gebhart/patrepeval huggingface dataset:
Inflammation during skeletal muscle regeneration and tissue remodeling: application to exercise‐induced muscle damage management (2015)

Increase in the practice of sport by more and more numerous people in the Western countries is associated with an increase in muscle injuries, and in demand for improving muscle function and acceleration of muscle recovery after damage. Most of the treatments used target inflammation. Indeed, several lines of experimental evidence in animal models that are supported by human studies identify inflammatory cells, and particularly macrophages, as essential players in skeletal muscle regeneration. Macrophages act not only through their immune functions, but also control myogenesis and extracellular matrix remodeling by directly acting on myogenic precursors and fibro-adipogenic precursors. In light of these recent biological advances, the question of early treatment aiming at blunting inflammation after exercise-induced muscle injury is discussed.
Delivery of the Immunosuppressive Antigen Salp15 to Antigen-Presenting Cells bySalmonella entericaSerovar TyphimuriumaroAMutants (2004)

A Salmonella enterica serovar Typhimurium aroA-deficient delivery system was used to target the immunosuppressive protein Salp15 to antigen-presenting cells. In vitro and in vivo infections with Salp15-containing Salmonella resulted in an impaired CD4(+)-T-cell activation, suggesting that the protein was produced by antigen-presenting cells in a physiologically active form.
Two Distinct Domains within CIITA Mediate Self-Association: Involvement of the GTP-Binding and Leucine-Rich Repeat Domains (2001)

CIITA is the master regulator of class II major histocompatibility complex gene expression. We present evidence that CIITA can self-associate via two domains: the C terminus (amino acids 700 to 1130) and the GTP-binding domain (amino acids 336 to 702). Heterotypic and homotypic interactions are observed between these two regions. Deletions within the GTP-binding domain that reduce GTP-binding and transactivation function also reduce self-association. In addition, two leucine residues in the C-terminal leucine-rich repeat region are critical for self-association as well as function. This study reveals for the first time a complex pattern of CIITA self-association. These interactions are discussed with regard to the apoptosis signaling proteins, Apaf-1 and Nod1, which share domain arrangements similar to those of CIITA.
In vitro selection of bacteria resistant to LY146032, a new cyclic lipopeptide (1988)

Isolates of Streptococcus pneumoniae, Enterococcus faecalis, Enterococcus faecium, and coagulase-positive and -negative staphylococci were investigated for their abilities, in vitro, to develop resistance to LY146032. Exposure of the organisms to incremental concentrations of LY146032 resulted in MICs 8- to 32-fold higher than those for the original isolates. After three passages on antibiotic-free medium, the high MICs were maintained for the coagulase-negative staphylococci and pneumococci, with a twofold decrease observed for the enterococci and a fourfold decrease observed for Staphylococcus aureus. The frequency of spontaneous emergence of resistance was highest with S. pneumoniae (1.2 X 10(-6) at 16 times the original MIC) and lowest with S. aureus (7.0 X 10(-10) at 8 times the original MIC). For bacteria For bacteria surviving time-kill studies MICs were also higher than were those for the original isolates. Exposure to LY146032 in vitro selected for strains with decreased susceptibilities to the antimicrobial agent. However, the emergence of resistance in vivo is unpredictable and can be evaluated only after prolonged clinical use of the drug.
Binding of amyloid β-peptide to ganglioside micelles is dependent on histidine-13 (2006)

Amyloid beta-peptide (Abeta) is a major component of plaques in Alzheimer's disease, and formation of senile plaques has been suggested to originate from regions of neuronal membrane rich in gangliosides. Here we demonstrate using NMR on 15N-labelled Abeta-(1-40) and Abeta-(1-42) that the interaction with ganglioside G(M1) micelles is localized to the N-terminal region of the peptide, particularly residues His13 to Leu17, which become more helical when bound. The key interaction is with His13, which undergoes a G(M1)-specific conformational change. The sialic acid residue of the ganglioside headgroup is important for determining the nature of the conformational change. The isolated pentasaccharide headgroup of G(M1) is not bound, suggesting the need for a polyanionic surface. Binding to heparin confirms this suggestion, since binding is of similar affinity but does not produce the same conformational changes in the peptide. A comparison of Abeta-(1-40) and Abeta-(1-42) indicates that binding to G(M1) micelles is not related to oligomerization, which occurs at the C-terminal end. These results imply that binding to ganglioside micelles causes a transition from random coil to alpha-helix in the N-terminal region, leaving the C-terminal region unstructured.
Phase I/II Trial of Epratuzumab (Humanized Anti-CD22 Antibody) in Indolent Non-Hodgkin’s Lymphoma (2003)

