gebhart/patrepeval huggingface dataset:
Tumor-Activated Monocytes Promote Expansion of IL-17–Producing CD8+ T Cells in Hepatocellular Carcinoma Patients (2010)

The proinflammatory IL-17-producing CD8(+) T cells (Tc17 cells) have recently been detected in tumors, but the nature and regulation of these cells in human tumors are presently unknown. We have recently found that IL-17(+) cells are accumulated in human hepatocellular carcinomas (HCC), where they promote disease progression by fostering angiogenesis. In this study, we showed that Tc17 cells constitute a remarkable portion of IL-17-producing cells in human HCC. Although most circulating Tc17 cells were negative for IFN-gamma, >80% of Tc17 cells in HCC tissues were positive for IFN-gamma, and they were enriched predominantly in invading tumor edge. Most CD68(+) cells located in invading tumor edge exhibited an activated phenotype and, accordingly, the activated monocytes isolated from HCC tissues were significantly superior to those isolated from nontumor tissues in inducing expansion of Tc17 cells in vitro with phenotypic features similar to those isolated from tumors. Compared with IL-17(-)IFN-gamma(+)CD8(+) cells, these IFN-gamma(+)Tc17 cells have significantly higher expression of proinflammatory cytokines (IL-2, IL-22, and TNF-alpha), but reduced expression of granzyme B and perforin. Moreover, we found that tumor-activated monocytes secreted a set of key cytokines (IL-1beta, IL-6, and IL-23) to trigger the proliferation of Tc17 cells. These data reveal an intriguing mechanism in which human Tc17 cells are generated by a fine-tuned collaborative action between different types of immune cells in distinct tumor microenvironments.
Diagnostic Accuracy of Fractional Flow Reserve From Anatomic CT Angiography (2012)

Although the study did not achieve its prespecified primary outcome goal for the level of per-patient diagnostic accuracy, use of noninvasive FFR(CT) plus CT among stable patients with suspected or known CAD was associated with improved diagnostic accuracy and discrimination vs CT alone for the diagnosis of hemodynamically significant CAD when FFR determined at the time of ICA was the reference standard.
Regulation of Vascular Endothelial Growth Factor Receptor KDR in vitro by a Soluble Factor in Confluent Endothelial Cells (1998)

Hypoxia regulates the expression of both vascular endothelial growth factor (VEGF) and its receptor (KDR). We have shown that cell density regulates VEGF expression in colon cancer and hypothesized that a similar mechanism regulates KDR in endothelial cells. Human umbilical vein endothelial cells were grown as sparse and confluent monolayers. Northern blot analysis revealed that KDR and VEGF mRNA expression in confluent cells was more than two-fold greater than in sparse cells. In contrast, flt-1 expression increased only slightly in cells grown to confluence. Cells were then plated at various concentrations and subjected to semi-quantitative PCR; KDR mRNA expression increased as cell density increased. Serum-free conditioned medium from cells grown to confluency for 48 h was added to sparsely plated cells, and KDR expression in the sparse cells increased twofold. We conclude that cell density regulates KDR endothelial cell expression via an unidentified soluble factor.
Antigen-Specific T-Cell Response from Dendritic Cell Vaccination Using Cancer Stem-Like Cell-Associated Antigens (2009)

