gebhart/patrepeval huggingface dataset:
New Stitching Algorithm Using an Approximated Reference Shape (2017)

A new stitching algorithm named ARSA (Approximated Reference Shape Algorithm) that connects multiple partial measurements and combines them into a whole shape is proposed. Compared to the conventional stitching method, the advantages of the new algorithm are that there is no need to precisely find the overlap area and no need to interpolate three dimensional point data. These are essential conditions in order to apply the method to a free form measurement machine whose measured data are sparse and three dimensional points. The performance of the algorithm is verified by simulation of a TMT (30 m telescope) segmented mirror.
Investigating Biogenetic Hypotheses of the Securinega Alkaloids: Enantioselective Total Syntheses of Secu’amamine E/ent-Virosine A and Bubbialine (2017)

The synthesis of the Securinega alkaloid secu'amamine E (ent-virosine A) has been accomplished for the first time in 12 steps and 8.5% overall yield. In addition, bubbialine has been prepared and characterized. These two alkaloids and bubbialidine, all featuring an azabicyclo[2.2.2]octane core, were rearranged to their azabicyclo[3.2.1]octane congeners, a framework found in many Securinega alkaloids. These experiments suggest that azabicyclo[2.2.2]octane derivatives could serve as intermediates in the biosynthesis of the rearranged azabicyclo[3.2.1]octane products.
Supplementary Figure 3 from Development and Characterization of a Novel CD19CherryLuciferase (CD19CL) Transgenic Mouse for the Preclinical Study of B-Cell Lymphomas (2023)

&lt;p&gt;PDF file, 576KB, Confocal analysis of PBMC of A) wild type and B) single transgenic mice. Mature naive B cells expressing the cherry protein were observed in freshly isolated PBMC stained with a, c, e and g) DAPI, to visualize nuclei. b, d, f and h) cherry cytoplasmatic fluorescence. a, b, c and d) 40X, e, f, g and h) 63X. C) Luciferase assay of cell extracts of CD19+ B cells isolated from PBMC of wild type and single transgenic mice.&lt;/p&gt;
Dinucleating Ligand Platforms Supporting Indium and Zinc Catalysts for Cyclic Ester Polymerization (2016)

The synthesis of the first alkoxide-bridged indium complex supported by a chiral dinucleating ligand platform (1), along with its zinc analogue (2), is reported. Both complexes are synthesized in a one-pot reaction starting from a chiral dinucleating bis(diamino)phenolate ligand platform, sodium ethoxide, and respective metal salts. The dinucleating indium analogue (7) based on an achiral ligand backbone is also reported. Indium complexes bearing either the chiral or achiral ligand catalyze the ring-opening polymerization of racemic lactide (rac-LA) to afford highly heterotactic poly(lactic acid) (PLA; Pr > 0.85). The indium complex bearing an achiral ligand affords essentially atactic PLA from meso-LA. The role of the dinucleating ligand structure in catalyst synthesis and polymerization activity is discussed.
Paleoenvironments (2018)

Abstract One of the most fascinating facets of eDNA lies in the possibility of exploiting it to reconstruct past environments in paleoecology and in archaeology. Chapter 15, entitled “Paleoenvironments,” reviews different pioneer studies that scrutinized ancient eDNA extracted from different substrates (e.g., lake sediments, permafrost, or archaeological midden material), to address a wide range of questions. These include, for example, the taxonomic identification of archaeological fish bones in Madagascar from bulk samples, the reconstruction of past plant communities based on the large-scale analysis of permafrost samples, or the assessment of past human diet in Greenland based on midden material. Midden material from archaeological sites represents a valuable source of information for tracking food habits of ancient human communities. It also provides information about the surrounding biodiversity, using humans as biodiversity samplers, which is also explored here.
Substrate specificity of protein kinase A in reaction with protein and peptide substrates (2001)

