gebhart/patrepeval huggingface dataset:
Terminal repetitive sequences in herpesvirus saimiri virion DNA (1985)

The H-DNA repeat unit of Herpesvirus saimiri strain 11 was cloned in plasmid vector pAGO, and the nucleotide sequence was determined by the dideoxy chain termination method. One unit of repetitive DNA has 1,444 base pairs with 70.8% G+C content. The structural features of repeat DNA sequences at the termini of intact virion M-DNA (160 kilobases) and orientation of reiterated DNA were analyzed by radioactive end labeling of M-DNA, followed by cleavage of the end fragments with restriction endonucleases. The termini appeared to be blunt ended with a 5'-phosphate group, probably generated during encapsidation by cleavage in the immediate vicinity of the single ApaI recognition site in the H-DNA repeat unit. The sequence did not reveal sizeable open reading frames, the longest hypothetical peptide from H-DNA being 85 amino acids. There was no evidence for an mRNA promoter or terminator element, and H-DNA-specific transcription could not be found in productively infected cells.
Phase 1b, multicenter, single blinded, placebo‐controlled, sequential dose escalation study to assess the safety and tolerability of topically applied AG013 in subjects with locally advanced head and neck cancer receiving induction chemotherapy (2013)

AG013 was safe and well tolerated. Preliminary efficacy data support further study.
Research progress of ctDNA in non-small cell lung cancer (2016)

Lung cancer is the malignant neoplasm with the highest incidence and mortality in the world.Early diagnosis and timely monitoring tumor relapse and metastasis are extremely important for improving five-year survival rate of lung cancer patients.Circulating tumor DNA (ctDNA) is the extracellular free DNA in human.The level of ctDNA in blood of non-small cell lung cancer patients is significantly higher than that of healthy controls.Furthermore, many studies have proved that ctDNA detection contributes to diagnosis, tumor stages, and prediction of therapeutic efficacy and prognosis.Many genetic changes, such as gene mutation, gene methylation, microsatellite instability, and loss of heterozygosity are also found in ctDNA of non-small cell lung cancer patients.These researches demonstrated that ctDNA could help to perform dynamic genetic surveillance.This study reviews the recent progress of ctDNA in non-small cell lung cancer.


Key words: 
Non-small cell lung cancer; Circulating tumor DNA
EndoS2 is a unique and conserved enzyme of serotype M49 group A Streptococcus that hydrolyses N-linked glycans on IgG and α1-acid glycoprotein (2013)

Many bacteria have evolved ways to interact with glycosylation functions of the immune system of their hosts. Streptococcus pyogenes [GAS (group A Streptococcus)] secretes the enzyme EndoS that cleaves glycans on human IgG and impairs the effector functions of the antibody. The ndoS gene, encoding EndoS, has, until now, been thought to be conserved throughout the serotypes. However, in the present study, we identify EndoS2, an endoglycosidase in serotype M49 GAS strains. We characterized EndoS2 and the corresponding ndoS2 gene using sequencing, bioinformatics, phylogenetic analysis, recombinant expression and LC-MS analysis of glycosidic activity. This revealed that EndoS2 is present exclusively, and highly conserved, in serotype M49 of GAS and is only 37% identical with EndoS. EndoS2 showed endo-β-N-acetylglucosaminidase activity on all N-linked glycans of IgG and on biantennary and sialylated glycans of AGP (α1-acid glycoprotein). The enzyme was found to act only on native IgG and AGP and to be specific for free biantennary glycans with or without terminal sialylation. GAS M49 expression of EndoS2 was monitored in relation to carbohydrates present in the culture medium and was linked to the presence of sucrose. We conclude that EndoS2 is a unique endoglycosidase in serotype M49 and differs from EndoS of other GAS strains by targeting both IgG and AGP. EndoS2 expands the repertoire of GAS effectors that modify key glycosylated molecules of host defence.
How to… (2013)

Abstract Spinal radiography can be used to diagnose many osseous and some soft tissue spinal lesions. Victoria Doyle discusses the technique’s uses and limitations, and how to interpret the radiographs.
Autoimmune Encephalomyelitis and Uveitis Induced by T Cell Immunity to Self β-Synuclein (2003)

