gebhart/patrepeval huggingface dataset:
Crystallization and Some Properties of Mannanase (1972)

A mannan-hydrolyzing enzyme produced by a certain strain of Bacillus subtilis was purified from the culture broth and isolated in a crystalline state by being treated with several ion-exchangers. The optimal pH of the enzyme was 6.0. The enzyme was stable in a pH region of 5.0 to 9.5 and at temperatures less than 55°C. The enzyme attacked only β-1,4-mannosidic linkages in the main chain of galactomannan of soybean seed coat, guar gum and coffee bean, and of glucomannan of konjak (Amorphophalus konjac). Investigation of the hydrolysis mode revealed that the enzyme attacked coffee bean galactomannan endowise to form mannobiose, mannotriose and mannotetraose. The action patterns on several mannohomooligomers prepared from a partial hydrolysate of coffee bean galactomannan were also investigated, indicating that the enzyme preferentially attacked the β-1,4-mannosidic linkages that were present apart three to four mannose residues from the non-reducing end of the mannose chain.
Synergistic effects of nisin and thymol on antimicrobial activities inListeria monocytogenesandBacillus subtilis (2000)

Nisin Z and thymol were tested, alone and in combination, for antibacterial activity against Listeria monocytogenes ATCC 7644 and Bacillus subtilis ATCC 33712. The antibacterial effect of nisin Z, produced by Lactococcus lactis KE3 isolated from the traditional Moroccan fermented milk, was greatly potentiated by sub-inhibitory concentrations of thymol in both bacterial strains. Our data showed that the concentration of nisin required for effective control of food-borne pathogenic bacteria could be considerably lowered by the use of thymol in combination. The use of low concentrations of nisin could lead to a less favourable condition for the occurrence of nisin-resistant bacterial sub-populations.
Inflammation, Neurodegenerative Diseases, and Environmental Exposures (2004)

The etiology of neurodegenerative disorders is multifactorial and consists of an interaction between aging, environmental factors, and genetic predisposition. Neuronal cell loss in specific regions of the central nervous system and the resulting clinical symptoms are used to characterize different neurological syndromes. While the selectivity of neuronal cell death is not clearly understood, it is in part attributed to the physiological role and microenvironment of the impacted cells. In this review, innate immune responses in the central nervous system are described. Chronic upregulation of this pathway, orchestrated mainly by microglial cells, may jeopardize neuronal integrity through the prolonged production of toxic inflammatory mediators. Environmental exposures that further enhance the innate immune response may accelerate microglia-driven neurodegeneration. Environmental factors that can trigger inflammatory events in the central nervous system are lipopolysaccharide, aluminum, and particulate matter present in air pollution. These factors may enhance existing age-related inflammation in the central nervous system and thus accelerate neuronal toxicity.
Treatment of Chronic Myeloid Leukemia Relapsing After Allogeneic Bone Marrow Transplantation: The Case for Giving Interferon (1998)

To the Editor:

Higano et al have recently communicated their experience with interferon-α (IFN-α) treatment in 14 chronic myeloid leukemia (CML) patients with cytogenetic relapse after unmanipulated allogeneic bone marrow transplantation (BMT).[1][1] Eighty percent of their patients obtained
Spectroscopic Optical Coherence Tomography and Microscopy (2007)

Imaging biological tissues using optical coherence tomography is enhanced with spectroscopic analysis, providing new metrics for functional imaging. Recent advances in spectroscopic optical coherence tomography (SOCT) include techniques for the discrimination of endogenous tissue types and for the detection of exogenous contrast agents. In this paper, we review these techniques and their associated signal processing algorithms, while highlighting their potential for biomedical applications. We unify the theoretical framework for time- and frequency-domain SOCT and introduce a noise correction method. Differences between spectroscopic Mie scatterers are demonstrated with SOCT, and spectroscopic imaging of macrophage and fibroblast cells in a 3-D scaffold is shown.
Fabrication and characterization of tough elastomeric fibrous scaffolds for tissue engineering applications (2010)

