gebhart/patrepeval huggingface dataset:
Effects of surface treatments and metal work functions on electrical properties at p-GaN/metal interfaces (1997)

In order to examine the possibility of preparing a nonreacted (nonalloyed) Ohmic contact to p-GaN, the effects of GaN surface treatments and work functions of the contact metals on the electrical properties between the metal contacts and p-GaN were investigated. A contamination layer consisting of GaOx and adsorbed carbons was found on the GaN substrate grown by metalorganic chemical vapor deposition. The contamination layer was not completely removed by sputtering the GaN surface with Ar and N ions where the ion densities were ∼10−2 μA/cm2. Although the contamination layer was partially removed by immersing in a buffered HF solution, little improvement of the electrical properties of the GaN/metal interfaces was obtained. Most of the contamination layer was removed by annealing the Ni and Ta contacts at temperatures close to 500 °C. These annealed contacts exhibited slightly enhanced current injection from the contact metal to the GaN. The present surface treatment study indicated that removal of the contamination layer did not significantly reduce the contact resistance. On the other hand, the resistance decreased exponentially with increasing the metal work functions, where Pt, Ni, Pd, Au, Cu, Ti, Al, Ta, and Ni/Au were deposited on the GaN. This result suggests that the Schottky barrier height at the p-GaN/metal interface might not be pinned at the GaN surface. The present study concluded that a contact metal with a large work function is desirable for nonreacted Ohmic contacts to p-GaN. However, these contacts did not provide the low contact resistance required for blue laser diodes.
Papillomavirus infection of the lower genital tract: Detection of viral DNA in gynecological swabs (1985)

A total of 311 smears from the lower genital tract were examined by the filter in situ hybridization method to identify human papillomavirus (HPV) DNA. Of these 311 smears, 229 came from clinically and cytologically negative patients and served as a control group. In this group HPV-DNA was detected in 5 cases (2.2%). Of 82 cytologically positive cases (25 confirmed by histology) 56 (68%) contained HPV-DNA. A high prevalence of HPV 6/11 and absence of HPV 16/18 was found in cases with cytological signs of permissive HPV infection. In mild and moderate dysplasia all viruses occurred at almost the same frequency. In severe dysplasia/carcinoma in situ HPV 16/18 was found 5 times more frequently than HPV 6/11. HPV 16/18 was identified in all 4 invasive cancer cases. Cervical irrigation of colposcopically suspect areas was performed in 15 cytologically and HPV-DNA positive cases using the hydrodynamic filtration method. In 12 cases only the cells obtained from the colposcopically positive areas contained HPV-DNA. The sensitivity and reproducibility of the filter in situ hybridization was shown by: comparing the results obtained by HPV-DNA hybridization using Southern blot analysis of tumor biopsies; analysing the correlation of cytologic diagnosis and presence of HPV-DNA in follow-up examinations, and diagnosing presence or absence of HPV-DNA in parallel filters from the same patients.
Antigen replacement of domains D2 and D3 in flagellin promotes mucosal IgA production and attenuates flagellin-induced inflammatory response after intranasal immunization (2013)

Targeting early infection in mucosal sites is one of the primary goals for mucosal vaccines so as to prevent pathogen mucosal transmission and infection. The TLR5 agonist flagellin was deemed to be a mucosal adjuvant candidate for clinical usage. However, the high antigenicity of flagellin and the possible inflammatory injury induced by flagellin might restrict its clinical usage. Here HIV-1 p24 protein was selected as an antigen model and we replaced the main antigenicity region domains D2 and D3 of non-pathogenic E.coli-derived flagellin (KF). The derived soluble protein KFD-p24 3D was then compared with KF-p24, which fused p24 directly to the C-terminal of KF. In vitro and ex vivo experiments showed that KFD-p24 3D has lower TLR5 agonist efficacy and less immunocyte-activating efficacy. Interestingly, the production of KF- specific antibody was highly reduced, and KFD-p24 3D induced IgA-biased antibody responses in mucosal sites. Moreover, KFD-p24 3D induced far fewer systemic inflammatory responses and abrogated detectable inflammatory side effects on mice, even at the high dose. The properties of enhanced IgA generation and attenuated inflammatory responses broaden the safe-dose range of KFD-p24 3D flagellin, creating a potentially promising mucosal adjuvant.
Distributed systems (3rd ed.): concepts and design (2000)

