gebhart/patrepeval huggingface dataset:
Extracellular ATP and Toll-Like Receptor 2 Agonists Trigger in Human Monocytes an Activation Program That Favors T Helper 17 (2013)

Strategically-paired Toll-like receptor (TLR) ligands induce a unique dendritic cell (DC) phenotype that polarizes Th1 responses. We therefore investigated pairing single TLR ligands with a non TLR-mediated danger signal to cooperatively induce distinct DC properties from cultured human monocytes. Adenosine triphosphate (ATP) and the TLR2 ligand lipoteichoic acid (LTA) selectively and synergistically induced expression of IL-23 and IL-1β from cultured monocytes as determined by ELISA assays. Flow cytometric analysis revealed that a sizable sub-population of treated cells acquired DC-like properties including activated surface phenotype with trans-well assays showing enhanced migration towards CCR7 ligands. Such activated cells also preferentially deviated, in an IL-23 and IL-1-dependent manner, CD4(pos) T lymphocyte responses toward the IL-22(hi), IL-17(hi)/IFN-γ(lo) Th17 phenotype in standard in vitro allogeneic sensitization assays. Although pharmacological activation of either ionotropic or cAMP-dependent pathways acted in synergy with LTA to enhance IL-23, only inhibition of the cAMP-dependent pathway antagonized ATP-enhanced cytokine production. ATP plus atypical lipopolysaccharide from P. gingivalis (signaling through TLR2) was slightly superior to E. coli-derived LPS (TLR4 ligand) for inducing the high IL-23-secreting DC-like phenotype, but greatly inferior for inducing IL-12 p70 production when paired with IFN-γ, a distinction reflected in activated DCs' ability to deviate lymphocytes toward Th1. Collectively, our data suggest TLR2 ligands encountered by innate immune cells in an environment with physiologically-relevant levels of extracellular ATP can induce a distinct activation state favoring IL-23- and IL-1β-dependent Th17 type response.
Strained ${\rm n}$-MOSFET With Embedded Source/Drain Stressors and Strain-Transfer Structure (STS) for Enhanced Transistor Performance (2008)

A novel-channel MOS transistor with a silicon-germanium (SiGe) heterostructure embedded beneath the channel and silicon-carbon source/drain (Si:C S/D) stressors was demonstrated. The additional SiGe structure couples additional strain from the S/D stressors to the overlying Si channel, leading to enhanced strain effects in the channel region. We termed the SiGe region a strain-transfer structure due to its role in enhancing the transfer of strain from lattice-mismatched S/D stressors to the channel region. Numerical simulations were performed using the finite-element method to explain the strain-transfer mechanism. A significant drive current I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DSAT</sub> improvement of 40% was achieved over the unstrained control devices, which is predominantly due to the strain-induced mobility enhancement. In addition, the impact of scaling the device design parameters on transistor drive current performance was investigated. Guidelines on further performance optimization in such a new device structure are provided.
The collagen matrix of the heart. (1981)

Scanning electron microscopy demonstrates an extensive and highly organized network of collagen in the left ventricle of all species examined. This system is arbitrarily divisible into three major components: a collagen weave network that surrounds groups of myocytes; an extensive array of collagen struts measuring 120 to 150 nm in diameter that extend from the basal lamina of a myocyte to the basal laminae of all contiguous myocytes; and an array of similar sized collagen struts that extend from the basal lamina of all capillaries to the basal laminae of all contiguous myocytes. The functions of the individual components of this complicated network are not well-defined. The weave network certainly contributes to the viscous and elastic properties of the heart. Myocyte-to-myocyte struts can prevent slippage of adjacent cells during the cardiac cycle and would ensure equal stretch of adjacent myocytes during diastole. Myocyte to capillary struts may be important in maintaining capillary patency during the early phases of systole. In rats. rabbits and hamsters this entire system is virtually absent at birth and develops rapidly to the adult form by 15 days.
Multiple sclerosis diagnostic criteria: three years later (2005)

