gebhart/patrepeval huggingface dataset:
Interresidue hydrogen bonding in a peptide nucleic acid.RNA heteroduplex. (1996)

Previous molecular mechanics calculations suggest that strands of peptide nucleic acids (PNAs) and complementary oligonucleotides form antiparallel duplexes stabilized by interresidue hydrogen bonds. In the computed structures, the amide carbonyl oxygen nearest the nucleobase (O7') forms an interresidue hydrogen bond with the backbone amide proton of the following residue, (n + 1)H1'. Of the 10 published two dimensional 1H NMR structures of a hexameric PNA.RNA heteroduplex. PNA(GAACTC).r(GAGUUC), 9 exhibit two to five potential interresidue hydrogen bonds. In our minimized average structure, created from the coordinates of these 10 NMR structures, three of the five possible interresidue hydrogen bond sites within the PNA backbone display the carbonyl oxygen (O7') and the amide proton (n + 1)H1' distances and N1'-H1'-(n - 1)O7' angles optimal for hydrogen bond formation. The finding of these interresidue hydrogen bonds supports the results of our previous molecular mechanics calculations.
Origin and use of embryonic and adult stem cells in differentiation and tissue repair (2003)

Stem cells are self-renewing, unspecialised cells that can give rise to multiple cell types of all tissues of the body. They can be derived from the embryo, foetus and adult. The ability of stem cells to divide but also to differentiate to specialised cell types like nerve and muscle, have made them candidates on which to base therapies for diseases and disorders for which no, or only partially effective, therapies are available. Replacement of defective or absent cells in defective tissues and organs could represent a cure. Here, we introduce the background to stem cell research and review the present state-of-the-art in stem cell biology, directed differentiation and tissue repair. In particular, we distinguish embryonic versus adult sources of stem cells and data derived from animal versus human experiments in order to place current research and perspectives for clinical application in their correct context.
pH-Defining Equilibrium between Water and Supercritical CO2. Influence on SFE of Organics and Metal Chelates (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTpH-Defining Equilibrium between Water and Supercritical CO2. Influence on SFE of Organics and Metal ChelatesKaren L. Toews, Robert M. Shroll, Chien M. Wai, and Neil G. SmartCite this: Anal. Chem. 1995, 67, 22, 4040–4043Publication Date (Print):November 15, 1995Publication History Published online1 May 2002Published inissue 15 November 1995https://pubs.acs.org/doi/10.1021/ac00118a002https://doi.org/10.1021/ac00118a002research-articleACS PublicationsRequest reuse permissionsArticle Views2834Altmetric-Citations332LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Affinity Chromatography of Splicing Complexes: U2, U5, and U4 + U6 Small Nuclear Ribonucleoprotein Particles in the Spliceosome (1986)

The splicing process, which removes intervening sequences from messenger RNA (mRNA) precursors is essential to gene expression in eukaryotic cells. This site-specific process requires precise sequence recognition at the boundaries of an intervening sequence, but the mechanism of this recognition is not understood. The splicing of mRNA precursors occurs in a multicomponent complex termed the spliceosome. Such an assembly of components is likely to play a key role in specifying those sequences to be spliced. In order to analyze spliceosome structure, a stringent approach was developed to obtain splicing complexes free of cellular contaminants. This approach is a form of affinity chromatography based on the high specificity of the biotin-streptavidin interaction. A minimum of three subunits: U2, U5, and U4 + U6 small nuclear ribonucleoprotein particles were identified in the 35S spliceosome structure, which also contains the bipartite RNA intermediate of splicing. A 25S presplicing complex contained only the U2 particle. The multiple subunit structure of the spliceosome has implications for the regulation of a splicing event and for its possible catalysis by ribozyme or ribozymes.
Differential information and excessive volatility in financial markets (1992)

It is analysed whether risk averse agents possessing different information have an incentive to trade in a zero-sum market. The key to generate trading in a zero-sum speculative market is whether expectations are »homogenized» through the trading process. If not, trading will take place and all agents expect to be able to exploit private information not fully revealed by market prices to make a speculative profit. The existence of a rational expectations equilibrium with heterogenous expectations is proven to exist, and shown to imply excessive volatility ofprices and trading volumes.
Wavelets in Temporal and Spatial Processing of Biomedical Images (2000)

We review some of the most recent advances in the area of wavelet applications in medical imaging. We first review key concepts in the processing of medical images with wavelet transforms and multiscale analysis, including time-frequency tiling, overcomplete representations, higher dimensional bases, symmetry, boundary effects, translational invariance, orientation selectivity, and best-basis selection. We next describe some applications in magnetic resonance imaging, including activation detection and denoising of functional magnetic resonance imaging and encoding schemes. We then present an overview in the area of ultrasound, including computational anatomy with three-dimensional cardiac ultrasound. Next, wavelets in tomography are reviewed, including their relationship to the radon transform and applications in position emission tomography imaging. Finally, wavelet applications in digital mammography are reviewed, including computer-assisted diagnostic systems that support the detection and classification of small masses and methods of contrast enhancement.
Molecular Cloning, Characterization, and Localization of the Human Homolog to the Reported Bovine NPY Y3 Receptor: Lack of NPY Binding and Activation (1993)

