gebhart/patrepeval huggingface dataset:
Mass Spectrometric Analysis of Protein Mixtures at Low Levels Using Cleavable 13C-Isotope-coded Affinity Tag and Multidimensional Chromatography (2003)

In order to identify and compare the protein content of very low quantity samples of high complexity, a protocol has been established that combines the differential profiling strength of a new cleavable 13C isotope-coded affinity tag (cICAT) reagent with the high sequence coverage provided by multidimensional liquid chromatography and two modes of tandem mass spectrometry. Major objectives during protocol optimization were to minimize sample losses and establish a robust procedure that employs volatile buffer systems that are highly compatible with mass spectrometry. Cleavable ICAT-labeled tryptic peptides were separated from nonlabeled peptides by avidin affinity chromatography. Subsequently, peptide samples were analyzed by nanoflow liquid chromatography electrospray ionization tandem mass spectrometry and liquid chromatography matrix-assisted laser desorption/ionization tandem mass spectrometry. The use of two ionization/instrumental configurations led to complementary peptide identifications that increased the confidence of protein assignments. Examples that illustrate the power of this strategy are taken from two different projects: i) immunoaffinity purified complexes containing the prion protein from the murine brain, and ii) human tracheal epithelium gland secretions. In these studies, a large number of novel proteins were identified using stringent match criteria, in addition to many that had been identified in previous experiments. In the latter case, the ICAT method produced significant new information on changes that occur in protein expression levels in a patient suffering from cystic fibrosis.
Characterization and Modeling of Temporal Variations on an Ultrawideband Radio Link (2006)

The development of efficient ultrawideband (UWB) systems for high-rate wireless links requires an accurate knowledge of the radio propagation mechanisms. Anticipated usage scenarios in office or residential environments predict a significant impact of mobile persons on the UWB radio link. However, the issue of temporal variations in the UWB propagation channel has been scarcely investigated so far. This paper presents a study of the time variance of a UWB channel induced by the motion of people, with a specific focus on the main path of a line-of-sight radio link. A real-time measurement campaign involving moving scatterers was performed in the 4-5 GHz band, in a hallway of a typical office building. The analysis of measured data, regarding the shadowing effect and fast signal fluctuations, provides a detailed description of the phenomena involved in a time varying UWB channel. As a result, a model is described for the temporal variations observed on the main propagation path in a fixed UWB link, accounting for both the nonstationary attenuation due to obstructing people and the small-scale signal variations due to scattered propagation paths
Potential for imaging cerebral amyloid deposits using 123I-labelled serum amyloid P component and SPET (1996)

The systemic and cerebral accumulation of 123I-labelled serum amyloid P component (123I-SAP) was studied in patients with hereditary cerebral amyloid angiopathy-Dutch type (HCHWA-D) to determine the usefulness of 123I-SAP imaging in cerebral amyloidosis. Whole-body and SPET scintigraphic imaging was performed in two patients with HCHWA-D and four controls after the intraveous injection of 123I-SAP. Venous 123I-SAP clearance was also determined. Accumulation of the tracer was observed in the cerebral cortex of both patients, whereas no accumulation was seen in the controls. Blood clearance of radioactivity was similar in the patients and controls, suggesting that the amount of uptake of 123I-SAP in the cerebral amyloid deposits is relatively small. We believe this to be the first demonstration of cerebral amyloid deposits in vivo. Our findings indicate that 123I-SAP scintigraphy has possibilities for the diagnosis of patients with cerebral amyloid diseases, in addition to its use in patients with systemic amyloid deposition.
On the computation of motion from sequences of images-A review (1988)

Recent developments are reviewed in the computation of motion and structure of objects in a scene from a sequence of images. Two distinct paradigms are highlighted: (i) the feature-based approach and (ii) the optical-flow-based approach. The comparative merits/demerits of these approaches are discussed. The current status of research in these areas is reviewed and future research directions are indicated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Role of Annexin II in Angiogenesis and Tumor Progression: A Potential Therapeutic Target (2007)

