gebhart/patrepeval huggingface dataset:
A new method for reconstruction of major defects in the cranial vault. (1976)

A new method for reconstruction of cranial vault defects is described. A combination graft made of both alloplastic and autogenous materials combines several advantages to produce adequate strength and a smooth contour.
Parallel Addressing Scheme for Voltage-Programmed Active-Matrix OLED Displays (2007)

This paper presents a novel parallel addressing scheme for voltage-programmed active-matrix organic light-emitting diode (OLED) displays which provides high precision recovery of the threshold voltage shift. As a result, the uniformity over the panel is significantly improved. In addition, a new pixel circuit is presented that is capable of providing a predictably higher current as the pixel ages, so as to compensate for the OLED luminance degradation
The rapid discovery of engineered antibodies. (2007)

Antibodies, in particular human antibodies, are a growing class of new agents with potential diagnostic and therapeutic applications. Advanced DNA and protein technologies allow for the generation of recombinant antibodies in vitro from large DNA libraries. Ribosome display is a cell-free protein display technology that selects desirable antibodies through an efficient search for novel diversity from large populations. The ribosome-selected pools can then be screened rapidly to identify individual antibodies possessing the required activity, without involving the need for cloning by Escherichia coli. The combination of ribosome display, selection and cell-free screening provides a rapid discovery tool for the generation, optimization and modification of antibody-combining sites.
On T2‐shortening by weakly magnetized particles: The chemical exchange model† (2001)

Chemical exchange (CE) theory is compared with two theories of T2-shortening caused by microscopic magnetic centers: inner- and outer-sphere relaxation theory (long-echo limit) and mean gradient diffusion theory (short-echo limit). The CE equation is shown to be identical to these theories in the respective limits and appropriate parameter relationships are derived for spherical particles. The theories are then compared with computer simulations of spherical particles and with a recent general theory, with good agreement in the asymptotic regions. The CE model also reproduces the essential relaxation characteristics in the intermediate range. Finally, good agreement of a CE model with simulations for magnetized cylinders is also demonstrated. The discussion is limited to weakly magnetized particles such that the maximum phase shift during an echo interval is less than one radian, permitting the use of the Luz-Meiboom CE equation. Published 2001 Wiley-Liss, Inc.
GMM foreground segmentation processor based on address free pixel streams (2012)

A compact implementation of a foreground segmentation processor in a multi-resolution transform domain has been proposed for HDTV signals. The proposed architecture is designed to simplify system controls by the hardware streaming and to reduce required memory capacities. It enables flowing pixels through all functional units in order, including multi-resolution spatial transform and temporal segmentation. The resultant architecture does not use memories except I/O buffers. Therefore, memory modules as well as complex address manipulation over the multiple global transforms and spatial/temporal interface is not required. The FPGA prototype chip dissipates 150 mW of power. This approach can be used for tablets and smart-phone by an ASIC implementation which will reduce the operation power to about 1/6.
An intronic element contributes to splicing repression in spinal muscular atrophy (2007)

The neurodegenerative disease spinal muscular atrophy is caused by mutation of the survival motor neuron 1 (SMN1) gene. SMN2 is a nearly identical copy of SMN1 that is unable to prevent disease, because most SMN2 transcripts lack exon 7 and thus produce a nonfunctional protein. A key cause of inefficient SMN2 exon 7 splicing is a single nucleotide difference between SMN1 and SMN2 within exon 7. We previously provided evidence that this base change suppresses exon 7 splicing by creating an inhibitory element, a heterogeneous nuclear ribonucleoprotein (hnRNP) A1-dependent exonic splicing silencer. We now find that another rare nucleotide difference between SMN1 and SMN2, in intron 7, potentially creates a second SMN2-specific hnRNP A1 binding site. Remarkably, this single base change does indeed create a high-affinity hnRNP A1 binding site, and base substitutions that disrupt it restore exon 7 inclusion in vivo and prevent hnRNP A1 binding in vitro. We propose that interactions between hnRNP A1 molecules bound to the exonic and intronic sites cooperate to exclude exon 7 and discuss the significance of this exclusion with respect to SMN expression and splicing control more generally.
Gender Differences in Hemodynamic Responses to Endothelin-1 (2000)