These results suggest that the reduction of bodyweight is a major key point for the improvement of FLD.
Radiation‐induced crystallinity changes in linear polyethylene (1983)

Abstract Two kinds of ultrahigh‐molecular‐weight linear polyethylene (UHMW PE), together with conventional high‐density polyethylene (HDPE), were subjected to β irradiation, and changes in their properties were monitored. Elastic modulus increased steadily with dose for all materials, as did the yield stress. A dramatic rise of density with dose was observed in the UHMW PE specimens accompanied by a corresponding increase in heat of fusion, x‐ray crystallinity, and peak melting temperature. The magnitude of such changes in HDPE was much smaller. In UHMW PE specimens, the x‐ray long period simultaneously decreased but crystal thickness remained constant. No changes in long period occurred in HDPE. The effects are attributed to the scission of tie molecules in UHMW PE followed by a growth in the perfection of the crystal lamellae, and suggest a method for assessing the tie‐molecule content of such materials.
Crystallization and preliminary X-ray analysis of alginate lyases A1-II and A1-II′ fromSphingomonassp. A1 (2005)

Alginate lyases depolymerize alginate, a heteropolysaccharide consisting of alpha-L-guluronate and beta-D-mannuronate, through a beta-elimination reaction. The alginate lyases A1-II (25 kDa) and A1-II' (25 kDa) from Sphingomonas sp. A1, which belong to polysaccharide lyase family PL-7, exhibit 68% homology in primary structure but have different substrate specificities. To determine clearly the structural basis for substrate recognition in the depolymerization mechanism by alginate lyases, both proteins were crystallized at 293 K using the vapour-diffusion method. A crystal of A1-II belonged to space group P2(1) and diffracted to 2.2 A resolution, with unit-cell parameters a = 51.3, b = 30.1, c = 101.6 A, beta = 100.2 degrees, while a crystal of A1-II' belonged to space group P2(1)2(1)2(1) and diffracted to 1.0 A resolution, with unit-cell parameters a = 34.6, b = 68.5, c = 80.3 A.
Low Dose Bexarotene Treatment Rescues Dopamine Neurons and Restores Behavioral Function in Models of Parkinson’s Disease (2013)

Nurr1 is a nuclear hormone receptor (NucHR) strongly implicated in the growth, maintenance, and survival of dopaminergic neurons. Nurr1 may be unable to bind ligands directly, but it forms heterodimers with other NucHRs that do. Using bioluminescence resonance energy transfer (BRET) assays to directly monitor interactions of Nurr1 with other NucHRs, we found the cancer drug bexarotene (Targretin, also LGD1069) displayed biased interactions with Nurr1-RXR heterodimers compared with RXR-RXR homodimers. Remarkably, at doses up to 100-fold lower than those effective in rodent cancer models, bexarotene rescued dopamine neurons and reversed behavioral deficits in 6-hydroxydopamine (6-OHDA) lesioned rats. Compared to the high doses used in cancer therapy, low doses of bexarotene have significantly milder side effects including a reduced increase in plasma triglycerides and less suppression of thyroid function. On the basis of extrapolations from rat to human doses, we hypothesize that low oral doses of bexarotene may provide an effective and tolerated therapy for Parkinson's disease (PD).
A 2ns-read-latency 4Mb embedded floating-body memory macro in 45nm SOI technology (2009)

To meet advancing market demands, microprocessor embedded memory applications require denser and faster memory arrays with each process generation. Recent work presented an 18.5 ns 128 Mb DRAM with a floating body cell for conventional DRAM products and a 4 Mb memory macro using a memory cell built with two floating body transistors. This paper presents a floating-body Z-RAM <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">reg</sup> memory cell to fabricate a high-density low-latency and high-bandwidth 4 Mb memory macro building block, targeted at the requirements of microprocessor caches. It uses a single transistor (1T), unlike traditional 1T1C DRAM, or six transistor 6T-SRAM memory cell.
Cost‐effectiveness of blood transfusion and white cell reduction in elective colorectal surgery (1995)

The use of WBC-reduced whole blood transfusions in elective colorectal surgery significantly reduces the frequency of postoperative infection, the length of hospital stay, and the total hospital charges for patients needing blood transfusion.
Kaposi's Sarcoma-Associated Herpesvirus Induces the Phosphatidylinositol 3-Kinase-PKC-ζ-MEK-ERK Signaling Pathway in Target Cells Early during Infection: Implications for Infectivity (2002)

