gebhart/patrepeval huggingface dataset:
Characterization of Malignant Melanoma Using Vibrational Spectroscopy (2005)

Malignant melanoma, a malignant neoplasm of epidermal melanocytes is the third most common skin cancer. In many cases, melanoma develops from nevus, which is considered as the nonmalignant stage. Fourier transform infrared microspectroscopy (FTIR-MSP), which is based on characteristic molecular vibrational spectra of cells, was used to investigate spectral differences between melanoma, nevus, and the corresponding normal epidermis. In the present work, FTIR-MSP was performed on formalin-fixed biopsies of melanoma and nevi along with the adjoining histologically normal epidermis to understand the biochemical variations from the epidermis and identify suitable parameters for differentiation of nevi from melanoma. The comparative analysis of various parameters calculated from the spectral data of the normal epidermis and the abnormal regions showed that the changes in the nucleic acids was a significant indicator of the abnormal nature of the tissues. The RNA/DNA ratio was decreased in case of both melanoma and nevus compared to the epidermis. The amide II/amide I ratio was greater for nevus and melanoma compared to the epidermis. In contrast to other organs, the analysis of carbohydrates was not found as a suitable indicator in case of malignant melanoma. Shifts in band wave number were found to be a major distinguishing feature between the melanoma and compound nevi. The present study helps in the identification of spectral features suitable for distinction of melanoma from nevus that appear similar even in FTIR spectral features and thus can pave the way for development of in vivo screening systems based on these diagnostic markers.
Elasticity as a biomarker for prostate cancer: a systematic review (2013)

To systematically review the range of methods available for assessing elasticity in the prostate and to examine its use as a biomarker for prostate cancer. A systematic review of the electronic database PubMed was performed up to December 2012. All relevant studies assessing the use of elasticity as a biomarker for prostate cancer were included except those not studying human prostates or reporting a sensitivity, specificity or quantitative elasticity value. There has been much interest in the use of elasticity in the detection of prostate cancer and there have been many publications using various methods of detection. The most common method of assessment is an imaging method, called sonoelastography. Further imaging methods include ultrasound (US), three-dimensional US and magnetic resonance elastography. These methods are reviewed for sensitivity and specificity. The other method of assessment is the mechanical method. These use quantitative elasticity values to differentiate benign from malignant areas of the prostate. This method of assessment has shown that the elasticity changes for differing Gleason grades and T stages of disease within the prostate. Quantitative elasticity values offer the potential of using 'threshold' elasticity values under which the prostate is benign. Tissue elasticity has great potential as a diagnostic and prognostic biomarker for prostate cancer and can be assessed using various methods. Currently transrectal sonoelastography has the most evidence supporting its use in clinical practice.
Modulation of nociceptive transmission by NMDA/glycine site receptor in the ventroposterolateral nucleus of the thalamus (2000)

NMDA-type glutamate receptors are involved in the generation and maintenance of altered pain states. In the present study, we examined the effect of an NMDA-glycine site antagonist, GV196771A [E-4, 6-dichloro-3-(2-oxo-1-phenyl-pyrrolidin-3-ylidenemethyl)-1H- indole-2- carboxylic acid sodium salt], on responses to noxious stimuli both in normal rats and during peripheral mononeuropathy induced by chronic constriction injury (CCI) of the sciatic nerve. In one series of experiments, activity of nociceptive neurons in the ventroposterolateral (VPL) nucleus of the thalamus was recorded in response to pressure stimuli to the contralateral hindpaw. Intravenous injection (iv) of the glycine antagonist had no effect on these cells in normal rats. When tested in rats with CCI induced 2-3 weeks previously, however, GV196771A (0.125, 0.5 and 2.0mg/kg) blocked responses to noxious stimulation in a dose-dependent and reversible manner. Morphine (0.5mg/kg, iv) and the NMDA channel blocker MK801 (0.1mg/kg, iv) suppressed noxious stimulus-evoked activity of VPL neurons in both normal and CCI-treated rats. MK801 also decreased the responses of non-nociceptive neurons to brush stimulation in both sets of animals, in contrast to the glycine antagonist which did not alter the responses of these cells. Similar results were obtained from a series of behavior experiments in which the latency for paw withdrawal from heat stimulation was measured in normal and CCI-treated rats. GV196771A (3 and 10mg/kg) injected orally, reduced the hyperalgesic response in the treated rats but did not change the withdrawal latency in normal rats. Taken together, these findings suggest that block of the NMDA receptor decreases nociceptive transmission in the thalamus and can modulate hyperalgesic states. GV196771A and glycine antagonists in general may represent innovative and safe agents for the treatment of neuropathic pain.
Antinociceptive Action of Isolated Mitragynine from Mitragyna Speciosa through Activation of Opioid Receptor System (2012)

