gebhart/patrepeval huggingface dataset:
H1- and H56- subunit vaccines against TB - an overview of the clinical development (2014)

Despite a very effective worldwide vaccination program, BCG vaccination has proven to be insufficient to provide protection against TB disease, and a better vaccine is urgently needed. Statens Serum Institut has developed two TB vaccine candidates, H1:IC and its improved successor H56:IC. Both candidates are currently being tested in human clinical trials although H1:IC development will end in 2014 as H56:IC program will take over. These vaccines candidates are intended to be used in adolescents and young adults, and are designed to be effective in both M. tuberculosis - uninfected and latently infected persons. Being a subunit vaccine, the H1 consists of a recombinant fusion protein of two secreted mycobacterial antigens, Ag85B and ESAT-6, and to this core H56 adds a third antigen - the latency antigen Rv2660c. Both vaccines are adjuvated with the IC31 adjuvant This presentation summarize results from preclinical studies in rodents and non-human primates to five clinical trials of the H1:IC and H56:IC vaccines. In preclinical studies, H56:IC provides superior protection against TB disease compared to BCG alone both pre- and post- infection with M.tb. In human trials, H1:IC has been shown to be safe and to induce long term immune responses characterized by T cells with sustained regenerative potential. Latest, this has been shown in HIV infected patients with latent infection in Tanzania and South Africa. Furthermore, a large dose- and schedule trial including 240 adolescents is currently ongoing in South Africa. Recently H56:IC proved similar safety and immunogenicity profile as H1:IC in a small first-in-man trial. These clinical data provides the groundwork for further clinical development of H56:IC.
Human TCR-Binding Affinity is Governed by MHC Class Restriction (2007)

T cell recognition is initiated by the binding of TCRs to peptide-MHCs (pMHCs), the interaction being characterized by weak affinity and fast kinetics. Previously, only 16 natural TCR/pMHC interactions have been measured by surface plasmon resonance (SPR). Of these, 5 are murine class I, 5 are murine class II, and 6 are human class I-restricted responses. Therefore, a significant gap exists in our understanding of human TCR/pMHC binding due to the limited SPR data currently available for human class I responses and the absence of SPR data for human class II-restricted responses. We have produced a panel of soluble TCR molecules originating from human T cells that respond to naturally occurring disease epitopes and their cognate pMHCs. In this study, we compare the binding affinity and kinetics of eight class-I-specific TCRs (TCR-Is) to pMHC-I with six class-II-specific TCRs (TCR-IIs) to pMHC-II using SPR. Overall, there is a substantial difference in the TCR-binding equilibrium constants for pMHC-I and pMHC-II, which arises from significantly faster on-rates for TCRs binding to pMHC-I. In contrast, the off-rates for all human TCR/pMHC interactions fall within a narrow window regardless of class restriction, thereby providing experimental support for the notion that binding half-life is the principal kinetic feature controlling T cell activation.
Functional Metamaterials for Nonlinear and Active Applications Using Embedded Devices (2014)

&lt;p&gt;Metamaterials have gained extensive attention in recent years due to their ability to exhibit material properties otherwise difficult or impossible to obtain using natural materials. Nonlinear and active metamaterials in particular exhibit great promise for exploring new effects and applications, from tunability to mixing. However, nonlinear and active metamaterials have been explored significantly less than linear metamaterials to this point and much work has focused on the fundamental physics of nonlinear metamaterials. Our aim is to further extend the knowledge of practical nonlinear metamaterials and to demonstrate how they can be transformed to real-world applications through the use of embedded devices. In this dissertation, we demonstrate a variety of ways that devices can be embedded within metamaterial unit cells to provide nonlinear and active effects. &lt;/p&gt;&lt;p&gt;Chapter 1 introduces the basic theory of metamaterials, background of existing work, and the current limitations of nonlinear and active metamaterial design. In Chapter 2, we present the design, simulation, fabrication, and verification of an RF limiter metamaterial. We show how a metamaterial can be designed using RF engineering principles to act as an effective limiter in a new topology, relying on nonlinear devices embedded within a metamaterial. Chapter 3 shows our design and demonstration of a power harvesting metamaterial. We design a nonlinear metamaterial towards a potential application, discussing how the selection of an appropriate embedded device provides our desired functionality. In Chapter 4 we show how nonlinear and active metamaterials can be used to realize phase conjugation, including demonstration of negative refraction and imaging through the use of these metamaterials. We also discuss design approaches to moving these metamaterials towards real-world applications. Chapter 5 discusses our work concerning metamaterials based on transistors. First we show that appropriate design of a transistor circuit allows us to tune the quality factor and resonant frequency of a metamaterial. We use this metamaterial for time-varying mixing, as well, demonstrating a mixing metamaterial that remains linear. We then illustrate how using transistors as nonlinear devices provides much greater design freedom for use with metamaterials. We show that the nonlinearity of a metamaterial can be dramatically enhanced through the use of transistors and even dynamically tuned, applying these nonlinear metamaterials to applications including phase conjugation and acoustoelectromagnetic modulation. In Chapter 6 we summarize the achievements of the presented research and directions for future work that build on the work described in this thesis.&lt;/p&gt;
TRANSPLANTATION IN MINIATURE SWINE (1977)

