gebhart/patrepeval huggingface dataset:
Coexpression of the c-met proto-oncogene and hepatocyte growth factor in human pancreatic cancer. (1994)

The c-met proto-oncogene encodes a transmembrane tyrosine kinase receptor (MET) that has the capacity to modulate cell proliferation and differentiation; it is activated by the hepatocyte growth factor. Using a highly specific anti-MET antibody we found mild MET immunoreactivity in acinar, ductal, and islet cells in the normal human pancreas and intense MET immunoreactivity in many of the duct-like cancer cells in 14 of 16 human pancreatic adenocarcinomas. Intense MET immunoreactivity was also evident in the ductal cells in regions adjacent to the cancer cells. Northern blot analysis of total RNA revealed that, by comparison with the normal pancreas, pancreatic cancers exhibited a 7-fold (P < 0.01) increase in c-met mRNA levels. Hepatocyte growth factor mRNA levels were increased 10-fold (P < 0.05) in the same cancers. The concomitant over-expression of c-met and hepatocyte growth factor in human pancreatic cancers suggests that there is excessive activation of c-met-dependent signaling pathways that may contribute to pancreatic cancer cell growth in vivo.
Control of strain in GaN using an In doping-induced hardening effect (2001)

We study the hardening effect by isoelectronic In doping on strain in GaN grown by metalorganic vapor phase epitaxy. Incorporated In into GaN was found to pin the slip of screw dislocations, producing internal resistance stress in GaN as a result of the hardening of GaN. We found that this result is due to the interaction between In atoms and screw dislocations. The calculated stress in GaN yielded by the interaction was found to be in good agreement with the measured stress by x-ray diffraction and Raman spectroscopy. The internal resistance stress was estimated to be 0.3 GPa at maximum.
Adeno-Associated Virus Serotype 9-Expressed ZMapp in Mice Confers Protection Against Systemic and Airway-Acquired Ebola Virus Infection (2016)

Adeno-associated viral vectors can be used as a platform for delivering biological countermeasures against pandemic and biological threats. We show that vector delivery of two antibody components of the ZMapp product is effective in mice against systemic and airway challenge with a mouse-adapted strain of Ebola virus. This platform provides a generic manufacturing solution and overcomes some of the delivery challenges associated with repeated administration of the protective protein.
Antimicrobial Preservative Efficacy Testing (2000)

A wide variety of products need to be protected from attack by micro-organisms during their period of use. This is both to protect the user from the dangers of infection and to prevent spoilage and deterioration of the product. In the case of medicines, foods and cosmetics, the safety of the user is the main priority, but maintenance of product quality and appearance and suitability of the product for its intended purpose are also important. Preservatives are intended to protect the product from spoilage due to organisms introduced by the user and those which unavoidably arise during the manufacturing process; preservatives should never be used to counter poor manufacturing procedures or poor-quality ingredients. Clearly, sterile products in single dose units do not require preservation, neither do non-sterile single dose units such as tablets and capsules which are unlikely to sustain microbial survival provided that they are contained within suitable packaging. The need for a preservative system, therefore, most commonly arises if the product is to be subject to microbial challenge during repeated use. Some products are self-preserving, either because the active ingredients are inhibitory, the pH is inimical to growth, or because they contain high concentrations of sugar or other solutes which act as osmotic preservatives. These types of formulations are rare in the pharmaceutical arena, and the majority of multi-dose water-containing medicines incorporate chemical preservatives to prevent microbial spoilage. The term preservative describes the function of a chemical agent in protecting a product from degradation or change which might arise if micro-organisms were to gain access and grow in it. However, this can be misleading since it might be thought that preservatives merely maintain the status quo (prevent micro-organisms growing, but not necessarily kill them), and as a result it is not uncommon to encounter the phrase preservative levels of biocide implying low concentrations of chemical agents which have only a bacteriostatic effect. In the majority of cases, however, the concentrations of preservatives used in product formulations are designed to give a rapid kill of any invading micro-organisms. Increasingly, preservatives are used in
Mechanical Imaging of the Breast (2008)

