gebhart/patrepeval huggingface dataset:
Intracisternal A-particle genes: identification in the genome of Mus musculus and comparison of multiple isolates from a mouse gene library. (1980)

The genome of Mus musculus contains multiple copies (500 -1000) of DNA sequences related to the 35S RNA of intracisternal type A particles (IAPs). Using labeled IAP RNA as a probe in blot-hybridization experiments, we have identified a characteristic electrophoretic pattern of reactive fragments generated by restriction endonuclease cleavage of mouse DNA. From the genomic blots, we deduced a composite restriction map for a 6.5- to 7-kilobase (kb) DNA region containing sequences homologous to the IAP RNA. Units of this type appeared to be interspersed without obvious regularity in nonhomologous flanking regions. A 5.2-kb segment of this unit was inserted directly into plasmid pBR322 from HindIII/EcoRI digest of mouse DNA. The fragment was cloned and then labeled by nick-translation and used to scan a mouse embryo gene library (average 16-kb inserts in lambda Charon 4A); 1% of the library samples hybridized, confirming the extensive reiteration of IAP genetic units. Among six different library isolates containing 6.5- to 7-kb IAP units, some restriction sites were highly conserved whereas others varied in both occurrence and position. Despite this variation, heteroduplexes between the individual isolates showed continuous IAP homology regions of 7 kb. No flanking region homologies were seen in this limited sample. Some evidence suggests that mouse DNA may contain other dispersed sequence elements related to but smaller than the genetic unit defined above.
Tree-Structured CRF Models for Interactive Image Labeling (2013)

We propose structured prediction models for image labeling that explicitly take into account dependencies among image labels. In our tree-structured models, image labels are nodes, and edges encode dependency relations. To allow for more complex dependencies, we combine labels in a single node and use mixtures of trees. Our models are more expressive than independent predictors, and lead to more accurate label predictions. The gain becomes more significant in an interactive scenario where a user provides the value of some of the image labels at test time. Such an interactive scenario offers an interesting tradeoff between label accuracy and manual labeling effort. The structured models are used to decide which labels should be set by the user, and transfer the user input to more accurate predictions on other image labels. We also apply our models to attribute-based image classification, where attribute predictions of a test image are mapped to class probabilities by means of a given attribute-class mapping. Experimental results on three publicly available benchmark datasets show that in all scenarios our structured models lead to more accurate predictions, and leverage user input much more effectively than state-of-the-art independent models.
An astrolabe from Passa Pau, Cape Verde Islands (2002)

Mariner's astrolabes seem to have been in use from the 15th to the end of the 18th centuries. They evolved at about the same time as quadrants and cross-staffs. Their precursor, the astronomer's astrolabe and kamal, were either too cumbersome or not sufficiently accurate for sea-going use. An astrolabe found on the Passa Pau wreck is unique in that it is the only know/specimen coated with silver. It is dated 1645 and has the maker's name, Nicolao Rvffo, inscribed on it.
CO{sub 2} capture, reuse, and sequestration technologies for mitigating global climate change (1998)

There are three levers that can be manipulated to help control emissions of CO{sub 2}--increase the efficiency of energy conversion and end-use processes, use fuels with lower carbon content, or sequester the carbon released in energy production. This paper looks at the third lever of carbon sequestration, with a focus on CO{sub 2} separation and capture from fossil fuel-fired power plants. the economics as they exist today are reviewed and pathways for significantly lowering costs are identified.
Investigation of Enzyme Activities of the Enzyme Immobilized on an AFM Tip (2003)

