gebhart/patrepeval huggingface dataset:
Comprehensive Immunophenotyping of Cerebrospinal Fluid Cells in Patients with Neuroimmunological Diseases (2014)

We performed unbiased, comprehensive immunophenotyping of cerebrospinal fluid (CSF) and blood leukocytes in 221 subjects referred for the diagnostic work-up of neuroimmunological disorders to obtain insight about disease-specific phenotypes of intrathecal immune responses. Quantification of 14 different immune cell subsets, coupled with the assessment of their activation status, revealed physiological differences between intrathecal and systemic immunity, irrespective of final diagnosis. Our data are consistent with a model where the CNS shapes intrathecal immune responses to provide effective protection against persistent viral infections, especially by memory T cells, plasmacytoid dendritic cells, and CD56(bright) NK cells. Our data also argue that CSF immune cells do not simply reflect cells recruited from the periphery. Instead, they represent a mixture of cells that are recruited from the blood, have been activated intrathecally and leave the CNS after performing effector functions. Diagnosis-specific differences provide mechanistic insight into the disease process in the defined subtypes of multiple sclerosis (MS), neonatal onset multisystem inflammatory disease, and Aicardi-Goutières syndrome. This analysis also determined that secondary-progressive MS patients are immunologically closer to relapsing-remitting patients as compared with patients with primary-progressive MS. Because CSF immunophenotyping captures the biology of the intrathecal inflammatory processes, it has the potential to guide optimal selection of immunomodulatory therapies in individual patients and monitor their efficacy. Our study adds to the increasing number of publications that demonstrate poor correlation between systemic and intrathecal inflammatory biomarkers in patients with neuroimmunological diseases and stresses the importance of studying immune responses directly in the intrathecal compartment.
Combining CD19 Redirection and Alloanergization to Generate Tumor-Specific Human T Cells for Allogeneic Cell Therapy of B-Cell Malignancies (2010)

Allogeneic hematopoietic stem-cell transplantation can cure some patients with high-risk B-cell malignancies, but disease relapse following transplantation remains a significant problem. One approach that could be used to augment the donor T-cell-mediated antitumor effect is the infusion of allogeneic donor-derived T cells expressing a chimeric antibody receptor (CAR) specific to the B-cell antigen CD19. However, the use of such cells might result in toxicity in the form of graft-versus-host disease mediated by CD19-specific (CD19-CAR) T cells possessing alloreactive endogenous T-cell receptors. We therefore investigated whether nonalloreactive tumor-specific human T cells could be generated from peripheral blood mononuclear cells of healthy donors by the combination of CD19 redirection via CAR expression and subsequent alloanergization by allostimulation and concomitant blockade of CD28-mediated costimulation. Alloanergization of CD19-CAR T cells resulted in efficient and selective reduction of alloresponses in both CD4(+) and CD8(+) T cells, including allospecific proliferation and cytokine secretion. Importantly, T-cell effector functions including CAR-dependent proliferation and specific target cytolysis and cytokine production were retained after alloanergization. Our data support the application of CD19 redirection and subsequent alloanergization to generate allogeneic donor T cells for clinical use possessing increased antitumor activity but limited capacity to mediate graft-versus-host disease. Immunotherapy with such cells could potentially reduce disease relapse after allogeneic transplantation without increasing toxicity, thereby improving the outcome of patients undergoing allogeneic transplantation for high-risk B-cell malignancies.
Molecular cloning and expression of two distinct cDNA-encoding heparan sulfate proteoglycan core proteins from a rat endothelial cell line. (1992)

