gebhart/patrepeval huggingface dataset:
Toll-like Receptor Agonist Imiquimod Facilitates Antigen-Specific CD8+ T-cell Accumulation in the Genital Tract Leading to Tumor Control through IFNγ (2014)

Several therapeutic HPV vaccination clinical trials using a spectrum of DNA vaccines, including vaccination in concert with cervical imiquimod, are ongoing. Our study identifies a mechanism by which these strategies could provide therapeutic benefit. Our findings support accumulating evidence that manipulation of the tumor microenvironment can enhance the therapeutic efficacy of strategies that induce tumor-specific T cells.
RETRACTED ARTICLE: TRIB2 confers resistance to anti-cancer therapy by activating the serine/threonine protein kinase AKT (2017)

Intrinsic and acquired resistance to chemotherapy is the fundamental reason for treatment failure for many cancer patients. The identification of molecular mechanisms involved in drug resistance or sensitization is imperative. Here we report that tribbles homologue 2 (TRIB2) ablates forkhead box O activation and disrupts the p53/MDM2 regulatory axis, conferring resistance to various chemotherapeutics. TRIB2 suppression is exerted via direct interaction with AKT a key signalling protein in cell proliferation, survival and metabolism pathways. Ectopic or intrinsic high expression of TRIB2 induces drug resistance by promoting phospho-AKT (at Ser473) via its COP1 domain. TRIB2 expression is significantly increased in tumour tissues from patients correlating with an increased phosphorylation of AKT, FOXO3a, MDM2 and an impaired therapeutic response. This culminates in an extremely poor clinical outcome. Our study reveals a novel regulatory mechanism underlying drug resistance and suggests that TRIB2 functions as a regulatory component of the PI3K network, activating AKT in cancer cells.
Ureteronephroscopic Endopyelotomy (1990)

The percutaneous nephrostomy tract has provided urologists with antegrade access to the upper urinary tract. Via this approach ureteropelvic junction obstruction has been treated with an endoscopically controlled incision with a cold knife. While less invasive than an open operation, we have noted significant discomfort from the 24 to 32F percutaneous tract. Accordingly, we sought to achieve the same results by using a less invasive approach, that is retrograde ureteronephroscopic endopyelotomy. A total of 10 patients (9 women and 1 man) with 5 primary and 5 secondary ureteropelvic junction obstructions underwent ureteroscopic endopyelotomy with a 3 or 5F Greenwald cutting electrode passed through a 12F rigid, 10.8F flexible or 9.8F flexible deflectable ureteronephroscope. Preoperatively, ureteropelvic junction obstruction was documented by a furosemide washout renal scan and/or a Whitaker test in 8 of 10 patients. In 2 patients an excretory urogram or retrograde pyelography was diagnostic. Duration of the procedure averaged 180 minutes (245 minutes with a concurrent Whitaker test). At the conclusion of the procedure a 7/14F indwelling ureteral stent was placed. The nephrostomy tube was removed after 3 days and average hospital stay was 5 days. The ureteral stents were routinely left in place for 6 weeks. Followup in 10 patients averaged 12 months. Flank pain was largely resolved in all patients. A followup Whitaker test, excretory urogram or renal scan ultimately has demonstrated decreased or no obstruction in 9 of 10 patients. In summary, early results with retrograde ureteronephroscopic endopyelotomy, specifically in female patients, appear to be promising. Morbidity is minimal and efficacy is satisfactory given the favorable objective response noted in 90% of the patients.
Direct endothelial junction restoration results in significant tumor vascular normalization and metastasis inhibition in mice (2014)

