gebhart/patrepeval huggingface dataset:
Immune Escape for Renal Cell Carcinoma: CD70 Mediates Apoptosis in Lymphocytes (2006)

Tumors can escape immune recognition and destruction through the induction of apoptosis in lymphocytes. Although renal cell carcinoma (RCC) is able to prevent immune recognition, only a few genes (such as FasL) that are relevant for RCC immune escape have been identified so far. We have previously shown that some apoptosis-inducing genes are overexpressed in RCC. We hypothesized that these genes could be part of the immune-escape strategy of these tumors. Here we report that CD70, a cytokine overexpressed in RCC, promotes lymphocyte apoptosis through interaction with its receptor CD27 and with the intracellular receptor-binding protein SIVA. Apoptosis increased after cocultivating lymphocytes with the RCC cell lines A498 and CAKI2. The addition of recombinant soluble CD70 to both native lymphocytes and a T-cell cell line resulted in increased lymphocyte apoptosis as well. Furthermore, induced apoptosis could be partially blocked with anti-CD27 and anti-CD70 antibodies. Our results strongly indicate a role for CD70 and CD27 receptor in lymphocyte apoptosis within the tumor environment. Apoptosis mediated by exposure to the CD70 secreted by tumor cells may contribute to the failure of RCC patients to develop an effective lymphocyte-mediated antitumor response.
Psilocybin produces substantial and sustained decreases in depression and anxiety in patients with life-threatening cancer: A randomized double-blind trial (2016)

ClinicalTrials.gov identifier: NCT00465595.
My Responsibilities as a Twentieth-CenturyAmerican (1955)

Non-fiction by Tom Willey
Oil accumulation in leaves directed by modification of fatty acid breakdown and lipid synthesis pathways (2009)

Plant oils in the form of triacylglycerol (TAG) are used for food, industrial feedstock and biofuel manufacture. Although TAG is typically harvested from the fruit or seeds of oil crop species, plants can also accumulate small amounts of TAG in the leaves and other vegetative tissues. Here we show that leaf TAG levels can be increased significantly (10-20 fold) by blocking fatty acid breakdown, particularly during extended dark treatments or leaf senescence in the model plant Arabidopsis. Generation of a double mutant in fatty acid breakdown and diacylglycerol acyltransferase 1 (DGAT1) resulted in a severe vegetative growth phenotype suggesting that partitioning of fatty acids to TAG in leaves is carried out predominantly by this acyltransferase. LEC2, a seed development transcription factor involved in storage product accumulation, was ectopically expressed during senescence in the fatty acid breakdown mutant COMATOSE (cts2). This resulted in accumulation of seed oil type species of TAG in senescing tissue. Our data suggests that recycled membrane fatty acids can be re-directed to TAG by expressing the seed-programme in senescing tissue or by a block in fatty acid breakdown. This work raises the possibility of producing significant amounts of oil in vegetative tissues of biomass crops such as Miscanthus.
Cancellation of SPM in self-homodyne coherent systems (2009)

The signal and local oscillator acquire identical nonlinear phase shifts during propagation in a selfhomodyne\ncoherent system. We exploit this to achieve cancellation of the phase distortion caused by self-phase\nmodulation.
Early versus Later Rhythm Analysis in Patients with Out-of-Hospital Cardiac Arrest (2011)

Among patients who had an out-of-hospital cardiac arrest, we found no difference in the outcomes with a brief period, as compared with a longer period, of EMS-administered CPR before the first analysis of cardiac rhythm. (Funded by the National Heart, Lung, and Blood Institute and others; ROC PRIMED ClinicalTrials.gov number, NCT00394706.).
TGFβ2 knockout mice have multiple developmental defects that are non-overlapping with other TGFβ knockout phenotypes (1997)

