gebhart/patrepeval huggingface dataset:
Molecular characterization of a mucin-type antigen associated with human pancreatic cancer. The DU-PAN-2 antigen. (1987)

This work describes the molecular characterization of a human pancreatic cancer-associated antigen defined by a murine monoclonal antibody (DU-PAN-2). DU-PAN-2 antigen was isolated from a pancreatic adenocarcinoma cell line (HPAF) or patient's ascitic fluid, and the antigenic activity was monitored by competitive inhibition radioimmunoassay. Affinity chromatography and CsCl/guanidine HCl density gradient centrifugation were employed to remove other populations of mucin-type glycoproteins and noncovalently associated proteins, respectively. Three electrophoretically distinct components were detected by 1% agarose gel electrophoresis and were resolved by chromatography on Sepharose CL-4B. The major fraction (FII) was subjected to carbohydrate and amino acid analyses. The sum of threonine, serine, proline, glycine, and alanine comprised more than 50% of the amino acid residues. The saccharide units, O-glycosidically linked to the peptide via GalNAc, contained fucose, galactose, GlcNAc, GalNAc, and sialic acid. The total carbohydrate content of FI and FII was 80.8% and 77.4% by weight, respectively. The molecular weight of FII antigen showed two species of molecules of 1.45 X 10(6) and 4.59 X 10(6) by analytical sedimentation equilibrium. DU-PAN-2 antigen was susceptible to neuraminidase, pepsin, Pronase, and papain digestion. These results suggest that both protein components and sialic acid residues may play important roles in the binding of DU-PAN-2 antibody.
Bromodomain protein inhibition: a novel therapeutic strategy in rheumatic diseases (2018)

The reading of acetylation marks on histones by bromodomain (BRD) proteins is a key event in transcriptional activation. Small molecule inhibitors targeting bromodomain and extra-terminal (BET) proteins compete for binding to acetylated histones. They have strong anti-inflammatory properties and exhibit encouraging effects in different cell types in vitro and in animal models resembling rheumatic diseases in vivo. Furthermore, recent studies that focus on BRD proteins beyond BET family members are discussed.
A neural network approach to broadcasting in multihop packet radio networks (1991)

A neural network model for broadcasting scheduling in multihop packet radio networks is presented. The problem of broadcast scheduling with a minimum number of time slots is NP-complete. The proposed neural network model finds a broadcasting schedule with a minimal number of time slots, and requires n processing elements for an n-node radio network. Fifteen different radio networks were examined where the neural network model found an m-time-slot solution in O(m) time with n processors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Greater glycosaminoglycan content in human patellar tendon biopsies is associated with more pain and a lower VISA score (2013)

Increased GAGs in the pathological human patellar tendon are related to a worse clinical status. These findings indicate that the VISA score reflects the extent of tendon tissue pathology.
Lasers for isotope separation processes and their properties (1976)

The laser system requirements for isotope enrichment are presented in the context of an atomic uranium vapor process. Coherently pumped dye lasers using as the pump laser either the frequency doubled Nd:YAG or copper vapor are seen to be quite promising for meeting the near term requirements of a laser isotope separation (LIS) process. The utility of electrical discharge excitation of the rare gas halogens in an LIS context is discussed.
Induction of Mxi1-SRα by FOXO3a Contributes to Repression of Myc-Dependent Gene Expression (2007)

Forkhead transcription factors of the O class (FOXOs) are important targets of the phosphatidylinositol 3-kinase (PI3-kinase)/Akt pathway. FOXOs have been implicated in the regulation of cell cycle progression, oxidative stress resistance, and apoptosis. Using DNA microarrays, we analyzed the transcriptional response to FOXO3a activation by gene expression analysis in DLD-1 colon cancer cells stably expressing a FOXO3a.A3-ER fusion protein. We found that activation of FOXO3a resulted in repression of a number of previously identified Myc target genes. Furthermore, FOXO3a activation induced expression of several members of the Mad/Mxd family of transcriptional repressors, most notably Mxi1. The induction of Mxi1 by FOXO3a was specific to the Mxi1-SR alpha isoform and was mediated by three highly conserved FOXO binding sites within the first intron of the gene. Activation of FOXO3a in response to inhibition of Akt also resulted in activation of Mxi1-SR alpha expression. Silencing of Mxi1 by small interfering RNA (siRNA) reduced FOXO3a-mediated repression of a number of Myc target genes. We also observed that FOXO3a activation induced a switch in promoter occupancy from Myc to Mxi1 on the E-box containing promoter regions of two Myc target genes, APEX and FOXM1. siRNA-mediated transient silencing of Mxi1 or all Mad/Mxd proteins reduced exit from S phase in response to FOXO3a activation, and stable silencing of Mxi1 or Mad1 reduced the growth inhibitory effect of FOXO3a. We conclude that induction of Mad/Mxd proteins contributes to the inhibition of proliferation in response to FOXO3a activation. Our results provide evidence of direct regulation of Mxi1 by FOXO3a and imply an additional mechanism through which the PI3-kinase/Akt/FOXO pathway can modulate Myc function.
Supplementary Figure S1 from USP9X Downregulation Renders Breast Cancer Cells Resistant to Tamoxifen (2023)

