gebhart/patrepeval huggingface dataset:
Application of time gating in the measurement of glucose level in a three-layer biotissue model by using ultrashort laser pulses (2008)

The efficiency of using the time-of-flight (TOF) method at a wavelength of 820 nm for detecting the changes in the optical properties of multilayer light scattering medium in connection with the problem of the glucose level detection in the human tissue is discussed. Pulses scattered from a three-layer biotissue phantom consisting of two skin layers and a blood layer between them, are calculated with the help of a program code based on the Monte Carlo algorithm for different glucose concentrations. Relative changes in the recorded signals caused by variations in the glucose content are analysed for different source – detector separations. It is shown that the maximum relative change in the total pulse energy is 7.2% and 4.8% for the anisotropy factor of the layer mimicking skin g = 0.9 and 0.7, respectively, and the change in the glucose concentration from 0 up to 500 mg dL-1. The use of time gating leads to the increase in these values up to 12% and 8.5%, respectively. The sensitivity maps are obtained which can be used to determine the optimal duration and the time delay of the time gate relative to the probe pulse for five values of the source – detector separations.
Isolation of an asparagus intracellular PR gene (AoPR1) wound‐responsive promoter by the inverse polymerase chain reaction and its characterization in transgenic tobacco (1993)

The Asparagus officinalis intracellular PR1 (AoPR1) gene is expressed in response to wounding and pathogen attack. We utilized the inverse polymerase chain reaction (IPCR) to isolate the cis-acting regulatory sequences of the AoPR1 gene following unsuccessful attempts to identify hybridizing clones in genomic libraries. Sequence analysis of two IPCR products revealed that a 347 bp intron was present in the AoPR1 gene and that it was probable that the AoPR1 regulatory sequence had been amplified. To test the AoPR1 cis-acting sequences for biological function a translational fusion was constructed with the beta-glucuronidase (GUS) reporter gene and tested in tobacco. These data demonstrated that sequences 982 bp from the probable start of transcription are sufficient to direct wound-inducible transcription and that there is no signal peptide encoded by the first 31 residues of the predicted AoPR1 protein. Histochemical localization of GUS activity in transgenic tobacco demonstrated strong activity localized to wound and pathogen invasion sites. GUS activity was also found in mature pollen grains.
Recognition of speech in additive and convolutional noise based on RASTA spectral processing (1993)

RASTA (relative spectral) processing is studied in a spectral domain which is linear-like for small spectral values and logarithmic-like for large spectral values. Experiments with a recognizer trained on clean speech and test data degraded by both convolutional and additive noise show that doing RASTA processing in the new domain yields results comparable with those obtained by training the recognizer on known noise.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Design and Performance of an ESI Interface for Selective External Ion Accumulation Coupled to a Fourier Transform Ion Cyclotron Mass Spectrometer (2000)

The coupling of Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) with electrospray ionization has advanced the analysis of large biopolymers and provided the basis for high-throughput protein characterization (e.g., for rapid "proteome" analyses). In this work, the combination of high-performance capillary liquid chromatography with FTICR mass spectrometry and external ion accumulation has been shown to increase both sensitivity and analysis duty cycle. Instrument versatility is further improved by ion preselection followed by ion accumulation in an external linear quadrupole ion trap. The interface was tested with a 3.5-T FTICR mass spectrometer and evaluated with a number of peptides and proteins whose molecular weights ranged from 500 to 66000. A significant increase in the sensitivity, duty cycle, and dynamic range over that of the previously used accumulated trapping was achieved, exhibiting a detection limit of approximately 10 zmol (approximately 6000 molecules) for smaller proteins such as cytochrome c. Capillary LC external accumulation interface with FTICR was successfully applied for the study of whole-proteome mouse tryptic digests.
Three-dimensional dosimetry for radioimmunotherapy treatment planning. (1993)

Absorbed-dose calculations for radioimmunotherapy are generally based on tracer imaging studies of the labeled antibody. Such calculations yield estimates of the average dose to normal and target tissues assuming idealized geometries for both the radioactivity source volume and the target volume. This work describes a methodology that integrates functional information obtained from SPECT or PET with anatomical information from CT or MRI. These imaging modalities are used to define the actual shape and position of the radioactivity source volume relative to the patient's anatomy. This information is then used to calculate the spatially varying absorbed dose, depicted in "colorwash" superimposed on the anatomical imaging study. By accounting for individual uptake characteristics of a particular tumor and/or normal tissue volume and superimposing resulting absorbed-dose distribution over patient anatomy, this approach provides a patient-specific assessment of the target-to-surrounding normal tissue absorbed-dose ratio. Such information is particularly important in a treatment planning approach to radioimmunotherapy, wherein a therapeutic administration of antibody is preceded by a tracer imaging study to assess therapeutic benefit.
Solvent screening for a hard-to-dissolve molecular crystal (2008)

