gebhart/patrepeval huggingface dataset:
Differential Impairment of Lytic and Cytokine Functions in Senescent Human Immunodeficiency Virus Type 1-Specific Cytotoxic T Lymphocytes (2003)

Telomere length is abnormally short in the CD8(+) T-cell compartment of human immunodeficiency virus type 1 (HIV-1)-infected persons, likely because of chronic cell turnover. Although clonal exhaustion of CD8(+) cytotoxic T lymphocytes (CTL) has been proposed as a mechanism for loss of antigen-specific responses, the functional consequences of exhaustion are poorly understood. Here we used telomerase transduction to evaluate the impact of senescence on CTL effector functions. Constitutive expression of telomerase in an HIV-1-specific CTL clone results in enhanced proliferative capacity, in agreement with prior studies of other human cell types. Whereas the CTL remain phenotypically normal in terms of antigenic specificity and requirements for proliferation, their cytolytic and antiviral capabilities are superior to those of control CTL. In contrast, their ability to produce gamma interferon and RANTES is essentially unchanged. The selective enhancement of cytolytic function in memory CTL by ectopic telomerase expression implies that loss of this function (but not cytokine production) is a specific consequence of replicative senescence. These data suggest a unifying mechanism for the in vivo observations that telomere lengths are shortened in the CD8(+) cells of HIV-1-infected persons and that HIV-1-specific CTL are deficient in perforin. Telomerase transduction could therefore be a tool with which to explore a potential therapeutic approach to an important pathophysiologic process of immune dysfunction in chronic viral infection.
Protein Antigens of Genital Mycoplasmas (1988)

Surface structures of the genital mycoplasmas Ureaplasma urealyticum and Mycoplasma hominis that are important in the human immune response and pathogenesis of disease are relatively poorly defined. In this study, an unusual antigen complex of U. urealyticum consisting of multiple bands forming a "ladder" pattern after electrophoretic separation was noted. It is similar to the variable V-1 surface antigen of Mycoplasma pulmonis. Data on U. urealyticum are only preliminary, but the ureaplasma antigen, if it proves to be analogous to V-1, may provide the antigenic determinants for distinguishing among serovars or serogroups and correlating them with pathogenicity. Surface proteins of M. hominis were identified with use of 125I surface labeling, [35S]methionine metabolic labeling, and immunoadsorption of rabbit antiserum. Comparison of M. hominis reference strains PG-21 and 4195 showed little homology between surface proteins, although with metabolic labeling they appeared essentially identical. Immunoblotting with patients' sera, using PG-21 as antigen, showed that most reactions were directed to surface proteins and that a 102K antigen (MH1) was recognized by 94% of the sera. MH1 was one of the few surface proteins of PG-21 that appeared to have counterparts in the other six reference strains, making MH1 a prime candidate for reliable and specific detection of M. hominis infection.
Detection and quantification of mutations in the plasma of patients with colorectal tumors (2005)

The early detection of cancers through analysis of circulating DNA could have a substantial impact on morbidity and mortality. To achieve this goal, it is essential to determine the number of mutant molecules present in the circulation of cancer patients and to develop methods that are sufficiently sensitive to detect these mutations. Using a modified version of a recently developed assay for this purpose, we found that patients with advanced colorectal cancers consistently contained mutant adenomatous polyposis coli (APC) DNA molecules in their plasma. The median number of APC DNA fragments in such patients was 47,800 per ml of plasma, of which 8% were mutant. Mutant APC molecules were also detected in >60% of patients with early, presumably curable colorectal cancers, at levels ranging from 0.01% to 1.7% of the total APC molecules. These results have implications for the mechanisms through which tumor DNA is released into the circulation and for diagnostic tests based on this phenomenon.
Cloning and characterization of murine 1-acyl-sn-glycerol 3-phosphate acyltransferases and their regulation by PPARα in murine heart (2005)