The growth and differentiation factor transforming growth factor-beta2 (TGFbeta2) is thought to play important roles in multiple developmental processes. Targeted disruption of the TGFbeta2 gene was undertaken to determine its essential role in vivo. TGFbeta2-null mice exhibit perinatal mortality and a wide range of developmental defects for a single gene disruption. These include cardiac, lung, craniofacial, limb, spinal column, eye, inner ear and urogenital defects. The developmental processes most commonly involved in the affected tissues include epithelial-mesenchymal interactions, cell growth, extracellular matrix production and tissue remodeling. In addition, many affected tissues have neural crest-derived components and simulate neural crest deficiencies. There is no phenotypic overlap with TGFbeta1- and TGFbeta3-null mice indicating numerous non-compensated functions between the TGFbeta isoforms.
Fast window correlations over uncooperative time series (2005)

Data arriving in time order (a data stream) arises in fields including physics, finance, medicine, and music, to name a few. Often the data comes from sensors (in physics and medicine for example) whose data rates continue to improve dramatically as sensor technology improves. Further, the number of sensors is increasing, so correlating data between sensors becomes ever more critical in order to distill knowlege from the data. In many applications such as finance, recent correlations are of far more interest than long-term correlation, so correlation over sliding windows (windowed correlation) is the desired operation. Fast response is desirable in many applications (e.g., to aim a telescope at an activity of interest or to perform a stock trade). These three factors -- data size, windowed correlation, and fast response -- motivate this work.Previous work [10, 14] showed how to compute Pearson correlation using Fast Fourier Transforms and Wavelet transforms, but such techniques don't work for time series in which the energy is spread over many frequency components, thus resembling white noise. For such "uncooperative" time series, this paper shows how to combine several simple techniques -- sketches (random projections), convolution, structured random vectors, grid structures, and combinatorial design -- to achieve high performance windowed Pearson correlation over a variety of data sets.
Compatibility of Lithium Ion Conductive Sulfide Glass with Carbon-Lithium Electrode (2003)

Electrochemical properties of graphite were investigated using -based glass or -based glass as a solid electrolyte. Graphite showed reversible electrode reactions in the -based glass, while it did not in the -based one. The results of X-ray diffractometry and Raman spectroscopy indicated that the -based glass was reduced as side reactions instead of the intercalation of lithium ions into graphite during the reduction, resulting in the poor reversibility. © 2003 The Electrochemical Society. All rights reserved.
Relationship Between Intracellular Calcium and Contractile Force in Stunned Myocardium (1995)

To elucidate the abnormalities of excitation-contraction coupling in stunned myocardium, we measured [Ca2+]i and force in thin fura 2-loaded ventricular trabeculae from control or stunned (20 minutes ischemia followed by 20 minutes reflow at 37 degrees C) rat hearts. At any given [Ca2+]o, force development was significantly lower in the stunned trabeculae than in control trabeculae. In contrast, there was no difference in the amplitude of Ca2+ transients between the two groups. The steady state force-[Ca2+]i relationship, assessed by tetanization in the presence of ryanodine, revealed both a decrease in maximal Ca(2+)-activated force and an increase in the [Ca2+]i required for 50% activation in stunned trabeculae. Postischemic myocardium also exhibited an accelerated rate of diastolic relaxation that was not due to changes in the rate of Ca2+ transient decay. Destabilization of attached cross-bridges in a quantitative model of cardiac myofibrils accurately reproduced the salient systolic and diastolic features of the stunned phenotype, suggesting an abnormality of the thin filaments. In response to supraphysiological increases in [Ca2+]o, diastolic [Ca2+]i and diastolic tone increased much more in stunned trabeculae than in controls, with the frequent occurrence of aftercontractions. This novel experimental model lends further support to the hypothesis that the primary lesion of excitation-contraction coupling resides at the level of the contractile proteins. The finding of enhanced susceptibility to calcium overload helps to rationalize the functional deterioration of stunned myocardium during intense inotropic stimulation and additionally suggests that stunned myocardium may represent a favorable substrate for triggered arrhythmias.
Pre- and Postexposure Prophylaxis of Ebola Virus Infection in an Animal Model by Passive Transfer of a Neutralizing Human Antibody (2002)