A selective breeding program based on serological techniques was used to establish three herds of miniature swine, each homozygous for a different allele at the major histocompatibility complex, termed MSLA. By selective immunization of these swine, high-titered antisera detecting the products of individual MSLA alleles were raised and used to confirm the genotype of offspring in these herds. Techniques for performing one-way mixed leukocyte cultures in these pigs were developed and demonstrated the presence of a strong mixed leukocyte culture locus (or loci) closely linked to the serologically defined MSLA locus. Cell-mediated cytotoxicity assays based on 51Cr release were developed to monitor the course of cellular immunity following allotransplantation and exhibited specificity identical to that predicted by the serological typing.
Near-Field Optical Flying Head with A Triangular Aperture (2008)

Heat assisted magnetic recording head needs near-field element as a micro heat generator and light guide structure. We have proposed a triangular aperture as a near-filed element. Computer simulation using finite difference time domain (FDTD) method shows that the triangular aperture has a near-field peak on the edge perpendicular to the polarization of the incident light. Therefore it achieves a near-field spot less than 20 nm (FWHM) in the direction of the polarization, which is not limited by the aperture size. SNOM and contact slider experiments in the previous study also show that the triangular aperture is effective. We have also proposed a compact light guide structure with an optical fiber. Using light guide structure with a polarization maintaining fiber and micro optics can achieve a thin and small (1.6x1.6x0.7 mm) near-field flying head. The head was fabricated. Signal readout was demonstrated in flying operation. It could read 300 nm L&S patterns.
[Reactivity differences between serums of patients infected with HIV-2 and HIV-1 antigens according to the patients' geographic origin]. (1994)

We tested 98 sera from HIV-2-infected patients for cross-reactivity with HIV-1 antigens in a competitive EIA test and western blotting. The sera were obtained during epidemiological surveys in Cape Verde Islands (n = 47) and Mali (n = 51). There were significantly more cross reactions with sera from Mali. Similar results were obtained with sera from African patients resident in France. Samples from HIV-2-infected patients from Burkina Faso, Ghana, Ivory Coast and Mali were more often reactive with HIV-1 antigens than were those from HIV-2-infected patients from the western Atlantic coast (Cape Verde, Guinea Bissau and Senegal). These data underline the importance of using specific tests for HIV-2 sero-positivity, and the need to include a panel of HIV-2-positive sera of different geographic origins in quality control kits.
The effect of three human recombinant hematopoietic growth factors (granulocyte-macrophage colony-stimulating factor, granulocyte colony- stimulating factor, and interleukin-3) on phagocyte oxidative activity (1993)