Human herpesvirus 8 (HHV-8) is implicated in the pathogenesis of Kaposi's sarcoma. HHV-8 envelope glycoprotein B (gB) possesses the RGD motif known to interact with integrin molecules, and HHV-8 infectivity was inhibited by RGD peptides, by antibodies against alpha3 and beta1 integrins, and by soluble alpha3beta1 integrin (S. M. Akula, N. P. Pramod, F.-Z. Wang, and B. Chandran, Cell 108:407-419, 2002). Anti-gB antibodies immunoprecipitated the virus alpha3 and beta1 complexes, and virus-binding studies suggest a role for alpha3beta1 in HHV-8 entry. HHV-8 infection induced the integrin-mediated activation of focal adhesion kinase (FAK), implicating a role for integrin and the associated signaling pathways in HHV-8 entry into the target cells. Immediately after infection, target cells exhibited morphological changes and cytoskeletal rearrangements, suggesting the induction of signal pathways. As early as 5 min postinfection, HHV-8 activated the MEK-ERK1/2 pathway. The focal adhesion components phosphatidylinositol 3-kinase (PI 3-kinase) and protein kinase C-zeta (PKC-zeta) were recruited as upstream mediators of the HHV-8-induced ERK pathway. Anti-HHV-8 gB-neutralizing antibodies and soluble alpha3beta1 integrin inhibited the virus-induced signaling pathways. Early kinetics of the cellular signaling pathway and its activation by UV-inactivated HHV-8 suggest a role for virus binding and/or entry but not viral gene expression in this induction. Studies with human alpha3 integrin-transfected Chinese hamster ovary cells and FAK-negative mouse DU3 cells suggest that the alpha3beta1 integrin and FAK play roles in the HHV-8 mediated signal induction. Inhibitors specific for PI 3-kinase, PKC-zeta, MEK, and ERK significantly reduced the virus infectivity without affecting virus binding to the target cells. Examination of viral DNA entry suggests a role for PI 3-kinase in HHV-8 entry into the target cells and a role for PKC-zeta, MEK, and ERK at a post-viral entry stage of infection. These findings implicate a critical role for integrin-associated mitogenic signaling in HHV-8's infection of target cells and suggest that, by orchestrating the signal cascade, HHV-8 may create an appropriate intracellular environment to facilitate the infection.
Imiquimod as an antiangiogenic agent. (2005)

Imiquimod (imidazoquinoline 5%) is a topical immune response modifier agent that inhibits angiogenesis, the growth of new blood vessels. In addition to its stimulation of cell-mediated immunity, imiquimod's antiangiogenic activity contributes to its clinical efficacy by interfering with pathological neovascularization that promotes disease progression. The antiangiogenic mechanisms of imiquimod are due to its: 1) induction of cytokines that themselves inhibit angiogenesis (interferons, IL-10, IL-12); 2) local up-regulation of endogenous angiogenesis inhibitors (TIMP, TSP-1); 3) local down-regulation of pro-angiogenic factors (bFGF, MMP-9); and 4) promotion of endothelial cell apoptosis. This report discusses these mechanisms and the rationale for imiquimod's use as an antiangiogenic agent. Key principles of antiangiogenic therapy are presented to describe how imiquimod may be applied in a well-tolerated fashion to treat a broad range of angiogenesis-dependent dermatological conditions, including actinic keratosis (AK), basal cell carcinoma (BCC), squamous cell carcinoma (SCC), lentigo maligna, hemangiomas, Kaposi's sarcoma, pyogenic granuloma, and external genital warts.
A Rapid Molecular Approach for Chromosomal Phasing (2015)

Determining the chromosomal phase of pairs of sequence variants - the arrangement of specific alleles as haplotypes - is a routine challenge in molecular genetics. Here we describe Drop-Phase, a molecular method for quickly ascertaining the phase of pairs of DNA sequence variants (separated by 1-200 kb) without cloning or manual single-molecule dilution. In each Drop-Phase reaction, genomic DNA segments are isolated in tens of thousands of nanoliter-sized droplets together with allele-specific fluorescence probes, in a single reaction well. Physically linked alleles partition into the same droplets, revealing their chromosomal phase in the co-distribution of fluorophores across droplets. We demonstrated the accuracy of this method by phasing members of trios (revealing 100% concordance with inheritance information), and demonstrate a common clinical application by phasing CFTR alleles at genomic distances of 11-116 kb in the genomes of cystic fibrosis patients. Drop-Phase is rapid (requiring less than 4 hours), scalable (to hundreds of samples), and effective at long genomic distances (200 kb).
Superparamagnetism (1959)

