gebhart/patrepeval huggingface dataset:
Therapy against murine collagen‐induced arthritis with T cell receptor Vβ‐specific antibodies (1991)

Immunization with native type II collagen (CII) of susceptible strains of mice (H-2q) induces a rheumatoid arthritis-like disease. Collagen-induced arthritis (CIA) is an experimental model for T cell-mediated autoimmune disease. To investigate the T cell receptor (TcR) repertoire involved in the pathogenesis of CIA, CII-primed DBA/1 mice were treated with various TcR V beta-specific monoclonal antibodies (mAb) using a protocol resulting in a long-term elimination of the target T cells. In vivo treatment with anti-CD4 mAb led to nearly complete protection against CIA. Mice injected with anti-V beta 8.1, 2 or anti-V beta 5.1, 2 mAb had a reduced incidence of arthritis (respectively 28.6% and 50% vs 84.6% for the control group). Administration of anti-V beta 2 mAb delayed the onset of the disease whereas injection of anti-V beta 6 or anti-V beta 11 mAb did not alter CIA. Moreover, the combined treatment with anti-V beta 2 and anti-V beta 5 mAb efficiently reduced the development of CIA. The humoral response to CII was down-regulated only in the groups of mice that were improved by the treatment. In vitro proliferative response to CII of lymph node cells from primed DBA/1 was partially blocked by addition of several anti-V beta mAb. Thus, our findings suggest that the overall T cell response to CII may be polyclonal while the T cell clones involved in the pathogenesis of CIA express a limited number of V beta chains.
The V‐stent: A novel technique for coronary bifurcation stenting (1996)

Intracoronary stenting as a transcatheter treatment for bifurcation stenoses remains controversial. A novel technique of coronary bifurcation stenting is reported. A 15 mm Palmaz-Schatz stent is bent 180° at its bridge articulation into a V- configuration and mounted on two balloon-catheters linked together by adhesive tape. This unified stent delivery system was used successfully in five cases of porcine coronary bifurcation stenting. © 1996 Wiley-Liss, Inc.
Sidewall oxidation of polycrystalline-silicon gate (1989)

Evidence is presented demonstrating that sidewall oxidation, a processing step needed for device reliability, can lead to gate oxide thickening in short-channel devices. This increase in thickness is the result of encroachment of bird's beaks from the edges of the gate structure into the channel region. The encroachment can be reduced by increasing oxidation temperature and/or using a dry ambient. With a judicious choice of polysilicon sidewall oxidation conditions, minimum gate-to-drain overlap capacitance and adequate device reliability can be achieved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evidence for novel fate of Flk1+ progenitor: Contribution to muscle lineage (2003)

Flk1 is one of the specific cell surface receptors for vascular endothelial growth factor and one of the most specific markers highlighting the earliest stage of hematopoietic and vascular lineages. However, recent new evidence suggests that these Flk1(+) mesodermal progenitor cells also contribute to muscle lineages. All evidence is based on the experiments using in vitro differentiation and in vivo transplantation systems. Although this approach revealed a differentiation potential range of Flk1(+) cells that is wider than previously expected, it fails to determine whether Flk1(+) cells contribute to muscle lineage as part of the normal developmental process. To obtain direct evidence for the fate of Flk1(+) cells in development, we used a knock-in mouse line where Cre is expressed in Flk1(+) cells. Studies with these Cre lines provide direct evidence that Flk1(+) cells are progenitors for muscles, in addition to hematopoietic and vascular endothelial cells.
Notch Signaling Alters Sensory or Neuronal Cell Fate Specification of Inner Ear Stem Cells (2011)