Materials with a high-degree of inter- and intra-molecular hydrogen bonding generally have limited solubility in conventional organic solvents. This presents a problem for the dissolution, manipulation and purification of these materials. Using a state-of-the-art density-functional-theory based quantum chemical solvation model we systematically evaluated solvents for a known hydrogen-bonded molecular crystal. This, coupled with direct solubility measurements, uncovered a class of ionic liquids involving fluoride anions that possess more than two orders of magnitude higher solvation power as compared with the best conventional solvents. The crystal structure of one such ionic liquid, determined by X-ray diffraction spectroscopy, indicates that F- ions are stabilized through H-bonded chains with water. The presence of coordinating water in such ionic liquids seems to facilitate the dissolution process by keeping the chemical activity of the F- ions in check.
Activation of the Pseudomonas aeruginosa lasI gene by LasR and the Pseudomonas autoinducer PAI: an autoinduction regulatory hierarchy (1995)

In Pseudomonas aeruginosa, the transcriptional activator LasR and the Pseudomonas autoinducer PAI, are necessary for efficient transcriptional activation of the lasB gene, encoding elastase (L. Passador, J. M. Cook, M.J. Gambello, L. Rust, and B. H. Iglewski, Science 260:1127-1130, 1993). The transcriptional start points of lasI in Escherichia coli and P. aeruginosa were determined by S1 nuclease mapping. In the presence of both LasR and PAI, the start site, T1, is located at position -25 relative to the ATG translational start codon. A minor transcriptional start, T2, is found at position -13 when lasI is transcribed in the absence of either LasR or PAI in P. aeruginosa and E. coli, respectively. To begin to closely examine the regulation of lasI, whose product is involved in the synthesis of PAI, a lasI-lacZ fusion on a lambda phage was constructed to form monolysogens of E. coli MG4. Lysogens supplied only with either lasI or lasR via multicopy plasmids demonstrated no significant increase in beta-galactosidase expression compared with control levels. Lysogens in which both lasR and lasI were supplied in multicopy exhibited a 62-fold increase in expression, and a lysogen in which lasR was supplied in trans and which was grown in the presence of exogenous PAI exhibited a 60-fold increase. Thus, LasR and PAI are necessary for the full expression of lasI in E. coli. The interchangeability of the P. aeruginosa and Vibrio fischeri homologs LasR and LuxR and their respective autoinducers, PAI and VAI, as activators of lasI-lacZ was examined. Only the combination of LasR and PAI significantly increased the expression of lasI. The comparison of lasI-lacZ and lasB-lacZ expression lysogens grown in the presence of lasR and PAI revealed that half-maximal expression of lasI required 0.1 nM PAI, in contrast to the 1.0 nM PAI necessary for lasB half-maximal expression. These results suggest an autoinduction regulatory hierarchy in which LasR and low PAI concentrations primarily activate lasI expression in a regulatory loop. With the accumulation of PAI, secondary activation of virulence product genes such as lasB occurs.
Hybrid modeling and simulation of manufacturing systems (2002)

In this paper, a new methodology for modeling and simulation of hybrid manufacturing systems is presented. This methodology which is based on an extension of Petri nets can be used to model, simulate and analyze systems with both time and event-driven parts. This new extension is called GPN (global Petri net). Here we show how it is used to model a jobshop at two abstraction levels. At the higher level the jobshop is modeled as a discrete-event system by a conventional PN. When more details about its behavior is required, we have modeled it as a hybrid system by a GPN. The modeling approach is very general and can be used for any type of hybrid systems. A simulation package developed based on the GPN modeling methodology is used for the simulation of the resulting nets. Various hybrid system properties such as boundedness stability, controllability and liveness can be investigated by the analysis methods developed for GPNs.
Pancreatic cysts (2009)

