens were equally distributed between the constitutive- and IFNγ-induced peptidome. We next examined additional HLA-matched patient-derived cell lines to investigate how frequently these peptides were identified and found that a high proportion of both linear and spliced peptides was conserved between individual patient tumors, drawing on data amassing to more than 100,000 peptide sequences. Several of these peptides showed &lt;i&gt;in vitro&lt;/i&gt; immunogenicity across multiple patients with melanoma. These observations highlight the breadth and complexity of the repertoire of immunogenic peptides that can be exploited therapeutically and suggest that spliced peptides are a major class of tumor antigens.&lt;/p&gt;&lt;/div&gt;
A Means to Accommodate Residual Limb Movement During Optical Scanning: A Technical Note (2008)

A technique is described for correcting for subject movement while imaging the residual limb of a person with a transtibial amputation. Small reflective markers were placed on the residual limb, and then their motions tracked during scanning using two stationary cameras. The marker position measurements were used to generate appropriate translational and rotational transformation matrices so that limb motion could be corrected for during the 1.5-s scan interval. Evaluation tests showed good performance for moderate (2-4 mm) to high (5-8 mm) motion cases. The difference in mean absolute cross-sectional area between the test scan and a stationary reference scan was reduced by approximately one half when motion correction was used compared with when motion correction was not used. The algorithm broke down for exaggerated motion ( >or= 9 mm) cases, particularly in areas outside the region encompassed by the markers. The developed method is useful in prosthetics research where high resolution shape measurement is needed, for example in cases where residual limb shape or volume change is of interest.
Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature (2018)

Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting evidence statements, and then send those annotations to any database in the world. Textpresso Central URL: http://www.textpresso.org/tpc.
Equivalence Ratio Dependence of Reactivity of Low and High Temperature Reactions for Ultra-Lean Gasoline Surrogate/Air Weak Flames in Micro Flow Reactor with Controlled Temperature Profile (2017)

A vertical-type micro flow reactor with a controlled temperature profile was used to investigate the effect of the equivalence ratio on low and high temperature reactions of ultra-lean gasoline surrogate/air weak flames. Surrogates of research octane number 90 and 100 were used at equivalence ratios between 0.50 and 1.00. In the experiments, leaner mixtures showed a higher reactivity as indicated by hot flames stabilizing at lower wall temperatures. In 1D steady computations by PREMIX only LLNL mechanism was able to reproduce this trend. This was accounted to difference in the reaction parameters of the chain termination reaction H+O2(+M)=HO2(+M) in the KUCRS mechanisms. Once LLNL's parameters were introduced, results by KUCRS and SIP mechanisms were able to reproduce the experimental results with higher accuracy.
Prolactin modulates the naive B cell repertoire (2003)

Prolactin is a peptide hormone produced by the anterior pituitary gland that is critical in lactation. Prolactin can also be produced by lymphocytes, and both B and T cells express prolactin receptors. These findings have suggested that prolactin has immunomodulatory functions. Studies in spontaneously autoimmune hosts have demonstrated a role for prolactin in augmenting autoreactivity. We chose to analyze prolactin effects on anti-DNA B cells in nonspontaneously autoimmune female BALB/c mice transgenic for the heavy chain of an anti-DNA antibody. Treatment with prolactin for 4 weeks induced a lupus-like phenotype with an increased number of transgene-expressing B cells, elevated serum anti-DNA antibody titers, and glomerular immunoglobulin deposits. Prolactin caused a decrease in the population of transitional B cells and an increase in mature follicular and marginal zone B cells. The DNA-reactive B cells had a follicular cell phenotype. Anti-DNA hybridomas demonstrated that prolactin alters selection of the naive B cell repertoire. The expansion and activation of anti-DNA B cells in prolactin-treated R4A-gamma2b BALB/c mice was dependent on the presence of CD4(+) T cells. Finally, treatment with prolactin was unable to break tolerance in R4A-gamma2b transgenic C57Bl/6 mice, suggesting that responsiveness of the immune system to prolactin is genetically determined.
Technical note: Mice produced by intracytoplasmic sperm injection using a modified conventional method1 (2012)