Multipotent progenitor cells in the otic placode give rise to the specialized cell types of the inner ear, including neurons, supporting cells, and hair cells. The mechanisms governing acquisition of specific fates by the cells that form the cochleovestibular organs remain poorly characterized. Here we show that whereas blocking Notch signaling with a γ-secretase inhibitor increased the conversion of inner ear stem cells to hair cells by a mechanism that involved the upregulation of bHLH transcription factor, Math1 (mouse Atoh1), differentiation to a neuronal lineage was increased by expression of the Notch intracellular domain. The shift to a neuronal lineage could be attributed in part to continued cell proliferation in cells that did not undergo sensory cell differentiation due to the high Notch signaling, but also involved upregulation of Ngn1. The Notch intracellular domain influenced Ngn1 indirectly by upregulation of Sox2, a transcription factor expressed in many neural progenitor cells, and directly by an interaction with an RBP-J binding site in the Ngn1 promoter/enhancer. The induction of Ngn1 was blocked partially by mutation of the RBP-J site and nearly completely when the mutation was combined with inhibition of Sox2 expression. Thus, Notch signaling had a significant role in the fate specification of neurons and hair cells from inner ear stem cells, and decisions about cell fate were mediated in part by a differential effect of combinatorial signaling by Notch and Sox2 on the expression of bHLH transcription factors.
Comparative Vaccine Studies in HLA-A2.1-Transgenic Mice Reveal a Clustered Organization of Epitopes Presented in Hepatitis C Virus Natural Infection (2002)

A polyepitopic CD8(+)-T-cell response is thought to be critical for control of hepatitis C virus (HCV) infection. Using transgenic mice, we analyzed the immunogenicity and dominance of most known HLA-A2.1 epitopes presented during infection by using vaccines that carry the potential to enter clinical trials: peptides, DNA, and recombinant adenoviruses. The vaccines capacity to induce specific cytotoxic T lymphocytes and interferon gamma-producing cells revealed that immunogenic epitopes are clustered in specific antigens. For two key antigens, flanking regions were shown to greatly enhance the scope of epitope recognition, whereas a DNA-adenovirus prime-boost vaccination strategy augmented epitope immunogenicity, even that of subdominant ones. The present study reveals a clustered organization of HCV immunogenic HLA.A2.1 epitopes and strategies to modulate their dominance.
Astaxanthin Limits Exercise-Induced Skeletal and Cardiac Muscle Damage in Mice (2003)

Dietary antioxidants may attenuate oxidative damage from strenuous exercise in various tissues. Beneficial effects of the antioxidant astaxanthin have been demonstrated in vitro, but not yet in vivo. We investigated the effect of dietary supplementation with astaxanthin on oxidative damage induced by strenuous exercise in mouse gastrocnemius and heart. C57BL/6 mice (7 weeks old) were divided into groups: rested control, intense exercise, and exercise with astaxanthin supplementation. After 3 weeks of exercise acclimation, both exercise groups ran on a treadmill at 28 m/min until exhaustion. Exercise-increased 4-hydroxy-2-nonenal-modified protein and 8-hydroxy-2'-deoxyguanosine in gastrocnemius and heart were blunted in the astaxanthin group. Increases in plasma creatine kinase activity, and in myeloperoxidase activity in gastrocnemius and heart, also were lessened by astaxanthin. Astaxanthin showed accumulation in gastrocnemius and heart from the 3 week supplementation. Astaxanthin can attenuate exercise-induced damage in mouse skeletal muscle and heart, including an associated neutrophil infiltration that induces further damage.
Gabriel: a design environment for DSP (1990)

Gabriel, a second-generation digital signal-processing (DSP) design environment, is described. The Gabriel experimental signal-processing software performs non-real-time algorithm simulations and code synthesis for real-time hardware based on programmable DSPs. Gabriel eases code development for architectures that are not easy targets for conventional compilers. The model of compilation used by Gabriel is discussed at length. Modification of the model to run in real time, target architectures, and scheduling are examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
CO2 Capture Technologies for Cement Industry (2009)