It is well established that human tumors overproduce plasmin a serine protease that is known to promote angiogenesis, tumor growth and metastasis. However, the mechanism by which endothelial or tumor cells regulate the proteolytic activity of plasmin is not well understood. Cell surface receptors regulate activation of plasminogen to plasmin and its proteolytic activity. Annexin II is one of the well studied receptors for plasminogen and tPA, which binds to plasminogen and converts it to plasmin. Plasmin is a highly reactive enzyme which is physiologically involved in fibrinolysis. Since the proteolytic activity of plasmin is very tightly regulated, uncontrolled production of plasmin can degrade extracellular matrix (ECM) and basement membrane (BM) of the surrounding blood vessels. Thus plasmin plays an important role in neoangiogenesis and cancer invasion and metastasis. Therefore, the receptor which regulates plasmin generation may be an attractive target for the development of anti-cancer/anti-metastatic agents. Angiostatin (AS), internal fragment of plasminogen, has been reported to inhibit human tumor growth and metastasis. We have shown that AS binds to endothelial/cancer cell surface annexin II with high affinity and interferes with plasmin generation suggesting that the role of plasmin/plasminogen system may be more complex than we previously thought. In this review we provide a comprehensive analysis of the literature in context of the role of annexin II in angiogenesis, tumor progression and metastasis. Compelling evidence from the literature and our own findings suggest that annexin II may be a potential target for the development of effective therapeutic strategies for the treatment of cancer and its induced metastasis.
Identification of an Exotic Pest Ant, Paratrechina sp. nr. pubens (Hymenoptera: Formicidae), in Texas (2008)

Invasive species are capable of causing considerable damage to natural ecosystems, agricultures and economies throughout the world. These invasive species must be identified to prevent and reduce the negative effects associated with exotic species. A recent introduction of an exotic ant, Paratrechina sp. nr. pubens, has caused tremendous economic and ecological damage in southeast Texas. Morphometric analyses ofworkers and male alates were used to identify this pest ant, P. sp. nr. pubens, in Southeast Texas. The populations in Texas were found to be slightly different, but were not discriminated from P. pubens Forel populations described in previous literature. Multivariate ANOVA identified significant differences (Wilke's λ = 0.006, F = 4.17, P < 0.001) among worker morphometrics from Texas populations of P. sp. nr. pubens and previously described populations from Florida and other locations. The ANOVA tests of equality of group means indicated nearly all characters of workers and male alates as significantly discriminating. Canonical discriminant analysis ofworkers also identified differences among the groups based on these data (Function 1; Wilks' λ = 0.02, df = 30, P < 0.001 and Function 2; Wilks' λ = 0.26, df= 14, P < 0.001). Along with the morphological findings, the densities demonstrated by P. sp. nr. pubens in Texas may also indicate a taxonomic classification of an undescribed species. Until more comprehensive sampling and/or diagnostic evidence is discovered for its current position; the taxonomic identity of P. sp. nr. pubens populations in Texas will remain unchanged.
Design Principles of Bipolar Electrochemical Co-Electrolysis Cells for Efficient Reduction of Carbon Dioxide from Gas Phase at Low Temperature (2019)

Cell designs for the electrochemical reduction of CO 2 from gas phase were developed and investigated, and the critical elements for an efficient process were identified. Various types of polymeric membrane were used to build membrane electrode assembly adapted for CO 2 reduction in gas phase: protonic and anion exchange membrane (AEM), bipolar membrane and a modified bipolar like membrane configuration. Configurations using anion exchange ionomer in the cathodic catalytic layer in contact with an AEM allow for a great enhancement of the cathode reaction selectivity toward CO. However, a severe problem was identified when co-electrolysis is performed using only an AEM: this type of membrane acts as a CO 2 "pump" meaning that for each molecule of CO 2 reduced at the cathode, one or two CO 2 molecules are produced at the anode by oxidation of the carbonate/bicarbonate anion transported in the membrane. A bipolar membrane system was shown to soften this problem, but only a newly developed cell design was able to fully prevent the parasitic CO 2 pumping. Using this new cell configuration, the faradaic efficiency of an alkaline environment is maintained, the parasitic CO 2 pumping to the anode side is completely suppressed, and the overall cell voltage efficiency is highly improved.
Borealin (2004)

