gebhart/patrepeval huggingface dataset:
Differences in DNA‐methylation are associated with a paramutation phenomenon in transgenic petunia (1993)

The transgenic petunia line 17-R contains one copy of the maize A1 gene which mediates brick-red pelargonidin pigmentation of the flower. A white derivative, 17-W, was isolated from homozygous progeny of this line in which no pelargonidin pigmentation was observed. In 17-W the 35S promoter driving the A1 gene was hypermethylated, in contrast to its hypomethylated state in 17-R. Progeny plants carrying both the 17-R and 17-W allele did not show the expected A1 phenotype. Predominantly white progeny and variable plants were observed which showed a continuous change in pattern and intensity of pelargonidin pigmentation. This reduction of A1 activity argues for a semidominant effect of the 17-W allele which inhibits the activity of its homologue, 17-R. This system shows striking similarities to some paramutation phenomena in plants which represent a heritable change in gene function of a paramutable allele directed by a paramutagenic homologue. The analysis of the methylation patterns of the A1 alleles suggests that interactions between differentially methylated alleles are responsible for the paramutation-like effect which is mediated by somatic pairing. The analogy of this system to other phenomena based on homology-dependent interlocus trans-inactivation supports the assumption that those may be based on a related mechanism which includes an interaction between ectopic homologues.
Lifestreams: Organizing your Electronic Life* (1995)

The &amp;quot;Web,&amp;quot; an attempt to organize the electronic world, has become the focus of a wide range of research activities from agents to information retrieval to virtual reality systems, and is a central focus of work presented at this symposium. Our work considers a more humble task: that of organizing our own electronic lives. We introduce a new metaphor, Lifestreams, for dynamically organizing a user&amp;apos;s personal files, electronic mail, schedules, rolodex and financial data. In this paper we describe our prototype Lifestreams system and in the process cover most of the topics of this symposium, including indexing, information retrieval, user interfaces, multisource integration and multimedia.
Antineoplastic agents. 278. Isolation and structure of axinastatins 2 and 3 from a Western Caroline Island marine sponge (1994)

The Republic of Palau marine sponge Axinella sp. was found to be an exceptionally productive source of cell growth inhibitory substances. The strongly antineoplastic polyether macrocyclic lactones halichondrin B (1) and homohalichondrin B (2) were isolated in 1.2 x 10(-6)% and 5.4 x 10(-7)% yields, respectively. In addition to axinastatin 1 (3), two new and cytostatic (GI50 values of 0.35 to 0.0072 microgram/mL against six human cancer cell lines) cycloheptapeptides designated axinastatins 2 (4) and 3 (5) were discovered in 1.4 x 10(-6)% and 1.25 x 10(-6)% yields. Structures were elucidated by high-resolution FABMS and tandem MS/MS techniques augmented by high-field (400 and 500 MHz) 2D-NMR spectral analyses. The absolute configurations were established by a combination of hydrolysis, derivatization, and chiral gas chromatographic methods.
New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization (2014)

Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
Management of Traumatic Foot Wounds (1994)

The foot is frequently exposed to direct trauma due to its role in weight-bearing. The soft-tissue wounds that commonly result interfere with ambulation due to complications such as tissue necrosis, scar formation, infection, and deformity. The five most common categories of foot injury are (1) low-velocity blunt trauma, (2) high-velocity blunt trauma, (3) low-velocity penetrating trauma, (4) highvelocity penetrating trauma, and (5) thermal injuries. For major wounds, the treatment is early aggressive debridement, copious irrigation, and skeletal stabilization with early coverage of skin defects. Local and systemic antibiotics are adjunctive to debridement to prevent infection. Prompt recognition and release of compartment syndrome of the foot are extremely important. Close observation is appropriate for wounds that appear minor on initial evaluation.
Overexpression of alpha4 chain-containing laminins in human glial tumors identified by gene microarray analysis. (2001)