Beta-synuclein is a neuronal protein that accumulates in the plaques that characterize neurodegenerative diseases such as Parkinson's and Alzheimer's diseases. It has been proposed that immunization to peptides of plaque-forming proteins might be used therapeutically to help dissociate pathogenic plaques in the brain. We now report that immunization of Lewis rats with a peptide from beta-synuclein resulted in acute paralytic encephalomyelitis and uveitis. T cell lines and clones reactive to the peptide adoptively transferred the disease to naive rats. Immunoblotting revealed the presence of beta-synuclein in heavy myelin, indicating that the expression of beta-synuclein is not confined to neurons. These results add beta-synuclein to the roster of encephalitogenic self Ags, point out the potential danger of therapeutic autoimmunization to beta-synuclein, and alert us to the unsuspected possibility that autoimmunity to beta-synuclein might play an inflammatory role in the pathogenesis of neurodegeneration.
Molecular Beacons: Nucleic Acid Hybridization and Emerging Applications (2001)

Molecular beacons (MBs) are a novel class of nucleic acid probes that become fluorescent when bound to a complementary sequence. Because of this characteristic, coupled with the sequence specificity of nucleic acid hybridization and the sensitivity of fluorescence techniques, MBs are very useful probes for a variety of applications requiring the detection of DNA or RNA. We survey various applications of MBs, including the monitoring of DNA triplex formation, and describe recent developments in MB design that enhance their sensitivity.
Transdermal uptake and organ distribution of silver from two different wound dressings in rats after a burn trauma (2014)

Silver-containing wound dressings are an integral part of wound therapy in adult and pediatric burn patients. The antimicrobial effect of silver is well known and has been described in numerous studies. Side effects are rarely reported from silver-containing wound care products, even though systemic absorption of silver has been shown by elevated levels of silver in the blood of patients after silver exposure during wound therapy. This animal study investigated the silver levels of blood and in which organs and tissues silver is detectable after long-term application of silver-containing wound dressings after a burn trauma. In male rats, a major full-thickness scald was created on their backs according to a standardized burn model. Two different silver-containing wound dressings (nanocrystalline silver [NCS] and silver sulphate foam [SSF]) were applied initially and changed every 7 days. Weekly blood drawings revealed an increase of blood silver in week three with significant higher values in the SSF compared with NCS group (Ag μg/kg 135.8 vs. 61.7; means; p ≤ 0.05). Thereafter, the NCS group showed significantly higher blood silver levels than the SSF group at week five (Ag μg/kg 192.3 vs. 81.3; means; p ≤ 0.01) and six (Ag μg/kg 168.2 vs. 32.9; means; p ≤ 0.01). After 6 weeks, the animals were sacrificed, and the organs and tissues were analyzed for their silver content by inductively coupled plasma mass-spectrometry. Silver was detectable in all analyzed organs and tissue samples, with higher silver values in parenchymatous organs in the NCS than SSF group (Ag μg/kg; spleen: 3,469 vs. 260; kidney: 3,186 vs. 289; liver: 2,022 vs. 313; means; p ≤ 0.05). Silver was also detectable in brain, testis, lung, heart, and muscle tissue.
Assessment of Pancreatic Islet Mass after Islet Transplantation Using In Vivo Bioluminescence Imaging (2005)

In vivo BLI allows for quantitative, serial measurements of pancreatic islet mass after transplantation and should be useful in assessing interventions to sustain or increase islet survival of transplanted islets.
Proapoptotic Bcl-2 Relative Bim Required for Certain Apoptotic Responses, Leukocyte Homeostasis, and to Preclude Autoimmunity (1999)

Apoptosis can be triggered by members of the Bcl-2 protein family, such as Bim, that share only the BH3 domain with this family. Gene targeting in mice revealed important physiological roles for Bim. Lymphoid and myeloid cells accumulated, T cell development was perturbed, and most older mice accumulated plasma cells and succumbed to autoimmune kidney disease. Lymphocytes were refractory to apoptotic stimuli such as cytokine deprivation, calcium ion flux, and microtubule perturbation but not to others. Thus, Bim is required for hematopoietic homeostasis and as a barrier to autoimmunity. Moreover, particular death stimuli appear to activate apoptosis through distinct BH3-only proteins.
Regulation of CAR T cell-mediated cytokine release syndrome-like toxicity using low molecular weight adapters (2019)