The chromosomal passenger complex of Aurora B kinase, INCENP, and Survivin has essential regulatory roles at centromeres and the central spindle in mitosis. Here, we describe Borealin, a novel member of the complex. Approximately half of Aurora B in mitotic cells is complexed with INCENP, Borealin, and Survivin; and Borealin binds Survivin and INCENP in vitro. A second complex contains Aurora B and INCENP, but no Borealin or Survivin. Depletion of Borealin by RNA interference delays mitotic progression and results in kinetochore-spindle misattachments and an increase in bipolar spindles associated with ectopic asters. The extra poles, which apparently form after chromosomes achieve a bipolar orientation, severely disrupt the partitioning of chromosomes in anaphase. Borealin depletion has little effect on histone H3 serine10 phosphorylation. These results implicate the chromosomal passenger holocomplex in the maintenance of spindle integrity and suggest that histone H3 serine10 phosphorylation is performed by an Aurora B-INCENP subcomplex.
Melanin and blood concentration in a human skin model studied by multiple regression analysis: assessment by Monte Carlo simulation (2001)

Measurement of melanin and blood concentration in human skin is needed in the medical and the cosmetic fields because human skin colour is mainly determined by the colours of melanin and blood. It is difficult to measure these concentrations in human skin because skin has a multi-layered structure and scatters light strongly throughout the visible spectrum. The Monte Carlo simulation currently used for the analysis of skin colour requires long calculation times and knowledge of the specific optical properties of each skin layer. A regression analysis based on the modified Beer-Lambert law is presented as a method of measuring melanin and blood concentration in human skin in a shorter period of time and with fewer calculations. The accuracy of this method is assessed using Monte Carlo simulations.
MULTICENTER RANDOMIZED TRIAL COMPARING TACROLIMUS (FK506) AND CYCLOSPORINE IN THE PREVENTION OF RENAL ALLOGRAFT REJECTION1 (1997)

The significant reduction in the incidence of episodes of allograft rejection observed with tacrolimus therapy may have important long-term implications given the prognostic influence of rejection on graft survival.
Enhanced expression of surface tumor-associated antigens on human breast and colon tumor cells after recombinant human leukocyte alpha-interferon treatment. (1984)

Treatment of human breast or colon carcinoma cells with recombinantly derived human leukocyte (clone A) interferon (IFN-alpha A) increases the surface expression of specific tumor-associated antigens (TAAs) recognized by monoclonal antibodies (MAbs). The MAbs used, B1.1, B6.2, and B72.3, recognize three distinct TAAs, i.e., the Mr 180,000 carcinoembryonic antigen, a Mr 90,000, and a Mr 220,000 to 400,000 glycoprotein, respectively. The binding of the MAbs to the surface of tumor cells increased in a dose-dependent manner, with optimal levels of TAA enhancement at 100 to 1,000 units IFN-alpha A/ml. Higher concentrations of IFN-alpha A that were cytostatic or cytotoxic were also less effective in enhancing TAA expression. Human melanoma (A375) cells and normal fibroblasts (WI-38 and Flow 4000) do not express any of the three TAAs, either before or after interferon treatment. The ability of IFN-alpha A to increase the expression of TAAs on human carcinoma cells was also temporally dependent, with optimal enhancement occurring after 16 to 24 hr. The enhancement of specific TAAs at the surface of the carcinoma cells by IFN-alpha A was confirmed, using fluorescence-activated cell sorter analysis. These data demonstrate that the IFN-alpha A-mediated increase of surface antigen is a result of both an accumulation of more antigen per cell, and an increase in the percentage of cells expressing the antigen. The ability of recombinant interferon to enhance specific TAAs on human carcinoma cells may be exploited in designing protocols for the in situ detection and therapy of human carcinoma lesions by MAbs, as well as in further defining the role of specific TAAs in the expression of the transformed phenotype.
The Carnegie Mellon TruckSim: a tool to improve driving safety (2002)