In this paper, we analyze the physical basis for elasticity imaging of the breast by measuring breast skin stress patterns that result from a force sensor array pressed against the breast tissue. Temporal and spatial changes in the stress pattern allow detection of internal structures with different elastic properties and assessment of geometrical and mechanical parameters of these structures. The method entitled mechanical imaging is implemented in the breast mechanical imager (BMI), a compact device consisting of a hand held probe equipped with a pressure sensor array, a compact electronic unit, and a touchscreen laptop computer. Data acquired by the BMI allows calculation of size, shape, consistency/hardness, and mobility of detected lesions. The BMI prototype has been validated in laboratory experiments on tissue models and in an ongoing clinical study. The obtained results prove that the BMI has potential to become a screening and diagnostic tool that could largely supplant clinical breast examination through its higher sensitivity, quantitative record storage, ease-of-use, and inherent low cost.
Hyperthermia from interstitial laser irradiation in normal rat brain (1987)

This study examined both the effect of variations in optical fiber tip and in light wavelength on laser-induced hyperthermia in rat brain. Normal rat brains were exposed to argon laser light (454-514.5 nm) delivered through an intracerebral end-emitting (bare-tipped) or a diffusion-emitting (sapphire-tipped) optical fiber probe. Interstitial thermistor probes recorded temperatures after thermal equilibration at varying distances from the emitting source. The end-emitting fiber produced significantly (P less than 0.05) higher elevations in tissue temperature than the diffusion-emitting fiber at the same laser power output. This is due to the smaller surface area (1.2 mm2 versus 7.8 mm2) of the end-emitting fiber, which results in a greater rate of energy delivery to tissue adjacent to the fiber tip. Changes in intracerebral temperature measurements were also recorded at similar distances from a diffusion-emitting fiber at a continuous total laser power output of 150 mW for light wavelengths of 454-514.5 nm, 700 nm, and 750 nm and at a total laser output of 1.1 W for 1,060 nm. Variations in brain tissue temperature with distance from the laser emission source were compared for each laser group with the tissue temperature profile generated by a radiofrequency (wavelength 600-625 m) interstitial probe. Similar temperature changes were found for all visible wavelengths near the probe, suggesting that the thermal response of brain adjacent to an interstitial laser fiber is primarily dependent upon the rate of energy delivery and not upon wavelength. The thermal profile versus distance from the light source depends mostly upon the level of temperature rise near the interstitial laser fiber tip and not the wavelength of laser light used. These results have important implications in interstitial applications of laser for hyperthermia and photochemotherapy.
Modifications of single-wall carbon nanotubes upon oxidative purification treatments (2003)

A systematic characterization of single-wall carbon nanotube (SWCNT) material after successive purification steps, including reflux treatment with nitric acid, air oxidation, and annealing, has been performed. Inductively coupled plasma–optical emission spectroscopy shows that a considerable reduction of the metal impurities by up to 95% can be obtained by the nitric acid reflux treatment. During this process, Raman spectroscopy clearly proves that HNO3 molecules are intercalated into the bundles of SWCNTs. At the same time, SWCNTs have suffered a high degree of degradation and defects are being introduced. The subsequent thermal processes lead to the removal of further defect carbon materials and to the almost complete de-intercalation of the HNO3 molecules. Transmission electron microscopy reveals that the remaining SWCNT bundles tend to form thick bundles. Thus the applied purification process results in a high-purity SWCNT material with a drastically reduced content of metal nanoparticles and composed of large bundles of SWCNTs.
Documentation of systemic perfusion in man and in an experimental model (1980)

Maintenance of arterial pressure and consciousness by vigorous coughing during ventricular fibrillation has been previously documented. Observations in 4 additional patients with unstable rhythms and in fibrillating dogs confirm that coughing: (1) produces an arterial pulse; (2) produces opening of the aortic valve; (3) generates forward blood flow; and (4) can maintain consciousness during circulatory arrest. The authors speculate that cough-induced systemic perfusion results from compression of the pulmonary vascular beds by a rise in intrathoracic pressure, the left heart acting only as a one-way conduit to the lower pressure extrathoracic vascular outlets. Recent data suggest that conventional CPR likewise produces blood flow by compression of the pulmonary vascular blood pool, and not by cardiac compression as previously thought.
Microengineering Aerospace Systems (1999)

This is a textbook tutorial encompassing MEMS (micro-electromechanical systems), nanoelectronics, packaging, processing and materials characterization for developing miniaturized smart instruments for aerospace systems, satellites and satellite subsystems.
Postmortem Stability of Ebola Virus (2015)