Preoperative diagnosis of pancreatic cysts benefits from integrating the clinical, radiological, and cytological features. As patient management algorithms evolve to increasingly nonsurgical options, accuracy in distinguishing mucinous from nonmucinous and benign from malignant mucinous cysts is important. This review focuses on pseudocysts, serous cystadenomas, intraductal papillary mucinous neoplasms (IPMNs), and mucinous cystic neoplasms. Patients with pseudocysts almost always present with pancreatitis and are usually medically managed. Radiological studies reveal a unilocular cyst mostly in the pancreatic tail. Cyst fluid is thin, with high amylase but low carcinoembryonic antigen (CEA) levels. DNA mutations are absent. Serous cystadenomas are benign and do not require resection. Patients are usually asymptomatic and have microcystic or macrocystic masses anywhere in the pancreas. Cytology is frequently nondiagnostic. CEA and amylase levels are low. DNA analysis may reveal loss of heterozygosity (LOH) at 3p if associated with Von Hippel-Lindau disease. Neoplastic mucinous cysts are highly variable in their presentation. Most are resected. Mucinous cystic neoplasms typically arise in the body or tail of the pancreas of middle-aged women and demonstrate a septated cyst without dilatation of the main pancreatic duct. Branch duct IPMNs are more common in the pancreatic head of elderly men. Main duct dilatation correlates with main duct or combined type IPMN. Both types of mucinous cysts produce variable amounts of mucin. Cytologically nonmalignant but atypical epithelial cells, even when scant, are an indication of a high risk for malignancy. High CEA level supports a mucinous cyst, as do KRAS mutation and good quality DNA levels. KRAS mutation and multiple LOH support malignancy.
Iron-Chelation Therapy with Oral Deferiprone in Patients with Thalassemia Major (1995)

Oral deferiprone induces sustained decreases in body iron to concentrations compatible with the avoidance of complications from iron overload. The risk of agranulocytosis associated with deferiprone may restrict its administration to patients who are unable or unwilling to use deferoxamine.
Evidence for Potent Autologous Neutralizing Antibody Titers and Compact Envelopes in Early Infection with Subtype C Human Immunodeficiency Virus Type 1 (2006)

Information about neutralizing antibody responses in subtype C-infected individuals is limited, even though this viral subtype causes the majority of AIDS cases worldwide. Here we compared the course and magnitude of the autologous neutralizing antibody (NAb) response against viral envelope (Env) glycoproteins present during acute and early infection with subtypes B and C human immunodeficiency virus type 1 (HIV-1). NAb responses were evaluated in 6 subtype B-infected and 11 subtype C-infected subjects over a mean evaluation period of 25 months using a pseudovirus reporter gene assay. All subjects in the C cohort were infected through heterosexual contact, while five of the six subjects in the B cohort were infected via male-to-male contact. The kinetics and magnitude of the NAb responses varied among subjects in the B and C cohorts; however, the median 50% inhibitory concentration (IC(50) titer) reached by antibody in the plasma of subtype C-infected subjects, overall, was 3.5-fold higher than in the subtype B-infected subjects (P = 0.06). The higher titers of NAbs in the C cohort were associated with viruses having significantly shorter amino acid length (P = 0.002) in the V1 to V4 region of the surface Env glycoprotein, gp120, compared to the B cohort. Despite the potency of the autologous subtype C NAb response, it was not directed against cross-neutralizing epitopes. These data demonstrate that subtype C Envs elicit a potent yet restricted NAb response early in infection that frequently reaches IC(50) titers in excess of 1:1,000 and suggest that clade-specific differences may exist in Env immunogenicity or susceptibility to neutralization.
Dark Green Islands in Plant Virus Infection are the Result of Posttranscriptional Gene Silencing (2001)

Dark green islands (DGIs) are a common symptom of plants systemically infected with a mosaic virus. DGIs are clusters of green leaf cells that are free of virus but surrounded by yellow, virus-infected tissue. We report here on two lines of evidence showing that DGIs are caused by posttranscriptional gene silencing (PTGS). First, transcripts of a transgene derived from the coat protein of Tamarillo mosaic potyvirus (TaMV) were reduced in DGIs relative to adjacent yellow tissues when the plants were infected with TaMV. Second, nontransgenic plants coinfected with TaMV and a heterologous virus vector carrying TaMV sequences showed reduced titers of the vector in DGIs compared with surrounding tissues. DGIs also were compared with recovered tissue at the top of transgenic plants because recovery has been shown previously to involve PTGS. Cytological analysis of the cells at the junction between recovered and infected tissue was undertaken. The interface between recovered and infected cells had very similar features to that surrounding DGIs. We conclude that DGIs and recovery are related phenomena, differing in their ability to amplify or transport the silencing signal.
Synthesis and Characterization of Biotin-Labeled Nucleotide Analogs (1986)

