gebhart/patrepeval huggingface dataset:
Sequence polymorphism of the predicted human metapneumovirus G glycoprotein (2004)

The putative G glycoprotein genes of 25 human metapneumovirus (hMPV) field isolates obtained during five consecutive epidemic seasons (1997 to 2002) were sequenced. Sequence alignments identified two major genetic groups, designated groups 1 and 2, and two minor genetic clusters within each major group, designated subgroups A and B. Extensive nucleotide and deduced amino acid sequence variability was observed, consisting of high rates of nucleotide substitutions, use of alternative transcription-termination codons and insertions that retained the reading frame. Deduced amino acid sequences showed the greatest variability, with most differences located in the extracellular domain of the protein: nucleotide and amino acid sequence identities for the entire open reading frame ranged from 52 to 58 % and 31 to 35 %, respectively, between the two major groups. Like the closely related avian pneumovirus and human and bovine respiratory syncytial viruses, the predicted G protein of hMPV shared the basic features of a type II mucin-like glycosylated protein. However, differences from these related viruses were also observed, e.g. lack of conserved cysteine clusters as seen in human respiratory syncytial virus and avian pneumovirus. The displacement of genetic groups of hMPV observed during the study period suggests that potential antigenic differences in the G glycoprotein, which have evolved in response to immune-mediated pressure, may influence the circulation patterns of hMPV strains.
Automated 2D IR spectroscopy using a mid-IR pulse shaper and application of this technology to the human islet amyloid polypeptide (2007)

The capability of 2D IR spectroscopy to elucidate time-evolving structures is enhanced by a programmable mid-IR pulse shaper that greatly improves the ease, speed, and accuracy of data collection. Traditional ways of collecting 2D IR spectra are difficult to implement, cause distorted peak shapes, and result in poor time resolution and/or phase problems. We report on several methods for collecting 2D IR spectra by using a computer-controlled germanium acoustooptic modulator that overcomes the above problems. The accuracy and resolution of each method is evaluated by using model metal carbonyl compounds that have well defined lineshapes. Furthermore, phase cycling can now be employed to largely alleviate background scatter from heterogeneous samples. With these methods in hand, we apply 2D IR spectroscopy to study the structural diversity in amyloid fibers of aggregated human islet amyloid polypeptide (hIAPP), which is involved with type 2 diabetes. The 2D IR spectra reveal that the beta-sheet fibers have a large structural distribution, as evidenced by an inhomogeneously broadened beta-sheet peak and strong coupling to random coil conformations. Structural diversity is an important characteristic of hIAPP because it may be that partly folded peptides cause the disease. This experiment on hIAPP is an example of how computer generation of 2D IR pulse sequences is a key step toward automating 2D IR spectroscopy, so that new pulse sequences can be implemented quickly and a diverse range of systems can be studied more easily.
Computational cardiac anatomy using MRI (2004)

Ventricular geometry and fiber orientation may undergo global or local remodeling in cardiac disease. However, there are as yet no mathematical and computational methods for quantifying variation of geometry and fiber orientation or the nature of their remodeling in disease. Toward this goal, a landmark and image intensity-based large deformation diffeomorphic metric mapping (LDDMM) method to transform heart geometry into common coordinates for quantification of shape and form was developed. Two automated landmark placement methods for modeling tissue deformations expected in different cardiac pathologies are presented. The transformations, computed using the combined use of landmarks and image intensities, yields high-registration accuracy of heart anatomies even in the presence of significant variation of cardiac shape and form. Once heart anatomies have been registered, properties of tissue geometry and cardiac fiber orientation in corresponding regions of different hearts may be quantified.
Rapid sampling for visualizations with ordering guarantees (2015)