Development of biodegradable tough elastomeric scaffolds are important for engineering tissues such as myocardium and heart valves that experience dynamic environments in vivo. Biomaterial scaffolds should ideally provide appropriate physical, chemical and mechanical cues to the seeded cells to closely mimic the native ECM. Collagen fibers form an important component of native myocardium as well as heart valve leaflets and provide necessary tensile properties to these tissues. Amongst various polymers, collagen mimicking biodegradable elastomer, Poly-(glycerol-sebacate) (PGS) has shown great promise in microfabricated scaffolds for cardiac tissue engineering. However, its use is limited by its solubility and the ability to cast nano-/microfibrous structures. For its superior mechanical properties, thermal or UV crosslinking of the pre-polymer is required under high temperatures and vacuum limiting fabrication of fibers. In this work, we fabricated electrospun PGS fibers were fabricated by simply blending it with biodegradable polycaprolactone (PCL) polymer without any post-processing. It was hypothesized that microfibrous PGS-PCL scaffolds would provide appropriate physical (fibrous structure) and chemical (balanced hydrophilicity and hydrophobicity) to the cells in addition to the mechanical properties.
Photothermal treatment of cutaneous lesions (2001)

This thesis reviews the understanding of the processes involved in the laser treatment of cutaneous blemishes. The current treatment protocol for the treatment of vascular lesions - double scanning with transient blanching used at St George's Hospital is shown to give excellent results. The protocol takes advantage of the precise control provided by the SCANALL automatic scanner and the 5 W, 578 nm output of the copper vapour laser. The clinical endpoint - transient blanching - is shown to be due to a temporary halting of blood flow (probably by vasoconstriction) rather than coagulation necrosis of overlying tissues. Various models of the laser treatment of vascular lesions are presented and examined. A histological study of the double scanning, transient blanching protocol shows that tissue damage is confined to vascular and perivascular tissue. Cosmetic lightening is due to a reduction in both the number and size of the vessels in the upper dermis. The protocol is also investigated by interview and postal survey. The incidence of adverse effects is small. For example, there are only two 1 cm² adverse skin texture changes in 64000cm² of treated area. Patients receiving treatment for telangiectasia and spider naevus are satisfied with the outcome after one or two treatments, but many with port-wine stain cease treatment after four sessions when government funding runs out. Patient perception of the success is compared with the surgeon's perception. Patients often needed to be reminded of the size and severity of their original lesion with a photograph. The thesis reports on a parallel investigation of the use of millisecond scale pulses of white light for the treatment of tattoos. A xenon flash-lamp system is designed, constructed, and used in a clinical trial. This includes building pulse forming networks to produce rectangular current pulses of differing lengths. During the clinical trial the system produced a strong inflammatory response in the skin adjacent to the pigment, and lightening of the tattoo. Modelling, histology and other literature studies lead to the conclusion that the pulse length is too long to cause the explosive rupture of pigment-containing cells observed after Q-switched laser treatment, and too short to cause sufficient necrosis and phagocytosis of the pigment-containing cells for it to be useful clinically. The thesis also describes the construction of a device to measure muscle tension during tendon transfer surgery. The device uses diffraction to measure the separation of the fundamental unit of muscle tissue - the sarcomere.
How Ebola Virus Infects Cells (2005)

A recent study provides insight into the way in which Ebola virus enters cells and may therefore suggest a new strategy for therapy.
Efficacy of cyclosporin A in rheumatoid arthritis: worldwide experience. (1993)

The effects of cyclosporin A (CyA) on the activity of RA have mainly been investigated in patients with active, refractory, long-term disease. The data obtained in these trials suggest that CyA is not only a symptomatic treatment for RA but can also be considered a DMARD. The potential benefits of CyA on one hand and its potential toxicity on the other indicate that a careful assessment should be made of its use in patients with early active RA.
NONLINEAR DYNAMICAL SYSTEM IDENTIFICATION FROM UNCERTAIN AND INDIRECT MEASUREMENTS (2004)

We review the problem of estimating parameters and unobserved trajectory components from noisy time series measurements of continuous nonlinear dynamical systems. It is first shown that in parameter estimation techniques that do not take the measurement errors explicitly into account, like regression approaches, noisy measurements can produce inaccurate parameter estimates. Another problem is that for chaotic systems the cost functions that have to be minimized to estimate states and parameters are so complex that common optimization routines may fail. We show that the inclusion of information about the time-continuous nature of the underlying trajectories can improve parameter estimation considerably. Two approaches, which take into account both the errors-in-variables problem and the problem of complex cost functions, are described in detail: shooting approaches and recursive estimation techniques. Both are demonstrated on numerical examples.
Automatic modeling of a 3D city map from real-world video (1999)