Glioblastoma multiforme (GBM) is the most aggressive primary brain tumor, with current treatment remaining palliative. Immunotherapies harness the body's own immune system to target cancers and could overcome the limitations of conventional treatments. One active immunotherapy strategy uses dendritic cell (DC)-based vaccination to initiate T-cell-mediated antitumor immunity. It has been proposed that cancer stem-like cells (CSCs) may play a key role in cancer initiation, progression, and resistance to current treatments. However, whether using human CSC antigens may improve the antitumor effect of DC vaccination against human cancer is unclear. In this study, we explored the suitability of CSCs as sources of antigens for DC vaccination again human GBM, with the aim of achieving CSC-targeting and enhanced antitumor immunity. We found that CSCs express high levels of tumor-associated antigens as well as major histocompatibility complex molecules. Furthermore, DC vaccination using CSC antigens elicited antigen-specific T-cell responses against CSCs. DC vaccination-induced interferon-gamma production is positively correlated with the number of antigen-specific T cells generated. Finally, using a 9L CSC brain tumor model, we demonstrate that vaccination with DCs loaded with 9L CSCs, but not daughter cells or conventionally cultured 9L cells, induced cytotoxic T lymphocytes (CTLs) against CSCs, and prolonged survival in animals bearing 9L CSC tumors. Understanding how immunization with CSCs generates superior antitumor immunity may accelerate development of CSC-specific immunotherapies and cancer vaccines.
Fast swept volume approximation of complex polyhedral models (2003)

We present an efficient algorithm to approximate the swept volume (SV) of a complex polyhedron along a given trajectory. Given the boundary description of the polyhedron and a path specified as a parametric curve, our algorithm enumerates a superset of the boundary surfaces of SV. It consists of ruled and developable surface primitives, and the SV corresponds to the outer boundary of their arrangement. We approximate this boundary by using a five-stage pipeline. This includes computing a bounded-error approximation of each surface primitive, computing unsigned distance fields on a uniform grid, classifying all grid points using fast marching front propagation, iso-surface reconstruction, and topological refinement. We also present a novel and fast algorithm for computing the signed distance of surface primitives as well as a number of techniques based on surface culling, fast marching level-set methods and rasterization hardware to improve the performance of the overall algorithm. We analyze different sources of error in our approximation algorithm and highlight its performance on complex models composed of thousands of polygons. In practice, it is able to compute a bounded error approximation in tens of seconds for models composed of thousands of polygons sweeping along a complex trajectory.
CD74 is a survival receptor on colon epithelial cells (2010)

CD74 is expressed on CEC and colon carcinoma cells and serves as a survival receptor in these cells. These results may have implications on colorectal cancer research.
REVIEWS (2003)

Hammurabi's Laws. Text, translation and glossary M.E.J.Richardson . Sheffield Academic Press, Sheffield , 2000. Pp. 423 Price: £56.00 . ISBN: 1-84127-030-X.
A distributed architecture for activating the peripheral nervous system (2009)

We present a new system for functional electrical stimulation (FES) applications based on networked stimulation units. They embed an advanced analog circuit, which provides multipolar and multiphasic stimulation profiles, and digital circuits, which ensure safety, locally executed programmed profiles, and communication with the master controller. This architecture is thus based on distributed stimulation units (DSU) that need only a two-wire bus to communicate, regardless of the number of poles of each DSU-driven electrode. This structure minimizes the required bandwidth between master and distributed units, increases the safety and stimulation features and decreases the complexity of the surgical approach. We have successfully tested this network-based stimulation architecture on benchtop stimulators. This original approach allows broad exploration of all possible methods to stimulate peripheral nerves, particularly in the goal of restoring the motor function. It provides a powerful research device to determine the optimal, least aggressive and the most efficient way to activate the peripheral nervous system using an implanted FES system that is less invasive than other existing devices.
Neonatal Pulmonary Hypertension (2001)

Infants with persistent pulmonary hypertension have low plasma concentrations of arginine and nitric oxide metabolites. The simultaneous presence of diminished concentrations of precursors and breakdown products suggests that inadequate production of nitric oxide is involved in the pathogenesis of neonatal pulmonary hypertension. Our preliminary observations suggest that the genetically predetermined capacity of the urea cycle--in particular, the efficiency of carbamoyl-phosphate synthetase--may contribute to the availability of precursors for nitric oxide synthesis.
Multicomponent Seismic Technology (2011)

A principle that is emphasized throughout this book is that the physics of any multicomponent seismic technology cannot be understood unless that technology is viewed in terms of the particle-displacement vectors associated with the various modes of a seismic wavefield. This material therefore begins with a discussion of seismic vector-wavefield behavior to set the stage for subsequent chapters.