A cDNA clone encoding the human homolog of the bovine cDNA clone LCR1 was isolated from a human lung cDNA library. The 1,670-bp-long nucleotide sequence predicts a single open reading frame of 352 amino acids, with a 92% amino acid identity to a bovine sequence reported to represent the neuropeptide Y (NPY) Y3 receptor. The amino acid sequence shares features common to many other G-protein-coupled receptors, including the seven transmembrane regions and putative glycosylation and phosphorylation sites. Polymerase chain reaction (PCR) analysis of human-hamster hybrid cell DNA reveals that the corresponding gene is located on human chromosome 2. Although the ligand for the bovine receptor has previously been identified as NPY in binding studies, extensive analysis with the human homolog transfected in several different cell lines failed to confirm this classification. Furthermore, the receptor shows 36% identity to both the human interleukin-8 (IL-8) and angiotensin II receptors but only 21% identity to the human NPY Y1 receptor. In addition, NPY and a number of other ligands fail to induce any change in cytosolic calcium levels in transfected cells, suggesting that this clone represents a novel neuropeptide receptor.
Ion concentration and haematocrit as determinants of impedance in an erythrocyte suspension model of renal medullary tissue (1990)

In order to analyse the respective roles of ion concentration and fractional volume of the interstitial compartment as determinants of the impedance, Z, of renal medullary tissue, a model was needed in which both these factors could be varied independently. An array of blood cell suspensions ions in saline (different haematocrit values and different NaCl concentrations) was used for this purpose. It was found that: (i) up to a measuring frequency of about 10 kHz, the complex consisting of needle electrodes and 'tissue' can be regarded as serially connected resistances, R, and capacitances; (ii) the frequency range 3-10 kHz can be regarded as optimal since it simultaneously assures low electrode polarization and a negligible role of tissue capacitance; (iii) increasing the haematocrit had two consequences--a reduced contribution of polarization impedance to the total impedance measured and a decreased sensitivity of ion concentration measurement from R-1 (conductance); (iv) passive electrical properties of renal medullary tissue were close to those of a 75% haematocrit cell suspension; (v) since in high haematocrit suspensions the resistive component of impedance predominates, within the frequency range 3-10 kHz either conductance or admittance, Z-1, can be used as an index of ion concentration; and (vi) impedance changes in kidney tissue are primarily determined by fluctuations of ion concentration with a less important contribution from interstitial volume changes.
Gene Expression Profiling of Mucosal Addressin Cell Adhesion Molecule-1+ High Endothelial Venule Cells (HEV) and Identification of a Leucine-Rich HEV Glycoprotein as a HEV Marker (2002)

High endothelial venule (HEV) cells support lymphocyte migration from the peripheral blood into secondary lymphoid tissues. Using gene expression profiling of mucosal addressin cell adhesion molecule-1(+) mesenteric lymph node HEV cells by quantitative 3'-cDNA collection, we have identified a leucine-rich protein, named leucine-rich HEV glycoprotein (LRHG) that is selectively expressed in these cells. Northern blot analysis revealed that LRHG mRNA is approximately 1.3 kb and is expressed in lymph nodes, liver, and heart. In situ hybridization analysis demonstrated that the mRNA expression in lymph nodes is strictly restricted to the HEV cells, and immunofluorescence analysis with polyclonal Abs against LRHG indicated that the LRHG protein is localized mainly to HEV cells and possibly to some lymphoid cells surrounding the HEVs. LRHG cDNA encodes a 342-aa protein containing 8 tandem leucine-rich repeats of 24 aa each and has high homology to human leucine-rich alpha(2)-glycoprotein. Similar to some other leucine-rich repeat protein family members, LRHG can bind extracellular matrix proteins that are expressed on the basal lamina of HEVs, such as fibronectin, collagen IV, and laminin. In addition, LRHG binds TGF-beta. These results suggest that LRHG is likely to be multifunctional in that it may capture TGF-beta and/or other related humoral factors to modulate cell adhesion locally and may also be involved in the adhesion of HEV cells to the surrounding basal lamina.
Direct Observation of Radical Intermediates in Protein-Dependent DNA Charge Transport (2001)