AGPAT (1-acyl-sn-glycerol 3-phosphate acyltransferase) exists in at least five isoforms in humans, termed as AGPAT1, AGPAT2, AGPAT3, AGPAT4 and AGPAT5. Although they catalyse the same biochemical reaction, their relative function, tissue expression and regulation are poorly understood. Linkage studies in humans have revealed that AGPAT2 contributes to glycerolipid synthesis and plays an important role in regulating lipid metabolism. We report the molecular cloning, tissue distribution, and enzyme characterization of mAGPATs (murine AGPATs) and regulation of cardiac mAGPATs by PPARalpha (peroxisome-proliferator-activated receptor alpha). mAGPATs demonstrated differential tissue expression profiles: mAGPAT1 and mAGPAT3 were ubiquitously expressed in most tissues, whereas mAGPAT2, mAGPAT4 and mAGPAT5 were expressed in a tissue-specific manner. mAGPAT2 expressed in in vitro transcription and translation reactions and in transfected COS-1 cells exhibited specificity for 1-acyl-sn-glycerol 3-phosphate. When amino acid sequences of five mAGPATs were compared, three highly conserved motifs were identified, including one novel motif/pattern KX2LX6GX12R. Cardiac mAGPAT activities were 25% lower (P<0.05) in PPARalpha null mice compared with wild-type. In addition, cardiac mAGPAT activities were 50% lower (P<0.05) in PPARalpha null mice fed clofibrate compared with clofibrate fed wild-type animals. This modulation of AGPAT activity was accompanied by significant enhancement/reduction of the mRNA levels of mAGPAT3/mAGPAT2 respectively. Finally, mRNA expression of cardiac mAGPAT3 appeared to be regulated by PPARalpha activation. We conclude that cardiac mAGPAT activity may be regulated by both the composition of mAGPAT isoforms and the levels of each isoform.
[Quantitative analysis of factors affected mortality trend in Chinese, 2002]. (2005)

The study showed that the risk factors had contributed to the increase of death rates, including behavioral risk factors described in the preceding 5 papers as smoking and passive smoking, unhealthy diet, sedentary life style, violating traffic regulation etc. In order to reduce the death rates on cancer, heart diseases, diabetes, traffic accidents, emphasis should be also laid on the change of unhealthy behaviors.
RTP Payload Format for JPEG-compressed Video (1998)

This memo describes the RTP payload format for JPEG video streams.The packet format is optimized for real-time video streams where codec parameters change rarely from frame to frame.
Reviving virus based cancer vaccines by using cytomegalovirus vectors expressing modified tumor antigens (2015)

Cancer vaccines that have utilized various immunization strategies to induce antitumor immunity have largely failed in clinical settings. We have recently developed a cancer vaccine using a cytomegalovirus (CMV) based vector that expressed a modified melanoma antigen that elicited a robust antitumor CD8<sup>+</sup> T cell response and tumor rejection.
Stopping Light All-Optically (2003)

We show that light pulses can be stopped and stored all-optically, with a process that involves an adiabatic and reversible pulse bandwidth compression occurring entirely in the optical domain. Such a process overcomes the fundamental bandwidth-delay constraint in optics, and can generate arbitrarily small group velocities for light pulses with a given bandwidth, without the use of any coherent or resonant light-matter interactions. We exhibit this process in optical resonator systems, where the pulse bandwidth compression is accomplished only by small refractive index modulations performed at moderate speeds. (Accepted for publication in Phys. Rev. Lett. Submitted on Sept. 10th 2003)
Prospects for hepatitis C virus therapeutics: levovirin and viramidine as improved derivatives of ribavirin. (2002)

Ribavirin, in combination with interferons, has proved clinically useful for the treatment of hepatitis C virus (HCV) infection despite uncertainty as to its true mechanism of action. Its immunomodulatory effects have been proposed to be crucial for its efficacy in HCV treatment. Two new derivatives of zibavirin, Levovirin and virmidine, are currently in development as HCV therapeutics. Both drugs retain ribavirin's immunomodulatory properties but appear to be less toxic than the parent drug. Clinical evaluation of these drugs may aid in understanding the relevant mechanism of action of ribavirin itself, as well as the role of immunomodulators in HCV therapy.
Synthesis, Structure, and DNA Cleavage Activity of New Trinuclear Zn3 and Zn2Cu Complexes of a Chiral Macrocycle:  Structural Correlation with the Active Center of P1 Nuclease (2002)

