gebhart/patrepeval huggingface dataset:
Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies (2016)

Current screening methods for ovarian cancer can only detect advanced disease. Earlier detection has proved difficult because the molecular precursors involved in the natural history of the disease are unknown. To identify early driver mutations in ovarian cancer cells, we used dense whole genome sequencing of micrometastases and microscopic residual disease collected at three time points over three years from a single patient during treatment for high-grade serous ovarian cancer (HGSOC). The functional and clinical significance of the identified mutations was examined using a combination of population-based whole genome sequencing, targeted deep sequencing, multi-center analysis of protein expression, loss of function experiments in an in-vivo reporter assay and mammalian models, and gain of function experiments in primary cultured fallopian tube epithelial (FTE) cells. We identified frequent mutations involving a 40kb distal repressor region for the key stem cell differentiation gene SOX2. In the apparently normal FTE, the region was also mutated. This was associated with a profound increase in SOX2 expression (p<2(-16)), which was not found in patients without cancer (n=108). Importantly, we show that SOX2 overexpression in FTE is nearly ubiquitous in patients with HGSOCs (n=100), and common in BRCA1-BRCA2 mutation carriers (n=71) who underwent prophylactic salpingo-oophorectomy. We propose that the finding of SOX2 overexpression in FTE could be exploited to develop biomarkers for detecting disease at a premalignant stage, which would reduce mortality from this devastating disease.
Raman spectroscopy as a tool for the identification and differentiation of neoplasias contained within lymph nodes of the head and neck (2010)

The use of Raman spectroscopy in the detection and classification of malignancy within lymph nodes of the head and neck has been evaluated. Currently histopathology is considered the diagnostic gold standard. A consensus (majority) opinion from three expert histopathologists has been obtained and spectral diagnostic models developed by correlation with their opinions.
Raman spectra have been measured at 830nm from 103 lymph nodes collected from patients undergoing surgery for a suspicious node. The pathologies covered reactive lymph nodes, primaries from Hodgkin's and non-Hodgkin's lymphomas and metastases from squamous cell carcinomas and adenocarcinomas. Spectral diagnostic models were
constructed using PCA-fed-LDA and tested using leave-one-specimen-out cross validation. Models were constructed to distinguish between reactive and malignant nodes as well as a four group model to distinguish between the benign, metastatic and primary conditions. They achieved 89% and 84% correct prediction by node versus the gold standard, majority histopathology.
Characterization of fourteen strains of Neisseria gonorrhoeae: structural analyses and serum reactivities (1990)

Resistance to normal human serum (NHS) killing in Neisseria gonorrhoeae has been associated with particular types of Protein I (PI) and lipopolysaccharide (LPS), but many exceptions exist, and the role of these structures in determining serum reactivities remains controversial. In reality, the response of the gonococcus to NHS is probably governed by several parameters involving a number of outer-membrane (OM) components. We surveyed the serum reactivities of 14 strains of N. gonorrhoeae and characterized each of their major OM components. The strains presented a spectrum of sensitivity to pooled NHS. As assessed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis, immunoblotting, and peptide mapping, the strains were also quite heterogeneous in terms of PI, H.8 antigen, and LPS type, and the presence of the 2-1-L8 epitope. Five of the strains had identical PIAs in varying LPS and H.8 backgrounds, and four had identical PIBs in varying LPS and H.8 backgrounds. As assessed by electrophoretic migration and monoclonal antibody binding, Protein III and the 44,000 Dalton protein were identical in these strains. We found no association between PI subclass and serum sensitivity, while H.8 and LPS variation appeared to be related to bactericidal responses. The diversity and close interaction of gonococcal components in the OM are undoubtedly involved in differential abilities to survive NHS killing.
Molecular dimensions of Hb-based O2carriers determine constriction of resistance arteries and hypertension (2000)

The effect of molecular dimension of hemoglobin (Hb)-based O(2) carriers on the diameter of resistance arteries (A(0), 158 +/- 21 microm) and arterial blood pressure were studied in the conscious hamster dorsal skinfold model. Cross-linked Hb (XLHb), polyethylene glycol (PEG)-conjugated Hb, hydroxyethylstarch-conjugated XLHb, polymerized XLHb, and PEG-modified Hb vesicles (PEG-HbV) were synthesized. Their molecular diameters were 7, 22, 47, 68, and 224 nm, respectively. The bolus infusion of 7 ml/kg of XLHb (5 g/dl) caused an immediate hypertension (+34 +/- 13 mmHg at 3 h) with a simultaneous decrease in A(0) diameter (79 +/- 8% of basal value) and a blood flow decrease throughout the microvascular network. The diameter of smaller arterioles did not change significantly. Infusion of larger O(2) carriers resulted in lesser vasoconstriction and hypertension, with PEG-HbV showing the smallest changes. Constriction of resistance arteries was found to be correlated with the level of hypertension, and the responses were proportional to the molecular dimensions of the O(2) carriers. The underlying mechanism is not evident from these experiments; however, it is likely that the effects are related to the diffusion properties of the different Hb molecules.
A Cost-Effective WDM-PON Using a Multiple Section Fabry–Pérot Laser Diode (2010)