The effect of the increasing concentration of CO2 in the atmosphere on climate change is a major driving force for the development of advanced energy cycles incorporating CO2 management options. Growing interest in the technical and economic feasibility of CO2 capture from large coal-based power plants has led to increased efforts worldwide to develop new concepts for greater CO2 reductions in the future. Greenhouse gas emissions, especially CO2, have to be reduced by 50–80% by 2050, according to the IPCC [1]. The type of fuel used in cement manufacture directly impacts on CO2 emissions, with coal accounting for around 60–70% of CO2 emissions from cement installations. Therefore, the large amount of carbon dioxide emitted during cement manufacturing process - 5% of the total emissions of CO2 from stationary sources worldwide - is a cause of great concern and has to be tack led in order to comply with current legislation. Several technologies are available and have been proposed for the separation of CO2 from the flue gases from new and existing plants with retrofit capture units. Few studies have been undertaken on CO2 capture in cement plants to assess the suitable technologies, with oxy-combustion and amine scrubbing as the possible options (pre-combustion capture not being viable). This paper summarises the different CO2 capture technologies suitable for cement industry and assesses the potential of the calcium looping cycle [2], [3] as a new route for CO2 capture in the cement industry. The potential advantage of this system is the very low efficiency penalty expected (<6%) compared with other capture technologies as the heat required for calcination is balanced by heat released during the carbonation (CO2 capture) step and can be utilized efficiently at high temperature in the plant’s steam cycle. Since limestone is already used for cement manufacture, and because it is a cheap material with good geographical distribution, it allows the use of local limestone resources with minimal limestone-related infrastructure investment. Another envisaged benefit of this new technology is that the lime purged from the cycle could be us ed as a raw material for the production of cement clinker. Therefore, the calcium looping cycle can potentially have an important impact in reducing CO2 emissions from the cement industry, and may also be applicable in other sectors.
Sp1 cooperates with c-Myc to activate transcription of the human telomerase reverse transcriptase gene (hTERT) (2000)

Telomerase activation is thought to be a critical step in cellular immortalization and carcinogenesis. The human telomerase catalytic subunit (hTERT) is a rate limiting determinant of the enzymatic activity of human telomerase. In the previous study, we identified the proximal 181 bp core promoter responsible for transcriptional activity of the hTERT gene. To identify the regulatory factors of transcription, transient expression assays were performed using hTERT promoter reporter plasmids. Serial deletion assays of the core promoter revealed that the 5'-region containing the E-box, which binds Myc/Max, as well as the 3'-region containing the GC-box, which binds Sp1, are essential for transactivation. The mutations introduced in the E-box or GC-box significantly decreased transcriptional activity of the promoter. Overexpression of Myc/Max or Sp1 led to significant activation of transcription in a cell type-specific manner, while Mad/Max introduction repressed it. However, the effects of Myc/Max on transactivation were marginal when Sp1 sites were mutated. Western blot analysis using various cell lines revealed a positive correlation between c-Myc and Sp1 expression and transcriptional activity of hTERT. Using fibroblast lineages in different stages of transformation, we found that c-Myc and Sp1 were induced to a dramatic extent when cells overcame replicative senescence and obtained immortal characteristics, in association with telomerase activation. These findings suggest that c-Myc and Sp1 cooperatively function as the major determinants of hTERT expression, and that the switching functions of Myc/Max and Mad/Max might also play roles in telomerase regulation.
Geo-material surface modification of microchips using layer-by-layer (LbL) assembly for subsurface energy and environmental applications (2017)

A key constraint in the application of microfluidic technology to subsurface flow and transport processes is the surface discrepancy between microchips and the actual rocks/soils. This research employs a novel layer-by-layer (LbL) assembly technology to produce rock-forming mineral coatings on microchip surfaces. The outcome of the work is a series of 'surface-mimetic micro-reservoirs (SMMR)' that represent multi-scales and multi-types of natural rocks/soils. For demonstration, the clay pores of sandstones and mudrocks are reconstructed by representatively coating montmorillonite and kaolinite in polydimethylsiloxane (PDMS) microchips in a wide range of channel sizes (width of 10-250 μm, depth of 40-100 μm) and on glass substrates. The morphological and structural properties of mineral coatings are characterized using a scanning electron microscope (SEM), optical microscope and profilometer. The coating stability is tested by dynamic flooding experiments. The surface wettability is characterized by measuring mineral oil-water contact angles. The results demonstrate the formation of nano- to micro-scale, fully-covered and stable mineral surfaces with varying wetting properties. There is an opportunity to use this work in the development of microfluidic technology-based applications for subsurface energy and environmental research.
Proteolytic inactivation of tissue factor pathway inhibitor by bacterial omptins (2008)