Single domain ferromagnetic particles at elevated temperatures can behave magnetically in a manner analogous to the Langevin paramagnetism of moment-bearing atoms. The main distinction is that the moment of the particle may be 105 times the atomic moment. The experimental and theoretical foundations of this effect are reviewed and indication is made of the applications of this phenomenon. Lastly, attention is drawn to some current problems in this area.
PBT2 Reduces Toxicity in a C. elegans Model of polyQ Aggregation and Extends Lifespan, Reduces Striatal Atrophy and Improves Motor Performance in the R6/2 Mouse Model of Huntington's Disease (2012)

Treatment with PBT2 may be beneficial as a disease modifying therapy for HD.
A phase I dose-escalation study of the Hsp90 inhibitor STA-9090 administered once weekly in patients with solid tumors. (2010)

2529 Background: STA-9090 is a potent, next-generation Hsp90 inhibitor that is structurally unrelated to the first-generation ansamycin class of Hsp90 inhibitors, such as 17-AAG and IPI-504, and has shown superior activity and an improved safety profile relative to these agents in preclinical studies. Methods: In a standard 3 + 3 dose escalation trial, advanced cancer patients received STA-9090 as a 1-hr infusion once weekly for 3 weeks of a 28-day cycle. Blood samples for PK and biomarker analyses were collected in cycle 1. Safety assessments included the number and grade of AEs, changes from baseline in laboratory parameters, and ECG changes. Results: 35 patients (17 M, 18 F; median age 61 yrs, range 37-87; ECOG status range 0-2) received doses ranging from 7-259 mg/m2 once weekly. There have been 3 DLTs: 1 at 150 mg/m2 (grade 3 amylase elevation) and 2 at 259 mg/m2 (grade 4 fatigue and grade 3 diarrhea). The MTD is 216 mg/m2. AEs reported in ≥ 20% of patients were diarrhea, anemia, fatigue, abdominal pain, nausea, elevated alk phos, constipation and dyspnea; most of these AEs were mild to moderate in severity. STA-9090 shows linear PK and has a mean terminal half life of 5-13 hours with no accumulation. Preliminary signs of clinical activity have been observed including a durable PR in a patient with rectal carcinoma, as well as several cases of tumor shrinkage and prolonged SD in patients with tumors including NSCLC, renal cell carcinoma and GIST, who were treated for 16 to 48 weeks. Conclusions: STA-9090 has been well tolerated up to dose levels of 216 mg/m2 given once weekly, without significant liver toxicity. Preliminary safety and activity signals warrant continued evaluation of single-agent STA-9090 using once weekly dosing. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Synta Synta
[Application of Arai's experimental spectral distribution data]. (2002)

A new spectral distribution data file is set up by handling Arai's experimental data of spectral distribution, through the procession of interpolation and fitting. The distance of wavelength is 0.002 nm. The data file is applied to our FPM program and then to the analysis of refractory steels GH131. Correlation between theoretical and measured intensities is good. Results of theoretical influence coefficient method and fundamental parameter method are consistent with certified values; the relative error is smaller than 1% to Cr and Ni. The results show the accuracy is improved and the application range of FP and SFP is enlarged.
Methy-Pipe: An integrated bioinformatics data analysis pipeline for whole genome methylome analysis (2010)

Bisulfite sequencing is used to detect the methylated status at single nucleotide resolution. Coupled with a recently developed next generation sequencing technology, it becomes a powerful tool for studying the epigenetic regulations in a variety of biological systems. However, due the large dataset generated from this kind of experiment, limited software packages are available for analyzing the resultant high-throughput bisulfite sequencing data with reasonable performance in terms of efficiency and accuracy. To solve this problem,, we developed an integrated data analysis pipeline Methy-Pipe for analyzing whole genome methylome data. The capability of it running in parallel on Linux cluster makes this pipeline superior to other exisetnent softwares.
Phenotypic Modulation of Vascular Smooth Muscle Cells Induced by Unsaturated Lysophosphatidic Acids (2001)