&lt;p&gt;Figure S1. ERÃŽÂ± positive breast cancer cells are rescued from tamoxifen induced growth arrest by USP9X knockdown, but ERÃŽÂ± negative breast cancer cells are not. Knockdown of USP9X rescues tamoxifen-induced growth arrest in T47D cells. T47D cells were infected with the shRNA against USP9X recovered from the initial screen, pRS-USP9X II or pRS-GFP as control. Cells were cultured for 4-6 weeks in the presence of 1ÃŽÂ¼M 4OH-tamoxifen. When colonies appeared cells were fixed and subsequently stained. Plate confluency was determined by calculating the number of cell-covered pixels related to the total surface area.&lt;/p&gt;
Tight bounds on the minimum average weight per branch for rate (N-1)/N convolutional codes (1997)

Consider a cycle in the state diagram of a convolutional code. The average weight per branch of the cycle is equal to the total Hamming weight of all labels on the branches divided by the number of branches. Let w/sub 0/ be the minimum average weight per branch over all cycles in the state diagram, except the zero state self-loop of weight zero. Codes with low w/sub 0/ result in high bit error probabilities when they are used with either Viterbi or sequential decoding. Hemmati and Costello (1980) showed that w/sub 0/ is upper-bounded by 2/sup /spl nu/-2//(3/spl middot/2/sup /spl nu/-2/-1) for a class of (2,1) codes where /spl nu/ denotes the constraint length. In the present correspondence it is shown that the bound is valid for a large class of (n,n-1) codes, n/spl ges/2. Examples of high-rate codes with w/sub 0/ equal to the upper bound are also given. Hemmati and Costello defined a class of codes to be asymptotically catastrophic if w/sub 0/ approaches zero for large /spl nu/. The class of (n,n-1) codes constructed by Wyner and Ash (1963) is shown to be asymptotically catastrophic. All codes in the class have minimum possible w/sub 0/ equal to 1//spl nu/.
FETC Programs for Reducing Greenhouse Gas Emissions (1998)

Mark Twain once quipped that everyone talks about the weather but no one does anything about it. With interest in global climate change on the rise, researchers in the fossil-energy sector are feeling the heat to provide new technology to permit continued use of fossil fuels but with reduced emissions of so-called `greenhouse gases.` Three important greenhouse gases, carbon dioxide, methane, and nitrous oxide, are released to the atmosphere in the course of recovering and combusting fossil fuels. Their importance for trapping radiation, called forcing, is in the order given. In this report, we briefly review how greenhouse gases cause forcing and why this has a warming effect on the Earth`s atmosphere. Then we discuss programs underway at FETC that are aimed at reducing emissions of methane and carbon dioxide.
Kidney injury molecule-1: a tissue and urinary biomarker for nephrotoxicant-induced renal injury (2004)

