gebhart/patrepeval huggingface dataset:
Metal Artifact Reduction for Clipping and Coiling in Interventional C-Arm CT (2009)

Our MAR method provided metal artifact-reduced images in every studied case. It reduced image noise and corrected CT values to levels comparable with images measured without metallic implants. An overall improvement of brain tissue modeling and implant visibility was achieved. MAR in neuroradiologic FDCT imaging is a promising step forward for better image quality and diagnosis in the presence of metallic implants.
24-Hour Monitoring of Cortisol and Corticotropin Secretion in Psychotic and Nonpsychotic Major Depression (2000)

In the population studied, PMD and NPMD patients have distinct profiles of HPA axis dysregulation.
Mobilization of bone marrow stem cells with StemEnhance® improves muscle regeneration in cardiotoxin-induced muscle injury (2010)

Bone marrow-derived stem cells have the ability to migrate to sites of tissue damage and participate in tissue regeneration. The number of circulating stem cells has been shown to be a key parameter in this process. Therefore, stimulating the mobilization of bone marrow stem cells may accelerate tissue regeneration in various animal models of injury. In this study we investigated the effect of the bone marrow stem cells mobilizer StemEnhance (SE), a water-soluble extract of the cyanophyta Aphanizomenon flos-aquae (AFA), on hematopoietic recovery after myeloablation as well as recovery from cardiotoxin-induced injury of the anterior tibialis muscle in mice. Control and SE-treated female mice were irradiated, and then transplanted with GFP(+) bone marrow stem cells and allowed to recover. Immediately after transplant, animals were gavaged daily with 300 mg/kg of SE in PBS or a PBS control. After hematopoietic recovery (23 days), mice were injected with cardiotoxin in the anterior tibialis muscle. Five weeks later, the anterior tibialis muscles were analyzed for incorporation of GFP(+) bone marrow-derived cells using fluorescence imaging. SE significantly enhanced recovery from cardiotoxin-injury. However, StemEnhance did not affect the growth of the animal and did not affect hematopoietic recovery after myeloablation, when compared to control. This study suggests that inducing mobilization of stem cells from the bone marrow is a strategy for muscle regeneration.
Neutralization of HTLV-III/LAV Replication by Antiserum to Thymosin α 1 (1986)

An antiserum prepared against thymosin alpha 1, a hormone secreted by the thymus gland, effectively neutralized the AIDS-associated virus [HTLV-III/LAV (clone BH-10)] and blocked its replication in H9 cells. Reverse transcriptase activity and expression of the HTLV-III/LAV antigens p15 and p24 were inhibited by purified immunoglobulin G preparations of antisera to thymosin alpha 1. The antiviral activity of the antiserum was found to be due to a region of homology between thymosin alpha 1 and p17, a product of the gag gene of HTLV-III/LAV. Comparison of the primary sequences of thymosin alpha 1 and the gag protein revealed a 44% to 50% homology in an 18-amino acid region, between positions 11 and 28 on thymosin alpha 1 and 92 and 109 on the gag protein. The effectiveness of the thymosin alpha 1 antiserum and of immunoglobulin G-enriched preparations in blocking replication of HTLV-III(BH-10) in H9 cells suggests a novel approach to the development of an AIDS vaccine. A vaccine directed against the gag protein might overcome the problem of genetic drift in the envelope region of the virus and be useful against all genetic variants of HTLV-III/LAV.
Primary Isolation ofEhrlichia chaffeensisfrom Patients with Febrile Illnesses: Clinical and Molecular Characteristics (2000)

Ehrlichia chaffeensis was sought among patients with a history of tick exposure and fever, and the accuracy of other diagnostic tests was compared with that of primary isolation. Among the 38 patients enrolled, E. chaffeensis was isolated from the blood of 7 (18%) and from cerebrospinal fluid specimens of 2 of these 7. All 7 patients also were positive by polymerase chain reaction (PCR) of blood, and 6 patients developed diagnostic titers of antibody to E. chaffeensis. The isolates were characterized by molecular analysis of the 16S rRNA gene, the 120-kDa protein gene, and the variable-length PCR target (VLPT) of E. chaffeensis. On the basis of the 120-kDa and VLPT genotypes, the cerebrospinal fluid and blood isolates from the same patients were identical. This study demonstrates that both PCR and culture of blood for E. chaffeensis have high diagnostic yields. More frequent isolation of E. chaffeensis from patients with infection should further our understanding of the pathogenesis of this infection.
Effects of laterally wedged insoles on symptoms and disease progression in medial knee osteoarthritis: a protocol for a randomised, double-blind, placebo controlled trial (2007)