The phenotypic modulation of vascular smooth muscle cells (VSMCs) from the differentiated state to the dedifferentiated one is critically involved in the development and progression of atherosclerosis. Although many cytokines and growth factors have been reported as atherogenic factors, the critical pathogens for inducing atherosclerosis remain unknown, largely because proper examining systems of them have not been developed. We recently established primary culture systems for visceral SMCs and VSMCs in which both SMCs, when cultured on laminin with insulin-like growth factor-I, show a differentiated phenotype, as indicated by a spindle-like shape, ligand-induced contractility, and a high level of SMC differentiation marker gene expression. In this study, we searched for critical dedifferentiation factors for these SMCs using our culture system. We found that polar lipids extracted from human serum markedly induced VSMC dedifferentiation, and this activity was solely present in the lysophosphatidic acid (LPA) fraction. Among several LPA species detected in human serum lipids, unsaturated LPAs were identified as major contributors to the induction of VSMC dedifferentiation. Signaling and phenotype analyses revealed that unsaturated LPA-induced VSMC dedifferentiation is mediated through the coordinated activation of extracellular signal-regulated kinase and p38 mitogen-activated protein kinase. Thus, this report demonstrates the first finding that unsaturated LPAs, but not saturated LPAs, specifically induce VSMC phenotypic modulation, suggesting that these molecules could function as atherogenic factors.
Nitric oxide: a possible etiologic factor in spinal cord cavitation. (1998)

To determine whether nitric oxide (NO) is related to spinal cord cavitation, we treated mice that underwent spinal cord injury with NG-mono-methyl-L-arginine (N-MMA). Spinal cord specimens were subjected to glial fibrillary acidic protein (GFAP) immunostaining, which is selective for astrocytes. Spinal cord cavities and GFAP-positive glial cells appeared simultaneously at 3 days after spinal cord injury, and the cavities enlarged at 7 days. In mice receiving N-MMA, the cavities were significantly smaller than those in the mice that underwent spinal cord injury only. However, the numbers of GFAP-positive cells showed no difference between these two groups. These experimental findings suggest that cavitation of the spinal cord is caused mainly by NO released from activated glial cells.
Mutational Analysis of the Saccharomyces cerevisiae SNF1 Protein Kinase and Evidence for Functional Interaction with the SNF4 Protein (1989)

The SNF1 gene of Saccharomyces cerevisiae encodes a protein-serine/threonine kinase that is required for derepression of gene expression in response to glucose limitation. We present evidence that the protein kinase activity is essential for SNF1 function: substitution of Arg for Lys in the putative ATP-binding site results in a mutant phenotype. A polyhistidine tract near the N terminus was found to be dispensable. Deletion of the large region C terminal to the kinase domain only partially impaired SNF1 function, causing expression of invertase to be somewhat reduced but still glucose repressible. The function of the SNF4 gene, another component of the regulatory system, was required for maximal in vitro activity of the SNF1 protein kinase. Increased SNF1 gene dosage partially alleviated the requirement for SNF4. C-terminal deletions of SNF1 also reduced dependence on SNF4. Our findings suggest that SNF4 acts as a positive effector of the kinase but does not serve a regulatory function in signaling glucose availability.
New perspectives and strategy research biomarkers for hepatocellular carcinoma (2007)

Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. Cirrhosis caused by hepatitis B virus, hepatitis C virus or chronic alcohol intake is associated with major risk. Systematic screening for HCC of asymptomatic patients with cirrhosis is needed for earlier detection of small tumors requiring treatment (liver transplantation, surgical resection, percutaneous techniques). The recommended screening strategy among cirrhotic patients is based on regular liver ultrasonography associated with serum alpha-fetoprotein (AFP) assay. As the performance of AFP is not satisfactory, additional tumoral markers are proposed (des-gamma-carboxyprothrombin, glycosylated AFP-L3 fraction). Currently, diagnosis of HCC in cirrhotic patients includes non-invasive tests (imaging after contrast administration, AFP assay); diagnostic biopsy is performed when imaging is limited. After treatment, tumor recurrence is assessed by regular follow-up (AFP assay and imaging). Despite the lack of accurate markers, recent developments in genomic and proteomic approaches will allow the discovery of new biomarkers for primary tumors, as well as for recurrence. This review summarizes the current state of biomarkers for screening, diagnosis and follow-up of HCC, and highlights new perspectives in the field.