A piezo-driven pipette that includes a small amount of mercury to enhance efficiency is widely used for mouse intracytoplasmic sperm injection (ICSI). Unfortunately, the use of toxic mercury is not permitted in hospital facilities and alternatives to mercury that enhance performance of the device do not work as well in the mouse. We have eliminated mercury toxicity and obtained acceptable ICSI efficiency using a modified conventional method. With this technique, oocyte survival, fertilization (number of 2-cell) and blastocyst rates were 77/126 (61.1%), 65/77 (84.4%), and 45/65 (69.2%), respectively. Eleven live pups were born from the transfer of thirty-two 2- to 4-cell embryos to 2 surrogate mothers. This conventional method is efficient, simple, and does not need the assistance of piezo-driven devices.
Robust Text Detection in Natural Scene Images by Generalized Color-Enhanced Contrasting Extremal Region and Neural Networks (2014)

This paper presents a robust text detection approach based on generalized color-enhanced contrasting extremal region (CER) and neural networks. Given a color natural scene image, six component-trees are built from its gray scale image, hue and saturation channel images in a perception-based illumination invariant color space, and their inverted images, respectively. From each component-tree, generalized color-enhanced CERs are extracted as character candidates. By using a "divide-and-conquer" strategy, each candidate image patch is labeled reliably by rules as one of five types, namely, Long, Thin, Fill, Square-large and Square-small, and classified as text or non-text by a corresponding neural network, which is trained by an ambiguity-free learning strategy. After pruning non-text components, repeating components in each component-tree are pruned by using color and area information to obtain a component graph, from which candidate text-lines are formed and verified by another set of neural networks. Finally, results from six component-trees are combined, and a post-processing step is used to recover lost characters and split text lines into words as appropriate. Our proposed method achieves 85.72% recall, 87.03% precision, and 86.37% F-score on ICDAR-2013 "Reading Text in Scene Images" test set.
Non-saturated throughput analysis for a QoS differentiated p-persistent CSMA protocol with the capture effect (2015)

Analysing the performance of WLANs in non-ideal channel conditions is a fundamental consideration in practical situations since wireless channels are error-prone. This paper presents a closed form analytical solution for the non-saturated throughput of a QoS differentiated p-persistent CSMA protocol that takes into account the capture effect in a Rayleigh multipath fading environment. The results show that the throughput performance with the capture effect depends on the absolute and relative p-persistent values, the total system offered load and relative offered loads per traffic type, as well as the thresholds for capture.
Improved Pr{sup 3+}-doped heavy metal fluoride glasses and fibers (1996)

Praseodymium doped heavy metal fluoride glass preforms were fabricated via a modified suction casting method. A subsequent redraw process was employed to obtain high quality single mode fluoride fiber. Modifications of the ZBLAN composition, including the incorporation of In{sup 3+}, Y{sup 3+} and Cs{sup +}, were undertaken in an attempt to improve optical properties while maintaining the inherent drawability of ZBLAN. Thermal analysis to determine the various draw parameters was conducted using Differential Scanning Calorimetry, while optical characterization included spectral absorption, fluorescence, and fluorescent lifetime measurements for all specimens. The modifications in composition resulted in an increase in the fluorescent lifetime of Pr{sup 3+} at 1.3{mu}m.
Abstract A023: RNF185 modulates prostate cancer metastatic potential through regulation of epithelial-mesenchymal transition (2023)

Abstract RNF185 is a RING finger domain-containing ubiquitin ligase which is anchored to the ER and resemble RNF5, a ubiquitin ligase implicated in ER associated degradation. In prostate cancer, deregulation of the expression or activity of several ubiquitin ligases has been shown to contribute to disease progression (e.g., Siah2, SPOP, RNF6). Analysis of prostate tumor patient data revealed a negative correlation between RNF185 expression and prostate adenocarcinoma progression and metastasis. Supporting these observations, several prostate cancer cell lines exhibited greater migration and invasion capabilities upon RNF185 depletion, in vitro. Subcutaneous inoculation of mouse prostate cancer MPC3 cells, stably expressing shRNA against RNF185, resulted in larger tumors and more frequent lung metastases in NSG mice. These results suggest that the increased metastatic potential associated with lower RNF185 levels may depend on molecular changes intrinsic to the tumors cells. RNA-sequencing and Ingenuity Pathway Analysis of RNF185-depleted compared to control MPC3 cells identified wound healing and cellular movement among the most significantly upregulated pathways in RNF185-depleted cells. Transcription regulators of Epithelial-Mesenchymal Transition (EMT) Snai2 and Zeb1 were among the most upregulated genes that were predicted to be activated based on the expression of their target genes. Comparison between differentially expressed genes in patients with low RNF185 expression, and RNF185-depleted cell lines (from mouse and human prostate tumors) confirmed deregulation of genes implicated in EMT. Taken together, our results identify RNF185 as gatekeeper of prostate cancer metastasis, via its control of EMT genes implicated in cell motility and metastasis. Citation Format: Benjamin Van Espen, Ladan Fazli, Htoo Z. Oo, Rabi Murad, Martin Gleave, Ze'ev A. Ronai. RNF185 modulates prostate cancer metastatic potential through regulation of epithelial-mesenchymal transition [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A023.
Synergistic Roles of Bone Morphogenetic Protein 15 and Growth Differentiation Factor 9 in Ovarian Function (2001)