The cloned rat fat pad endothelial cell (RFP-EC) line synthesizes anticoagulantly active heparan sulfate proteoglycans (HSPGact) and anticoagulantly inactive heparan sulfate proteoglycans (HSPGinact), both of which exhibit 25-, 30-, and 50-kDa core proteins of extremely similar structure. The primary sequences of internal peptides obtained from HSPGinact core proteins and the NH2-terminal sequence analyses of the 25-kDa component from the HSPGinact core proteins demonstrate that the 30-kDa component is a previously unidentified species, designated as ryudocan, with the 25-kDa component representing a proteolytic degradation product, while the 50-kDa component is the rat homolog of syndecan (Saunders, S. Jalkanen, M., O'Farrell, S., and Bernfield, M. (1989) J. Cell Biol. 108, 1547-1556). Specific oligonucleotide probes were obtained for ryudocan and syndecan by polymerase chain reaction, and the corresponding cDNAs were isolated from a RFP-EC library. The cDNAs encode type I integral membrane proteins of 202 and 313 amino acids, respectively, which have homologous transmembrane and intracellular domains but very distinct extracellular regions. In particular, ryudocan exhibits only three potential glycosaminoglycan attachment sites within the extracellular region while syndecan has five glycosaminoglycan attachment sites within the same domain. Both species are expressed in RFP-EC lines, primary rat aortic smooth muscle cells and primary rat skin fibroblast cells. The levels of ryudocan and syndecan mRNA were measured by quantitative polymerase chain reaction in primary microvascular endothelial cells and closely associated non-endothelial cells isolated by cell sorting. Ryudocan and syndecan mRNAs were abundantly expressed in both populations representing about 0.1-0.5% of mRNA.
International network of cancer genome projects (2010)

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
A Massively Parallel Architecture for a Self-Organizing Neural Pattern Recognition Machine (1991)

A neural network architecture for the learning of recognition categories is derived. Real-time network dynamics are completely characterized through mathematical analysis and computer simulations. The architecture self-organizes and self-stabilizes its recognition codes in response to arbitrary orderings of arbitrarily many and arbitrarily complex binary input patterns. Top-down attentional and matching mechanisms are critical in self-stabilizing the code learning process. The architecture embodies a parallel search scheme which updates itself adaptively as the learning process unfolds. After learning self-stabilizes, the search process is automatically disengaged. Thereafter input patterns directly access their recognition codes without any search. Thus recognition time does not grow as a function of code complexity. A novel input pattern can directly access a category if it shares invariant properties with the set of familiar exemplars of that category. These invariant properties emerge in the form of learned critical feature patterns, or prototypes. The architecture possesses a context-sensitive self-scaling property which enables its emergent critical feature patterns to form. They detect and remember statistically predictive configurations of featural elements which are derived from the set of all input patterns that are ever experienced. Four types of attentional process—priming, gain control, vigilance, and intermodal competition—are mechanistically characterized. Top—down priming and gain control are needed for code matching and self-stabilization. Attentional vigilance determines how fine the learned categories will be. If vigilance increases due to an environmental disconfirmation, then the system automatically searches for and learns finer recognition categories. A new nonlinear matching law (the ⅔ Rule) and new nonlinear associative laws (the Weber Law Rule, the Associative Decay Rule, and the Template Learning Rule) are needed to achieve these properties. All the rules describe emergent properties of parallel network interactions. The architecture circumvents the noise, saturation, capacity, orthogonality, and linear predictability constraints that limit the codes which can be stably learned by alternative recognition models.
MicroRNA signature in diabetic wound healing: promotive role of miR‐21 in fibroblast migration (2011)

A major complication of diabetes mellitus is the disruption of normal wound repair process, characterised by insufficient production of growth factors. A molecular genetic approach wherein resident cells synthesise and deliver the growth factors to the wound site would be a powerful therapeutic strategy to treat diabetic wounds. One such molecular approach could be the application of microRNAs (miRNAs). This study reports differential expression of miRNAs related to cell development and differentiation, during wound healing in diabetic mice. Comparison of skin tissue from normal and diabetic mice showed that 14 miRNAs were differentially expressed in diabetic skin; miR-146b and miR-21 were the most noteworthy. Expression pattern of these miRNAs was also altered during healing of diabetic wounds. A subset of miRNAs (miR-20b, miR-10a, miR-10b, miR-96, miR-128, miR-452 and miR-541) exhibited similar basal levels in normal and diabetic skins, but displayed dysregulation during healing of diabetic wounds. Amongst the miRNAs studied, miR-21 showed a distinct signature with increased expression in diabetic skin but decreased expression during diabetic wound healing. We analysed the role of miR-21 in fibroblast migration, because migration of fibroblasts into the wound area is an important landmark facilitating secretion of growth factors and migration of other cell types into the wound, thus enhancing the healing process. Using gain-of and loss-of function approaches, we show that miR-21 is involved in fibroblast migration. Our preliminary studies implicate an important role for miRNAs in the pathogenesis of diabetic wounds.
Two-phase modelling of a fluid mixing layer (1999)

