gebhart/patrepeval huggingface dataset:
Data from Measles Virus Vaccine–Infected Tumor Cells Induce Tumor Antigen Cross-Presentation by Human Plasmacytoid Dendritic Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Plasmacytoid dendritic cells (pDC) are antigen-presenting cells specialized in antiviral response. The measles virus vaccine is proposed as an antitumor agent to target and specifically kill tumor cells without infecting healthy cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Here, we investigated, &lt;i&gt;in vitro&lt;/i&gt;, the effects of measles virus vaccine–infected tumor cells on the phenotype and functions of human pDC. We studied maturation and tumor antigen cross-presentation by pDC, exposed either to the virus alone, or to measles virus vaccine–infected or UV-irradiated tumor cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We found that only measles virus vaccine–infected cells induced pDC maturation with a strong production of IFN-α, whereas UV-irradiated tumor cells were unable to activate pDC. This IFN-α production was triggered by the interaction of measles virus vaccine single-stranded RNA (ssRNA) with TLR7. We observed that measles virus vaccine–infected tumor cells were phagocytosed by pDC. Interestingly, we showed cross-presentation of the tumor antigen NYESO-1 to a specific CD8&lt;sup&gt;+&lt;/sup&gt; T-cell clone when pDC were cocultured with measles virus vaccine–infected tumor cells, whereas pDC were unable to cross-present NYESO-1 after coculture with UV-irradiated tumor cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Altogether, our results suggest that the use of measles virus vaccine in antitumor virotherapy induces immunogenic tumor cell death, allowing pDC to mature, produce high amounts of IFN-α, and cross-present tumor antigen, thus representing a mode of recruiting these antigen-presenting cells in the immune response. &lt;i&gt;Clin Cancer Res; 19(5); 1147–58. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Electrically Tunable Mid-Infrared Metamaterials based on Semiconductor Device Structures. (2012)

Abstract not provided.
Development of candidate vaccines against infection caused by shiga-toxin producing Escherichia coli. Part 1 (2020)

Shiga-toxin producing Escherichia coli (STEC) strains cause serious and life-threatening diseases, hemorrhagic colitis (HC) and associated hemolytic uremic syndrome (HUS). Antibacterial etiotropic therapy against these diseases are not recommended. There are no vaccines against human HA and HUS. The review provides materials on the design of various types of candidate vaccines against STEC strains and assessment of their immunogenic and protective properties in experiments on laboratory and farm animals. The prospects for the use of inactivated corpuscular and live (vector) vaccines, lipopolysaccharide vaccines, DNA vaccines and nanovaccines, vaccines based on bacterial cell membranes (ghost), as well as vaccines created by reverse vaccinology methods in practice are considered. Key words: STEC, hemorrhagic colitis, immunodominant antigens, shiga toxins, EspA, EspB, Tir, intimine, IgG, sIgA
Versatile Stereoselective Synthesis of Completely Protected Trifunctional α‐Methylated α‐Amino Acids Starting from Alanine (1991)

Abstract A new route to completely protected α‐methylated α‐amino acids starting from alanine is described (see Scheme ). These derivatives, which are obtained via base‐catalyzed opening of the oxazolidinones (2 S ,4 R )‐ and (2 R ,4 S )‐ 2 , can be directly employed in peptide synthesis. The synthesis of both enantiomers of Z‐protected α‐methylaspartic acid β‐( tert ‐butyl)ester ( O 4 ‐( tert ‐butyl) hydrogen 2‐methylaspartates ( R ) or ( S )‐ 4a ), α‐methyl‐glutamic acid γ‐( tert ‐butyl) ester ( O 5 ‐( tert ‐butyl) hydrogen 2‐methylglutamate ( R )‐ or ( S )‐ 4b ), and of N ε ‐bis‐Boc‐protected α‐methyllysine ( N 6 , N 6 ‐bis[( tert ‐butyloxy)carbonyl]‐2‐methyllysine ( R )‐ or ( S )‐ 4c ) is described in full detail.
New Performance Motors Set New Benchmarks in Drilling Performance (2003)

