gebhart/patrepeval huggingface dataset:
Molecular Diversity in Gene-Encoded, Cationic Antimicrobial Polypeptides (2002)

Gene-encoded, ribosomally synthesised antimicrobial peptides (AMPs) are an ancient and pervasive component of the innate defence mechanisms used by multicellular organisms to control the natural flora and combat pathogens. Bacteria also produce such AMPs to maintain ecological niches free of rival strains. Several hundred different peptides have been characterised to date, and they show a marked degree of variability in both sequence and structure, having evolved to act against distinct microbial targets in different physiological contexts. Many of these peptides appear to function via a selective, but not receptor-mediated, permeabilisation of microbial membranes, while others interact with specific membrane associated or intracellular targets. This review presents a broad survey of different amp structural classes, emphasising both their molecular diversity and underlying similarities. The mode of action of these peptides and potential for biomedical and other application is also briefly discussed.
Error Control to Increase the Yield of Semiconductor RAM's (2005)

A hard defect in a semiconductor random access memory (RAM) is a cell which is stuck-at a certain value or is otherwise consistently unreliable. The most commonly used technique to correct hard defects during manufacturing is row/column replacement, wherein redundant rows and columns are added on to each memory array and are used to replace rows and columns which contain defective cells. This method has been applied to memory chips of modest sizes (in the 64 K - 4 M bit range). However, the strategy of replacing an entire row or column because of a single defective cell seems likely to be inefficient as the size of the memory array grows. Our research effort was motivated by a recent paper [l] in which this technique is shown to be asymptotically ineffective: as the size of the memory array grows, regardless of the rate (the amount of redundancy) the probability of obtaining an error-free array approaches zero. We consider implementing an error correcting code (ECC) on the memory array in order to control hard defects. A simple single-errorcorrecting code is used over the rows, each row containing an integral number of codewords. Since each codeword can tolerate up to one defect, this technique allows the array to suffer some defective cells and still exhibit no loss of fidelity. We analyze the yield (the probability that a chip is defect-free) due to this method, using a shortenend Hamming code to illustrate our results. The presence of multiple defective cells in some codewords would cause these codewords to become undecodable, causing the chip to be rejected. In order to further improve the yield, we also consider using redundant rows and columns in conjunction with an ECC to correct undecodable codewords in the memory array. It is to be noted that we are interested in improving the yield of memory chips which suffer from single cell defects. In the case of an entire row or column failing (due to the failure of a row driver or a column decoder) we cannot, of course, do any better than to replace the entire row or column. Algorithms to switch rows and columns are examined, and three separate cases are considered: (1) redundant rows, (2) redundant columns, and (3) redundant rows and columns. Case (1) is easily analyzed. Cases (2) and (3) are much more difficult: it is shown that the problem of finding an optimal algorithm to switch columns (case (2)) is inherently intractable, and we prove that this problem is NP - complete. As a corollary, the problem of simultaneously switching rows and columns is also shown to be NP - complete. Heuristics for cases (2) and (3) are presented, and bounds on the yield due to these techniques are derived. References
Ecology and economy decide for 50000 HP electric turbocompressor drivers (2003)

Since the summer of 1997 three natural gas turbocompressors are driven by adjustable speed supersynchronous motors of 38 MW @4200 rpm-the largest LCI drives ever built for that speed up to now. Restrictions on harmonics imposed by the utility, special network conditions, pressure by ecological political groups, and life-cycle economics were decisive in the choice of drive systems. Selection and design criteria for the drivers, network considerations, and first year positive operating experience are addressed by the client and the manufacturer. A subsequent project involving similar high speed electric motor drivers of 25 MW with active magnetic bearings for a "dry" turbocompressor string concludes the paper that primarily addresses prospective users of such systems.
The imidazoquinolines and their place in the therapy of cutaneous disease (2003)