We analyse and improve a recently-proposed two-phase flow model for the statistical evolution of two-fluid mixing. A hyperbolic equation for the volume fraction, whose characteristic speed is the average interface velocity v *, plays a central role. We propose a new model for v * in terms of the volume fraction and fluid velocities, which can be interpreted as a constitutive law for two-fluid mixing. In the incompressible limit, the two-phase equations admit a self-similar solution for an arbitrary scaling of lengths. We show that the constitutive law for v * can be expressed directly in terms of the volume fraction, and thus it is an experimentally measurable quantity. For incompressible Rayleigh–Taylor mixing, we examine the self-similar solution based on a simple zero-parameter model for v *. It is shown that the present approach gives improved agreement with experimental data for the growth rate of a Rayleigh–Taylor mixing layer. Closure of the two-phase flow model requires boundary conditions for the surfaces that separate the two-phase and single-phase regions, i.e. the edges of the mixing layer. We propose boundary conditions for Rayleigh–Taylor mixing based on the inertial, drag, and buoyant forces on the furthest penetrating structures which define these edges. Our analysis indicates that the compatibility of the boundary conditions with the two-phase flow model is an important consideration. The closure assumptions introduced here and their consequences in relation to experimental data are compared to the work of others.
Concepts (1990)

This chapter considers the concepts of power in use in sixth- to eleventh-century Wales, and ideas about it. It describes a great variety of ruler terms and examines they ways in which they are used in the early middle ages. The notions of rule and rulers existed in early medieval Wales from the terms available for rulers and from their context of use. The use of the word rex or ‘king’ is predominant, and where rex is not used, the numerically significant exceptions are of two types: first, dux in the singular, ‘duke’ or ‘leader’, is used specifically to designate English royal officers and also some other people with a military following; the second type of alternative Latin usage involves worlds like seniores, meliores, and optimates, in the plural, ‘elders’ or ‘worthies’.
600 mW CW single-mode GaAlAs triple-quantum-well laser with a new index guided structure (1993)

A very-high-power, single-mode GaAlAs triple-quantum-well (TQW) laser with a novel real refractive index guided structure has been developed. The maximum output power of 720 mW CW and single transverse- and longitudinal-mode operation up to 600 mW CW have been achieved in a single-element device. This excellent mode operation is attained by using the real refractive index guided structure with a GaAlAs current-blocking layer which gives a low effective refractive index step, suppressing the spatial hole-burning effect in the high-power range.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Occurrence of sulphate‐reducing bacteria in human faeces and the relationship of dissimilatory sulphate reduction to methanogenesis in the large gut (1988)

Sulphate-reducing bacteria (SRB) were enumerated in 40 faecal samples obtained from two different human populations in the United Kingdom and rural South Africa. Species able to metabolize acetate, lactate, propionate, butyrate, H2/CO2, succinate, pyruvate, valerate, ethanol and a glutamate/serine/alanine mixture were found in faeces from both populations. Although a variety of nutritionally and morphologically distinct species of SRB belonging to the genera Desulfotomaculum, Desulfobacter, Desulfomonas and Desulfobulbus were identified, Desulfovibrio types always predominated. Significant numbers of SRB were present only in faecal samples from subjects whose breath methane excretion was low or undetectable. Reduced or absent methanogenesis in the presence of SRB was confirmed in fermentation studies with faecal slurries. Fourteen of 20 (70%) British faecal samples contained SRB and the remainder produced methane. The reverse was the case with 20 rural black South Africans, where only three (15%) of the samples had significant levels of SRB; the remaining 85% produced methane. These results suggest that to a large extent, dissimilatory sulphate reduction and methanogenesis are mutually exclusive in the human large gut.
World Perspective and Celiac Disease Epidemiology (2015)

