gebhart/patrepeval huggingface dataset:
SPARC correlation with response to gemcitabine (G) plus nab-paclitaxel (nab-P) in patients with advanced metastatic pancreatic cancer: A phase I/II study (2009)

4525 Background: Pancreatic cancer cells and surrounding stroma are known to overexpress SPARC (secreted protein acid rich in cysteine), which is associated with poor clinical outcomes. nab-P, an albumin-bound nanoparticle form of paclitaxel increased tumor accumulation of paclitaxel through binding of albumin to SPARC. This disease specific phase 1 study was designed to evaluate the safety and efficacy of G + nab-P and the correlation of response with tumor SPARC and serum CA19–9 levels. Methods: nab-P doses (100–150 mg/m 2 ) + (G) (1000 mg/m 2 ) were given on days 1, 8, and 15 of a 28-day cycle to pts with metastatic pancreatic adenocarcinoma and with no prior chemotherapy for their metastatic disease. Level 3 SPARC staining by immunohistochemistry was considered positive. Results: 63 pts received treatment. The most common grade 3 and 4 adverse event that occurred in &gt;20% of pts was neutropenia. Nine (18%) pts and 4 (8%) pts had a grade 3/4 event, respectively. Neuropathy was also observed. One combination-associated death due to sepsis occurred at the 150 mg/m 2 nab-P level. Serial PET scans of 53 pts with outside adjudication to date showed 12 (23%) complete responses, 29 (55%) partial responses (PRs) and 4 (8%) stable disease (SD). By RECIST criteria, of the 49 pts evaluable to date, 1(2%) had CR, 12 (24%) had PR, and 20 (41%) had SD. The median survival was 9 months to date. SPARC data were available for 35 pts, of which 10 (29%) were SPARC+ and 25 (71%) were SPARC-. Of these, 27 pts had evaluable response data. Pts that were SPARC+ (8/27) were more likely to be responders (6/8, 75%) than pts who were SPARC- (5/19, 26%), P = 0.03, Fisher's exact test. Median progression-free survival (PFS) increased from 4.8 months for SPARC- pts (22 pts) to 6.2 months for SPARC+ pts (9 pts); however, these data are still immature. Of 45 pts with elevated CA19–9 at baseline, 42 (93%) had maximum decrease of &gt;40% with a median maximum decrease of 92%. Conclusions: The combination of nab-P and G was generally well tolerated and had substantial enough antitumor activity in patients with pancreatic cancer to warrant a phase III clinical trial. SPARC+ status in these patients was associated with higher response rate and longer PFS. [Table: see text]
Common Dermatologic Presentations: The Red Face (2004)

• Objective: To review common dermatologic causes of the “red face.” • Methods: Qualitative assessment of the literature. • Results: Patients with dermatologic problems frequently present in the primary care setting. The most common causes of “red face” are rosacea, acne, actinic keratoses, seborrheic dermatitis, and atopic dermatitis. In cases without complicating factors, the primary care physician can make a clinical diagnosis and initiate treatment. If the diagnosis is in question or the patient has many complicating factors, a referral to a dermatologist or other specialist may be indicated. • Conclusion: Prompt recognition and understanding of common causes of red face will prevent costly diagnostic studies and direct essential therapy.
EnterotoxigenicBacteroides fragilis: a Rogue among Symbiotes (2009)

Enterotoxigenic Bacteroides fragilis (ETBF) strains are strains of B. fragilis that secrete a 20-kDa heat-labile zinc-dependent metalloprotease toxin termed the B. fragilis toxin (BFT). BFT is the only recognized virulence factor specific for ETBF. ETBF strains are associated with inflammatory diarrheal disease in children older than 1 year of age and in adults; limited data suggest an association of ETBF colonization with inflammatory bowel disease flare-ups and colorectal cancer. ETBF secretes one of three highly related BFT isoforms. The relationship between BFT isoform and disease expression is unknown. Although the mechanism of action of BFT is incompletely understood, available data suggest that BFT binds to a specific intestinal epithelial cell receptor, stimulating intestinal cell signal transduction pathways that result in cell morphology changes, cleavage of E-cadherin, reduced colonic barrier function, and increased epithelial cell proliferation and cytokine expression (such as the proinflammatory chemokine interleukin-8). Together, the data suggest that in some hosts, ETBF acts via secretion of BFT to induce colitis. However, the full spectrum of clinical disease related to ETBF and the impact of chronic ETBF colonization on the host remain to be defined.
Hydrotreatment of Fast Pyrolysis Oil Using Heterogeneous Noble-Metal Catalysts (2009)