ACTR12605000503628; NCT00415259.
Functional map of human cytomegalovirus AD169 defined by global mutational analysis (2003)

Human cytomegalovirus has a complex double-stranded DNA genome of approximately 240,000 bp that contains approximately 150 ORFs likely to encode proteins, most of whose functions are not well understood. We have used an infectious bacterial artificial chromosome to introduce 413 defined insertion and substitution mutations into the human cytomegalovirus AD169 genome by random and site-directed transposon mutagenesis. Mutations were produced in all unique ORFs with a high probability of encoding proteins for which mutants have not been previously documented and in many previously characterized ORFs. The growth of selected mutants was assayed in cultured human fibroblasts, and we now recognize 41 essential, 88 nonessential, and 27 augmenting ORFs. Most essential and augmenting genes are located in the central region, and nonessential genes generally cluster near the ends of the viral genome.
Glycosphingolipids Promote Entry of a Broad Range of Human Immunodeficiency Virus Type 1 Isolates into Cell Lines Expressing CD4, CXCR4, and/or CCR5 (2000)

Treatment of human osteosarcoma cells, expressing CD4 and various chemokine receptors, with the glucosylceramide synthase inhibitor 1-phenyl-2-hexadecanoylamino-3-morpholino-1-propanol (PPMP), blocked target membrane glycosphingolipid (GSL) biosynthesis and reduced the susceptibility of cells to infection and fusion mediated by envelope glycoproteins from a variety of human immunodeficiency virus type 1 (HIV-1) isolates that utilize CXCR4 and/or CCR5. PPMP treatment of the cell lines did not significantly change the cell surface expression of CD4, CXCR4, and/or CCR5, nor did it alter the chemokine receptor association with CD4. PPMP-treated cells exhibited no changes in chemokine-induced Ca(2+) mobilization and chemotaxis. However, massive envelope glycoprotein conformational changes triggered by CD4 and the appropriate chemokine receptor on the target membrane were inhibited when the target cells were treated with PPMP. Addition of various purified GSLs to PPMP-treated target cells showed that for all isolates tested, globotriaosylceramide (Gb3) was the most potent GSL in restoring the fusion susceptibility of target cells with cells expressing HIV-1 envelope glycoproteins; addition of the monosialoganglioside GM3 yielded a slight enhancement of fusion susceptibility. Our data are consistent with the notion that a limited number of specific GSL species serve as crucial elements in organizing gp120-gp41, CD4, and an appropriate chemokine receptor into a membrane fusion complex.
Journal of Liposome Research: a Journal Born Again (1992)

(1992). Journal of Liposome Research: a Journal Born Again. Journal of Liposome Research: Vol. 2, No. 2, pp. iii-iii.
최적의 서포트 벡터 머신을 이용한 유방암 분류 (2013)

Objectives: This paper is to examine breast cancer classification using support vector machine (SVM). SVM with optimal parameters obtained using the improved grid search with 5-fold cross validation has been proposed to reach the optimal classification performance. Methods: Two data sets, Wisconsin Original Breast Cancer (WOBC) and Wisconsin Diagnostic Breast Cancer (WDBC) data set, were used to classify tumors as benign and malignant. SVM model performs the classification tasks using optimal kernel parameter and penalty parameter using 5-fold cross validation. Discriminant analysis, logistic regression analysis, decision tree, support vector machines were applied to analyze two data sets. Performance of these techniques was compared through accuracy, ROC curves and c-statistics. Results: Our analysis showed that SVMs predicted breast cancer with highest accuracy and c-statistics among four classification models. A comparison of these SVMs indicated that SVM with optimal parameters has much superior performance than SVM with default parameters. Conclusions: Research efforts have reported with increasing confirmation that SVMs have greater accurate diagnosis ability. In this paper, breast cancer diagnosis based on SVM with optimal parameters obtained using the improved grid search with 5-fold cross validation has been proposed. The performance of the method is evaluated using classification accuracy, ROC curves and c-statistics.
Evaluation of Selectable Markers for Rice Transformation (1989)

