gebhart/patrepeval huggingface dataset:
QSAR modeling and computer‐aided design of antimicrobial peptides (2007)

The drastic increase in multi-drug-resistant bacteria has created an urgent need for new therapeutic interventions, including antimicrobial peptides, an interesting template for novel drug development. However, the process of optimizing peptide antimicrobial activity and specificity using large peptide libraries is both tedious and expensive. Here we confirm the use of a mathematical model for prediction, prior to synthesis, of peptide antibacterial activity toward the antibiotic resistant pathogen Pseudomonas aeruginosa. By the use of novel descriptors quantifying the contact energy between neighboring amino acids, as well as a set of inductive and conventional QSAR descriptors, we were able to model the antibacterial activity of peptides. Cross-correlation and optimization of the implemented descriptor values enabled us to build two models, using very limited sets of peptides, which were able to correctly predict the activity of 85 or 71% of the tested peptides, within a twofold deviation window of the corresponding previously assessed IC(50) values, measured earlier. Though these two models were significantly different in size, they demonstrated no significant difference in their predictive power, implying that it is possible to build powerful predictive models using even small sets of structurally different peptides, when using contact-energy descriptors and inductive and conventional QSAR descriptors in the model design.
Nucleotide Sequence of the Envelope Gene of Gardner-Arnstein Feline Leukemia Virus B Reveals Unique Sequence Homologies with a Murine Mink Cell Focus-Forming Virus (1983)

The nucleotide sequence of the envelope gene and the adjacent 3' long terminal repeat (LTR) of Gardner-Arnstein feline leukemia virus of subgroup B (GA-FeLV-B) has been determined. Comparison of the derived amino acid sequence of the gp70-p15E polyprotein to those of several previously reported murine retroviruses revealed striking homologies between GA-FeLV-B gp70 and the gp70 of a Moloney virus-derived mink cell focus-forming virus. These homologies were located within the substituted (presumably xenotropic) portion of the mink cell focus-forming virus envelope gene and comprised amino acid sequences not present in three ecotropic virus gp70s. In addition, areas of insertions and deletions, in general, were the same between GA-FeLV-B and Moloney mink cell focus-forming virus, although the sizes of the insertions and deletions differed. Homologies between GA-FeLV-B and mink cell focus-forming virus gp70s is functionally significant in that they both possess expanded host ranges, a property dictated by gp70. The amino acid sequence of FeLV-B contains 12 Asn-X-Ser/Thr sequences, indicating 12 possible sites of N-linked glycosylation as compared with 7 or 8 for its murine counterparts. Comparison of the 3' LTR of GA-FeLV-B to AKR and Moloney virus LTRs revealed extensive conservation in several regions including the "CCAAT" and Goldberg-Hogness (TATA) boxes thought to be involved in promotion of transcription and in the repeat region of the LTR. The inverted repeats that flanked the LTR of GA-FeLV-B were identical to the murine inverted repeats, but were one base longer than the latter. The region of U3 corresponding to the approximately 75-nucleotide "enhancer sequence" is present in GA-FeLV-B, but contains deletions relative to AKR and Moloney virus and is not repeated. An interesting pallindrome in the repeat region immediately 3' to the U3 region was noted in all the LTRs, but was particularly pronounced in GA-FeLV-B. Possible roles for this structure are discussed.
Homogeneous Amplification and Mutation Scanning of the p53 Gene Using Fluorescent Melting Curves (2002)

p53 mutation scanning by single-labeled hybridization probes is a homogeneous, rapid, and sensitive method with application in both research and clinical diagnostics.
Synthesis of poly‐ϵ‐caprolactone via a free radical mechanism. Free radical ring‐opening polymerization of 2‐methylene‐1,3‐dioxepane (1982)

Abstract 2‐Methylene‐1,3‐dioxepane 6 polymerized with a quantitative ring opening to form poly‐ϵ‐caprolactone via a free radical mechanism. On the other hand, 2‐methylene‐1,3‐dioxolane (ethylene ketene acetal) 4 and 2‐methylene‐1,3‐dioxane 5, under the same conditions, generated polymers with mixed ring‐opened and nonring‐opened structures. In copolymerization monomer 6 also showed a high tendency toward ring opening by which the ester functionality could be conveniently introduced into the backbone of the addition polymers.
Lysosomal Trafficking and Cysteine Protease Metabolism Confer Target-specific Cytotoxicity by Peptide-linked Anti-CD30-Auristatin Conjugates (2006)