In Europe and the USA, the mean frequency of celiac disease (CD) in the general population is approximately 1%, with some regional differences, the reasons for which remain elusive. A similar disease prevalence has been found in other countries mostly populated by individuals of European origin, e.g. Australia and Argentina. In Western countries, a true rise in overall CD prevalence of CD has been documented. CD is a common disorder in North Africa, the Middle East and India; however, the diagnostic rate is low in these countries due to low availability of diagnostic facilities and poor disease awareness. The highest CD prevalence in the world (5.6%) has been described in an African population originally living in Western Sahara, the Saharawi, of Arab-Berber origin. The reasons for this high CD frequency are unclear but could be primarily related to recent dietary changes and genetic factors, given the high level of consanguinity of this population. Further studies are needed to quantify the incidence of the celiac condition in apparently 'celiac-free' areas such as Sub-Saharan Africa and the Far East. In many developing countries, the frequency of CD is likely to increase in the near future given the diffuse tendency to adopt Western, gluten-rich dietary patterns. As most cases currently escape diagnosis all over the world, an effort should be made to increase the awareness of CD polymorphism. A cost-effective case-finding policy and new strategies of mass CD screening could significantly reduce the morbidity and mortality associated with untreated disease. The current high prevalence of CD is just the last link in a chain of events started about 10,000 years ago after wheat domestication and diffusion from the Middle East. We hypothesize different mechanisms to explain the so-called evolutionary celiac paradox of co-localization of gluten consumption and HLA CD-predisposing genotypes.
Enol Ethers as Substrates for Efficient Z- and Enantioselective Ring-Opening/Cross-Metathesis Reactions Promoted by Stereogenic-at-Mo Complexes: Utility in Chemical Synthesis and Mechanistic Attributes (2012)

The first examples of catalytic enantioselective ring-opening/cross-metathesis (EROCM) reactions that involve enol ethers are reported. Specifically, we demonstrate that catalytic EROCM of several oxa- and azabicycles, cyclobutenes and a cyclopropene with an alkyl- or aryl-substituted enol ether proceed readily in the presence of a stereogenic-at-Mo monopyrrolide-monoaryloxide. In some instances, as little as 0.15 mol % of the catalytically active alkylidene is sufficient to promote complete conversion within 10 min. The desired products are formed in up to 90% yield and >99:1 enantiomeric ratio (er) with the disubstituted enol ether generated in >90% Z selectivity. The enol ether of the enantiomerically enriched products can be easily differentiated from the terminal alkene through a number of functionalization procedures that lead to the formation of useful intermediates for chemical synthesis (e.g., efficient acid hydrolysis to afford the enantiomerically enriched carboxaldehyde). In certain cases, enantioselectivity is strongly dependent on enol ether concentration: larger equivalents of the cross partner leads to the formation of products of high enantiomeric purity (versus near racemic products with one equivalent). The length of reaction time can be critical to product enantiomeric purity; high enantioselectivity in reactions that proceed to >98% conversion in as brief a reaction time as 30 s can be nearly entirely eroded within 30 min. Mechanistic rationale that accounts for the above characteristics of the catalytic process is provided.
Differential expression of invertase genes in internal and external phloem tissues of potato ( Solanum tuberosum L.) (2000)