The ongoing Ebola virus outbreak in West Africa has highlighted questions regarding stability of the virus and detection of RNA from corpses. We used Ebola virus-infected macaques to model humans who died of Ebola virus disease. Viable virus was isolated <7 days posteuthanasia; viral RNA was detectable for 10 weeks.
Nucleotide sequence of theLuxCgene and the upstream DNA from the bioluminescent system ofVibrio harveyi (1988)

The nucleotide sequence of the luxC gene (1431 bp) and the upstream DNA (1049 bp) of the luminescent bacterium Vibrio harveyi has been determined. The luxC gene can be translated into a polypeptide of 55 kDa in excellent agreement with the molecular mass of the reductase polypeptide required for synthesis of the aldehyde substrate for the bioluminescent reaction. Analyses of codon usage showed a high frequency (1.9%) of the isoleucine codon, AUA, in the luxC gene compared to that found in Escherichia coli genes (0.2%) and its absence in the luxA, B and D genes. The low G/C content of the luxC gene and upstream DNA (38-39%) compared to that found in the other lux genes of V. harveyi (45%) was primarily due to a stretch of 500 nucleotides with only a 24% G/C content, extending from 200 bp inside lux C to 300 bp upstream. Moreover, an open reading frame did not extend for more than 48 codons between the luxC gene and 600 bp upstream at which point a gene transcribed in the opposite direction started. As the lux system in the luminescent bacterium, V. fischeri, contains a regulatory gene immediately upstream of luxC transcribed in the same direction, these results show that the organization and regulation of the lux genes have diverged in different luminescent bacteria.
Biodegradation of 1,2,3-Trichloropropane through Directed Evolution and Heterologous Expression of a Haloalkane Dehalogenase Gene (2002)

Using a combined strategy of random mutagenesis of haloalkane dehalogenase and genetic engineering of a chloropropanol-utilizing bacterium, we constructed an organism that is capable of growth on 1,2,3-trichloropropane (TCP). This highly toxic and recalcitrant compound is a waste product generated from the manufacture of the industrial chemical epichlorohydrin. Attempts to select and enrich bacterial cultures that can degrade TCP from environmental samples have repeatedly been unsuccessful, prohibiting the development of a biological process for groundwater treatment. The critical step in the aerobic degradation of TCP is the initial dehalogenation to 2,3-dichloro-1-propanol. We used random mutagenesis and screening on eosin-methylene blue agar plates to improve the activity on TCP of the haloalkane dehalogenase from Rhodococcus sp. m15-3 (DhaA). A second-generation mutant containing two amino acid substitutions, Cys176Tyr and Tyr273Phe, was nearly eight times more efficient in dehalogenating TCP than wild-type dehalogenase. Molecular modeling of the mutant dehalogenase indicated that the Cys176Tyr mutation has a global effect on the active-site structure, allowing a more productive binding of TCP within the active site, which was further fine tuned by Tyr273Phe. The evolved haloalkane dehalogenase was expressed under control of a constitutive promoter in the 2,3-dichloro-1-propanol-utilizing bacterium Agrobacterium radiobacter AD1, and the resulting strain was able to utilize TCP as the sole carbon and energy source. These results demonstrated that directed evolution of a key catabolic enzyme and its subsequent recruitment by a suitable host organism can be used for the construction of bacteria for the degradation of a toxic and environmentally recalcitrant chemical.
Human metabolism : functional diversity and integration (1999)

I. GENERAL FEATURES OF METABOLISM. 1. An Overview of Metabolism 2. Carbohydrate Metabolism 3. Lipid Metabolism 4. Nitrogen Metabolism II. DIFFERENT ORGANS HAVE SPECIALIZED AREAS OF METABOLISM. 5. What Do Different Organs Contribute to the Body's Metabolism 6. The Liver 7. Adipose Tissue 8. Muscles 9. The Pancreas 10. Intestinal Metabolism and nutrient Absorption 11. Metabolism and the Central Nervous System 12. Blood 13. The Kidneys III. INTEGRATION AND CONTROL OF TISSUE METABOLISM. 14. Hoe the Integration and Control of Metabolism Can be Altered 15. The Influence of Starvation on Tissue Metabolism 16. How Does Exercise Alter the Metabolic Balance?
PERIOPERATIVE FEVER AND OUTCOME IN SURGICAL PATIENTS WITH ANEURYSMAL SUBARACHNOID HEMORRHAGE (2009)