Cannabinoids and opioids systems share numerous pharmacological properties and antinociception is one of them. Previous findings have shown that mitragynine (MG), a major indole alkaloid found in Mitragyna speciosa (MS) can exert its antinociceptive effects through the opioids system. In the present study, the action of MG was investigated as the antinociceptive agent acting on Cannabinoid receptor type 1 (CB1) and effects on the opioids receptor. The latency time was recorded until the mice showed pain responses such as shaking, licking or jumping and the duration of latency was measured for 2 h at every 15 min interval by hot plate analysis. To investigate the beneficial effects of MG as antinociceptive agent, it was administered intraperitoneally 15 min prior to pain induction with a single dosage (3, 10, 15, 30, and 35 mg/kg b.wt). In this investigation, 35 mg/kg of MG showed significant increase in the latency time and this dosage was used in the antagonist receptor study. The treated groups were administered with AM251 (cannabinoid receptor-1 antagonist), naloxone (non-selective opioid antagonist), naltrindole (δ-opioid antagonist) naloxonazine (μ(1)-receptor antagonist) and norbinaltorpimine (κ-opioid antagonist) respectively, prior to administration of MG (35 mg/kg). The results showed that the antinociceptive effect of MG was not antagonized by AM251; naloxone and naltrindole were effectively blocked; and norbinaltorpimine partially blocked the antinociceptive effect of MG. Naloxonazine did inhibit the effect of MG, but it was not statistically significant. These results demonstrate that CB1 does not directly have a role in the antinociceptive action of MG where the effect was observed with the activation of opioid receptor.
Optimal design of a PZT bimorph actuator for minimally invasive surgery (2000)

A metamodel-based presented is developed to optimize the force and displacement performance of a piezoceramic bimorph actuator. A segmented design with a variable piezoceramic layer thickness is proposed, where the thicknesses of discrete piezoceramic segments are used as the design variables. Design of experiments and metamodeling techniques are employed to construct computationally inexpensive approximations of finite element simulations of the PZT bimorph actuator. The metamodels are then used in lieu of the actual FEM for optimization. Design objectives include maximum tip deflection, maximum grasping force, and maximum work available at the tip. The metamodels are also used to rapidly generate the design space and identify the Pareto frontier for the competing design objectives of maximum deflection and maximum force. The accuracy and efficacy of two types of metamodels -- response surfaces and kriging models -- are compared in this study. By optimizing the thickness of the piezoceramic layers, and by allowing the voltage applied to each segment to vary, dramatic improvements in deflection and force are obtained when compared to a standard straight bimorph actuator. The motivation for this design is the need in the field of minimally invasive surgery for improved grasping tools, where a pair of optimized bimorph actuators can be used as a simple grasping device.
Phase II Study of a Liposome-Entrapped Cisplatin Analog (L-NDDP) Administered Intrapleurally and Pathologic Response Rates in Patients With Malignant Pleural Mesothelioma (2005)

Intrapleural L-NDDP therapy in this patient population is feasible with significant but manageable toxicity. Although pathologic responses are highly encouraging, areas of mesothelioma that are not in direct communication with the pleural space will evade drug exposure and limit efficacy in some patients. The optimal role of intrapleural L-NDDP therapy currently remains to be determined.
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom <i>Coprinopsis cinerea</i> ( <i>Coprinus cinereus</i> ) (2010)

The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.
Normal Collagen and Bone Production by Gene-targeted Human Osteogenesis Imperfecta iPSCs (2011)

Osteogenesis imperfecta (OI) is caused by dominant mutations in the type I collagen genes. In principle, the skeletal abnormalities of OI could be treated by transplantation of patient-specific, bone-forming cells that no longer express the mutant gene. Here, we develop this approach by isolating mesenchymal cells from OI patients, inactivating their mutant collagen genes by adeno-associated virus (AAV)-mediated gene targeting, and deriving induced pluripotent stem cells (iPSCs) that were expanded and differentiated into mesenchymal stem cells (iMSCs). Gene-targeted iMSCs produced normal collagen and formed bone in vivo, but were less senescent and proliferated more than bone-derived MSCs. To generate iPSCs that would be more appropriate for clinical use, the reprogramming and selectable marker transgenes were removed by Cre recombinase. These results demonstrate that the combination of gene targeting and iPSC derivation can be used to produce potentially therapeutic cells from patients with genetic disease.
Posttransfusion survival of red cells frozen for 8 weeks after 42‐day liquid storage in AS‐3 (1989)