Visualizations are frequently used as a means to understand trends and gather insights from datasets, but often take a long time to generate. In this paper, we focus on the problem of <i>rapidly generating approximate visualizations while preserving crucial visual properties of interest to analysts</i>. Our primary focus will be on sampling algorithms that preserve the visual property of <i>ordering</i>; our techniques will also apply to some other visual properties. For instance, our algorithms can be used to generate an approximate visualization of a bar chart very rapidly, where the comparisons between any two bars are correct. We formally show that our sampling algorithms are generally applicable and provably optimal in theory, in that they do not take more samples than necessary to generate the visualizations with ordering guarantees. They also work well in practice, correctly ordering output groups while taking orders of magnitude fewer samples and much less time than conventional sampling schemes.
The Credit Union Industry: An Overview (1996)

An introduction to the credit union industry's structure and regulatory environment, offering a brief look at some safety and soundness issues.
INTERNET OF THINGS BASED HEALTH MONITORING SYSTEM : OPPORTUNITIES AND CHALLENGES (2018)

Internet of Things (IoT) is a new and fast growing technology in which everything ( smart objects and smart devices) are connected to the internet for effective communication between these connected things. Internet of things serves as a catalyst for the healthcare and plays very important role in wide range of healthcare monitoring applications. Networked sensors devices, either worn on the body or embedded in living environments, make possible the gathering of rich information to evaluate physical and mental health condition of the patient by collecting body temperature, blood pressure, sugar level etc. Communicating this collected information to the doctor, making accurate decision on the data collected and notifying the patient is the challenging task in the Internet of things. In this paper author focus on review of IoT based Healthcare System and outline about Opportunities and Challenges for Internet of Things based Patient Health Monitoring System.
The evolution of a high-performing Java virtual machine (2000)

Early Java™ virtual machines (Jvms) possessed several significant performance bottlenecks that inhibited the speed of Java workloads. This paper presents the methodology that was used by IBM to identify and eliminate these bottlenecks for improving the performance of Java applications running on several operating system platforms. In addition, several of the key performance problems that were common to all early Java virtual machine implementations and how they were solved for IBM enhanced Jvms are described in detail. The issues discussed in this paper are focused on problems found in core Jvm components, such as object synchronization, object allocation, heap management, text rendering, run-time resolution, and Java class library methods. The results obtained from applying the described methodology and eliminating the identified performance bottlenecks increased the performance of IBM Java virtual machines by as much as four times on some workloads. The technology discussed in this paper is applica ble to other Jvm implementations.
Physical Absorption Of CO2 in Protic and Aprotic Ionic Liquids: An Interaction Perspective (2015)

The physical absorption of CO2 by protic and aprotic ionic liquids such as 1-ethyl-3-methyl-imidazolium tetrafluoroborate was examined at the molecular level using symmetry adapted perturbation theory (SAPT) and density functional techniques through comparison of interaction energies of noncovalently bound complexes between the CO2 molecule and a series of ionic liquid ions and ion pairs. These energies were contrasted with those for complexes with model amines such as methylamine, dimethylamine, and trimethylamine. Detailed analysis of the five fundamental forces that are responsible for stabilization of the complexes is discussed. It was confirmed that the nature of the anion had a greater effect upon the physical interaction energy in non functionalized ionic liquids, with dispersion forces playing an important role in CO2 solubility. Hydrogen bonding with protic cations was shown to impart additional stability to the noncovalently bound CO2···IL complex through inductive forces. Two solvation models, the conductor-like polarizable continuum model (CPCM) and the universal solvation model (SMD), were used to estimate the impact of solvent effects on the CO2 binding. Both solvent models reduced interaction energies for all types of ions. These interaction energies appeared to favor imidazolium cations and carboxylic and sulfonic groups as well as bulky groups (e.g., NTf2) in anions for the physical absorption of CO2. The structure-reactivity relationships determined in this study may help in the optimization of the physical absorption process by means of ionic liquids.
Membrane-bound Na,K-ATPase: target size and radiation inactivation size of some of its enzymatic reactions. (1988)