Fast pyrolysis oils from lignocellulosic biomass are promising second-generation biofuels. Unfortunately, the application range for such oils is limited because of the high acidity (pH∼2.5) and the presence of oxygen in a variety of chemical functionalities, and upgrading of the oils is required for most applications. Herein, we report an experimental study on the upgrading of fast pyrolysis oil by catalytic hydrotreatment. A variety of heterogeneous noble-metal catalysts were tested for this purpose (Ru/C, Ru/TiO2, Ru/Al2O3, Pt/C, and Pd/C), and the results were compared to those obtained with typical hydrotreatment catalysts (sulfided NiMo/Al2O3 and CoMo/Al2O3). The reactions were carried out at temperatures of 250 and 350 °C and pressures of 100 and 200 bar. The Ru/C catalyst was found to be superior to the classical hydrotreating catalysts with respect to oil yield (up to 60 wt %) and deoxygenation level (up to 90 wt %). The upgraded products were less acidic and contained less water than the original fast pyrolysis oil. The HHV was about 40 MJ/kg, which is about twice the value of pyrolysis oil. Analyses of the products by 1H NMR spectroscopy and 2D GC showed that the upgraded pyrolysis oil had lower contents of organic acids, aldehydes, ketones, and ethers than the feed, whereas the amounts of phenolics, aromatics, and alkanes were considerably higher.
Role of Vif in human immunodeficiency virus type 1 reverse transcription (1996)

The Vif protein of human immunodeficiency virus type 1 (HIV-1) is important for virion infectivity. Previous studies have shown that vif mutant HIV-1 virions are defective in their ability to synthesize proviral DNA in vivo. Here, we examine the role of Vif in viral DNA synthesis in the endogenous reverse transcriptase (RT) reaction, an in vitro assay in which virions synthesize viral DNA by using endogenous viral RNA as a template. vif mutant virions showed a significant reduction in endogenous RT activity despite similar levels of exogenous RT activity. Analysis of the viral DNA products on agarose gels demonstrated that this reflects reduced synthesis of short minus- and plus-strand DNA products in addition to those of full genomic length. Quantitative PCR analysis of endogenous reverse transcription provided further evidence for reduced formation of both initial and completed reverse transcripts. Vif had no effect on genomic RNA dimerization or the stability of the RNA dimer linkage. These results suggest that Vif is important for an early event after virus entry but preceding or during the early stages of viral DNA synthesis. This may be due to an intrinsic effect on reverse transcription or a preceding postentry event(s), such as virion uncoating or disassembly of the virion core. Drugs targeted to Vif function may provide a new therapeutic approach to inhibiting HIV-1 reverse transcription.
Comparison of the Structures of Three Circoviruses: Chicken Anemia Virus , Porcine Circovirus Type 2 , and Beak and Feather Disease Virus (2003)