Current standards recommend that red cells (RBCs) should be frozen within 6 days of donation. There are situations, however, in which it is desirable to freeze RBCs that are older than 6 days, such as for the salvage of rare or autologous units. To determine the therapeutic efficacy of RBCs frozen after prolonged liquid storage, standard units were drawn from nine normal donors and stored at 4 degrees C for 42 days in a nutrient-additive solution, AS-3. 51CrRBC survival assays were performed (24-hour survival: 78.2 +/- 12.4%; n = 8) and the units were frozen at -80 degrees C in glycerol for 8 weeks. After deglycerolization, the mean RBC recovery was 81.0 +/- 4.1 percent and the mean 24-hour 51Cr survival was 78.0 +/- 9.1 percent. The index of therapeutic effectiveness (ITE) was determined by multiplying the postdeglycerolization 24-hour 51Cr survival by the mean RBC recovery (63.3 +/- 9.2). ITE values greater than 60 percent (75% 51Cr survival x 80% RBC recovery) were considered acceptable. Mean adenosine triphosphate levels declined from an initial 3.81 +/- 0.56 micromol per g of hemoglobin to 2.33 +/- 0.55 micromol per g after frozen storage. These findings show that an acceptable percentage of RBCs survives frozen storage after maximum liquid storage (mean ITE greater than 60%). If necessary, RBCs stored in AS-3 can be frozen at any time before 42 days.
Microwave Fixation of Brain Tissue as a Neurochemical Technique— A Review (1977)

Microwave devices have been developed for rapidly inactivating brain enzymes by focusing the power output into the heads of small laboratory animals. The rapid inactivation achieved prevents postmortem changes and permits the measurement of neurochemicals such as acetylcholine at concentrations close to those obtained in vivo. The technique promises the assay of neurochemical parameters not possible before.
Microfluorometer Assay to Measure the Expression of β-Galactosidase and Green Fluorescent Protein Reporter Genes in Single <i>Drosophila</i> Flies (2001)

beta-galactosidase and green fluorescent protein (GFP) are among the most commonly used reporter genes to monitor gene expression in various organisms including Drosophila melanogaster. Their expression is usually detected in a qualitative way by direct microscopic observations of cells, tissues, or whole animals. To measure in vivo the inducibility of two antimicrobial peptide genes expressed during the Drosophila innate immune response, we have adapted two reporter gene systems based on the beta-galactosidase enzymatic activity and GFP. We have designed a 96-well microplate fluorometric assay sensitive enough to quantify the expression of both reporter genes in single flies. The assay has enabled us to process efficiently and rapidly a large number of individual mutant flies generated during an ethylmethane sulfonate saturation mutagenesis of the Drosophila genome. This method may be used in any screen that requires the quantification of reporter gene activity in individual insects.
Acute Pancreatitis in Patients With End-Stage Renal Disease Without Transplantation (1986)

Acute pancreatitis is infrequently described in patients with end-stage renal disease (ESRD) who have not undergone transplantation. We observed 35 attacks of acute pancreatitis in 23 of 1001 patients with ESRD and one additional patient with irreversible acute renal failure, during a ten-year period. Pancreatitis occurred more frequently in association with peritoneal dialysis than with hemodialysis. Four patients died of complications related to a pancreatic pseudocyst, and a fifth died from hemorrhagic pancreatitis. The ten-year incidence of pancreatitis was 2.3% and the overall mortality was 20.8% in patients with ESRD treated without transplantation. We conclude that clinically evident acute pancreatitis occurs more often than has been previously recognized in patients with ESRD who have not undergone transplantation and, particularly, in those patients managed with peritoneal dialysis.
Torsional waves propagation along a waveguide of arbitrary cross section immersed in a perfect fluid (2008)

Guided torsional waves in a bar with a noncircular cross section have been exploited by previous researchers to measure the density of fluids. However, due to the complexity of the wave behavior in the noncircular cross-sectional shape, the previous theory can only provide an approximate prediction; thus the accuracy of the measurement has been compromised. In this paper, a semianalytical finite element method is developed to model accurately the propagation velocity and leakage of guided waves along an immersed waveguide with arbitrary noncircular cross section. An accurate inverse model is then provided to measure the density of the fluid by measuring the change of the torsional wave speed. Experimental results obtained with a rectangular bar in a range of fluids show very good agreement with the theoretical predictions. Finally, the potentials to use the model for sensor optimization are discussed.
The Formation of the Diffraction Image with Electrons in the Gabor Diffraction Microscope (1952)