We demonstrated a wavelength-division-multiplexing passive optical network using a multiple section Fabry-Pérot laser diode without a seed light. The electrical envelope tuning of the laser enables color-free operation at 1.25 Gb/s with 100-GHz channel spacing. The mode partition noise is mitigated by shifting the signal spectrum.
Further Characterization of the Capsule-Like Complex (CLC) Produced by Francisella tularensis Subspecies tularensis: Protective Efficacy and Similarity to Outer Membrane Vesicles (2018)

<i>Francisella tularensis</i> is the etiologic agent of tularemia, and subspecies <i>tularensis</i> (type A) is the most virulent subspecies. The live vaccine strain (LVS) of subspecies <i>holarctica</i> produces a capsule-like complex (CLC) that consists of a large variety of glycoproteins. Expression of the CLC is greatly enhanced when the bacteria are subcultured in and grown on chemically defined medium. Deletion of two genes responsible for CLC glycosylation in LVS results in an attenuated mutant that is protective against respiratory tularemia in a mouse model. We sought to further characterize the CLC composition and to determine if a type A CLC glycosylation mutant would be attenuated in mice. The CLCs isolated from LVS extracted with 0.5% phenol or 1 M urea were similar, as determined by gel electrophoresis and Western blotting, but the CLC extracted with urea was more water-soluble. The CLC extracted with either 0.5% phenol or 1 M urea from type A strains was also similar to the CLC of LVS in antigenic properties, electrophoretic profile, and by transmission electron microscopy (TEM). The solubility of the CLC could be further enhanced by fractionation with Triton X-114 followed by N-Lauroylsarcosine detergents; the largest (>250 kDa) molecular size component appeared to be an aggregate of smaller components. Outer membrane vesicles/tubules (OMV/T) isolated by differential centrifugation and micro-filtration appeared similar to the CLC by TEM, and many of the proteins present in the OMV/T were also identified in soluble and insoluble fractions of the CLC. Further investigation is warranted to assess the relationship between OMV/T and the CLC. The CLC conjugated to keyhole limpet hemocyanin or flagellin was highly protective against high-dose LVS intradermal challenge and partially protective against intranasal challenge. A protective response was associated with a significant rise in cytokines IL-12, IL-10, and IFN-γ. However, a type A CLC glycosylation mutant remained virulent in BALB/c mice, and immunization with the CLC did not protect mice against high dose respiratory challenge with type A strain SCHU S4.
Simultaneous inhibition of human CD4 and 4-1BB biogenesis suppresses cytotoxic T lymphocyte proliferation (2021)

ABSTRACT The small molecule cyclotriazadisulfonamide (CADA) down-modulates the human CD4 receptor, an important factor in T cell activation. Here, we addressed the immunosuppressive potential of CADA using in vitro activation models. CADA inhibited lymphocyte proliferation in a mixed lymphocyte reaction, and when human PBMCs were stimulated with CD3/CD28 beads or phytohemagglutinin. The immunosuppressive effect of CADA involved both CD4 + and CD8 + T cells but was, surprisingly, most prominent in the CD8 + T cell subpopulation where it inhibited cell-mediated lympholysis. We discovered a direct down-modulatory effect of CADA on 4-1BB (CD137) expression, a survival factor for activated CD8 + T cells. More specifically, CADA blocked 4-1BB protein biosynthesis by inhibition of its co-translational translocation across the ER membrane in a signal peptide-dependent way. This study demonstrates that CADA, as potent down-modulator of human CD4 and 4-1BB, has promising in vitro immunomodulatory characteristics for future in vivo exploration as immunosuppressive drug.
Re-Oxidation of Thermally Nitrided Silicon Dioxide Thin Films (1995)