Frozen samples of membrane-bound pig kidney Na,K-ATPase were subjected to target size analysis by radiation inactivation with 10-MeV electrons at -15 degrees C. The various properties investigated decreased monoexponentially with radiation dose, and the decay constants, gamma, were independent of the presence of other proteins and of sucrose concentrations above 0.25 M. The temperature factor was the same as described by others. Irradiation of four proteins of known molecular mass, m, showed that gamma for protein integrity was proportional to m with a proportionality factor about 20% higher than that conventionally used. By this standard curve, glucose-6-phosphate dehydrogenase activity used as internal standard gave a radiation inactivation size of 110 +/- 5 kDa, very close to m = 104-108 kDa for the dimer, as expected. For Na+/K+-transporting ATPase the following target sizes and radiation inactivation size values were very close to m = 112 kDa for the alpha-peptide: peptide integrity of alpha, 115 kDa; unmodified binding sites for ATP and vanadate, 108 kDa; K+-activated p-nitrophenylphosphatase activity, 106 kDa. There was thus no sign of dimerization of the alpha-peptide or involvement of the beta-peptide. In contrast, optimal Na+/K+-transporting ATPase activity had a radiation inactivation size = 189 +/- 7 kDa, and total nucleotide binding capacity corresponded to 72 +/- 3 kDa. These latter results will be extended and discussed in a forthcoming paper.
A distributed transducer system for functional electrical stimulation (2002)

Implanted transducers for functional electrical stimulation (FES) powered by inductive links are subject to conflicting requirements arising from low link efficiency, a low power budget and the need for protection of the weak signals against strong RF electromagnetic fields. We propose a solution to these problems by partitioning the RF transceiver and sensor/actuator functions onto separate integrated circuits. By amplifying measured neural signals directly at the measurements site and converting them into the digital domain before passing them to the transceiver the signal integrity is less likely to be affected by the inductive link. Neural stimulators are affected to a lesser degree, but still benefit from the partitioning. As a test case, we have designed a transceiver and a sensor chip which implement this partitioning policy. The transceiver is designed to operate in the 6.78 MHz ISM band and consumes approximately 360 /spl mu/W. Both chips were implemented in a standard 0.5 /spl mu/m CMOS technology, and use a 3 V supply voltage.
First Total Synthesis of the Re-Type Lipopolysaccharide (2001)

Drei aufeinander folgende effiziente Glycosylierungen ausgehend von D-Glucosamin sind Teil der ersten Totalsynthese des Re-Typ-Lipopolysaccharids aus Escherichia coli, eines der einfachsten Lipopolysaccharide, die auf der Oberfläche lebender Bakterien nachgewiesen wurden.
Nucleic Acids Research annual Web Server Issue in 2009 (2009)

The 2009 Web Server Issue of Nucleic Acids Research is the seventh in a series of annual special issues dedicated to webbased software resources for analysis and visualization of molecular biology data.It is freely available online under NAR's open access policy.The present issue reports on 112 web servers. TOPICSThis year's special emphasis was on metagenomics, molecular network and pathway analysis and biological text mining.Fourteen papers deal with these topics.Another 14 papers involve web services, biocomputing workbenches or bioinformatics tools for such tasks as clustering, genome browsing, deep sequencing and homology search.By far, the largest number of papers covers DNA and RNA (17) and proteins (36).The remainder cover a variety of topics, including gene annotation, gene set enrichment analysis, phylogeny, microarrays and SNPs.Also included in the present issue is the Bioinformatics Links Directory 2009 update by Michelle Brazas, Francis Ouellette and their colleagues at the Ontario Institute for Cancer Research.The directory, at http://bioinformatics.ca/ links_directory, is a searchable compilation of web servers published in this and previous Web Server issues together with other useful tools, databases and resources for life sciences research.
Differentially regulated and evolved genes in the fully sequenced Xq/Yq pseudoautosomal region (2000)

