gebhart/patrepeval huggingface dataset:
Bionic wavelet transform: a new time-frequency method based on an auditory model (2001)

In this paper, a new adaptive wavelet transform, named bionic wavelet transform (BWT), is developed based on a model of the active auditory system. The most distinguishing characteristic of BWT is that its resolution in the time-frequency domain can be adaptively adjusted not only by the signal frequency but also by the signal instantaneous amplitude and its first-order differential. The automatically adjusted resolution, even in a fixed frequency along the time-axis, is achieved by introducing the active control of the auditory system into the wavelet transform (WT). Other properties of BWT include that: 1) BWT is a nonlinear transform that has high sensitivity and frequency selectivity; 2) BWT represents the signal with a concentrated energy distribution; and 3) the inverse BWT can reconstruct the original signal from its time-frequency representation. In order to compare these three properties between BWT and WT, experiments were conducted on both constructed signals and real speech signals. The results show that BWT performs better than WT in these three aspects, and that BWT is appropriate for speech signal processing, especially for cochlear implants.
A wavelet-based method for action potential detection from extracellular neural signal recording with low signal-to-noise ratio (2003)

We present a method for the detection of action potentials, an essential first step in the analysis of extracellular neural signals. The low signal-to-noise ratio (SNR) and similarity of spectral characteristic between the target signal and background noise are obstacles to solving this problem and, thus, in previous studies on experimental neurophysiology, only action potentials with sufficiently large amplitude have been detected and analyzed. In order to lower the level of SNR required for successful detection, we propose an action potential detector based on a prudent combination of wavelet coefficients of multiple scales and demonstrate its performance for neural signal recording with varying degrees of similarity between signal and noise. The experimental data include recordings from the rat somatosensory cortex, the giant medial nerve of crayfish, and the cutaneous nerve of bullfrog. The proposed method was tested for various SNR values and degrees of spectral similarity. The method was superior to the Teager energy operator and even comparable to or better than the optimal linear detector. A detection ratio higher than 80% at a false alarm ratio lower than 10% was achieved, under an SNR of 2.35 for the rat cortex data where the spectral similarity was very high.
Optogenetic reporters (2012)

The discovery of naturally evolved fluorescent proteins and their subsequent tuning by protein engineering provided the basis for a large family of genetically encoded biosensors that report a variety of physicochemical processes occurring in living tissue. These optogenetic reporters are powerful tools for live-cell microscopy and quantitative analysis at the subcellular level. In this review, we present an overview of the transduction mechanisms that have been exploited for engineering these genetically encoded reporters. Finally, we discuss current and future efforts towards the combined use of various optogenetic actuators and reporters for simultaneously controlling and imaging the physiology of cells and tissues.
Homocitrate Formation in Neurospora crassa (1968)

Abstract Neurospora crassa lysine auxotrophs 33933 and STL-7 which on nutritional grounds are known to be blocked at an early stage of lysine biosynthesis via the aminoadipic acid pathway, were found to accumulate homocitrate and malate plus citrate, respectively. Such accumulations predominate only when these mutants are grown in a medium containing minimal, but not excess, lysine. The acids were isolated by two-phase partition chromatography on silicic acid, and their structures were adduced from appropriate chemical and spectral data. Homocitrate was formed from acetate and α-ketoglutarate under suitable conditions by cell-free extracts of mutant 33933, but such homocitrate-condensing enzyme activity could not be shown in mutant STL-7 under the conditions of assay. Homocitrate-condensing enzyme activity of mutant 33933 extracts was subject to repression and feedback inhibition by lysine. The significance, if any, of malate and citrate accumulation to lysine metabolism in mutant STL-7 remains to be elucidated. This paper extends present knowledge, derived exclusively from studies in yeast, and shows that, in Neurospora, the initial step of lysine biosynthesis is via a homocitrate-condensing enzyme which is under effective end product control by lysine.
Dual primer emulsion PCR for next-generation DNA sequencing (2010)