Epratuzumab was well tolerated at up to 1,000 mg/m2/wk (for 4 weeks) and had clinical activity. One third of responding patients achieved CR. A 43% objective response rate in follicular NHL patients treated at 360 mg/m2/wk indicates that this dose should be explored in additional studies.
A Central Role of Salicylic Acid in Plant Disease Resistance (1994)

Transgenic tobacco and Arabidopsis thaliana expressing the bacterial enzyme salicylate hydroxylase cannot accumulate salicylic acid (SA). This defect not only makes the plants unable to induce systemic acquired resistance, but also leads to increased susceptibility to viral, fungal, and bacterial pathogens. The enhanced susceptibility extends even to host-pathogen combinations that would normally result in genetic resistance. Therefore, SA accumulation is essential for expression of multiple modes of plant disease resistance.
Improved Artificial Death Switches Based on Caspases and FADD (1999)

A number of "suicide genes" have been developed as safety switches for gene therapy vectors or as potential inducible cytotoxic agents for hyperproliferative disorders, such as cancer or restenosis. However, most of these approaches have relied on foreign proteins, such as HSV thymidine kinase, that primarily target rapidly dividing cells. In contrast, novel artificial death switches based on chemical inducers of dimerization (CIDs) and endogenous proapoptotic molecules function efficiently in both dividing and nondividing cells. In this approach, lipid-permeable, nontoxic CIDs are used to conditionally cross-link target proteins that are fused to CID-binding domains (CBDs), thus activating signaling cascades leading to apoptosis. In previous reports, CID-regulated Fas and caspases 1, 3, 8, and 9 were described. Since the maximum efficacy of these artificial death switches requires low basal and high specific activity, we have optimized these death switches for three parameters: (1) extent of oligomerization, (2) spacing between CBDs and target proteins, and (3) intracellular localization. We describe improved conditional Fas and caspase 1, 3, 8, and 9 alleles that function at subnanomolar levels of the CID AP1903 to trigger apoptosis. Further, we demonstrate for the first time that oligomerization of the death effector domain of the Fas-associated protein, FADD, is sufficient to trigger apoptosis, suggesting that the primary function of FADD, like that of Apaf-1, is oligomerization of associated caspases. Finally, we demonstrate that nuclear-targeted caspases 1, 3, and 8 can trigger apoptosis efficiently, implying that the cleavage of nuclear targets is sufficient for apoptosis.
Improved characteristics of InGaN multiple-quantum-well light-emitting diode by GaN/AlGaN distributed Bragg reflector grown on sapphire (2000)

An InGaN multiple-quantum-well light-emitting diode (LED) containing a GaN/AlGaN distributed Bragg reflector has been grown on a sapphire substrate by metalorganic chemical vapor deposition. Comparing with the conventional LED, the output power has been improved from 79 to 120 μW under 20 mA direct current biasing condition and the external quantum efficiency has been also improved from 0.16% to 0.23% under 10 mA dc current.
Molecular Signature of Quiescent Satellite Cells in Adult Skeletal Muscle (2007)

Skeletal muscle satellite cells play key roles in postnatal muscle growth and regeneration. To study molecular regulation of satellite cells, we directly prepared satellite cells from 8- to 12-week-old C57BL/6 mice and performed genome-wide gene expression analysis. Compared with activated/cycling satellite cells, 507 genes were highly upregulated in quiescent satellite cells. These included negative regulators of cell cycle and myogenic inhibitors. Gene set enrichment analysis revealed that quiescent satellite cells preferentially express the genes involved in cell-cell adhesion, regulation of cell growth, formation of extracellular matrix, copper and iron homeostasis, and lipid transportation. Furthermore, reverse transcription-polymerase chain reaction on differentially expressed genes confirmed that calcitonin receptor (CTR) was exclusively expressed in dormant satellite cells but not in activated satellite cells. In addition, CTR mRNA is hardly detected in nonmyogenic cells. Therefore, we next examined the expression of CTR in vivo. CTR was specifically expressed on quiescent satellite cells, but the expression was not found on activated/proliferating satellite cells during muscle regeneration. CTR-positive cells reappeared at the rim of regenerating myofibers in later stages of muscle regeneration. Calcitonin stimulation delayed the activation of quiescent satellite cells. Our data provide roles of CTR in quiescent satellite cells and a solid scaffold to further dissect molecular regulation of satellite cells. Disclosure of potential conflicts of interest is found at the end of this article.
Hybrid fiber-optic sensor using true heterodyne measurement techniques (1991)