Abstract The elastomer and its bonding system has always been the one of the most critical areas in downhole motor design. The elastomer's physical properties change due to temperature or from reactions with certain chemicals commonly used in drilling applications. This limits both the motor's operational temperature range and the chemicals that can be used in the mud system. While drilling with a conventional motor, heat is concentrated in a regular elastomer power section's lobes forming hot spots which contribute to a premature heat aging of the elastomer. Today, however, a new manufacturing process for stator tubes permits the forging of a pre-contoured lobe configuration — significantly reducing the elastomer content in the power section. This new design broadens motor capabilities by allowing heat to radiate faster from the thin elastomer and significantly improving the motor's mechanical and volumetric efficiency. The power output of all sizes of positive displacement downhole motors has more than tripled during the past fifteen years. For example, today's 4–3/4″ motors are significantly stronger than the 9–1/2″ motors built in the 1980's. The latest step change in motor power was achieved in the manufacturing processes that eliminated 60%-80% of the elastomer used in the power section's stator. These latest generation downhole motors are used as performance motors — delivering over 50% more power output compared to the previous generation motors of the same length and diameter and permitting the operator to select more aggressive bit designs. As a result, operators have experienced Rates of Penetration (ROP) improvements of 100%-300%. In addition, high speed configurations with bit speeds up to 1200 RPM are used in hard and abrasive formations with temperatures up to 160°C (320°F). These configurations outperform previously used turbines where the motors have greater torque capabilities while maintaining full steerability throughout the entire run. Typical performance drilling applications cover re-entry, deepwater and extended reach wells in all parts of the world. This paper describes the technical features of the latest generation downhole motors in detail and documents their capabilities with case histories from various worldwide applications.
Supplementary Figure S3 from Predictive Biomarkers for Adjuvant Capecitabine Benefit in Early-Stage Triple-Negative Breast Cancer in the FinXX Clinical Trial (2023)

&lt;p&gt;Supplementary Figure S3 shows the expression levels of immune-related genes and metagenes against basal status&lt;/p&gt;
vpsA-andluxO-independent biofilms ofVibrio cholerae (2007)

The natural life cycle of Vibrio cholerae involves the transitioning of cells between different environmental surfaces such as the chitinous shell of Crustaceae and the epithelial layer of the human intestine. Previous studies using static biofilm systems showed a strict dependence of biofilm formation on the vps and lux genes, which are essential for exopolysaccharide formation and cell-cell signaling, respectively. The authors' report here that in biofilms grown under hydrodynamic conditions, DeltavpsA and DeltaluxO mutants of V. cholerae do form pronounced, three-dimensional biofilms that resemble all aspects of wild-type biofilms. By genetic experiments, it was shown that in hydrodynamically grown biofilms this independence of vpsA is due to the expression of rpoS, which is a negative regulator of vpsA expression. Biofilms also underwent substantial dissolution after 96 h that could be induced by a simple stop of medium flow. The studies indicate that metabolic conditions control the reversible attachment of cells to the biofilm matrix and are key in regulating biofilm cell physiology via RpoS. Furthermore, the results redefine the roles of vps and quorum-sensing in V. cholerae biofilms.
Data from Cell-Type-Specific Responses to Chemotherapeutics in Breast Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Recent microarray studies have identified distinct subtypes of breast tumors that arise from different cell types and that show statistically significant differences in patient outcome. To gain insight into these differences, we identified &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; changes in gene expression induced by chemotherapeutics. We treated two cell lines derived from basal epithelium (immortalized human mammary epithelial cells) and two lines derived from luminal epithelium (MCF-7 and ZR-75–1) with chemotherapeutics used in the treatment of breast cancer and assayed for changes in gene expression using DNA microarrays. Treatment doses for doxorubicin and 5-fluorouracil were selected to cause comparable cytotoxicity across all four cell lines. The dominant expression response in each of the cell lines was a general stress response; however, distinct expression patterns were observed. Both cell types induced DNA damage-response genes such as &lt;i&gt;p21&lt;/i&gt;&lt;sup&gt;&lt;i&gt;waf1&lt;/i&gt;&lt;/sup&gt;, but the response in the luminal cells showed higher fold changes and included more p53-regulated genes. Luminal cell lines repressed a large number of cell cycle-regulated genes and other genes involved in cellular proliferation, whereas the basal cell lines did not. Instead, the basal cell lines repressed genes that were involved in differentiation. These &lt;i&gt;in vitro&lt;/i&gt; responses were compared with expression responses in breast tumors sampled before and after treatment with doxorubicin or 5-fluorouracil/mitomycin C. The &lt;i&gt;in vivo&lt;/i&gt; data corroborated the cell-type-specific responses to chemotherapeutics observed &lt;i&gt;in vitro&lt;/i&gt;, including the induction of &lt;i&gt;p21&lt;/i&gt;&lt;sup&gt;&lt;i&gt;waf1&lt;/i&gt;&lt;/sup&gt;. Similarities between &lt;i&gt;in vivo&lt;/i&gt; and &lt;i&gt;in vitro&lt;/i&gt; responses help to identify important response mechanisms to chemotherapeutics.&lt;/p&gt;&lt;/div&gt;
A Transient Homotypic Interaction Model for the Influenza A Virus NS1 Protein Effector Domain (2011)