We have developed a highly sensitive single-molecule clonal amplification method called dual primer emulsion PCR (DPePCR) for next-generation DNA sequencing. The approach is similar in concept to standard emulsion PCR; however, in DPePCR both primers are attached to the beads, therefore following PCR amplification, both strands of the PCR products are attached to the beads. The ends of each strand can be freed for analysis by restriction digestion of the bridged PCR fragments, which allows efficient paired-end sequencing of fragment libraries.
Delaying the onset of Alzheimer disease (2010)

The present data confirm results from an earlier study, and thus we conclude that lifelong bilingualism confers protection against the onset of AD. The effect does not appear to be attributable to such possible confounding factors as education, occupational status, or immigration. Bilingualism thus appears to contribute to cognitive reserve, which acts to compensate for the effects of accumulated neuropathology.
Overcoming the global crisis: “Yes, we can”, but also for TB … ? (2009)

Tuberculosis (TB) poses formidable challenges to global health at the public health-, scientific- and political level. Causing almost two million deaths every year, this ancient disease represents a continuing global crisis. The writing on the wall is that TB is resurging in more virulent and treatment-resistant forms. Our tools to combat TB are dangerously out of date and ineffective. Besides new tools (TB drugs, vaccines, diagnostics), we also need new strategies to identify key Mycobacterium tuberculosis/human host interactions, since it is here that we can most likely find Mtb's Achilles' heel. Equally important is that we build high-quality clinical trial capacity and biobanks for TB biomarker identification. But most important is a global commitment at all levels to roll back TB before it outwits us again.
Structure of Two Iron-binding Proteins from Bacillus anthracis (2002)

Bacillus anthracis is currently under intense investigation due to its primary importance as a human pathogen. Particularly important is the development of novel anti-anthrax vaccines, devoid of the current side effects. A novel class of immunogenic bacterial proteins consists of dodecamers homologous to the DNA-binding protein of Escherichia coli (Dps). Two Dps homologous genes are present in the B. anthracis genome. The crystal structures of these two proteins (Dlp-1 and Dlp-2) have been determined and are presented here. They are sphere-like proteins with an internal cavity. We also show that they act as ferritins and are thus involved in iron uptake and regulation, a fundamental function during bacterial growth.
The occurrence of families of repetitive sequences in a library of cloned cDNA from human lymphocytes (1981)

A library of cloned cDNAs representative of lymphocyte total poly(A)+ RNA was screened with total DNA probes at high clone density. 10% of the recombinants showed the presence of sequences which are repeated in the genome. Further analysis of six such isolated cDNA clones indicated that they contain different families of repetitive sequences with reiteration frequencies of between 150 and 45,000 copies per haploid genomes. Five of the six clones were found to contain single copy sequences as well as a repetitive sequence. cDNA clones containing repetitive sequences have been found to be derived from high, intermediate and low abundance classes of lymphocyte poly(A)+ RNA.
Memory B cells: Effectors of long‐lived immune responses (2009)

Immunological memory is the phenomenon whereby B and T cells have the unique ability to respond with heightened kinetics and efficacy to subsequent encounter with Ag relative to the initial exposure. In this review, we examine recent developments in the phenotypic characterisation of memory B cells, with an emphasis on the definition and functional properties of memory B-cell subsets in humans. Gene expression differences are also considered in light of the unique functional and survival properties of memory B cells, and mutations that alter memory formation and function are also examined. Finally, we consider recent advances in the understanding of germinal center B-cell differentiation through analysis of transcription factor networks operating in these B cells.
L-diversity: privacy beyond k-anonymity (2006)

Publishing data about individuals without revealing sensitive information about them is an important problem. In recent years, a new definition of privacy called \kappa-anonymity has gained popularity. In a \kappa-anonymized dataset, each record is indistinguishable from at least k—1 other records with respect to certain "identifying" attributes. In this paper we show with two simple attacks that a \kappa-anonymized dataset has some subtle, but severe privacy problems. First, we show that an attacker can discover the values of sensitive attributes when there is little diversity in those sensitive attributes. Second, attackers often have background knowledge, and we show that \kappa-anonymity does not guarantee privacy against attackers using background knowledge. We give a detailed analysis of these two attacks and we propose a novel and powerful privacy definition called \ell-diversity. In addition to building a formal foundation for \ell-diversity, we show in an experimental evaluation that \ell-diversity is practical and can be implemented efficiently.
Tau Oligomers in Sera of Patients with Alzheimer’s Disease and Aged Controls (2017)