New homo trinuclear Zn(II) complexes [Zn(3)L(1)(micro-OAc)](ClO(4))(2).3CHCl(3).H(2)O, 1, and [Zn(3)L(1)(micro-OAc)].ClO(4).PF(6).5CH(3)OH.H(2)O, 2, and hetero trinuclear complex [Zn(2)CuL(1)(micro-OAc)](ClO(4))(2).3CHCl(3).H(2)O,3, of optically active hexaaza triphenolic macrocycle H(3)L(1) were synthesized and crystallographically characterized. The cation [Zn(3)L(1)(micro-OAc)](+) structure of 1 and 2 closely resembles the trinuclear Zn(II) active site of P1 nuclease. The distorted tetrahedral geometry of Zn3 was successfully reproduced at Cu1 in complex 3. The complexes 2 and 3 cleave CT DNA at 37 and 50 degrees C.
Two-dimensional optics with surface plasmon polaritons (2002)

We report the experimental realization of highly efficient optical elements built up from metal nanostructures to manipulate surface plasmon polaritons propagating along a silver/polymer interface. Mirrors, beamsplitters, and interferometers produced by electron-beam lithography are investigated. The plasmon fields are imaged by detecting the fluorescence of molecules dispersed in the polymer.
Selective Interaction of Voltage-gated K+ Channel β-Subunits with α-Subunits (1996)

To begin to study the molecular bases that determine the selective interaction of the beta-subunits of voltage-gated K+ channels with alpha-subunits observed in situ, we have expressed these polypeptides in transfected mammalian cells. Analysis of the specificity of alpha/bet a-subunit interaction indicates that both the Kvbeta1 and Kvbeta2 beta-subunits display robust and selective interaction with the five members of the Shaker-related (Kv1) alpha-subunit subfamily tested. The interaction of these beta-subunits with Kv1 alpha-subunits does not require the beta-subunit N-terminal domains. Thus, the previously observed failure of N-terminal mutants of Kv beta1 to modulate inactivation kinetics of Kv1 family members is not simply due to a lack of subunit interaction. Interaction of these beta-subunits with members of two other subfamilies (Shab- and Shaw-related) could not be detected. Somewhat surprisingly, a member of the Shal-related subfamily was found to interact with beta-subunits; however, this interaction had biochemical characteristics distinct from the beta-subunit interaction with Kv1 family members. In all cases, Kvbeta1 and Kvbeta2 exhibited indistinguishable alpha-subunit selectivity. These studies point to a selective interaction between K+ channel alpha- and beta-subunits mediated through conserved domains in the respective subunits.
Diastereoselective allylation and crotylation of N-unsubstituted imines derived from ketones (2005)

A wide variety of tertiary carbinamines are synthesized in high yields via diastereoselective allylation and crotylation of in situ generated N-unsubstituted ketimines.
Treatment of Osteoporotic Fractures (2002)

Fractures are the most common problem associated with osteoporosis and despite advances in prevention and treatment of osteoporosis the number of fractures continue to increase. Along with the three classic locations hip, spine and wrist, there are several other fractures that commonly are related to osteoporosis. The weak bone makes it difficult to achieve a stable bone-implant construct and general weakness of the patient often prevents reduction of load on the injured extremity during healing. The main treatment goal should be preservation of function even at the expense of restoration of exact anatomy. By development of dynamic load-sharing implants and less invasive techniques the results following fixation of osteoporotic fractures has improved. A new strategy has also been to develop materials that will enhance the strength of the cancellous bone that surrounds the metal implant. By using bioactive cement in conjunction with metal implants improved strength has been shown in internally fixed metaphyseal fractures. Encouraging results have also been reported after cement injection into compressed vertebral fractures, so called vertebroplasty. The specific demands involved in the treatment of osteoporotic fractures calls for specific solutions. Apart from augmentation of the cancellous bone and development of new load-sharing devices, endoprosthetic replacement with specially designed fracture prosthesis has become more frequent.
Pervaporation and Vapor Permeation Tutorial: Membrane Processes for the Selective Separation of Liquid and Vapor Mixtures (2013)

