gebhart/patrepeval huggingface dataset:
REGULATION OF THE PHOSPHORELAY AND THE INITIATION OF SPORULATION IN BACILLUS SUBTILIS (1993)

The initiation of sporulation of bacteria is a complex cellular event controlled by an extensive network of regulatory proteins that serve to ensure that a cell embarks on this differentiation process only when appropriate conditions are met. The major signal-transduction pathway for the initiation of sporulation is the phosphorelay, which responds to environmental, cell cycle, and metabolic signals, and phosphorylates the Spo0A transcription factor activating its function. Signal input into the phosphorelay occurs through activation of kinases to phosphorylate a secondary-messenger protein, Spo0F. Spo0F-P serves as a substrate for phosphoprotein phosphotransferase, Spo0B, which phosphorylates Spo0A. The pathway is regulated by transcriptional control of its component proteins and by regulating phosphate flux through the pathway. This is accomplished by several regulatory proteins, and by activated Spo0A, which regulates transcription of genes for its own synthesis. Spo0A-P indirectly controls the transcription of numerous genes by regulating the level of other transcription regulators and directly activates the transcription of several regulatory proteins and sigma factors required for progression to the second stage of sporulation. Although the pathway and regulatory proteins have been identified, the signals and effectors for these regulators remain a mystery.
Characterization of self-formed Ti-based barrier layers in Cu(Ti)/dielectric-layer samples using X-ray Photoelectron Spectroscopy (2010)

In this paper, the amorphous phases in the Ti-based barrier layers are identified. More so, X-ray photoelectron spectroscopy (XPS) technique is employed to study its composition.
Triterpenoid CDDO-Me Blocks the NF-κB Pathway by Direct Inhibition of IKKβ on Cys-179 (2006)

The novel oleanane triterpenoid 2-cyano-3,12-dioxooleana-1,9,-dien-28-oic acid (CDDO) and the C-28 methyl ester (CDDO-Me) induce apoptosis of human tumor cells by disruption of redox balance and are currently in clinical trials. The present studies show that CDDO and CDDO-Me block tumor necrosis factoralpha-induced targeting of NF-kappaB p65 to the nucleus. CDDO-Me also blocked tumor necrosis factor alpha-induced phosphorylation of IkappaBalpha. In concert with these results, we found that CDDO-Me inhibits IkappaBalpha kinasebeta (IKKbeta) activity in cells. In support of a direct mechanism, CDDO-Me inhibited recombinant IKKbeta activity in vitro. The results also demonstrate that (i) CDDO and CDDO-Me form adducts with IKKbeta, but not IKKbeta with mutation of Cys-179 to Ala, and (ii) CDDO-Me inhibits IKKbeta by a mechanism dependent on oxidation of Cys-179. These findings indicate that CDDO and CDDO-Me directly block IKKbeta activity and thereby the NF-kappaB pathway by interacting with Cys-179 in the IKKbeta activation loop.
Disialoganglioside GD2 distributes preferentially into substrate-associated microprocesses on human melanoma cells during their attachment to fibronectin. (1986)

Human melanoma cells (M21) actively attach and spread on a fibronectin substrate. Indirect immunofluorescence assays with specific monoclonal antibodies directed to the disialoganglioside GD2, the major ganglioside expressed on M21 melanoma cells, indicate that during the cell attachment process this molecule redistributes into microprocesses that make direct contact with the fibronectin substrate. Scanning and transmission immunoelectron microscopic studies with anti-GD2 monoclonal antibodies and immuno-gold staining demonstrate that GD2 preferentially localizes into substrate-associated microprocesses that emanate from the plasma membrane of the M21 cells. Staining with monoclonal antibodies directed to other melanoma surface antigens fails to demonstrate a similar distribution pattern on these cells. Direct evidence is provided that GD2 is involved in M21 cell attachment to fibronectin, since treatment of these cells with anti-GD2 monoclonal antibodies causes cell rounding and detachment from a fibronectin substrate. Moreover, scanning electron microscopy demonstrates that this loss of attachment of fibronectin is characterized by a perturbation of the cell attachment-promoting microprocesses that in the presence of these antibodies lose contact with the fibronectin substrate.
The outer membranes of Brucella spp. are not barriers to hydrophobic permeants (1993)