Although tau protein was long regarded as an intracellular protein with several functions inside the cell, new evidence has shown tau secretion into the extracellular space. The active secretion of tau could be a physiological response of neurons to increased intracellular amounts of tau during the progression of tau pathology. We looked for potential differences in the serum levels of toxic tau oligomers in regards to cognitive impairment of subjects. We detected tau oligomers in the serum of Alzheimer's disease (AD) patients, but they were also present to some extent in the serum of healthy older subjects where the levels positively correlated with aging (Spearman r = 0.26, p = 0.016). On the contrary, we found lower levels of tau oligomers in the serum of mild cognitive impairment (MCI) (p = 0.033) and MCI-AD (p = 0.006) patients. These results could suggest that clearance of extracellular tau proteins takes place, in part, in the periphery. In the case of MCI patients, the lower levels of tau oligomers could be the result of impaired clearance of tau protein from interstitium to blood and consequent accumulation of tau aggregates in the brain.
A Potential Role for U2AF-SAP 155 Interactions in Recruiting U2 snRNP to the Branch Site (1998)

Base pairing between U2 snRNA and the branchpoint sequence (BPS) is essential for pre-mRNA splicing. Because the metazoan BPS is short and highly degenerate, this interaction alone is insufficient for specific binding of U2 snRNP. The splicing factor U2AF binds to the pyrimidine tract at the 3' splice site in the earliest spliceosomal complex, E, and is essential for U2 snRNP binding in the spliceosomal complex A. We show that the U2 snRNP protein SAP 155 UV cross-links to pre-mRNA on both sides of the BPS in the A complex. SAP 155's downstream cross-linking site is immediately adjacent to the U2AF binding site, and the two proteins interact directly in protein-protein interaction assays. Using UV cross-linking, together with functional analyses of pre-mRNAs containing duplicated BPSs, we show a direct correlation between BPS selection and UV cross-linking of SAP 155 on both sides of the BPS. Together, our data are consistent with a model in which U2AF binds to the pyrimidine tract in the E complex and then interacts with SAP 155 to recruit U2 snRNP to the BPS.
Impulse generation with appropriate amplitude, length, inter-arrival, and spectral characteristics (2002)

This paper proposes a suitable method for simulating impulses with appropriate amplitude, spectral, and inter-arrival characteristics. The statistics used to develop the parameters of this model are based on statistics derived from observations of impulse noise on the telephone networks of British Telecom (BT) and Deutsche Telekom (DT). This paper initially reviews the former DT approach to impulse noise generation for testing digital subscriber line systems, so called xDSL systems. Some problems are highlighted and an alternative technique is suggested that is capable of generating impulses with both appropriate amplitude an spectral characteristics.
Connective tissue growth factor (CCN2, CTGF) and organ fibrosis: lessons from transgenic animals (2009)

In recent months, four different systems have been reported in the literature in which CCN2 transgenes were individually expressed in podocytes, hepatocytes, cardiomyocytes or respiratory epithelial cells to achieve overexpression in, respectively, the kidney, liver, heart, or lung. These transgenic systems have provided valuable information about the contribution of CCN2 to fibrosis in vivo and have begun to reveal the complexities of the underlying mechanisms involved. On the one hand, studies of these animals have revealed that CCN2 overexpression does not necessarily lead directly to fibrotic pathology but may cause severe non-fibrotic tissue damage due to its other effects on cell function (e.g. heart). On the other hand, overexpression of CCN2 in concert with signaling pathways associated with development (e.g. lung) or fibrosing injuries (e.g. kidney, liver) can lead to the initiation or exacerbation of fibrosis. The significance of these studies is discussed in the context of the requirement for interactions between CCN2 and co-stimulatory factors in the microenvironment for the manifestation of CCN2-dependent fibrosis.
Filters and components with inductance cancellation (2003)

