gebhart/patrepeval huggingface dataset:
The Cys(X)5Arg Catalytic Motif in Phosphoester Hydrolysis (1994)

The Yersinia protein tyrosine phosphatase (PTPase) was identified in the genus of bacteria responsible for the plague or the Black Death and was shown to be essential for pathogenesis. The three-dimensional structure of the catalytic domain of the Yersinia PTPase has been solved, and this information along with a detailed kinetic analysis has led to a better understanding of the catalytic mechanism of the PTPase. Mutational and chemical modification experiments have established that an invariant Cys residue (Cys403) is directly involved in formation of a covalent phosphoenzyme intermediate. We have shown that Arg409 plays a critical role in PTPase action and that the Cys(X)5Arg active site motif forms a phosphate-binding loop which appears to represent the essential features necessary for catalysis by the PTPases, the dual specific phosphatases, and the low molecular weight acid phosphatases.
On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction (2010)

We estimated the reproducibility of tandem mass spectra for the widely used collision-induced dissociation (CID) of peptide ions. Using the Pearson correlation coefficient as a measure of spectral similarity, we found that the within-experiment reproducibility of fragment ion intensities is very high (about 0.85). However, across different experiments and instrument types/setups, the correlation decreases by more than 15% (to about 0.70). We further investigated the accuracy of current predictors of peptide fragmentation spectra and found that they are more accurate than the ad-hoc models generally used by search engines (e.g., SEQUEST) and, surprisingly, approaching the empirical upper limit set by the average across-experiment spectral reproducibility (especially for charge +1 and charge +2 precursor ions). These results provide evidence that, in terms of accuracy of modeling, predicted peptide fragmentation spectra provide a viable alternative to spectral libraries for peptide identification, with a higher coverage of peptides and lower storage requirements. Furthermore, using five data sets of proteome digests by two different proteases, we find that PeptideART (a data-driven machine learning approach) is generally more accurate than MassAnalyzer (an approach based on a kinetic model for peptide fragmentation) in predicting fragmentation spectra but that both models are significantly more accurate than the ad-hoc models.
Integrated epigenomics identifies <i>BMP4</i> as a modulator of cisplatin sensitivity in gastric cancer (2012)

BMP4 epigenetic and expression status may represent promising biomarkers for GC cisplatin resistance. Targeting BMP4 may sensitise GC cells to cisplatin. Oxaliplatin, a clinically acceptable cisplatin alternative, may represent a potential therapeutic option for BMP4-positive GCs.
The use of Millipore filter discs in axenic culture of flax rust (1971)

The presence of Millipore filter discs on the agar medium resulted in more uniform, vigorous colonies of flax rust than were found when the colonies were grown directly on the agar surface. In addition, transferring and subculturing were greatly facilitated, and losses were greatly reduced.
Feasibility of using ultrasound phased arrays for MRI monitored noninvasive surgery (1996)

The purpose of this paper was to evaluate the in vivo feasibility of using phased arrays for MRI guided ultrasound surgery. Two different array concepts were investigated: a spherically curved concentric ring array to move the focus along the central axis and a spherically curved 16 square element array to make the focus larger. Rabbit thigh muscles were exposed in vivo in a 1.5 T MRI scanner to evaluate the array performance. The results showed that both of the arrays performed as expected, and the focus could be moved and enlarged. In addition, adequate power could be delivered from the arrays to necrose in vivo muscle tissue in 10 s. This study was the first implementation of phased arrays for MRI guided ultrasound surgery. The results demonstrate that phased arrays have significant potential for noninvasive tissue coagulation.
An active vision system for a location task using an inhomogeneously blurred image (2002)

This paper describes a simple method to detect a location of each object using an inhomogeneously blurred image, and the implementation of the method to an active vision system in order to execute a location task. In the proposed method, which is based on our previous theoretical study on the early vision, a camera-taken image is processed with high resolution near the optical axis of the camera, and with low resolution in the periphery. Using such an inhomogeneously blurred image, the objects are classified by neural networks with respect to their location in view . This method is implemented to our proposed mobile camera as the active vision system. The experimental results show that every object in view is easily foveated one after another.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
On the Length Estimation of Digital Curves (1999)