Two biotin-labeled nucleotide analogs, Bio-4-dUTP and Bio-12-SS-dUPT, were synthesized by a modification of the procedure described by Langer et al. (1981). Deoxyuridine 5'-triphosphate was first mercurated at the 5-C and subsequently reacted with allylamine to form 5-(3-amino)allyldeoxyuridine 5'-triphosphate (AA-dUTP). AA-dUTP was purified and reacted with either N-hydroxysuccinimide-activated biotin to form Bio-4-dUTP, or with N-hydroxysuccinimide-activated 2-(biotinamido)ethyl-1,3'-dithiopropionate to form Bio-12-SS-dUTP. Bio-12-SS-dUTP is a chemically cleavable biotinylated nucleotide analog containing a disulfide bond in the 12-atom linker arm joining biotin to the pyrimidine base. Both biotinylated nucleotide analogs were purified either by ion-exchange chromatography or by ion-pair reverse-phase HPLC. Bio-4-dUTP was identified by (i) its unique absorbance spectrum, (ii) its coelution with 3H-Bio-4-dUTP during reverse-phase HPLC, and (iii) its ability to bind to avidin agarose. As a functional assay for both the synthesis and purification of the biotinylated nucleotide analogs, each nucleotide was incorporated into DNA by nick-translation. The nick-translated DNA was shown to contain biotinylated nucleotides by its ability to bind to biotin-cellulose affinity columns following incubation with soluble avidin. DNA nick-translated in the presence of Bio-12-SS-dUTP was recovered from the biotin-cellulose column following incubation in buffer containing 50 mM dithiothreitol. The susceptibility of the disulfide bond in the linker arm of Bio-12-SS-dUTP to cleavage by dithiothreitol was shown to be unaffected by the presence of avidin bound to the biotin group.
Fibroblast Growth Factor 2 Is Required for Epithelial Recovery, but Not for Pulmonary Fibrosis, in Response to Bleomycin (2014)

The pathogenesis of pulmonary fibrosis involves lung epithelial injury and aberrant proliferation of fibroblasts, and results in progressive pulmonary scarring and declining lung function. In vitro, fibroblast growth factor (FGF) 2 promotes myofibroblast differentiation and proliferation in cooperation with the profibrotic growth factor, transforming growth factor-β1, but the in vivo requirement for FGF2 in the development of pulmonary fibrosis is not known. The bleomycin model of lung injury and pulmonary fibrosis was applied to Fgf2 knockout (Fgf2(-/-)) and littermate control mice. Weight loss, mortality, pulmonary fibrosis, and histology were analyzed after a single intranasal dose of bleomycin. Inflammation was evaluated in bronchoalveolar lavage (BAL) fluid, and epithelial barrier integrity was assessed by measuring BAL protein and Evans Blue dye permeability. Fgf2 is expressed in mouse and human lung epithelial and inflammatory cells, and, in response to bleomycin, Fgf2(-/-) mice have significantly increased mortality and weight loss. Analysis of BAL fluid and histology show that pulmonary fibrosis is unaltered, but Fgf2(-/-) mice fail to efficiently resolve inflammation, have increased BAL cellularity, and, importantly, deficient recovery of epithelial integrity. Fgf2(-/-) mice similarly have deficient recovery of club cell secretory protein(+) bronchial epithelium in response to naphthalene. We conclude that FGF2 is not required for bleomycin-induced pulmonary fibrosis, but rather is essential for epithelial repair and maintaining epithelial integrity after bleomycin-induced lung injury in mice. These data identify that FGF2 acts as a protective growth factor after lung epithelial injury, and call into question the role of FGF2 as a profibrotic growth factor in vivo.
Initiation of Base Excision Repair: Glycosylase Mechanisms and Structures (1999)

