gebhart/patrepeval huggingface dataset:
Genome-based Identification and Analysis of Collagen-related Structural Motifs in Bacterial and Viral Proteins (2003)

Collagens are extended trimeric proteins composed of the repetitive sequence glycine-X-Y. A collagen-related structural motif (CSM) containing glycine-X-Y repeats is also found in numerous proteins often referred to as collagen-like proteins. Little is known about CSMs in bacteria and viruses, but the occurrence of such motifs has recently been demonstrated. Moreover, bacterial CSMs form collagen-like trimers, even though these organisms cannot synthesize hydroxyproline, a critical residue for the stability of the collagen triple helix. Here we present 100 novel proteins of bacteria and viruses (including bacteriophages) containing CSMs identified by in silico analyses of genomic sequences. These CSMs differ significantly from human collagens in amino acid content and distribution; bacterial and viral CSMs have a lower proline content and a preference for proline in the X position of GXY triplets. Moreover, the CSMs identified contained more threonine than collagens, and in 17 of 53 bacterial CSMs threonine was the dominating amino acid in the Y position. Molecular modeling suggests that threonines in the Y position make direct hydrogen bonds to neighboring backbone carbonyls and thus substitute for hydroxyproline in the stabilization of the collagen-like triple-helix of bacterial CSMs. The majority of the remaining CSMs were either rich in proline or rich in charged residues. The bacterial proteins containing a CSM that could be functionally annotated were either surface structures or spore components, whereas the viral proteins generally could be annotated as structural components of the viral particle. The limited occurrence of CSMs in eubacteria and lower eukaryotes and the absence of CSMs in archaebacteria suggests that DNA encoding CSMs has been transferred horizontally, possibly from multicellular organisms to bacteria.
Bluetooth in industrial environment (2002)

An initial study of the use of Bluetooth in an industrial environment is presented. The tests have been performed at a paper mill, and in an office environment at Halmstad University. It shows the possibility to use Bluetooth for wireless short range communication in an industrial environment.
<title>Large-scale sensing arrays based on fiber Bragg gratings</title> (2002)

In this paper a new quasi-distributed sensor suitable for multi-point detection and localizing of alarm conditions along large structures is presented. The sensor is based on a serial array of equal low-reflective fiber Bragg gratings. The sensor interrogation employs measurement of light intensity at a fixed reference wavelength. Difference between the reference wavelength and the Bragg wavelength in normal conditions set a threshold level for detection. Method was tested experimentally in two different configurations. A simple design of the sensor in combination with the economical interrogation technique makes this sensor interesting for real applications.
Assessing aneuploidy with repetitive element sequencing (2020)

We report a sensitive PCR-based assay called Repetitive Element AneupLoidy Sequencing System (RealSeqS) that can detect aneuploidy in samples containing as little as 3 pg of DNA. Using a single primer pair, we amplified ∼350,000 amplicons distributed throughout the genome. Aneuploidy was detected in 49% of liquid biopsies from a total of 883 nonmetastatic, clinically detected cancers of the colorectum, esophagus, liver, lung, ovary, pancreas, breast, or stomach. Combining aneuploidy with somatic mutation detection and eight standard protein biomarkers yielded a median sensitivity of 80% in these eight cancer types, while only 1% of 812 healthy controls scored positive.
A Hybrid of Dual and Meet-in-the-Middle Attack on Sparse and Ternary Secret LWE. (2019)

