gebhart/patrepeval huggingface dataset:
Tumor-Specific CD8+ T Cells Expressing Interleukin-12 Eradicate Established Cancers in Lymphodepleted Hosts (2010)

T-cell-based immunotherapies can be effective in the treatment of large vascularized tumors, but they rely on adoptive transfer of substantial numbers ( approximately 20 million) of tumor-specific T cells administered together with vaccination and high-dose interleukin (IL)-2. In this study, we report that approximately 10,000 T cells gene-engineered to express a single-chain IL-12 molecule can be therapeutically effective against established tumors in the absence of exogenous IL-2 and vaccine. Although IL-12-engineered cells did not perist long-term in hosts, they exhibited enhanced functionality and were detected in higher numbers intratumorally along with increased numbers of endogenous natural killer and CD8(+) T cells just before regression. Importantly, transferred T cells isolated from tumors stably overproduced supraphysiologic amounts of IL-12, and the therapeutic effect of IL-12 produced within the tumor microenvironment could not be mimicked with high doses of exogenously provided IL-12. Furthermore, antitumor effects could be recapitulated by engineering wild-type open-repertoire splenocytes to express both the single-chain IL-12 and a recombinant tumor-specific T-cell receptor (TCR), but only when individual cells expressed both the TCR and IL-12, indicating that arrested migration of T cells at the tumor site was required for their activities. Successful tumor eradication was dependent on a lymphodepleting preconditioning regimen that reduced the number of intratumoral CD4(+) Foxp3(+) T regulatory cells. Our findings reveal an approach to genetically modify T cells to reduce the cell number needed, eliminate the need for vaccines or systemic IL-2, and improve immunotherapy efficacy based on adoptive transfer of gene-engineered T cells.
Induced endogenous autotoxicity in Camptotheca (2010)

Are plants always immune to their endogenous toxic secondary metabolites? Without disturbance, fast-growing Camptotheca plants can avoid poison by its endogenous camptothecin (DNA topoisomerase I inhibitor) at more than 10 times higher than the fatal concentration of exogenous application to the plant. Pruning has been long known to promote lateral growth; however, here we report that auxin-reducing pruning can induce endogenous autotoxicity in Camptotheca: dramatic deviations from normal morphogenesis, including serrated or lobed leaves, disturbed phyllotaxis, and fasciated stems. The abnormal morphogenesis appears correlatively with the elevated camptothecin contents following decapitation pruning. Plants resume their normal morphogenesis when camptothecin is reduced to natural levels after stress discontinuation. Exogenously applied auxin restores a dwarf mutant of high camptothecin yield to its parent type of lower yield, suggesting that auxin may be a triggering factor for the observed autotoxicity. Autotoxicity induced by endogenous compounds has not been reported before.
PD-L1 blockade synergizes with IL-2 therapy in reinvigorating exhausted T cells (2013)

The inhibitory receptor programmed cell death 1 (PD-1) plays a major role in functional exhaustion of T cells during chronic infections and cancer, and recent clinical data suggest that blockade of the PD-1 pathway is an effective immunotherapy in treating certain cancers. Thus, it is important to define combinatorial approaches that increase the efficacy of PD-1 blockade. To address this issue, we examined the effect of IL-2 and PD-1 ligand 1 (PD-L1) blockade in the mouse model of chronic lymphocytic choriomeningitis virus (LCMV) infection. We found that low-dose IL-2 administration alone enhanced CD8+ T cell responses in chronically infected mice. IL-2 treatment also decreased inhibitory receptor levels on virus-specific CD8+ T cells and increased expression of CD127 and CD44, resulting in a phenotype resembling that of memory T cells. Surprisingly, IL-2 therapy had only a minimal effect on reducing viral load. However, combining IL-2 treatment with blockade of the PD-1 inhibitory pathway had striking synergistic effects in enhancing virus-specific CD8+ T cell responses and decreasing viral load. Interestingly, this reduction in viral load occurred despite increased numbers of Tregs. These results suggest that combined IL-2 therapy and PD-L1 blockade merits consideration as a regimen for treating human chronic infections and cancer.
Kinetic and Spectroscopic Characterization of the Gamma-Carbonic Anhydrase from the Methanoarchaeon Methanosarcina thermophila (1999)