Enzyme activities of V8 protease on AFM tip were investigated by measuring its force curves. The enzyme was immobilized onto the surface of the chemically modified AFM tip; two kinds of peptides were immobilized to the mica surface by a hetero‐reactive reagent. One peptide was designed to be recognized and digested by the enzyme. Another was designed so as not to be recognized by the enzyme. Force curves were obtained by plotting the applied force on the cantilever as a function of the sample displacement. Force applied on the cantilever, over 1.5 nN, was often observed when the tip contacted to a peptide that was digestible by the enzyme. In contrast a force of less than 0.4 nN was observed for contact with other peptides. Large force over 1.5 nN seemed to be caused by rupturing of the intermediate form of the enzyme and the peptide. It was suggested that enzyme molecules on the AFM tip can recognize the target sequence of the peptide. This method can be a tool to analyze biomolecules on a surface.
Systematic Mutagenesis of the Escherichia coli Genome (2004)

A high-throughput method has been developed for the systematic mutagenesis of the Escherichia coli genome. The system is based on in vitro transposition of a modified Tn5 element, the Sce-poson, into linear fragments of each open reading frame. The transposon introduces both positive (kanamycin resistance) and negative (I-SceI recognition site) selectable markers for isolation of mutants and subsequent allele replacement, respectively. Reaction products are then introduced into the genome by homologous recombination via the lambdaRed proteins. The method has yielded insertion alleles for 1976 genes during a first pass through the genome including, unexpectedly, a number of known and putative essential genes. Sce-poson insertions can be easily replaced by markerless mutations by using the I-SceI homing endonuclease to select against retention of the transposon as demonstrated by the substitution of amber and/or in-frame deletions in six different genes. This allows a Sce-poson-containing gene to be specifically targeted for either designed or random modifications, as well as permitting the stepwise engineering of strains with multiple mutations. The promiscuous nature of Tn5 transposition also enables a targeted gene to be dissected by using randomly inserted Sce-posons as shown by a lacZ allelic series. Finally, assessment of the insertion sites by an iterative weighted matrix algorithm reveals that these hyperactive Tn5 complexes generally recognize a highly degenerate asymmetric motif on one end of the target site helping to explain the randomness of Tn5 transposition.
Integrin αvβ3 Antagonists for Anti-Angiogenic Cancer Treatment (2007)

Direct contact between cellular and extracellular matrix (ECM) proteins is necessary for a diverse array of physiologic processes including cellular activation, migration, proliferation, and differentiation. These direct interactions are modulated by cell adhesion molecules (CAMs) such as integrins, selectins, cadherins, and immunoglobulins. Integrin signaling also plays a key role in tumor growth, angiogenesis, and metastasis. Recent advances in the discovery and characterization of CAMs and their receptors, most notably integrin alpha(v)beta(3), and the clarification of their roles in disease states have laid the groundwork for the development and clinical implementation of novel anti-cancer treatments. Integrin alpha (v)beta(3) is a glycoprotein membrane receptor which recognizes ECM proteins expressing an arginine-glycine-aspartic acid (RGD) peptide sequence. The receptor is highly expressed on activated tumor endothelial cells, but not resting endothelial cells and normal organ systems, thus making alpha(v)beta(3) an appropriate target for anti-angiogenic therapeutics. In addition, alpha(v)beta(3) is also expressed on tumor cells, allowing for both tumor cell and tumor vasculature targeting of anti-integrin therapy. Throughout the past decade, numerous patents have been published and issued using alpha(v)beta(3) antagonists for the prevention and/or treatment of cancer, with many antagonists demonstrating positive pre-clinical anti-angiogenic and anti-tumor results. This review will focus on the key points and distinguishing factors for patents which use antibodies, RGD peptides, non-RGD peptides, peptidomimetics, and amine salts as alpha(v)beta(3) antagonists.
Back‐Scattering Interferometry: A Versatile Platform for the Study of Free‐Solution versus Surface‐Immobilized Hybridization (2010)

The first direct comparison of surface immobilization and free-solution oligonucleotide hybridization using back-scattering interferometry (BSI) showed that surface immobilization perturbs hybridization by as much as 50 %. BSI can distinguish between a perfect complement and a two-base-pair mismatch with an internal mismatch significantly destabilizing the duplex.
Vibration control of a two-link flexible robot arm (2002)