Nephrotoxicity is a common side effect of therapeutic interventions, environmental insults, and exposure to toxicants in the workplace. Although biomarkers for nephrotoxicity are available, they often lack sensitivity and are not specific as indicators of epithelial cell injury. Kidney injury molecule-1 (Kim-1) is a type 1 membrane protein with extracellular immunoglobulin and mucin domains. The mRNA and protein for Kim-1 are expressed at very low levels in normal rodent kidney, but expression increases dramatically after injury in proximal tubule epithelial cells in postischemic rodent kidney and in humans during ischemic acute renal failure. To evaluate the utility of Kim-1 as a biomarker for other types of renal injury, we analyzed tissue and urinary expression in response to three different types of nephrotoxicants in the rat: S-(1,1,2,2-tetrafluoroethyl)-l-cysteine (TFEC), folic acid, and cisplatin. Marked increases in Kim-1 expression were confirmed by immunoblotting in all three models. The protein was shown to be localized to the proximal tubule epithelial cell by immunofluorescence. Furthermore, Kim-1 protein was detected in urine of toxicant-treated rats. The temporal pattern of expression in response to TFEC is similar to the Kim-1 expression pattern in the postischemic kidney. In folic acid-treated kidneys, Kim-1 is clearly localized to the apical brush border of the well-differentiated proximal tubular epithelial cells. After folic acid treatment, expression of Kim-1 is present in the urine despite no significant increase in serum creatinine. Cisplatin treatment results in early detection of urinary Kim-1 protein and diffuse Kim-1 expression in S3 cells of the proximal tubule. Kim-1 can be detected in the tissue and urine on days 1 and 2 after cisplatin administration, occurring before an increase in serum creatinine. The upregulation of expression of Kim-1 and its presence in the urine in response to exposure to various types of nephrotoxicants suggest that this protein may serve as a general biomarker for tubular injury and repair processes.
The Development of Organometallic Methodologies For the Stereospecific Introduction of Cephalosporin Side Chains (1994)

A variety of 3-substituted cephems has become available via the coupling of 3-trifloxycephems with organostannanes, by a modified Stille coupling procedure that includes a new palladium ligand, tri(2-furyl)phosphine. A complementary cuprate coupling via the same intermediates is also described. A cheaper alternative to the triflates are the enol fluorosulfonates, which also undergo Stille and organocuprate couplings. A radically different approach to cephaosporins from penicillins involves a modification of the Morin rearrangement that involves the intermediacy of allenylazetidinones; these undergo chemoselective addition of cuprates to the allene central carbon, followed by rapid cyclization by intramolecular sulfenylation. The process was applied, i.a., to the efficient synthesis of the new oral antibiotic Cefprozil. 1. Introduction 2. The Stille Approach to Novel Cephalosporins 3. Other Cross-Coupling Approaches 4. The synthesis of Cephalosporins via Allenylazetidinones 5. Conclusion
In Vivo Application of Short-Lag Spatial Coherence and Harmonic Spatial Coherence Imaging in Fetal Ultrasound (2014)

Fetal scanning is one of the most common applications of ultrasound imaging and serves as a source of vital information about maternal and fetal health. Visualization of clinically relevant structures, however, can be severely compromised in difficult-to-image patients due to poor resolution and the presence of high levels of acoustical noise or clutter. We have developed novel coherence-based beamforming methods called Short-Lag Spatial Coherence (SLSC) imaging and Harmonic Spatial Coherence imaging (HSCI), and applied them to suppress the effects of clutter in fetal imaging. This method is used to create images of the spatial coherence of the backscattered ultrasound as opposed to images of echo magnitude. We present the results of a patient study to assess the benefits of coherence-based beamforming in the context of first trimester fetal exams. Matched fundamental B-mode, SLSC, harmonic B-mode, and HSCI images were generated using raw radio frequency data collected on 11 volunteers in the first trimester of pregnancy. The images were compared for qualitative differences in image texture and target conspicuity as well as using quantitative imaging metrics such as signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and contrast. SLSC and HSCI showed statistically significant improvements across all imaging metrics compared with B-mode and harmonic B-mode, respectively. These improvements were greatest for poor quality B-mode images where contrast of anechoic targets was improved from 15 dB in fundamental B-mode to 27 dB in SLSC and 17 dB in harmonic B-mode to 30 dB in HSCI. CNR improved from 1.4 to 2.5 in the fundamental images and 1.4 to 3.1 in the harmonic case. These results exhibit the potential of coherence-based beamforming to improve image quality and target detectability, especially in high noise environments.
Comparison of Calcium-Induced Associations of Bovine and Caprine Caseins and the Relationship of αs1-Casein Content to Colloidal Stabilization: A Thermodynamic Linkage Analysis (1993)