Tumor blood vessels are leaky and immature, which causes inadequate blood supply to tumor tissues resulting in hypoxic microenvironment and promotes metastasis. Here we have explored tumor vessel modulating activity of Sac-1004, a recently developed molecule in our lab, which directly potentiates VE-cadherin-mediated endothelial cell junction. Sac-1004 could enhance vascular junction integrity in tumor vessels and thereby inhibit vascular leakage and enhance vascular perfusion. Improved perfusion enabled Sac-1004 to have synergistic anti-tumor effect on cisplatin-mediated apoptosis of tumor cells. Interestingly, characteristics of normalized blood vessels namely reduced hypoxia, improved pericyte coverage and decreased basement membrane thickness were readily observed in tumors treated with Sac-1004. Remarkably, Sac-1004 was also able to inhibit lung and lymph node metastasis in MMTV and B16BL6 tumor models. This was in correlation with a reduction in epithelial-to-mesenchymal transition of tumor cells with considerable diminution in expression of related transcription factors. Moreover, cancer stem cell population dropped substantially in Sac-1004 treated tumor tissues. Taken together, our results showed that direct restoration of vascular junction could be a significant strategy to induce normalization of tumor blood vessels and reduce metastasis.
Fingerprinting Cryptographic Protocols with Key Exchange Using an Entropy Measure (2018)

Encryption has become increasingly prevalent in many applications and for various purposes, but its use also brings big challenges to network security. In this paper, we take the first steps towards addressing some of these challenges by introducing a novel system to identify key exchange protocols. These protocols are usually required if encryption keys are not shared in advance. We observed that key exchange protocols yield certain patterns of high-entropy data blocks, such as those found in key material. We propose a multi-resolution approach to accurately detect high-entropy data blocks and a method of generating fingerprints for cryptographic protocols. We provide experimental evidence that our approach has the potential to identify cryptographic protocols by their unique key exchanges, leading to the ability to detect malware traffic that includes customized key exchange protocols.
Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue (2023)

The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. We developed and validated a novel method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and used solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise two protofilaments with pseudo-2<sub>1</sub> helical screw symmetry, very low twist and an interface formed by antiparallel beta strands of residues 85-93. The fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural landscape of LBD Asyn fibrils and inform further studies of disease mechanisms, imaging agents and therapeutics targeting Asyn.
Phenylpyrrole Fungicides (2012)

This chapter contains sections titled: Introduction History Synthesis Mode of Action Biological Activity Structure–Activity Relationship References
Practical Data Processing Approach for RNA Sequencing of Microorganisms (2017)

The rapid evolvement of sequencing technology has generated huge amounts of DNA/RNA sequences, even with the continuous performance acceleration. Due to the wide variety of basic studies and applications derived from the huge number of species and the microorganism diversity, the targets to be sequenced are also expanding. The huge amounts of data generated by recently developed high-throughput sequencers have required highly efficient data analysis algorithms using recently developed high-performance computers. We have developed a highly accurate and cost-effective mapping strategy that includes the exclusion of unreliable base calls and correction of the reference sequence through provisional mapping of RNA sequencing reads. The use of mapping software tools, such as HISAT and STAR, precisely aligned RNA-Seq reads to the genome of a filamentous fungus considering exon-intron boundaries. The accuracy of the expression analysis through the refinement of gene models was achieved by the results of mapped RNA-Seq reads in combination with ab initio gene finding tools using generalized hidden Markov models (GHMMs). Visualization of the mapping results greatly helps evaluate and improve the entire analysis in terms of both wet experiment and data processing. We believe that at least a portion of our approach is useful and applicable to the analysis of any microorganism.
αL-Integrin I domain cyclic peptide antagonist selectively inhibits T cell adhesion to pancreatic islet microvascular endothelium (2004)

Insulitis is a hallmark feature of autoimmune diabetes that ultimately results in islet beta-cell destruction. We examined integrin requirements and specific inhibition of integrin structure in T cell and monocyte adhesion to pancreatic islet endothelium. Examination of cell surface integrin expression on WEHI 7.1 T cells revealed prominent expression of beta-, beta(1)-, alpha(L)-integrins, and low expression of alpha(M)-integrins; whereas WEHI 274.1 monocytes showed significant staining for beta(2)-, beta(1)-, alpha(M)-molecules and no expression of alpha(L)-molecules. Unstimulated islet endothelium showed constitutive levels of ICAM-1 counter-ligand expression with minimal VCAM-1 expression; however, TNF-alpha stimulation increased cell surface density of both molecules. TNF-alpha increased T cell and monocyte rolling and adhesion under hydrodynamic flow conditions. Administration of a cyclic peptide competitor for the alpha(L)-integrin I domain binding sites (cyclo1,12-PenITDGEATDSGC) blocked T cell adhesion without inhibiting monocyte adhesion. Examination of T cell rolling revealed that cLAB.L treatment increased the average rolling velocity on activated endothelium and significantly decreased the fraction of T cells rolling at < or =50 microm/s, suggesting that cLAB.L treatment interferes with signal activation events required for the conversion of T cell rolling to firm adhesion. These data demonstrate for the first time that cyclic peptide antagonists against alpha(L)-integrin I domain attenuate T cell recruitment to islet endothelium.
CGALmesh: a Generic Framework for Delaunay Mesh Generation (2014)