Analysis and experimentation are described for a two-link apparatus in which both members are very flexible. Attention is focused on endpoint position control for point-to-point movements, assuming a fixed reference frame for the base, with two rotary joints. Each link in instrumented with acceleration sensing and is driven by a separate motor equipped with velocity and position sensing. The control perspective adopted is to implement a two-stage control in which the vibration control problem for fine motion endpoint positioning is considered separately from the gross motion, large angle skew problem. In the first stage the control law shapes the actuator inputs for the large angle movement in such a way that minimal energy is injected into the flexible modes, while in the second phase an endpoint acceleration feedback scheme is employed in independent joint control for vibration suppression at the link endpoints.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effect of grapefruit juice and naringin on nisoldipine pharmacokinetics (1993)

The bioavailability of some dihydropyridine calcium antagonists can be markedly augmented by grapefruit juice and may involve the bioflavonoid naringin. The pharmacokinetics of nisoldipine coat-core tablet were studied in a Latin square-designed trial in which 12 healthy men were administered the drug with water, grapefruit juice, or encapsulated naringin powder at the same amount as that assayed in the juice. Compared with water, grapefruit juice increased the maximum concentration of nisoldipine to 406% +/- 73% (mean +/- SEM; range, 107% to 836%; p < 0.001), increased the area under the plasma concentration-time curve to 198% +/- 46% (range, 81% to 682%; p < 0.001), and reduced time to reach maximum nisoldipine concentration to 58% +/- 9% (range, 13% to 100%; p < 0.01), probably by inhibition of presystemic metabolism and possibly by enhancement of drug dissolution. The interaction could not be predicted from baseline pharmacokinetics with water and resulted in greater interindividual variability. The naringin capsule did not change nisoldipine pharmacokinetics. All treatments produced minor effects on supine blood pressure and heart rate, probably because subjects were normotensive. Current information supports the cautioning of patients about concomitant ingestion of grapefruit juice and nisoldipine.
Polar heterojunction interfaces (1978)

A study of heterojunction interface geometry based on our measured differences in $3d$ core-state binding energies for germanium and gallium at Ge-GaAs heterojunctions of different crystallographic orientations is reported. For the interfaces which have been studied, i.e., (110), (100) Ga, (100) As, (111) Ga, and ($\overline{1}\overline{1}\overline{1}$) As, orientation-dependent variations in dipole contributions to valence-band discontinuities of about 0.2 eV have been observed. From electrostatic considerations we deduce the simplest interface geometries consistent with the facts that the differences are small and no large charge accumulations can occur at the junction. An abrupt planar junction is allowed for the (110) interface, but the polar interfaces require at least two transition planes of atoms with compositions which are deduced from the two conditions above. The electrostatic calculations were based upon the differences in nuclear charge and are unaffected by the resulting polarization of the bonds if that polarization is described in an "electronegativity" approximation. In this approximation there would in fact be no dipole shift for the ideal geometries proposed. An improved treatment of the bond polarization based upon the bond-orbital model gives residual dipole shifts somewhat smaller than those observed, and in poor agreement with our measurements. Inclusion of lattice-distortion effects at the interface also fails to account for the observed dipole shifts. We conclude that the experimentally prepared junctions must contain deviations from the ideal atom arrangements. The number of these deviations required to account for the observed shifts is on the order of one for every fifteen interface atoms.
Orientation of LamB Signal Peptides in Bilayers:  Influence of Lipid Probes on Peptide Binding and Interpretation of Fluorescence Quenching Data (1999)