ABSTRACT A neutralizing human monoclonal antibody, KZ52, protects guinea pigs from lethal Ebola Zaire virus challenge. Administration before or up to 1 h after challenge resulted in dose-dependent protection by the antibody. Interestingly, some antibody-treated animals survived despite developing high-level viremia, suggesting that the mechanism of protection by KZ52 may extend beyond reduction of viremia by virus neutralization. KZ52 is a promising candidate for immunoprophylaxis of Ebola virus infection.
Ultra-compact, low RF power, 10 Gb/s silicon Mach-Zehnder modulator (2007)

Silicon p(+)-i-n(+) diode Mach-Zehnder electrooptic modulators having an ultra-compact length of 100 to 200 mum are presented. These devices exhibit high modulation efficiency, with a V(pi)L figure of merit of 0.36 V-mm. Optical modulation at data rates up to 10 Gb/s is demonstrated with low RF power consumption of only 5 pJ/bit.
Control of Ethylene Synthesis by Expression of a Bacterial Enzyme in Transgenic Tomato Plants (1991)

Harry J. Klee, Maria B. Hayford, Keith A. Kretzmer, Gerard F. Barry, Ganesh M. Kishore, Control of Ethylene Synthesis by Expression of a Bacterial Enzyme in Transgenic Tomato Plants, The Plant Cell, Vol. 3, No. 11 (Nov., 1991), pp. 1187-1193
Epitope and isotype specificities of antibodies to β-amyloid peptide for protection against Alzheimer's disease-like neuropathology (2003)

Transgenic PDAPP mice, which express a disease-linked isoform of the human amyloid precursor protein, exhibit CNS pathology that is similar to Alzheimer's disease. In an age-dependent fashion, the mice develop plaques containing beta-amyloid peptide (Abeta) and exhibit neuronal dystrophy and synaptic loss. It has been shown in previous studies that pathology can be prevented and even reversed by immunization of the mice with the Abeta peptide. Similar protection could be achieved by passive administration of some but not all monoclonal antibodies against Abeta. In the current studies we sought to define the optimal antibody response for reducing neuropathology. Immune sera with reactivity against different Abeta epitopes and monoclonal antibodies with different isotypes were examined for efficacy both ex vivo and in vivo. The studies showed that: (i) of the purified or elicited antibodies tested, only antibodies against the N-terminal regions of Abeta were able to invoke plaque clearance; (ii) plaque binding correlated with a clearance response and neuronal protection, whereas the ability of antibodies to capture soluble Abeta was not necessarily correlated with efficacy; (iii) the isotype of the antibody dramatically influenced the degree of plaque clearance and neuronal protection; (iv) high affinity of the antibody for Fc receptors on microglial cells seemed more important than high affinity for Abeta itself; and (v) complement activation was not required for plaque clearance. These results indicate that antibody Fc-mediated plaque clearance is a highly efficient and effective process for protection against neuropathology in an animal model of Alzheimer's disease.
Regulation of IL-2 receptor subunit genes in human monocytes. Differential effects of IL-2 and IFN-gamma (1992)

We investigated the effects of IFN-gamma and IL-2 on IL-2R alpha and beta mRNA expression in human monocytes. Low basal expression of IL-2R beta mRNA was detected in fresh monocytes. Stimulation of monocytes with IL-2 induced a significant increase of IL-2R beta mRNA, but did not induce IL-2R alpha mRNA. In contrast, stimulation of monocytes with IFN-gamma-induced IL-2R alpha mRNA, but did not modify IL-2R beta mRNA. Five U/ml of IFN-gamma induced IL-2R alpha mRNA and 2.2 nM of IL-2 induced IL-2R beta mRNA, both within 3 h. Nuclear run-on experiments demonstrated that the induction of IL-2R alpha mRNA by IFN-gamma is controlled, at least in part, at the transcriptional level. In contrast, the enhancement of IL-2R beta mRNA by IL-2 is controlled at a posttranscriptional level and is associated with an increase in the half-life of IL-2R beta mRNA. The results of studies on the cytotoxic activity and on the expression of c-fms mRNA of monocytes activated by the combination of IFN-gamma and IL-2 show that pretreatment with IFN-gamma renders monocytes more sensitive to activation by IL-2. These results demonstrate that the IL-2R alpha and IL-2R beta subunits are induced by different lymphokines through distinct mechanisms and that both receptor subunits can influence the response of monocytes to IL-2.
Different tumors in bone each give rise to a distinct pattern of skeletal destruction, bone cancer‐related pain behaviors and neurochemical changes in the central nervous system (2003)