The imidazoquinolines arose from efforts to develop a nucleoside analogue. Although molecularly similar to nucleosides, the imidazoquinolines did not have nucleoside-like activity. However, the imidazoquinolines induced immune modulatory cytokines, in part, because of their ability to activate toll receptors (TLR)s. Imiquimod, the first FDA-approved imidazoquinoline, has been marketed as a 5% cream, which is approved for the therapy of genital warts. The advantage of imiquimod therapy over other therapies for genital warts is the decrease in recurrence rate with the establishment of an adaptive immunological response or immunological memory/surveillance response. As tumours and viral infections are handled similarly by the immune system, there has been great interest in the use of topical imiquimod for the treatment of cutaneous neoplasms, particularly non-melanoma skin cancers. Future efforts in imidazoquinoline research is focused around the development of analogues with modifications in the immunological profiles, potency and penetration parameters that better focus these new analogues for the therapy of specific intracellular infections and neoplasms, as well as the development of imidazoquinolines for conditions related either directly or indirectly to patterns of immune dysregulation.
Inhibition of Clostridium tyrobutyricum by Bacteriocin-Like Substances Produced by Lactic Acid Bacteria (1991)

Lactic acid bacteria were selected for their inhibitory activity against Clostridium tyrobutyricum under conditions that eliminate the effects of lactic acid and hydrogen peroxide. Four strains were isolated belonging to the species Lactococcus lactis ssp. lactis. The sensitivity of the inhibitory substances to pronase and trypsine indicates that they are proteins or peptides different from nisin. Their resistance to phospholipase D indicates that they are also different from lactostrepcin. The inhibitory substances are produced during the exponential phase of growth. Their activity is bactericidal and directed toward some strains of Clostridium tyrobutyricum, Lactobacillus helveticus, and Streptococcus thermophilus, but strains used as dairy starters, Lactobacillus lactis, Streptococcus thermophilus, and Propionibacterium shermanii, are not all affected by the inhibition.
Nitrogen and hydrogen plasma treatments of multiwalled carbon nanotubes (2008)

This article investigates plasma treatment of vertically aligned multiwall carbon nanotube (CNT) films in different plasma environments for modification of surface chemistry and morphology. The surfaces of the CNTs were functionalized with a pulsed dc plasma treatment, where the power was directly applied to the nanotube film in low pressure argon/nitrogen and argon/hydrogen backgrounds. Optical emission spectroscopy was used to detect atomic and molecular excitations in the gas mixtures as well as in pure gases in the vicinity of the CNT films. In situ x-ray photoelectron spectroscopy was performed on the treated samples to examine CNT surface chemistry after treatment. The analysis of CNT films after nitrogen and hydrogen treatment indicated formation of both CN and CH bonds, respectively. Correlations of the plasma characteristics to the surface chemistry and morphology of the CNT surfaces are discussed.
A parallel hybrid learning approach to artificial neural nets (2002)

The requirements of well chosen applications are of great importance for developing new parallel computer architectures. The algorithms presented are implemented on the EDS (European Declarative System) parallel computer. By using a hybrid approach of genetic and gradient descend algorithms in an appropriate manner the advantages of both methods are combined. It is shown how artificial neural networks can be modelled to make the application of the hybrid learning paradigm possible. This hybrid learning approach was implemented in a simulation environment (NNSIM) and compared with standard learning algorithms on a phoneme recognition example.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Accumulation of amino-terminally formylated tryptophan synthase in amplifying conditions. (1983)

Protein synthesis in prokaryotes is initiated with formylated methionyl r-RNA. The amino-terminal formyl residue, and often also amino-terminal methionyl residue, is removed from the finished polypeptide. Wehave previously reported that an amino-terminally formylated
Prefibrillar Amyloid Aggregates Could Be Generic Toxins in Higher Organisms (2006)