The immune response to infection includes activation of the blood clotting system, leading to extravascular fibrin deposition to limit the spread of invasive microorganisms. Some bacteria have evolved mechanisms to counteract this host response. Pla, a member of the omptin family of Gram-negative bacterial proteases, promotes the invasiveness of the plague bacterium, Yersinia pestis, by activating plasminogen to plasmin to digest fibrin. We now show that the endogenous anticoagulant tissue factor pathway inhibitor (TFPI) is also highly sensitive to proteolysis by Pla and its orthologs OmpT in Escherichia coli and PgtE in Salmonella enterica serovar Typhimurium. Using gene deletions, we demonstrate that bacterial inactivation of TFPI requires omptin expression. TFPI inactivation is mediated by proteolysis since Western blot analysis showed that TFPI cleavage correlated with loss of anticoagulant function in clotting assays. Rates of TFPI inactivation were much higher than rates of plasminogen activation, indicating that TFPI is a better substrate for omptins. We hypothesize that TFPI has evolved sensitivity to proteolytic inactivation by bacterial omptins to potentiate procoagulant responses to bacterial infection. This may contribute to the hemostatic imbalance in disseminated intravascular coagulation and other coagulopathies accompanying severe sepsis.
Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root (2009)

Regulated cell division is critical for the development of multi-cellular organisms. In the Arabidopsis root, SCARECROW (SCR) is required for the first cell division, but represses the subsequent, longitudinal asymmetric cell divisions that generate the two cell types of the ground tissue - cortex and endodermis. To elucidate the molecular basis of the role of SCR in ground tissue patterning, we screened for SCR-interacting proteins using the yeast two-hybrid method. A number of putative SCR-interacting proteins were identified, among them LIKE HETEROCHROMATIN PROTEIN 1 (LHP1). In lhp1 mutants, a second longitudinal asymmetric cell division occurs in the ground tissue earlier than in wild-type plants. Similar to the scr mutant, this premature middle cortex phenotype is suppressed by the phytohormone gibberellin (GA). We provide evidence that the N-terminal domain of SCR is required for the interaction between SCR and LHP1 as well as with other interacting partners, and that this domain is essential for repression of asymmetric cell divisions. Consistent with a role for GA in cortex proliferation, mutants of key GA signaling components produce a middle cortex precociously. Intriguingly, we found that the spindly (spy) mutant has a similar middle cortex phenotype. As SPY homologs in animals physically interact with histone deacetylase, we examined the role of histone deacetylation in middle cortex formation. We show that inhibition of histone deacetylase activity causes premature middle cortex formation in wild-type roots. Together, these results suggest that epigenetic regulation is probably the common basis for SCR and GA activity in cortex cell proliferation.
Footprinting RNA-protein complexes following gel retardation assays: application to the R-17-procoat-RNA and tat-TAR interactions (1994)

RNA-protein complexes isolated following a gel retardation assay can be footprinted within the gel matrix using the chemical nuclease activities of 4,7-dimethyl-, 5,6-dimethyl-, and 3,4,7,8-tetramethyl-1,10-phenanthroline-copper. These complexes are more reactive than 1,10-phenanthroline-copper but share its reaction preference for bulges and loops. The interaction of the coat protein of R-17 with its viral RNA target and tat- and tat-derived peptides with HIV TAR RNA have been studied. In both cases, the RNA sequence opposite a 2-3 nucleotide bulge are protected. Tat-derived peptides inhibit cleavage at sites which intact tat does not protect. These results are consistent with transcription studies which have suggested that truncation of tat increases nonspecific binding.
Counting Single Native Biomolecules and Intact Viruses with Color-Coded Nanoparticles (2006)