New diagnostic criteria for multiple sclerosis (MS) were developed by an International Panel in 2001 and have had wide distribution and discussion since publication. These provided the first formal incorporation of magnetic resonance imaging (MRI) in a diagnosis work-up for patients suspected of having MS. The so-called McDonald criteria have been studied in retrospective and prospective analyses for sensitivity, specificity and utility, and have been proven to compare favourably or to be an improvement upon prior MS diagnostic criteria. The purpose of the current review is to present and evaluate the key studies that have been performed using the McDonald criteria since 2001 and to set the stage for an upcoming re-evaluation of the new criteria based on data-driven information gathered since their development.
Efficient Methano[70]fullerene/MDMO‐PPV Bulk Heterojunction Photovoltaic Cells (2003)

Owing to their increased absorption of light in the visible region, [70]fullerene derivatives provide a high photocurrent when incorporated as the electron acceptor in thin-film polymer photovoltaic cells. An incident-photon-to-current efficiency of 66 % is obtained when [70]PCBM (see picture) is used in combination with a poly(p-phenylene vinylene). These high currents originate from an ultrafast charge transfer that occurs upon photoexcitation of either the fullerene or the polymer. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z51647_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Nonmitogenic CD3 Antibody Reverses Virally Induced (Rat Insulin Promoter-Lymphocytic Choriomeningitis Virus) Autoimmune Diabetes Without Impeding Viral Clearance (2002)

Treatment with nonmitogenic CD3 Ab reverses established autoimmune diabetes in nonobese diabetic mice by restoring self-tolerance, and is currently under clinical evaluation in patients presenting recent onset type I diabetes. Due to the immunosuppressive potential of this strategy, it was relevant to explore how this treatment would influence the outcome of concomitant viral infections. In this study, we used a transgenic model of virally induced autoimmune diabetes (rat insulin promoter-lymphocytic choriomeningitis virus) that allows for more precise tracking of the autoaggressive response and choice of the time point for initiation of autoimmunity. CD3 was most effective during a clearly defined prediabetic phase and prevented up to 100% of diabetes by drastically lowering activation of autoaggressive CD8 lymphocytes and their production of inflammatory cytokines. Interestingly, reversion of established disease could be achieved as well, when nonmitogenic CD3 was administered late during pathogenesis to overtly diabetic recipients. Most importantly, competence to clear viral infections was maintained. Thus, administration of nonmitogenic CD3 prevents diabetes by sufficient systemic reduction of (auto)aggressive lymphocytes, but without compromising antiviral immune competence.
Increased Plasma Levels of Adrenomedullin in Patients with Systemic Inflammatory Response Syndrome (1999)

We measured the plasma levels of adrenomedullin (AM), a novel vasodilating peptide, in 89 patients with various forms of systemic inflammatory response syndrome (SIRS) and 13 healthy volunteers serving as controls. Plasma levels of AM in SIRS (burns: 20.5 +/- 3. 2 fmol/ml [mean +/- SEM]; pancreatitis: 13.8 +/- 3.8 fmol/ml; trauma: 14.9 +/- 2.5 fmol/ml; traumatic shock: 41.1 +/- 7.8 fmol/ml; severe sepsis: 59.9 +/- 11.2 fmol/ml; septic shock: 193.5 +/- 30.1 fmol/ml) were significantly increased over those of controls (5.1 +/- 0.2 fmol/ml). The patients with traumatic shock or septic shock especially had higher levels of plasma AM than those with trauma or severe sepsis, respectively. These data showed that in patients with SIRS, plasma AM levels increased in proportion to the severity of illness. Subsequently, we measured the plasma levels of mediators such as tumor necrosis factor (TNF)-alpha, interleukin (IL)-6, IL-8, plasminogen activator inhibitor (PAI)-1, and thrombomodulin (TM) in patients with traumatic shock and septic shock. A significant correlation was observed between plasma AM and TNF-alpha levels in patients with septic shock, suggesting an important role for AM as well as of TNF-alpha in the pathophysiology of inflammation. Plasma AM and IL-8 levels correlated positively with Acute Physiology and Chronic Health Evaluation (APACHE) II score, peak multiple organ failure (MOF) score during the first month and prognosis in patients with septic shock, as did plasma IL-6 levels in patients with traumatic shock. The plasma AM level might serve as a useful marker for evaluating the severity of disease and as an early predictor of subsequent organ failure and outcome in septic shock.
Antibacterial activity of the human host defence peptide LL-37 and selected synthetic cationic lipids against bacteria associated with oral and upper respiratory tract infections (2012)