Human sex chromosomes, which are morphologically and genetically different, share few regions of homology. Among them, only pseudoautosomal regions (PARs) pair and recombine during meiosis. To better address the complex biology of these regions, we sequenced the telomeric 400 kb of the long arm of the human X chromosome, including 330 kb of the human Xq/YqPAR and the telomere. Sequencing reveals subregions with distinctive regulatory and evolutionary features. The proximal 295 kb contains two genes inactivated on both the inactive X and Y chromosomes [ SYBL1 and a novel homologue ( HSPRY3 ) of Drosophila sprouty ]. The GC-rich distal 35 kb, added in stages and much later in evolution, contains the X/Y expressed gene IL9R and a novel gene, CXYorf1, only 5 kb from the Xq telomere. These properties make Xq/YqPAR a model for studies of region-specific gene inactivation, telomere evolution, and involvement in sex-limited conditions.
Molecular cloning of epithelial cell invasion determinants from enterotoxigenic Escherichia coli (1992)

Although penetration of the epithelial mucosa has not been identified as a virulence mechanism in enterotoxigenic Escherichia coli (ETEC), we have found that this pathogen is capable of invading human intestinal cell lines. Classical ETEC strain H10407 was most invasive for epithelial cell lines derived from ileocecal and colonic tissues. An ETEC cosmid library was screened for clones that could direct E. coli HB101 to invade cultured human ileocecal epithelial cells (HCT 8 cells). Three invasive recombinant cosmid clones were isolated. These cosmids could direct HB101 invasion at an efficiency that was equal to or greater than that of the parent ETEC strain. The invasion cosmids also allowed for enhanced HCT 8 cell adherence by HB101. Electron micrographs of ETEC and recombinant HB101 strains revealed intracellular bacteria contained within endocytic vacuoles. Restriction endonuclease mapping and hybridization analyses showed that the three ETEC clones represent two separate invasion systems present in the parent ETEC strain and that both systems are chromosomally encoded. The parent ETEC strain and one cloned invasion system did not invade HeLa cells. Interestingly, one cloned invasion system was capable of directing HB101 to invade HeLa cells. Invasion of HCT 8 cells by recombinant HB101 strains and the parent ETEC strain was inhibited by cytochalasin D, indicating that the wild-type and both cloned invasion systems trigger an actin polymerization-dependent uptake process. It is not known whether the invasive phenotype of ETEC is relevant for enterotoxigenic disease. However, the parent ETEC strain, as well as recombinant HB101 strains, was capable of transcytosis through polarized HCT 8 monolayers. This transcytosis suggests that ETEC may cross the gut epithelium in vivo and that this invasion may have a previously unrecognized role in the disease process.
Temporal distribution, localization and metabolism of all-trans-retinol, didehydroretinol and all-trans-retinal during Xenopus development (1994)

Recently, the temporal and spatial distribution patterns of the retinoid receptor ligands 9-cis-retinoic acid and all-trans-retinoic acid were described in Xenopus embryos during early development [Creech Kraft, Schuh, Juchau and Kimelman (1994) Proc. Natl. Acad. Sci. U.S.A., in the press]. The present study demonstrates the presence and distribution of their likely precursors, all-trans-retinol, didehydroretinol, didehydroretinal and all-trans-retinal, as well as the occurrence of 4-oxo metabolites, in Xenopus embryos. The temporal and spatial distribution patterns of all-trans-retinol, didehydroretinol and all-trans-retinal did not coincide with that observed for 9-cis-retinoic acid but, in certain regards, were similar to the patterns delineated for all-trans-retinoic acid and all-trans-retinoyl beta-glucuronide. Evidence is presented that 9-cis-retinoic acid can be synthesized from both all-trans-retinoic acid and all-trans-retinol in Xenopus embryos, suggesting that the difference between the distributions of 9-cis-retinoic acid and the other retinoids may be caused by selective synthesis and/or protein binding of the 9-cis isomer.
Wnt-Signaling in Retinal Development and Disease (2008)