Differential gene expression in tumors often involves growth factors and extracellular matrix/basement membrane components. Here, 11,000- gene microarray was used to identify gene expression profiles in brain tumors including high-grade gliomas [glioblastoma multiforme (GBM) and anaplastic astrocytoma], low-grade astrocytomas, or benign extra-axial brain tumors (meningioma) in comparison with normal brain tissue. Histologically normal tissues adjacent to GBMs were also studied. All GBMs studied overexpressed 14 known genes compared with normal human brain tissue. Overexpressed genes belonged to two broad groups: (a) growth factor-related genes; and (b) structural/extracellular matrix-related genes. For most of these 14 genes, expression levels were lower in low-grade astrocytoma than in GBM and were barely detectable in normal brain. Despite normal-appearing histology, gene expression patterns of tissues immediately adjacent to GBM were similar to those of their respective primary GBMs. Two genes were consistently up-regulated in both high-grade and low-grade gliomas, as well as in histologically normal tissues adjacent to GBMs. These genes coded for the epidermal growth factor receptor (previously reported to be overexpressed in gliomas) and for the alpha4 chain of laminin, a major blood vessel basement membrane component. Changes in expression of this laminin chain have not been previously associated with malignant tumors. Overexpression of laminin alpha4 chain in GBM and astrocytoma grade II by gene microarray analysis was confirmed by semiquantitive reverse transcription-PCR and immunohistochemistry. Importantly, an alpha4 chain-containing laminin isoform, laminin-8 (alpha4beta1gamma1), was expressed mainly in blood vessel walls of GBMs and histologically normal tissues adjacent to GBMs, whereas another alpha4 chain-containing laminin isoform, laminin-9 (alpha4beta2gamma1), was expressed mainly in blood vessel walls of low-grade tumors and normal brain. GBMs that overexpressed laminin-8 had a shorter mean time to tumor recurrence (4.3 months) than GBMs with overexpression of laminin-9 (9.7 months, P = 0.0007). Up-regulation of alpha4 chain-containing laminins could be important for the development of glioma-induced neovascularization and glial tumor progression. Overexpression of laminin-8 may be predictive of glioma recurrence.
Biosynthesis of novel copolyesters containing 3-hydroxypivalic acid by Rhodococcus ruber NCIMB 40126 and related bacteria (1998)

Rhodococcus ruber and related Gram-positive bacteria synthesized and accumulated novel copolyesters containing 3-hydroxypivalic acid as constituent if the cells were cultivated in a mineral salts medium containing 3-hydroxypivalic acid and glucose as carbon sources. The copolyesters contributed 0.4–10% of the cellular dry mass, and they contained up to 78 mol% of 3-hydroxypivalic acid in addition to 3-hydroxybutyric acid and 3-hydroxyvaleric acid; a homopolyester of 3-hydroxypivalic acid was also synthesized under certain conditions. The presence of 3-hydroxypivalic acid in the accumulated copolyesters was confirmed by nuclear magnetic resonance spectrometry as well by coupled gas chromatography/mass spectrometry. This is the first time that the incorporation of 3-hydroxypivalic acid and therefore of a hydroxyalkanoic acid with two methyl group substituents at the α-carbon atom in a naturally occurring copolyester is reported. It indicates that 3-hydroxypivalic acid-coenzyme A is accepted by polyhydroxyalkanoic acid synthase as a substrate.
Total Reconstitution of Copper-Zinc Superoxide Dismutase (1974)

Abstract The total reconstitution of copper-zinc superoxide dismutase by stoichiometric addition of the metals to completely metal-free apoprotein is described. Reconstitution has been monitored by electron paramagnetic resonance (EPR) and absorption spectroscopy, enzymic activity, and acrylamide gel electrophoresis. Under the same conditions, it has been possible to prepare highly active enzymes with cobalt, mercury, or cadmium in place of zinc. The properties of these derivatives demonstrate that the replacement is exact, that copper has the major influence on the spectral properties of the enzyme, and that occupation of the zinc site is necessary in order to attain fully native properties. A technique is described which allows the extraction of superhyperfine patterns from the bulk of magnetic resonance spectra. Use of this technique shows that the superhyperfine patterns of superoxide dismutase from animal sources differ from those of fungal enzymes. In addition, the technique of shows that the superhyperfine patterns in the EPR spectra reconstituted Cu2-, Cu2, Cd2-, Cu2, Hg2-, and Cu2, Zn2-derivatives are very similar to that in the EPR spectrum of native enzyme. Reconstitution with 63Cu and treatment with cyanide demonstrates that three magnetically equivalent nitrogens are the source of these patterns. The results of this study are shown to be consistent with the copper binding site being a distorted square planar arrangement of ligands and neighboring the zinc-binding site.
CAD for low power: status and promising directions (2002)