Re-oxidation of thermally nitrided SiO 2 thin films was studied. The SiO 2 growth rate at re-oxidation is reduced until a certain time (the “oxidation delay time” or “ODT”) has passed. During the ODT, thermally nitrided SiO 2 at the Si-SiO 2 interface is re-oxidized. the ODT is the time required for complete oxidation of nitrided SiO 2 . Re-oxidation of thermally nitrided SiO 2 thin films is limited not by diffusion of oxidizing species, but by oxidation of nitrided SiO 2 . The ODT is proportional to the nitrided SiO 2 thickness. Nitrided SiO 2 formation at the Si-SiO 2 interface is mass-transfer controlled by nitriding species through nitrided SiO 2 to Si substrate. As an application of thermal nitridation of SiO 2 , thermal nitridation of the local oxidation of silicon (LOCOS) pad oxide can shorten the bird's beak of LOCOS.
Thyroxine-Triiodothyronine Combination TherapyVersusThyroxine Monotherapy for Clinical Hypothyroidism: Meta-Analysis of Randomized Controlled Trials (2006)

T(4) monotherapy should remain the treatment of choice for clinical hypothyroidism.
Fiber Optic Sensing Technology for Measuring In-Cylinder Pressure in Automotive Engines (2006)

A new fiber optic sensing technology for measuring in-cylinder pressure in automotive engines was investigated. The metal-protected fiber sensor is embedded into a small cut in the metal casing of the spark plug.
Tetra-MnIII-Containing 30-Tungsto-4-phosphate, [MnIII4(H2O)2(P2W15O56)2]12–: Synthesis, Structure, XPS, Magnetism, and Electrochemical Study (2020)

Reaction of the mixed-valent Mn<sub>12</sub>-acetato complex [Mn<sup>III</sup><sub>8</sub>Mn<sup>IV</sup><sub>4</sub>O<sub>12</sub>(CH<sub>3</sub>COO)<sub>16</sub>(H<sub>2</sub>O)<sub>4</sub>] with the trilacunary Wells-Dawson-type heteropolytungstate [P<sub>2</sub>W<sub>15</sub>O<sub>56</sub>]<sup>12-</sup> in acidic acetate solution (pH 1.1) resulted in the tetra-Mn<sup>III</sup>-containing polyanion [Mn<sup>III</sup><sub>4</sub>(H<sub>2</sub>O)<sub>2</sub>(P<sub>2</sub>W<sub>15</sub>O<sub>56</sub>)<sub>2</sub>]<sup>12-</sup> (<b>1</b>). Single-crystal XRD on Na<sub>12</sub>[Mn<sup>III</sup><sub>4</sub>(H<sub>2</sub>O)<sub>2</sub>(P<sub>2</sub>W<sub>15</sub>O<sub>56</sub>)<sub>2</sub>]·84H<sub>2</sub>O (<b>1a</b>) revealed that four Mn<sup>III</sup> ions form a rhombic Mn<sub>4</sub>O<sub>16</sub> core encapsulated by two [P<sub>2</sub>W<sub>15</sub>O<sub>56</sub>]<sup>12-</sup> units. X-ray photoelectron spectroscopy (XPS) data confirm the +3 oxidation state of the four manganese ions in <b>1</b>. Magnetic measurements from 1.8-300 K in a 100 Oe magnetic field allowed for the extraction of full fitting parameters from the susceptibility data for <b>1</b>. The negative <i>J</i><sub>a</sub> value (<i>J</i><sub>a</sub> = -2.16 ± 0.08 K, <i>J</i><sub>b</sub> = 3.24 ± 1.73 K, <i>g</i> = 2.35 ± 0.040, and ρ = 0.34 ± 0.03) suggests a dominant antiferromagnetic spin exchange interaction between the four Mn<sup>III</sup> ions, with the positive <i>J</i><sub>b</sub> being an accompanying result of <i>J</i><sub>a</sub>. Electrochemical studies revealed a reversible Mn<sup>IV</sup>/Mn<sup>III</sup> redox couple in <b>1</b> at the +0.80 to +1.1 V potential region with <i>E</i><sub>1/2</sub> = +0.907 V.
Security, Trust and Privacy in the SEcure MObile Payment Service (2004)

In this analysis, a distinct learning curve for uniportal video-assisted thoracoscopic surgery lobectomy was observed. Procedure time decreased sharply at approximately the 60th procedure, but 80 additional lobectomies were required to master the approach.
The Prophylaxis and Treatment with Antiviral Agents of Respiratory Syncytial Virus Infections (2011)

In this review, we consider recent advances in the discovery and development of antiviral agents for respiratory syncytial virus (RSV) infections. A background to the various manifestations of human RSV infection and current treatments is provided. The technical, clinical and commercial issues surrounding the development of such antiviral agents are discussed.
A 60 GHz CMOS Rectifier with -27.5 dBm Sensitivity for mm-Wave Power Detection and Its Application (2013)