Knockout mouse technology has been used over the last decade to define the essential roles of ovarian-expressed genes and uncover genetic interactions. In particular, we have used this technology to study the function of multiple members of the transforming growth factor-beta superfamily including inhibins, activins, and growth differentiation factor 9 (GDF-9 or Gdf9). Knockout mice lacking GDF-9 are infertile due to a block in folliculogenesis at the primary follicle stage. In addition, recombinant GDF-9 regulates multiple cumulus granulosa cell functions in the periovulatory period including hyaluronic acid synthesis and cumulus expansion. We have also cloned an oocyte-specific homolog of GDF-9 from mice and humans, which is termed bone morphogenetic protein 15 (BMP-15 or Bmp15). To define the function of BMP-15 in mice, we generated embryonic stem cells and knockout mice, which have a null mutation in this X-linked gene. Male chimeric and Bmp15 null mice are normal and fertile. In contrast to Bmp15 null males and Gdf9 knockout females, Bmp15 null females (Bmp15(-/-)) are subfertile and usually have minimal ovarian histopathological defects, but demonstrate decreased ovulation and fertilization rates. To further decipher possible direct or indirect genetic interactions between GDF-9 and BMP-15, we have generated double mutant mice lacking one or both alleles of these related homologs. Double homozygote females (Bmp15(-/-)Gdf9(-/-)) display oocyte loss and cysts and resemble Gdf9(-/-) mutants. In contrast, Bmp15(-/-)Gdf9(+/-) female mice have more severe fertility defects than Bmp15(-/-) females, which appear to be due to abnormalities in ovarian folliculogenesis, cumulus cell physiology, and fertilization. Thus, the dosage of intact Bmp15 and Gdf9 alleles directly influences the destiny of the oocyte during folliculogenesis and in the periovulatory period. These studies have important implications for human fertility control and the maintenance of fertility and normal ovarian physiology.
Supplemental Figures S1-S10 from Histone Deacetylase Inhibitors Synergize with Catalytic Inhibitors of EZH2 to Exhibit Antitumor Activity in Small Cell Carcinoma of the Ovary, Hypercalcemic Type (2023)

&lt;p&gt;Fig.S1 shows that SCCOHT cells are sensitive to HDAC inhibition. Fig. S2 shows that SCCOHT cells are sensitive to HDAC inhibition or depletion. Fig.S3 shows that SMARCA4/A2 dual deficiency is not associated with hypersensitivity to HDAC inhibitors in lung and pancreatic cancer cell lines. Fig.S4 shows that pan-HDAC inhibitors induce cell morphology changes in SCCOHT cells. Fig.S5 shows that SMARCA2 activation is partially required for the hypersensitivity of SCCOHT cells to HDAC inhibition. Fig. S6 shows the effect of quisinostat on mouse body weights in BIN67 mouse xenograft models. Fig.S7 shows the synergistic effects between HDAC inhibitors and EZH2 inhibitors in SWI/SNF deficiency-driven tumor cells. Fig. S8 shows that depletion of HDAC2 increased sensitivity of BIN67 cells to EPZ-6438 treatment. Fig.S9 shows the synergistic effects between HDAC inhibitors and EZH2 inhibitors in SCCOHT cells. Fig.S10 shows the effect of combined treatment of EPZ-6438 and quisinostat on mouse body weight and survival.&lt;/p&gt;
Out of thin air: In-situ formation of diamond-like nanocomposite films. (2020)

Abstract not provided.