You are granted permission for the non-commercial reproduction, distribution, display, and performance of this technical report in any format, BUT this permission is only for a period of 45 (forty-five) days from the most recent time that you verified that this technical report is still available from the original CITR web site; http://citr.auckland.ac.nz/techreports/ under terms that include this permission. All other rights are reserved by the author(s).
<i>Griffonia simplicifolia</i> I isolectin as a functionally monovalent probe for use in flow cytometry (1986)

The inherent tendency of lectins to agglutinate cells has limited their use as reagents for the detection of carbohydrate groups on cell surfaces by flow cytometry. In the current study, we demonstrate a method for the use of a fluoresceinated tetrameric isolectin (Griffonia simplicifolia I-A3B, FITC-GS I-A3B) as a functionally monovalent, nonagglutinating probe in flow cytometry. This isolectin contains three A subunits and one B subunit. Both types of subunits bind alpha-D-galactopyranosyl (alpha-D-galp-) end groups with similar affinities; however, the A subunits have a 1,000-fold greater affinity for N-Acetyl-D-galactosamine (GalNAc) than does the B subunit. The addition of low (1-2 mM) concentrations of GalNAc to the FITC-GS I-A3B isolectin results in blockage of the three A subunits without significantly affecting the B subunit; this yields a functionally monovalent probe for the detection of cell surface alpha-D-Galp end groups. This approach has been used to examine two types of cells: Ehrlich ascites tumor cells and rat alveolar macrophages, both of which are known to express cell surface alpha-D-Galp end groups. Lectin binding, as determined by number of positive cells and fluorescence intensity, was dependent upon concentration of the lectin and haptenic sugar. Specificity of the staining was demonstrated by the ability of methyl alpha-D-galactopyranoside (Met alpha-D-Galp) to abolish the binding of the lectin to the cells. Elimination of both GalNAc and Met alpha-D-Galp from the staining solution resulted in agglutination of the cells, indicating that the A subunits were active in the absence of GalNAc.
Ordinal measures for image correspondence (1998)

We present ordinal measures of association for image correspondence in the context of stereo. Linear correspondence measures like correlation and the sum of squared difference between intensity distributions are known to be fragile. Ordinal measures which are based on relative ordering of intensity values in windows-rank permutations-have demonstrable robustness. By using distance metrics between two rank permutations, ordinal measures are defined. These measures are independent of absolute intensity scale and invariant to monotone transformations of intensity values like gamma variation between images. We have developed simple algorithms for their efficient implementation. Experiments suggest the superiority of ordinal measures over existing techniques under nonideal conditions. These measures serve as a general tool for image matching that are applicable to other vision problems such as motion estimation and texture-based image retrieval.
Possible role for the essential GTP-binding protein Obg in regulating the initiation of sporulation in Bacillus subtilis (1995)

We fused obg, encoding an essential GTP-binding protein in Bacillus subtilis, to the LacI-repressible, IPTG (isopropyl-beta-D-thiogalactopyranoside)-inducible promoter Pspac. Depletion of Obg, following removal of IPTG, caused a defect in sporulation and in expression of sporulation genes that are activated by Spo0A approximately P. These defects were significantly relieved by a mutation in spo0A (rvtA11) that bypasses the normal phosphorylation pathway, indicating that Obg might normally be required, either directly or indirectly, to stimulate activity of the phosphorelay that activates Spo0A.
Classifying and using motion in organic indoor positioning (2012)

Current mobile devices continuously estimate their locations, allowing users to “check in”, find nearby friends and interests, and determine routes to their destinations. While underlying satellite, cell, and WiFi-based positioning systems can return an accurate and meaningful position in many cases, extending them to work energy-efficiently, particularly indoors, remains an open problem. In this work, we study energy-efficient and robust human-scale motion classifiers and their use in room-grain, collaborative indoor positioning systems. Previous work on improving energy-efficiency in positioning systems has assumed sensor input from an energy-cheaper alternative: using an accelerometer in lieu of GPS, for example. Unfortunately, even these alternative sensors are not practical for everyday use because of their own energy consumption, at least when sampled continuously. After studying what accelerometer sampling rates are feasible, we compare six methods for motion classification, two of which are new. We find that the existing simple statistical methods are not sufficiently robust with respect to different kinds of movement and different users, because the thresholds between movement and non-movement are too tight. In contrast we find that the two new, more sophisticated models, one based on Page-Hinkley statistics, and the other inspired by the Discrete Fourier Transform, provide a clearer differentiation between the two states. Only the Page-Hinkley-based one is as energy-efficient as the simple statistical methods, however. Through a WiFi geolocation system that relies on motion detection, we show how the choice of the underlying motion classifier can have a significant impact on user-perceived performance.
[<i>cis</i>‐(1,3‐Diene)<sub>2</sub>W(CO)<sub>2</sub>] Complexes as MOCVD Precursors for the Deposition of Thin Tungsten – Tungsten Carbide Films (2010)