Hematopoietic growth factors not only modulate blood progenitor cell activity but also alter the function of mature phagocytes. Recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF; 1 ng/mL for 60 min) did not stimulate luminol-enhanced chemiluminescence of polymorphonuclear leukocytes (PMNs) in suspension but primed PMN for as much as a 15-fold increase in chemiluminescence in response to f-met-leu-phe (fMLP). Mixed mononuclear leukocytes (monocytes [approximately 20%] and lymphocytes [approximately 80%]; MNL) chemiluminescence was very low even after rhGM-CSF priming, but MNLs added to the PMNs (PMN-MNL) resulted in near doubling of rhGM-CSF-primed PMN fMLP-stimulated chemiluminescence. The enhancing factor(s) from MNLs were inherent rather than induced by the GM-CSF, and purified lymphocytes increased GM-CSF-primed PMN chemiluminescence equal to mixed MNLs. We could not detect cell-free "enhancing factor(s)," but cell-to-cell contact further enhanced rhGM-CSF-primed fMLP-stimulated PMN-MNL oxidative activity by 40%. Polyclonal rabbit anti-tumor necrosis factor (TNF) (but not preimmune serum) decreased both fMLP-stimulated rhGM-CSF-primed PMNs and PMN-MNL chemiluminescence, suggesting that TNF on the PMN surface is enhancing GM-CSF-primed chemiluminescence. GM-CSF priming markedly increased PMN superoxide release (sevenfold), but PMN superoxide release was not further enhanced by the presence of MNLs. Recombinant human granulocyte colony-stimulating factor (rhG-CSF) and interleukin-3 (rhIL-3) displayed much smaller effects on pure PMNs and mixed PMN-MNL chemiluminescence and superoxide release than rhGM-CSF. rhGM-CSF primes PMNs for increased oxidative activity more than rhG-CSF and rhIL-3. Maximal oxidative activity was observed when mixed PMN-MNL were primed with GM-CSF in a cell pellet-promoting cell-to-cell contact. This enhanced activity can be attributed, in part, to both inherent enhancing factor(s) on lymphocytes and PMN-associated TNF induced by GM-CSF.
Design and functionalization of responsive hydrogels for photonic crystal biosensors (2016)

In this review, the molecular-level design and fabrication of photonic crystal hydrogels is presented, and their application as biosensors for many biologically important analytes is highlighted.
EFFECTS OF SELECTIVE 5-HT1/2 RECEPTOR AGONISTS ON OPERANT FOOD INTAKE IN RATS (1999)

s of the First Congress of the Behavioral Pharmacology Society and the European Behavioural Pharmacology Society: PDF Only
Electric-Field-Induced Orientation of Surfactant-Templated Nanoscopic Silica (2007)

While exhibiting a well-defined nanometer-level structure, surfactant-templated nanoscopic silicas produced via self-assembly do not always possess long-range order. We demonstrate that long-range order can be controlled by guiding the self-assembly of nanostructured silica-surfactant hybrids with low-strength electric fields (E approximately 200 V/m) to produce nanoscopic silica with both the micrometer- and nanometer-level structures oriented parallel to the applied field. Under the influence of the electric field, nanoscopic silica particles migrate, elongate, and merge into fibers with a rate of migration proportional to the applied field strength. The linear dependence with the field strength indicates that the process is governed by electroosmotic flow but not by polarization effects. Realignment of the short-range ordered surfactant nanochannels along the fiber axis accompanies the migration.
Genomics of the Genus Lactobacillus (2011)

Part 1 chap 1
SYNTHESIS OF 2′-C-METHYL-4′-THIO RIBONUCLEOSIDES (2005)

Starting from 2-C-methyl-ribonolactone, 1,2,3,5-tetra-O-acetyl-2-C-methyl-4-thioribofuranose was synthesized and condensed with heterocyclic bases to afford 2-C-methyl-4'-thioribonucleosides.
Zur Hydrierung von Δ2‐5‐Isoxazolonen (1973)

Abstract Die Δ 2 ‐5‐Isoxazolone 1, 5, 8a–c und 11a, b werden bei der katalytischen Hydrierung unter reduktiver Ringöffnung zu β‐Enamino‐β'‐ketocarbonsäuren 6a, b gespalten Dabei cyclisieren die Derivate 8a–c, 11a, b intramolekular zu den Diazepinen 10a–c und Pyrazolen 12, 13 . Die Strukturen werden durch NMR‐ und IR‐Spektren bewiesen.
A Study on the TTI Service Delivery via Digital Terrestrial UHD Broadcasting Network (2019)

As technology develops, vehicles evolve to support connected car, autonomous driving, etc. In the era of connected car and autonomous driving, traffic and travel information is essential to drivers or cars. To send this information efficiently, it needs to make good use of the merits of the broadcasting. This paper introduces mechanisms to transmit traffic and travel information efficiently using terrestrial UHD broadcasting.
Repellency and Toxicity of Oil from <I>Artemisia annua</I> to Certain Stored-Product Beetles (2000)