Low power design is gaining increasing attention as the market for battery powered portable products expands and as power consumption becomes the stumbling block for further system integration. This paper examines strategies to minimize power consumption of digital circuits by reducing the supply voltage, by using power-conscious design methodologies and tools at the behavioral, logic and circuit levels, and by dynamic power management. The paper highlights some of the more effective and promising approaches for achieving ultra low power VLSI circuits and systems.
One-Step18F-Labeling of Carbohydrate-Conjugated Octreotate-Derivatives Containing a Silicon-Fluoride-Acceptor (SiFA): In Vitro and in Vivo Evaluation as Tumor Imaging Agents for Positron Emission Tomography (PET) (2010)

The synthesis, radiolabeling, and initial evaluation of new silicon-fluoride acceptor (SiFA) derivatized octreotate derivatives is reported. So far, the main drawback of the SiFA technology for the synthesis of PET-radiotracers is the high lipophilicity of the resulting radiopharmaceutical. Consequently, we synthesized new SiFA-octreotate analogues derivatized with Fmoc-NH-PEG-COOH, Fmoc-Asn(Ac₃AcNH-β-Glc)-OH, and SiFA-aldehyde (SIFA-A). The substances could be labeled in high yields (38 ± 4%) and specific activities between 29 and 56 GBq/μmol in short synthesis times of less than 30 min (e.o.b.). The in vitro evaluation of the synthesized conjugates displayed a sst2 receptor affinity (IC₅₀ = 3.3 ± 0.3 nM) comparable to that of somatostatin-28. As a measure of lipophilicity of the conjugates, the log P(ow) was determined and found to be 0.96 for SiFA-Asn(AcNH-β-Glc)-PEG-Tyr³-octreotate and 1.23 for SiFA-Asn(AcNH-β-Glc)-Tyr³-octreotate, which is considerably lower than for SiFA-Tyr³-octreotate (log P(ow) = 1.59). The initial in vivo evaluation of [¹⁸F]SiFA-Asn(AcNH-β-Glc)-PEG-Tyr³-octreotate revealed a significant uptake of radiotracer in the tumor tissue of AR42J tumor-bearing nude mice of 7.7% ID/g tissue weight. These results show that the high lipophilicity of the SiFA moiety can be compensated by applying hydrophilic moieties. Using this approach, a tumor-affine SiFA-containing peptide could successfully be used for receptor imaging for the first time in this proof of concept study.
Effect of Potassium Citrate Therapy on Stone Recurrence and Residual Fragments after Shockwave Lithotripsy in Lower Caliceal Calcium Oxalate Urolithiasis: A Randomized Controlled Trial (2002)

Potassium citrate therapy significantly alleviated calcium oxalate stone activity after SWL for lower pole stones in patients who were stone free. An important observation was the beneficial effect of medical treatment on stone activity after SWL among patients with residual calculi.
The Enterotoxin from Clostridium difficile (ToxA) Monoglucosylates the Rho Proteins (1995)