The cloning of promoter sequences of two invertase genes from potato ( Solanum tuberosum L.) is described. Histochemical analysis of series of reporter transgenic lines reveals phloem‐expression from both promoters, with one expressed preferentially in internal phloem and the other in external phloem of stem vascular bundles.
Thrombopoietin from human embryonic kidney cells stimulates an increase in megakaryocyte size of sublethally irradiated mice. (1993)

Previous work showed that treatment of irradiated mice with a thrombocytopoiesis-stimulating factor (TSF or thrombopoietin) decreased the degree and duration of thrombocytopenia in the period after irradiation. In an attempt to elucidate the radio-protective effects of TSF, femoral megakaryocyte sizes and numbers were measured in mice treated with 3.0 Gy of 137Cs gamma rays and TSF. For controls, other irradiated mice were given human serum albumin (HSA), the carrier protein for TSF, rabbit anti-mouse platelet serum (RAMPS), or normal rabbit serum (NRS); megakaryocyte sizes and numbers were studied on Days 7-14. The results showed that irradiated, TSF-treated mice had significantly larger megakaryocytes on all days assessed compared to HSA-treated control mice. Likewise, RAMPS-treated mice had significantly larger megakaryocytes 14 days after irradiation compared to NRS-treated mice. Megakaryocyte numbers were significantly depressed in TSF-treated mice on Days 7-10 and 14 and on Day 10 in RAMPS-treated mice, compared to their respective controls. Therefore, irradiated mice treated with TSF yielded results similar to RAMPS-treated mice. Megakaryocyte sizes and numbers were also determined for mice treated with 40,000 U/mouse of interleukin-6 (IL-6), 227 U/mouse of granulocyte-macrophage colony-stimulating factor (GM-CSF), or a combination of both cytokines; bovine serum albumin (BSA) was used as a control for these cytokine treatments. Unlike TSF treatment, GM-CSF significantly increased megakaryocyte numbers on both Days 10 and 14; the combination of both growth factors also increased megakaryocyte numbers on Day 14 compared to BSA-treated control mice. However, megakaryocyte size was decreased in GM-CSF-treated mice and in mice treated with both growth factors on Day 10. High levels of IL-6 failed to affect megakaryocyte size or number significantly on any day evaluated. The data of the present report, showing that TSF significantly increases megakaryocyte sizes and platelet counts of sublethally irradiated mice, indicate that thrombopoietin will be useful in treating patients undergoing bone marrow transplantation and/or patients with platelet production problems.
RANTES and MCP-3 Antagonists Bind Multiple Chemokine Receptors (1996)

Antagonists of multiple chemokines could be more effective than inhibitors of specific chemokines for controlling cell migration and inflammation. To attempt to identify such antagonists we characterized a number of truncated analogs of regulated on activation normal T cell expressed protein (RANTES), monocyte chemoattractant protein (MCP)-3, and MCP-1. On the basis of their ability to compete for binding of their parent chemokines, three analogs were selected for cross-reactivity studies: RANTES (9-68), MCP-3 (10-76), and MCP-1 (9-76). These analogs bound to THP-1 monocytic cells with dissociation constants that were within 4-6-fold of their native counterparts, but they did not promote detectable chemotaxis of THP-1 cells or enzyme release from purified human monocytes. The RANTES (9-68) analog competed for the binding and inhibited the activities of all three chemokines. In contrast, native RANTES was specific for RANTES binding sites. However, truncation of either MCP-1 or MCP-3 did not change their respective binding specificity. MCP-3 and MCP-3 (10-76) competed for binding of all three labeled chemokines. MCP-1 (9-76) competed strongly for binding of labeled MCP-1, but only weakly for the other two labeled ligands and inhibited the activities induced by MCP-1 and MCP-3 but not RANTES. Although RANTES (9-68) and MCP-3 (10-76) inhibited all three chemokines, the RANTES analog was significantly more potent for RANTES-induced activity. The results indicate that NH2-terminal residues partly determine the receptor specificity of RANTES, and deletions within this region permit binding to multiple chemokine receptors. The findings suggest the feasibility of design of high affinity multi-specific CC chemokine antagonists.