Mixed reality (MR) systems which integrate the virtual world and the real world have become a major topic in the research area of multimedia. As a practical application of these MR systems, we propose an efficient method for making a 3D map from real-world video data. The proposed method is an automatic organization method focusing on video objects to describe video data in an efficient way, i.e., by collating the real-world video data with map information using DP matching. To demonstrate the reliability of this method, we describe successful experiments that we performed using 3D information obtained from the real-world video data.
A 62-kD Sucrose Binding Protein Is Expressed and Localized in Tissues Actively Engaged in Sucrose Transport (1992)

Howard D. Grimes, Paul J. Overvoorde, Kevin Ripp, Vincent R. Franceschi, William D. Hitz, A 62-kD Sucrose Binding Protein Is Expressed and Localized in Tissues Actively Engaged in Sucrose Transport, The Plant Cell, Vol. 4, No. 12 (Dec., 1992), pp. 1561-1574
<b>IMMUNOCYTOCHEMICAL LOCALIZATION OF THE DIFFERENT GASTRIN FORMS IN THE PYLORIC </b><b>ANTRUM </b> (1980)

Localization of big gastrin, G34, and little gastrin, G17, in the pyloric antrum of mammals including man was investigated by immunocytochemical technique. The antisera used were raised either against synthetic N-terminal fragment of hG34 [hG34 (1-15)] or against synthetic hG17. The antigenic determinant of the anti-hG34(1~15) serum was shown to reside in the 1-5 sequence of hG34 and that of the anti-G17 serum in the 6-12 sequence of hG17. Immunostaining using the anti-hG34 (1-15) serum differentiated the G17 antiserum-positive cells in the antrum into two groups: one reactive with the anti-hG34(1-15) serum which, therefore, contains G34 or / and its N-terminal fragment immunoreactivities a.nd the other not reactive or only very weakly reactive with the antiserum. The present result posed a question on classification of the gastrin cells and the anti-hG34(1-15) serum devoid of any antibodies against the G17 portion of G34 was suggested to be useful substrate for immunocytochemical elucidation of the prohormone-hormone relationship in the gastrin cells.
Synthesis of PMN and 65PMN‐35PT Ceramics and Films by a New Suspension Method (2006)

This chapter contains sections titled: Introduction Experimental Procedure Results and discussion Conclusion
New founder germline mutations of CDKN2A in melanoma‐prone families and multiple primary melanoma development in a patient receiving levodopa treatment (2007)

Germline mutations in the CDKN2A gene have been shown to predispose individuals to cutaneous malignant melanoma. Here, we describe three melanoma-prone families and one isolated patient affected by multiple melanoma who carried a tandem germline mutation of CDKN2A at the nucleotide level, [c.339G>C;c.340C>T], [p.Leu113Leu;p.Pro114Ser]. We also describe three other melanoma-prone families that carried a missense germline CDKN2A mutation, c.167G>T, p.Ser56Ile. All these families and patients resided in southeast France. We analyzed six 9p21 markers where the CDKN2A gene is located and found that carrier haplotypes for both mutations were consistent with two respective common founder ancestors. In one family, we identified two fourth-degree relatives homozygous for the Ser56Ile mutation, indicating a possible consanguinity. Furthermore, we observed that a carrier of the founder CDKN2A [p.Leu113Leu;p.Pro114Ser] mutation as well as two MC1R moderate-risk variants, [p.Arg151Cys(+)p.Arg163Gln] developed 22 primary melanomas in the three years that followed initiation of levodopa therapy for Parkinson's disease. This observation suggests that there is a need for reconsideration of the hypothesis that levodopa may play a role in melanoma development, at least when in the context of a high-risk genetic background.
Proteome Changes after Metabolic Engineering to Enhance Aerobic Mineralization of cis-1,2-Dichloroethylene (2006)