CGALmesh is the mesh generation software package of the Computational Geometry Algorithm Library (CGAL). It generates isotropic simplicial meshes -- surface triangular meshes or volume tetrahedral meshes -- from input surfaces, 3D domains as well as 3D multi-domains, with or without sharp features. The underlying meshing algorithm relies on restricted Delaunay triangulations to approximate domains and surfaces, and on Delaunay refinement to ensure both approximation accuracy and mesh quality. CGALmesh provides guarantees on approximation quality, as well as on size and shape of the mesh elements. It provides four optional mesh optimization algorithms to further improve the mesh quality. A distinctive property of CGALmesh is its high flexibility with respect to the input domain representation. Flexibility is achieved through a careful software design, gathering into a single abstract concept, denoted by the oracle, all required interface features between the meshing engine and the input domain. We already provide oracles for domains defined by polyhedral and implicit surfaces.
The Power of One Qubit in Machine Learning (2019)

Kernel methods are used extensively in classical machine learning, especially in the field of pattern analysis. In this paper, we propose a kernel-based quantum machine learning algorithm that can be implemented on a near-term, intermediate scale quantum device. Our proposal is based on estimating classically intractable kernel functions, using a restricted quantum model known as deterministic quantum computing with one qubit. Our method provides a framework for studying the role of quantum correlations other than quantum entanglement for machine learning applications.
Erratum: Impact-energy dependence of hydrogenated Si cluster deposition onSi(111)−(7×7)[Phys. Rev. B61, 7219 (2000)] (2004)

We have realized that the Si 6 H 13 + cluster ion beam used for the deposition experiment was heavily contaminated by an unidentified species, probably organic molecules originating in vacuum pump oil. This fact was reflected in the mass spectrum shown in Ref. 1 (Fig. We confirmed that the mass-selecting resolution of our cluster ion source was not enough to suppress the satellite peaks. Thus the results and conclusion of the article were not relevant to the hydrogenated Si clusters but for unidentified organic molecules having a mass number of 181 amu. We regret that we did not notice this error earlier.
A Z-axis differential capacitive SOI accelerometer with vertical comb electrodes (2004)

This paper describes a differentially detecting capacitive Z-axis SOI accelerometer using a set of vertical comb electrodes. The device structure has only one silicon layer and there are no lower or upper electrodes. Z-axis acceleration was differentially detected by using a set of newly proposed vertical comb electrodes of different movable and fixed heights. The sensing area was 1.1 mm/spl times/1.1 mm/spl times/15 /spl mu/m. The performance of the accelerometer was calculated and measured experimentally to determine its linear capacitance change and voltage output against input acceleration. The measured capacitance sensitivity and its linearity were 1.1 fF/G and 0.21%, respectively.
Gender HCI Issues in End-User Software Engineering Environments (2007)

Although gender differences in a technological world are receiving significant research attention, much of the research and practice has aimed at how society and education can impact the successes and retention of female computer science professionals. The possibility of gender issues within software, however, has received almost no attention. We hypothesize that factors within software have a strong impact on how well female problem solvers can make use of the software. Evidence from other fields and investigations of our own have revealed evidence supporting this hypothesis.
Lipid Composition but Not Curvature Is the Determinant Factor for the Low Molecular Mobility Observed on the Membrane of Virus-Like Vesicles (2018)