Although chimeric antigen receptor (CAR) T cell therapies have demonstrated considerable success in treating hematologic malignancies, they have simultaneously been plagued by a cytokine release syndrome (CRS) that can harm or even kill the cancer patient. We describe a CAR T cell strategy in which CAR T cell activation and cancer cell killing can be sensitively regulated by adjusting the dose of a low molecular weight adapter that must bridge between the CAR T cell and cancer cell to initiate tumor eradication. By controlling the concentration and dosing schedule of adapter administration, we document two methods that can rapidly terminate (<3 h) a pre-existing CRS-like toxicity and two unrelated methods that can pre-emptively prevent a CRS-like toxicity that would have otherwise occurred. Because all four methods concurrently enhance CAR T cell potency, we conclude that proper use of bispecific adapters could potentially avoid a life-threatening CRS while enhancing CAR T cell tumoricidal activity.
The Soluble Form of Alzheimer′s Amyloid β Protein Is Complexed to High Density Lipoprotein 3 and Very High Density Lipoprotein in Normal Human Plasma (1994)

The amyloid fibrils of Alzheimer's neuritic plaques and cerebral blood vessels are mainly composed of aggregated forms of a 39 to 44 amino acids peptide, named amyloid beta (A beta). A similar although soluble form of A beta (sA beta) has been identified in plasma, cerebrospinal fluid and cell culture supernatants, indicating that it is produced under physiologic conditions. We report here that sA beta in normal human plasma is associated with lipoprotein particles, in particular to the HDL3 and VHDL fractions where it is complexed to ApoJ and, to a lesser extent, to ApoAI. This was assessed by immunoprecipitation experiments of purified plasma lipoproteins and lipoprotein-depleted plasma and confirmed by means of amino acid sequence analysis. Moreover, biotinylated synthetic peptide A beta 1-40 was traced in normal human plasma in in vitro experiments. As in the case of sA beta, biotinylated A beta 1-40 was specifically recovered in the HDL3 and VHDL fractions. This data together with the previous demonstration that A beta 1-40 is taken up into the brain via a specific mechanism and possibly as an A beta 1-40-ApoJ complex indicate a role for HDL3- and VHDL-containing ApoJ in the transport of the peptide in circulation and suggest their involvement in the delivery of sA beta across the blood-brain barrier.
Neurodegeneration associated with genetic defects in phospholipase A 2 (2008)

Defects in phospholipase A(2) lead to a range of phenotypes. PLA2G6 mutations are associated with nearly all cases of classic infantile neuroaxonal dystrophy but a minority of cases of idiopathic neurodegeneration with brain iron accumulation, and genotype correlates with phenotype. Cerebellar atrophy predicts which patients are likely to be mutation-positive. The neuropathologic changes that are caused by defective phospholipase A(2) suggest a shared pathogenesis with both Parkinson and Alzheimer diseases.
Initial testing of topotecan by the pediatric preclinical testing program (2009)

Topotecan demonstrated broad activity in vitro and in vivo against both the solid tumor and ALL panels, with significant tumor growth delay generated in all the panels. These results further demonstrate the validity of the PPTP panel for preclinical testing of new drugs.
MALDI Quadrupole Time-of-Flight Mass Spectrometry:  A Powerful Tool for Proteomic Research (2000)

A MALDI QqTOF mass spectrometer has been used to identify proteins separated by one-dimensional or two-dimensional gel electrophoresis at the femtomole level. The high mass resolution and the high mass accuracy of this instrument in both MS and MS/MS modes allow identification of a protein either by peptide mass fingerprinting of the protein digest or from tandem mass spectra acquired by collision-induced dissociation of individual peptide precursors. A peptide mass map of the digest and tandem mass spectra of multiple peptide precursor ions can be acquired from the same sample in the course of a single experiment. Database searching and acquisition of MS and MS/MS spectra can be combined in an interactive fashion, increasing the information value of the analytical data. The approach has demonstrated its usefulness in the comprehensive characterization of protein in-gel digests, in the dissection of complex protein mixtures, and in sequencing of a low molecular weight integral membrane protein. Proteins can be identified in all types of sequence databases, including an EST database. Thus, MALDI QqTOF mass spectrometry promises to have remarkable potential for advancing proteomic research.
Calcium Carbonate Biphasic Cement Concept to Control Cement Resorption (2006)