More than 40 human diseases are associated with fibrillar deposits of specific peptides or proteins in tissue. Amyloid fibrils, or their precursors, can be highly toxic to cells, suggesting their key role in disease pathogenesis. Proteins not associated with any disease are able to form oligomers and amyloid assemblies in vitro displaying structures and cytotoxicity comparable with those of aggregates of disease-related polypeptides. In isolated cells, such toxicity has been shown to result from increased membrane permeability with disruption of ion homeostasis and oxidative stress. Here we microinjected into the nucleus basalis magnocellularis of rat brains aggregates of an Src homology 3 domain and the N-terminal domain of the prokaryotic HypF, neither of which is associated with amyloid disease. Prefibrillar aggregates of both proteins, but not their mature fibrils or soluble monomers, impaired cholinergic neuron viability in a dose-dependent manner similar to that seen in cell cultures. Contrary to the situation with cultured cells, however, under our experimental conditions, cell stress in tissue is not followed by a comparable level of cell death, a result that is very likely to reflect the presence of protective mechanisms reducing aggregate toxicity. These findings support the hypothesis that neurodegenerative disorders result primarily from a generic cell dysfunction caused by early misfolded species in the aggregation process.
Role of Peripheral Tachykinin Receptors in Neurogenic Inflammation of the Respiratory, Genitourinary and Gastrointestinal Systems (2003)

A wide distribution of tachykinin-containing projections of capsaicin-sensitive primary afferent neurons is present in the peripheral organs of respiratory, gastrointestinal and genitourinary systems. Tachykinins, along with calcitonin gene-related peptide (CGRP) and other neuropeptides, can be released by adequate stimuli having pathological rather than physiological relevance. In most cases these stimuli are represented by chemical irritants penetrating through the respiratory tree or alimentary channel to the body, or being removed through the urinary system. Tachykinins produce in the visceral organs part of the responses obtained at somatic level by antidromic activation of capsaicin-sensitive nerve terminals and known as “neurogenic inflammation” that is, increase in vascular permeability and plasma protein leakage followed by oedema. In addition tachykinins produce at visceral level smooth muscle contraction, neuronal stimulation, mucus secretion and recruitment / activation of immune cells. The physiological significance of these effects is to afford protection toward chemical irritants or noxious stimuli by facilitating their removal from the body. Nonetheless, a large body of preclinical evidence exists indicating that tachykinins participate in the genesis and/or maintenance of symptoms accompanying various human diseases, such as asthma / bronchial hyperreactivity, cystitis of various aetiologies, inflammatory bowel diseases and irritable bowel syndrome. Tachykinin receptor antagonists, proved capable of preventing/reducing tachykinin-mediated effects in experimental animal models of these pathologies, are expected to afford therapeutically relevant effects in humans. Keywords: capsaicin, neurogenic inflammation, neuropeptides, substance p (sp), tackykinin(s), tackykinin receptors
Estimating Malaria Parasitaemia from Blood Smear Images (2006)

A technique is proposed for estimating parasitaemia from blood smear images by extracting healthy and parasite infected red blood cells. The developed approach accounts for uncertain imaging conditions due to microscope settings as well as the quality of the blood smear preparation. The solution is based on a multi-stage estimation process with minimal prior knowledge starting from a model representation of red blood cells. Based on pattern matching with parameter optimisation and cross-validation against the expected biological characteristics, red blood cells are determined. In a final stage, the parasitaemia measure is carried out by partitioning the uninfected and infected cells using an unsupervised and in comparison a training-based technique. Finally, the obtained estimates were analysed with respect to manually acquired results from professionals. Red blood cells detection resulted in precision and recall rates of 80-88% and 92-98%, respectively. By using a training-based method, the precision and recall rates were improved to 92% and 95%, respectively
Gene Expression in Autumn Leaves (2003)

Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula x tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10% of that in young leaves.
An improved synthesis of N4-aminocytidine. (1987)

N4-Aminocytidine, a mutagenic nucleoside, was obtained as crystals on reaction of cytidine with a reagent mixture consisting of hydrazine, bisulfite and phosphate buffer at pH 7. The product can be precipitated directly from the reaction mixture, and therefore the procedure is suitable for preparing N4-aminocytidine in large quantities.
Channel aging effects in CoMP transmission: gains from linear channel prediction (2011)