The zinc and cobalt forms of the prototypic gamma-carbonic anhydrase from Methanosarcina thermophila were characterized by extended X-ray absorption fine structure (EXAFS) and the kinetics were investigated using steady-state spectrophotometric and (18)O exchange equilibrium assays. EXAFS results indicate that cobalt isomorphously replaces zinc and that the metals coordinate three histidines and two or three water molecules. The efficiency of either Zn-Cam or Co-Cam for CO(2) hydration (k(cat)/K(m)) was severalfold greater than HCO(3-) dehydration at physiological pH values, a result consistent with the proposed physiological function for Cam during growth on acetate. For both Zn- and Co-Cam, the steady-state parameter k(cat) for CO(2) hydration was pH-dependent with a pK(a) of 6.5-6.8, whereas k(cat)/K(m) was dependent on two ionizations with pK(a) values of 6.7-6.9 and 8.2-8.4. The (18)O exchange assay also identified two ionizable groups in the pH profile of k(cat)/K(m) with apparent pK(a) values of 6.0 and 8.1. The steady-state parameter k(cat) (CO(2) hydration) is buffer-dependent in a saturable manner at pH 8. 2, and the kinetic analysis suggested a ping-pong mechanism in which buffer is the second substrate. The calculated rate constant for intermolecular proton transfer is 3 x 10(7) M(-1) s(-1). At saturating buffer concentrations and pH 8.5, k(cat) is 2.6-fold higher in H(2)O than in D(2)O, suggesting that an intramolecular proton transfer step is at least partially rate-determining. At high pH (pH > 8), k(cat)/K(m) is not dependent on buffer and no solvent hydrogen isotope effect was observed, consistent with a zinc hydroxide mechanism. Therefore, at high pH the catalytic mechanism of Cam appears to resemble that of human CAII, despite significant structural differences in the active sites of these two unrelated enzymes.
Immunoliposomes: A Targeted Delivery Tool for Cancer Treatment (2002)

Within the last decade, we have seen a rapid expansion in the use of monoclonal antibodies as targeting molecules in medicine. However, the disadvantages associated with intact antibodies has limited their therapeutic usefulness. The development of small biologically active antibody fragments, such as the scFv molecules, has provided a way to circumvent some of these problems. This, coupled with the use of liposomes as drug and gene delivery vehicles, has broadened the potential of immunotherapy for cancer. In this chapter we examine some of the factors influencing, and review some of the latest reports describing, the ability of antibody targeted immunoliposomal complexes to target both primary tumors and metastases as we work toward more effective therapeutic modalities.
The Potential Role of Proteoglycans in Cationic Lipid-mediated Gene Delivery (2001)

Recent evidence supports a role for proteoglycans in polycation-mediated gene delivery. Therefore, the interaction of glycosaminoglycans with cationic lipid-DNA complexes (CLDCs) has been characterized using a combination of biophysical approaches. At low ionic strength, CLDCs bind to heparin-derivatized Sepharose particles, with the ratio of cationic lipid to DNA controlling the binding. Incorporation of the helper lipids cholesterol or 1,2-dioleoyl-phosphatidylethanolamine increases the amount of bound CLDC. Heparin also induces the aggregation of CLDCs, with cholesterol reducing this effect. Isothermal titration calorimetry demonstrates an endothermic heat for the binding of heparin to CLDCs at low ionic strength, whereas circular dichroism studies suggest a heparin-stimulated release of DNA from CLDCs at a greater than 20-fold charge excess. Increasing the ionic strength to 0.11 reduces CLDC binding to heparin beads, and greatly enhances the release of DNA from CLDCs by heparin. The ability of the cell surface glycosaminoglycan heparan sulfate to release DNA from CLDCs is more sensitive than heparin to the incorporation of the cholesterol or 1,2-dioleoyl-phosphatidylethanolamine. Titration calorimetry reveals an exothermic heat for the interaction glycosaminoglycans with CLDCs at higher ionic strength. These results are consistent with the direct involvement of proteoglycans in transfection.
The sunflower HD-Zip transcription factor HAHB4 is up-regulated in darkness, reducing the transcription of photosynthesis-related genes (2008)

