gebhart/patrepeval huggingface dataset:
Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropsis gaditana (2012)

The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a genetic transformation method for the marine microalga Nannochloropsis gaditana CCMP526. We show that N. gaditana has highly favourable lipid yields, and is a promising production organism. The genome assembly includes nuclear (~29 Mb) and organellar genomes, and contains 9,052 gene models. We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis. Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed. The availability of a genome sequence and transformation methods will facilitate investigations into N. gaditana lipid biosynthesis and permit genetic engineering strategies to further improve this naturally productive alga.
Human thyroid peroxidase: complete cDNA and protein sequence, chromosome mapping, and identification of two alternately spliced mRNAs. (1987)

Two forms of human thyroid peroxidase cDNAs were isolated from a lambda gt11 cDNA library, prepared from Graves disease thyroid tissue mRNA, by use of oligonucleotides. The longest complete cDNA, designated phTPO-1, has 3048 nucleotides and an open reading frame consisting of 933 amino acids, which would encode a protein with a molecular weight of 103,026. Five potential asparagine-linked glycosylation sites are found in the deduced amino acid sequence. The second peroxidase cDNA, designated phTPO-2, is almost identical to phTPO-1 beginning 605 base pairs downstream except that it contains 1-base-pair difference and lacks 171 base pairs in the middle of the sequence. This results in a loss of 57 amino acids corresponding to a molecular weight of 6282. Interestingly, this 171-nucleotide sequence has GT and AG at its 5' and 3' boundaries, respectively, that are in good agreement with donor and acceptor splice site consensus sequences. Using specific oligonucleotide probes for the mRNAs derived from the cDNA sequences hTPO-1 and hTPO-2, we show that both are expressed in all thyroid tissues examined and the relative level of two mRNAs is different in each sample. These results suggest that two thyroid peroxidase proteins might be generated through alternate splicing of the same gene. By using somatic cell hybrid lines, the thyroid peroxidase gene was mapped to the short arm of human chromosome 2.
Solutions to Point-to-Point Control Problems using Laplace Transform Technique (1990)

The governing equations of point-to-point control problems are converted using Laplace transform from a set of linear ordinary differential equations into an equivalent set of linear algebraic equations embedded with the boundary conditions. A simple analytical procedure for evaluating open-loop control input using these algebraic equations is presented. A new concept of feedback control is also developed which involves a recursive evaluation of the open-loop control input.
Plasma excitatory amino acids in autism. (1996)

Plasma amino acid levels were measured by high pressure liquid chromatography (HPLC) in fourteen autistic children, all below 10 years of age. Mean glutamic and aspartic acid valued were elevated (169 +/- 142 uM and 22.1 +/- 13 uM respectively) together with taurine (90.1 +/- 78.7 uM) (p > 0.1). All affected children had low levels of glutamine (241 +/- 166 uM; p < 0.01) and asparagine (22.9 +/- 12.9 uM; p < 0.01) as compared to normal values (585 +/- 25 and 59.2 +/- 4.2 uM respectively); eleven children had increased aspartic acid and eight children had high levels of glutamate; seven of these children had a concomitant increment of taurine. The increment of the three above mentioned compounds was observed at the same time only in five children. These findings demonstrate that abnormal plasmatic levels of neurotransmitter amino acids may be found in some autistic children. Increased glutamatemia may be dietary in origin or may arise endogenously for several reasons, among others, metabolic derrangements in glutamate metabolism perhaps involving vitamin B6, defects or blockage of the glutamate receptor at the neuronal compartment, or alterations in the function of the neurotransmitters transporters. Increments of taurine, an inhibitor, is likely compensatory and calcium dependent.
Ricin linked to monophosphopentamannose binds to fibroblast lysosomal hydrolase receptors, resulting in a cell-type-specific toxin. (1979)

The receptor specificity of the plant seed toxin ricin, which ordinarily binds to galactose-containing receptors, has been altered by coupling monophosphopentamannose residues to ricin by reductive amination and by reversibly binding lactose to the modified ricin. The added monophosphopentamannose residues provide ricin with the recognition factor common to fibroblast lysosomal hydrolases and enable the modified ricin (Man6P-ricin) to bind to the fibroblast Man6P receptor and inhibit protein synthesis in the cells via this receptor. The addition of lactose to Man6P-ricin saturates the galactose site on Man6P-ricin and prevents the binding of Man6P-ricin to cells via galactose-containing ricin receptors. The Man6P receptor-mediated toxicity of Man6P-ricin, identified in human fibroblasts by competition by Man6P and blockade by alkaline phosphatase treatment, was not detected in HeLa cells or human amnion cells. Consequently, in the presence of lactose, the fibroblasts were 8 and 13 times more sensitive than amnion and HeLa cells, respectively. These results show that highly toxic cell-type-specific reagents can be made by the proper alteration of toxin receptor specificities. An attempt to construct a highly toxic altered toxin by adding Man6P residues to diphtheria toxin fragment A was unsuccessful. A possible explanation is that in Man6P-ricin the ricin B chain performs some entry function, even though the initial binding step occurs at the Man6P receptor.
Cardiac perforation due to Wallstent embolization: a fatal complication of the transjugular intrahepatic portosystemic shunt procedure. (1997)