Abstract Pervaporation and vapor permeation are membrane-based processes proposed as alternatives to conventional separation technologies. Applications range from organic solvent removal from water, ethanol, or butanol recovery from fermentation broths, solvent/biofuel dehydration to meet dryness specifications, and organic-organic separations such as the removal of sulfur compounds from gasoline. Unlike membrane filtration processes, which rely on an applied liquid pressure gradient and size sieving to accomplish a separation, pervaporation and vapor permeation separate compounds based on a chemical activity driving force and the sorption and diffusion of the compounds through the membrane. These properties enable the separation of even miscible liquid mixtures. Keywords: membrane separationpervaporationsolution diffusionvapor permeation ACKNOWLEDGEMENTS The views expressed in this article are those of the author and do not necessarily reflect the views or policies of the U.S. Environmental Protection Agency. Notes Review articles and overviews: Mass transfer: Hybrid processes: Preferred performance measures: *This manuscript is part of an evolving virtual issue on Water Treatment and Re-Use and the Water-Energy Nexus which was facilitated by the Engineering Conferences International Meeting (of the same name) held in Cancun, Mexico January 8–12, 2012 and supported by NSF CBET 1157131 and W. L. Gore, Inc.
Stem cells at the dawn of the 21st century (2003)

Understanding and controlling the interaction of graphene-based materials with cell membranes is key to the development of graphene-enabled biomedical technologies and to the management of graphene health and safety issues. Very little is known about the ...
Prevalence of associated deformities and hip pain in patients with cam-type femoroacetabular impingement (2009)

Femoroacetabular impingement is a cause of hip pain in adults and is potentially a precursor of osteoarthritis. Our aim in this study was to determine the prevalence of bilateral deformity in patients with symptomatic cam-type femoroacetabular impingement as well as the presence of associated acetabular abnormalities and hip pain. We included all patients aged 55 years or less seen by the senior author for hip pain, with at least one anteroposterior and lateral pelvic radiograph available. All patients with dysplasia and/or arthritis were excluded. A total of 113 patients with a symptomatic cam-impingement deformity of at least one hip was evaluated. There were 82 men and 31 women with a mean age of 37.9 years (16 to 55). Bilateral cam-type deformity was present in 88 patients (77.8%) while only 23 of those (26.1%) had bilateral hip pain. Painful hips had a statistically significant higher mean alpha angle than asymptomatic hips (69.9 degrees vs 63.1 degrees , p < 0.001). Hips with an alpha angle of more than 60 degrees had an odds ratio of being painful of 2.59 (95% confidence interval 1.32 to 5.08, p = 0.006) compared with those with an alpha angle of less than 60 degrees . Of the 201 hips with a cam-impingement deformity 42% (84) also had a pincer deformity. Most patients with cam-type femoroacetabular impingement had bilateral deformities and there was an associated acetabular deformity in 84 of 201 patients (42%). This information is important in order to define the natural history of these deformities, and to determine treatment.
Fungal and Parasitic Infections of the Eye (2000)

The unique structure of the human eye as well as exposure of the eye directly to the environment renders it vulnerable to a number of uncommon infectious diseases caused by fungi and parasites. Host defenses directed against these microorganisms, once anatomical barriers are breached, are often insufficient to prevent loss of vision. Therefore, the timely identification and treatment of the involved microorganisms are paramount. The anatomy of the eye and its surrounding structures is presented with an emphasis upon the association of the anatomy with specific infection of fungi and parasites. For example, filamentous fungal infections of the eye are usually due to penetrating trauma by objects contaminated by vegetable matter of the cornea or globe or, by extension, of infection from adjacent paranasal sinuses. Fungal endophthalmitis and chorioretinitis, on the other hand, are usually the result of antecedent fungemia seeding the ocular tissue. Candida spp. are the most common cause of endogenous endophthalmitis, although initial infection with the dimorphic fungi may lead to infection and scarring of the chorioretina. Contact lens wear is associated with keratitis caused by yeasts, filamentous fungi, and Acanthamoebae spp. Most parasitic infections of the eye, however, arise following bloodborne carriage of the microorganism to the eye or adjacent structures.
Targeted Chromosomal Cleavage and Mutagenesis in Drosophila Using Zinc-Finger Nucleases (2002)