The patterns of susceptibility to hydrophobic and hydrophilic drugs and the uptake of the fluorescent probe N-phenyl-naphthylamine in Brucella spp., Haemophilus influenzae, Escherichia coli, and deep rough Salmonella minnesota mutants were compared. The results show that the outer membranes of smooth and naturally rough Brucella spp. do not represent barriers to hydrophobic permeants and that this absence of a barrier relates at least in part to the properties of Brucella lipopolysaccharide.
The cell-free protein biosynthesis--applications and analysis of the system. (2001)

The in vitro protein biosynthesis has the potentials to become a powerful technology for biochemical research. Beside the determination of structure and function the in vitro evolution of proteins is also of great interest. The system described was used to produce bovine heart fatty acid binding protein (FABP) and bacterial chloramphenicol acetyltransferase (CAT) with and without fusion of the Strep-tag II affinity peptide. The proteins were purified after and during protein biosynthesis by using a StrepTactin Sepharose matrix. No significant influence of the Strep-tag and the conditions during the affinity chromatography on maturation or activity of the protein was observed. The in vitro evolution of proteins is feasible by means of ribosome display. The selection of a specific mRNA coding for a shortened FABP with a N-terminal His-tag via the accompanying protein property was shown. Goal of the selection was to bind the FABP via the His-tag on Ni(II)-IDA-agarose. After nine cycles of transcription, translation, affinity selection and RT-PCR the protein with the His-tag could be enriched 10(8)-fold. In order to correlate a possible relationship between changes in protein population and biological function studies were initiated in which 2-dimensional protein patterns of the total in vitro system were compared after 0 and 2 h reaction time. The very interesting findings are that a number of proteins disappear, while others are newly formed during protein synthesis.
Analysis of Paramagnetic NMR Spectra of Triple-Helical Lanthanide Complexes with 2,6-Dipicolinic Acid Revisited:  A New Assignment of Structural Changes and Crystal-Field Effects 25 Years Later (2002)

Variable-temperature (1)H and (13)C NMR measurements of the D(3)-symmetrical triple-helical complexes [Ln(L1-2H)(3)](3)(-) (L1 = pyridine-2,6-dicarboxylic acid; Ln = La-Lu) show evidence of dynamic intermolecular ligand-exchange processes whose activation energies depend on the size of the metal ion. At 298 K, the use of diastereotopic probes in [Ln(L3-2H)(3)](3)(-) (L3 = 4-ethyl-pyridine-2,6-dicarboxylic acid) shows that fast intramolecular P <==> M interconversion between the helical enantiomers occurs on the NMR time scale. Detailed analyses of the paramagnetic NMR hyperfine shifts according to crystal-field independent techniques demonstrate the existence of two different helical structures, one for large lanthanides (Ln = La-Eu) and one for small lanthanides (Ln = Tb-Lu), in complete contrast with the isostructurality proposed 25 years ago. A careful reconsideration of the original crystal-field-dependent analysis shows that an abrupt variation of the axial crystal-field parameter A(0)2<r (2)> parallels the structural change leading to some accidental compensation effects that prevent the detection of structural variations according to the classical one-nucleus method. Crystal structures in the solid state and density functional theory calculations in the gas phase provide structural models that rationalize the paramagnetic NMR data. A regular triple-helical structure is found for small lanthanides (Ln = Tb-Lu) in which the terdentate chelating ligands are rigidly tricoordinated to the metals. A flexible and distorted structure is evidenced for Ln = La-Eu in which the central pyridine rings interact poorly with the metal ion. The origin of the simultaneous variation of structural parameters and crystal-field and hyperfine constants near the middle of the lanthanide series is discussed together with the use of crystal-field-independent techniques for the interpretation of paramagnetic NMR spectra in axial lanthanide complexes.
KNN Classifier with Self Adjusting Memory for Heterogeneous Concept Drift (2016)