Influenza A virus NS1 protein is a multifunctional virulence factor consisting of an RNA binding domain (RBD), a short linker, an effector domain (ED), and a C-terminal 'tail'. Although poorly understood, NS1 multimerization may autoregulate its actions. While RBD dimerization seems functionally conserved, two possible apo ED dimers have been proposed (helix-helix and strand-strand). Here, we analyze all available RBD, ED, and full-length NS1 structures, including four novel crystal structures obtained using EDs from divergent human and avian viruses, as well as two forms of a monomeric ED mutant. The data reveal the helix-helix interface as the only strictly conserved ED homodimeric contact. Furthermore, a mutant NS1 unable to form the helix-helix dimer is compromised in its ability to bind dsRNA efficiently, implying that ED multimerization influences RBD activity. Our bioinformatical work also suggests that the helix-helix interface is variable and transient, thereby allowing two ED monomers to twist relative to one another and possibly separate. In this regard, we found a mAb that recognizes NS1 via a residue completely buried within the ED helix-helix interface, and which may help highlight potential different conformational populations of NS1 (putatively termed 'helix-closed' and 'helix-open') in virus-infected cells. 'Helix-closed' conformations appear to enhance dsRNA binding, and 'helix-open' conformations allow otherwise inaccessible interactions with host factors. Our data support a new model of NS1 regulation in which the RBD remains dimeric throughout infection, while the ED switches between several quaternary states in order to expand its functional space. Such a concept may be applicable to other small multifunctional proteins.
A Method for Improving Power Grid Resilience to Electromigration-Caused via Failures (2014)

Electromigration (EM) has become a major power grid reliability problem in VLSI. In this paper, we first demonstrate that EM reliability analysis of a power grid can be converted to analyzing EM reliability of the grid vias. We develop a model for calculating EM lifetime of via-arrays and observe that making power grid EM-immortal carries a huge metal area overhead and possibly makes routing of both power and signal networks too difficult to complete. We propose a method for trading off power grid integrity and reliability to minimize the total metal area overhead needed to achieve the desired grid life time under power integrity constraints. Experimental results show that using our method, both EM reliability and power integrity can be met, while the additional metal area used is significantly reduced.
Partitioning programs for parallel execution (1988)