Carnegie Mellon Driving Research Center is presently involved in the design and development of an Advanced Human Factors Research and Driving Training Research Facility. The facility has been designed to address human factors issues and driver training issues. Human factors interests include development countermeasures for fatigue and driver/vehicle interface issues. Driver training issues include validating the usefulness of simulators for driver training, developing effective curricula and investigating simulator fidelity needed for effective training. A key component of the facility is that the Carnegie Mellon TruckSim will be capable of simulating a variety of commercial and emergency vehicles using interchangeable cabs mounted to a common motion platform. TruckSim's modular configuration will allow for rapid and cost effective design of experiments and training scenarios. A first research program to evaluate fatigue countermeasures is presented as an example.
In vivo osmoregulation of Na/myo-inositol cotransporter mRNA in rat kidney medulla. (1994)

myo-Inositol, a major compatible osmolyte in renal medulla, is accumulated in kidney-derived epithelial cells cultured in hypertonic media via Na/myoinositol cotransporter (SMIT). The altered medium osmolality of Madin-Darby canine kidney cells leads to changes in the transcription of the SMIT gene and mRNA abundance. To investigate whether SMIT is regulated by tonicity in vivo, renal medullary myoinositol and SMIT mRNA was measured in rats in hydrated and dehydrated states. Rats were divided into two groups: (1) hydrated rats, free access to 3% sucrose water; (2) dehydrated rats, 3 days of water deprivation. Urine sodium, potassium, urea, and osmolality in dehydrated rats were significantly higher than in hydrated rats. Renal medullary sodium, urea, and myo-inositol in dehydrated rats were significantly higher than in hydrated rats. Northern analysis revealed that there was a message hybridized to SMIT cDNA in the cortex and outer and inner medulla of the kidney. Compared with hydrated rats, SMIT mRNA in dehydrated rats was 2.6-fold higher in the outer medulla and 2.5-fold higher in the inner medulla. These results indicate that there is osmoregulatory SMIT in the outer and inner medulla of the kidney and that myo-inositol accumulation in this region is probably due to the increased expression of the SMIT gene.
Corynebacteriumsp. U-96 Contains a Cluster of Genes of Enzymes for the Catabolism of Sarcosine to Pyruvate (2005)

The sarcosine oxidase gene and nearby genes from Corynebacterium sp. U-96 were determined. The genes for serine hydroxymethyltransferase, the beta, delta, alpha, and gamma subunits of sarcosine oxidase, serine dehydratase, and 10-formyltetrahydrofolate hydrolase are arranged in this order. This suggests that the bacteria contain a cluster of genes for the catabolism of sarcosine to pyruvate. The possibility that the gene cluster is a merit for the cellular energy demands of the bacteria is discussed. Functional expression of sarcosine oxidase in Escherichia coli was accomplished, but the beta subunit and the betadelta complex were expressed at a low level as a soluble protein.
Genetic status of KRAS modulates the role of Neuropilin-1 in tumorigenesis (2017)

Neuropilin-1 (NRP1), a non-tyrosine kinase receptor, is overexpressed in many cancers including pancreatic and lung cancers. Inhibition of NRP1 expression, however, has differing pro-tumor vs. anti-tumor effects, depending on the cancer types. To understand the differential role of NRP1 in tumorigenesis process, we utilized cells from two different cancer types, pancreatic and lung, each containing either wild type KRAS (KRAS <sup>wt</sup>) or mutant KRAS (KRAS <sup>mt</sup>). Inhibition of NRP1 expression by shRNA in both pancreatic and lung cancer cells containing dominant active KRAS <sup>mt</sup> caused increased cell viability and tumor growth. On the contrary, inhibition of NRP1, in the tumor cells containing KRAS <sup>wt</sup> showed decreased tumor growth. Importantly, concurrent inhibition of KRAS <sup>mt</sup> and NRP1 in the tumor cells reverses the increased viability and leads to tumor inhibition. We found that NRP1 shRNA expressing KRAS <sup>mt</sup> tumor cells caused increased cell viability by decreasing SMAD2 phosphorylation. Our findings demonstrate that the effects of NRP1 knockdown in cancer cells are dependent on the genetic status of KRAS.
Black-box Concurrent Data Structures for NUMA Architectures (2017)