Abstract Tungsten ‐ tungsten carbide thin films are deposited by metal‐organic (MO)CVD on silica‐coated silicon wafers using [ cis ‐(1,3‐butadiene) 2 W(CO) 2 ] and [ cis ‐(1,3‐cyclohexadiene) 2 W(CO) 2 ], respectively, as tunable precursor complexes. The compounds are prepared through photochemical ligand exchange reactions from [W(CO) 6 ] and fully characterized, including X‐ray structure determination and detailed differential thermal analysis (DTA)/thermogravimetry (TG) investigations. Gas‐phase diffusion coefficients and the vapor pressure of the compounds are calculated. The MOCVD experiments are performed in a vertical cold‐wall reactor and the exhaust gas is analyzed by gas chromatography (GC). X‐ray photoelectron spectroscopy (XPS), X‐ray diffraction (XRD), atomic force microscopy (AFM), and scanning electron microscopy (SEM) measurements are utilized for film characterization. Consequences of the high oxophilicity of freshly formed tungsten surfaces, consecutive surface reactions of the complex ligands, film growth, and film properties are discussed. Inside the layers, tungsten carbide is identified as the main component.
MULINEX: Multilingual Web Search and Navigation (1998)

MULINEX is a multilingual search engine for the WWW. During the phase of document gathering, the system extracts information about documents by making use of language identification, thematic classification and automatic summarisation. In the search phase, the users&apos; query terms are translated in order to enable search in different languages. Search results are presented with a summary and information about the language and thematic categories to which the document belongs. Summaries and documents are translated on demand by making use of the LOGOS machine translation system. The system is to be deployed in the online services of Bertelsmann Telemedia and Grolier Interactive Europe, and supports French, German and English. The current MULINEX prototype is the first system for translingual information access integrating retrieval, summarisation and translation. Keywords translingual information retrieval, categorisation, summarisation, language identification, query translation, mac...
Solid phase extraction on multiwalled carbon nanotubes and flame atomic absorption spectrometry combination for determination of some metal ions in environmental and food samples (2011)

Abstract In this study, a new sensitive and simple method for simultaneous separation and preconcentration of Cu2+, Zn2+, Pb2+, and Cd2+ ions from various real samples prior to their measurements by flame atomic absorption spectrometry has been developed. The proposed method is based on the utilization of multiwalled carbon nanotube in combination with (E)-N1-(4-nitro-benzylidene)-N2-(2-((E)-4-nitrobenzylideneamino)ethyl) ethane-1,2-diamine as a solid phase extractant. The separation parameters for effective adsorption of Cu2+, Zn2+, Pb2+, and Cd2+ ions, including the effects of pH, amount of ligand, sample and eluent flow rate, and common coexisting ions were examined. The optimum pH for the separation of Cu2+, Zn2+, Pb2+, and Cd2+ ions on the new sorbent was 6.0. The detection limits based on 3 sigma (n = 15) for Cu2+, Zn2+, Pb2+, and Cd2+ ions was 0.69, 0.48, 8.9, and 0.25 ng mL−1 while respective preconcentration factor for Cu2+, Zn2+ ions was 80 and for Pb2+ and Cd2+ ion was 20 and 60, respectively, with relative standard deviations between 0.7% and 5.8%. The proposed preconcentration procedure was applied to the analysis of various real samples. Keywords: (E)-N1-(4-nitrobenzylidene)-N2-(2-((E)-4-nitrobenzylideneamino)ethyl) ethane-1,2-diaminesolid phase extractionmetal ionsflame atomic absorption spectrometry
Rapid Detection of Ricin in Serum Based on Cu-Chelated Magnetic Beads Using Mass Spectrometry (2016)