Summary: We investigated whether gender affects the pressor and constrictor effects of endothelin-1 (ET-1) in anesthetized rats. Baseline values for arterial blood pressure (mmHg) and hindquarter resistance (HQR, mmHg/ml/min/100 g), respectively, were similar in male (96.0 ± 3.1 and 13.9 ± 0.6) and female (103.1 ± 5.6 and 12.8 ± 2.3) rats. ET-1 (1 and 3 μg/kg) produced rapid and transient falls in arterial blood pressure and HQR, followed by long-lasting increases in blood pressure and HQR. The initial ET-1-induced hypotension and vasodilation were similar in both groups. However, the pressor and hindquarter vasoconstrictor effects were significantly higher (p < 0.05) in male than female rats. Thus, the increases in blood pressure and HQR to ET-1 (3 μg/kg) were attenuated in female (+15.3 ± 3.4 mmHg and +3.7 ± 1.6 mmHg/ml/min/100 g) compared to male (+24.9 ± 2.3 mmHg and +8.0 ± 1.6 mmHg/ml/min/100 g) rats. These results indicate that there is a gender difference in the vasoconstrictor, but not the vasodilator effects of ET-1. We suggest that the lower ET-1-induced hypertension and hindlimb vasoconstrictions observed in female rats may be responsible for the lower risk of developing coronary heart disease in premenopausal women.
Purification of rat hepatic stellate cells by side scatter-activated cell sorting (1998)

In this study, we present a new method to obtain pure, viable, freshly isolated hepatic stellate cells. Stellate cells were purified by cell sorting using their high side scatter (SSC) of incident light. Purity of the cells was established by light and transmission electron microscopy (TEM). Starting from stellate cells that were 50% to 70% enriched by centrifugation in 11% Nycodenz, the cell purity after sorting was found to be 96.6% +/- 2.9%. Viability of the sorted cells was 90.8% +/- 2.2% as measured by the Trypan blue exclusion test and was confirmed by cell culturing. Per hour of sorting, 1.4 +/- 0.4 million stellate cells were obtained. Sorting runs of up to 4 hours were practically feasible, resulting in yields of 5 to 6 million cells per rat liver. Cells attached to plastic substratum within 24 hours. Subsequently, they spread and underwent spontaneous transition into myofibroblast-like cells. The purity of sorted cells was documented by reverse-transcriptase polymerase chain reaction (RT-PCR) experiments using specific primer pairs for messenger RNA (mRNA) species that were only present in parenchymal (preproalbumin), endothelial (endothelial cell nitric oxide synthase [eNOS]), stellate (desmin), or Kupffer cells (77- to 88-kd fucose receptor). Contaminating mRNA species were absent in sorted stellate cells. Next, we examined freshly sorted stellate cells by Western blotting to confirm the presence of relevant cytoskeletal proteins. Cells were positive for vimentin, desmin, and glial fibrillary acidic protein (GFAP), but negative for alpha-smooth muscle actin (alpha-SMA). Sorted and cultured cells were immunophenotyped for the presence of collagen types I, III, and IV, laminin, and the cytoskeletal proteins, alpha-SMA, desmin, vimentin, and GFAP. At 90 hours in culture, cells expressed all the investigated extracellular matrix proteins. Desmin was present in 82% +/- 1%, vimentin in 96% +/- 2.5%, and GFAP in 91% +/- 4.5% of cells. Alpha-SMA was present in 91% +/- 2% of cultured cells. We conclude that cell sorting based on SSC of incident light is a convenient method to obtain virtually pure stellate cells that can be used for direct analysis or for culturing. Although the yields obtained with this method are lower than with standard methods, and additional equipment is required, SSC-activated sorting offers the possibility of very pure cells when essential for analyses based on sensitive detection methods such as RT-PCR.
An activity gradient of decapentaplegic is necessary for the specification of dorsal pattern elements in the Drosophila embryo (1993)

decapentaplegic (dpp) is a zygotically expressed gene encoding a TGF-beta-related ligand that is necessary for dorsal-ventral patterning in the Drosophila embryo. We show here that dpp is an integral part of a gradient that specifies many different cell fates via intercellular signalling. There is a graded requirement for dpp activity in the early embryo: high levels of dpp activity specify the amnioserosa, while progressively lower levels specify dorsal and lateral ectoderm. This potential for dpp to specify cell fate is highly dosage sensitive. In the wild-type embryo, increasing the gene dosage of dpp can shift cell fates along the dorsal-ventral axis. Furthermore, in mutant embryos, in which only a subset of the dorsal-ventral pattern elements are represented, increasing the gene dosage of dpp can specifically transform those pattern elements into more dorsal ones. We present evidence that the zygotic dpp gradient and the maternal dorsal gradient specify distinct, non-overlapping domains of the dorsal-ventral pattern.
Current density and electric field analysis of microelectrodes using finite element modeling (2002)