Protein kinases are enzymes that catalyse the phosphoryl transfer from the g-phosphate of ATP to acceptor amino acids in proteins. The specificity of selected model protein kinases was studied at three different levels using a) novel bi-substrate-analogue inhibitors, b) synthetic peptide substrates and c) mutated protein substrate analogues. A new class of protein kinase bi-substrate-analogue inhibitors was designed on the basis of adenosine-5’-carboxylic acid derivatives, where a short arginine containing peptide was attached to the 5'-carbon atom of the adenosine sugar moiety via a linker chain. These compounds showed high inhibitory potential against two basophilic protein kinases, the protein kinase A (PKA) and protein kinase C (PKC), with IC50 values in the nanomolar range, but no inhibitory activity towards the acidophilic kinases CK1 and CK2. The inhibitors were efficiently applied for affinity purification of PKA using MgATP as well as L-arginine as eluting agents. Ca2+-dependent protein kinase (CDPK-1) was purified from maize seedlings and its substrate specificity was studied using a set of synthetic peptides. These were derived from the phosphorylatable sequence RVLSRLHS(15)VRER of maize sucrose synthase 2 (SuSy2), and a consensus sequence motif A/LXRXXSXRZR (where X denotes a position with no strict amino acid requirements and Z a position strictly not tolerating arginine) was defined from a study using arrays of systematically varied peptides attached to cellulose membrane (SPOTsTM membranes). The SuSy2 derived peptides were also found to be efficient substrates for mammalian PKC, but showed low reactivity in the case of PKA. On the basis of this peptide motif, a positionally oriented peptide library approach based on ESI-MS detection of phosphopeptides in initial velocity conditions was designed for quantitative kinetic characterization of protein kinase specificity profiles. On the basis of the obtained data an optimal peptide substrate for PKC, FRRRRSFRRR, was designed. The specificity of protein kinase A was studied using site-directed mutagenesis in the phosphorylation site of L-type pyruvate kinase (L-PK), and comparison of the obtained data with the data from previous studies on structurally altered peptide substrates revealed that amino acid alterations in short peptide substrates cause stronger effects on the phosphorylation rate than the corresponding alterations in the protein substrate L-PK.
Structure and immunological function of oxidised albumin in lung cancer: its potential role as a biomarker of elevated oxidative stress (2009)

"Structure and immunological function of oxidised albumin in lung cancer: its potential role as a biomarker of elevated oxidative stress." British Journal of Biomedical Science, 66(3), p. 166This article refers to:Structure and immunological function of oxidised albumin in lung cancer: its potential role as a biomarker of elevated oxidative stress
Reflections on a distance education experiment in DSP (1999)

Distance education is becoming an increasingly important means of reaching a wider variety of traditional and non-traditional students and of developing unique educational partnerships between universities. In an effort to assist engineering departments just beginning to pursue distance education, the authors reflect on an innovative four year experiment in Internet based distance education involving students and faculty from the University of Colorado at Boulder, George Mason University, Rice University, Cornell University, and Sandia National Labs. The educational and research benefits to both the students and faculty are discussed in detail. In addition, the weaknesses and limitations of this experiment are also addressed. It is hoped that these comments and observations will benefit other institutions beginning to pursue similar distance education programs.
The circumstances surrounding the outbreak and spread of equine influenza in South africa (1999)

Equine-2 influenza A virus (H3N8) infection first occurred among naïve horses in South Africa in December 1986. The virus was introduced following the importation of six horses from the United States of America. While the release of in-contact horses from quarantine three days after the arrival of these six horses played a role in the rapid spread of the disease in South Africa, other outbreaks of disease were associated with viral introduction by personnel or contaminated instruments. The control measures and implications of the introduction of equine influenza to South Africa are also discussed.
Atomic force microscopy using optical interferometry (1988)

An atomic force microscope using optical interferometry as the lever detection method is presented. Topographic images of graphite with 50-Å lateral resolution have been obtained using repulsive contact forces. Images of the graphite surface showing the atomic periodicity were also recorded; in this case, the image contrast does not represent surface topography, but rather variations in the lateral frictional force on the tip. Images using attractive electrostatic forces to map topographic features are shown. The instrument has also been operated as a scanning tunneling microscope while simultaneously measuring the contact force between the tip and a graphite surface.
Application of Improved Particle Swarm Optimization Algorithm Based on GSO in Optimization Design of FIR Digital Filter (2018)