The essential oil of Artemisia annua L. was tested for its toxic repellent and development inhibitory activities against 2 economically important stored product insects: Tribolium castaneum (Herbst) and Callosobruchus maculatus (L.). Adult beetles of T. castaneum were repelled significantly by oil of A. annua at 1% concentration (vol:vol) and above in filter paper arena test. Dose-response relationship of A. annua oil revealed a significant negative correlation between larval survival; pupal survival and adult emergence of T. castaneum (i.e., increase in dose caused decrease in survival and adult emergence). Effective concentration (EC50) to reduce F1 progeny by 50% was calculated to be 2.6 and 4.1 microl/ml solvent against both the insect species, C. maculatus and T. castaneum, respectively. The relationship between bioactivity of oil from A. annua and responses of T. castaneum and C. maculatus is discussed. We found that oil from A. annua was largely responsible for both repellent (behavioral) and toxic (physiological) actions on 2 species of insect tested.
T-CAM, a fastatin-FIII 9-10 fusion protein, potently enhances anti-angiogenic and anti-tumor activity αvβ3 and α5β1 integrins (2008)

We made fusion protein of fastatin and FIII 9-10, termed tetra-cell adhesion molecule (T-CAM) that can interact simultaneously with alphavbeta3 and alpha5beta1 integrins, both playing important roles in tumor angiogenesis. T-CAM can serve as a cell adhesion substrate mediating adhesion and migration of endothelial cells in alphavbeta3 and alpha5beta1 integrin-dependent manner. T-CAM showed pronounced anti-angiogenic activities such as inhibition of endothelial cell tube formation, endothelial cell proliferation, and induction of endothelial cell apoptosis. T-CAM also inhibited angiogenesis and tumor growth in mouse xenograft model. The anti-angiogenic and anti-tumoral activity of molecule like fastatin could be improved by fusing it with integrin-recognizing cell adhesion domain from other distinct proteins. The strategy of combining two distinct anti-angiogenic molecules or cell adhesion domains could facilitate designing improved anticancer agent of therapeutic value.
Tuning second-order NLO responses through halogen bonding (2007)

As a function of the ability of the solvent to behave as acceptor of halogen bonding, the NLO-phores under study give rise to microbeta(lambda) values ranging from +192 x 10(-48) esu to -465 x 10(-48) esu.
Bio-based amines through sustainable heterogeneous catalysis (2017)

Heterogeneous catalysis offers a sustainable toolbox for the synthesis of a wide variety of biomass-derived amines.
Correction: Interactions between the breast cancer-associated MUC1 mucins and C-type lectin characterized by optical tweezers (2018)

[This corrects the article DOI: 10.1371/journal.pone.0175323.].
Abstract 119: Pan-cancer analysis of HIF pathways defines a robust molecular signature that reflects tissue and cellular hypoxia in bulk and single-cell RNA-seq analyses (2022)

Abstract Low levels of tissue oxygen, or intra-tumor hypoxia, is a common feature of many solid cancers in which dysregulated cell proliferation often outstrips the ability to develop new functional blood vessels. Furthermore, hypoxia pathways may also be activated in response to mutation in key tumor suppressor genes or oncogenes. Importantly, in many types of cancer, activation of hypoxia pathways is associated with a clinically aggressive phenotype as well as with resistance to therapy. Indeed, hypoxia drives many of the “hallmarks” of cancer, including cell proliferation, apoptosis, metabolism, immune responses, genomic instability, vascularization, invasion and metastasis. However, the full-range of genes activated by hypoxia varies greatly between cell-types and for many this remains uncharacterized. The key mediator of the cellular transcriptional response to hypoxia is the HIF (hypoxia-inducible factor) family of transcription factors. Here, we generate pan-genomic datasets encompassing HIF ChIP-seq and RNA-seq across cancer cell lines from diverse common tumor types. We then employ integrated analysis of our 72 transcriptome and whole-genome-binding datasets to define a core set of HIF-target genes that are conserved across multiple cell types. We show that these genes can be used to identify HIF activation and tumor hypoxia in bulk RNA-seq analysis of solid tumors, and that this can be applied to large tumor databases (TCGA). We then leverage this analysis to identify tumor-type-specific HIF-associated genes in 32 different cancer types, including those lacking cell-culture models. We further show that these conserved HIF-target genes can be applied to single cell RNA-seq datasets from solid tumors and used to examine intra-tumor heterogeneity in HIF-pathway activation within individual cancer samples. Importantly, using a panel of genes reduces the phenomenon of “drop-out” typically observed in gene-level expression in these datasets. Lastly, applying this gene signature to single cell data allows the hypoxia response to be deconvoluted across diverse cell-types in heterogenous tumor samples. This includes not only the identification of HIF-activity in cancer cells, but also in non-cancer cells within the tumor, thereby allowing the effects of intra-tumor hypoxia on stromal responses (such as tumor angiogenesis) to be studied in vivo in solid tumors. Citation Format: Olivia Lombardi, Ran Li, Silvia Halim, Peter J. Ratcliffe, David R. Mole. Pan-cancer analysis of HIF pathways defines a robust molecular signature that reflects tissue and cellular hypoxia in bulk and single-cell RNA-seq analyses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 119.
Visualization of Intracellular PP1 Targeting Through Transiently and Stably Expressed Fluorescent Protein Fusions (2007)