In milk, O(sl-, O(s2-, {3-, and K-caseins undergo association into colloidal complexes (casein micelles) that are visible with the electron microscope. Hydrophobic interactions and ea 2 + bonding are among the major causes of colloidal complex formation. In model systems, stable colloidal casein micelles can be obtained in a calcium caseinate solution by centrifugation at 1500 x g. The stabilities of colloidal complexes of bovine and two caprine caseins, selected for their O(sl-casein contents, were tested and thermodynamically linked with the calcium-induced changes in the amount of stable colloid present. Analysis of the data according to this thermodynamic linkage approach for bovine and caprine caseins indicates colloid formation at low calcium concentrations .015 M). However, at increased calcium ion concentrations, these colloids are destabilized. Bovine casein (O(sl-casein = 38% of total casein) was most stable with respect to added calcium ion concentration, and caprine casein, low in O(slcasein (5% of total casein), was least stable. The high caprine (O(sl-casein = 17% of total casein) was intermediate in stability. After destabilization, bovine
Evaluation of a New Etest Vancomycin-Teicoplanin Strip for Detection of Glycopeptide-Intermediate Staphylococcus aureus (GISA), in Particular, Heterogeneous GISA (2008)

Glycopeptide-intermediate Staphylococcus aureus (GISA) and, in particular, heterogeneous GISA (hGISA) are difficult to detect by standard MIC methods, and thus, an accurate detection method for clinical practice and surveillances is needed. Two prototype Etest strips designed for hGISA/GISA resistance detection (GRD) were evaluated using a worldwide collection of hGISA/GISA strains covering the five major clonal lineages. A total of 150 strains comprising 15 GISA and 60 hGISA strains (defined by population analysis profiles-area under the curve [PAP-AUC]), 70 glycopeptide-susceptible S. aureus (GSSA) strains, and 5 S. aureus ATCC reference strains were tested. For standardized Etest vancomycin (VA) MIC testing, the modified Etest macromethod with VA and teicoplanin (TP) strips tested with a heavier inoculum using brain heart infusion agar (BHI) and two glycopeptide screening agar plates (6 microg/ml VA/BHI and 5 microg/ml Mueller-Hinton agar [MHA]) were tested in parallel with the two new Etest GRD strips: a VA 32 (0.5-microg/ml)-TP 32 (0.5-microg/ml) double-sided gradient (E-VA/TP) with one prototype overlaid with a nutrient (E-VA/TP+S) to enhance the growth of hGISA. The Etest GRD strips were tested with a standard 0.5-McFarland standard inoculum using MHA and MHA plus 5% blood (MHB) and were read at 18 to 24 and 48 h. The interpretive MIC cutoffs used for the new Etest GRD strips at 24 and 48 h were as follows: for GISA, TP or VA, >or=8, and a standard VA MIC of >or=6; for hGISA, TP or VA, >or=8, and a standard VA MIC of <or=4. The results on MHB at 48 h showed that E-VA/TP+S had high specificity (94%) and sensitivity (95%) in comparison to PAP-AUC and was able to detect all GISA (n = 15) and 98% of hGISA (n = 60) strains. In contrast, the glycopeptide screening plates performed poorly for hGISA. The new Etest GRD strip (E-VA/TP+S), utilizing standard media and inocula, is a simple and acceptable tool for detection of hGISA/GISA for clinical and epidemiologic purposes.
The effects of a variable temperature regime on the physiology of the reef-building coralSeriatopora hystrix: results from a laboratory-based reciprocal transplant (2012)

To understand the effects of global climate change on reef-building corals, a thorough investigation of their physiological mechanisms of acclimatization is warranted. However, static temperature manipulations may underestimate the thermal complexity of the reefs in which many corals live. For instance, corals of Houbihu, Taiwan, experience changes in temperature of up to 10°C over the course of a day during spring-tide upwelling events. To better understand the phenotypic plasticity of these corals, a laboratory-based experiment was conducted whereby specimens of Seriatopora hystrix from an upwelling reef (Houbihu) and conspecifics from a non-upwelling reef (Houwan) were exposed to both a stable seawater temperature (26°C) regime and a regime characterized by a 6°C fluctuation (23-29°C) over a 12 h period for 7 days. A suite of physiological and molecular parameters was measured in samples of both treatments, as well as in experimental controls, to determine site of origin (SO) and temperature treatment (TT) responses. Only chlorophyll a (chl a) concentration and growth demonstrated the hypothesized trend of higher levels when exposed to a TT that mimicked SO conditions. In contrast, chl a, maximum dark-adapted quantum yield of photosystem II (F(v)/F(m)), and Symbiodinium ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL), photosystem I (psI, subunit III) and phosphoglycolate phosphatase (pgpase) mRNA expression demonstrated significant TT effects. Specifically, levels of these response variables were higher in samples exposed to a variable temperature regime, suggesting that S. hystrix may acclimate to fluctuating temperatures by increasing its capacity for photosynthesis.
Formation of Optical Images by X-Rays (1948)