The protein toxin ricin obtained from castor bean plant (Ricinus communis) seeds is a potent biological warfare agent due to its ease of availability and acute toxicity. In this study, we demonstrated a rapid and simple method to detect ricin in serum in vitro. The ricin was mixed with serum and digested by trypsin, then all the peptides were efficiently extracted using Cu-chelated magnetic beads and were detected with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The specific ricin peptides were identified by Nanoscale Ultra Performance liquid chromatography coupled to tandem mass spectrometry according to their sequences. The assay required 2.5 hours, and a characteristic peptide could be detected down to 4 ng/μl and used as a biomarker to detect ricin in serum. The high sensitivity and simplicity of the procedure makes it valuable in clinical practice. Graphical Abstract ᅟ.
Notizen: Bildung eines Derivats von 1-Aza-8-sila-bicyclo [4.2.0] oktan unter C-H-Spaltung. / Formation of 1-Aza-8-sila-bicyclo[4,2,0]octane under Cleavage of a C-Η Bond (1976)

The reaction of tert-butylamino-fluoro-phenyl -tetramethylpiperidino-silane and butyllithium takes places under LiF- and C 4 H 10 -elimination. The proton, required for the formation of butane, is not transferred from the amino but from one of the methyl substituents of the piperidino ring under formation of a bicyclic structure
Increased Sequestration of Matrix Metalloproteinases in Ageing Human Bruch's Membrane: Implications for ECM Turnover (2010)

The ageing of Bruch's membrane was associated with progressive sequestration of MMPs reducing the free concentration and potential for activation. These changes may underlie the reduction in degradation that leads to the age-related increase in the thickness of the membrane.
C≡C Triple Bond Activation by Heterocyclic Aluminum Phosphinides (2010)

Treatment of aryl-di(tert-butylethynyl)phosphines Aryl-P(C≡C-CMe3)2 [Aryl = C6H5 (4) 2,4,6-Me3C6H2 (5)] with dialkylaluminum hydrides, R2Al−H (R = CMe3, CH2CMe3), afforded heterocyclic, zwitterionic compounds 6−9 by hydroalumination and release of the corresponding dimeric tert-butylethynyl-dialkylaluminum derivatives, [R2Al-C≡C-CMe3]2 (10 and 11). The molecular structures of 6−8 reveal a P2C2Al ring with a tetracoordinated aluminum atom, two exocyclic C═C double bonds, a tricoordinated phosphorus atom, and a phosphonium cation carrying an aryl and an alkynyl group. The C≡C triple bond of 7 was inserted into the Al−P bonds of the heterocycles upon warming to give the bicyclic compound 13. A similar compound (12) was directly formed when the bisalkyne 4 was treated with dineopentylaluminum hydride. Their molecular structures show the annulated four- (AlC2P) and five-membered heterocycles (P2C3) to contain three different C═C double bonds. The sterically most shielded monocyclic compound (8; Aryl = 2,4,5-Me3C6H2; R = CMe3) decomposed upon warming. DFT calculations were used to examine these reactions.
A new stereophonic stethoscope. (1990)

A new stereophonic stethoscope is presented. It is characterized by a single chest piece construction housing paired open-bell type sound accumulating chambers and paired diaphragm type sound accumulating chambers. A pair of separate ear tubes connected to each of the paired sound chambers establish two cross talk-free channels for collecting and delivering auscultatory sounds. Selective use of the open-bell and diaphragm sound chambers is assured with this new stethoscope. Advantages of stereophonic auscultation are discussed.
A robust immunoassay for pregnancy-associated plasma protein-A2 based on analysis of circulating antigen: establishment of normal ranges in pregnancy (2013)