The dual attack is one of the most efficient attack algorithms for learning with errors (LWE) problem. Recently, an efficient variant of the dual attack for sparse and small secret LWE was reported by Albrecht (Eurocrypt 2017), which forces some LWE-based cryptosystems, especially fully homomorphic encryptions (FHE), to change parameters. In this paper, we propose a new hybrid of dual and meet-in-themiddle (MITM) attack, which outperforms the improved variant on the same LWE parameter regime. To this end, we adapt the MITM attack for NTRU due to Odlyzko to LWE and give a rigorous analysis for it. The performance of our MITM attack depends on the relative size of error and modulus, and hence, for a large modulus LWE samples, our MITM attack works well for quite large error. We then combine our MITM attack with Albrecht's observation that understands the dual attack as a dimension-error tradeoff, which finally yields our hybrid attack. We also implement a sage module that estimates the attack complexity of our algorithm upon LWE-estimator, and our attack shows significant performance improvement for the LWE parameter for FHE. For example, for the LWE problem with dimension n = 2
 15
, modulus q = 2
 628
, and ternary secret key with Hamming weight 64 which is one parameter set used for HEAAN bootstrapping (Eurocrypt 2018), our attack takes 2
 112.5
 operations and 2
 70.6
 bit memory, while the previous best attack requires 2
 127.2
 operations as reported by the LWE-estimator.
Dysregulation of Inflammatory and Hemostatic Markers in Sepsis and Suspected Disseminated Intravascular Coagulation (2013)

Inflammatory mediators and hemostatic markers were evaluated in patients enrolled in a phase-2b study evaluating the safety and efficacy of recombinant thrombomodulin (ART-123) in patients with sepsis and suspected disseminated intravascular coagulation (DIC). In contrast to controls, patients with sepsis and suspected DIC showed an increase in the circulating levels of inflammatory and fibrinolytic markers. The levels of procalcitonin (PCT), interleukin 6 (IL-6), interleukin 10 (IL-10), anaphylatoxin C5a, plasminogen activator inhibitor 1 (PAI-1), and myeloperoxidase were higher in the patients with sepsis and suspected DIC, whereas protein C (PrC) exhibited a significant decrease. When the patients with overt and nonovert DIC were compared, the PrC level was lower, and PCT, PAI-1, IL-6, and IL-10 levels were higher in the patients with overt DIC. These results indicate that inflammation is elevated in sepsis and suspected DIC, and inflammation, impairment of fibrinolysis, and overconsumption of PrC may play a key role in the pathogenesis of DIC.
The Non-Diaryl Heterocycle Classes of p38 MAP Kinase Inhibitors (2002)

The p38 mitogen activated protein (MAP) kinase is an integral enzyme involved in the production of a wide variety of pro-inflammatory cytokines from various cell types. The identification of this kinase and of the diaryl imidazole containing inhibitor, SB203580, initiated an intense discovery effort in this field. Numerous inhibitors were subsequently produced containing replacements for the imidazole, as well as some of the pharmacophores attached to it. During this time many other classes of potent p38 inhibitors emerged containing scaffolds and binding components not found in the diaryl imidazole group. This review summarizes nine of those classes. At least one of these classes requires the kinase to undergo reorganization prior to binding. From this diverse set of inhibitors four compounds have been reported advancing into human clinical trials.
Early high-affinity neutralizing anti-viral IgG responses without further overall improvements of affinity. (1995)

Affinity maturation of IgG antibodies in adaptive immune responses is a well-accepted mechanism to improve effector functions of IgG within 2 weeks to several months of antigen encounter. This concept has been defined mainly for IgG responses against chemically defined haptens. We have evaluated this concept in a viral system and analyzed neutralizing IgG antibody responses against vesicular stomatitis virus (a close relative of rabies virus) with a panel of monoclonal antibodies obtained early (day 6 or 12) and late (day 150) after hyperimmunization. These neutralizing IgG antibodies recognize a single major antigenic site with high affinities (Ka of 10(8)-10(10) liter.mol-1) and with rapid on-rates already on day 6 of a primary response and with no evidence for further antigen dose- and time-dependent overall improvement of affinity. This type of IgG response is probably representative for viruses or bacterial toxins which are crucially controlled by neutralizing antibodies.
On the Bandwidth of the Plenoptic Function (2011)