These findings suggest that fever is associated with worsened outcome in surgical subarachnoid hemorrhage patients, although, because the association between fever and the primary outcome measure for the trial is dependent on the covariates used in the analysis (particularly operative events and delayed ischemic neurological deficits), we cannot rule out the possibility that fever is a marker for other events. Only a formal trial of fever treatment or prevention can address this issue.
MOC31 Immunoreactivity in Primary and Metastatic Carcinoma of the Liver (2000)

Differentiating between primary tumors of the liver and metastatic lesions can, at times, be difficult. Various histochemical and immunohistochemical methods have been used in an effort to better delineate between hepatocellular carcinoma (HCC), especially the microglandular variant, primary cholangiocarcinoma, and metastatic adenocarcinoma; these ancillary studies can yield less than satisfactory results. Recently, anti-MOC31, a monoclonal antibody directed against a cell surface glycoprotein, has been shown to be helpful in distinguishing between adenocarcinoma and mesothelioma. This study addresses whether this antibody might be helpful in distinguishing between HCC, primary cholangiocarcinoma, and metastatic adenocarcinoma in the liver. Formalin-fixed, paraffin-embedded tissue sections from 15 HCC (including 10 microglandular variants), 14 primary cholangiocarcinomas, and 33 metastatic adenocarcinomas (7 colon, 1 lung, 8 breast, 4 GE jct/gastric, 9 pancreas, 2 small intestine, 1 renal, 1 ovary) were immunostained with anti-MOC 31 (1:40, Dako) after protease digestion and biotin block using a modified ABC technique. Positive staining was limited to membrane based reactivity; controls stained appropriately. Immunoreactivity for MOC31 was observed in 14 of 14 cholangiocarcinomas and 33 of 33 metastatic tumors. Staining was diffuse, intense, and readily interpretable, with rare exceptions. All 15 cases of HCC were negative. We conclude that cholangiocarcinoma and metastatic adenocarcinoma from a variety of sites express MOC31; HCC is uniformly negative for this marker. Anti-MOC31 may prove useful in the evaluation of liver neoplasms where primary hepatocellular and adenocarcinoma enter the differential diagnosis; it is not useful in separating primary cholangiocarcinoma from metastatic adenocarcinoma.
Redundancy and Specificity of Escherichia coli Iron Acquisition Systems during Urinary Tract Infection (2011)

Uropathogenic Escherichia coli (UPEC), the predominant cause of uncomplicated urinary tract infection (UTI), utilizes an array of outer membrane iron receptors to facilitate siderophore and heme import from within the iron-limited urinary tract. While these systems are required for UPEC in vivo fitness and are assumed to be functionally redundant, the relative contributions of specific receptors to pathogenesis are unknown. To delineate the relative roles of distinct UPEC iron acquisition systems in UTI, isogenic mutants in UPEC strain CFT073 or 536 lacking individual receptors were competed against one another in vivo in a series of mixed infections. When combinations of up to four mutants were coinoculated using a CBA/J mouse model of ascending UTI, catecholate receptor mutants (ΔfepA, Δiha, and ΔiroN mutants) were equally fit, suggesting redundant function. However, noncatecholate siderophore receptor mutants, including the ΔiutA aerobactin receptor mutant and the ΔfyuA yersiniabactin receptor mutant, were frequently outcompeted by coinoculated mutants, indicating that these systems contribute more significantly to UPEC iron acquisition in vivo. A tissue-specific preference for heme acquisition was also observed, as a heme uptake-deficient Δhma ΔchuA double mutant was outcompeted by siderophore receptor mutants specifically during kidney colonization. The relative contribution of each receptor to UTI only partially correlated with in vivo levels of receptor gene expression, indicating that other factors likely contributed to the observed fitness differences. Overall, our results suggest that UPEC iron receptors provide both functional redundancy and niche specificity for this pathogen as it colonizes distinct sites within the urinary tract.
An RNA Hairpin to G-Quadruplex Conformational Transition (2012)