The base excision repair pathway is an organism's primary defense against mutations induced by oxidative, alkylating, and other DNA-damaging agents. This pathway is initiated by DNA glycosylases that excise the damaged base by cleavage of the glycosidic bond between the base and the DNA sugar-phosphate backbone. A subset of glycosylases has an associated apurinic/apyrimidinic (AP) lyase activity that further processes the AP site to generate cleavage of the DNA phosphate backbone. Chemical mechanisms that are supported by biochemical and structural data have been proposed for several glycosylases and glycosylase/AP lyases. This review focuses on the chemical mechanisms of catalysis in the context of recent structural information, with emphasis on the catalytic residues and the active site conformations of several cocrystal structures of glycosylases with their substrate DNAs. Common structural motifs for DNA binding and damage specificity as well as conservation of acidic residues and amino groups for catalysis are discussed.
Increased antibody responses to human papillomavirus type 16 L1 protein expressed by recombinant vaccinia virus lacking serine protease inhibitor genes (1990)

The L1 gene of human papillomavirus type 16 (HPV-16) driven by the vaccinia virus major late 4b gene promoter has been inserted into three different sites of the vaccinia virus genome. Insertion into the thymidine kinase (TK) gene was achieved by selection of TK- mutants in BUdR on TK- cells. Insertion into two vaccinia virus serine protease inhibitor (serpin) genes was achieved by co-insertion of the Escherichia coli xanthine guanine phosphoribosyltransferase gene linked to the vaccinia virus 7.5K promoter and selection of mycophenolic acid-resistant recombinant viruses. Each recombinant virus expressed a 57K L1 protein at similar levels and with similar kinetics. However, immunization of mice with these recombinant viruses induced different levels of antibody to the L1 protein. Viruses lacking serpin genes B13R and B24R induced significantly higher antibody levels than did viruses lacking the TK gene. The presence of functional B13R and B24R gene products is therefore somehow immunosuppressive at least for antibody responses to the L1 protein of HPV-16.
MTAP Gene Deletion in Endometrial Cancer (1998)

A gene (MTAP) that encodes the enzyme 5'-deoxy-5'-methylthioadenosine (MTA) phosphorylase has been identified on chromosome 9p21 and cloned. The substrate of this enzyme, MTA, inhibits aminopropyltransferases that synthesize polyamines from putrescine and decarboxylated S-adenosylmethionine. This enzyme normally cleaves MTA to adenine and 5'-methylthioribose-1-phosphate, which are recycled to adenine nucleotides and methionine, respectively. Cancers with deletions of the MTAP gene may be especially susceptible to chemotherapeutic regimes which interfere with purine or methionine utilization. The purpose of this study was to determine deletion of the MTAP gene in endometrial cancer using a polymerase chain reaction-based method. Therefore, 50 endometrial adenocarcinomas were studied. Partial or total deletions of the MTAP gene were detected in 7 (14%) of these cancers. There were no significant relationships between gene deletion and patient age, pathological grade or clinical stage (p > 0.05). The findings indicate that deletion of the MTAP gene does occur in a subgroup of endometrial cancer. The present work may be extended to the development of molecular diagnosis of MTAP gene deletion in other cancers and assist in selecting appropriate chemotherapy.
Rheological properties of thermoresponsive nanocomposite hydrogels (2015)

ABSTRACT Highly elastic and robust nanocomposite hydrogels based on N ‐isopropylacrylamide (NIPAM) and cationic (3‐acrylamidopropyl) trimethylammonium chloride (AMPTMA) were synthesized by photopolymerization. Nanoscopic clay, laponite XLS, was added in the gels during the synthesis. The effect of a hydrophobic salt, lithium bis(trifluoromethane) sulfonimide (LiNTf 2 ), and clay content on the viscoelastic properties, swelling ratio, and stiffness of the nanocomposite hydrogels were investigated as a function of temperature. Synthetic clay served as a multifunctional cross‐linker, producing hydrogels with enhanced elastic properties. Anionic NTf 2 binds to the cationic comonomer units and significantly affected the viscoelasticity and thermal properties. DSC measurements showed that the volume phase transition temperature and its enthalpy changed with the clay content and with introducing the cationic comonomer (AMPTMA) in the PNIPAM network. With the addition of either laponite XLS or the comonomer and 5 mM solution of LiNTf 2 , a fourfold and fivefold increase in elastic modulus was obtained, respectively, compared to that of the homopolymer PNIPAM hydrogel. With increasing the temperature from 20 to 45°C for the copolymer gel with 10% AMPTMA in 5 mM LiNTf 2 , the elastic modulus grew 15 times larger. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016 , 133 , 43123.