Biodegradation and bioactivity properties of ceramics and cements have often been related to the solubility of their&#13;\nconstitutive phases. The concept of biphasic calcium phosphate (BCP) ceramics based on an optimum balance between a sparingly soluble phase (hydroxyapatite) and more soluble phase tricalcium phosphate) to control material resorption has however rarely been applied to control the resorption of ionic cements.
Activatable Photosensitizers for Imaging and Therapy (2010)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTActivatable Photosensitizers for Imaging and TherapyJonathan F. Lovell†, Tracy W. B. Liu‡, Juan Chen‡, and Gang Zheng*†‡View Author Information Institute of Biomaterials and Biomedical Engineering and Department of Medical Biophysics, Ontario Cancer Institute, University of Toronto, Ontario M5G 1L7, Canada* To whom correspondence should be addressed. E-mail: [email protected]†Institute of Biomaterials and Biomedical Engineering.‡Department of Medical Biophysics.Cite this: Chem. Rev. 2010, 110, 5, 2839–2857Publication Date (Web):January 27, 2010Publication History Received1 July 2009Published online27 January 2010Published inissue 12 May 2010https://pubs.acs.org/doi/10.1021/cr900236hhttps://doi.org/10.1021/cr900236hreview-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views19425Altmetric-Citations1445LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Fluorescence,Oxygen,Peptides and proteins,Photosensitization,Quenching Get e-Alerts
Nerve injury induced by vibration: prevention of the effect of a conditioning lesion by D600, a Ca2+ channel blocker. (1997)

Local administration of a Ca2+ channel blocker D600 can prevent the effect of a conditioning lesion-that is, the nerve injury induced by vibration can be inhibited by D600. This may have implications for the treatment of patients with neuropathy of the hand induced by vibration.
Recovery of Heavy Oils Using Vapourized Hydrocarbon Solvents: Further Development of the Vapex Process (1993)

Abstract There are extensive deposits of heavy oil in Saskatchewan and Alberta which can only be recovered with low efficiency by conventional methods. Primary recovery in the best of these heavy oil reservoirs can yield about 6 percent of the OOIP. Waterflooding can improve the recovery, but only to an extent of 1–2 percent because of the adverse mobility ratio. Thermal recovery processes using steam can be effective, but these are uneconomic in many Lloydminister type reservoirs because the deposits are relatively thin and heat losses to the overburden and underburden are excessive. One potential means for overcoming the problem of heat loss is to make use of vapourized hydrocarbon solvents at their dew point. This paper discusses the results of experiments withangleflags heavy oil and propane carried out in a large, scaled physical model. It focuses on the area of potential problems encountered with the use of saturated hydrocarbon vapour as a solvent. In particular, it addresses the issue of precipitation of asphaltenes which may lead to reduced permeability and lower production rates. Rates, recoveries, gas to oil ratios and other important parameters will be presented and field performance ofhe process will be predicted from the data obtained in the scaled laboratory model. Introduction Production of heavy oils anti bitumens from the extensive Deposits in Alberta and Saskatchewan hampered by the high viscosity of these materials caused by the high content ofsphaltenes. After these heavy crudes have been produced, often by thermal methods, dilution with light hydrocarbons is required to facilitate transport through pipelines to upgrading plants and refineries. The cost of steam injection to mobilize the heavy crude is large, mostly because there are inherent heat losses associated with heatingsurrounding rock formations that do not bear oil. This situation is further exacerbated in thinner reservoirs. A new idea is to be recover heavy oils using saturated hydrocarbon vapours under carefully controlled conditions which lead to eparation of asphaltenes from the heavy crude. The asphaltenes thus left behind are deposited on the reservoir matrix while the much lighter oil is recovered. The handling, processing and transport of such in situ upgraded oil is easier and more economical. In our previous paper(1) we described a new process for recovering heavy oil with the aid of a saturated Hydrocarbon vapour. In this paper we present further experimental data to support the feasibility of the Process and explore the benefits of an in situ upgrading by asphaltene removal and deposition on the rock matrix. Experimental Work -Hot Water-propane Injection into a Packed Cell: Apparatus Development The purpose of this work was to extend the body of knowledge obtained in our original development of the Vapex process(1) to a larger physical model in which problems not apparent to a small cell come into focus. The previous work was carried out with a small cell with inside dimensions 7 cm × 7 cm × 2.5 cm. The results were encouraging.
STUDIES ON A NEUTRALIZING ANTIBODY AGAINST CANINE DISTEMPER VIRUS FOUND IN MAN (1955)

