gebhart/patrepeval huggingface dataset:
Embolization: An adjunctive measure for removal of carotid body tumors (1988)

Small carotid body tumors that do not encircle the internal carotid artery are excised with relative ease and minimal risk by the conventional subadventicial approach. Large carotid body tumors frequently encircle the internal and external carotid arteries, and extensive bleeding often complicates the resection, increasing the risk of carotid artery rupture and damage to major cranial nerves. Recent improvements in surgical techniques and selective embolization have lessened the risks of surgical excision, decreased the blood loss, and diminished the time required for resection. Experiences in the resection of carotid tumors with and without embolization are compared. Early resection of carotid body tumors, before involvement of the internal carotid artery and carotid bulb, is advocated.
Steps Toward Safe Cell Therapy Using Induced Pluripotent Stem Cells (2013)

The enthusiasm for producing patient-specific human embryonic stem cells using somatic nuclear transfer has somewhat abated in recent years because of ethical, technical, and political concerns. However, the interest in generating induced pluripotent stem cells (iPSCs), in which pluripotency can be obtained by transcription factor transduction of various somatic cells, has rapidly increased. Human iPSCs are anticipated to open enormous opportunities in the biomedical sciences in terms of cell therapies for regenerative medicine and stem cell modeling of human disease. On the other hand, recent reports have emphasized the pitfalls of iPSC technology, including the potential for genetic and epigenetic abnormalities, tumorigenicity, and immunogenicity of transplanted cells. These constitute serious safety-related concerns for iPSC-based cell therapy. However, preclinical data supporting the safety and efficacy of iPSCs are also accumulating. In this Review, recent achievements and future tasks for safe iPSC-based cell therapy are summarized, using regenerative medicine for repair strategies in the damaged central nervous system (CNS) as a model. Insights on safety and preclinical use of iPSCs in cardiovascular repair model are also discussed.
Effects of oligo sequence and chemistry on the efficiency of oligodeoxyribonucleotide-mediated mRNA cleavage (1990)

Using the endogenous histone H4 mRNA of Xenopus oocytes as a target, we have previously shown that 20mer oligos complementary to different parts of this sequence vary in their effectiveness at causing mRNA cleavage in vivo, and that some of the RNA can never be cleaved. In this paper we show that the resistant RNA is not localised within one part of the oocyte, and that the relative resistance in vivo of endogenous or synthetic H4 mRNA to the different oligos is preserved in an in vitro assay system using deproteinised RNA. If an prior annealing step is included in vitro, all resistance is abolished. Chemical modification of one oligo by end substitution with methylphosphonate or phosphorothioate residues did not improve cleavage efficiency. Oligos with complete phosphorothioate substitution cause slower cleavage in vivo but persist for longer. Consequently phosphorothioate oligos are effective at lower doses than phosphodiester ones, provided that the incubation time is long enough (24 hours). Increasing oligo length from 20nt to 30nt increases phosphorothioate oligo efficiency over long reaction times in vivo, but decreases efficiency during short in vitro assays. Similar increases in length did not affect phosphodiester oligo performance in vivo, but caused a decrease in efficiency in vitro which was overcome by an annealing step.
Fluid-based analysis of a network of AQM routers supporting TCP flows with an application to RED (2000)

In this paper we use jump process driven Stochastic Differential Equations to model the interactions of a set of TCP flows and Active Queue Management routers in a network setting. We show how the SDEs can be transformed into a set of Ordinary Differential Equations which can be easily solved numerically. Our solution methodology scales well to a large number of flows. As an application, we model and solve a system where RED is the AQM policy. Our results show excellent agreement with those of similar networks simulated using the well known ns simulator. Our model enables us to get an in-depth understanding of the RED algorithm. Using the tools developed in this paper, we present a critical analysis of the RED algorithm. We explain the role played by the RED configuration parameters on the behavior of the algorithm in a network. We point out a flaw in the RED averaging mechanism which we believe is a cause of tuning problems for RED. We believe this modeling/solution methodology has a great potential in analyzing and understanding various network congestion control algorithms.
Analyzing Radioligand Binding Data (2002)

Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.
Reprogramming of Various Cell Types to a Beta-Like State by Pdx1, Ngn3 and MafA (2013)

The three transcription factors, PDX1, NGN3 and MAFA, are very important in pancreatic development. Overexpression of these three factors can reprogram both pancreatic exocrine cells and SOX9-positive cells of the liver into cells resembling pancreatic beta cells. In this study we investigate whether other cell types can be reprogrammed. Eight cell types are compared and the results are consistent with the idea that reprogramming occurs to a greater degree for developmentally related cells (pancreas, liver) than for other types, such as fibroblasts. Using a line of mouse hepatocyte-derived cells we screened 13 compounds for the ability to increase the yield of reprogrammed cells. Three are active and when used in combination they can increase the yield of insulin-immunopositive cells by a factor of six. These results should contribute to the eventual ability to develop a new cure for diabetes based on the ability to reprogram other cells in the body to a beta cell phenotype.
Mast cell subpopulations in the synovial tissue of patients with osteoarthritis: selective increase in numbers of tryptase‐positive, chymase‐negative mast cells (1998)

Although there is relatively little evidence of inflammation in osteoarthritis (OA), increases in mast cell numbers and mast cell activation are prominent features of the synovial tissue. As little is known of the types of mast cells which may be involved, the numbers and distribution of mast cell subpopulations have been investigated as defined according to their content of proteases. Tissue was obtained from patients with OA undergoing total knee replacement surgery (n=14) and from control subjects either post-mortem (n=11) or following leg amputation for peripheral vascular disease (n=3); a double-labelling immunocytochemical procedure with monoclonal antibodies specific for tryptase and chymase was applied to identify those mast cells which contain both tryptase and chymase (MCTC) and those with tryptase but not chymase (MCT). There was considerable variation between individual tissues and between sites of tissue sampling, but cells of the MCTC subset were predominant in the synovial layer of both groups of subjects without joint disease, accounting for some 60 per cent of all mast cells present. In tissue from OA patients, however, there appeared to have been a striking shift in the relative proportions of mast cells from the MCTC to the MCT phenotype, with many more MCT cells present in the synovial tissues of OA patients (median 53 MCT/mm2) than in tissue from post-mortem (7·5 MCT/mm2, P<0·0001) or amputation controls (12 MCT/mm2). In contrast, numbers of synovial MCTC cells in the synovium of OA patients (20 MCTC/mm2) differed little from those in either of the control groups (both 12 MCTC/mm2). In several other conditions, the MCT cells have been linked with inflammatory events, but it seems that in OA, other factors may be operating to induce a selective expansion of this subpopulation.
The amino acid sequence of a crystal protein from Bacillus thuringiensis deduced from the DNA base sequence. (1985)

We have determined the nucleotide sequence of a 4222-base segment of DNA which contains the promoter, the coding region, and the terminator of a crystal protein gene cloned from a Bacillus thuringiensis plasmid. A sequence of 1176 amino acids encoding a Mr 133,500 peptide was deduced from the single open reading frame. This protein-coding region was analyzed for codon usage, predicted hydropathy, and predicted secondary structure. Examination of the base sequence revealed the presence of several inverted and direct repeats located in both the coding and noncoding regions. S1 nuclease mapping was used to locate the transcription termination point at a site following a potentially very stable stem-and-loop structure.
Human and guinea pig immune responses to Legionella pneumophila protein antigens OmpS and Hsp60 (1994)