A CMOS rectifier that converts 60 GHz signal to DC voltage is presented for millimeter-Wave (mm-Wave) power detection. The sensitivity of the rectifier is -27.5 dBm, which is the highest sensitivity compared with previous works. The optimization method for the rectifier is proposed considering the power matching design and loss of the passive devices at 60 GHz. According to the proposed method, the number of stage should be decreased because the stacked structure that is often used at frequency of several GHz doesn't increase the sensitivity in the case of 60 GHz. The loss of the passive devices is minimized by adopting the proposed optimization method. Additionally, the 60 GHz Wake up Receiver (WuRX) is discussed as application of the rectifier proposed in this work.
Direct Organocatalytic Asymmetric α‐Oxidation of Ketones with Iodosobenzene and N‐Sulfonyloxaziridines. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
NEDD9 targets COL3A1 to promote endothelial fibrosis and pulmonary arterial hypertension (2018)

Germline mutations involving small mothers against decapentaplegic-transforming growth factor-β (SMAD-TGF-β) signaling are an important but rare cause of pulmonary arterial hypertension (PAH), which is a disease characterized, in part, by vascular fibrosis and hyperaldosteronism (ALDO). We developed and analyzed a fibrosis protein-protein network (fibrosome) in silico, which predicted that the SMAD3 target neural precursor cell expressed developmentally down-regulated 9 (NEDD9) is a critical ALDO-regulated node underpinning pathogenic vascular fibrosis. Bioinformatics and microscale thermophoresis demonstrated that oxidation of Cys<sup>18</sup> in the SMAD3 docking region of NEDD9 impairs SMAD3-NEDD9 protein-protein interactions in vitro. This effect was reproduced by ALDO-induced oxidant stress in cultured human pulmonary artery endothelial cells (HPAECs), resulting in impaired NEDD9 proteolytic degradation, increased NEDD9 complex formation with Nk2 homeobox 5 (NKX2-5), and increased NKX2-5 binding to <i>COL3A1</i> Up-regulation of NEDD9-dependent collagen III expression corresponded to changes in cell stiffness measured by atomic force microscopy. HPAEC-derived exosomal signaling targeted NEDD9 to increase collagen I/III expression in human pulmonary artery smooth muscle cells, identifying a second endothelial mechanism regulating vascular fibrosis. ALDO-NEDD9 signaling was not affected by treatment with a TGF-β ligand trap and, thus, was not contingent on TGF-β signaling. Colocalization of NEDD9 with collagen III in HPAECs was observed in fibrotic pulmonary arterioles from PAH patients. Furthermore, <i>NEDD9</i> ablation or inhibition prevented fibrotic vascular remodeling and pulmonary hypertension in animal models of PAH in vivo. These data identify a critical TGF-β-independent posttranslational modification that impairs SMAD3-NEDD9 binding in HPAECs to modulate vascular fibrosis and promote PAH.
An investigation of the performance of various instruction-issue buffer topologies (1995)

In out-of-order issue superscalar microprocessors, instructions must be buffered before they are issued. This buffer can be either unified (one buffer linked to all functional units) as in the P6, distributed among the units as in the PowerPC 620, or semi-unified (a few buffers each shared by several units) as in the MIPS R10000. Of course, the size of this buffer also plays a leading role in the performance of the processor. Intensive trace-driven simulations on the SPEC92 suite have been made in order to determine the best designs and relevant choices are pointed out according to the dispatch width of the processor.
Singapore KneE osTeoarthritis CoHort (SKETCH): protocol for a multi-centre prospective cohort study (2023)

The study has been registered under clinicaltrials.gov registry (Identifier: NCT04942236).
The Convenient Synthesis of Hydrogen‐Bonded Ureidopyrimidinones. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Synergistic effect of Indium and Gallium co-doping on growth behavior and physical properties of hydrothermally grown ZnO nanorods (2017)

We synthesized ZnO nanorods (NRs) using simple hydrothermal method, with the simultaneous incorporation of gallium (Ga) and indium (In), in addition, investigated the co-doping effect on the morphology, microstructure, electronic structure, and electrical/optical properties. The growth behavior of the doped NRs was affected by the nuclei density and polarity of the (001) plane. The c-axis parameter of the co-doped NRs was similar to that of undoped NRs due to the compensated lattice distortion caused by the presence of dopants that are both larger (In<sup>3+</sup>) and smaller (Ga<sup>3+</sup>) than the host Zn<sup>2+</sup> cations. Red shifts in the ultraviolet emission peaks were observed in all doped NRs, owing to the combined effects of NR size, band gap renormalization, and the presence of stacking faults created by the dopant-induced lattice distortions. In addition, the NR/p-GaN diodes using co-doped NRs exhibited superior electrical conductivity compared to the other specimens due to the increase in the charge carrier density of NRs and the relatively large effective contact area of (001) planes. The simultaneous doping of In and Ga is therefore anticipated to provide a broader range of optical, physical, and electrical properties of ZnO NRs for a variety of opto-electronic applications.
A PDMS membrane microvalve with one-dimensional line valve seat for robust microfluidics (2014)