Geometrically and electrically accurate finite element models of microelectrodes used in microstimulation of the central nervous system were created to examine the current density along the surface of the electrode as well as the electric field generated within the tissue medium. Sharp tipped microelectrodes (tip radius=15 /spl mu/m; cone angle=10/spl deg/) were examined with electrode surface areas that ranged from 250-1000 /spl mu/m/sup 2/. Analysis of these models showed that the current density was concentrated at the tip of the microelectrode, and increasing the surface area of the electrode has little effect on reducing the peak current density. The models also showed that as the surface area of the microelectrode was increased, the gradient of the electric field within the tissue decreased, and the modeling of the electric field generated by a sharp tipped microelectrode by a theoretical point source electrode was valid only for distances greater than 20 /spl mu/m from the electrode tip. The results of this study have important implications for electrochemical reactions at the electrode surface, and for modeling of neural excitation with metal microelectrodes.
Melatonin inhibition of cancer growth in vivo involves suppression of tumor fatty acid metabolism via melatonin receptor-mediated signal transduction events. (1999)

The growth of rat hepatoma 7288CTC in vivo is stimulated by the uptake of linoleic acid (LA) and its metabolism to 13-hydroxyoctadecadienoic acid (13-HODE), an important mitogenic signaling molecule within this tumor. Conversely, the growth of a variety of experimental cancers in vivo is inhibited by either physiological or pharmacological levels of the pineal gland hormone melatonin, although the mechanism(s) are unknown. We tested the hypothesis that the mechanism of melatonin's anticancer action in vivo involves the inhibition of tumor LA uptake and metabolism to 13-HODE in hepatoma 7288CTC. Tumor uptake of LA and release of 13-HODE, measured in tissue-isolated rat hepatoma 7288CTC at 4-h intervals over a 24-h period, were highest during the light phase and lowest during the mid-dark phase, when plasma melatonin levels were lowest and highest, respectively. Pinealectomy eliminated this rhythm of tumor LA uptake and 13-HODE production, indicating that it was driven by the circadian melatonin rhythm. Perfusion of tissue-isolated tumors in situ with melatonin (1 nM) rapidly and reversibly inhibited the uptake of plasma fatty acids (FAs), including LA, and its metabolism to 13-HODE. These inhibitory effects of melatonin on tumor FA uptake and 13-HODE release were completely reversed by perfusion of tumors in situ with melatonin receptor antagonist S-20928, pertussis toxin, forskolin, or 8-bromo-cAMP. Perfusion of tumors in situ with melatonin also decreased tumor [3H]thymidine incorporation and DNA content; these effects on DNA synthesis were also prevented by the coperfusion of tumors with melatonin and S-20928, pertussis toxin, forskolin, 8-Br-cAMP, or 13-HODE. Pinealectomy stimulated tumor growth, LA uptake and metabolism to 13-HODE, and FA storage in hepatoma 7288CTC, whereas melatonin administration (200 microg/day) was inhibitory in vivo. Northern blot analysis revealed that, compared with normal liver tissue, hepatoma 7288CTC overexpressed mRNA transcripts for a plasma membrane-associated FA transport protein (FATP). FATP mRNA expression was unaffected by the treatment of tumor-bearing rats with daily afternoon melatonin injections or exposure to constant light. These results support a novel mechanism of tumor growth inhibition by melatonin involving a melatonin receptor-mediated suppression of cAMP levels, resulting in diminished tumor FA transport, possibly via decreased FATP function. The inhibition of these signal transduction events by melatonin culminates in the suppression of LA uptake, LA metabolism to the mitogenic signaling molecule 13-HODE, and cancer growth.
Issues in wireless mobile computing (2003)