The orientation in lipid bilayers of the signal sequence of the bacterial protein LamB was studied using binding, circular dichroism, and fluorescence quenching experiments. Measurements were made of binding modifications caused by the incorporation of lipid probes (brominated or nitroxide-labeled phospholipids) used in the parallax fluorescence quenching method of determining peptide penetration depth [Abrams, F. S., and London, E. (1992) Biochemistry 31, 5312-5322]. The signal peptide bound to a similar extent to neutral bilayers composed of either egg phosphatidylcholine (EPC) or phosphatidylcholines brominated at various positions on their acyl chains. The fluorescence of a tryptophan in either the 18 or 24 position of the peptide was quenched more by bromines in the 6 and 7 than in the 9 and 10 positions on the lipid hydrocarbon chain. Parallax calculations showed that tryptophan-18 was located only 4 A from the hydrocarbon-water interface, consistent with the peptide adopting a "hammock" configuration in the bilayer, with both termini exposed to the aqueous phase and the central alpha-helix located near the hydrocarbon-water interface. In contrast, the incorporation of 10% nitroxide-labeled lipids into EPC bilayers modified peptide binding in a manner dependent on the position of the nitroxide on the hydrocarbon chain; 7-Doxyl PC reduced the percent peptide bound by about one-half, whereas 12-Doxyl PC had little effect on binding. These binding differences modified tryptophan quenching by these probes, making parallax analysis problematical. In the presence of the positively charged LamB peptide, the incorporation of negatively charged phospholipids into EPC bilayers increased the level of peptide binding and modified tryptophan quenching by nitroxide probes. These results suggest that the nitroxide probe could be partially excluded from negatively charged lipid domains where the peptide preferentially bound. Quite different binding and quenching results were obtained with a negatively charged peptide analogue, showing that the charge on both the peptide and bilayer affects peptide-nitroxide probe interactions.
Discovering relations among named entities from large corpora (2004)

Discovering the significant relations embedded in documents would be very useful not only for information retrieval but also for question answering and summarization. Prior methods for relation discovery, however, needed large annotated corpora which cost a great deal of time and effort. We propose an unsupervised method for relation discovery from large corpora. The key idea is clustering pairs of named entities according to the similarity of context words intervening between the named entities. Our experiments using one year of newspapers reveals not only that the relations among named entities could be detected with high recall and precision, but also that appropriate labels could be automatically provided for the relations.
Nanoscale Magnesium Hydroxide and Magnesium Oxide Powders:  Control over Size, Shape, and Structure via Hydrothermal Synthesis (2001)

Mg(OH)2 nanocrystallines with rod-, tube-, needle-, or lamella-like morphologies have been synthesized by a hydrothermal reaction using different magnesium precursors and solvents as the reactants. The products appeared to have narrow size distributions with a monodisperse nature. Subsequent thermal decomposition at 450 °C gave nanosized MgO, which preserved well the morphological features of the Mg(OH)2 samples. The specific surface areas of the MgO samples were determined by the BET technique, which gave a feature of high surface area generally larger than 100 m2/g. The channels formed in the thermal dehydroxylation process may account for this feature of the MgO nanocrystallines.
In vivo depth-resolved birefringence measurements of the human retinal nerve fiber layer by polarization-sensitive optical coherence tomography (2002)

To our knowledge, this is the first demonstration of in vivo depth-resolved birefringence measurements of the human retinal nerve fiber layer (RNFL) by use of polarization-sensitive optical coherence tomography (PS-OCT). Because glaucoma causes nerve fiber layer damage, which may cause loss of retinal birefringence, PS-OCT is a potentially useful technique for the early detection of glaucoma. We built a fiber-based PS-OCT setup that produces quasi-real-time images of the human retina in vivo . Preliminary measurements of a healthy volunteer showed that the double-pass phase retardation per unit depth of the RNFL near the optic nerve head is 39+/-6( degrees )/100microm .
Hermes: a distributed event-based middleware architecture (2003)

In this paper, we argue that there is a need for an event-based middleware to build large-scale distributed systems. Existing publish/subscribe systems still have limitations compared to invocation-based middlewares. We introduce Hermes, a novel event-based distributed middleware architecture that follows a type- and attribute-based publish/subscribe model. It centres around the notion of an event type and supports features commonly known from object-oriented languages like type hierarchies and super-type subscriptions. A scalable routing algorithm using an overlay routing network is presented that avoids global broadcasts by creating rendezvous nodes. Fault-tolerance mechanisms that can cope with different kinds of failures in the middleware are integrated with the routing algorithm resulting in a scalable and robust system.
Influenza Viruses, Cell Enzymes, and Pathogenicity (1995)