We have developed a monolithic polydimethylsiloxane (PDMS) membrane microvalve with an isotropically etched valve seat for robust microfluidics. In order to avoid bonding or sticking of the PDMS membrane to the valve seat during the bonding process, the valve seat was wet-etched to be a one-dimensional line instead of a plane. The simple wet-etching technique allowed for the fabrication of an anti-bonding architecture in a scalable manner, and it intrinsically prevented contact between the PDMS membrane and valve seat when no external force was applied (i.e., normally open). This approach enables the permanent device assembly so that the microfluidic chip can be operable in a wide range of fluid pressures (e.g., over 200 kPa) without any leakage and sticking problems.
Abstract 3421: Twist1 and clusterin regulate epithelial-mesenchymal transition (2011)

Abstract INTRODUCTION AND OBJECTIVE: Clusterin (CLU) is a stress-activated, cytoprotective molecular chaperone, and is highly expressed in cells surviving apoptotic stimuli and in advanced and treatment-resistant cancers. In addition, CLU has recently been reported to be implicated in epithelial-mesenchymal transition (EMT). Similarly, oncogenic transcription factor Twist1 which binds to E-box (core sequence, 5’-CANNTG-3’) is known to be a master regulator of EMT. Although CLU is known to be transcriptionally activated by heat-shock factor 1, the mechanism CLU expression in EMT is not fully elucidated. This study begins to define mechanism of CLU expression and relevance in EMT of prostate cancer. METHODS: Human prostate cancer PC-3 and LNCaP cells were used to examine whether the manipulation of Twist1 expression affected CLU expression using quantitative real-time PCR, Western blotting and luciferase reporter assay using CLU promoter region. Chromatin-immunoprecipitation (ChIP) assays were used to determine whether Twist1 binds to CLU promoter region. We also examined markers of EMT after treatment with TGF-β1 and manipulation of Twist1/CLU expression. RESULTS: Twist1 overexpression was shown to upregulate CLU expression whereas Twist1 knockdown reduced CLU expression. ChIP assay and luciferase reporter assay revealed that Twist1 was bound to CLU promoter region and regulated CLU transcription. Treatment with TGF-β1, which is known to be an EMT-inducing cytokine, upregulated Twist1 expression followed by CLU expression. Furthermore, CLU knockdown ameliorated EMT induced by TGF-β1 and Twist1. CONCLUSIONS: This study indicates that CLU regulates EMT induced by TGF-β1 and Twist1 in prostate cancer cells. Modulation of CLU expression may be a useful strategy for developing novel therapeutics regulating EMT. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3421. doi:10.1158/1538-7445.AM2011-3421
[Complications of percutaneous nephrostomy. Apropos of 481 procedures: the value of puncture of the median calices]. (1999)

The authors report on a series of 481 percutaneous nephrostomy procedures, and describe the complications encountered. 163 percutaneous nephrostomies for drainage and 318 percutaneous stone removals, were performed between 1985 and 1995 in the Radiology Department of Hôtel-Dieu de France Hospital under fluoroscopy. One tract was needed for PN but more than one was sometimes necessary for percutaneous stone removal. Complication rate was identical to the results reported in the literature. Complications were more frequently encountered when the upper calyx was punctured (intercostal approach), mostly pleural lesions. Puncture of the middle and inferior calyx were associated with the same rate of complications, but with different degrees of severity. Major complications (80% of cases of hemorrhage, including all arteriovenous fistulae and pseudoaneurysms) were encountered with the puncture of the lower calyx while those associated with the puncture of the middle calyx were minimal. Thus, puncture of the middle calyx is the least morbid. It is recommended by the authors, whenever possible.
Effect of pretreatment on the enzymatic synthesis of rosin acid starch (2016)

Esterification reaction efficiency was improved by pretreatment of starch, and the high DS of RAS was achieved.
Synthesis of a Novel Class of Water-Soluble and Bioavailable Antioxidants: 5-Hydroxycoumaran Derivatives Possessing Imidazole Group (1997)

The 5-hydroxycoumaran derivative 1 possessing imidazole group was synthesized from 2-isopropyl-6-methylphenol with high regioselectivity. The compound 1 was the water-soluble antioxidant with potent bioavailability and showed TXA2 synthase inhibition.