The ability of parallel computers to execute multiple instruction streams (tasks) simultaneously gives rise to the problem of partitioning a program into a set of tasks that can be assigned to different processors. The degree to which parallelism can be exploited, the amount of overhead involved during parallel execution of a program and a number of other factors depend directly on partitioning. A good partitioning scheme must take into account all these factors. In this paper we present algorithms to compute optimal partitions in diverse models of the problem. Both directed and undirected graph representations of a parallel program are considered. For some instances of the problem where practical optimal schemes are not possible we suggest simple and efficient heuristics. Finally, a polynomial time algorithm to compute optimal partitions for chains is given.
ATRIAL NATURIURETIC PEPTIDE LEVELS IN RESPONSE TO PHENYLEPHRINE PRESSOR CHALLENGE DURING CORONARY ARTERY BYPASS GRAFT SURGERY (1988)

SChwinn, Debra A. M.D.; McIntyre, William R. M.D.; Xuan, Yu-Ting M.D.; Watkins, David W. M.D., Ph.D. Author Information
Arylarsonate- and Phosphonate-Capped Polyoxomolybdates, [(RC6H4As)2Mo6O24]n− and [(R′C6H4P)2Mo5O21]n− (2021)

We report on the synthesis and structural characterization of four arylarsonate- and phosphonate-capped polyoxomolybdates that exhibit different organic substituents in the para position of the phenyl group. The reaction of arylarsonates (RAsO<sub>3</sub>, wherein R = 4-BrC<sub>6</sub>H<sub>4</sub> or 4-N<sub>3</sub>C<sub>6</sub>H<sub>4</sub>) with molybdate in aqueous pH 3.5 media resulted in the cyclic hexamolybdates [(BrC<sub>6</sub>H<sub>4</sub>As)<sub>2</sub>Mo<sub>6</sub>O<sub>24</sub>]<sup>4-</sup> (<b>Mo</b><sub><b>6</b></sub><b>As</b><sub><b>2</b></sub><b>L</b><sub><b>a</b></sub>) and [(N<sub>3</sub>C<sub>6</sub>H<sub>4</sub>As)<sub>2</sub>Mo<sub>6</sub>O<sub>24</sub>]<sup>4-</sup> (<b>Mo</b><sub><b>6</b></sub><b>As</b><sub><b>2</b></sub><b>L</b><sub><b>b</b></sub>), whereas the reaction of arylphosphonates (R'PO<sub>3</sub>, wherein R' = 4-O<sub>2</sub>CC<sub>6</sub>H<sub>4</sub> or 4-O<sub>2</sub>CC<sub>6</sub>H<sub>4</sub>CH<sub>2</sub>) with molybdate in aqueous pH 3 media resulted in the cyclic pentamolybdates [(O<sub>2</sub>CC<sub>6</sub>H<sub>4</sub>P)<sub>2</sub>Mo<sub>5</sub>O<sub>21</sub>]<sup>6-</sup> (<b>Mo</b><sub><b>5</b></sub><b>P</b><sub><b>2</b></sub><b>L</b><sub><b>c</b></sub>) and [(HO<sub>2</sub>CC<sub>6</sub>H<sub>4</sub>CH<sub>2</sub>P)<sub>2</sub>Mo<sub>5</sub>O<sub>21</sub>]<sup>4-</sup> (<b>Mo</b><sub><b>5</b></sub><b>P</b><sub><b>2</b></sub><b>L</b><sub><b>d</b></sub>), respectively. Polyanions <b>Mo</b><sub><b>6</b></sub><b>As</b><sub><b>2</b></sub><b>L</b><sub><b>a</b></sub> and <b>Mo</b><sub><b>6</b></sub><b>As</b><sub><b>2</b></sub><b>L</b><sub><b>b</b></sub> comprise a ring of six MoO<sub>6</sub> octahedra that is capped on either side by an organoarsonate group, whereas <b>Mo</b><sub><b>5</b></sub><b>P</b><sub><b>2</b></sub><b>L</b><sub><b>c</b></sub> and <b>Mo</b><sub><b>5</b></sub><b>P</b><sub><b>2</b></sub><b>L</b><sub><b>d</b></sub> consist of a ring of five MoO<sub>6</sub> octahedra that is capped on either side by an organophosphonate group, with the organic arms protruding away from the metal-oxo core of the polyanions. All four polyanions <b>Mo</b><sub><b>6</b></sub><b>As</b><sub><b>2</b></sub><b>L</b><sub><b>a</b></sub>, <b>Mo</b><sub><b>6</b></sub><b>As</b><sub><b>2</b></sub><b>L</b><sub><b>b</b></sub>, <b>Mo</b><sub><b>5</b></sub><b>P</b><sub><b>2</b></sub><b>L</b><sub><b>c</b></sub>, and <b>Mo</b><sub><b>5</b></sub><b>P</b><sub><b>2</b></sub><b>L</b><sub><b>d</b></sub> have been characterized in the solid state by single-crystal X-ray diffraction, IR spectroscopy, and thermogravimetric and elemental analysis and in solution by multinuclear NMR (<sup>31</sup>P, <sup>13</sup>C, and <sup>1</sup>H). The synthetic procedure of (4-bromophenyl)arsonic acid, BrC<sub>6</sub>H<sub>4</sub>AsO<sub>3</sub>H<sub>2</sub>, is reported here for the first time.
Inhibition of Chk1 by the G2 DNA damage checkpoint inhibitor isogranulatimide (2004)