We describe a hybrid, coherent, fiber-optic sensor for the measurement of phenomena that lead to birefringence, polarization rotation, or differential phase shifts in a remote-sensing element. By utilizing a single fiber that carries two orthogonally linearly polarized laser beams of different frequencies to the sensor and true heterodyne detection, we obtain high common-mode rejection of any unwanted intrinsic sensitivity of the fiber itself. The sensor is resistant to fading and has a high dynamic range. For demodulation we use high-frequency phase-locked loop detection that is insensitive to slowly varying phase shifts.
Structure-Activity Relationships in a Series of 5-[(2,5-Dihydroxybenzyl)amino]salicylate Inhibitors of EGF-Receptor-Associated Tyrosine Kinase: Importance of Additional Hydrophobic Aromatic Interactions (1994)

Potent inhibitors of EGF-dependent protein tyrosine kinase (PTK) activity were synthesized in a series of 5-[(2,5-dihydroxybenzyl)amino]salicylates. Several of these compounds inhibited EGF-dependent DNA synthesis in ER 22 cells with IC50 < 1 microM. In this series of PTK inhibitors, the role of the salicylate moiety as a potential divalent ion chelator was tested and found to be nonessential in all cases. The length and ramification of the substituting carboxyl group were investigated to improve cellular bioavailability, and this analysis provided compounds with increased inhibitory effect on EGF-induced DNA synthesis. Salicylates esterified with long hydrophobic chains were shown to be noncompetitive inhibitors of ATP, in contrast to the free acid and methyl salicylate. Moreover, all the tested inhibitors were shown to be noncompetitive inhibitors of the peptide substrate. Structure-activity relationships allowed us to suspect a hydrophobic pocket in the tyrosine kinase domain, preferentially interacting with aromatic rings. Finally, the selectivity of the best inhibitors was tested against other kinases, and they were found to be selective for tyrosine kinase. They were also shown to be good inhibitors of EGF-receptor autophosphorylation.
Barbiturate Inhibition of GLUT-1 Mediated Hexose Transport in Human Erythrocytes Exhibits Substrate Dependence for Equilibrium Exchange but Not Unidirectional Sugar Flux (1996)

Barbiturates inhibit GLUT-1 mediated hexose transport both in vivo [Gjedde & Rasmussen (1980) J. Neurochem. 35, 1382-1387; Otsuka et al. (1991) Am. J. Physiol. 261, R265-R275] and in vitro [Honkanen et al. (1995) Biochemistry 34, 535-544]. In the present study, the mechanism by which barbiturates inhibit GLUT-1 mediated hexose transport was examined by measuring both unidirectional zero trans and equilibrium exchange fluxes of hexoses in the functionally well-characterized, GLUT-1 rich human erythrocyte system. Unidirectional influx were both inhibited (> 80%) by 10 mM pentobarbital (PB). This symmetrical inhibition of unidirectional flux by PB was virtually independent of cis sugar concentration (2-130 mM) and exhibited an IC50 of approximately 2 mM. In contrast to unidirectional sugar flux, PB inhibition of equilibrium exchange sugar flux is attenuated by increased substrate concentration (e.g., 88% inhibition at 1 mM Glc versus 40% inhibition at 130 mM Glc in the presence of 10 mM PB) and exhibits an IC50 of approximately 10 mM at 100 mM Glc. Other barbiturates were found to inhibit sugar flux in human erythrocytes in this differential manner. These findings, when viewed with kinetic models proposed for GLUT-1 mediated transport [Carruthers (1990) Physiol. Rev. 70, 1135-1176], are consistent with barbiturates being noncompetitive inhibitors of Glc translocation and preferentially inhibiting the unoccupied form of the carrier protein. We propose, therefore, that barbiturates may prevent or alter the conformational changes associated with the reorientation of the carrier protein within the membrane. Overall, these results imply that barbiturates may more strongly inhibit GLUT-1 mediated Glc flux in vivo when the trans Glc is near zero as a result of either metabolism or another transport process.
Imagable 4T1 model for the study of late stage breast cancer (2008)