Aiming at the problem that the particle swarm optimization algorithm will fall into the local optimum, and improve the convergence speed of the algorithm as much as possible, an improved particle swarm optimization algorithm based on firefly position optimization is proposed, which is improved based on the standard firefly position optimization algorithm. Adaptive inertia weights are introduced and flight factors, chaos and mutation strategies are introduced. The improved algorithm is applied to the optimization design of FIR digital filter. The optimization algorithm is used to efficiently search the whole particle swarm space and obtain the optimal parameters. The simulation proves the superiority of the algorithm in convergence speed and precision.
Doppler radar sensor for occupancy monitoring (2013)

This paper investigates the use of Doppler radar sensor for occupancy monitoring. The feasibility of true presence is explored with Doppler radar occupancy sensors to overcome the limitations of the common occupancy sensors. The common occupancy sensors are more of a motion sensor than a presence detector. Existing cost effective off the shelf System-on-Chip CC2530 RF transceiver is used for developing the radio. The transmitter sends continuous wave signal at 2.405 GHz. Different levels of activity is detected by post-processing sensor signals. Heart and respiratory signals are extracted in order to improve stationary subject detection.
Substrate-Specific Conformational Regulation of the Receptor Tyrosine Kinase VEGFR2 Catalytic Domain (2013)

The contributions of the phosphoacceptor and the catalytic domain context to protein kinase biology and inhibitor potency are routinely overlooked, which can lead to mischaracterization of inhibitor and receptor functions. The receptor tyrosine kinase vascular endothelial growth factor receptor-2 (VEGFR2) is studied as a model system using a series of phosphoacceptor substrates (k(cat)/K(m) 684-116,000 M(-1) s(-1)) to assess effects on catalysis and inhibitor binding. ATP-competitive inhibitor potency toward the VEGFR2 catalytic domain (VEGFR2-CD) varies with different phosphoacceptor substrates, which is unexpected because the phosphoacceptors do not affect K(m,ATP) values. Indazole-based inhibitors are up to 60-fold more potent with two substrates (gastrin, minigastrin) relative to the others. Thus there is a component of uncompetitive inhibition because a specific phosphoacceptor enhances potency but is not strictly required. This substrate-specific inhibitory potency enhancement correlates with phosphoacceptor active site saturation and is not observed with other related kinases. The effect is confined to a specific catalytic domain conformation because autophosphorylation eliminates the potency enhancement as does the addition of the juxtamembrane domain (20 amino acids). Indazole inhibitor structure-activity analysis reveals that the magnitude of potency enhancement correlates with the size of the substituent that binds in a regulatory region of the active site. VEGFR drugs profiled with VEGFR2-CD using minigastrin have potency well-correlated with inhibition of full-length, cellular VEGFR2 autophosphorylation, an indication that the minigastrin-induced conformation is biologically relevant. These findings raise the possibility that inhibitors directed toward a common target can have different biological effects based on the kinase-substrate complexes present in different cellular contexts.
A cyclotron for medical research (1957)

The paper describes the design and construction of the Medical Research Council fixed-frequency cyclotron, which is to be used for research in radiotherapy and radiobiology and for the production of radioactive isotopes for diagnostic, therapeutic and medical research purposes.The machine is designed to maintain an output of 200 μA of 15 MeV deuterons in an external beam under routine operating conditions.Special care has been taken throughout the design to ensure ease of maintenance and reliable routine operation.
Bias correction for selecting the minimal-error classifier from many machine learning models (2014)

Supplementary data are available at Bioinformatics online.
ChemInform Abstract: Catalysis with Doped Sol‐Gel Silicates. (2011)

Abstract Review: 56 refs.
Signed Link Prediction with Sparse Data: The Role of Personality Information (2019)