The plenoptic function (POF) provides a powerful conceptual tool for describing a number of problems in image/video processing, vision, and graphics. For example, image-based rendering is shown as sampling and interpolation of the POF. In such applications, it is important to characterize the bandwidth of the POF. We study a simple but representative model of the scene where band-limited signals (e.g., texture images) are "painted" on smooth surfaces (e.g., of objects or walls). We show that, in general, the POF is not band limited unless the surfaces are flat. We then derive simple rules to estimate the essential bandwidth of the POF for this model. Our analysis reveals that, in addition to the maximum and minimum depths and the maximum frequency of painted signals, the bandwidth of the POF also depends on the maximum surface slope. With a unifying formalism based on multidimensional signal processing, we can verify several key results in POF processing, such as induced filtering in space and depth-corrected interpolation, and quantify the necessary sampling rates.
Identification and characterization of two functional domains in cytochrome P-450BM-3, a catalytically self-sufficient monooxygenase induced by barbiturates in Bacillus megaterium. (1987)

In a previous publication (Narhi, L. O. and Fulco, A. J. (1986) J. Biol. Chem. 261, 7160-7169) we described the characterization of a soluble 119,000-dalton P-450 cytochrome (P-450BM-3) that was induced by barbiturates in Bacillus megaterium. This single polypeptide contained 1 mol each of FAD and FMN/mol of heme and, in the presence of NADPH and O2, catalyzed the oxygenation of long-chain fatty acids without the aid of any other protein. We have now utilized limited trypsin proteolysis in the presence of substrate to cleave P-450BM-3 into two polypeptides (domains) of about 66,000 and 55,000 daltons. The 66-kDa domain contains both FAD and FMN but no heme, reduces cytochrome c in the presence of NADPH, and is derived from the C-terminal portion of P-450BM-3. The 55-kDa domain is actually a mixture of three discrete peptides (T-I, T-II, and T-III) separable by high performance liquid chromatography. All three contain heme and show a P-450 absorption peak in the presence of CO and dithionite. The major component, T-I (Mr = 55 kDa), binds fatty acid substrate and has an N-terminal amino acid sequence identical to that of intact P-450BM-3, an indication that this domain constitutes the N-terminal portion of the 119-kDa protein. T-II (54 kDa) is the same as T-I except that it is missing the first nine N-terminal amino acids and does not bind substrate. T-III (Mr = 53.5 kDa) has lost the first 15 N-terminal residues and does not bind substrate. Since trypsin digestion of P-450BM-3 carried out in the absence of substrate yields T-II and T-III but no T-I, it appears that 1 or more residues of the first nine N-terminal amino acids of this protein are intimately involved in substrate binding. Although both the heme- and flavin-containing tryptic peptides retain their original half-reactions, fatty acid monooxygenase activity cannot be reconstituted after proteolysis, and the two domains, once separated, show no affinity for each other. In most respects, the reductase domain of P-450BM-3 more closely resembles the mammalian microsomal P-450 reductases than it does any known bacterial protein.
Superior Efficacy of Tumor Cell Vaccines Grown in Physiologic Oxygen (2010)

Tissue culture oxygen functions as an "immunologic switch" by dictating the cellular and humoral immune responses elicited by tumor cell lysates. These results have profound implications for cancer vaccines that utilize tumor cells as the source of antigen.
Enzymatic Properties and Intracellular Localization of the Novel Trichoderma reesei β-Glucosidase BGLII (Cel1A) (2002)

This paper describes the characterization of an intracellular beta-glucosidase enzyme BGLII (Cel1a) and its gene (bgl2) from the cellulolytic fungus Trichoderma reesei (Hypocrea jecorina). The expression pattern of bgl2 is similar to that of other cellulase genes known from this fungus, and the gene would appear to be under the control of carbon catabolite repression mediated by the cre1 gene. The BGLII protein was produced in Escherichia coli, and its enzymatic properties were analyzed. It was shown to be a specific beta-glucosidase, having no beta-galactosidase side activity. It hydrolyzed both cellotriose and cellotetraose. BGLII exhibited transglycosylation activity, producing mainly cellotriose from cellobiose and sophorose and cellobiose from glucose. Antibodies raised against BGLII showed the presence of the enzyme in T. reesei cell lysates but not in the culture supernatant. Activity measurements and Western blot analysis of T. reesei strains expressing bgl2 from a constitutive promoter further confirmed the intracellular localization of this beta-glucosidase.
Light-evoked Somatosensory Perception of Transgenic Rats That Express Channelrhodopsin-2 in Dorsal Root Ganglion Cells (2012)