Pregnancy-associated plasma protein-A (PAPP-A) and PAPP-A2, two homologous metzincin metalloproteases, are both tightly linked to regulation within the insulin-like growth factor (IGF) system because of their specific cleavage of IGF binding proteins. Recent studies suggest that PAPP-A may be involved in clinical conditions related to unwanted cellular growth, and the circulating levels of PAPP-A is an established biomarker in prenatal screening for chromosomal abnormalities. Microarray data indicate that PAPP-A2 has potential as a biomarker for pre-eclampsia. However, well-characterized immunological methods of quantification are not available. We therefore developed monoclonal antibodies against recombinant PAPP-A2. The antibodies were epitope mapped against recombinantly expressed chimeras between PAPP-A2 and PAPP-A. Furthermore, circulating PAPP-A2 was immunoaffinity purified and characterized by sequence analysis and mass spectrometry. Unlike PAPP-A, PAPP-A2 is a noncovalent dimer in which each subunit of 1558 amino acids originates from all of the 22 predicted coding exons. A previously hypothesized variant (PAPP-E) does not exist, but low amounts of a C-terminally truncated PAPP-A2 variant was detected. A sensitive and robust ELISA for full-length PAPP-A2 was developed and used to establish normal ranges of PAPP-A2 through pregnancy. The functional sensitivity of this ELISA at 20% CV was 0.08 ng/ml, and the serum concentration of PAPP-A2 was found to increase during pregnancy in agreement with placental synthesis. The existence of this assay will enable an assessment of the biomarker potential of PAPP-A2 in pre-eclampsia as well as other clinical conditions.
Low Overhead Hardware-Assisted Virtual Machine Analysis and Profiling (2016)

Cloud infrastructure providers need reliable performance analysis tools for their nodes. Moreover, the analysis of Virtual Machines (VMs) is a major requirement in quantifying cloud performance. However, root cause analysis, in case of unexpected crashes or anomalous behavior in VMs, remains a major challenge. Modern tracing tools such as LTTng allow fine grained analysis - albeit at a minimal execution overhead, and being OS dependent. In this paper, we propose HAVAna, a hardware-assisted VM analysis algorithm that gathers and analyzes pure hardware trace data, without any dependence on the underlying OS or performance analysis infrastructure. Our approach is totally non-intrusive and does not require any performance statistics, trace or log gathering from the VM. We used the recently introduced Intel PT ISA extensions on modern Intel Skylake processors to demonstrate its efficiency and observed that, in our experimental scenarios, it leads to a tiny overhead of up to 1%, as compared to 3.6-28.7% for similar VM trace analysis done with software-only schemes such as LTTng. Our proposed VM trace analysis algorithm has also been open-sourced for further enhancements and to the benefit of other developers. Furthermore, we developed interactive Resource and Process Control Flow visualization tools to analyze the hardware trace data and present a real-life usecase in the paper that allowed us to see unexpected resource consumption by VMs.
Generation of Induced Pluripotent Stem Cells from Human Renal Proximal Tubular Cells with Only Two Transcription Factors, Oct4 and Sox2 (2012)

The tubular epithelium of the kidney is susceptible to injury from a number of different causes, including inflammatory and immune disorders, oxidative stress, and nephrotoxins, among others. Primary renal epithelial cells remain one of the few tools for studying the biochemical and physiological characteristics of the renal tubular system. Nevertheless, differentiated primary cells are not suitable for recapitulation of disease properties that might arise during embryonic kidney formation and further maturation. Thus, cellular systems resembling kidney characteristics are in urgent need to model disease as well as to establish reliable drug-testing platforms. Induced pluripotent stem cells (iPSCs) bear the capacity to differentiate into every cell lineage comprising the adult organism. Thus, iPSCs bring the possibility for recapitulating embryonic development by directed differentiation into specific lineages. iPSC differentiation ultimately allows for both disease modeling in vitro and the production of cellular products with potential for regenerative medicine. Here, we describe the rapid, reproducible, and highly efficient generation of iPSCs derived from endogenous kidney tubular renal epithelial cells with only two transcriptional factors, OCT4 and SOX2. Kidney-derived iPSCs may provide a reliable cellular platform for the development of kidney differentiation protocols allowing drug discovery studies and the study of kidney pathology.
A design methodology of the wideband orthogonal mode transducer for the SKA Band 2 feed (2016)

A methodology for fast design of a compact wideband orthogonal mode transducer (OMT) matched to a wide flare angle axially corrugated conical horn for the Band 2 feed of the Square Kilometer Array (SKA) is presented. The design takes into account, through full-wave electromagnetic analyses, interactions that occur in the feed over the entire frequency band. To lower the computational cost and make the model suitable for optimization, problem decomposition together with a combination of high fidelity and physics-based models are employed. The reflection coefficients of the feed are designed to be less than -20 dB.