We studied the immune responses of guinea pigs and humans to two Legionella pneumophila antigens. Guinea pigs surviving a lethal intraperitoneal challenge dose of virulent L. pneumophila exhibited strong cutaneous delayed-type hypersensitivity (DTH) reactions to purified OmpS (28-kDa major outer membrane protein) and Hsp60 (heat shock protein or common antigen), while weak DTH reactions were noted for extracellular protease (major secretory protein [MSP] [ProA]) and no reaction was observed with an ovalbumin (OA) control. Lymphocyte proliferation responses (LPRs) were measured for peripheral blood and spleen lymphocytes from guinea pigs surviving sublethal and lethal challenge doses of L. pneumophila. Lymphocytes from uninfected animals showed no proliferation to Hsp60 or OmpS, while lymphocytes from sublethally and lethally challenged animals exhibited strong proliferative responses to Hsp60 and OmpS. Guinea pigs vaccinated with purified OmpS exhibited low antibody titers and strong DTH and LPRs to OmpS, whereas lymphocytes from animals vaccinated with Hsp60 exhibited weak DTH responses and high antibody titers to Hsp60. All guinea pigs immunized with OmpS survived experimental challenge with L. pneumophila (two of two in a pilot study and seven of seven in trial 2) versus zero of seven OA-immunized controls (P = 0.006 by Fisher's exact test). In three vaccine trials in which animals were vaccinated with Hsp60, only 1 guinea pig of 15 survived lethal challenge. Peripheral blood lymphocytes (PBLs) from humans with legionellosis showed stronger LPRs to OmpS than PBLs from humans with no history of legionellosis (P = 0.0002 by Mann-Whitney test). PBLs of humans surviving legionellosis exhibited a lower but highly significant proliferative response to Hsp60 (P < 0.0001 compared with controls by Mann-Whitney test). These studies indicate that OmpS and Hsp60 are important antigens associated with the development of protective cellular immunity. However, as determined in vaccine trial studies in the guinea pig model for legionellosis, the species-specific antigen OmpS proved much more effective than the genus-common Hsp60 antigen.
The Plastidic Pentose Phosphate Translocator Represents a Link between the Cytosolic and the Plastidic Pentose Phosphate Pathways in Plants (2002)

Plastids are the site of the reductive and the oxidative pentose phosphate pathways, which both generate pentose phosphates as intermediates. A plastidic transporter from Arabidopsis has been identified that is able to transport, in exchange with inorganic phosphate or triose phosphates, xylulose 5-phosphate (Xul-5-P) and, to a lesser extent, also ribulose 5-phosphate, but does not accept ribose 5-phosphate or hexose phosphates as substrates. Under physiological conditions, Xul-5-P would be the preferred substrate. Therefore, the translocator was named Xul-5-P/phosphate translocator (XPT). The XPT shares only approximately 35% to 40% sequence identity with members of both the triose phosphate translocator and the phosphoenolpyruvate/phosphate translocator classes, but a higher identity of approximately 50% to glucose 6-phosphate/phosphate translocators. Therefore, it represents a fourth group of plastidic phosphate translocators. Database analysis revealed that plant cells contain, in addition to enzymes of the oxidative branch of the oxidative pentose phosphate pathway, ribose 5-phosphate isomerase and ribulose 5-phosphate epimerase in both the cytosol and the plastids, whereas the transketolase and transaldolase converting the produced pentose phosphates to triose phosphates and hexose phosphates are probably solely confined to plastids. It is assumed that the XPT function is to provide the plastidic pentose phosphate pathways with cytosolic carbon skeletons in the form of Xul-5-P, especially under conditions of a high demand for intermediates of the cycles.
NCAM polysialic acid can regulate both cell-cell and cell-substrate interactions. (1991)