Proteolytic cleavage of the influenza virus hemagglutinin glycoprotein (HA) by cellular proteases is a prerequisite for virus infectivity, spread of the virus in the infected organism, tissue tropism, and viral pathogenicity. Production of infectious virus depends upon the structure at the HA cleavage site as well as the substrate specificity and the distribution of appropriate enzymes. Differences exist in the specificities of the endoproteases that recognize the different sequence motifs at the cleavage site. With avian influenza viruses that cause lethal systemic infections, the cleavage site consists of multibasic amino acids. Furin, which activates this type of HA, is a member of the subtilisin family and represents the prototype of ubiquitously occurring membrane-bound proteases. On the other hand, serine proteases secreted from a restricted number of cell types and some bacterial enzymes recognize a monobasic cleavage signal at HA of the mammalian and the apathogenic avian influenza viruses. The limited occurrence of these proteases results in only localized infection. Implementation of these defined conditions for virus activation may represent a novel type of disease control.
Human mesenchymal stem cells modulate allogeneic immune cell responses (2004)

Mesenchymal stem cells (MSCs) are multipotent cells found in several adult tissues. Transplanted allogeneic MSCs can be detected in recipients at extended time points, indicating a lack of immune recognition and clearance. As well, a role for bone marrow-derived MSCs in reducing the incidence and severity of graft-versus-host disease (GVHD) during allogeneic transplantation has recently been reported; however, the mechanisms remain to be investigated. We examined the immunomodulatory functions of human MSCs (hMSCs) by coculturing them with purified subpopulations of immune cells and report here that hMSCs altered the cytokine secretion profile of dendritic cells (DCs), naive and effector T cells (T helper 1 [T(H)1] and T(H)2), and natural killer (NK) cells to induce a more anti-inflammatory or tolerant phenotype. Specifically, the hMSCs caused mature DCs type 1 (DC1) to decrease tumor necrosis factor alpha (TNF-alpha) secretion and mature DC2 to increase interleukin-10 (IL-10) secretion; hMSCs caused T(H)1 cells to decrease interferon gamma (IFN-gamma) and caused the T(H)2 cells to increase secretion of IL-4; hMSCs caused an increase in the proportion of regulatory T cells (T(Regs)) present; and hMSCs decreased secretion of IFN-gamma from the NK cells. Mechanistically, the hMSCs produced elevated prostaglandin E2 (PGE(2)) in co-cultures, and inhibitors of PGE(2) production mitigated hMSC-mediated immune modulation. These data offer insight into the interactions between allogeneic MSCs and immune cells and provide mechanisms likely involved with the in vivo MSC-mediated induction of tolerance that could be therapeutic for reduction of GVHD, rejection, and modulation of inflammation.
The Matrisome: In Silico Definition and In Vivo Characterization by Proteomics of Normal and Tumor Extracellular Matrices (2011)

The extracellular matrix (ECM) is a complex meshwork of cross-linked proteins providing both biophysical and biochemical cues that are important regulators of cell proliferation, survival, differentiation, and migration. We present here a proteomic strategy developed to characterize the in vivo ECM composition of normal tissues and tumors using enrichment of protein extracts for ECM components and subsequent analysis by mass spectrometry. In parallel, we have developed a bioinformatic approach to predict the in silico "matrisome" defined as the ensemble of ECM proteins and associated factors. We report the characterization of the extracellular matrices of murine lung and colon, each comprising more than 100 ECM proteins and each presenting a characteristic signature. Moreover, using human tumor xenografts in mice, we show that both tumor cells and stromal cells contribute to the production of the tumor matrix and that tumors of differing metastatic potential differ in both the tumor- and the stroma-derived ECM components. The strategy we describe and illustrate here can be broadly applied and, to facilitate application of these methods by others, we provide resources including laboratory protocols, inventories of ECM domains and proteins, and instructions for bioinformatically deriving the human and mouse matrisome.