The trend toward possible computers with interfaces to wireless network technologies is examined. The question of needed research and specification of hardware is discussed, the major challenges, such as services for the mobile user, mobile internetworking and adjusting to new technologies are described, and a listing of outstanding questions which must be resolved is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Systemic Administration of IL-15 Augments the Antigen-Specific Primary CD8+ T Cell Response Following Vaccination with Peptide-Pulsed Dendritic Cells (2002)

The systemic administration of IL-2 can act as a potent adjuvant for T cell-directed vaccine strategies. However, not only is the administration of IL-2 potentially toxic, but recent evidence suggests that it may also paradoxically limit the duration and magnitude of the cytotoxic T cell response. A recently identified cytokine, IL-15, shares many properties with IL-2 and may provide a preferential means of augmenting T cell-directed vaccine responses. Although well characterized in vitro, there are few data on the ability of IL-15 to augment T cell-mediated responses in vivo. We therefore evaluated the ability of systemic IL-15 to function as a T cell adjuvant in a murine vaccine model. To establish a population of easily identifiable Ag-responsive T cells, naive CD8(+) (OT-1) T cells were first adoptively transferred into mice. Vaccination with peptide-pulsed dendritic cells induced a modest expansion of OT-1 T cells. The addition of systemic IL-15 for 7 days following vaccination resulted in a significant increase in the expansion of responding T cells in the PBL, spleen, and lymph nodes. Importantly, the responding T cells were cytotoxic and maintained a Tc1-biased phenotype. We did not observe either enhanced resistance to activation-induced cell death or preferential generation of memory T cells as a result of treatment with IL-15 compared with IL-2. These studies show for the first time that IL-15 is capable of augmenting the primary CD8(+) T cell response to vaccination and contribute to the basis for future experiments exploring the clinical role of IL-15.
Opposing regulatory effects of thioredoxin and eosinophil cytotoxicity-enhancing factor on the development of human immunodeficiency virus 1. (1994)

Exogenous recombinant human thioredoxin (rTRX, &amp;gt; or = 500 nM), a dithiol reductase enzyme, inhibited the expression of human immunodeficiency virus (HIV) 1BaL in human macrophages (M phi) by 71% (range, 26-100%), as evaluated by p24 antigen production and the integration of provirus at 14 d after infection. The stoichiometric reducing agent N-acetylcysteine (NAC) also inhibited HIV production, but to a lesser degree, and only at 30,000-fold higher concentrations. Exogenous rTRX is cleaved by M phi to generate the inflammatory cytokine, eosinophil cytotoxicity-enhancing factor (ECEF). In contrast to rTRX, rECEF (concentrations from 50 pM to 2 microM) enhanced the production of HIV by 67% (range, 33-92%). Thus, whereas TRX is a potent inhibitor of the expression of HIV in human M phi, cleavage of TRX to ECEF creates a mediator with the opposite effect. TRX also inhibited the expression of integrated provirus in the chronically infected OM 10.1 cell line, showing that it can act at a step subsequent to viral infection and integration.
Grid metadata catalog service-based OGC web registry service (2004)

Grid is a promising e-Science infrastructure that promotes and facilitates the sharing and collaboration in the use of distributed heterogeneous resources through Virtual Organization (VO). A critical factor to the overall utility of Grid is a scalable, flexible and robust registry mechanism. Although it provides some mechanisms to store and access metadata for publishing and discovering resources, such as MCS (Metadata Catalog Service), the Grid registry is inadequate for dealing with domain-specific resources. To enhance the earth science Grid systems, this paper presents a geospatial registry approach in which the OGC (Open GIS Consortium) WRS (Web Registry Service), a <i>de facto</i> standard that supports the publishing of and run-time access to geospatial resources, as a wrapper is used to extend the capabilities of the conventional Grid MCS to the processing of geospatial queries against multiple heterogeneous spatial data sources and services. The approach presented not only focuses on the specifics of descriptive information about spatial data, services, and relevant information objects, but also emphasizes using ontology to infer the semantic relationships between vocabularies for integrating different information models. The implementation of presented approach used in NASA Grid Data Service environment is also illustrated in this paper.
Stable aluminium fluoride chelates with triazacyclononane derivatives proved by X-ray crystallography and 18F-labeling study (2011)