We have proposed previously that the polysialic acid (PSA) moiety of NCAM can influence membrane-membrane apposition, and thereby serve as a selective regulator of a variety of contact-dependent cell interactions. In this study, cell and tissue culture models are used to obtain direct evidence that the presence of PSA on the surface membrane can affect both cell-cell and cell-substrate interactions. Using a neuroblastoma/sensory neuron cell hybrid, it was found that removal of PSA with a specific neuraminidase (endo-N) augments cell-cell aggregation mediated by the L1 cell adhesion molecule as well as cell attachment to a variety of tissue culture substrates. In studies of embryonic spinal cord axon bundling, which involves both cell-cell and cell-substrate interactions, the pronounced defasciculation produced by removal of PSA is most easily explained by an increase in cell-substrate interaction. The fact that in both studies NCAM's intrinsic adhesion function was found not to be an important variable further illustrates that regulation of the cell surface by PSA can extend beyond binding mediated by the NCAM polypeptide.
Discourses, actors and instruments in international forest governance (2010)

Politics are not only about interests and institutions but discourses as well. Discourses are (dominant) ideas, concepts and categorisations in a society that give meaning to reality and that shape the identities, interests and preferences of individuals and groups. The assumption of this chapter is that forest discourses are constitutive to global forest politics. Three forest-related types of discourses are distinguished: meta discourses that relate to global economics, politics and culture; regulatory discourses that deal with the regulation and instrumentation of policy issues; and forest discourses that shape forest issues and policies in specific ways. On the basis of a scientific literature review, the main discourses within these three categories (meta, regulatory and forest discourses) as well as three regional forest discourses (Africa, Asia and Latin-America) are analysed. This analysis leads to a number of policy messages: (1) policy makers should try to understand and embrace discursive complexity (instead of artificially reducing it); (2) awareness of this discursive complexity improves global forest negotiations; (3) orchestrated collective action might lead to discursive change; and (4) there is a need for new, open, discursive arenas to improve global forest policymaking. (Less)
Frequency of Tau Gene Mutations in Familial and Sporadic Cases of Non-Alzheimer Dementia (2001)

We conclude that tau mutations are uncommon in a neurology referral population with non-Alzheimer dementia, even in those with a clinical diagnosis of FTD. However, a positive family history and/or tau pathologic findings increase the likelihood of a tau mutation. There must be other genetic and nongenetic causes of FTD and non-Alzheimer dementia, similar to the etiologic heterogeneity present in Alzheimer disease.
Reproducibility of Impedance Cardiography Hemodynamic Measures in Clinically Stable Heart Failure Patients (2000)

BACKGROUND AND AIMS. One of the greatest challenges confronting physicians who are managing the care of patients with heart failure is to acquire objective data that signals treatment effectiveness and/or disease progression. The aim of this study was twofold: 1) to determine the extent to which (real time) impedance cardiography measurements obtained with a specific medical device (the BioZ) were reproducible in outpatients with clinically stable heart failure; and 2) to establish "normal" ranges of one week hemodynamic variability in this population of patients. Information of this nature would help clinical cardiologists and primary care practitioners to evaluate the implications of their patient's visit-to-visit hemodynamic variability. METHODS. A one group, prospective, time series design was used. The sample consisted of 62 patients who had clinically stable heart failure and who were being treated in an outpatient heart failure clinic at a university medical center. BioZ hemodynamic measures of cardiac output, contractility, and after load were obtained at five points in time: two, 10, and 60 minutes resting following a 40-50 foot walk on the first day and at two and 10 minutes resting following a 40-50 foot walk on the second day, one week later. RESULTS. Small but significant changes in cardiac output and cardiac index (mainly due to changes in heart rate) were seen during the 60-minute period on week one. Stroke index did not change during this period. In general, reproducibility between measurements taken on the same day and between days was quite good. Establishment of 95% confidence intervals helped define boundaries of variability in this population. Further clinical evaluation of the four patients whose values exceeded the 95% confidence intervals revealed unexpected, potentially relevant changes that could have accounted for their interday variability. Conclusion. The BioZ impedance cardiography measurements are responsive to hemodynamic activity-rest changes and are reproducible at a one week interval in clinically stable heart failure patients being treated in an outpatient clinic. Stroke index is a better measure of patient status than cardiac output or cardiac index. (c)2000 by CHF, Inc.
Therapy for colon carcinoma xenografts with bispecific antibody‐targeted, iodine‐131‐labeled bivalent hapten (1997)