Human Immunodeficiency Virus type-1 (HIV-1) acquires its lipid membrane from the plasma membrane of the infected cell from which it buds out. Previous studies have shown that the HIV-1 envelope is an environment of very low mobility, with the diffusion of incorporated proteins two orders of magnitude slower than in the plasma membrane. One of the reasons for this difference is thought to be the HIV-1 membrane composition that is characterised by a high degree of rigidity and lipid packing, which has, until now, been difficult to assess experimentally. To further refine the model of the molecular mobility on the HIV-1 surface, we herein investigated the relative importance of membrane composition and curvature in simplified model membrane systems, large unilamellar vesicles (LUVs) of different lipid compositions and sizes (0.1⁻1 µm), using super-resolution stimulated emission depletion (STED) microscopy-based fluorescence correlation spectroscopy (STED-FCS). Establishing an approach that is also applicable to measurements of molecule dynamics in virus-sized particles, we found, at least for the 0.1⁻1 µm sized vesicles, that the lipid composition and thus membrane rigidity, but not the curvature, play an important role in the decreased molecular mobility on the vesicles' surface. This observation suggests that the composition of the envelope rather than the particle geometry contributes to the previously described low mobility of proteins on the HIV-1 surface. Our vesicle-based study thus provides further insight into the dynamic properties of the surface of individual HIV-1 particles, as well as paves the methodological way towards better characterisation of the properties and function of viral lipid envelopes in general.
Deep‐vein thrombosis and coumarin skin necrosis associated with a factor V inhibitor with lupus‐like features (1998)

We report a 71-year-old man who developed deep-vein thrombosis after major surgery. Coumarin skin necrosis developed after starting oral anticoagulant therapy. An inhibitor to factor V (61 Bethesda units) with lupus-like features was found as well as a low protein C level. The occurrence of these very rare findings indicates that despite profound procoagulant inhibition (factor V inhibition and anticoagulant therapy), hypercoagulation can occur. Am. J. Hematol. 57:176–178, 1998. © 1998 Wiley-Liss, Inc.
Carbonate‐Induced Electrosynthesis of Hydrogen Peroxide via Two‐Electron Water Oxidation (2021)

Electrochemical synthesis of hydrogen peroxide (H<sub>2</sub> O<sub>2</sub> ), via the two-electron water oxidation reaction (2e<sup>-</sup> WOR), is an attractive method for the sustainable production of valuable chemicals in place of oxygen during water electrolysis. While the majority of 2e<sup>-</sup> WOR studies have focussed on electrocatalyst design, little research has been carried out on the selection of the supporting electrolyte. In this work, we investigate the impact of potassium carbonate (K<sub>2</sub> CO<sub>3</sub> ) electrolytes, and their key properties, on H<sub>2</sub> O<sub>2</sub> production. We found that at electrolyte pH values (>9.5) where the carbonate anion (CO<sub>3</sub> <sup>2-</sup> ) was prevalent in the mixture, a 26.5 % increase in the Faraday efficiency (%FE) for H<sub>2</sub> O<sub>2</sub> production was achieved, compared to bicarbonate (HCO<sub>3</sub> <sup>-</sup> ) dominant solutions. Utilising boron-doped diamond (BDD) in highly concentrated K<sub>2</sub> CO<sub>3</sub> solutions, current densities of up to 511 mA cm<sup>-2</sup> (in 4 m) and %FEs of 91.5 % (in 5 m) could be attained. The results presented in this work highlight the influence of CO<sub>3</sub> <sup>2-</sup> on electrochemical H<sub>2</sub> O<sub>2</sub> generation via the 2e<sup>-</sup> WOR and provide novel pathways to produce desirable commodities at the anode during electrochemical water splitting.
ABNO: a feasible SDN approach for multi-vendor IP and optical networks (2014)

ABNO architecture is proposed in IETF as a framework which enables network automation and programmability thanks to the utilization of standard protocols and components. This work not only justifies the architecture but also presents the first experimental demonstration.
40 Gbit/s photonic receivers integrating UTC photodiodes with high- and low-confinement SOAs using quantum well intermixing and MOCVD regrowth (2006)