Data Mining in non-stationary data streams is gaining more attentionrecently, especially in the context of Internet of Things and Big Data. It is a highly challenging task, since the fundamentally different typesof possibly occurring drift undermine classical assumptions such asi.i.d. data or stationary distributions. Available algorithms are either struggling with certain forms of drift or require a priori knowledge in terms of a task specific setting. We propose the Self Adjusting Memory (SAM) model for the k Nearest Neighbor (kNN) algorithm since kNN constitutes a proven classifier within the streaming setting. SAM-kNN can deal with heterogeneous concept drift, i.e different drift types and rates, using biologically inspiredmemory models and their coordination. It can be easilyapplied in practice since an optimization of the meta parameters is not necessary. The basic idea is to construct dedicated models for thecurrent and former concepts and apply them according tothe demands of the given situation. An extensive evaluation on various benchmarks, consisting of artificial streamswith known drift characteristics as well as real world datasets is conducted. Thereby, we explicitly add new benchmarks enabling a precise performance evaluation on multiple types of drift. The highly competitive results throughout all experiments underline the robustness of SAM-kNN as well as its capabilityto handle heterogeneous concept drift.
Immunization with hybrid hepatitis B virus core particles carrying circumsporozoite antigen epitopes protects mice against Plasmodium yoelii challenge. (1997)

The hepatitis B virus nucleocapsid antigen (HBcAg) was investigated as a carrier moiety for circumsporozoite protein (CS) repeat B cell epitopes of the rodent malaria agent Plasmodium yoelii. A vector expressing a hybrid gene coding for the dominant CS repeat epitope (QGPGAP)4 was constructed and transformed into avirulent Salmonella typhimurium. The resulting hybrid HBcAg-CS polyproteins were purified from recombinant Salmonella typhimurium. They purified as particles and displayed HBc as well as P. yoelii CS antigenicity. To investigate immunogenicity and protective efficacy, BALB/c mice were immunized with the hybrid HBcAg-CS particles. Immunization resulted in high titered antinative CS serum IgG antibody litres. BALB/c mice immunized with hybrid HBcAgCS particles were between 90-100% protected against subsequent P. yoelli challenge. Protective immunity persisted for a minimum of three months. These data confirm the previous suggestion (Schödel et al., 1994), that hybrid HBcAg particles could become a useful component of future human malaria vaccines.
Viewdata—a Post Office interactive information medium for the general public (1977)

In the year of the Caxton quincentenary celebrations, it is fitting to write about Viewdata, the most recent development in the art and technology of electronic communication by means of the written word, intended for members of the general public
Fluorescence-intensity distribution analysis and its application in biomolecular detection technology (1999)

A methodology, fluorescence-intensity distribution analysis, has been developed for confocal microscopy studies in which the fluorescence intensity of a sample with a heterogeneous brightness profile is monitored. An adjustable formula, modeling the spatial brightness distribution, and the technique of generating functions for calculation of theoretical photon count number distributions serve as the two cornerstones of the methodology. The method permits the simultaneous determination of concentrations and specific brightness values of a number of individual fluorescent species in solution. Accordingly, we present an extremely sensitive tool to monitor the interaction of fluorescently labeled molecules or other microparticles with their respective biological counterparts that should find a wide application in life sciences, medicine, and drug discovery. Its potential is demonstrated by studying the hybridization of 5'-(6-carboxytetramethylrhodamine)-labeled and nonlabeled complementary oligonucleotides and the subsequent cleavage of the DNA hybrids by restriction enzymes.
Additions to the Human Plasma Proteome via a Tandem MARS Depletion iTRAQ-Based Workflow (2013)

Robust platforms for determining differentially expressed proteins in biomarker and discovery studies using human plasma are of great interest. While increased depth in proteome coverage is desirable, it is associated with costs of experimental time due to necessary sample fractionation. We evaluated a robust quantitative proteomics workflow for its ability (1) to provide increased depth in plasma proteome coverage and (2) to give statistical insight useful for establishing differentially expressed plasma proteins. The workflow involves dual-stage immunodepletion on a multiple affinity removal system (MARS) column, iTRAQ tagging, offline strong-cation exchange chromatography, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Independent workflow experiments were performed in triplicate on four plasma samples tagged with iTRAQ 4-plex reagents. After stringent criteria were applied to database searched results, 689 proteins with at least two spectral counts (SC) were identified. Depth in proteome coverage was assessed by comparison to the 2010 Human Plasma Proteome Reference Database in which our studies reveal 399 additional proteins which have not been previously reported. Additionally, we report on the technical variation of this quantitative workflow which ranges from ±11 to 30%.
Diagnostic Usefulness of the ABCD 2 Score to Distinguish Transient Ischemic Attack and Minor Ischemic Stroke From Noncerebrovascular Events (2009)