Protein phosphatase 1 (PP1) is a ubiquitous serine/threonine phosphatase that regulates many cellular processes, including cell division, signaling, differentiation, and metabolism. It is expressed in mammalian cells as three closely related isoforms: alpha, beta/delta, and gamma1. These isoforms differ in their relative affinities for proteins, termed targeting subunits, that mediate their intracellular localization and substrate specificity. Because of the dynamic nature of these interactions, it is important to find experimental approaches that permit direct analyses of PP1 localization and PP1-targeting subunit interactions in live cells. When transiently or stably expressed as fluorescent protein (FP) fusions, the three isoforms are active phosphatases with distinct localization patterns and can interact with both endogenous and exogenous targeting subunits. Their changing spatio-temporal distributions can be monitored both throughout the cell cycle and following cellular perturbations by time-lapse fluorescence microscopy, and turnover rates of intracellular pools of the protein calculated by fluorescence recovery after photobleaching (FRAP). Interactions with targeting subunits can be visualized in vivo by fluorescence resonance energy transfer (FRET), using techniques such as sensitized emission, acceptor photobleaching, or fluorescence lifetime imaging.
Renewable Gasoline, Solvents, and Fuel Additives from 2,3‐Butanediol (2016)

2,3-Butanediol (2,3-BD) is a renewable alcohol that can be prepared in high yield from biomass sugars. 2,3-BD was selectively dehydrated in a solvent-free process to a complex mixture of 2-ethyl-2,4,5-trimethyl-1,3-dioxolanes and 4,5-dimethyl-2isopropyl dioxolanes with the heterogeneous acid catalyst Amberlyst-15. The purified dioxolane mixture exhibited an anti-knock index of 90.5, comparable to high octane gasoline, and a volumetric net heat of combustion 34 % higher than ethanol. The solubility of the dioxolane mixture in water was only 0.8 g per 100 mL, nearly an order of magnitude lower than the common gasoline oxygenate methyl tert-butyl ether. The dioxolane mixture has potential applications as a sustainable gasoline blending component, diesel oxygenate, and industrial solvent.
Design for manufacturability: a path from system level to high yielding chips (2000)

No abstract available.
Polymer Brushes in a Poor Solvent (1995)

The structure of an end-grafted polymer layer immersed in poor solvent is investigated through Monte Carlo simulation based on Edward's Hamiltonian. When the solvent quality becomes sufficiently poor, lateral inhomogeneities are observed to develop in the monomer density in the direction parallel to the grafting plane. A micro-phase-separated conformation is observed at long times. The length scale characteristic of the micro-phase structure is found to be consistent with a two-dimensional random walk. The simulation gives results consistent with the stability line predicted by Yeung, Balazs and Jasnow (Macromolecules, 26 (1993) 1914).
Study of TFET non-ideality effects for determination of geometry and defect density requirements for sub-60mV/dec Ge TFET (2015)

Tunneling Field Effect Transistor (TFET) has attracted interest due to its steep-SS prospects [1]. Although a number of sub-60mV/dec TFETs were demonstrated [2], many failed to realize this feat due to non-optimized geometry, material choice [3], and material defects [4, 5]. In this paper, we clearly distinguish the requirement for i) geometry, ii) semiconductor BTBT characteristics, iii) semiconductor defects and iv) oxide interface defects. Using Ge as a case study, multi-temperature characterization of experimental PIN diodes is used to separate bulk properties from the interface effects, calibrating the models for BTBT, trap-assisted-tunneling (TAT) and SRH. The measured BTBT characteristic of a material is as important as the effect of defects; even a zero-defect TFET using the calibrated Ge material requires thin body and thin oxide. Bulk SRH and TAT is found to be a less critical issue for thin body TFETs, whereas interface defect density ∼1012cm−2 is low enough to only degrade TFET SS <10mV/dec. The method of current component segmentation using multi-temperature short-intrinsic PIN diodes is essential for evaluation of materials for TFETs.