Several approaches can be used to explain why each wave mode of nine-component (9C) and three-component (3C) seismic data that propagates through subsurface geology provides a different amount and type of rock/fluid information about the geology that the wave modes illuminate. Some approaches appeal to people who have limited interest in mathematics. Other options need to be structured for people who have an appreciation of the mathematics of wavefield reflectivity. Another argument that can be used focuses on the fundamental differences in P-wave and S-wave radiation patterns and the distinctions in target illuminations associated with 9C and 3C seismic sources. We will consider all of those paths of logic.

A principle that will be stressed is that each mode of a multicomponent seismic wavefield senses a different earth fabric along its propagation path because its particle-displacement vector is oriented in a different direction than are the particle-displacement vectors of its companion modes. Although estimations of earth fabric obtained from various modes of a multicomponent seismic wavefield can differ, each estimate still can be correct because each wave mode deforms a unit volume of rock in a different direction, depending on the orientation of its particle-displacement vector. Those deformations sense a different earth resistance in directions parallel to and normal to various symmetry planes in real-earth media. The logic of that nonmathematical approach appeals to people who are interested in the geologic and petrophysical information that multicomponent seismic data can provide and are less concerned about theory and mathematics.

A second approach that is helpful for distinguishing one-component (1C), 3C, and 9C wavefield behavior focuses on the mathematics of the reflectivity equation associated with each mode of the full-elastic seismic wavefield. The mathematical structure of the reflectivity equation associated with each seismic wave mode describes why and how petrophysical properties of the propagation medium affect different wave modes in different ways. The logic of that analytical approach is appreciated by scientists who are comfortable with mathematics.

All of these concepts lead to the development of a new seismic-interpretation science based on multicomponent seismic data called elastic wavefield seismic stratigraphy.
Cloning and expression of the Bacillus thuringiensis crystal protein gene in Escherichia coli. (1981)

Sau 3A1 partial digestion fragments from Bacillus thuringiensis var. kurstaki HD-1 plasmid DNA were ligated into the BamHI site of the cloning vector pBR322 and transformed into Escherichia coli strain HB101. Colonies presumed to contain recombinant plasmids were screened for production of an antigen that would react with antibody made against B. thuringiensis crystals. One strain, ES12, was isolated by using this procedure. ES12 contains a plasmid of Mr 11 X 10(6) that has DNA sequence homology with pBR322 as well as with Mr 30 X 10(6) and Mr 47 X 10(6) plasmids of B. thuringiensis. It makes a protein antigen, detected by antibodies to crystal, which has the same electrophoretic mobility as the B. thuringiensis crystal protein. Protein extracts of ES12 are toxic to larvae of the tobacco hornworm Manduca sexta.
Does Perioperative Myocardial Ischemia Lead to Postoperative Myocardial Infarction? (1985)

To determine if a relationship exists between perioperative myocardial ischemia (ST segment depression greater than or equal to 0.1 mV) and postoperative myocardial infarction (PMI), nonparticipating observers recorded all ECG, hemodynamic, and other events between arrival of patients in the operating room and onset of cardiopulmonary bypass during 1,023 elective coronary artery bypass operations (CABG). The roles of preoperative patient characteristics, quality of the operation limited by disease as rated by the surgeon and duration of ischemic cardiac arrest as risk factors for PMI also were quantified. ECG ischemia occurred in 36.9% of all patients, with almost half the episodes occurring before induction of anesthesia. PMI was almost three times as frequent in patients with ischemia (6.9% vs. 2.5%) and was independent of when ischemia occurred. Ischemia was related significantly to tachycardia but not hypertension nor hypotension and was frequent in the absence of any hemodynamic abnormalities. The anesthesiologist whose patients had the highest rate of tachycardia and ischemia had the highest rate of PMI. Although neither single nor multiple preoperative patient characteristics related to PMI, suboptimal quality of operation and prolonged ischemic cardiac arrest increased the likelihood of PMI independent of the occurrence of myocardial ischemia. The authors conclude that perioperative myocardial ischemia is common in patients undergoing CABG, occurs randomly as well as in response to hemodynamic abnormalities, and is one of three independent risk factors the authors identified as related to PMI. PMI is unrelated to preoperative patient characteristics such as ejection fraction and left main coronary artery disease, and its frequency will relate primarily to perioperative management rather than patient selection.
Ceritinib in ALK -Rearranged Non–Small-Cell Lung Cancer (2014)