RNA molecules can fold into noncanonical structures such as the four-stranded structures known as G-quadruplexes. G-quadruplexes in the transcriptome have recently emerged as relevant regulatory elements of gene expression. Conformational transitions in RNA molecules offer an important way to regulate their biological functions. Here we report on the competition between a canonical hairpin structure and a G-quadruplex structure within an RNA molecule. We show that the conformational preference strongly depends on the relative amounts of mono- and divalent metal ions present in solution. In our system, the G-quadruplex, whose formation is not predicted by available predictive RNA folding programs, is the major conformer at physiologically relevant K(+) and Mg(2+) concentrations. Furthermore, we show that a synthetic small molecule can displace the structural dynamic equilibrium in favor of the hairpin conformer. This work highlights a new and important level of complexity in RNA folding that could be relevant to the biological functions and targeting of RNAs comprising G-quadruplex motifs.
Interleukin 12–dependent Interferon γ Production by CD8α+Lymphoid Dendritic Cells (1999)

We investigated the role of antigen-presenting cells in early interferon (IFN)-gamma production in normal and recombinase activating gene 2-deficient (Rag-2(-/-)) mice in response to Listeria monocytogenes (LM) infection and interleukin (IL)-12 administration. Levels of serum IFN-gamma in Rag-2(-/-) mice were comparable to those of normal mice upon either LM infection or IL-12 injection. Depletion of natural killer (NK) cells by administration of anti-asialoGM1 antibodies had little effect on IFN-gamma levels in the sera of Rag-2(-/-) mice after LM infection or IL-12 injection. Incubation of splenocytes from NK cell-depleted Rag-2(-/-) mice with LM resulted in the production of IFN-gamma that was completely blocked by addition of anti-IL-12 antibodies. Both dendritic cells (DCs) and monocytes purified from splenocytes were capable of producing IFN-gamma when cultured in the presence of IL-12. Intracellular immunofluorescence analysis confirmed the IFN-gamma production from DCs. It was further shown that IFN-gamma was produced predominantly by CD8alpha+ lymphoid DCs rather than CD8alpha- myeloid DCs. Collectively, our data indicated that DCs are potent in producing IFN-gamma in response to IL-12 produced by bacterial infection and play an important role in innate immunity and subsequent T helper cell type 1 development in vivo.
Constant-time filtering with space-variant kernels (1988)

Filtering is an essential but costly step in many computer graphics applications, most notably in texture mapping. Several techniques have been previously developed which allow prefiltering of a texture (or in general an image) in time that is independent of the number of texture elements under the filter kernel. These are limited, however, to space-invariant kernels whose shape in texture space is the same independently of their positions, and usually are also limited to a small range of filters.We present here a technique that permits constant-time filtering for space-variant kernels. The essential step is to approximate a filter surface in texture space by a sum of suitably-chosen basis functions. The convolution of a filter with a texture is replaced by the weighted sum of the convolution of the basis functions with the texture, which can be precomputed. To achieve constant time, convolutions with the basis functions are computed and stored in a pyramidal fashion, and the right level of the pyramid is selected so that only a constant number of points on the filter kernel need be evaluated.The technique allows the use of arbitrary filters, and as such is useful to explore interesting mappings and special filtering techniques. We give examples of applications to perspective and conformal mappings, and to the use of filters such as gaussians and sinc functions.
Recent Molecular Insights into Rickettsial Pathogenesis and Immunity (2013)

Human infections with arthropod-borne Rickettsia species remain a major global health issue, causing significant morbidity and mortality. Epidemic typhus due to Rickettsia prowazekii has an established reputation as the 'scourge of armies', and as a major determinant of significant 'historical turning points'. No suitable vaccines for human use are currently available to prevent rickettsial diseases. The unique lifestyle features of rickettsiae include obligate intracellular parasitism, intracytoplasmic niche within the host cell, predilection for infection of microvascular endothelium in mammalian hosts, association with arthropods and the tendency for genomic reduction. The fundamental research in the field of Rickettsiology has witnessed significant recent progress in the areas of pathogen adhesion/invasion and host immune responses, as well as the genomics, proteomics, metabolomics, phylogenetics, motility and molecular manipulation of important rickettsial pathogens. The focus of this review article is to capture a snapshot of the latest developments pertaining to the mechanisms of rickettsial pathogenesis and immunity.