The ABCD(2) score had significant diagnostic usefulness for discrimination of true TIA and MIS from noncerebrovascular events, which may contribute to its predictive usefulness.
Human Cord Blood Progenitors Sustain Thymic T-Cell Development and a Novel Form of Angiogenesis (1999)

There is growing interest in using human umbilical cord blood (CB) for allogeneic bone marrow transplantation (BMT), particularly in children. Thus, CB has been identified as a rich source of hematopoietic progenitors of the erythroid, myeloid, and B-cell lineages. Whether CB blood cells engrafting in the BM space also comprise T-cell progenitors capable of trafficking to the thymus and reconstituting a functional thymopoiesis in young recipients is presently unknown. Here, we show that CB progenitors, engrafted in the BM of immunodeficient mice, sustain human thymopoiesis by generating circulating T-cell progenitors capable of homing to and developing within a human thymic graft. Surprisingly, development of CB stem cells in this in vivo model extended to elements of the endothelial cell lineage, which contributed to the revascularization of transplants and wound healing. These results demonstrate that human CB stem cell transplantation can reconstitute thymic-dependent T-cell lymphopoiesis and show a novel role of CB-derived hematopoietic stem cells in angiogenesis.
Cognitive radio: brain-empowered wireless communications (2005)

Cognitive radio is viewed as a novel approach for improving the utilization of a precious natural resource: the radio electromagnetic spectrum. The cognitive radio, built on a software-defined radio, is defined as an intelligent wireless communication system that is aware of its environment and uses the methodology of understanding-by-building to learn from the environment and adapt to statistical variations in the input stimuli, with two primary objectives in mind: /spl middot/ highly reliable communication whenever and wherever needed; /spl middot/ efficient utilization of the radio spectrum. Following the discussion of interference temperature as a new metric for the quantification and management of interference, the paper addresses three fundamental cognitive tasks. 1) Radio-scene analysis. 2) Channel-state estimation and predictive modeling. 3) Transmit-power control and dynamic spectrum management. This work also discusses the emergent behavior of cognitive radio.
TOE-27 VOLTAGE CONTROLLED OSCILLATOR, (1953)

The specification includes requirements for: serial numbering, visual inspection, test data, test equipment, calibration procedure and vibration tests.
Intracoronary Delivery of Adenovirus Encoding Adenylyl Cyclase VI Increases Left Ventricular Function and cAMP-Generating Capacity (2000)

Intracoronary injection of a recombinant adenovirus encoding AC provides enduring increases in cardiac function.
Protein Modifications as Potential Biomarkers in Breast Cancer (2009)

A variety of post-translational protein modifications (PTMs) are known to be altered as a result of cancer development. Thus, these PTMs are potentially useful biomarkers for breast cancer. Mass spectrometry, antibody microarrays and immunohistochemistry techniques have shown promise for identifying changes in PTMs. In this review, we summarize the current literature on PTMs identified in the plasma and tumor tissue of breast-cancer patients or in breast cell lines. We also discuss some of the analytical techniques currently being used to evaluate PTMs.
Microarray-Based Analysis of Methylation Status of CpGs in Placental DNA and Maternal Blood DNA – Potential New Epigenetic Biomarkers for Cell Free Fetal DNA-Based Diagnosis (2015)

Epigenetic markers for cell free fetal DNA in the maternal blood circulation are highly interesting in the field of non-invasive prenatal testing since such markers will offer a possibility to quantify the amount of fetal DNA derived from different chromosomes in a maternal blood sample. The aim of the present study was to define new fetal specific epigenetic markers present in placental DNA that can be utilized in non-invasive prenatal diagnosis. We have conducted a high-resolution methylation specific beadchip microarray study assessing more than 450.000 CpG sites. We have analyzed the DNA methylation profiles of 10 maternal blood samples and compared them to 12 1st trimesters chorionic samples from normal placentas, identifying a number of CpG sites that are differentially methylated in maternal blood cells compared to chorionic tissue. To strengthen the utility of these differentially methylated CpG sites to be used with methyl-sensitive restriction enzymes (MSRE) in PCR-based NIPD, we furthermore refined the list of selected sites, containing a restriction sites for one of 16 different methylation-sensitive restriction enzymes. We present a list of markers on chromosomes 13, 18 and 21 with a potential for aneuploidy testing as well as a list of markers for regions harboring sub-microscopic deletion- or duplication syndromes.
The Columbia-Presbyterian Medical Center decision-support system as a model for implementing the Arden Syntax. (1991)