The transjugular intrahepatic portosystemic shunt procedure is an effective intervention for patients with bleeding esophageal varices. Potential complications are numerous but rarely serious. A case of hemopericardium, cardiac tamponade, and death caused by perforation of the right atrium and aorta by a stent after embolization from the liver during stent placement is reported.
Breed and Species Differences in the Hair Proteins of Four Genera of Caprini (1971)

A study has been made of the high-sulphur protein components of wools from goats and a variety of sheep using electrophoresis in starch gels at pH 2·4 and chromatography on DEAE-cellulose at pH 4·5 as methods for characterization. The high-sulphur proteins prepared from ovine wools, from domestic (10 breeds and strains), feral (Soay and Shetland), or wild (Bighorn, O. canadensis; Mouflon, O. mU8'imon) sheep are very heterogeneous. Of the two methods gel electrophoresis gives the better resolution with a characteristic pattern in which upwards of 20 components can be seen and 12 are sufficiently well separated to be readily identifiable. This pattern is unaffected by the diet or by the age of the sheep (up to 5 yr) and would seem to be characteristic for ovine wools. One or other of two of these bands may be missing from the wool of some individuals, particularly of wild sheep.
Clearing and release of basement membrane proteins from substrates by metastatic tumor cell variants. (1986)

A variety of normal cells and tumor cell lines of differing metastatic potential were evaluated for their effect on various substrates consisting of purified preparations of the basement membrane-associated proteins fibronectin, laminin, and type IV collagen, which were labeled with tritium and/or rhodamine isothiocyanate. Different degrees of clearing or release of material from the substrate were observed, depending on the cell-protein combination. Normal fibroblasts as well as transformed cells and cells of low metastatic potential showed extensive clearing of surfaces coated with fibronectin, laminin, and type IV collagen. This clearing of protein began at sites of initial cell adhesion and was restricted to areas beneath and/or along the apparent paths of cell migration and beneath cellular processes. Covalent attachment of adhesion proteins to glass coverslips nearly eliminated clearing and release. Studies showed that a substantial amount of the fibronectin released from the substrate by HT-1080 fibrosarcoma cells is due to proteolysis. Release and clearing of substratum-attached protein is reduced by approximately 50% by antibodies specific for the protein on the substrate. Tumor cells with low metastatic potential were found to produce higher levels of clearing and release of protein adsorbed to the substrate than tumor cells with high metastatic potential. This was true for variants of the murine K-1735 melanoma and the UV-2237 fibrosarcoma with high and low metastatic capability on all three basement membrane-associated protein substrates. The differences in clearing and release between high and low metastatic cells were not due to differences in initial cell adhesion to the substrates but may be associated with differences in the affinity, type of cell-substrate interactions, proteases, or other variables.
Redundant phenazine operons in Pseudomonas aeruginosa exhibit environment-dependent expression and differential roles in pathogenicity (2012)

Evolutionary biologists have postulated that several fitness advantages may be conferred by the maintenance of duplicate genes, including environmental adaptation resulting from differential regulation. We examined the expression and physiological contributions of two redundant operons in the adaptable bacterium Pseudomonas aeruginosa PA14. These operons, phzA1-G1 (phz1) and phzA2-G2 (phz2), encode nearly identical sets of proteins that catalyze the synthesis of phenazine-1-carboxylic acid, the precursor for several phenazine derivatives. Phenazines perform diverse roles in P. aeruginosa physiology and act as virulence factors during opportunistic infections of plant and animal hosts. Although reports have indicated that phz1 is regulated by the Pseudomonas quinolone signal, factors controlling phz2 expression have not been identified, and the relative contributions of these redundant operons to phenazine biosynthesis have not been evaluated. We found that in liquid cultures, phz1 was expressed at higher levels than phz2, although phz2 showed a greater contribution to phenazine production. In colony biofilms, phz2 was expressed at high levels, whereas phz1 expression was not detectable, and phz2 was responsible for virtually all phenazine production. Analysis of mutants defective in quinolone signal synthesis revealed a critical role for 4-hydroxy-2-heptylquinoline in phz2 induction. Finally, deletion of phz2, but not of phz1, decreased lung colonization in a murine model of infection. These results suggest that differential regulation of the redundant phz operons allows P. aeruginosa to adapt to diverse environments.
Therapeutic Utility and Medicinal Chemistry of Cathepsin C Inhibitors (2010)