BACKGROUND One of the main limitations of radioimmunotherapy (RIT) is the secondary toxicity related to the poor therapeutic indices achieved with labeled whole immunoglobulin (Ig)G or F(ab')2 fragments. To overcome this problem, we have developed a two-step targeting method, which we refer to as the Affinity Enhancement System (AES), using a radiolabeled bivalent hapten and a bispecific antibody recognizing the hapten and a target cell antigen. This method has been applied successfully to immunoscintigraphy in carcinoembryonic antigen (CEA)-expressing carcinoma patients and increased tumor to normal tissue uptake ratios have been achieved. The aim of the current study was to evaluate the application of AES to RIT of CEA-expressing solid tumors in an animal model. METHODS Nude mice grafted with LS174T human colorectal carcinoma were treated either with 111 megabecquerels (MBq) of iodine-131 labeled bivalent diethylenetriamine pentaacetic acid (DTPA) hapten 20 hours after pretargeting by anti-CEA × anti-DTPA-indium bispecific antibody or 12 MBq of iodine-131 labeled anti-CEA IgG. RESULTS Treatment with the IgG induced only a growth delay of 53 ± 5 days but all tumors progressed. Treatment with the AES was highly efficient because tumor growth inhibition was achieved over 150 days. Hematologic and overall toxicity of both treatments were equivalent. CONCLUSIONS The long term tumor regression consecutive to AES RIT represents a very significant improvement over the use of directly labeled IgG. Toxicity consecutive to AES or IgG RIT were similar despite an administered activity nearly ten times higher with the AES. However, given the efficacy of the AES treatment, a lower dose may afford lower toxicity and significant antitumor effect. Cancer 1997; 80:2618-23. © 1997 American Cancer Society.
SnO2/graphene composite with high lithium storage capability for lithium rechargeable batteries (2010)

SnO2/graphene nanocomposites have been fabricated by a simple chemical method. In the fabrication process, the control of surface charge causes echinoid-like SnO2 nanoparticles to be formed and uniformly decorated on the graphene. The electrostatic attraction between a graphene nanosheet (GNS) and the echinoid-like SnO2 particles under controlled pH creates a unique nanostructure in which extremely small SnO2 particles are uniformly dispersed on the GNS. The SnO2/graphene nanocomposite has been shown to perform as a high capacity anode with good cycling behavior in lithium rechargeable batteries. The anode retained a reversible capacity of 634 mA·h·g−1 with a coulombic efficiency of 98% after 50 cycles. The high reversibility can be attributed to the mechanical buffering by the GNS against the large volume change of SnO2 during delithiation/lithiation reactions. Furthermore, the power capability is significantly enhanced due to the nanostructure, which enables facile electron transport through the GNS and fast delithiation/lithiation reactions within the echinoid-like nano-SnO2. The route suggested here for the fabrication of SnO2/graphene hybrid materials is a simple economical route for the preparation of other graphene-based hybrid materials which can be employed in many different fields.
Epigenetic Natural Variation in Arabidopsis thaliana (2007)

Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ecotypes, Columbia and Landsberg erecta. We also used comparative genome hybridization to profile copy number polymorphisms. Repeated sequences and transposable elements (TEs), especially long terminal repeat retrotransposons, are densely methylated, but one third of genes also have low but detectable methylation in their transcribed regions. While TEs are almost always methylated, genic methylation is highly polymorphic, with half of all methylated genes being methylated in only one of the two ecotypes. A survey of loci in 96 Arabidopsis accessions revealed a similar degree of methylation polymorphism. Within-gene methylation is heritable, but is lost at a high frequency in segregating F(2) families. Promoter methylation is rare, and gene expression is not generally affected by differences in DNA methylation. Small interfering RNA are preferentially associated with methylated TEs, but not with methylated genes, indicating that most genic methylation is not guided by small interfering RNA. This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means.