These data suggest that cationic lipids such as ceragenins warrant further testing as potential novel antibacterial agents.
Fluorescence Imaging of Electrical Activity in Cardiac Cells Using An All-Solid-State System (2004)

Tracking spatial and temporal determinants of cardiac arrhythmogenesis at the cellular level presents challenges to the optical mapping techniques employed. In this paper, we describe a compact system combining two nontraditional low-cost solutions for excitation light sources and emission filters in fluorescence measurements of transmembrane potentials, Vm, or intracellular calcium, [Ca2+]i in cardiac cell networks. This is the first reported use of high-power blue and green light emitting diodes (LEDs), to excite cell monolayers stained with Vm - (di-8-ANEPPS) or [Ca2+]i - (Fluo-3) sensitive dyes. In addition, we use simple techniques for fabrication of suitable thin emission filters with uniform properties, no auto-fluorescence, high durability and good flexibility for imaging Vm or [Ca2+]i. The battery-operated LEDs and the fabricated emission filters, integrated with a fiber-optic system for contact fluorescence imaging, were used as tools to characterize conduction velocity restitution at the macro-scale. The versatility of the LEDs for illumination is further emphasized through 1) demonstration of their usage for epi-illumination recordings at the single-cell level, and 2) demonstration of their unique high-frequency light modulation ability. The LEDs showed excellent stability as excitation light sources for fluorescence measurements; acceptable signal-to-noise ratio and negligible cell photodamage and indicator dye photobleaching were observed.
Sequential development of interleukin 2–dependent effector and regulatory T cells in response to endogenous systemic antigen (2005)

Transfer of naive antigen-specific CD4(+) T cells into lymphopenic mice that express an endogenous antigen as a systemic, secreted protein results in severe autoimmunity resembling graft-versus-host disease. T cells that respond to this endogenous antigen develop into effector cells that cause the disease. Recovery from this disease is associated with the subsequent generation of FoxP3(+)CD25(+) regulatory cells in the periphery. Both pathogenic effector cells and protective regulatory cells develop from the same antigen-specific T cell population after activation, and their generation may occur in parallel or sequentially. Interleukin (IL)-2 plays a dual role in this systemic T cell reaction. In the absence of IL-2, the acute disease is mild because of reduced T cell effector function, but a chronic and progressive disease develops late and is associated with a failure to generate FoxP3(+) regulatory T (T reg) cells in the periphery. Thus, a peripheral T cell reaction to a systemic antigen goes through a phase of effector cell-mediated pathology followed by T reg cell-mediated recovery, and both require the growth factor IL-2.
MapReduce/Bigtable for Distributed Optimization (2010)

With large data sets, it can be time consuming to run gradient based optimization, for example to minimize the log-likelihood for maximum entropy models. Distributed methods are therefore appealing and a number of distributed gradient optimization strategies have been proposed including: distributed gradient, asynchronous updates, and iterative parameter mixtures. In this paper, we evaluate these various strategies with regards to their accuracy and speed over MapReduce/Bigtable and discuss techniques and configurations needed for high performance. 1
Sequence of gene E15 of bacteriophage D108 and comparison with phage Mu (1990)

The genomes of bacteriophage Mu and the closely related, heteroimmune bacteriophage D108 are greater than 90% homologous, with three small regions of nonhomology at the left end of the genomes and a 520-bp insertion near the right end of the D108 genome The first region of nonhomology encompasses the genes for the two regulatory proteins, repressor (c) and ner, and about 180-bp of the N- terminus of the A, or transposase, gene (Priess et al., 1982; Toussaint et al., 1983; Mizuuchi et al., 1986) and extends from about 200 bp to 1500 bp from the left end of the genomes. The second region of nonhomology between the two genomes contains the 3' portion of gene E6 (in the nomenclature of Priess et al., 1987) and lies between 4817-5044 bp from the left end of the Mu genome (Waggoner et al., 1988).
PNA-nucleic acid complexes. Structure, stability and dynamics (1996)