Charge migration through the DNA base stack has been probed both spectroscopically, to observe the formation of radical intermediates, and biochemically, to assess irreversible oxidative DNA damage. Charge transport and radical trapping were examined in DNA assemblies in the presence of a site-specifically bound methyltransferase HhaI mutant and an intercalating ruthenium photooxidant using the flash-quench technique. The methyltransferase mutant, which can flip out a base and insert a tryptophan side chain within the DNA cavity, is found to activate long-range hole transfer through the base pair stack. Protein-dependent DNA charge transport is observed over 50 A with guanine radicals formed >10(6) s(-1); hole transport through DNA over this distance is not rate-limiting. Given the time scale and distance regime, such protein-dependent DNA charge transport chemistry requires consideration physiologically.
SCONE: secure Linux containers with Intel SGX (2016)

In multi-tenant environments, Linux containers managed by Docker or Kubernetes have a lower resource footprint, faster startup times, and higher I/O performance compared to virtual machines (VMs) on hypervisors. Yet their weaker isolation guarantees, enforced through software kernel mechanisms, make it easier for attackers to compromise the confidentiality and integrity of application data within containers.We describe SCONE, a secure container mechanism for Docker that uses the SGX trusted execution support of Intel CPUs to protect container processes from outside attacks. The design of SCONE leads to (i) a small trusted computing base (TCB) and (ii) a low performance overhead: SCONE offers a secure C standard library interface that transparently encrypts/decrypts I/O data; to reduce the performance impact of thread synchronization and system calls within SGX enclaves, SCONE supports user-level threading and asynchronous system calls. Our evaluation shows that it protects unmodified applications with SGX, achieving 0.6×-1.2× of native throughput.
Metaqueries for data mining (1996)

This chapter presents a framework that uses metaqueries to integrate inductive learning methods with deductive database technologies in the context of knowledge discovery from databases. Metaqueries are second-order predicates or templates, and are used for (1) Guiding deductive data collection, (2) Focusing attention for inductive learning, and (3) Assisting human analysts in the discovery loop. We describe in detail a system that uses this idea to unify a Bayesian Data Cluster with the Logical Data Language (LDL++), and show the results of three case studies, namely, discovering regularities from a knowledge base, discovering patterns and errors from a large telecommunication database, and discovering patterns and errors from a large chemical database. The patterns discovered using metaqueries are implication rules with probabilities. These rules can link information from many tables in databases, and they can be stored persistently for multiple purposes, including error detection, i...
Low-density parity-check codes from combinatorial designs (2004)

Abstract Recent breakthroughs in forward error correction, in the form of low-density parity-check(LDPC) and turbo codes, have seen the promise of near Shannon limit information trans-mission realised. The deterministic construction of good codes, for LDPC codes in par-ticular, is currently the subject of intense interest in the research and development com-munity. This thesis adds to this ﬁeld, developing methods and supporting theory for thedesign of algebraic LDPC codes using incidence structures from combinatorial designs.The beneﬁts of this approach are guaranteed code properties, parameter ﬂexibility, easeof implementation and reduced encoding complexity.In the ﬁrst part of this thesis Steiner 2-designs and partial geometries are used toprovide systematic constructions of regular LDPC codes with Tanner graphs free of 4-cyclesandwithdeterministiccodeproperties. Drawingextensivelyfromexistingincidencestructures we present new families of algebraic LDPC codes with beneﬁts over traditionalrandomly constructed regular codes, particularly where small-to-medium length codes areconcerned. We focus in particular on exploring the eﬀect of diﬀerent design propertieson the code parameters by deriving the rate, minimum distance, girth, and stopping setdistribution of LDPC codes from designs.In the second part of this thesis resolvable designs are employed to create regularLDPC codes free of 4-cycles with the parameter ﬂexibility and decoding performance ofrandomly constructed regular LDPC codes. Employing resolvability greatly extends theclass of LDPC codes that can be algebraically constructed. These codes can oﬀer sig-niﬁcant implementation advantages due to the deterministic structure of their resolutionclasses and in some cases their simple encoding.A shortcoming of LDPC codes is their potentially high encoding complexity, whichis generally quadratic in the code length. Finding computationally eﬃcient encodersis therefore critical for LDPC codes to be considered as serious contenders for futuregenerations of forward error correction devices. As a result the purpose of the last part ofthis thesis is to design codes which have the graph-based properties necessary to performwell with sum-product decoding but which are also cyclic or quasi-cyclic and so can beencoded simply. The main focus is regular codes but we also extend our constructionof quasi-cyclic codes to produce irregular LDPC codes with simple linear-time encodingcircuits.
African Traditional Religion in Igaland, Nigeria (c. 1000 – present) (2017)