The projection and transmission methods of diffraction image formation with electrons are discussed in relation to their practical application.The significance of the two methods as limiting cases of one general method is shown. Analysis shows that the projection method is limited in a practical sense by the combination of a chromatic variation in magnification and path difference. This effect leads either to a severely limited field or a much more stringent electrical stability requirement. Analysis of the transmission method shows it to be free from the above effect, besides having other practical advantages. Some initial results of the application of this method are shown.
Effect of Process Parameters on Tensile Mechanical Properties of 3D Printing Continuous Carbon Fiber-Reinforced PLA Composites (2020)

Three-dimensional (3D) printing continuous carbon fiber-reinforced polylactic acid (PLA) composites offer excellent tensile mechanical properties. The present study aimed to research the effect of process parameters on the tensile mechanical properties of 3D printing composite specimens through a series of mechanical experiments. The main printing parameters, including layer height, extrusion width, printing temperature, and printing speed are changed to manufacture specimens based on the modified fused filament fabrication 3D printer, and the tensile mechanical properties of 3D printing continuous carbon fiber-reinforced PLA composites are presented. By comparing the outcomes of experiments, the results show that relative fiber content has a significant impact on mechanical properties and the ratio of carbon fibers in composites is influenced by layer height and extrusion width. The tensile mechanical properties of continuous carbon fiber-reinforced composites gradually decrease with an increase of layer height and extrusion width. In addition, printing temperature and speed also affect the fiber matrix interface, i.e., tensile mechanical properties increase as the printing temperature rises, while the tensile mechanical properties decrease when the printing speed increases. Furthermore, the strengthening mechanism on the tensile mechanical properties is that external loads subjected to the components can be transferred to the carbon fibers through the fiber-matrix interface. Additionally, SEM images suggest that the main weakness of continuous carbon fiber-reinforced 3D printing composites exists in the fiber-matrix interface, and the main failure is the pull-out of the fiber caused by the interface destruction.
An integrated approach to studying regulation of production of the antibiotic methylenomycin by Streptomyces coelicolor A3(2) (1992)

A physiological and molecular biological study was made of the control of methylenomycin biosynthesis by Streptomyces coelicolor A3(2). A simple and reliable assay for this antibiotic was developed. Conditions that permit the synthesis of methylenomycin by S. coelicolor cultures grown in defined medium were elucidated: a readily assimilated carbon and nitrogen source is required. Under these conditions methylenomycin is produced late in the growth phase, at the time of transition from exponential to linear growth. Provided that the phosphate concentration in the medium is kept high, there is synthesis of methylenomycin but not of the other secondary metabolites that this strain can produce. These conditions were used to study the transcription of the methylenomycin gene cluster during the transition from primary to secondary metabolism. The biosynthetic genes of at least one of the mmy transcription units appear to be transcribed before the mmr resistance determinant. The possibility that methylenomycin induces the transcription of mmr is discussed.
Contribution of TNF-α Converting Enzyme and Proteinase-3 to TNF-α Processing in Human Alveolar Macrophages (2005)

Membrane-associated TNF-alpha cleavage is required to yield the 17.5-kD soluble product. This process is poorly understood in human cells, and no studies have related this process to the alveolar macrophage (AM). TNF-alpha-converting enzyme (TACE) is known to cleave TNF at the Ala-76-Val-77 site. We have evaluated the expression, regulation, and catalytic function of TACE in healthy human AMs. TACE was detected on the surface of AMs using flow cytometry. TACE protein can be upregulated by LPS (P = 0.036) and IFN-gamma. LPS-induced expression is downregulated by IL-10 (P = 0.04) and TNF-alpha. TACE regulation was observed at the mRNA level. TACE catalytic activity as assessed by cleavage of glutathione S-transferase-proTNF fusion protein correlates significantly with TACE protein expression (P = 0.04). However, cleavage and soluble TNF-alpha release by AMs was inhibited by matrix metalloproteinase and serine protease inhibitors, suggesting a role for a serine protease in this process. We confirmed the presence of proteinase-3 (PR-3) on the AM surface that was functionally capable of TNF cleavage. PR-3 mRNA expression was not found in AMs. However, we determined that PR-3 from neutrophil supernatants could bind to the AM membrane, suggesting that AM-derived PR-3 is from an exogenous source, which is important in the context of inflammation.
A Review Of Contrast In Positive Photoresists (1985)

The literature dealing with contrast in positive photoresists is reviewed. Pertinent definitions are relayed followed by a survey of the various methods proposed for the measurement of contrast. The processing techniques used to improve contrast are also enumerated along with the advantages and disadvantages of each.