The production of factors that stimulate angiogenesis and ECM modification and induce hematopoiesis, recruitment and activation of leukocytes suggest that 4T1 tumor cells play a more direct role than previously appreciated in orchestrating changes in the tumor environment conducive to tumor cell dissemination and metastasis. The new cell lines will greatly facilitate the study of late stage breast and preclinical assessment of cancer drugs and other therapeutics particularly those targeting immune system effects on tumor metastasis.
Novel treatment strategies in clear-cell metastatic renal cell carcinoma (2005)

Metastatic renal-cell carcinoma (mRCC) is highly resistant to cytotoxic agents or hormones and is currently mainly treated with cytokine-based therapy. Transient responses and moderate survival advantages have been achieved in a subset of patients with these aspecific biological response modifiers. Side-effects are considerable, especially with high-dose interleukin (IL)-2. Efforts made in the field of specific immunotherapy have focused on optimization of dendritic cell vaccination and on administration of monoclonal antibodies, either cold (unconjugated) or hot (radioactively labeled). Furthermore, allogeneic bone marrow transplantation is able to induce remissions but, regrettably, is related to substantial morbidity and mortality. Neutralization of the biological activity of some immunosuppressive cytokines produced by RCC (IL-6 and tumor necrosis factor-alpha) with monoclonal antibodies is currently under investigation. Insights gained into the processes and pathways underlying carcinogenesis have led to the development of new treatment strategies. These treatments can be used for clear cell RCC, since they focus on blocking gene products that are upregulated by mutations in the von Hippel-Lindau gene. Specific strategies include anti-vascular endothelial growth factor monoclonal antibody (bevacizumab) or inhibition of its receptor kinases (oral SU11248 or PTK787), or targeting the Raf kinase pathway (by BAY 43-9006) or the mammalian target of rapamycin (mTOR) pathway (by CCI-779). Early clinical results are promising, but their place in the treatment of RCC has to be determined.
Polarization-insensitive arrayed-waveguide wavelength multiplexer with birefringence compensating film (1993)

An integrated-optic polarization-insensitive wavelength multiplexer that is based on an arrayed-waveguide grating is described. Polarization dependence due to thermal stress was eliminated by depositing an a-Si birefringence compensation film on the arrayed-waveguide. The multiplexing operation of 16 wavelength channels with a 0.8 nm spacing was confirmed to be independent of the polarization state.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Gene expression in melanoma cell lines and cultured melanocytes: correlation between levels of c-src-1, c-myc and p53. (1990)

The molecular genetics of melanoma is little understood and has concentrated largely on DNA analyses. We have examined mRNA levels of 21 different oncogenes, antioncogenes, growth factors and proteases in cultured melanocytes and 17 melanoma cell lines. C-mel, c-erb-B2, c-myc, c-src-1, p53, platelet derived growth factor A chain, gro, transforming growth factor alpha, epidermal growth factor receptor and tissue plasminogen activator were all expressed in at least some cell lines. Most striking was the finding that there are significant intercorrelations of c-myc, p53 and c-src-1 levels, and between p53 and c-erb-B2, which may be due to common regulatory control of these genes in cells of the melanocytic lineage.
Characterization of the rnpB gene and RNase P RNA in the order Chlamydiales. (2000)

The sequence of the RNase P RNA gene (rnpB) was determined for 60 strains representing all nine species in the family Chlamydiaceae and for the related Chlamydiales species, Parachlamydia acanthamoebae and Simkania negevensis. These sequences were used to infer evolutionary relationships among the Chlamydiaceae. The analysis separated Chlamydophila and Chlamydia into two lineages, with Chlamydophila forming three distinct clusters: the Chlamydophila pneumoniae strains; the Chlamydophila pecorum strains; and a third cluster comprising the species Chlamydophila psittaci, Chlamydophila abortus, Chlamydophila caviae and Chlamydophila felis. The Chlamydia line of descent contained two clusters, with the Chlamydia suis strains distinctly separated from strains of Chlamydia trachomatis and Chlamydia muridarum. This analysis indicated that the rnpB sequence and structure are distinctive markers for species in the Chlamydiaceae. It was also demonstrated that the RNase P RNA derived from Chlamydia trachomatis is able to cleave a tRNA precursor in the absence of protein. These findings are discussed in relation to the structure of Chlamydia RNase P RNA.
Infants' Physical World (2004)

Investigations of infants' physical world over the past 20 years have revealed two main findings. First, even very young infants possess expectations about physical events. Second, these expectations undergo significant developments during the first year of life, as infants form event categories, such as occlusion, containment, and covering events, and identify the variables relevant for predicting outcomes in each category. A new account of infants' physical reasoning integrates these findings. Predictions from the account are examined in change-blindness and teaching experiments.
Free-Flow Electrophoresis System for Proteomics Applications (2008)