Electrical filters are important for attenuating electrical ripple, eliminating electromagnetic interference (EMI) and susceptibility, improving power quality, and minimizing electromagnetic signature. Capacitors are critical elements in such filters, and filter performance is strongly influenced by the capacitor parasitics. This paper introduces a new design technique that overcomes the capacitor parasitic inductance that limits filter performance at high frequencies. Coupled magnetic windings are employed to effectively cancel the parasitic inductance of capacitors, and to add inductance in filter branches where it is desired. The underlying basis of the new technique is treated in detail, and its application to the design of both discrete filters and integrated LC filter components is described. Numerous experimental results demonstrating the high performance of the approach in both discrete filters and integrated filter elements are provided.
Evaluation of Surface-Enhanced Resonance Raman Scattering for Quantitative DNA Analysis (2003)

The labeling of biological species using dyes has become common practice to aid in their detection, and immediate positive identification of specific dyes in high dilution is a key requirement. Here the detection by surface-enhanced resonance Raman scattering (SERRS) of eight commercially available dye labels (ROX, rhodamine 6G, HEX, FAM, TET, Cy3, Cy5, TAMRA) attached to oligonucleotide strands is reported. Each of the eight labels was easily detected by using the SERRS from silver nanoparticles to produce a unique, molecularly specific spectrum. The conditions were optimized to obtain the best signal enhancement, and linear concentration graphs at low oligonucleotide concentrations were obtained. At higher concentrations (above approximately 10(-)(8) mol dm(-)(3)), curvature was introduced into the concentration graphs with the exception of rhodamine 6G, TET, and FAM, which gave linearity over the entire concentration range studied. Detection limits as low as 0.5 fmol were obtained, with lower possible if a smaller sample was analyzed. Investigation was also carried out into the effect of a Tris-HCl buffer containing the surfactant Tween 20 to aid in the prevention of surface adhesion of the oligonucleotides to the sample vessels at ultralow concentrations. The Tween 20 allowed lower detection limits to be obtained for each of the labels studied. This study shows that the different dyes commonly used with oligonucleotides can give quantitative SERRS at concentration levels not possible when the same dyes are used with fluorescence detection.
Viral-Induced Rhinitis (1998)

Upper respiratory viruses cause self-limited illness characterized by acute rhinitis. In rhinovirus colds the symptoms are thought to be caused by the host response rather than viral damage of the nasal epithelium. Rhinovirus triggers an inflammatory cascade, evidenced by the presence of inflammatory mediators (e.g., IL-8) and proinflammatory cytokines (e.g., kinins) in nasal secretions, which results in symptomatic illness. In contrast to rhinovirus and coronavirus, which do not cause discernible epithelial damage, influenza virus and adenovirus do damage the nasal epithelium. Appropriate antiviral therapy will depend on the causative virus. Treatment of rhinovirus colds may require an antiviral agent (e.g., interferon alpha) in combination with antiinflammatory medication.
Continuous Quadrupole Magnetic Separation of Islets during Digestion Improves Purified Porcine Islet Viability (2016)

Islet transplantation (ITx) is an emerging and promising therapy for patients with uncontrolled type 1 diabetes. The islet isolation and purification processes require exposure to extended cold ischemia, warm-enzymatic digestion, mechanical agitation, and use of damaging chemicals for density gradient separation (DG), all of which reduce viable islet yield. In this paper, we describe initial proof-of-concept studies exploring quadrupole magnetic separation (QMS) of islets as an alternative to DG to reduce exposure to these harsh conditions. Three porcine pancreata were split into two parts, the splenic lobe (SPL) and the combined connecting/duodenal lobes (CDL), for paired digestions and purifications. Islets in the SPL were preferentially labeled using magnetic microparticles (MMPs) that lodge within the islet microvasculature when infused into the pancreas and were continuously separated from the exocrine tissue by QMS during the collection phase of the digestion process. Unlabeled islets from the CDL were purified by conventional DG. Islets purified by QMS exhibited significantly improved viability (measured by oxygen consumption rate per DNA, <i>p</i> < 0.03) and better morphology relative to control islets. Islet purification by QMS can reduce the detrimental effects of prolonged exposure to toxic enzymes and density gradient solutions and substantially improve islet viability after isolation.
Separation of DNA sequencing fragments at 53 bases/minute by capillary gel electrophoresis (1992)