A single crystal structure of an aluminium-fluoride complex of a model compound (NODA-benzyl) was studied to understand the co-ordination chemistry. Series of ligands with an extra carboxylic acid linker for biomolecule conjugation were studied for improved (18)F-labeling applications.
Evidence for Antibody-Catalyzed Ozone Formation in Bacterial Killing and Inflammation (2002)

Recently, we showed that antibodies catalyze the generation of hydrogen peroxide (H2O2) from singlet molecular oxygen (1O2*) and water. Here, we show that this process can lead to efficient killing of bacteria, regardless of the antigen specificity of the antibody. H2O2 production by antibodies alone was found to be not sufficient for bacterial killing. Our studies suggested that the antibody-catalyzed water-oxidation pathway produced an additional molecular species with a chemical signature similar to that of ozone. This species is also generated during the oxidative burst of activated human neutrophils and during inflammation. These observations suggest that alternative pathways may exist for biological killing of bacteria that are mediated by potent oxidants previously unknown to biology.
The Crystal Structure of Lysin, a Fertilization Protein (1993)

Lysin, a protein from abalone sperm, creates a hole in the envelope of the egg, permitting the sperm to pass through the envelope and fuse with the egg. The structure of lysin, refined at 1.9 angstroms resolution, reveals an alpha-helical, amphipathic molecule. The surface of the protein exhibits three features: two tracks of basic residues that span the length of the molecule, a solvent-exposed cluster of aromatic and aliphatic amino acids, and an extended amino-terminal hypervariable domain that is species-specific. The structure suggests possible mechanisms of action.
Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation (2013)

The detection and quantification of genetic heterogeneity in populations of cells is fundamentally important to diverse fields, ranging from microbial evolution to human cancer genetics. However, despite the cost and throughput advances associated with massively parallel sequencing, it remains challenging to reliably detect mutations that are present at a low relative abundance in a given DNA sample. Here we describe smMIP, an assay that combines single molecule tagging with multiplex targeted capture to enable practical and highly sensitive detection of low-frequency or subclonal variation. To demonstrate the potential of the method, we simultaneously resequenced 33 clinically informative cancer genes in eight cell line and 45 clinical cancer samples. Single molecule tagging facilitated extremely accurate consensus calling, with an estimated per-base error rate of 8.4 × 10(-6) in cell lines and 2.6 × 10(-5) in clinical specimens. False-positive mutations in the single molecule consensus base-calls exhibited patterns predominantly consistent with DNA damage, including 8-oxo-guanine and spontaneous deamination of cytosine. Based on mixing experiments with cell line samples, sensitivity for mutations above 1% frequency was 83% with no false positives. At clinically informative sites, we identified seven low-frequency point mutations (0.2%-4.7%), including BRAF p.V600E (melanoma, 0.2% alternate allele frequency), KRAS p.G12V (lung, 0.6%), JAK2 p.V617F (melanoma, colon, two lung, 0.3%-1.4%), and NRAS p.Q61R (colon, 4.7%). We anticipate that smMIP will be broadly adoptable as a practical and effective method for accurately detecting low-frequency mutations in both research and clinical settings.
Functional expression of B7/BB1 on activated T lymphocytes. (1993)

B7/BB1 is a membrane differentiation antigen expressed on activated B cells, macrophages, and dendritic cells that binds to a counter-receptor, CD28, expressed on T lymphocytes and thymocytes. Interaction between CD28 and B7 results in potent costimulation of T cell activation initiated via the CD3/T cell receptor complex. We now report that B7 is also expressed on activated human peripheral blood T cells, CD4 T cell clones, CD8 T cell clones, and natural killer cell clones. B7 appears relatively late after T cell activation, can be detected on both CD4 and CD8 T cell subsets, and is present on antigen-specific, major histocompatibility complex-restricted CD4 and CD8 T cell clones. Expression of B7 on activated T cells was confirmed by immunoprecipitation from 125I-labeled activated T cells and by detection of B7 transcripts. A B7+ CD4+ T cell clone was able to stimulate a primary allogeneic mixed lymphocyte response using small, resting peripheral blood T cells as responders. The alloantigen-induced proliferative response and cytokine production was partially inhibited by anti-B7 monoclonal antibody. Since activated T cells can coexpress both CD28 and its counter-receptor, B7, this suggests that activated T cells may be capable of autocrine costimulation via the CD28 activation pathway.