Pain is the most common presenting symptom in patients with bone cancer and bone cancer pain can be both debilitating and difficult to control fully. To begin to understand the mechanisms involved in the generation and maintenance of bone cancer pain, we implanted 3 well-described murine tumor cell lines, 2472 sarcoma, B16 melanoma and C26 colon adenocarcinoma into the femur of immunocompromised C3H-SCID mice. Although each of the tumor cell lines proliferated and completely filled the intramedullary space of the femur within 3 weeks, the location and extent of bone destruction, the type and severity of the pain behaviors and the neurochemical reorganization of the spinal cord was unique to each tumor cell line injected. These data suggest that bone cancer pain is not caused by a single factor such as increased pressure induced by intramedullary tumor growth, but rather that multiple factors are involved in generating and maintaining bone cancer pain.
The response of pregnant gilts previously given an inactivated preparation of porcine parvovirus (PPV) to challenge infection with a fully virulent PPV. (1992)

Eight 40-day pregnant gilts, previously treated with an adjuvanted-inactivated viral preparation (AIVP) obtained with a field strain of porcine parvovirus (PPV) together with 4 pregnant untreated controls, were subjected to challenge infection with a virulent strain of PPV at the 40th day of gestation. After challenge, all controls became febrile for 2 to 8 days, whereas only one gilt among those which had been treated with the AIVP experienced fever which lasted 4 days. Virus was consistently recovered from fecal swabs obtained from the controls and only sporadically from feces of AIVP-treated gilts. When the gilts were killed 53 days after challenge infection, no macroscopic lesions were found in any of the gilts in either groups, but fetal death was observed in the two groups of animals. However, the rate of dead fetuses was much higher among the control (70.5%) than among those from the AIVP-treated gilts (10.1%). Virus was recovered from 23 of the 24 dead fetuses in the control group and only from 3 among the 8 dead fetuses which were reported for the AIVP-treated gilts.
Semisynthetic Di- and Tri-Functionalized Non-Immunosuppressive Cyclosporin A Derivatives as Potential Anti-HIV 1 Drugs (2004)

A regio- and stereoselective synthesis of original semisynthetic di- and tri-functionalized non-immunosuppressive ­cyclosporins by way of a Barton ester decarboxylation and a C-thioalkylation starting from cyclosporin A (CsA) and [4′-hydroxy-­MeLeu]4-CsA is described.
Tumor-specific lysis of human renal cell carcinomas by tumor-infiltrating lymphocytes. I. HLA-A2-restricted recognition of autologous and allogeneic tumor lines. (1993)