This study examines various aspects of African traditional religious beliefs in Igalaland which have been largely neglected by indigenous scholars with a view to bridge the gap in the historiography of the people from c.1000 to present. The period marked the beginning of Igalaland as a people with central authority. This study thus, adopts the use of primary and secondary sources. Data was obtained from in-depth interviews with traditional priests, elders, archival documents, historical sites, textbooks and journals articles. It is therefore, imperative to note that the root of African traditional religion in Igalaland goes back into primeval times. The Ifa oracle plays vital roles, as it dictated the reverential and sacrificial life of the people by which they get cleansed of their abominations and gain the aids of divinities. They also believed in the spirit of the departed. Unlike the western man, religion permeated every aspect of their life.
Mitochondrial Aspects of Synaptic Dysfunction in Alzheimer’s Disease (2016)

Alzheimer's disease (AD) is characterized by brain deposition of amyloid plaques and tau neurofibrillary tangles along with steady cognitive decline. Synaptic damage, an early pathological event, correlates strongly with cognitive deficits and memory loss. Mitochondria are essential organelles for synaptic function. Neurons utilize specialized mechanisms to drive mitochondrial trafficking to synapses in which mitochondria buffer Ca2+ and serve as local energy sources by supplying ATP to sustain neurotransmitter release. Mitochondrial abnormalities are one of the earliest and prominent features in AD patient brains. Amyloid-β (Aβ) and tau both trigger mitochondrial alterations. Accumulating evidence suggests that mitochondrial perturbation acts as a key factor that is involved in synaptic failure and degeneration in AD. The importance of mitochondria in supporting synaptic function has made them a promising target of new therapeutic strategies for AD. Here, we review the molecular mechanisms regulating mitochondrial function at synapses, highlight recent findings on the disturbance of mitochondrial dynamics and transport in AD, and discuss how these alterations impact synaptic vesicle release and thus contribute to synaptic pathology associated with AD.
Preadipocyte Function and Aging: Links Between Age‐Related Changes in Cell Dynamics and Altered Fat Tissue Function (1997)

Intrinsic aging changes in fat cells and preadipocytes as well as in factors extrinsic to fat tissue (such as food intake and absorption and hormonal status) contribute to age-related alterations in fat tissue function and cellularity. Changes with age in preadipocyte number, replicative potential, and capacity for differentiation, which may be linked to aging changes in fat cell size, number, and function, have been identified. The decline in preadipocyte capacity for differentiation and the associated decline in fat cell lipogenic capacity may be particularly important in contributing to the decrease in fat mass and alterations in fat tissue function that occur between middle- and old age. These declines result from blunting of the changes in gene expression that occur during preadipocyte differentiation and may, in turn, be related to altered regulation of particular transcription factors that control the preadipocyte differentiation program and maintenance of fat cell function.
Synthesis and Photophysical Investigation of Squaraine Rotaxanes by “Clicked Capping” (2008)

Pseudorotaxane complexes of squaraine dyes and tetralactam macrocycles are converted into permanently interlocked rotaxane structures using copper-catalyzed and copper-free cycloaddition reactions with bulky stopper groups. The photophysical properties of the encapsulated squaraine depend on the structure of the macrocycle. In one case, squaraine rotaxanes are produced in near-quantitative yields and with intense near-IR fluorescence. In another case, squaraine fluorescence is greatly diminished upon macrocyclic encapsulation but the signal can be restored by dye displacement with anions.
Localization of a Short-Term Memory in <i>Drosophila</i> (2000)

Memories are thought to be due to lasting synaptic modifications in the brain. The search for memory traces has relied predominantly on determining regions that are necessary for the process. However, a more informative approach is to define the smallest sufficient set of brain structures. The rutabaga adenylyl cyclase, an enzyme that is ubiquitously expressed in the Drosophila brain and that mediates synaptic plasticity, is needed exclusively in the Kenyon cells of the mushroom bodies for a component of olfactory short-term memory. This demonstrates that synaptic plasticity in a small brain region can be sufficient for memory formation.
THE ROLE OF THE ORGANIC SOLVENT IN OBTAINING HYDROTALCITE - LIKE ANIONIC CLAY NANOPOWDERS WITH SPECIFIC TEXTURAL AND POROUS PROPERTIES ♦ (2006)

Hydrotalcite - like anionic clays were synthesized by the sol-gel method while ethanol and phenol were used as organic solvents in the synthesis medium. The X-ray diffraction analysis points out that the obtained nanopowders possess a well crystallized hydrotalcite - like anionic clay structure. The N2 adsorption analysis reveals that the features of the nanoparticles ensemble pattern and the textural properties of the mesoporous structure are dependent on the nature of the organic solvent. When ethanol is used in the synthesis medium the emerged nanoclay present a relatively uniform porous structure with a specific surface area of 140 m 2 /g and the value of N2 adsorption volume is equal to 270 mL/g. On the contrary when phenol is present as major organic solvent in the synthesis medium a lower specific surface area is obtained (77 m 2 /g) while the value decreases to 170 mL/g. These results point out that the nature of the organic solvent is important for tailoring the textural and porous properties of hydrotalcite - like anionic clay nanostructures.