Columbia-Presbyterian Medical Center is implementing a decision-support system based on the Arden Syntax for Medical Logic Modules (MLM's). The system uses a compiler-interpreter pair. MLM's are first compiled into pseudo-codes, which are instructions for a virtual machine. The MLM's are then executed using an interpreter that emulates the virtual machine. This design has resulted in increased portability, easier debugging and verification, and more compact compiled MLM's. The time spent interpreting the MLM pseudo-codes has been found to be insignificant compared to database accesses. The compiler, which is written using the tools "lex" and "yacc," optimizes MLM's by minimizing the number of database accesses. The interpreter emulates a stack-oriented machine. A phased implementation of the syntax was used to speed the development of the system.
FOXA1: Growth inhibitor and a favorable prognostic factor in human breast cancer (2006)

The transcription factor Forkhead-box A1 (Foxa1), a member of the FOX class of transcription factors, has been implicated in the pathogenesis of lung, esophageal and prostate cancers. We have recently identified transcriptional activation of p27 by FOXA1. In this study, we analyzed the activities and expression pattern of FOXA1 in breast cancer. Forced expression of FOXA1 inhibited clonal growth of breast cancer cell lines, and FOXA1 levels inversely correlated with growth stimuli. In the estrogen receptor (ER)-positive MCF-7 cells, FOXA1 increased p27 promoter activity and inhibited the ER pathway activity. Analysis of FOXA1 expression in breast tissue arrays revealed significantly higher expression in pure ductal carcinomas in situ compared to invasive ductal carcinomas (IDC); and in IDC, high expression of FOXA1 was associated with favorable prognostic factors. Yet, FOXA1 expression was noted in a subset of the ER-negative tumors. Taken together, our findings suggest a growth inhibitory role for FOXA1, and identify it as a novel, potential prognostic factor in breast cancer.
Extracting a Mobility Model from Real User Traces (2006)

Understanding user mobility is critical for simula- tions of mobile devices in a wireless network, but current mobility models often do not reflect real user movements. In this paper, we provide a foundation for such work by exploring mobility characteristics in traces of mobile users. We present a method to estimate the physical location of users from a large trace of mobile devices associating with access points in a wireless network. Using this method, we extracted tracks of always-on Wi-Fi devices from a 13-month trace. We discovered that the speed and pause time each follow a log-normal distribution and that the direction of movements closely reflects the direction of roads and walkways. Based on the extracted mobility characteristics, we developed a mobility model, focusing on movements among popular regions. Our validation shows that synthetic tracks match real tracks with a median relative error of 17%.
Borate melt structure: Temperature‐dependent B–O bond lengths and coordination numbers from high‐energy X‐ray diffraction (2018)

Abstract Borate melts containing &lt;20 mol% Na 2 O have been studied using high‐energy synchrotron X‐ray diffraction. Temperature dependencies of the mean B–O bond lengths are shown to vary strongly with soda content, by comparison to previous measurements on liquid B 2 O 3 and Na 2 B 4 O 7 . Whereas in liquid B 2 O 3 linear thermal expansion of the BØ 3 units is observed, with coefficient α BO = 3.7(2) × 10 −6 K −1 , this expansion is apparently slightly suppressed in melts containing &lt;20 mol% Na 2 O, and is dramatically reversed at the diborate composition. These effects are interpreted in terms of changes in the mean B–O coordination number, where the reaction BØ 4 − + BØ 3 ⇌ BØ 3 + BØ 2 O − shifts to the right with increasing temperature. The empirical bond‐valence relationship is used to convert measured bond lengths, r BO , to coordination numbers, n BO , including a correction for the expected thermal expansion. This method is more accurate and precise than direct determination of n BO from peak areas in the radial distribution functions. Gradients of Δ n BO /Δ T = −3.4(3) × 10 −4 K −1 close to the diborate composition, and Δ n BO /Δ T = −0.3(1) × 10 −4 K −1 for a 13(3) mol% Na 2 O melt are observed, in reasonable agreement with Raman spectroscopic observations and thermodynamic modeling, with some quantitative differences. These observations go toward explaining isothermal viscosity maxima and changes in fragility across the sodium borate system.