Abstract Polyacrylamide gels are unstable in 50‐μm internal diameter capillaries at electric fields greater than about 500 V cm −1 due to the formation of bubbles, which destroy the separation. We describe the use of a modified polyacrylamide capillary gel that is stable at electric fields of at least 800 V cm −1 . This capillary gel produces sequencing rates of 3,200 bases h −1 for fragments up to 250 bases in length; a total of 7 min are required to separate fragments of 250 bases in length. Longer fragments tend to coelute and do not generate useful sequencing information. This sequencing rate is a factor of 40 times higher than that produced by conventional sequencing gels and a factor of 3 faster than previous reports in the literature.
Structure and function of cholera toxin and the related Escherichia coli heat-labile enterotoxin. (1992)

Cholera and the related Escherichia coli-associated diarrheal disease are important problems confronting Third World nations and any area where water supplies can become contaminated. The disease is extremely debilitating and may be fatal in the absence of treatment. Symptoms are caused by the action of cholera toxin, secreted by the bacterium Vibrio cholerae, or by a closely related heat-labile enterotoxin, produced by Escherichia coli, that causes a milder, more common traveler's diarrhea. Both toxins bind receptors in intestinal epithelial cells and insert an enzymatic subunit that modifies a G protein associated with the adenylate cyclase complex. The consequent stimulated production of cyclic AMP, or other factors such as increased synthesis of prostaglandins by intoxicated cells, initiates a metabolic cascade that results in the excessive secretion of fluid and electrolytes characteristic of the disease. The toxins have a very high degree of structural and functional homology and may be evolutionarily related. Several effective new vaccine formulations have been developed and tested, and a growing family of endogenous cofactors is being discovered in eukaryotic cells. The recent elucidation of the three-dimensional structure of the heat-labile enterotoxin has provided an opportunity to examine and compare the correlations between structure and function of the two toxins. This information may improve our understanding of the disease process itself, as well as illuminate the role of the toxin in studies of signal transduction and G-protein function.
A new family of heparin-binding growth/differentiation factors: increased midkine expression in Wilms' tumor and other human carcinomas. (1993)

Midkine (MK) and heparin-binding growth-associated molecule/pleiotrophin form a new family of heparin-binding growth/differentiation factors. We studied MK gene expression in human tumors. In normal human reference tissues, MK was highly expressed in the mucosal tissue of the small intestine, moderately in the thyroid, weakly in the tissues of the lung, colon, stomach, kidney, and spleen, and not at all in the liver. All of 6 surgically removed specimens of Wilms' tumor highly expressed MK. Also, a moderate to intense level of MK expression was noted in the majority of surgically removed hepatocellular carcinomas. The MK mRNA level was analyzed in a number of cultured and nude mice-transplanted lines of human tumors. In stomach, colon, pancreatic, lung, and esophageal carcinomas, a moderate to high level of MK expression was found in the majority of them. These results suggest an important role of MK in the development and/or biological behavior of tumors and raised a possibility to use MK as a diagnostic marker. Heparin-binding growth associated molecule/pleiotrophin mRNA was low or scarcely detectable in samples analyzed thus far except for significant levels of the expression that were observed in PA-1 teratocarcinoma cells and in some surgical specimens of Wilms' tumor.
<title>Using behavior modeling for proximity correction</title> (1994)

A proximity correction system supporting zone-sampling behavior modeling (see SPIE 2197- 28, `Fast proximity correction with zone sampling,') is described. The data flow for correcting integrated circuit layout patterns is explained. We outline the steps needed to generate and optimize behavior models, that serve as correction `rules.'