Metabolically engineered Escherichia coli has previously been used to degrade cis-1,2-dichloroethylene (cis-DCE). The strains express the six genes of an evolved toluene ortho-monooxygenase from Burkholderia cepacia G4 (TOM-Green, which formed a reactive epoxide) with either (1) gamma-glutamylcysteine synthetase (GSHI, which forms glutathione) and the glutathione S-transferase IsoILR1 from Rhodococcus AD45 (which adds glutathione to the reactive cis-DCE epoxide) or (2) with an evolved epoxide hydrolase from Agrobacterium radiobacter AD1 (EchA F108L/I219L/C248I which converts the reactive cis-DCE epoxide to a diol). Here, the impact of this metabolic engineering for bioremediation was assessed by investigating the changes in the proteome through a quantitative shotgun proteomics technique (iTRAQ) by tracking the changes due to the sequential addition of TOM-Green, IsoILR1, and GSHI and due to adding the evolved EchA versus the wild-type enzyme to TOM-Green. For the TOM-Green/EchA system, 8 proteins out of 268 identified proteins were differentially expressed in the strain expressing EchA F108L/I219L/C248I relative to wild-type EchA (e.g., EchA, protein chain elongation factor EF-Ts, 50S ribosomal subunits L7/L12/L32/L29, cysteine synthase A, glycerophosphodiester phosphodiesterase, iron superoxide dismutase). For the TOM-Green/IsoILR1/GSHI system, the expression level of 49 proteins was changed out of 364 identified proteins. The induced proteins due to the addition of TOM-Green, IsoILR1, and GSHI were involved in the oxidative defense mechanism, pyruvate metabolism, and glutathione synthesis (e.g., 30S ribosomal subunit proteins S3 and S16, 50S ribosomal subunit protein L20, alkyl hydroperoxide reductase, lactate dehydrogenase, acetate kinase, cysteine synthase A). Enzymes involved in indole synthesis, fatty acid synthesis, gluconeogenesis, and the tricarboxylic acid cycle were repressed (e.g., tryptophanase, acetyl-CoA carboxylase, phosphoenolpyruvate carboxykinase, malate dehydrogenase). Hence, the metabolic engineering that leads to enhanced aerobic degradation of 1 mM cis-DCE (2.4-4-fold more chloride ions released) and reduced toxicity from cis-DCE epoxide results in enhanced synthesis of glutathione coupled with an induced stress response as well as repression of fatty acid synthesis, gluconeogenesis, and the tricarboxylic acid cycle.
Development of a Crohn's disease activity index. National Cooperative Crohn's Disease Study. (1976)

Needing a single index of degree of illness in Crohn's disease, the National Cooperative Crohn's Disease Study group collected data prospectively from 187 visits of 112 patients with Crohn's disease of the small bowel, colon, or both. Information on 18 predictor variables was gathered at each visit. In addition, the attending physician rated his over-all evaluation of how well the patient was doing and compared the patient's status with that at the previous visit. A multiple regression computer program was utilized to derive an equation for prediction of the physician's over-all ratings from a subset of the predictor variables fulfilling a combination of constraints. This equation, numerically simplified and utilizing eight selected variables, is the Crohn's Disease Activity Index. Index values of 150 and below are associated with quiescent disease; values above that indicate active disease, and values above 450 are seen with extremely severe disease.
A longitudinal study of angiogenic (placental growth factor) and anti-angiogenic (soluble endoglin and soluble vascular endothelial growth factor receptor-1) factors in normal pregnancy and patients destined to develop preeclampsia and deliver a small for gestational age neonate (2008)

(1) Changes in the maternal plasma concentration of s-Eng, sVEGFR-1, and PlGF precede the clinical presentation of PE, but only changes in s-Eng and PlGF precede the delivery of an SGA neonate; and (2) differences in the profile of angiogenic and anti-angiogenic response to intrauterine insults may determine whether a patient will deliver an SGA neonate, develop PE, or both.
High speed DNA sequencing by capillary electrophoresis (1990)

A major challenge of the Human Genome Initiative is the development of a rapid, accurate, and efficient DNA sequencing technology. A major limitation of current technology is the relatively long time required to perform the gel electrophoretic separations of DNA fragments produced in the sequencing reactions. We demonstrate here that it is possible to increase the speed of sequence analysis by over an order of magnitude by performing the electrophoresis and detection in ultra thin capillary gels. An instrument which utilizes these high speed separations to simultaneously analyze many samples will constitute a second generation automated DNA sequencer suitable for large-scale sequence analysis.
The C-Terminal Half of the Human Immunodeficiency Virus Type 1 Gag Precursor Is Sufficient for Efficient Particle Assembly (1998)