CoMP transmission gains attraction for future releases of LTE-Advanced specifications. It is considered for downlink cochannel interference mitigation of OFDMA systems operated at full frequency reuse. However, channel knowledge at the transmitter side will be required, where its usability reduces over time, even under quasi-static mobility. This work studies the range of performance degradation caused by channel aging and delayed utilization for the purpose of joint zero-forcing precoding from a subset of base stations. We demonstrate that channel prediction significantly improves the CoMP performance: There is hardly any difference between ideal and delayed feedback when utilizing prediction filters in low mobility regime.
Characteristics of the eukaryotic initiation factor 2 associated 67-kDa polypeptide (1993)

A eukaryotic initiation factor 2 (eIF-2) associated 67-kDa polypeptide (p67) protects the eIF-2 alpha-subunit from eIF-2 kinase(s) catalyzed phosphorylation, and this promotes protein synthesis in the presence of active eIF-2 kinase(s), [Datta, B., et al. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 3324-3328]. This report presents the results of studies related to characteristics of p67 action and the mechanism of p67:eIF-2 interaction: (1) p67 antibodies inhibited protein synthesis in hemin-supplemented rabbit reticulocyte lysates, and such inhibition was reversed by preincubation of the antibodies, specifically with p67. (2) p67 inhibited HRI- and dsI-catalyzed phosphorylations of the eIF-2 alpha-subunit and histones, but it did not inhibit casein kinase catalyzed phosphorylation of the eIF-2 beta-subunit. (3) p67 bound specifically to the eIF-2 gamma-subunit. p67 co-immunoprecipitated with the eIF-2 subunits when a p67/eIF-2 mixture was treated with p67 or eIF-2 subunit antibodies and protein A agarose. However, when eIF-2 was preincubated specifically with the eIF-2 gamma-subunit antibodies, subsequent co-immunoprecipitation of p67 with the eIF-2 subunits was completely inhibited. Similarly, preincubation of p67 and p67 antibodies prevented subsequent p67 binding to eIF-2. Preincubation of eIF-2, with either eIF-2 alpha- or beta-subunit antibodies, had no effect on p67 co-immunoprecipitation with the eIF-2 subunits. (4) p67:eIF-2 interaction is necessary for p67 activity to protect the eIF-2 alpha-subunit from eIF-2 kinase(s) catalyzed phosphorylation.(ABSTRACT TRUNCATED AT 250 WORDS)
Resonant Properties of Long-Range Surface Plasmons in an Arbitrary Multilayer Structure (1999)

In this study, properties of long-range surface plasmons (LRSPs) in an arbitrary multilayer structure have been investigated. We derived an approximation of the reflectivity from Fresnel formulas. Furthermore, the resonant properties of LRSPs have been calculated. As a result of the simulations, we conclude that the difference in resonant angles decreases as the metal thickness increases, and the damping rate obtained from the Sarid geometry is lower than that obtained from the Kretschmann geometry. The resonant half-width obtained from the Sarid geometry is narrower than those obtained from the Kretschmann and Otto geometries. As far as SP chemical sensors are concerned, the system based on the Sarid geometry is better than that based on the Kretschmann or Otto geometry.
First Emergence of acrAB and oqxAB Mediated Tigecycline Resistance in Clinical Isolates of Klebsiella pneumoniae Pre-Dating the Use of Tigecycline in a Chinese Hospital (2014)