In vertebrate somatosensory systems, each mode of touch-pressure, temperature or pain is sensed by sensory endings of different dorsal root ganglion (DRG) neurons, which conducted to the specific cortical loci as nerve impulses. Therefore, direct electrical stimulation of the peripheral nerve endings causes an erroneous sensation to be conducted by the nerve. We have recently generated several transgenic lines of rat in which channelrhodopsin-2 (ChR2) transgene is driven by the Thy-1.2 promoter. In one of them, W-TChR2V4, some neurons were endowed with photosensitivity by the introduction of the ChR2 gene, coding an algal photoreceptor molecule. The DRG neurons expressing ChR2 were immunohistochemically identified using specific antibodies to the markers of mechanoreceptive or nociceptive neurons. Their peripheral nerve endings in the plantar skin as well as the central endings in the spinal cord were also examined. We identified that ChR2 is expressed in a certain population of large neurons in the DRG of W-TChR2V4. On the basis of their morphology and molecular markers, these neurons were classified as mechanoreceptive but not nociceptive. ChR2 was also distributed in their peripheral sensory nerve endings, some of which were closely associated with CK20-positive cells to form Merkel cell-neurite complexes or with S-100-positive cells to form structures like Meissner's corpuscles. These nerve endings are thus suggested to be involved in the sensing of touch. Each W-TChR2V4 rat showed a sensory-evoked behavior in response to blue LED flashes on the plantar skin. It is thus suggested that each rat acquired an unusual sensory modality of sensing blue light through the skin as touch-pressure. This light-evoked somatosensory perception should facilitate study of how the complex tactile sense emerges in the brain.
Standards of Time and Frequency at the Outset of the 21st Century (2004)

After 50 years of development, microwave atomic clocks based on cesium have achieved fractional uncertainties below 1 part in 10(15), a level unequaled in all of metrology. The past 5 years have seen the accelerated development of optical atomic clocks, which may enable even greater improvements in timekeeping. Time and frequency standards with various levels of performance are ubiquitous in our society, with applications in many technological fields as well as in the continued exploration of the frontiers of basic science. We review state-of-the-art atomic time and frequency standards and discuss some of their uses in science and technology.
Quantification of cholesterol in all lipoprotein classes by the VAP-II method. (1994)

We have developed a high resolution microvolume Vertical Auto Profile (VAP) method for the simultaneous measurement of cholesterol in all lipoprotein classes, including lipoprotein[a] (Lp[a]) and intermediate density lipoprotein (IDL). This method, designated as VAP-II, uses a non-segmented continuous flow (controlled-dispersion flow) analyzer for the enzymatic analysis of cholesterol in lipoprotein classes separated by a short spin (47 min) single vertical ultracentrifugation. Cholesterol concentrations of high (HDL), low (LDL), very low (VLDL), and intermediate (IDL) density lipoproteins, as well as Lp[a], are determined by decomposing the spectrophotometric absorbance curve, obtained from the continuous analysis of the centrifuged sample, into its components using software developed in this laboratory. Analysis by VAP-II is rapid and sensitive (as little as 40 microliters plasma is required per assay). The resolution of lipoprotein peaks is considerably enhanced in the present analyzer compared to the previous analyzer (VAP-I, which used the Technicon AutoAnalyzer); improvement is especially noticeable for Lp[a] and IDL. Total and lipoprotein cholesterol values obtained by VAP-II correlated well with the values obtained by Northwest Lipid Research Laboratories (NWLRL). VAP-II Lp[a] cholesterol values also correlated well with the Lp[a] mass values obtained by an immunoassay technique performed at NWLRL (r = 0.907). The reproducibility and accuracy of the method are within the requirements of the CDC-NHLBI (Centers for Disease Control-National Heart, Lung, and Blood Institute) Lipid Standardization Program.
Role of cellular lipoteichoic acids in mediating adherence of serotype III strains of group B streptococci to human embryonic, fetal, and adult epithelial cells (1984)