Zinc-finger nucleases (ZFNs) are hybrids between a nonspecific DNA-cleavage domain and a DNA-binding domain composed of Cys(2)His(2) zinc fingers. Because zinc fingers can be manipulated to recognize a broad range of sequences, these enzymes have the potential to direct cleavage to arbitrarily chosen targets. We have tested this idea by designing a pair of ZFNs that recognize a unique site in the yellow (y) gene of Drosophila. When these nucleases were expressed in developing larvae, they led to somatic mutations specifically in the y gene. These somatic mosaics were observed in approximately one-half of the males expressing both nucleases. Germline y mutations were recovered from 5.7% of males, but from none of the females, tested. DNA sequences were determined and showed that all of the mutations were small deletions and/or insertions located precisely at the designed target. These are exactly the types of alterations expected from nonhomologous end joining (NHEJ) following double-strand cleavage of the target. This approach promises to permit generation of directed mutations in many types of cells and organisms.
Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury (2004)

We have identified cellular and molecular features of the stem cell niche required for marked amplification of mouse colonic epithelial progenitors (ColEPs) that occurs in response to wounding of the epithelium with dextran sodium sulfate. This regenerative response in areas adjacent to breaches in the epithelial barrier depends on the gut microbiota because ColEP proliferation is markedly diminished in germ-free animals. Analysis of conventionally raised C57BL/6 (B6) knockout mice lacking the Toll-like receptor signal transduction pathway component Myd88 and wild-type animals transplanted with Myd88(-/-) bone marrow, revealed that Myd88-mediated signaling through mesenchymal cells is also required for the ColEP response. Studies of B6 Csf1(op/op) (lacking macrophages) mice, Rag1(-/-) mice, and wild-type mice treated with neutrophil-specific Gr1 mAbs, disclosed that macrophages but not lymphocytes or neutrophils are necessary. GeneChip analysis of laser-capture-microdissected mesenchymal cells coupled with immunohistochemical and electron microscopic studies showed that, during the regenerative response, macrophages in the pericryptal stem cell niche express genes associated with their activation and extend processes to directly contact ColEPs near the crypt base. GeneChip analysis also identified a number of potential molecular mediators of regeneration expressed in the pericryptal progenitor niche, including secreted factors that stimulate epithelial proliferation and proteins involved in extracellular matrix and basement membrane function, stability, and growth factor binding. Together, these studies indicate that the colonic epithelial progenitor niche is a dynamic structure in which macrophages function as mobile "cellular transceivers" that coordinate inputs from luminal microbes and injured epithelium and transmit regenerative signals to neighboring ColEPs.
Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfA (2003)

PrfA is the major regulator of Listeria virulence gene expression. This protein is a member of the Crp/Fnr family of transcription regulators. To gain a deeper understanding of the PrfA regulon, we constructed a whole-genome array based on the complete genome sequence of Listeria monocytogenes strain EGDe and evaluated the expression profiles of the wild-type EGDe and a prfA-deleted mutant (EGDe Delta prfA). Both strains were grown at 37 degrees C in brain-heart infusion broth (BHI) and BHI supplemented with either activated charcoal, a compound known to enhance virulence gene expression, or cellobiose, a sugar reported to downregulate virulence gene expression in spite of full expression of PrfA. We identified three groups of genes that are regulated differently. Group I comprises, in addition to the 10 already known genes, two new genes, lmo2219 and lmo0788, both positively regulated and preceded by a putative PrfA box. Group II comprises eight negatively regulated genes: lmo0278 is preceded by a putative PrfA box, and the remaining seven genes (lmo0178-lmo0184) are organized in an operon. Group III comprises 53 genes, of which only two (lmo0596 and lmo2067) are preceded by a putative PrfA box. Charcoal addition induced upregulation of group I genes but abolished regulation by PrfA of most group III genes. In the presence of cellobiose, all the group I genes were downregulated, whereas group III genes remained fully activated. Group II genes were repressed in all conditions tested. A comparison of the expression profiles between a second L. monocytogenes strain (P14), its spontaneous mutant expressing a constitutively active PrfA variant (P14prfA*) and its corresponding prfA-deleted mutant (P14 Delta prfA) and the EGDe strain revealed interesting strain-specific differences. Sequences strongly similar to a sigma B-dependent promoter were identified upstream of 22 group III genes. These results suggest that PrfA positively regulates a core set of 12 genes preceded by a PrfA box and probably expressed from a sigma A-dependent promoter. In contrast, a second set of PrfA-regulated genes lack a PrfA box and are expressed from a sigma B-dependent promoter. This study reveals that PrfA can act as an activator or a repressor and suggests that PrfA may directly or indirectly activate different sets of genes in association with different sigma factors.