Growing interest in gene targeting drugs has inspired the development of a multitude of nucleic acid analogues, many of which feature substitutions in the phosphodiester moiety of the backbone (reviewed by Mesmaeker et al . 1995 and Nielsen, 1995). Peptide nucleic acid (PNA) is an example of a more radical redesign of DNA. The entire sugar-phosphate backbone is substituted by a chain of peptide-like N-(2-aminoethyl)glycine units so that an achiral and uncharged DNA-mimic is obtained (Fig. 1; Nielsen et al . 1991). The synthesis is based on standard peptide chemistry (Christensen et al . 1995) and has been automated. PNA can relatively easily be modified to include modifications of the backbone as well as of the bases (Hyrup &amp; Nielsen, 1996). PNA is chemically stable and, in contrast to natural nucleic acids and peptides, PNA is expected to remain intact in living cells since it is not a substrate for natural hydrolytic enzymes and is not degraded by cell extracts (Demidov et al . 1994).
Patch-Based Progressive 3D Point Set Upsampling (2019)

We present a detail-driven deep neural network for point set upsampling. A high-resolution point set is essential for point-based rendering and surface reconstruction. Inspired by the recent success of neural image super-resolution techniques, we progressively train a cascade of patch-based upsampling networks on different levels of detail end-to-end. We propose a series of architectural design contributions that lead to a substantial performance boost. The effect of each technical contribution is demonstrated in an ablation study. Qualitative and quantitative experiments show that our method significantly outperforms the state-of-the-art learning-based and optimazation-based approaches, both in terms of handling low-resolution inputs and revealing high-fidelity details.
Crystallization and cryocrystallography inside X-ray capillaries (2001)

This paper presents a modification of the gel acupuncture method to grow isolated crystals inside X-ray capillaries. Protein crystals are grown from 2–12 µl of gelled agarose–protein solution, cryoprotected and immobilized by the gel matrix. The same X-ray capillary that acts as a crystallization reactor is used to transport the crystals to the X-ray source and to collect data at both room temperature and 100 K, without any post-crystallization manipulation. To enhance the flash-cooling stage, two additional elements are proposed for inclusion in the cryosystems currently in use: a laser pointer to illuminate the crystal to be flash-cooled and a trap to divert the N 2 flow and switch from room temperature to 100 K without misalignment of the crystal. With the proposed implementation, data can be collected at different temperatures from the same crystal in exactly the same orientation. This permits the study, at lattice level, of changes in unit-cell parameters, mosaic spread and crystal quality induced by cryogenic temperatures and annealing techniques.
Video mosaic (1994)

Paper video storyboards are still in use by even very experienced video producers with access to the most advanced video editing software. An analysis of the characteristics of paper and on-line editing provide an overlapping but distinct set of benefits (and problems). Paper provides the user with the ability to lay out various temporal sequences over a large spatial area and the ability to quickly sketch, annotate and rearrange the relevant video clips. On-line editing provides users with the ability to generate and store a variety of video arrangements. Video Mosaic provides users with the ability to combine the best of both worlds: elements of a paper video storyboard are used as input to an on-line video editing system to take advantage of the best aspects of each. We developed a Unix and a Macintosh version of Video Mosaic. This paper describes the design of Video Mosaic, compares alternative approaches to creating this type of application, and suggests directions for future work.
Gene cloning: an introduction. (1990)

The basic principles of gene cloning - why gene cloning is important vehicles - plasmids and bacteriophages purification of DNA from living cells manipulation of purified DNA introduction of DNA into living cells cloning vectors for E. coli cloning vectors for organisms other than E. coli the applications of cloning in gene analysis how to obtain a clone of a specific gene studying gene and genome structure studying gene expression the polymerase chain reaction gene cloning in research and biotechnology production of protein from cloned genes gene cloning in medicine gene cloning in agriculture what to read next.
Synthesis and Application of Novel Glyoxylate-derived Chloroformates (2002)