The chimeric anti-CD30 monoclonal antibody cAC10, linked to the antimitotic agents monomethyl auristatin E (MMAE) or F (MMAF), produces potent and highly CD30-selective anti-tumor activity in vitro and in vivo. These drugs are appended via a valine-citrulline (vc) dipeptide linkage designed for high stability in serum and conditional cleavage and putative release of fully active drugs by lysosomal cathepsins. To characterize the biochemical processes leading to effective drug delivery, we examined the intracellular trafficking, internalization, and metabolism of the parent antibody and two antibody-drug conjugates, cAC10vc-MMAE and cAC10vc-MMAF, following CD30 surface antigen interaction with target cells. Both cAC10 and its conjugates bound to target cells and internalized in a similar manner. Subcellular fractionation and immunofluorescence studies demonstrated that the antibody and antibody-drug conjugates entering target cells migrated to the lysosomes. Trafficking of both species was blocked by inhibitors of clathrin-mediated endocytosis, suggesting that drug conjugation does not alter the fate of antibody-antigen complexes. Incubation of cAC10vc-MMAE or cAC10vc-MMAF with purified cathepsin B or with enriched lysosomal fractions prepared by subcellular fractionation resulted in the release of active, free drug. Cysteine protease inhibitors, but not aspartic or serine protease inhibitors, blocked antibody-drug conjugate metabolism and the ensuing cytotoxicity of target cells and yielded enhanced intracellular levels of the intact conjugates. These findings suggest that in addition to trafficking to the lysosomes, cathepsin B and perhaps other lysosomal cysteine proteases are requisite for drug release and provide a mechanistic basis for developing antibody-drug conjugates cleavable by intracellular proteases for the targeted delivery of anti-cancer therapeutics.
Dynamic resetting of the human circadian pacemaker by intermittent bright light (2000)

In humans, experimental studies of circadian resetting typically have been limited to lengthy episodes of exposure to continuous bright light. To evaluate the time course of the human endogenous circadian pacemaker's resetting response to brief episodes of intermittent bright light, we studied 16 subjects assigned to one of two intermittent lighting conditions in which the subjects were presented with intermittent episodes of bright-light exposure at 25- or 90-min intervals. The effective duration of bright-light exposure was 31% or 63% compared with a continuous 5-h bright-light stimulus. Exposure to intermittent bright light elicited almost as great a resetting response compared with 5 h of continuous bright light. We conclude that exposure to intermittent bright light produces robust phase shifts of the endogenous circadian pacemaker. Furthermore, these results demonstrate that humans, like other species, exhibit an enhanced sensitivity to the initial minutes of bright-light exposure.
Electrochemical Polymerization of (2‐Dodecyl‐4, 7‐di (thiophen‐2‐yl)‐2H‐benzo[d][1,2,3] triazole): A Novel Matrix for Biomolecule Immobilization (2010)

A recently synthesized conducting polymer [poly(2-dodecyl-4,7-di(thiophen-2-yl)-2H-benzo[d][1,2,3]triazole (PTBT)] was tested as a platform for biomolecule immobilization. After electrochemical polymerization of the monomer (TBT) on graphite electrodes, immobilization of glucose oxidase (GOx,β-D-glucose: oxygen-1-oxidoreductase, EC 1.1.3.4) was carried out. To improve the interactions between the enzyme and hydrophobic alkyl chain on the polymeric structure, GOx and isoleucine (Ile) amino acid were mixed in sodium phosphate buffer (pH 7.0) with a high ionic strength (250 × 10(-3) M). The solution is then casted on the polymer film, and the amino groups in the protein structure were crosslinked using glutaraldehyde (GA) as the bifunctional agent. Finally, the surface was covered with a perm-selective membrane. Consequently, cross-linked enzyme crystal (CLEC) like assembles with regular shapes were observed after immobilization. Microscopic techniques such as scanning electron microscopy (SEM) and fluorescence microscopy were used to monitor the surface morphologies of both the polymer and the bioactive layer. Electrochemical responses of the enzyme electrodes were measured by monitoring O(2) consumption in the presence of glucose at -0.7 V. The optimized biosensor showed a very good linearity between 0.05 and 2.5 × 10(-3) M with a 52 s response time and a detection limit (LOD) of 0.029 × 10(-3) M to glucose. Also, kinetic parameters, operational and storage stabilities were determined. K(m) and I(max) values were found as 4.6 × 10(-3) M and 2.49 µA, respectively. It was also shown that no activity was lost during operational and storage conditions. Finally, proposed system was applied for glucose biomonitoring during fermentation in yeast culture where HPLC was used as the reference method to verify the data obtained by the proposed biosensor.
The efficacy of the heat killing of Mycobacterium tuberculosis (2002)