HAHB4 belongs to the sunflower subfamily I of HD-Zip proteins and is involved in drought-tolerance response and ethylene-mediated senescence. Cross-talk between these two processes through this transcription factor was recently described. In this study it is shown that the expression of HAHB4 is induced in darkness and quickly disappears when plants are exposed to light. This regulation of HAHB4 was confirmed at the transcriptional level through the use of transgenic Arabidopsis plants bearing constructs in which different segments of the HAHB4 promoter were fused with the reporter gene GUS. Together with electrophoretic mobility shift assays performed with sunflower nuclear proteins, these experiments allowed a cis-acting element involved in this response to be located. Transient overexpression of the HAHB4 cDNA in sunflower leaf discs and HAHB4 knockdown by iRNA were performed, demonstrating the participation of this transcription factor in the transcriptional down-regulation of a large group of photosynthesis-related genes. In accordance with the reduction in the transcripts encoding chlorophyll a/b-binding proteins, the content of these pigments is diminished in Arabidopsis HAHB4-expressing transgenic plants. Thus, it appears that HAHB4 may participate with other factors in the intricate regulation mechanism of the photosynthetic machinery in darkness.
Human cytomegalovirus serum neutralizing antibodies block virus infection of endothelial/epithelial cells, but not fibroblasts, early during primary infection (2008)

A panel of human sera exhibited a >or=128-fold higher neutralizing potency against a human cytomegalovirus (HCMV) clinical isolate propagated and tested in endothelial (or epithelial) cells than against the same virus infecting human fibroblasts. In a group of 18 primary infections, the reverse geometric mean titre was in the range of 10-15 in human fibroblasts within the first 3 months after the onset of infection, whereas the endothelial cell infection-neutralizing activity was already present within the first 10 days, reaching median levels of 122, 320 and 545 at respectively 30, 60 and 90 days after onset, then declining slowly. This difference was also confirmed in the majority of reactivated and remote HCMV infections, as well as in a hyperimmune globulin preparation. The antibody response to HCMV pUL131A, pUL130 and pUL128 locus products, which are required for endothelial/epithelial cell infection, provided a potential molecular basis for such a differential neutralizing activity. In addition, monoclonal/monospecific antibodies raised against the pUL131A, pUL130 and pUL128 proteins were found to display an inhibitory activity on HCMV plaque formation and HCMV leukocyte transfer from HCMV-infected cells. Hence, conventional determination of the neutralizing activity of human sera in fibroblasts is misleading. Antibodies to pUL131A, pUL130 and pUL128 appear to display a major HCMV-neutralizing and dissemination-inhibiting activity.
A Systematic Review of Drug Therapy to Delay or Prevent Type 2 Diabetes (2005)

Currently, no single agent can be definitively recommended for diabetes prevention. Future studies should be designed with diabetes incidence as the primary outcome and should be of sufficient duration to differentiate between genuine diabetes prevention as opposed to simple delay or masking of this condition.
Constraint-Induced Movement Therapy: a new family of techniques with broad application to physical rehabilitation--a clinical review. (1999)

A new family of rehabilitation techniques, termed Constraint-Induced Movement Therapy or CI Therapy, has been developed that controlled experiments have shown is effective in producing large improvements in limb use in the real-world environment after cerebrovascular accident (CVA). The signature therapy involves constraining movements of the less-affected arm with a sling for 90% of waking hours for 2 weeks, while intensively training use of the more-affected arm. The common therapeutic factor in all CI Therapy techniques would appear to be inducing concentrated, repetitive practice of use of the more-affected limb. A number of neuroimaging and transcranial magnetic stimulation studies have shown that the massed practice of CI Therapy produces a massive use-dependent cortical reorganization that increases the area of cortex involved in the innervation of movement of the more-affected limb. The CI Therapy approach has been used successfully to date for the upper limb of patients with chronic and subacute CVA and patients with chronic traumatic brain injury and for the lower limb of patients with CVA, incomplete spinal cord injury, and fractured hip. The approach has recently been extended to focal hand dystonia of musicians and possibly phantom limb pain.
Contribution of OX40/OX40 ligand interaction to the pathogenesis of rheumatoid arthritis (2000)