Tigecycline is one of the few therapeutic options for treating infections caused by some multi-drug resistant pathogens, such as Klebsiella pneumoniae. However, tigecycline-resistant K. pneumoniae has been discovered recently in China. From 2009 to 2013, nine tigecycline-resistant K. pneumoniae isolates were identified in our hospital. Six of nine strains were identified before using tigecycline. To investigate the efflux-mediated resistance mechanisms of K. pneumoniae, the expression of efflux pump genes (acrA, acrB, tolC, oqxA and oqxB) and pump regulators (acrR, marA, soxS, rarA, rob and ramA) were examined by real-time RT-PCR. Molecular typing of the tigecycline resistant strains was performed. ST11 was the predominant clone of K. pneumoniae strains, while ST1414 and ST1415 were novel STs. Efflux pump inhibitor (EPI)-carbonyl cyanide chlorophenylhydrazone (CCCP) was able to reverse the resistance patterns of 5 resistant K. pneumoniae strains. In comparison with strain A111, a tigecycline-susceptible strain (negative control), we found that the expression levels of efflux pump genes and pump regulators were higher in a majority of resistant strains. Higher expression levels of regulators rarA (2.41-fold, 9.55-fold, 28.44-fold and 18.31-fold, respectively) and pump gene oqxB (3.87-fold, 31.96-fold, 50.61-fold and 29.45-fold, respectively) were observed in four tigecycline resistant strains (A363, A361, A368, A373, respectively). Increased expression of acrB was associated with ramA and marA expression. To our knowledge, studies on tigecycline resistance mechanism in K. pneumoniae are limited especially in China. In our study, we found that both efflux pump AcrAB-TolC and OqxAB contributed to tigecycline resistance in K. pneumoniae isolates.
In vivo administration of recombinant methionyl human stem cell factor expands the number of human marrow hematopoietic stem cells (1993)

A growing number of in vitro studies suggest that recombinant human stem cell factor (SCF) is capable of augmenting the proliferative capacity of human hematopoietic progenitor cells (HPC) and stem cells (HSC). We further evaluated this biologic effect by analyzing the response of bone marrow (BM) HPCs and HSCs to the administration of SCF in eight patients with locally advanced or metastatic breast cancer who were enrolled in an ongoing phase I study. SCF was administered for 14 days by daily subcutaneous injection at dosages of 10, 25, or 50 micrograms/kg/d. BM CD34+ HLA-DR+ and CD34+ HLA-DR- CD15- cells, previously shown by our laboratory to be enriched for various classes of differentiated and primitive HPCs, respectively, were quantitated in BM samples on day 0 (pretreatment) and day 15 (posttreatment). These CD34+ HLA-DR+ and CD34+ HLA-DR- CD15- cells were then isolated by cell- sorting and assayed for several classes of HPCs, including the high-- proliferative potential colony-forming cell (HPP-CFC), the burst- forming unit--megakaryocyte (BFU-MK), and the long-term BM culture-- initiating cell (LTBMC-IC). SCF administration resulted in a 3.3-fold (range, 1.4- to 18.8-fold; P = .018) increase in the absolute numbers of CD34+ cells, a 3.7-fold (range, 1.2- to 8.2-fold; P = .028) increase in the absolute numbers of CD34+ HLA-DR+ cells, and a 2.4-fold (range, 1.1- to 29.3-fold; P = .010) increase in the absolute numbers of CD34+ HLA-DR- CD15- cells. Following the infusion of SCF, a statistically significant increase in the absolute numbers of HPP-CFC (P = .018), BFU- MK (P = .046), CFU-granulocyte, erythrocyte, monocyte, megakaryocyte (CFU-GEMM: P = .043), BFU-erythrocyte (BFU-E; P = .043), CFU- granulocyte, macrophage (CFU-GM; P = .045), and CFU-megakaryocyte (CFU- MK; P = .028) per milliliter of marrow was observed. Stromal cell-free LTBMCs supplemented with SCF and interleukin-3 (IL-3), initiated with CD34+ HLA-DR- CD15- cells obtained on day 0, produced viable cells for 9.6 weeks, compared with 11.5 weeks for LTBMCs initiated with CD34+ HLA- DR- CD15- cells obtained on day 15. Cumulative cellular production by LTBMCs initiated with day 15 CD34+ HLA-DR- CD15- cells was statistically greater than that by day 0 LTBMCs (P = .031). These same cultures produced CFU-GM for 6.3 weeks (day 0) versus 9 weeks (day 15).(ABSTRACT TRUNCATED AT 400 WORDS)