High-performance servers are Non-Uniform Memory Access (NUMA) machines. To fully leverage these machines, programmers need efficient concurrent data structures that are aware of the NUMA performance artifacts. We propose Node Replication (NR), a black-box approach to obtaining such data structures. NR takes an arbitrary sequential data structure and automatically transforms it into a NUMA-aware concurrent data structure satisfying linearizability. Using NR requires no expertise in concurrent data structure design, and the result is free of concurrency bugs. NR draws ideas from two disciplines: shared-memory algorithms and distributed systems. Briefly, NR implements a NUMA-aware shared log, and then uses the log to replicate data structures consistently across NUMA nodes. NR is best suited for contended data structures, where it can outperform lock-free algorithms by 3.1x, and lock-based solutions by 30x. To show the benefits of NR to a real application, we apply NR to the data structures of Redis, an in-memory storage system. The result outperforms other methods by up to 14x. The cost of NR is additional memory for its log and replicas.
Near-field scanning optical microscope with a metallic probe tip (1994)

A near-field scanning optical microscope with a metallic probe tip was developed for detecting localized photons near the surface of the fine structure of a sample. In this microscope a metallic probe is used for converting the evanescent photons localized near the sample surface to the propagating scattering light wave; the scattered light is detected in the far field with external condenser optics. During the measurement the probe tip vibrates normal to the surface with an amplitude of ~5 nm at 2.5 kHz, and the light intensity modulated with this frequency is lock-in detected. This operation permits the removal of stray-light noise contribution. Experimental results of the measurements of the exponential decay of the evanescent field produced by total internal reflection are given with and without the probe vibration. Image data of the surface profile of an optical compact disk are also shown.
[Lysosomotropic agents inhibit the penetration of arenaviruses into a culture of BHK-21 and Vero cells]. (1990)

Lysosomotropic agents (NH4Cl, amantadine, chloroquine, monensin) which prevent acidification of intracellular vacuoles, when introduced into the culture medium before or during inoculation of cells (BHK-21, Vero) with arenaviruses inhibit reproduction of these viruses completely or significantly. Mozambique virus proved to be 10 times more sensitive to the effect of lysosomotropic agents than Pichinde and Lassa viruses. Thus, arenaviruses have a pH-dependent stage at the beginning of the reproduction cycle which is indirectly indicative of their penetration into cells by receptor endocytosis.
The three-dimensional structure of ricin at 2.8 A. (1987)

The x-ray crystallographic structure of the heterodimeric plant toxin ricin has been determined at 2.8-A resolution. The A chain enzyme is a globular protein with extensive secondary structure and a reasonably prominent cleft assumed to be the active site. The B chain lectin folds into two topologically similar domains, each binding lactose in a shallow cleft. In each site a glutamine residue forms a hydrogen bond to the OH-4 of galactose, accounting for the epimerimic specificity of binding. The interface between the A and B chains shows some hydrophobic contacts in which proline and phenylalanine side chains play a prominent role.
Particle Manipulation Inside a Grooved Microfluidic Channel (2009)

The manipulation of particles and cells in micro-fluids, such as cell suspensions, is a fundamental task in Lab-on-a-Chip applications. According to their analysis purposes in either the pre- or post-processing stage, particles/cells flowing inside a microfluidic channel are handled by means of enriching, trapping, separating or sorting. In this study, we report the use of patterning flows produced by a series of grooved surfaces with different geometrical setups integrated into a microfluidic device, to continuously manipulate the flowing particles (5 to 20 μm in diameters) of comparable sizes to the depth of the channel in ways of: 1) concentrating, 2) focusing, and 3) potential separating. The device is fabricated using soft lithographic techniques and is composed of inlets, microfluidic channels, and outlets for loading, manipulating and retrieving cell suspensions, respectively. Such fabrication methods allow rapid prototyping of micron or submicron structures with multiple layers and replica molding on those fabricated features in a clear polymer. The particles are evenly distributed in the entrance of the microchannel and illustrate the enriching, focusing, or size-selective profiles after passing through the patterning grooves. We expect that the techniques of manipulating cell suspensions from this study can facilitate the development of cell-based devices on 1) the visualization of counting, 2) the visualization of sizing, and 3) the particle separating.