A variety of expression systems and selection régimes have been developed to transform plants such as tobacco, petunia, and tomato. We investigated several of these to determine whether the promoters and selectable markers used in dicotyledonous plants are suitable for selecting transformed rice callus. We compared transient expression driven by constitutive and regulated promoters in rice (Oryza sativa) protoplasts and found that the 2' promoter of the octopine T-DNA is approximately 3 to 4 times more efficient than the CAMV 35S promoter, 10 times more efficient than the nos promoter and the 1' promoter, and more than 100 times better than two other regulated plant promoters. Similar results were obtained in tobacco (Nicotiana tabacum) protoplasts with the exception that the nos promoter was expressed nearly 10 times better in rice. Further studies demonstrated that rice callus growth is sensitive to low concentrations of methotrexate, phosphinothricin, and bleomycin, and to moderate concentrations of G418 and hygromycin, but is only partially inhibited by relatively high concentrations of kanamycin. Finally, we tested the ability of stably introduced resistance genes to protect callus against some of the selective agents. Genes that inactivated phosphinothricin or G418 permitted transformed calli to grow almost unimpeded on toxic concentrations of these selective agents. However, a gene conferring resistance to methotrexate could not be used to select for activily growing transformants. Southern analysis of the transformed cell lines demonstrated that 50% of the transformants contained a single plasmid copy and that nearly all integrated copies showed rearrangements. These results on the use of selectable markers in rice should facilitate efforts to obtain transformants of this important grain.
Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome (2010)

Bi-directional gene set enrichment analysis more accurately reflects dynamic regulatory behaviour in biochemical pathways, and as such highlighted biologically relevant changes that were not detected using a traditional approach. In such cases where transcriptomic response to treatment is exceptionally large, canonical correlation analysis in conjunction with Fisher's exact test highlights the subset of pathways showing strongest correlation with the clinical markers of interest. In this case, we have identified selenoamino acid metabolism and steroid biosynthesis as key pathways mediating the observed relationship between metabolic health and high-CLA beef. These results indicate that this type of analysis has the potential to generate novel transcriptome-based biomarkers of disease.
Mining the melanosome for tumor vaccine targets: P.polypeptide is a novel tumor-associated antigen. (2001)

To identify novel, tumor-specific target antigens for vaccine development, we studied immune responses to P.polypeptide, an M(r) 110,000 integral melanosomal membrane protein associated with the Prader-Willi syndrome. Together with expressed sequence tag (EST) and serial analyses of gene expression (SAGE) library analyses, reverse transcription-PCR and Northern blotting verified that P.polypeptide expression was limited to melanoma and melanocytes. A single dominant epitope corresponding to positions 427-435 (IMLCLIAAV) was identified using allele-specific epitope forecasting combined with work in HLA-A*0201/K(b) transgenic mice. This epitope was then used to generate de novo human P.polypeptide-specific CD8+ T cells capable of recognizing P.polypeptide expressing human tumor cell lines in an HLA-A*0201-restricted fashion. Thus, P.polypeptide may be valuable in the creation of novel therapeutic anticancer vaccines.
Lambda Red Recombineering in Escherichia coli Occurs Through a Fully Single-Stranded Intermediate (2010)

The phage lambda-derived Red recombination system is a powerful tool for making targeted genetic changes in Escherichia coli, providing a simple and versatile method for generating insertion, deletion, and point mutations on chromosomal, plasmid, or BAC targets. However, despite the common use of this system, the detailed mechanism by which lambda Red mediates double-stranded DNA recombination remains uncertain. Current mechanisms posit a recombination intermediate in which both 5' ends of double-stranded DNA are recessed by λ exonuclease, leaving behind 3' overhangs. Here, we propose an alternative in which lambda exonuclease entirely degrades one strand, while leaving the other strand intact as single-stranded DNA. This single-stranded intermediate then recombines via beta recombinase-catalyzed annealing at the replication fork. We support this by showing that single-stranded gene insertion cassettes are recombinogenic and that these cassettes preferentially target the lagging strand during DNA replication. Furthermore, a double-stranded DNA cassette containing multiple internal mismatches shows strand-specific mutations cosegregating roughly 80% of the time. These observations are more consistent with our model than with previously proposed models. Finally, by using phosphorothioate linkages to protect the lagging-targeting strand of a double-stranded DNA cassette, we illustrate how our new mechanistic knowledge can be used to enhance lambda Red recombination frequency. The mechanistic insights revealed by this work may facilitate further improvements to the versatility of lambda Red recombination.
Transporter (TAP)‐independent processing of a multiple membrane‐spanning protein, the Epstein‐Barr virus latent membrane protein 2 (1996)