Circoviruses are small, nonenveloped icosahedral animal viruses characterized by circular single-stranded DNA genomes. Their genomes are the smallest possessed by animal viruses. Infections with circoviruses, which can lead to economically important diseases, frequently result in virus-induced damage to lymphoid tissue and immunosuppression. Within the family Circoviridae, different genera are distinguished by differences in genomic organization. Thus, Chicken anemia virus is in the genus Gyrovirus, while porcine circoviruses and Beak and feather disease virus belong to the genus CIRCOVIRUS: Little is known about the structures of circoviruses. Accordingly, we investigated the structures of these three viruses with a view to determining whether they are related. Three-dimensional maps computed from electron micrographs showed that all three viruses have a T=1 organization with capsids formed from 60 subunits. Porcine circovirus type 2 and beak and feather disease virus show similar capsid structures with flat pentameric morphological units, whereas chicken anemia virus has stikingly different protruding pentagonal trumpet-shaped units. It thus appears that the structures of viruses in the same genus are related but that those of viruses in different genera are unrelated.
Carbon-13 nuclear magnetic resonance spectrometric study of wood and wood pulping with cross polarization and magic-angle spinning (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbon-13 nuclear magnetic resonance spectrometric study of wood and wood pulping with cross polarization and magic-angle spinningJames F. Haw, Gary E. Maciel, and Herbert A. SchroederCite this: Anal. Chem. 1984, 56, 8, 1323–1329Publication Date (Print):July 1, 1984Publication History Published online1 May 2002Published inissue 1 July 1984https://doi.org/10.1021/ac00272a028RIGHTS & PERMISSIONSArticle Views312Altmetric-Citations142LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (864 KB) Get e-Alerts Get e-Alerts
An encryption scheme using DNA technology (2008)

The vast parallelism, exceptional energy efficiency and extraordinary information density inherent in DNA molecules are being explored for computing, data storage and cryptography. DNA cryptography is a new field of cryptography arising with the research of DNA computing in recent years. In this paper, an encryption scheme is designed by using the technologies of DNA synthesis, PCR amplification and DNA digital coding as well as the theory of traditional cryptography. By applying the special function of primers to PCR amplification, the primers and coding mode are used as the key of the scheme. The traditional encryption method and DNA digital coding are used to preprocess to the plaintext, which can effectively prevent attack from a possible word as PCR primers. Biological difficult issues and cryptography computing difficulties provide a double security safeguards for the scheme. And the security analysis shows that the encryption scheme has high confidential strength. To demonstrate the performance, we present an interesting example to encode and decode message just between specific two persons using the proposed scheme.
Comparative study of DNA encapsulation into PLGA microparticles using modified double emulsion methods and spray drying techniques (2005)

Recently, several research groups have shown the potential of microencapsulated DNA as adjuvant for DNA immunization and in tissue engineering approaches. Among techniques generally used for microencapsulation of hydrophilic drug substances into hydrophobic polymers, modified WOW double emulsion method and spray drying of water-in-oil dispersions take a prominent position. The key parameters for optimized microspheres are particle size, encapsulation efficiency, continuous DNA release and stabilization of DNA against enzymatic and mechanical degradation. This study investigates the possibility to encapsulate DNA avoiding shear forces which readily degrade DNA during this microencapsulation. DNA microparticles were prepared with polyethylenimine (PEI) as a complexation agent for DNA. Polycations are capable of stabilizing DNA against enzymatic, as well as mechanical degradation. Further, complexation was hypothesized to facilitate the encapsulation by reducing the size of the macromolecule. This study additionally evaluated the possibility of encapsulating lyophilized DNA and lyophilized DNA/PEI complexes. For this purpose, the spray drying and double emulsion techniques were compared. The size of the microparticles was characterized by laser diffractometry and the particles were visualized by scanning electron microscopy (SEM). DNA encapsulation efficiencies were investigated photometrically after complete hydrolysis of the particles. Finally, the DNA release characteristics from the particles were studied. Particles with a size of <10 microm which represent the threshold for phagocytic uptake could be prepared with these techniques. The encapsulation efficiency ranged from 100-35% for low theoretical DNA loadings. DNA complexation with PEI 25?kDa prior to the encapsulation process reduced the initial burst release of DNA for all techniques used. Spray-dried particles without PEI exhibited high burst releases, whereas double emulsion techniques showed continuous release rates.
Maximum-likelihood approach to strain imaging using ultrasound (2000)