OX40 ligand (OX40L) and OX40 (CD134) are a pair of cell surface molecules belonging to the TNF/TNF receptor family. Interaction of OX40L with its receptor OX40 is thought to be important in T cell activation through T cell/antigen-presenting cell interaction. However, involvement of these molecules in the pathogenesis of rheumatoid arthritis (RA) remains unclear. To explore the contribution of OX40/OX40L interaction to the pathogenesis of RA in vivo, we evaluated the effect of a neutralizing anti-OX40L monoclonal antibody (mAb) on the development of collagen-induced arthritis (CIA) in DBA/1 mice as an animal model for RA. Administration of anti-OX40L mAb into type II collagen (CII) -immunized DBA/1 mice dramatically ameliorated the disease severity. In vivo treatment with anti-OX40L mAb did not inhibit the expansion of CII-reactive T cells, but suppressed IFN-gamma and anti-CII IgG2a production. Therefore, OX40/OX40L interaction appears to play a critical role in the development of CIA by enhancing Th1-type autoimmune response. In addition, T lymphocytes in synovial fluid and synovial tissue from RA patients expressed OX40, while OX40L was expressed on sublining cells in synovial tissue. These results indicate that OX40/OX40L interaction may play a critical role in the development of RA.
Structural requirements of substrate DNA for binding to and cleavage by RuvC, a Holliday junction resolvase. (1994)

To elucidate the molecular mechanism of the resolution of Holliday junctions by Escherichia coli RuvC protein, we studied biochemical properties of the protein using various synthetic DNA junctions as model substrates. RuvC cleaves not only a four-way junction but also three-way junctions efficiently. The central core of homology in the junction is essential for the substrates to be cleavable by RuvC. Although the divalent cations are essential for the endonuclease activity, RuvC efficiently forms specific complexes with four-way junctions in the absence of the cations, irrespective of the presence of homologous core sequences. By using T7 endonuclease I as a probe, we studied the topology of the substrate junctions used in our study. The results suggest that RuvC cleaves the three-way junctions with homology core when they become four-way conformers. From the present studies, we propose that RuvC initially binds mostly nonproductively to four-way junctions, which does not require divalent metals, and subsequently cleaves the junctions by a mechanism dependent on a divalent cation and a particular topological conformer that is induced by the sequences at the mobile junctions.
Technology assessment for the implementation of magnetoresistive elements with semiconductor components in magnetic random access memory (MRAM) architectures (1999)

We describe the DRAM-like approach towards a non-volatile magnetoresistive memory integrating magnetic and semiconductor devices into one cell. The speed at which the magnetic memory signal can be read depends on many factors. An important factor is the magnetic element itself, the size, magnetic characteristics and absolute resistance. Secondly, the design of the read-out electronics is a key issue. A third determining factor is the technology in which the electronics are fabricated. Some features are indicated that are essential in optimizing MRAM in future.
Modification of Cysteine Residues by Alkylation. A Tool in Peptide Mapping and Protein Identification (1998)

Although mass spectrometric peptide mapping has become an established technique for the rapid identification of proteins isolated by polyacrylamide gel electrophoresis (PAGE), the results of the identification procedure can sometimes be ambiguous. Such ambiguities become increasingly prevalent for proteins isolated as mixtures or when only very small amounts of the proteins are isolated. The quality of the identification procedure can be improved by increasing the number of peptides that are extracted from the gel. Here we show that cysteine alkylation is required to ensure maximal coverage in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) peptide mapping of proteins isolated by PAGE. In the described procedure, alkylation was performed prior to electrophoresis to avoid the adventitious formation of acrylamide adducts during electrophoresis. In this way, homogeneous alkylation was obtained with three different alkylating reagents (4-vinylpyridine, iodoacetamide, acrylamide). Cysteine alkylation was also used as a tool for the identification of cysteine-containing peptides. Using a 1:1 mixture of unlabeled acrylamide and deuterium-labeled acrylamide ([2,3,3'-D3]acrylamide), the proteins of interest were alkylated prior to electrophoretic separation. Peptide mixtures produced by trypsin digestion of the resulting protein bands were analyzed by MALDI-TOF MS, and the cysteine content of the peptides was inferred from the isotopic distributions. The cysteine content information was readily obtained and used to improve the protein identification process.
Anti-epidermal growth factor receptor antibody C225 inhibits angiogenesis in human transitional cell carcinoma growing orthotopically in nude mice. (1999)