Antigen presentation to CD8+ cytotoxic T lymphocytes (CTL) usually involves proteolytic cleavage of antigen in the cytosol and the delivery of epitope peptides onto major histocompatibility complex class I molecules in the endoplasmic reticulum (ER) via the heterodimeric peptide transporter TAP1/TAP2. In the few exceptional cases where TAP-independent presentation of an endogenously expressed protein has been observed, the epitope-containing domain of the protein either has naturally accessed or has been directed into the ER lumen where it is thought to become susceptible to ER proteases. Here, we describe a novel example of TAP-independent processing involving the Epstein-Barr virus (EBV) latent membrane protein LMP2, a multiple membrane-spanning protein with minimal projection into the ER. Expression of LMP2 in the TAP-T2 cell line, whether from the resident EBV genome or from a recombinant vaccinia virus vector vacc-LMP2, rendered the cells sensitive to recognition by CTL clones specific for two HLA-A2.1-restricted peptide epitopes, LMP2 329-337 or 426-434. Vacc-LMP2-mediated sensitization to lysis required expression of the antigen de novo in T2 cells and was blocked by brefeldin A. In the same experiments, two other EBV-specific CTL epitopes, one derived from LMP2 but restricted through a different HLA allele (A11), the other restricted through A2.1 but derived from a different viral protein (BMLF1), did not display TAP-independent processing. The results are discussed in relation to the unusual topology of LMP2 in the membrane and the position of the epitope peptides within that structure.
Immunization with recombinant MAGE-A3 protein combined with adjuvant systems AS15 or AS02B in patients with unresectable and progressive metastatic cutaneous melanoma: A randomized open-label phase II study of the EORTC Melanoma Group (16032- 18031) (2008)

9065 Background: The MAGE-A3 antigen, expressed in ±60% of metastatic melanomas, is a target of anti-tumor CD4+ and CD8+ T-cells. Previous data showed a few clinical responses of MAGE-A3 Antigen-Specific Cancer Immunotherapeutic in melanoma. This study was designed to evaluate MAGE-A3 recombinant protein combined with different Adjuvant Systems (AS). Methods: Patients (pts) with measurable metastatic MAGE-A3 (+) cutaneous melanoma (unresectable or in transit stage III or stage IV M1a) were randomized between immunization with MAGE-A3 protein combined with AS15 (CpG/MPL/QS21) or with AS02B (MPL/QS 21) as 1st line metastatic treatment. Pts received immunizations every 2 weeks for 6 doses. Those with clinical benefit received additional maintenance treatment for up to 4 yrs. Primary endpoints were CTC grade III/IV toxicity, objective response rate; secondary endpoints were immune response, progression- free survival. Planned sample size was 68 pts. Results: 91 out of 165 screened (55%) had MAGE-A3 (+) tumor biopsies and 75 pts were randomized. Among 72 eligible pts median age: 66 y (range 29–866 y), male: 36%, ECOG = 0: 93%, stage III in-transit: 26%, unresectable stage III: 46%, stage IV M1a: 28%. Toxicity in both treatment arms was comparable, mainly grade I/II with injection site reaction and constitutional symptoms (96%), rarely grade III/IV. Median number of immunizations was 9 (range 2–22). Objective responses (CR, PR) were reported in 3 pts (11, 23+, 24+ mns), 1 pt (5 mns) (AS15) and 0, 1 pt (6 mns) (AS02B). Stable disease (SD) > 16 wk was reported in 6 vs 5 pts in the 2 arms respectively. Anti-MAGE-3 antibody titers were higher in AS15 arm than in AS02B arm. CD4+ T-cell responses were observed in 72% (AS15) versus 36% (AS02B). Conclusions: The combination of MAGE-A3 + AS15 yielded higher specific Ab titers, more robust T-cell induction and long-lasting clinical responses or SD in metastatic melanoma. This warrants further development. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration GlaxoSmithKline GlaxoSmithKline
Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas (2015)