Inhibitors of the G(2) DNA damage checkpoint can selectively sensitize cancer cells with mutated p53 to killing by DNA-damaging agents. Isogranulatimide is a G(2) checkpoint inhibitor containing a unique indole/maleimide/imidazole skeleton identified in a phenotypic cell-based screen; however, the mechanism of action of isogranulatimide is unknown. Using natural and synthetic isogranulatimide analogues, we show that the imide nitrogen and a basic nitrogen at position 14 or 15 in the imidazole ring are important for checkpoint inhibition. Isogranulatimide shows structural resemblance to the aglycon of UCN-01, a potent bisindolemaleimide inhibitor of protein kinase C beta (IC(50), 0.001 micromol/L) and of the checkpoint kinase Chk1 (IC(50), 0.007 micromol/L). In vitro kinase assays show that isogranulatimide inhibits Chk1 (IC(50), 0.1 micromol/L) but not protein kinase C beta. Of 13 additional protein kinases tested, isogranulatimide significantly inhibits only glycogen synthase kinase-3beta (IC(50), 0.5 micromol/L). We determined the crystal structure of the Chk1 catalytic domain complexed with isogranulatimide. Like UCN-01, isogranulatimide binds in the ATP-binding pocket of Chk1 and hydrogen bonds with the backbone carbonyl oxygen of Glu(85) and the amide nitrogen of Cys(87). Unlike UCN-01, the basic N15 of isogranulatimide interacts with Glu(17), causing a conformation change in the kinase glycine-rich loop that may contribute importantly to inhibition. The mechanism by which isogranulatimide inhibits Chk1 and its favorable kinase selectivity profile make it a promising candidate for modulating checkpoint responses in tumors for therapeutic benefit.
Durable Suppression of Established Transmitted Founder Replication in Infected BLT Humanized Mice by Vectored ImmunoTherapy (2014)