Metastatic renal cell carcinoma (RCC), like melanoma, belongs to the small group of human tumors in which partial or complete remission has been observed in some patients after treatment with various forms of immunotherapy. In contrast to melanoma, CTL showing MHC-restricted lysis of RCC have not been easily found among tumor-infiltrating lymphocytes (TIL). This has led to the suggestion by some that responses to immunotherapy are mediated predominantly by non-MHC-restricted effector cells. We have characterized an MHC-restricted, CD8+ CTL line obtained from an uncloned TIL population of a primary RCC using a low concentration of rIL-2; in fact, these CTL represented a majority of the short-term cultured TIL population. The CTL lysed autologous tumor cells but not normal kidney cells or target cells sensitive to non-MHC-restricted effector cells. In contrast, lymphokine-activated killer (LAK) cells grown in a high concentration of rIL-2 from the patient's PBL lysed autologous tumor and normal kidney cells in addition to several allogeneic tumors. The TIL could be expanded optimally using an autologous tumor line retrovirally transduced with the human cDNA encoding IL-2. TIL were 20-fold more potent than LAK cells in eliminating the IL-2 expressing tumor cells in vitro. The cultured TIL utilized a restricted number of V alpha gene families, suggesting that they may recognize only a limited number of MHC-peptide complexes presented by autologous tumor cells. HLA-A2 was identified as an MHC restriction molecule for presentation of one tumor-derived peptide to these CTL. Only some allogeneic HLA-A2 RCC tumors were lysed. Sequencing of the second and third exons of the HLA-A2 alleles of these cells revealed that both heterogeneity in MHC and peptide availability influenced CTL recognition. These studies demonstrate that some RCC express common antigenic determinants that can be recognized by MHC-restricted CTL and open the possibility of defining the nature of RCC-derived peptides, which, combined with HLA-A2, can generate specific immune responses.
Nuclear Magnetic Resonance: A Noninvasive Approach to Cancer (1977)

Malignant cells differ in chemical composition from normal cells, and nuclear magnetic resonance can detect such differences, thereby offering a new biophysical approach to diagnosis. An instrument that focuses the NMR beam has been developed and has already proved successful in detecting a tumor in a living experimental animal. Other implications of the technique for human cancer are discussed.
Mutagenesis and Functional Characterization of the Four Domains of GlnD, a Bifunctional Nitrogen Sensor Protein (2010)

GlnD is a bifunctional uridylyltransferase/uridylyl-removing enzyme (UTase/UR) and is believed to be the primary sensor of nitrogen status in the cell by sensing the level of glutamine in enteric bacteria. It plays an important role in nitrogen assimilation and metabolism by reversibly regulating the modification of P(II) protein; P(II) in turn regulates a variety of other proteins. GlnD appears to have four distinct domains: an N-terminal nucleotidyltransferase (NT) domain; a central HD domain, named after conserved histidine and aspartate residues; and two C-terminal ACT domains, named after three of the allosterically regulated enzymes in which this domain is found. Here we report the functional analysis of these domains of GlnD from Escherichia coli and Rhodospirillum rubrum. We confirm the assignment of UTase activity to the NT domain and show that the UR activity is a property specifically of the HD domain: substitutions in this domain eliminated UR activity, and a truncated protein lacking the NT domain displayed UR activity. The deletion of C-terminal ACT domains had little effect on UR activity itself but eliminated the ability of glutamine to stimulate that activity, suggesting a role for glutamine sensing by these domains. The deletion of C-terminal ACT domains also dramatically decreased UTase activity under all conditions tested, but some of these effects are due to the competition of UTase activity with unregulated UR activity in these variants.
Single-Cell Gene Expression Profiling (2002)

A key goal of biology is to relate the expression of specific genes to a particular cellular phenotype. However, current assays for gene expression destroy the structural context. By combining advances in computational fluorescence microscopy with multiplex probe design, we devised technology in which the expression of many genes can be visualized simultaneously inside single cells with high spatial and temporal resolution. Analysis of 11 genes in serum-stimulated cultured cells revealed unique patterns of gene expression within individual cells. Using the nucleus as the substrate for parallel gene analysis, we provide a platform for the fusion of genomics and cell biology: "cellular genomics."
Tunable polarization diversity liquid-crystal wavelength filter (1991)

A compact polarization-insensitive liquid crystal filter is demonstrated using the polarization diversity technique. The incoming signal is split into two orthogonally polarized beams with a calcite crystal and the beams are filtered using two regions of the liquid crystal Fabry-Perot filter. The optic axes in these two regions are made orthogonal by controlling the surface structure. It is shown that a wide tuning range of 70 nm is possible with a band-pass of about 0.6 nm. Using arbitrarily polarized input light it is demonstrated that polarization-dependent power fluctuations are less than 1 dB.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>