There is concern that current procedures for the heat inactivation of Mycobacterium tuberculosis may not be adequate. This raises serious safety issues for laboratory staff performing molecular investigations such as IS6110 restriction fragment length polymorphism typing. This paper confirms that the protocol of van Embden et al, as performed routinely in this laboratory, is safe and effective for the heat inactivation of M tuberculosis. This procedure involves complete immersion of a tube containing a suspension of one loopfull of growth in a water bath at 80 degrees C for 20 minutes. Seventy four isolates were included in this investigation. Despite prolonged incubation for 20 weeks, none of the heat killed M tuberculosis suspensions produced visible colonies or gave a positive growth signal from liquid culture. This method did not affect the integrity of the DNA for subsequent molecular investigations.
Ca2+-Binding and Structural Dynamics in the Functions of Calmodulin (1994)

Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and ...Read More
Formation of Amyloid-Like Substance from Beta-2-Microglobulin in vitro (1994)

Although the pathogenesis has yet to be fully understood, beta 2-microglobulin (beta 2m) related amyloidosis is a frequent complication in long-term hemodialysis (HD) patients. In an attempt to clarify the association of two potential candidates with amyloidogenesis from beta 2m in HD patients, human urine-derived beta 2m solution alone or combined with glycosaminoglycans: hyaluronic acid, heparan sulfate, or serum amyloid P component (SAP) were dialyzed against physiological buffered solution (pH 7.4) using a microdialyzer in vitro for 72 h at 4 degrees C. This study demonstrates for the first time that SAP can play a crucial role in the formation of amyloid-like fibrils from beta 2m. This occurs by a direct influence on either the processing of a precursor protein, or protein folding, in vitro, by a short-period dialysis against a physiological buffered solution.
Fetal RHD genotype detection from circulating cell‐free fetal DNA in maternal plasma in non‐sensitized RhD negative women (2011)

Fetal RHD genotyping can accurately be determined using ccff DNA in the first and second trimesters of pregnancy.
Effect of different intravenous nutrients on metabolic changes in short-term fasted man. (1987)

It is well documented (1-3) that a balanced use of nutritive solutions is important to maintain metabolic homeostasis and a better control of nutrient flux in fasting patients. In this trial, 10 healthy males, aged 30-50 years, fasted for 12 h, were subjected to intravenous nutrient loads in three separate trials. In the first trial they received only a fat emulsion, in the second fat emulsion and L-amino acid solution, and in the third fat emulsion, L-amino acid solution and glucose solution, 240 and 480 min after intravenous infusion plasma triglycerides, serum cholesterol, free fatty acids, lactate, glucose and plasma amino acids were determined. Significant biochemical changes were detected with regard to triglycerides, lactic acid, free fatty acids, alanine, glutamine, lysine and proline concentrations, depending on the different mixtures utilized.
Software controlled memory layout reorganization for irregular array access patterns (2007)

Many embedded array-intensive applications have irregular access patterns that are not amenable to static analysis for extraction of access patterns, and thus prevent efficient use of a Scratch Pad Memory (SPM) hierarchy for performance and power improvement. We present a profiling based strategy that generates a memory access trace which can be used to identify data elements with fine granularity that can profitably be placed in the SPMs to maximize performance and energy gains. We developed an entire toolchain that allows incorporation of the code required to profitably move data to SPMs; visualization of the extracted access pattern after profiling; and evaluation/exploration of the generated application code to steer mapping of data to the SPM to yield performance and energy benefits.We present a heuristic approach that efficiently exploits the SPM using the profiler-driven access pattern behaviors. Experimental results on EEMBC and other industrial codes obtained with our framework show that we are able to achieve 36% energy reduction and reduce execution time by up to 22% compared to a cache based system.
Irradiation-free, columnar defects comprised of self-assembled nanodots and nanorods resulting in strongly enhanced flux-pinning in YBa2Cu3O7−δfilms (2005)