Lipoteichoic acids (LTA) of serotype III strains of group B streptococci (GBS) were shown to mediate adherence of these organisms to human embryonic (HEC), fetal (HFC), and adult buccal (HBEC) epithelial cells. The binding of GBS was temperature dependent, and maximum attachment occurred at 37 degrees C. HEC, HFC, and HBEC preincubated with purified LTA significantly inhibited attachment of GBS, whereas the group B and type III antigens had no effect. Under phosphate-limiting conditions in which cell-associated LTA could not be detected in these organisms, bacterial adherence did not take place. GBS (virulent) that were isolated from infected infants and previously shown to have significantly higher quantities of cell-associated LTA in comparison to GBS strains from asymptomatically colonized infants adhered with greater binding avidity to HEC and HFC and in greater numbers than to HBEC. It was determined that the mechanism of LTA-mediated adherence of GBS to HBEC differed from adherence to embryonic and fetal cells for both virulent and asymptomatic GBS strains bound to HBEC in a similar manner, enhanced by the lipid portion of the LTA. In contrast, the binding of GBS to HEC and HFC was mediated by hydrophobic as well as specific interactions due to the glycerolphosphate polymer of LTA. These results indicate that possible receptor sites for LTA present on cells in prenatal stages of development may differ from those of adult cells, which may result in increased susceptibility of newborn infants to group B streptococcal disease. The implications of LTA-mediated adherence of GBS and their possible role as virulence factors are discussed.
A continuous friction model for servo systems with stiction (2002)

Introduces a continuous model for friction torque of servo systems which involve stiction at extremely low velocities. This new friction model can be applied to both away from zero and close to zero velocity regimes. For high velocities this model reduces to the classical friction model while for very low velocities it allows for the realization of pre-sliding phenomena without the hysteresis effect.
Variable-dimension vector quantization (1996)

In many signal compression applications, the evolution of the signal over time can be represented by a sequence of random vectors with varying dimensionality. Frequently, the generation of such variable-dimension vectors can be modeled as a random sampling of another signal vector with a large but fixed dimension. Efficient quantization of these variable-dimension vectors is a challenging task and a critical issue in speech coding algorithms based on harmonic spectral modeling. We introduce a simple and effective formulation of the problem and present a novel technique, called variable-dimension vector quantization (VDVQ), where the input variable-dimension vector is directly quantized with a single universal codebook. The application of VDVQ to low bit-rate speech coding demonstrates significant gain in subjective quality as well as in rate-distortion performance over prior indirect methods.
Tumor microenvironment complexity and therapeutic implications at a glance (2020)

The dynamic interactions of cancer cells with their microenvironment consisting of stromal cells (cellular part) and extracellular matrix (ECM) components (non-cellular) is essential to stimulate the heterogeneity of cancer cell, clonal evolution and to increase the multidrug resistance ending in cancer cell progression and metastasis. The reciprocal cell-cell/ECM interaction and tumor cell hijacking of non-malignant cells force stromal cells to lose their function and acquire new phenotypes that promote development and invasion of tumor cells. Understanding the underlying cellular and molecular mechanisms governing these interactions can be used as a novel strategy to indirectly disrupt cancer cell interplay and contribute to the development of efficient and safe therapeutic strategies to fight cancer. Furthermore, the tumor-derived circulating materials can also be used as cancer diagnostic tools to precisely predict and monitor the outcome of therapy. This review evaluates such potentials in various advanced cancer models, with a focus on 3D systems as well as lab-on-chip devices. Video abstract.
Analyzing time series gene expression data (2004)

We present a comprehensive review of the current research in time series expression data analysis. We divide the computational challenges into four analysis levels: experimental design, data analysis, pattern recognition and networks. For each of these levels, we discuss computational and biological problems at that level and point out some of the methods that have been proposed to deal with these issues. Many open problems in all these levels are discussed. This review is intended to serve as both, a point of reference for experimental biologists looking for practical solutions for analyzing their data, and a starting point for computer scientists interested in working on the computational problems related to time series expression analysis.