Several conceivable methods for the formation of optical images by x-rays are considered, and a method employing concave mirrors is adopted as the most promising. A concave spherical mirror receiving radiation at grazing incidence (a necessary arrangement with x-rays) images a point into a line in accordance with a focal length f=Ri/2 where R is the radius of curvature and i the grazing angle. The image is subject to an aberration such that a ray reflected at the periphery of the mirror misses the focal point of central rays by a distance given approximately by S=1.5Mr2/R, where M is the magnification of the image and r is the radius of the mirror face. The theoretically possible resolving power is such as to resolve point objects separated by about 70A, a limit which is independent of the wave-length used. Point images of points and therefore extended images of extended objects may be produced by causing the radiation to reflect from two concave mirrors in series. Sample results are presented.
Beyond Just Text (2017)

Emoji, a set of pictographic Unicode characters, have seen strong uptake over the last couple of years. All common mobile platforms and many desktop systems now support emoji entry, and users have embraced their use. Yet, we currently know very little about what makes for good emoji entry. While soft keyboards for text entry are well optimized, based on language and touch models, no such information exists to guide the design of emoji keyboards. In this article, we investigate of the problem of emoji entry, starting with a study of the current state of the emoji keyboard implementation in Android. To enable moving forward to novel emoji keyboard designs, we then explore a model for emoji similarity that is able to inform such designs. This semantic model is based on data from 21 million collected tweets containing emoji. We compare this model against a solely description-based model of emoji in a crowdsourced study. Our model shows good perfor mance in capturing detailed relationships between emoji.
Induction of Interleukin 8 (IL‐8) Production by Pseudomonas Nitrite Reductase in Human Alveolar Macrophages and Epithelial Cells (1999)

Interleukin-8 (IL-8) participates in the generation of dense neutrophil accumulations in bronchopulmonary infections caused by Pseudomonas aeruginosa (P. aeruginosa). We have recently reported that nitrite reductase, a bifunctional enzyme located in the periplasmic space of P. aeruginosa, induces IL-8 generation in bronchial epithelial cells (K. Oishi et al. Infect. Immun. 65: 2648-2655, 1997). We examined whether or not Pseudomonas nitrite reductase (PNR) could also stimulate human alveolar macrophages (AM) and pulmonary type II epithelial-like cells (A549) to induce IL-8 production and mRNA expression as well as the production of TNF alpha and IL-1beta. We demonstrated a time- and dose-dependent IL-8 protein synthesis and IL-8 mRNA expression, but no TNF alpha or IL-1beta production, by A549 cells in response to PNR. New protein translation was not required for PNR-mediated IL-8 mRNA expression in the same cells. Furthermore, simultaneous stimulation of PNR with serial doses of TNF alpha or IL-1beta resulted in additive IL-8 production in A549 cells. In adherent AM, PNR enhanced IL-8 protein synthesis and IL-8 mRNA expression in a time-dependent fashion. PNR similarly induced a time-dependent production of TNF alpha and IL-1beta by human adherent AM. Neutralization of TNF alpha or IL-1beta did not influence the levels of IL-8 production in adherent AM culture. We also evaluated whether the culture supernatants of the A549 cells or AM stimulated with PNR could similarly mediate neutrophil migration in vitro. When anti-human IL-8 immunoglobulin G was used for neutralizing neutrophil chemotactic factor (NCF) activities in the culture supernatants of these cells stimulated with 5 microg/ml of PNR, the mean percent reduction of NCF activities were 49-59% in A549 cells and 24-34% in AM. Our present data support that PNR directly stimulates AM and pulmonary epithelial cells to produce IL-8. PNR also mediates neutrophil migration, in part, through IL-8 production from AM and pulmonary epithelial cells. These data suggest the contribution of PNR to the pathogenesis of bronchopulmonary infections due to P. aeruginosa.