The Wnt-signaling pathway is a known regulator of stem cell maintenance, cellular proliferation and differentiation, and cancer development in various tissues. Wnt proteins play a central role during various stages of retinal development; retinal field establishment, retinal and hyaloid vasculogenesis, cornea and lens development, eye field formation, and maintenance of retinal stem cell and neuronal specification in many species are Wnt-regulated processes. Uncontrolled Wnt signaling may cause retinal diseases such as familial exudative vitroretinopathy, retinitis pigmentosa, and Norrie's disease, further underscoring the importance of the Wnt-signaling pathway in the retina. This review summarizes major developments and discoveries regarding the role of the Wnt-signaling pathway as it pertains to retinal development and disease.
Synthetic Ligands Discovered by in Vitro Selection (2007)

The recognition and catalytic properties of biopolymers derive from an elegant evolutionary mechanism, whereby the genetic material encoding molecules with superior functional attributes survives a selective pressure and is propagated to subsequent generations. This process is routinely mimicked in vitro to generate nucleic-acid or peptide ligands and catalysts. Recent advances in DNA-programmed organic synthesis have raised the possibility that evolutionary strategies could also be used for small-molecule discovery, but the idea remains unproven. Here, using DNA-programmed combinatorial chemistry, a collection of 100 million distinct compounds is synthesized and subjected to selection for binding to the N-terminal SH3 domain of the proto-oncogene Crk. Over six generations, the molecular population converges to a small number of novel SH3 domain ligands. Remarkably, the hits bind with affinities similar to those of peptide SH3 ligands isolated from phage libraries of comparable complexity. The evolutionary approach has the potential to drastically simplify and accelerate small-molecule discovery.
Ar implantation effects in SOI NMOSFET's under low voltage operation (2002)

To reduce the parasitic bipolar gain of an SOI device, several techniques have been proposed. This paper reveals the advantage and disadvantage of Ar implant plus shallow S/D technique, highlighting process, temperature. and frequency dependent device characteristics of V/sub D/ below 1.5V.
Partial zero-forcing adaptive MMSE receiver for DS-CDMA uplink in multicell environments (2002)

Adaptive multi-user detection techniques for interference suppression in direct-sequence code division multiple access (DS-CDMA) systems have gained much attention since they do not require any information on interfering users. In the uplink of DS-CDMA systems, however, the base station receiver typically knows the spreading waveforms of the users within its cell but does not know those of the users in other cells. We propose a partial zero-forcing adaptive minimum mean squared error (MMSE) receiver for the DS-CDMA uplink utilizing the spreading waveforms known at the base station as well as training data. The proposed receiver first removes the intracell interference using a linear filter based on the knowledge of the spreading waveforms of the interfering users within the cell. Then the intercell interference remaining in the output of the linear filter is mitigated by adaptive MMSE detection. To speed up the convergence of the adaptive filter weights without loss of the steady-state performance, we develop a modified least mean square (LMS) algorithm based on the canonical representation of the filter weights. It is shown through analysis and simulation results that the proposed receiver improves the convergence speed and the steady-state performance.
Respiratory mutants of Azotobacter vinelandii with elevated levels of cytochrome d (1984)

A method is described for the isolation of respiratory mutants of Azotobacter vinelandii with increased amounts of d-type cytochrome by selecting for the inability to reduce tetrazolium red. Five stable mutants were obtained that had six-fold higher levels of cytochrome d, increased amounts of b-type and lower amounts of o-type and c-type cytochromes than the wild-type strain. Spectral alterations in cytochrome alpha 1 were also observed in the mutants. NADH and succinate oxidase activities of membrane particles were about two fold higher in the mutants compared to the wild-type strain. Ascorbate-N,N,N',N'-tetramethyl-p-phenylene diamine oxidase activity was barely detectable in membrane particles of the mutants. These results are consistent with an increase in the amount of the cytochrome d oxidase branch and a decrease in the amount and activity of the cytochrome o, alpha 1 oxidase branch in the mutants. Growth rates under oxygen-excess conditions and respiratory-linked proton translocation ratios of the mutant and wild-type stains were similar as were the photochemical spectral and kinetic properties of cytochrome d.