Predicting signed links in social networks often faces the problem of signed link data sparsity, i.e., only a small percentage of signed links are given. The problem is exacerbated when the number of negative links is much smaller than that of positive links. Boosting signed link prediction necessitates additional information to compensate for data sparsity. According to psychology theories, one rich source of such information is user's personality such as optimism and pessimism that can help determine her propensity in establishing positive and negative links. In this study, we investigate how personality information can be obtained, and if personality information can help alleviate the data sparsity problem for signed link prediction. We propose a novel signed link prediction model that enables empirical exploration of user personality via social media data. We evaluate our proposed model on two datasets of real-world signed link networks. The results demonstrate the complementary role of personality information in the signed link prediction problem. Experimental results also indicate the effectiveness of different levels of personality information for signed link data sparsity problem.
A 2.7 V only 8 Mb×16 NOR flash memory (2002)

This paper describes a 80 ns, 2.7 V to 3.6 V single voltage supply 8 Mb/spl times/16 flash memory. It uses a high speed Vcc detector to control the wordline boost level and an intelligent programming algorithm to optimize the program time. Erase is achieved by a new low Vcc negative charge pump. The device is fabricated using a 0.5 /spl mu/m design rule, double layer metal, dual layer polysilicon, and triple well CMOS. The single transistor cell size is 1.7/spl times/1.7 /spl mu/m/sup 2/. The memory cell uses a conventional drain side channel hot electron for programming and negative gate Fowler-Nordheim tunneling on the source side for erase.
Upper and lower stiffness bounds for porous anisotropic rocks (2008)

We derive double inequalities providing the bounds for components of the effective stiffness tensor of a two-phase, porous-cracked medium with aligned ellipsoidal inclusions. The bounds are derived on the basis of the Hashin-Shtrikman variational principle, and the conditions for positive semi-definiteness of quadratic forms. Inequalities are presented for isotropic, cubic, hexagonal and orthorhombic overall symmetries. The results obtained for orthorhombic symmetry are valid for the general determination of transport properties (effective permeability, thermal and electrical conductivity). We conclude that inequalities for diagonal components of the effective tensor have the form of bounds, whereas in general these bounds do not exist for off-diagonal components. One important implication of this is that Voigt-Reuss averages do not provide the upper and lower bounds for off-diagonal components of the effective tensor, as is sometimes assumed. We also present numerical results for stiffness bounds obtained by modelling various shales with isotropic, transverse isotropic and orthorhombic overall symmetries.
Identification of critical barriers in cloud computing adoption by enterprises using systematic review methodology (2017)

Cloud computing has been an area of research interest recently because of its unrivalled advantages to the computing world. However, businesses are still sceptical of adopting it because of the different issues that come with it. This study uses systematic literature review (SLR) process to identify and analyse potential barriers in cloud adaptation. The data required to conduct this study is extracted from 84 research studies via SLR process. The studies selection and data extraction process is based on a well-documented protocol. A list of 50 barriers has been identified after synthesising the extracted data. These identified barriers have been categorised in five main domains, i.e., organisational barriers, technical barriers, legal barriers, financial barriers, and environmental barriers. The proactive management of the identified barriers might allow enterprises to adopt cloud computing successfully.
Natively Interpretable Machine Learning and Artificial Intelligence: Preliminary Results and Future Directions (2019)

Machine learning models have become more and more complex in order to better approximate complex functions. Although fruitful in many domains, the added complexity has come at the cost of model interpretability. The once popular k-nearest neighbors (kNN) approach, which finds and uses the most similar data for reasoning, has received much less attention in recent decades due to numerous problems when compared to other techniques. We show that many of these historical problems with kNN can be overcome, and our contribution has applications not only in machine learning but also in online learning, data synthesis, anomaly detection, model compression, and reinforcement learning, without sacrificing interpretability. We introduce a synthesis between kNN and information theory that we hope will provide a clear path towards models that are innately interpretable and auditable. Through this work we hope to gather interest in combining kNN with information theory as a promising path to fully auditable machine learning and artificial intelligence.
Assessing and Interpreting Real‐World Evidence Studies: Introductory Points for New Reviewers (2021)