Photonic receivers integrating unitravelling carrier (UTC) photodiodes with high saturation power/high gain semiconductor optical amplifiers (SOAs) are presented. The SOAs demonstrated up to 28 dB of gain with saturation output powers of up to 18.6 dBm, while the UTC photodiodes were capable of 40 Gbit/s operation under high photocurrent operation. The chip-coupled receiver sensitivity was better than −20 dBm at 40 Gbit/s. A high-flexibility quantum well intermixing and MOCVD regrowth integration method was used for device fabrication.
Supplementary Figure S5 from Bispecific Antibodies and Antibody–Drug Conjugates (ADCs) Bridging HER2 and Prolactin Receptor Improve Efficacy of HER2 ADCs (2023)

&lt;p&gt;In T47D/HER2 cells, HER2xPRLR bsAb1 augments HER2 ADCinduced cell cycle arrest in G2M phase.&lt;/p&gt;
Nitrite enhances ischemia‐induced angiogenesis by Nitric Oxide dependent pathway (2007)

Purpose: We tested the hypothesis that in permanent ischemia, nitrite would enhance angiogenesis as compared to nitrate or PBS Methods: Hind limb ischemia was induced by femoral artery ligation. Nitrite and nitrate were given intraperitoneally in 2 doses 3.3mg/kg and 165μg/kg twice a day for 7 days. PBS injections served as control. Blood flow was measured with Laser Doppler on days 0, 3, 5 and 7. Angiogenic index (AI), cGMP, tissue and blood nitrite (TBN) were done on days 3 and 7. Next, NO scavenger PTIO was used with nitrite 165μg/kg Results: Blood Flow and AI were significantly increased in nitrite treated ischemic limbs vs. control (AI 165: 1.2 vs. 0.4; AI 3.3: 0.6 vs. 0.3 p&lt;0.0001) Both doses of nitrite were better than nitrate. AI was better with the lower dose of 165μg/kg of nitrite as compared to 3.3mg/kg. At day 3, TBN increased in nitrite treated ischemic limbs but this resolved by day 7. Tissue cGMP was elevated in nitrite treated limbs compared to nitrate ischemic limbs at 3.3mg/kg dose but was lower than nitrate at 165μg/kg dose. Blood flow response with 165μg/kg nitrite was completely abolished in presence of PTIO demonstrating NO dependence. Conclusion: Nitrite enhances angiogenesis in response to permanent ischemia via nitric oxide pathway and is a novel therapy in peripheral artery disease and transplant medicine.
Absence of ST7 gene alterations in human cancer. (2002)

The ST7 gene was cloned and mapped to chromosome 7q31.1-q31.2, a region suspected of containing a tumor suppressor gene involved in a variety of human cancers. Subsequent investigation described the presence of ST7 mutations in human cell lines derived from breast tumors and primary colon carcinoma. Introduction of the ST7 cDNA into a prostate cancer-derived cell line abrogated in vivo tumorigenecity in nude mice. To clarify the role of the ST7 gene in cancer, we scrutinized primary head and neck squamous cell carcinomas, invasive ductal carcinomas of the breast, and adenocarcinomas of the colon. Loss of heterozygosity of D7S522/D7S677 was detected in 24% (4 of 17) of head and neck squamous cell carcinomas, 17% (2 of 12) of invasive ductal carcinomas of the breast, and 33% (8 of 24) of adenocarcinomas of the colon, but no somatic mutations were found in any of these specimens. We then searched for mutations in breast cancer cell lines and found a complete wild-type sequence in all, including cell lines previously reported to harbor mutations. We believe that the ST7 gene is not a primary target of inactivation in most human cancers with loss of heterozygosity at 7q31.1-q31.2.
Characterization of GaN based Schottky UV detectors in the vacuum UV (VUV) and the soft X-ray (SX) region (10–100 nm) (2003)

Responsivity spectra of GaN based Schottky type ultraviolet (UV) photodetectors with transparent electrode from the Vacuum Ultraviolet (VUV) region to soft X-ray (SX) region (10–100 nm, 124–12.4 eV) are described for the first time. The calculated transmittance of 10 nm-thick transparent Ni/Au electrode from the transmittance of Ti/Au membrane is about 0.5–0.7 in the VUV and SX region (10–100 eV). Thus it is considered that the 10-nm-transparent Ni/Au electrode is thin enough to transmit VUV and SX light into the transparent electrode. The value of responsivity in the SX region (at 13 nm) is about 0.05 A/W. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)