Ceritinib was highly active in patients with advanced, ALK-rearranged NSCLC, including those who had had disease progression during crizotinib treatment, regardless of the presence of resistance mutations in ALK. (Funded by Novartis Pharmaceuticals and others; ClinicalTrials.gov number, NCT01283516.).
Use of Monoclonal Antibodies in Renal Transplantation (2011)

Monoclonal antibodies are applied in various settings in renal transplantation. Depleting T-cell antibodies are used for treatment of steroid-resistant acute rejection and as induction therapy to reduce the intensity of concomitant immunosuppressive drug therapy. Induction therapy with the nondepleting IL-2 receptor antagonists basiliximab and daclizumab, added to cyclosporine-based regimens, reduces the incidence of acute rejection without side effects. However, an increase in long-term graft and patient survival has not been demonstrated yet. The B-cell-targeting antibody rituximab is used in blood group ABO-incompatible transplantation, in desensitization protocols, and for treatment of antibody-mediated rejection. Eculizumab interrupts the complement pathway and is a promising tool for the treatment of antibody-mediated rejection and post-transplant hemolytic-uremic syndrome. Future options are monoclonal antibodies with new molecular targets and antibodies that can be used for maintenance immunosuppression in order to avoid the toxicity of existing drugs. However, in several cases, the development of new monoclonal antibodies has been hampered by safety issues.
A new approach to optimal nonlinear filtering (2002)

The classical approach to designing filters for systems where system equations are linear and measurement equations are nonlinear is to linearise measurement equations, and apply an extended Kalman filter (EKF). This results in suboptimal, biased, and often divergent filters. Many schemes proposed to improve the performance of the EKF concentrated on better linearisation techniques, iterative techniques and adaptive schemes. The improvements achieved were marginal and often reduced the bias and divergence problems but were far from optimal unbiased estimators. In this paper, we present a new approach to optimal nonlinear filtering in linear systems-nonlinear measurements case. It is based on approximation of evolved probability density functions using quasi-moments followed by numerical evaluation of Bayes' conditional density equation.
Acute blood flow changes and efficacy of vagus nerve stimulation in partial epilepsy (1999)

Increased thalamic synaptic activities probably mediate some antiseizure effects of VNS. Future studies should examine neurotransmitter-receptor alterations in reticular and specific thalamic nuclei during VNS.
Identification of a gene for aerobic growth with a SoxS binding sequence in Escherichia coli by operon fusion techniques (2001)

Eight Escherichia coli cells with aerobic growth defects were isolated by the insertion of λplacMu53, a hybrid bacteriophage of λ and Mu, which created transcriptional fusion to lacZY Two of these mutants, CL10 and CL12, were irradiated with UV to obtain specialized transducing phages. The phages that took out the neighboring chromosomal DNA of the related gene responsible for defective aerobic growth were identified. The in vivo cloned chromosomal sequence revealed that the mutated gene of CL10 was located at min 34.5 on the Escherichia coli linkage map and 1,599,515 on the physical map. The physical map indicated that there were 7 cistrons in the operon. We named this operon oxg10. The promoter sequence of oxgl0 exhibited a possible binding site for SoxS, a transcriptional regulator that activates the transcription of various SoxRS regulon genes. Transferring the oxg10::λplacMu53 mutation into the wild-type strain, RZ4500, resulted in the inhibition of normal aerobic growth, while the same mutation in strain MO inhibited aerobic cell growth completely. The full operon sequences of oxg10 were cloned from the Escherichia coli genomic library. The mutated gene of CL12 was identified to be a sucA gene encoding the α-ketoglutarate dehydrogenase E1 component in the TCA cycle.
Synthesis and Antifeedant Activity of New Oxadiazolyl 3(2H)-Pyridazinones (2002)