Nonrandomized real-world evidence (RWE) studies are conducted using healthcare data collected as part of clinical practice. As RWE studies are increasingly considered for regulatory, coverage, and other clinical decision making, nonspecialists will find themselves in the position of assessing the validity of RWE studies, a field that may be less familiar to them. This introductory guide provides conceptual guidance for reviewing RWE studies and is particularly directed at professionals for whom this is new or whose prior experience has primarily been in reviewing randomized controlled trial evidence. We focus on RWE studies that make causal inference, evaluating whether one treatment option is better, worse, or neutral compared to another. Although we provide citations to direct the reader to resources with more details on complex issues, this guide cannot substitute for years of training and expertise in the field.
LLM-Domain Containing B-GATA Factors Control Different Aspects of Cytokinin-Regulated Development in Arabidopsis thaliana (2016)

Leu-Leu-Met (LLM)-domain B-GATAs are a subfamily of the 30-membered GATA transcription factor family from Arabidopsis. Only two of the six Arabidopsis LLM-domain B-GATAs, i.e. GATA, NITRATE-INDUCIBLE, CARBON METABOLISM-INVOLVED (GNC) and its paralog GNC-LIKE/CYTOKININ-RESPONSIVE GATA FACTOR1 (GNL), have already been analyzed with regard to their biological function. Together, GNC and GNL control germination, greening, flowering time, and senescence downstream from auxin, cytokinin (CK), gibberellin (GA), and light signaling. Whereas overexpression and complementation analyses suggest a redundant biochemical function between GNC and GNL, nothing is known about the biological role of the four other LLM-domain B-GATAs, GATA15, GATA16, GATA17, and GATA17L (GATA17-LIKE), based on loss-of-function mutant phenotypes. Here, we examine insertion mutants of the six Arabidopsis B-GATA genes and reveal the role of these genes in the control of greening, hypocotyl elongation, phyllotaxy, floral organ initiation, accessory meristem formation, flowering time, and senescence. Several of these phenotypes had previously not been described for the gnc and gnl mutants or were enhanced in the more complex mutants when compared to gnc gnl mutants. Some of the respective responses may be mediated by CK signaling, which activates the expression of all six GATA genes. CK-induced gene expression is partially compromised in LLM-domain B-GATA mutants, suggesting that B-GATA genes play a role in CK responses. We furthermore provide evidence for a transcriptional cross regulation between these GATAs that may, in at least some cases, be at the basis of their apparent functional redundancy.
A Ligation-Triggered DNAzyme Cascade for Amplified Fluorescence Detection of Biological Small Molecules with Zero-Background Signal (2011)

Many types of fluorescent sensing systems have been reported for biological small molecules. Particularly, several methods have been developed for the recognition of ATP or NAD(+), but they only show moderate sensitivity, and they cannot discriminate either ATP or NAD(+) from their respective analogues. We have addressed these limitations and report here a dual strategy which combines split DNAzyme-based background reduction with catalytic and molecular beacon (CAMB)-based amplified detection to develop a ligation-triggered DNAzyme cascade, resulting in ultrahigh sensitivity. First, the 8-17 DNAzyme is split into two separate oligonucleotide fragments as the building blocks for the DNA ligation reaction, thereby providing a zero-background signal to improve overall sensitivity. Next, a CAMB strategy is further employed for amplified signal detection achieved through cycling and regenerating the DNAzyme to realize the true enzymatic multiple turnover (one enzyme catalyzes the cleavage of several substrates) of catalytic beacons. This combination of zero-background signal and signal amplification significantly improves the sensitivity of the sensing systems, resulting in detection limits of 100 and 50 pM for ATP and NAD(+), respectively, much lower than those of previously reported biosensors. Moreover, by taking advantage of the highly specific biomolecule-dependence of the DNA ligation reaction, the developed DNAzyme cascades show significantly high selectivity toward the target cofactor (ATP or NAD(+)), and the target biological small molecule can be distinguished from its analogues. Therefore, as a new and universal platform for the design of DNA ligation reaction-based sensing systems, this novel ligation-triggered DNAzyme cascade method may find a broad spectrum of applications in both environmental and biomedical fields.