The development of biaxially textured, second-generation, high-temperature superconducting (HTS) wires is expected to enable most large-scale applications of HTS materials, in particular electric-power applications. For many potential applications, high critical currents in applied magnetic fields are required. It is well known that columnar defects generated by irradiating high-temperature superconducting materials with heavy ions significantly enhance the in-field critical current density. Hence, for over a decade scientists world-wide have sought means to produce such columnar defects in HTS materials without the expense and complexity of ionizing radiation. Using a simple and practically scalable technique, we have succeeded in producing long, nearly continuous vortex pins along the c-axis in YBa2Cu3O7−δ (YBCO), in the form of self-assembled stacks of BaZrO3 (BZO) nanodots and nanorods. The nanodots and nanorods have a diameter of ∼2–3 nm and an areal density ('matching field') of 8–10 T for 2 vol.% incorporation of BaZrO3. In addition, four misfit dislocations around each nanodot or nanorod are aligned and act as extended columnar defects. YBCO films with such defects exhibit significantly enhanced pinning with less sensitivity to magnetic fields H. In particular, at intermediate field values, the current density, Jc, varies as Jc∼H−α, with α∼0.3 rather than the usual values 0.5–0.65. Similar results were also obtained for CaZrO3 (CZO) and YSZ incorporation in the form of nanodots and nanorods within YBCO, indicating the broad applicability of the developed process. The process could also be used to incorporate self-assembled nanodots and nanorods within matrices of other materials for different applications, such as magnetic materials.
Bell pepper fruit fatty acid hydroperoxide lyase is a cytochrome P450 (CYP74B) (1996)

Fatty acid hydroperoxide lyases cleave a C-C bond adjacent to a hydroperoxide group in lipoxygenase derived lipid hydroperoxides to form short-chain aldehydes and oxo-acids. Previously, we showed that fatty acid hydroperoxide lyase from bell pepper fruits is a heme protein whose spectrophotometric properties greatly resemble a cytochrome P450. In order to ascertain the relationship of it to the P450 gene family, we have cloned cDNA encoding fatty acid hydroperoxide lyase from immature bell pepper fruits. The cDNA encodes 480 amino acids, and shares homology with P450s mostly at the C terminus. The heme binding cysteine is recognizable at position 441. The most closely related P450 is allene oxide synthase (CYP74A), with which it has 40% identity. It qualifies the lyase as a member of a new P450 subfamily, CYP74B. From this finding, the enzyme is thought to be a novel member of P450 specialized for the metabolism of lipid peroxides.
Using Public Network Infrastructures for UAV Remote Sensing in Civilian Security Operations (2011)

This article appeared in Homeland Security Affairs (March 2011), Supplement no.3
Solitons in Molecular Systems (1979)

In the paper basic properties of solitons and excitons and the conditions for their formation are discussed. It is shown that solitons are perfect carriers of the energy of hydrolysis of the molecules ATP along x-helical protein molecules without significant losses. The concept of solitons is used to explain the contraction mechanism of animal muscles at the molecular level. The role of excitons is considered for light absorption processes in three-dimensional structures, with the exciton relaxation processes taken into account.
The N-CoR/Histone Deacetylase 3 Complex Is Required for Repression by Thyroid Hormone Receptor (2003)

Nuclear receptor corepressors (N-CoR) and silencing mediator for retinoid and thyroid receptors (SMRT) have both been implicated in thyroid hormone receptor (TR)-mediated repression. Here we show that endogenous N-CoR, TBL1, and histone deacetylase 3 (HDAC3), but not HDAC1, -2, or -4, are recruited to a stably integrated reporter gene repressed by unliganded TR as well as the orphan receptor RevErb. Unliganded TR also recruits this complex to a transiently transfected reporter, and transcriptional repression is associated with local histone deacetylation that is reversed by the presence of thyroid hormone. Knockdown of N-CoR using small interfering RNAs markedly reduces repression by the TR ligand binding domain in human 293T cells, whereas knockdown of SMRT has little effect. RevErb repression appears to involve both corepressors in this system. Knockdown of HDAC3 markedly reduces repression by both TR and RevErb, while knockdown of HDAC1 or 2 has more modest, partly nonspecific effects. Thus, HDAC3 is critical for repression by multiple nuclear receptors and the N-CoR HDAC3 complex plays a unique and necessary role in TR-mediated gene repression in human 293T cells.
Could STAT3 provide a link between respiration and cell cycle progression? (2010)