A total of 20 new compounds containing the oxadiazolyl 3(2H)-pyridazinone moiety were synthesized. The structures of all the compounds were confirmed by (1)H NMR, IR, MS, and elemental analysis. Their insect antifeedant activities against Asiatic corn borer Ostrinia furnacalis (Guenee) were examined and compared with commercial azadirachtin. The compounds exhibited significant levels of activity. The feeding deterrency values of IIIa,j were 57% and 51% at 500 mg/kg concentration, respectively.
Characterization and Differentiation of Human Embryonic Stem Cells (2003)

Cell replacement therapies have been limited by the availability of sufficient quantities of cells for transplantation. Human ES (hES) cell lines have recently been generated by several laboratories. When maintained for over 1 year in vitro, they remain karyotypically and phenotypically stable and may therefore provide an excellent source material for cell therapies. Currently, data is available for 26 hES cell lines. Although limited characterization has been performed on most of these lines, there are remarkable similarities in expression of markers. hES cell lines derived in different laboratories show similar expression profiles of surface markers, including SSEA-4, Tra-1-60, and Tra-1-81. In addition, markers associated with pluripotent cells such as OCT-4 are expressed at in all cell lines tested. These cells express high levels of telomerase and appear to have indefinite growth potential. The generation of the large quantities of cells necessary for cell replacement therapies will require a cell population which is stable over long term culture. We have characterized the properties of multiple hES cell lines that have been maintained in culture for extended periods. Quantitative analyses demonstrate that all of the cell lines examined show consistent marker expression and retain a normal karyotype after long-term culture. hES cells have been differentiated into the derivatives of all three germ layers. Specifically this includes cardiomyocytes, neural cells, hepatocyte-like cells, endothelial cells and hematopoietic progenitor cells. These data demonstrating the karyotypic and phenotypic stability of hES cells and their extensive differentiative capacity indicate that they may be an appropriate source of cells for multiple regenerative medicine applications.
Pathogenesis of chronic hepatitis C: Immunological features of hepatic injury and viral persistence (1999)

The immune response to viral antigens is thought to be responsible for viral clearance and disease pathogenesis during hepatitis C virus (HCV) infection. In chronically infected patients, the T-cell response to the HCV is polyclonal and multispecific, although it is not as strong as the response in acutely infected patients who display a more vigorous T-cell response. Importantly, viral clearance in acutely infected patients is associated with a strong CD4(+) helper T-cell response. Thus, the dominant cause of viral persistence during HCV infection may be the development of a weak antiviral immune response to the viral antigens, with corresponding inability to eradicate infected cells. Alternatively, if clearance of HCV from the liver results from the antiviral effect of T-cell-derived cytokines, as has been demonstrated recently for the hepatitis B virus, chronic HCV infection could occur if HCV is not sensitive to such cytokines or if insufficient quantities of cytokines are produced. Liver cell damage may extend from virally infected to uninfected cells via soluble cytotoxic mediators and recruitment and activation of inflammatory cells forming the necroinflammatory response. Additional factors that could contribute to viral persistence are viral inhibition of antigen processing or presentation, modulation of the response to cytotoxic mediators, immunological tolerance to HCV antigens, mutational inactivation of cytotoxic T lymphocyte (CTL) epitopes, mutational conversion of CTL epitopes into CTL antagonists, and infection of immunologically privileged tissues. Analysis of the basis for viral persistence is hampered because the necessary cell culture system and animal model to study this question do not yet exist.