To explore the potential of tumor-specific DNA as a biomarker for head and neck squamous cell carcinomas (HNSCC), we queried DNA from saliva or plasma of 93 HNSCC patients. We searched for somatic mutations or human papillomavirus genes, collectively referred to as tumor DNA. When both plasma and saliva were tested, tumor DNA was detected in 96% of 47 patients. The fractions of patients with detectable tumor DNA in early- and late-stage disease were 100% (n = 10) and 95% (n = 37), respectively. When segregated by site, tumor DNA was detected in 100% (n = 15), 91% (n = 22), 100% (n = 7), and 100% (n = 3) of patients with tumors of the oral cavity, oropharynx, larynx, and hypopharynx, respectively. In saliva, tumor DNA was found in 100% of patients with oral cavity cancers and in 47 to 70% of patients with cancers of the other sites. In plasma, tumor DNA was found in 80% of patients with oral cavity cancers, and in 86 to 100% of patients with cancers of the other sites. Thus, saliva is preferentially enriched for tumor DNA from the oral cavity, whereas plasma is preferentially enriched for tumor DNA from the other sites. Tumor DNA in saliva was found postsurgically in three patients before clinical diagnosis of recurrence, but in none of the five patients without recurrence. Tumor DNA in the saliva and plasma appears to be a potentially valuable biomarker for detection of HNSCC.
Origin of thermal fixing in photorefractive lithium niobate crystals (1997)

Macroscopic light patterns are thermally fixed in photorefractive iron- or copper-doped ${\mathrm{LiNbO}}_{3}$ crystals with different hydrogen concentrations. Spatially resolved absorption measurements reveal unambiguously that migrating hydrogen ions compensate for the space-charge fields at enhanced temperatures if the hydrogen concentration is large enough. However, in crystals with small hydrogen concentrations thermal fixing is also possible and another compensation mechanism appears. Partial depolarization of the crystals does not contribute to the charge compensation processes. The refractive-index pattern is developed by homogeneous illumination and measured by an interferometric technique. The development process is described considering the spatially modulated concentrations of filled and empty electron traps, which cause spatially modulated currents, even for homogeneous illumination.
Isolation and characterization of the alpha-sialyl-beta-2,3-galactosyl-specific adhesin from fimbriated Escherichia coli. (1987)

The alpha-sialyl-beta-2,3-galactosyl-specific adhesin (S adhesin) was isolated from cells of a recombinant Escherichia coli K-12 strain expressing the S-fimbrial adhesin complex. A crude cell extract was partially dissociated into fimbriae and an adhesin-enriched fraction by heating to 70 degrees C. From the latter, adhesin was purified to apparent homogeneity (by fast protein liquid chromatography, immunoblot, and NaDodSO4/PAGE) by differential ammonium sulfate precipitation, dissociation in 8 M guanidine hydrochloride, and high-resolution anion-exchange chromatography in 8 M urea. The purified adhesin formed an aggregate of Mr approximately 10(6) that was made up of one type of 12-kDa polypeptide (fimbrillin is 16.5 kDa). It had pI value of 4.7 (fimbriae has a pI value of 6). Adhesin and fimbrillin had different amino acid compositions. The purified adhesins agglutinated human and bovine erythrocytes with the same specificity as the whole bacteria; purified fimbriae were not adhesive. Monoclonal anti-adhesin and anti-fimbriae antibodies were obtained. Monoclonal anti-adhesin, but none of the anti-fimbriae, antibodies inhibited the agglutination of erythrocytes. The anti-adhesive antibodies were used in immuno-gold electron microscopy to localize adhesin exclusively on the fimbriae, with a possible preference to their tips.
A High-Efficiency Dimmable LED Driver for Low-Power Lighting Applications (2009)

This paper presents a dimmable light-emitting diode (LED) driver with adaptive feedback control for low-power lighting applications. An improved pulsewidth modulation dimming technique is studied for regulating the LED current and brightness. Under universal input voltage operation, high efficiency and high power factor can be achieved by a coupled inductor single-ended primary inductance converter power factor correction (PFC) converter with a simple commercial transition-mode PFC controller. The operation principles and design considerations of the studied LED driver are analyzed and discussed. A laboratory prototype is also designed and tested to verify the feasibility.