Epidermal growth factor receptor (EGFR) regulates the growth and progression of human transitional cell carcinoma (TCC) of the bladder. We have shown that therapy targeting EGFR inhibited the growth of human TCC established orthotopically in nude mice. The purpose of this study was to evaluate whether EGFR-directed therapy affects angiogenesis associated with the growth and metastasis of human TCC. We determined the cytostatic effect and the effect on production of angiogenic factors after in vitro treatment of the human TCC cell line 253J B-V with MAb C225, a chimerized monoclonal anti-EGFR antibody. The 253J B-V cells were implanted orthotopically into athymic nude mice, and established tumors (4 weeks) were treated with i.p. MAb C225. Expression of the angiogenic factors vascular endothelial growth factor (VEGF), interleukin-8 (IL-8), and basic fibroblast growth factor (bFGF) was evaluated by immunohistochemistry and in situ mRNA hybridization analyses and correlated with microvessel density evaluated after immunohistochemical staining with anti-CD31. In vitro treatment with MAb C225 inhibited mRNA and protein production of VEGF, IL-8, and bFGF by 253J B-V cells in a dose-dependent manner. MAb C225 therapy of nude mice with established TCCs growing orthotopically resulted in inhibition of growth and metastasis compared with controls (P <0.0005). VEGF, IL-8, and bFGF expression was significantly lower in treated tumors than in controls. The down-regulation of these angiogenic factors preceded the involution of blood vessels. These studies indicate that therapy with anti-EGFR MAb C225 has a significant antitumor effect mediated, in part, by inhibition of angiogenesis.
FormatGuard: automatic protection from printf format string vulnerabilities (2001)

format bugs&amp;quot; was discovered when an vulnerability in WU-FTP appeared that acted almost like a buffer overflow, but wasn&amp;apos;t. Since then, dozens of format string vulnerabilities have appeared. This paper describes the format bug problem, and presents FormatGuard: our proposed solution. FormatGuard is a small patch to glibc that provides general protection against format bugs. We show that FormatGuard is effective in protecting several real programs with format vulnerabilities against live exploits, and we show that FormatGuard imposes minimal compatibility and performance costs.
Velocity-Difference Induced Focusing of Nucleotides in Capillary Electrophoresis with a Dynamic pH Junction (2000)

Velocity-difference induced focusing (V-DIF) of nucleotides was achieved by using a dynamic pH junction in capillary electrophoresis (CE) with UV detection. The influence of specific analyte properties, such as nucleotide base structure, sugar structure, and degree of phosphorylation, is examined. The pKa values and borate complexation with vicinal diols are important factors that caused the focusing. Therefore, the pH and borate content in the sample and background electrolyte can be adjusted to optimize the focusing effect. This method allows the injection of large volumes of sample (approximately 300 nL), resulting in at least 50-fold improvement in concentration sensitivity. The detection limit of 4.0 x 10(-8) M for nucleotides can be achieved in favorable conditions. V-DIF can be also applied to nucleotide pool analysis from cell extracts to improve the concentration sensitivity of CE and to reduce the time-consuming steps of desalting and off-line preconcentration that are often required for assays of nucleotides from biological samples.
Evaluation of indium-111- and yttrium-90-labeled linker-immunoconjugates in nude mice and dogs. (1993)

Rapid uptake and slow transit of radioactivity from normal organs are detrimental to any clinical utilized radioimmunoconjugate because they lower the target-to-nontarget ratio and deliver undesirable radiation to normal organs. To mitigate this problem, two labile chemical linkages (EGS and DST) were introduced between a monoclonal antiferritin antibody (QCI) and a chelating agent (DTPA). The biodistribution of labile-linker immunoconjugates (EGS and DST) and stable linker immunoconjugates (DSS and ITCB) were compared. In a nude mouse model, all of the four immunoconjugates labeled with 111In targeted subcutaneously-implanted human tumor cells. Tumor-to-normal organ ratios were enhanced for the EGS linkage in comparison to the two stable linkages. Serial whole-body immunoscintigraphy confirmed the biodistribution study. The EGS and ITCB 90Y-labeled immunoconjugates had biodistributions similar to their respective 111In-labeled immunoconjugates. As the mouse model is not representative of the high uptake of monoclonal antibodies in the human liver, beagle dogs were used to further explore the retention of radiolabel in normal liver. The EGS-linked immunoconjugate significantly reduced the dog liver activity when compared to the ITCB immunoconjugate. The combination of the animal models (mouse and dog) appears to allow for a more compete and optimal preclinical analysis of chelated radiolabeled monoclonal antibodies for diagnosis or treatment and illustrates the potential clinical improvements possible with labile chemical linkages in radioimmunoconjugates.