Nanometer-sized particles such as semiconductor quantum dots and energy-transfer nanoparticles have novel optical properties such as tunable light emission, signal brightness, and multicolor excitation that are not available from traditional organic dyes and fluorescent proteins. Here we report the use of color-coded nanoparticles and dual-color fluorescence coincidence for real-time detection of single native biomolecules and viruses in a microfluidic channel. Using green and red nanoparticles to simultaneously recognize two binding sites on a single target, we demonstrate that individual molecules of genes, proteins, and intact viruses can be detected and identified in complex mixtures without target amplification or probe/target separation. Real-time coincidence analysis of single-photon events allows rapid detection of bound targets and efficient discrimination of excess unbound probes. Quantitative studies indicate that the counting results are remarkably precise when the total numbers of counted molecules are more than 10. The use of bioconjugated nanoparticle probes for single-molecule detection is expected to have important applications in ultrasensitive molecular diagnostics, bioterrorism agent detection, and real-time imaging and tracking of single-molecule processes inside living cells.
Monocarboxylate transporter 4 (MCT4) and CD147 overexpression is associated with poor prognosis in prostate cancer (2011)

Our data provides novel evidence for the involvement of MCTs in prostate cancer. According to our results, we consider that MCT2 should be further explored as tumour marker and both MCT4 and CD147 as markers of poor prognosis in prostate cancer.
Experimental treatments for Ebola (2014)

The Ebola virus disease outbreak in West Africa is a tragedy of mass proportions. It has afflicted a region with poor public health infrastructure, communities fearful of medical intervention due to past atrocities, and in a situation where the people are protective of themselves and their families. As the death toll continues to rise, experimental treatments are being offered as a solution. The widespread use and management of these treatments is a challenge due to the social and cultural structures that exists in these communities. An approach that is sensitive to these experiences needs to be observed.
What is the Efficiency of ATP Signaling from Erythrocytes to Regulate Distribution of O2 Supply Within the Microvasculature? (2012)

Erythrocytes appear to be ideal sensors for regulating microvascular O(2) supply as they release the potent vasodilator ATP in an O(2) saturation-dependent manner. Whether erythrocytes play a significant role in regulating O(2) supply in the complex environment of diffusional O(2) exchange among capillaries, arterioles, and venules, depends on the efficiency with which erythrocytes signal the vascular endothelium. If one assumes that the distribution of purinergic receptors is uniform throughout the microvasculature, then the most efficient site for signaling should occur in capillaries, where the erythrocyte membrane is in close proximity to the endothelium. ATP released from erythrocytes would diffuse a short distance to P(2y) receptors inducing an increase in blood flow, possibly the result of endothelial hyperpolarization. We hypothesize that this hyperpolarization varies across the capillary bed depending upon erythrocyte supply rate and the flux of O(2) from these erythrocytes to support O(2) metabolism. This would suggest that the capillary bed would be the most effective site for erythrocytes to communicate tissue oxygen needs. Electrically coupled endothelial cells conduct the integrated signal upstream where arterioles adjust vascular resistance, thus enabling ATP released from erythrocytes to regulate the magnitude and distribution of O(2) supply to individual capillary networks.
Linguistic Diversity in a Deaf Prison Population: Implications for Due Process (2004)

The entire deaf prison population in the state of Texas formed the basis for this research. The linguistic skills of prison inmates were assessed using the following measures: (1) Kannapell's categories of bilingualism, (2) adaptation of the diagnostic criteria for Primitive Personality Disorder, (3) reading scores on the Test of Adult Basic Education, and (4) an evaluation of sign language use and skills by a certified sign language interpreter who had worked with deaf inmates for the past 17 years. Deaf inmates with reading scores below the federal standard for literacy (grade level 2.9) were the group most likely to demonstrate linguistic incompetence to stand trial, meaning that they probably lacked the ability to understand the charges against them and/or were unable to participate in their own defenses. Based on the language abilities and reading scores of this population, up to 50% of deaf state prison inmates may not have received due process throughout their arrest and adjudication. Despite their adjudicative and/or linguistic incompetence, these individuals were convicted in many cases, possibly violating their constitutional rights and their rights under the Americans with Disabilities Act.