The enterotoxin from Clostridium difficile (ToxA) is one of the causative agents of the antibiotic-associated pseudomembranous colitis. In cultured monolayer cells ToxA exhibits cytotoxic activity to induce disassembly of the actin cytoskeleton, which is accompanied by morphological changes. ToxA-induced depolymerization of actin filaments is correlated with a decrease in the ADP-ribosylation of the low molecular mass GTP-binding Rho proteins (Just, I., Selzer, J., von Eichel-Streiber, C., and Aktories, K. (1995) J. Clin. Invest. 95, 1026-1031). Here we report on the identification of the ToxA-induced modification of Rho. Applying electrospray mass spectrometry, the mass of the modification was determined as 162 Da, which is consistent with the incorporation of a hexose into Rho. From several hexoses tested UDP-glucose selectively served as cosubstrate for ToxA-catalyzed modification. The acceptor amino acid of glucosylation was identified from a Lys-C-generated peptide by tandem mass spectrometry as Thr-37. Mutation of Thr-37 to Ala completely abolished glucosylation. The members of the Rho family (RhoA, Rac1, and Cdc42Hs) were substrates for ToxA, whereas H-Ras, Rab5, and Arf1 were not glucosylated. ToxA-catalyzed glucosylation of lysates from ToxA-pretreated rat basophilic leukemia (RBL) cells resulted in a decreased incorporation of [14C]glucose, indicating previous glucosylation in the intact cell. Glucosylation of the Rho subtype proteins appears to be the molecular mechanism by which C. difficile ToxA mediates its cytotoxic effects on cells.
CUBIC (2008)

CUBIC is a congestion control protocol for TCP (transmission control protocol) and the current default TCP algorithm in Linux. The protocol modifies the linear window growth function of existing TCP standards to be a cubic function in order to improve the scalability of TCP over fast and long distance networks. It also achieves more equitable bandwidth allocations among flows with different RTTs (round trip times) by making the window growth to be independent of RTT -- thus those flows grow their congestion window at the same rate. During steady state, CUBIC increases the window size aggressively when the window is far from the saturation point, and the slowly when it is close to the saturation point. This feature allows CUBIC to be very scalable when the bandwidth and delay product of the network is large, and at the same time, be highly stable and also fair to standard TCP flows. The implementation of CUBIC in Linux has gone through several upgrades. This paper documents its design, implementation, performance and evolution as the default TCP algorithm of Linux.
Wafer bonding of GaAs, InP, and Si annealed without hydrogen for advanced device technologies (1997)

In this paper the authors report on the direct bonding of compound semiconductors and silicon annealed at low temperatures (400 C) using hydrogen and nitrogen. Pressure and temperature relationships on interface characteristics were investigated with high resolution transmission electron microscopy and energy dispersive x-ray spectroscopy. It was found that no morphology differences existed between hydrogen and nitrogen annealed samples. applying the N{sub 2} bonding process, 850nm bottom emitting vertical cavity surface emitting lasers (VCSELs), were bonded to a transparent AlGaAs substrate. Finally, high anneal temperatures (up to 450 C) and shear stress values (> 1.6 MPa) were obtained for GaAs bonded to Si using a dry (plasma) activation technique.
Defect Structure in Thin Films of a Lamellar Block Copolymer Self-Assembled on Neutral Homogeneous and Chemically Nanopatterned Surfaces (2006)

Various defect structures in a symmetric block copolymer self-assembled in thin films on neutral homogeneous and chemically nanopatterned surfaces were investigated. On neutral homogeneous surfaces, a lamellar morphology lacking long-range order was observed with a high density of defects such as dislocations and disclinations in the two-dimensional plane of the film. On chemically patterned surfaces, the commensurability between the periodicity of the surface pattern and the block copolymer lamellae determined the final structure. When the surface pattern period was commensurate with the natural lamellar period, well-registered defect-free lamellar structures were obtained. In contrast, if the length scales were incommensurate, the formation of new structures such as dislocation dipoles, undulated lamellae, and tilted lamellae was observed. Our present work provides a detailed analysis of these new defect structures. In particular, a model describing the three-dimensional structure of the undulated morphology is suggested.
High-Throughput Single Copy DNA Amplification and Cell Analysis in Engineered Nanoliter Droplets (2008)