A maximum-likelihood (ML) strategy for strain estimation is presented as a framework for designing and evaluating bioelasticity imaging systems. Concepts from continuum mechanics, signal analysis, and acoustic scattering are combined to develop a mathematical model of the ultrasonic waveforms used to form strain images. The model includes three-dimensional (3-D) object motion described by affine transformations, Rayleigh scattering from random media, and 3-D system response functions. The likelihood function for these waveforms is derived to express the Fisher information matrix and variance bounds for displacement and strain estimation. The ML estimator is a generalized cross correlator for pre- and post-compression echo waveforms that is realized by waveform warping and filtering prior to cross correlation and peak detection. Experiments involving soft tissuelike media show the ML estimator approaches the Cramer-Rao error bound for small scaling deformations: at 5 MHz and 1.2% compression, the predicted lower bound for displacement errors is 4.4 microns and the measured standard deviation is 5.7 microns.
[Neonatal bacterial infection]. (2002)

In our NICU, 70 patients with sepsis were examined and analyzed by birth weight, onset day, causative pathogens, clinical symptoms and clinical examination values. Our study result showed the relationship between the birth weight and bacteriological infection rate: the lower birth weight was, the greater infection rate was. For low birth weight newborns, their onset were relatively late as horizontal transmission. For 50% of matured infants, they showed clinical symptom by 6 days after the birth. E. coli or/and S. agalactiae were identified from 57% patients of vertical transmission, and S. aureus and E. cloacae were the major pathogens of horizontal transmission. Low birth weight newborns did not show typical clinical symptoms and examination values. To prevent nosocomial infection, it is important to culture for monitoring and management of skin in addition to taking standard precaution.
Interaction of the adeno-associated virus Rep protein with a sequence within the A palindrome of the viral terminal repeat (1994)

We have characterized a Rep binding sequence which is within the A stem region of the adeno-associated virus terminal repeat (TR) and compared its affinity with that of the complete hairpinned TR for pure Rep68. Both the A stem and the complete TR substrates produced a complex pattern of protein-DNA complexes in which at least six different bound species could be distinguished. Competition experiments suggested that the dissociation constant for the A stem sequence is approximately 125-fold higher than that for the complete TR. The competition experiments also suggested that the average number of Rep molecules per TR substrate molecule under conditions of saturating substrate is 3.7:1, while for the A stem substrate, the ratio is 10:1. In spite of the apparent difference in protein-to-DNA ratio in the complexes, no major difference was seen in the mobility or the pattern of the protein-DNA complexes with the two kinds of substrates, suggesting that the difference in protein-to-DNA ratio was due to the lower stability of the A stem complex rather than the actual number of Rep molecules per DNA molecule. At least some of the difference in stability of the two kinds of complexes was due to the fact that the dissociation rate of the A stem substrate from the protein-DNA complexes was approximately fourfold faster than that of the complete TR. The dissociation rate curves for both substrates, however, were complex, suggesting that substrate was being released from at least two different kinds of protein-DNA complexes at different rates. In addition, we have analyzed binding to several substitution mutants within the A stem of the TR. A five-base mutant near the terminal resolution site (trs site) had little effect on binding. Two other mutants produced seven- or five-base substitutions within the 25-bp sequence of the A stem that had been identified in the accompanying report (D. M. McCarty, D. J. Pereira, I. Zolotukhin, X. Zhou, J. H. Ryan, and N. Muzyczka, J. Virol. 68:4988-4997, 1994) as essential for binding. Each of these mutants eliminated some but not all of the repeating GAGC motifs in the 25-bp A stem region. Both of these mutants completely abolished binding to the A stem substrate but only partially reduced binding in the context of the complete hairpinned TR. Furthermore, neither mutant altered the pattern of Rep-DNA complexes produced.(ABSTRACT TRUNCATED AT 400 WORDS)
Scene segmentation and definition for autonomous robotic navigation using structured light processing (1988)