ABSTRACT Human immunodeficiency virus type 1 particle assembly is directed by the Gag polyprotein Pr55 gag , the precursor for the matrix (MA), capsid (CA), and nucleocapsid proteins of the mature virion. We now show that CA sequences N terminal to the major homology region (MHR), which form a distinct domain, are dispensable for particle formation. However, slightly larger deletions which extend into the MHR severely impair particle production. Remarkably, a deletion which removed essentially all MA and CA sequences between the N-terminal myristyl anchor and the MHR reduced the yield of extracellular particles only moderately. Particle formation even exceeded wild-type levels when additional MA sequences, either from the N or the C terminus of the domain, were retained. We conclude that no distinct region between the myristyl anchor and the MHR is required for efficient particle assembly or release.
A catalytic antibody against cocaine prevents cocaine’s reinforcing and toxic effects in rats (1998)

Cocaine addiction and overdose have long defied specific treatment. To provide a new approach, the high-activity catalytic antibody mAb 15A10 was elicited using a transition-state analog for the hydrolysis of cocaine to nontoxic, nonaddictive products. In a model of cocaine overdose, mAb 15A10 protected rats from cocaine-induced seizures and sudden death in a dose-dependent fashion; a noncatalytic anticocaine antibody did not reduce toxicity. Consistent with accelerated catalysis, the hydrolysis product ecgonine methyl ester was increased >10-fold in plasma of rats receiving mAb 15A10 and lethal amounts of cocaine. In a model of cocaine addiction, mAb 15A10 blocked completely the reinforcing effect of cocaine in rats. mAb 15A10 blocked cocaine specifically and did not affect behavior maintained by milk or by the dopamine reuptake inhibitor bupropion. This artificial cocaine esterase is a rationally designed cocaine antagonist and a catalytic antibody with potential for medicinal use.
Detection of Human Papillomavirus in Formalin-Fixed, Invasive Squamous Carcinomas Using the Polymerase Chain Reaction (1989)

We analyzed 88 formalin-fixed, paraffin-embedded invasive squamous carcinomas for human papillomavirus-related DNA sequences (HPV types 16 and 18) following in vitro gene amplification using the polymerase chain reaction. HPV DNA sequences were found in 35 of 50 (70%) carcinomas of the anogenital region, including four of four (100%) anal, six of eight (75%) vulvar, nine of 14 (64%) vaginal, two of five (40%) penile, and 14 of 19 (74%) cervical tumors. Nine of 25 (36%) oropharyngeal squamous carcinomas contained HPV DNA sequences, including four of 10 (40%) laryngeal, three of eight (38%) buccal, and two of seven (29%) glossal tumors. HPV DNA sequences were not found in 13 esophageal carcinomas. Of the 44 cases that contained viral DNA, HPV-16 was detected in 41 cases (93%) and HPV-18 in five cases (11%), while both types were found in two cases (one anal and one vulvar). HPV DNA sequences were found in 43 of 83 (52%) nonverrucous and in one of five (20%) verrucous carcinomas, but this difference was not significant. These findings demonstrate that HPV DNA sequences are more frequently associated with anogenital than oropharyngeal squamous carcinomas and can be readily detected in routinely processed tissues using the polymerase chain reaction.
Allelic Exclusion and Peripheral Reconstitution by TCR Transgenic T Cells Arising From Transduced Human Hematopoietic Stem/Progenitor Cells (2013)

Transduction and transplantation of human hematopoietic stem/progenitor cells (HSPC) with the genes for a T-cell receptor (TCR) that recognizes a tumor-associated antigen may lead to sustained long-term production of T cells expressing the TCR and confer specific antitumor activity. We evaluated this using a lentiviral vector (CCLc-MND-F5) carrying cDNA for a human TCR specific for an HLA-A*0201-restricted peptide of Melanoma Antigen Recognized by T cells (MART-1). CD34(+) HSPC were transduced with the F5 TCR lentiviral vector or mock transduced and transplanted into neonatal NSG mice or NSG mice transgenic for human HLA-A*0201 (NSG-A2). Human CD8(+) and CD4(+) T cells expressing the human F5 TCR were present in the thymus, spleen, and peripheral blood after 4-5 months. Expression of human HLA-A*0201 in NSG-A2 recipient mice led to significantly increased numbers of human CD8(+) and CD4(+) T cells expressing the F5 TCR, compared with control NSG recipients. Transduction of the human CD34(+) HSPC by the F5 TCR transgene caused a high degree of allelic exclusion, potently suppressing rearrangement of endogenous human TCR-β genes during thymopoiesis. In summary, we demonstrated the feasibility of engineering human HSPC to express a tumor-specific TCR to serve as a long-term source of tumor-targeted mature T cells for immunotherapy of melanoma.