A high-throughput single copy genetic amplification (SCGA) process is developed that utilizes a microfabricated droplet generator (microDG) to rapidly encapsulate individual DNA molecules or cells together with primer functionalized microbeads in uniform PCR mix droplets. The nanoliter volume droplets uniquely enable quantitative high-yield amplification of DNA targets suitable for long-range sequencing and genetic analysis. A hybrid glass-polydimethylsiloxane (PDMS) microdevice assembly is used to integrate a micropump into the microDG that provides uniform droplet size, controlled generation frequency, and effective bead incorporation. After bulk PCR amplification, the droplets are lysed and the beads are recovered and rapidly analyzed via flow cytometry. DNA targets ranging in size from 380 to 1139 bp at single molecule concentrations are quantitatively amplified using SCGA. Long-range sequencing results from beads each carrying approximately 100 amol of a 624 bp product demonstrate that these amplicons are competent for achieving attomole-scale Sanger sequencing from a single bead and for advancing pyrosequencing read-lengths. Successful single cell analysis of the glyceraldehyde 3 phosphate dehydrogenase (GAPDH) gene in human lymphocyte cells and of the gyr B gene in bacterial Escherichia coli K12 cells establishes that SCGA will also be valuable for performing high-throughput genetic analysis on single cells.
Reflection: A Solution For Highly Adaptive Mobile Systems (2000)

Mobile systems are characterised by the fact that they operate in an environment prone to rapid and drastic changes [4]. More specifically, attributes like network quality of service (QoS) or power availability can vary significantly compared to non-mobile systems. Mobile applications should be capable of being informed of such changes and should also be able to adapt their behaviour accordingly in order to deliver the best level of service to the end-user. Moreover, future mobile systems should be capable of adapting to general environmental and contextual triggers such as the system&amp;apos;s physical location [2]. As presented in [3], current middleware support lacks the required level of control for co-ordinating highly adaptive systems triggered by multiple contextual attributes. Reflection has been suggested as a solution for adaptive middleware [1]. The benefits of being able to open the implementation of the platform, inspect and adapt the behaviour of the system have already been rec...
LDPC code construction with flexible hardware implementation (2004)

This paper presents an LDPC code construction technique for irregular codes of various block sizes and code rates, thus obtaining the performance benefit of irregular distributions. It represents an extension of the methods presented by Sridhara et al. [2001] for regular codes. More importantly, an efficient and practical decoder architecture is also presented that achieves flexibility in block size and code rate for this broad family of codes, a capability not present in other approaches. This decoder can also achieve a high degree of parallelism, thus exploiting one of the benefits of belief propagation.
PET of Malignant Melanoma Using 18F-Labeled Metallopeptides (2009)

Specific in vivo targeting of (18)F-FB-RMSH-1 to malignant melanoma was successfully achieved in preclinical models with high MC1R expression. Thus, the radiofluorinated metallopeptide (18)F-FB-RMSH-1 is a promising molecular probe for PET of MC1R-positive tumors.
Molecular aspects of rheumatoid arthritis: chemokines in the joints of patients (2008)

Rheumatoid arthritis (RA) is a chronic symmetric polyarticular joint disease that primarily affects the small joints of the hands and feet. The inflammatory process is characterized by infiltration of inflammatory cells into the joints, leading to proliferation of synoviocytes and destruction of cartilage and bone. In RA synovial tissue, the infiltrating cells such as macrophages, T cells, B cells and dendritic cells play important role in the pathogenesis of RA. Migration of leukocytes into the synovium is a regulated multi-step process, involving interactions between leukocytes and endothelial cells, cellular adhesion molecules, as well as chemokines and chemokine receptors. Chemokines are small, chemoattractant cytokines which play key roles in the accumulation of inflammatory cells at the site of inflammation. It is known that synovial tissue and synovial fluid from RA patients contain increased concentrations of several chemokines, such as monocyte chemoattractant protein-4 (MCP-4)/CCL13, pulmonary and activation-regulated chemokine (PARC)/CCL18, monokine induced by interferon-gamma (Mig)/CXCL9, stromal cell-derived factor 1 (SDF-1)/CXCL12, monocyte chemotactic protein 1 (MCP-1)/CCL2, macrophage inflammatory protein 1alpha (MIP-1alpha)/CCL3, and Fractalkine/CXC3CL1. Therefore, chemokines and chemokine-receptors are considered to be important molecules in RA pathology.