Recent reports in humanized mice and monkeys have found that broadly neutralizing antibodies (bNAbs) can suppress the replication of laboratory strains of HIV and SHIV while bNAb concentration remains high. Vectored ImmunoProphylaxis&#13;\n(VIP) results in long-lived bNAb expression following a single intramuscular {IM) injection of a specialized viral vector, and this approach has been demonstrated as a means&#13;\nof durably suppressing viral load. However, previous reports of VIP-delivered bNAbs for HIV therapy required prior antiretroviral drug therapy to reduce viral load to prevent escape.&#13;\nMethods: Humanized BLT mice were infected IV with the&#13;\nREJO.c transmitted molecular founder strain of HIV. A low dose of combination antiretroviral therapy (ART) was administered to these animals for 5 weeks, followed by a single IM injection of VIP expressing VRC07 or luciferase. Mouse plasma was analyzed by ELISA to determine antibody concentration and by qPCR to determine viral load. Cellular fractions were analyzed by flow cytometry to quantify human CD4 cells over time. After sacrifice, plasma was subjected to a clinically validated ultrasensitive PCR-based viral load assay.&#13;\nResults: We detected viral loads of 10^5 copies/mL in infected mice prior to low-dose ART treatment, which resulted in a transient reduction and rebound to pre-therapy loads. Following VIP administration, we observed a rapid increase in the blood concentration of VRC07. Mice expressing VRC07 exhibited a sharp decline in viral load to undetectable levels and an increase in CD4 cells over four weeks and this effect was sustained for the&#13;\nremaining 8 weeks of the study. In contrast, mice expressing&#13;\nluciferase exhibited increasing viral loads with concomitant&#13;\ndecreases in CD4 cells throughout the study. &#13;\nConclusions: Our results demonstrate that VIP expressing VRC07 is sufficient to suppress actively replicating transmitted founder virus at high viral load and support efforts to move Vectored Immuno Therapy into clinical trials with infected patients.
Transthyretin participates in beta-amyloid transport from the brain to the liver- involvement of the low-density lipoprotein receptor-related protein 1? (2016)

Transthyretin (TTR) binds Aβ peptide, preventing its deposition and toxicity. TTR is decreased in Alzheimer's disease (AD) patients. Additionally, AD transgenic mice with only one copy of the TTR gene show increased brain and plasma Aβ levels when compared to AD mice with both copies of the gene, suggesting TTR involvement in brain Aβ efflux and/or peripheral clearance. Here we showed that TTR promotes Aβ internalization and efflux in a human cerebral microvascular endothelial cell line, hCMEC/D3. TTR also stimulated brain-to-blood but not blood-to-brain Aβ permeability in hCMEC/D3, suggesting that TTR interacts directly with Aβ at the blood-brain-barrier. We also observed that TTR crosses the monolayer of cells only in the brain-to-blood direction, as confirmed by in vivo studies, suggesting that TTR can transport Aβ from, but not into the brain. Furthermore, TTR increased Aβ internalization by SAHep cells and by primary hepatocytes from TTR+/+ mice when compared to TTR-/- animals. We propose that TTR-mediated Aβ clearance is through LRP1, as lower receptor expression was found in brains and livers of TTR-/- mice and in cells incubated without TTR. Our results suggest that TTR acts as a carrier of Aβ at the blood-brain-barrier and liver, using LRP1.
Subwavelength diffractive optics for complete micropolarizer arrays in the short-wave and mid-wave IR (2004)

Numerical and experimental results are presented on polarizers and waveplates, arrayed for snap-shot imaging polarimeter applications. Design, material, and fabrication issues are discussed as the wavelength moves from the mid-wave IR to the visible waveband.
Multiaxial Fatigue of Preloaded Threaded Fasteners (2015)

This experimental study investigates the effect of cyclic multiaxial loading on the High Cycle Fatigue (HCF) life of preloaded threaded fasteners. A special fixture is used for orienting test bolts at different angles relative to the direction of the cyclic load applied by an MTS fatigue testing system. The orientation angle converts the external cyclic load to a combined cyclic axial and shear loading on test bolts. Test data is used for creating the S-N curves for various multiaxial load combinations. The effect of cyclic stress amplitude and mean stress level are investigated.
Multichannel intermodulation distortion in high-speed GaInAsP lasers (1987)

We present an experimental study of intermodulation distortion (IMD) in high-speed, long-wavelength GaInAsP lasers modulated up to 8 GHz. It is found that three-tone distortion products are the dominant contribution to IMD interference when the number of subcarriers is large. These distortion data are used with a simple theory to predict accurately the measured signal/noise ratio for each channel of a multichannel subcarrier system.