A convenient process for the synthesis of glyoxylate-derived chloroformates has been developed. The approach involves the reaction of glyoxylate esters with triphosgene and pyridine in various solvent systems. These novel glyoxylate-derived chloroformates are multifunctional, possessing a chloroformate, ester, and haloalkyl moiety. Further elaboration via a thiocarbonate route afforded highly functionalized carboxylic acid-derived alkoxycarbonyl-chlorocarbonyloxy-methyl esters. Application of a benzyl glyoxylate-derived chloroformate to halofenozide was also accomplished, affording halofenozide-N-carbonyloxy-chloro/iodoacetic acid benzyl ester derivatives, which were further derivatized to carboxylic acid-derived (halofenozide-N-carbonyloxy)-benzyloxycarbonyl-methyl esters. The trifunctional nature of the glyoxylate moiety was demonstrated through conversion of the benzyloxycarbonyl moiety of a carboxylic acid-derived (halofenozide-N-carbonyloxy)-benzyloxycarbonyl-methyl ester to its respective diethyl-amide.
Designing super selectivity in multivalent nano-particle binding (2011)

A key challenge in nano-science is to design ligand-coated nano-particles that can bind selectively to surfaces that display the cognate receptors above a threshold (surface) concentration. Nano-particles that bind monovalently to a target surface do not discriminate sharply between surfaces with high and low receptor coverage. In contrast, "multivalent" nano-particles that can bind to a larger number of ligands simultaneously, display regimes of "super selectivity" where the fraction of bound particles varies sharply with the receptor concentration. We present numerical simulations that show that multivalent nano-particles can be designed such that they approach the "on-off" binding behavior ideal for receptor-concentration selective targeting. We propose a simple analytical model that accounts for the super selective behavior of multivalent nano-particles. The model shows that the super selectivity is due to the fact that the number of distinct ligand-receptor binding arrangements increases in a highly nonlinear way with receptor coverage. Somewhat counterintuitively, our study shows that selectivity can be improved by making the individual ligand-receptor bonds weaker. We propose a simple rule of thumb to predict the conditions under which super selectivity can be achieved. We validate our model predictions against the Monte Carlo simulations.
TGF-beta1 and Ha-Ras collaborate in modulating the phenotypic plasticity and invasiveness of epithelial tumor cells. (1996)

Metastasis of epithelial tumor cells can be associated with the acquisition of fibroblastoid features and the ability to invade stroma and blood vessels. Using matched in vivo and in vitro culture systems employing fully polarized, mammary epithelial cells, we report here that TGF-beta1 brings about these changes in Ras-transformed cells but not in normal cells. When grown in collagen gels in the absence of TGF-beta, both normal and Ras-transformed mammary epithelial cells form organ-like structures in which the cells maintain their epithelial characteristics. Under these conditions, treatment of normal cells with TGF-beta results in growth arrest. The same treatment renders Ras-transformed epithelial cells fibroblastoid, invasive, and resistant to growth inhibition by TGF-beta. After this epithelial-fibroblastoid conversion, the Ras-transformed cells start to secrete TGF-beta themselves, leading to autocrine maintenance of the invasive phenotype and recruitment of additional cells to become fibroblastoid and invasive. More important, this cooperation of activated Ha-Ras with TGF-beta1 is operative during in vivo tumorigenesis and, as in wound healing processes, is dependent on epithelial-stromal interactions.
Bempegaldesleukin selectively depletes intratumoral Tregs and potentiates T cell-mediated cancer therapy (2020)

High dose interleukin-2 (IL-2) is active against metastatic melanoma and renal cell carcinoma, but treatment-associated toxicity and expansion of suppressive regulatory T cells (Tregs) limit its use in patients with cancer. Bempegaldesleukin (NKTR-214) is an engineered IL-2 cytokine prodrug that provides sustained activation of the IL-2 pathway with a bias to the IL-2 receptor CD122 (IL-2Rβ). Here we assess the therapeutic impact and mechanism of action of NKTR-214 in combination with anti-PD-1 and anti-CTLA-4 checkpoint blockade therapy or peptide-based vaccination in mice. NKTR-214 shows superior anti-tumor activity over native IL-2 and systemically expands anti-tumor CD8<sup>+</sup> T cells while inducing Treg depletion in tumor tissue but not in the periphery. Similar trends of intratumoral Treg dynamics are observed in a small cohort of patients treated with NKTR-214. Mechanistically, intratumoral Treg depletion is mediated by CD8<sup>+</sup> Teff-associated cytokines IFN-γ and TNF-α. These findings demonstrate that NKTR-214 synergizes with T cell-mediated anti-cancer therapies.