A reproducible test is described for the measurement of serum neutralizing capacity against a strain of CDV adapted to the chick embryo. A heat-stable neutralizing substance against CDV was demonstrated in human serum and in high titer in the gamma globulin fraction. The neutralizing substance is transmitted via the placenta quantitatively from the mother to the newborn infant. It is lost by the sixth month and reappears in the population between the second and tenth years of life. It reaches an incidence of almost 100 per cent in adults. The evidence so far available indicates that the neutralizing substance has the properties of a true antibody, formed in response to an as yet unidentified infection with an agent identical to or bearing an antigenic structure in common with CDV.
NUP98-HOXA9 Induces Long-term Proliferation and Blocks Differentiation of Primary Human CD34+ Hematopoietic Cells (2006)

NUP98-HOXA9, the chimeric protein resulting from the t(7;11)(p15;p15) chromosomal translocation, is a prototype of several NUP98 fusions that occur in myelodysplastic syndromes and acute myeloid leukemia. We examined its effect on differentiation, proliferation, and gene expression in primary human CD34+ hematopoietic cells. Colony-forming cell (CFC) assays in semisolid medium combined with morphologic examination and flow cytometric immunophenotyping revealed that NUP98-HOXA9 increased the numbers of erythroid precursors and impaired both myeloid and erythroid differentiation. In continuous liquid culture, cells transduced with NUP98-HOXA9 exhibited a biphasic growth curve with initial growth inhibition followed by enhanced long-term proliferation, suggesting an increase in the numbers of primitive self-renewing cells. This was confirmed by a dramatic increase in the numbers of long-term culture-initiating cells, the most primitive hematopoietic cells detectable in vitro. To understand the molecular mechanisms underlying the effects of NUP98-HOXA9 on hematopoietic cell proliferation and differentiation, oligonucleotide microarray analysis was done at several time points over 16 days, starting at 6 hours posttransduction. The early growth suppression was preceded by up-regulation of IFNbeta1 and accompanied by marked up-regulation of IFN-induced genes, peaking at 3 days posttransduction. In contrast, oncogenes such as homeobox transcription factors, FLT3, KIT, and WT1 peaked at 8 days or beyond, coinciding with increased proliferation. In addition, several putative tumor suppressors and genes associated with hematopoietic differentiation were repressed at later time points. These findings provide a comprehensive picture of the changes in proliferation, differentiation, and global gene expression that underlie the leukemic transformation of human hematopoietic cells by NUP98-HOXA9.
Antibiotics Reduce the Growth Rate and Differentiation of Embryonic Stem Cell Cultures (2006)

Embryonic stem cells (ESCs) are being investigated increasingly for their potential as a cell source for tissue engineering. Antibiotics are regularly used in ESC culture media to control contamination, although they can be cytotoxic and interfere with protein synthesis. Our aim was to examine the effects of the frequently used antibiotics gentamicin and combined penicillin and streptomycin on ESC culture using differentiation of murine ESC into type II pneumocytes as a model. Antibiotics reduced the expression of the specific marker for type II pneumocytes, SPC mRNA, by up to 60%. We also identified an adverse effect on the growth rate of differentiating embryoid bodies, causing a significant ( p < 0.05) reduction of up to 40%, and an increase in population doubling time of up to 48%. No contamination was seen in any of the cultures. Our findings suggest that the routine use of antibiotics in ESC culture should be avoided as it may reduce the efficiency of the culture system.