This dissertation proposes a new method for segmenting images of three-dimensional scenes for pathway estimation as required for robotic vision. Specifically, morphologically based processing of images of laser projected, scanned, structured light is applied to segment and define a three-dimensional scene. The structured light, viewed by a stereoscopically located, single video camera, results in an image in which the regional three-dimensional characteristics of the scene are represented by corresponding distortion of the structure of the projected light. The segmentation methods are based on this region specific distortion in the image of the structured light by applying morphological image filtering techniques to sense and locate these distortions. In addition, an extension of the segmentation process yields a three-dimensional planar fit of the region of interest in the scene. The scene segmentation and definition capabilities of this method can provide essential input to an autonomous navigation system for an off-road or planetary exploration vehicle.
Immunological Evidence for the Presence of Advanced Glycosylation End Products in Atherosclerotic Lesions of Euglycemic Rabbits (1995)

Atherosclerosis is known to be accelerated in diabetic patients, but the mechanisms of this acceleration are poorly understood. Nonenzymatic glycosylation of long-lived proteins results in the formation of advanced glycosylation end products (AGEs), which are extensively cross-linked and could contribute to atherogenesis. Oxidative modification of LDL is also an important process in atherogenesis. In vitro evidence suggests that hyperglycemia may enhance lipid peroxidation, and conversely, that increased lipid peroxidation may enhance AGE formation. If such interactions occur in vivo, we hypothesized that AGE should be found in atherosclerotic lesions of euglycemic LDL receptor-deficient rabbits in areas rich in lipids and oxidized lipoproteins. To demonstrate the presence of AGEs, we developed antisera against a specific "model" compound of AGE, 2-furoyl-4(5)-(2-furanyl)-1H-imidazole (FFI) by using FFI-hexanoic acid (FFI-HA)-protein adducts as the antigen and against AGEs in general by using AGE-albumin as the antigen. Antisera generated with FFI-HA-protein adducts recognized FFI-HA alone as well as FFI-protein adducts. Native proteins or proteins conjugated with aldehydes formed during lipid peroxidation in vitro were not recognized by these antisera. Immunocytochemistry with both FFI-specific and AGE-specific antisera revealed the presence of these epitopes in atherosclerotic lesions of euglycemic LDL receptor-deficient rabbits but not in normal aortic tissues. AGE epitopes within atherosclerotic lesions were predominantly found in similar locations as epitopes generated during modification of the lipoproteins by oxidation, consistent with the hypothesized interactions between oxidation and glycosylation. Indirect evidence in support of the in vivo presence of FFI-like structures was also obtained by the observation that both diabetic and euglycemic human subjects contained autoantibodies that recognize FFI-protein adducts. Taken together, these data provide immunological evidence for the in vivo presence of FFI-like structures and other AGE-protein adducts in atherosclerotic lesions, even in euglycemic conditions.
Amorphous silica nanoparticles trigger nitric oxide/peroxynitrite imbalance in human endothelial cells: inflammatory and cytotoxic effects (2011)

The [NO]/[ONOO(-)] imbalance induced by amorphous silica nanoparticles indicates a potentially deleterious effect of silica nanoparticles on vascular endothelium.
Resilient device authentication system (RDAS) through SIOMETRICS (2013)

In recent decades, human biometrics have been used authenticate the identity of human beings and provide access control. In this paper, we describe the use of Silicon-based "Biometrics" (SIOMETRICS) as the root of trust for Identity Management. This disruptive technological approach is a result of a combination of recent advances in Physical Unclonable Function (PUF) technology, which uses the inherent minute manufacturing variations in semiconductor devices as a silicon "fingerprint," and advanced identity management techniques. Collaboration between academia, leading industry innovators, and a high assurance security DoD provider has resulted in an architectural approach to change the paradigm in cyber security by reducing the attack surface and total cost of security. This approach is applicable to addressing the supply chain risk management problem by providing a lifecycle chain of custody/trust and securing: content/services ("the Cloud"), Mobile Device Integrity (MDI), Bring Your Own Device (BYOD), weapon systems, critical infrastructure protection, and other use cases.