Maintaining the intracellular environment is important for the survival and proliferation of eukaryotic cells. How a cell regulates its redox potential during fluctuations in the generation of intracellular reactive oxygen species and exposure to extracellular oxidants is unclear. The recent findings that Signal Transducer and Activator of Transcription 3 (STAT3) regulates mitochondrial respiration and can be oxidised directly by peroxide to form multimers may have revealed features of a homeostatic mechanism coupling cell cycle progression to the intracellular redox potential.
Multiresolution gray-scale and rotation invariant texture classification with local binary patterns (2002)

Presents a theoretically very simple, yet efficient, multiresolution approach to gray-scale and rotation invariant texture classification based on local binary patterns and nonparametric discrimination of sample and prototype distributions. The method is based on recognizing that certain local binary patterns, termed "uniform," are fundamental properties of local image texture and their occurrence histogram is proven to be a very powerful texture feature. We derive a generalized gray-scale and rotation invariant operator presentation that allows for detecting the "uniform" patterns for any quantization of the angular space and for any spatial resolution and presents a method for combining multiple operators for multiresolution analysis. The proposed approach is very robust in terms of gray-scale variations since the operator is, by definition, invariant against any monotonic transformation of the gray scale. Another advantage is computational simplicity as the operator can be realized with a few operations in a small neighborhood and a lookup table. Experimental results demonstrate that good discrimination can be achieved with the occurrence statistics of simple rotation invariant local binary patterns.
Optical and MRI Multifunctional Nanoprobe for Targeting Gliomas (2005)

A multifunctional nanoprobe capable of targeting glioma cells, detectable by both magnetic resonance imaging and fluorescence microscopy, was developed. The nanoprobe was synthesized by coating iron oxide nanoparticles with covalently bound bifunctional poly(ethylene glycol) (PEG) polymer, which were subsequently functionalized with chlorotoxin and the near-infrared fluorescing molecule Cy5.5. Both MR imaging and fluorescence microscopy showed significant preferential uptake of the nanoparticle conjugates by glioma cells. Such a nanoprobe could potentially be used to image resections of glioma brain tumors in real time and to correlate preoperative diagnostic images with intraoperative pathology at cellular-level resolution.
Biochemical and molecular characterization of a succinate semialdehyde dehydrogenase involved in the catabolism of 4-hydroxybutyric acid inRalstonia eutropha (1999)

A succinate semialdehyde dehydrogenase gene (gabD) was identified to be disrupted in a transposon-induced mutant of Ralstonia eutropha exhibiting the phenotype 4-hydroxybutyric acid-leaky. The native gabD gene was cloned by colony hybridization using a homologous gabD-specific DNA probe. DNA sequencing revealed an 1452-bp open reading frame, and the deduced amino acid sequence showed strong similarities to NADP(+)-dependent succinate semialdehyde dehydrogenases from Escherichia coli, Rhizobium sp., Homo sapiens and Rattus norvegicus. The gabD gene was heterologously expressed in a recombinant E. coli strain harboring plasmid pSK::EE6.8. Similar to the molecular organization of the gab cluster in E. coli, additional genes encoding enzymes for the degradation of gamma-aminobutyrate are closely related to gabD in R. eutropha. Enzymatic studies indicated the existence of a second NAD(+)-dependent succinate semialdehyde dehydrogenase in R. eutropha.
Inhibitory activity of the novel CB2receptor agonist, GW833972A, on guinea‐pig and human sensory nerve function in the airways (2008)

This confirms and extends previous studies highlighting the role of CB(2) receptors in the modulation of sensory nerve activity elicited both by the exogenous ligands capsaicin and hypertonic saline but also by endogenous modulators such as PGE(2) and low pH stimuli. These data establish the CB(2) receptor as an interesting target for the treatment of chronic cough.