This chapter describes the technology and selected applications in the field of protein analysis for free flow electrophoresis (FFE). FFE is a highly versatile technology for applications in this field as a result of its continuous processing of sample and the possibility of separating almost any kind of charged or chargeable particles in an aqueous medium without any solid matrix such as acrylamide. Possible applications are separation of ions, proteins, peptides, organelles, or whole cells for subsequent analysis.
Immunologic Tolerance: Collaboration Between Antigen and Lymphokines (1989)

Immunologic tolerance is the process whereby limits are placed on the degree to which lymphocytes respond to an animal's inherent antigens. It is a quantitative rather than an absolute term, as some autoantibody formation is common. Contrary to early hopes, it is not due to some single, simple causative mechanism confined to early developmental stages of the fetal immune system. Rather, self-tolerance results from a variety of complementary mechanisms and feedback loops in the immune system and is thus best seen as part of the general process of immunoregulation.
Resistance-Modifying Agents. 9. Synthesis and Biological Properties of Benzimidazole Inhibitors of the DNA Repair Enzyme Poly(ADP-ribose) Polymerase (2000)

The nuclear enzyme poly(ADP-ribose) polymerase (PARP) facilitates the repair of DNA strand breaks and is implicated in the resistance of cancer cells to certain DNA-damaging agents. Inhibitors of PARP have clinical potential as resistance-modifying agents capable of potentiating radiotherapy and the cytotoxicity of some forms of cancer chemotherapy. The preclinical development of 2-aryl-1H-benzimidazole-4-carboxamides as resistance-modifying agents in cancer chemotherapy is described. 1H-Benzimidazole-4-carboxamides, particularly 2-aryl derivatives, are identified as a class of potent PARP inhibitors. Derivatives of 2-phenyl-1H-benzimidazole-4-carboxamide (23, K(i) = 15 nM), in which the phenyl ring contains substituents, have been synthesized. Many of these derivatives exhibit K(i) values for PARP inhibition < 10 nM, with 2-(4-hydroxymethylphenyl)-1H-benzimidazole-4-carboxamide (78, K(i) = 1.6 nM) being one of the most potent. Insight into structure-activity relationships (SAR) for 2-aryl-1H-benzimidazole-4-carboxamides has been enhanced by studying the complex formed between 2-(3-methoxyphenyl)-1H-benzimidazole-4-carboxamide (44, K(i) = 6 nM) and the catalytic domain of chicken PARP. Important hydrogen-bonding and hydrophobic interactions with the protein have been identified for this inhibitor. 2-(4-Hydroxyphenyl)-1H-benzimidazole-4-carboxamide (45, K(i) = 6 nM) potentiates the cytotoxicity of both temozolomide and topotecan against A2780 cells in vitro (by 2.8- and 2.9-fold, respectively).
A specific and potent immunotoxin composed of antibody ZME-018 and the plant toxin gelonin. (1991)

Murine monoclonal antibody ZME-018 recognizes a 240 Kda glycoprotein present on the surface of most human melanoma cells and on over 80% of human biopsy specimens tested. Gelonin is a ribosome-inactivating plant toxin similar in nature and rivaling the activity of ricin A chain. ZME-018 was coupled to purified gelonin using the reagents SPDP and 2-iminothiolane. The ZME-gelonin conjugate was purified by S-300 Sephacryl and Blue Sepharose chromatography, removing unreacted gelonin and antibody, respectively. PAGE analysis showed that ZME was coupled to 1, 2, or 3 gelonin molecules. The ZME-gelonin conjugate was 10(6)-fold more active than gelonin itself in inhibiting the growth of log-phase human melanoma cells in culture. The immunoconjugate was not cytotoxic to antigen negative T-24 (human bladder carcinoma) cells. Treatment of melanoma cells with recombinant IFN-alpha or TNF substantially augmented the cytotoxicity of the immunoconjugate while treatment with IFN-gamma had a minor effect. Using the human tumor colony assay of melanoma cells obtained from fresh biopsy specimens, greater than 90% growth suppression was observed in 2 of 4 samples tested at a concentration of 250 ng/ml. In addition, 25% growth suppression was observed with a third sample tested, and no growth suppression was observed in 1 sample. Thus, clonogenic melanoma cells are sensitive in vitro to the cytotoxic activity of this immunotoxin at concentrations which we presume are pharmacologically relevant.