The lysosomal cysteine protease cathepsin C (Cat C), also known as dipeptidyl peptidase I, activates a number of granule-associated serine proteases with pro-inflammatory and immune functions by removal of their inhibitory N-terminal dipeptides. Thus, Cat C is a therapeutic target for the treatment of a number of inflammatory and autoimmune diseases. Cathepsin C null mice and humans with Cat C loss of function mutations (Papillon-Lefèvre syndrome) show deficiencies in disease-relevant proteases including neutrophil elastase, cathepsin G, chymases and granzymes and the Cat C mice are protected in a number of disease models. Several methodologies have been recently reported for assessing the effects of Cat C inhibitors on serine protease activities in cellular assays and prolonged treatment of rats with a reversible, selective Cat C inhibitor reduced the activity of three leukocyte serine proteases. Nearly all potent and selective Cat C inhibitors described are based on the preferred dipeptide substrates bearing either irreversible (e.g. diazomethylketone, acyloxymethyl ketone, o-acyl hydroxamic acid and vinyl sulfone) or reversible (e.g. semicarbazide, nitrile and cyanamide) electrophilic warheads. While potent and highly selective, the best inhibitors described to date still have poor stability and/or rodent pharmacokinetics, likely resulting from their peptidic nature. The lack of selective compounds with appropriate rodent pharmacokinetic properties has hampered the assessment of the effects of Cat C inhibitors on the activation of disease-relevant proteases in vivo and the full evaluation of the therapeutic utility of Cat C inhibitors.
The State of Record Linkage and Current Research Problems (1999)

This paper provides an overview of methods and systems developed for record linkage. Modern record linkage begins with the pioneering work of Newcombe and is especially based on the formal mathematical model of Fellegi and Sunter. In their seminal work, Fellegi and Sunter introduced many powerful ideas for estimating record linkage parameters and other ideas that still influence record linkage today. Record linkage research is characterized by its synergism of statistics, computer science, and operations research. Many difficult algorithms have been developed and put in software systems. Record linkage practice is still very limited. Some limits are due to existing software. Other limits are due to the difficulty in automatically estimating matching parameters and error rates, with current research highlighted by the work of Larsen and Rubin. Keywords: computer matching, modeling, iterative fitting, string comparison, optimization RsSUMs Cet article donne une vue d&amp;apos;ensemble sur les ...
Antimicrobial peptides in the stomach of Xenopus laevis. (1991)

Antimicrobial peptides are widely distributed in nature and appear to play a role in the host defense of plants and animals. In this study we report the existence of antimicrobial peptides in the stomach of the vertebrate Xenopus laevis, an animal previously shown to store high concentrations of antimicrobial peptides in its skin. Antimicrobial activity was detected in extracts of X. laevis stomach tissue and nine antimicrobial peptides were then purified. A novel 24-amino acid peptide, designated PGQ, was isolated from these extracts, and has the following amino acid sequence: GVLSNVIGYLKKLGTGALNAVLKQ. PGQ is relatively basic and has the potential to form an amphipathic alpha-helix. The other peptides isolated are members of the magainin family of antimicrobial peptides, and include magainins I and II, PGLa, xenopsin precursor fragment, and four caerulein precursor fragments. None of these peptides had been previously identified in tissues other than the skin. The purification of the peptides from stomach extracts and subsequent protein sequence analysis reveals that the peptides have undergone the same processing as their dermal counterparts, and that they are stored in their processed forms. Northern blot analysis indicates that the magainin family of peptides are synthesized in the stomach, and immunohistochemical studies demonstrate that magainin is stored in a novel granular multinucleated cell in the gastric mucosa of Xenopus. This study demonstrates that the magainin family of antimicrobial peptides is found in the gastrointestinal system of X. laevis and offers an opportunity to further define the physiological role of these defense peptides.
2 × 2 Single-mode fiber routing switch (1996)

An all-fiber 2 x 2 acousto-optic routing switch is described that has an insertion loss of 0.11 dB, a drive power of 1.5 mW, and a switching time of 80 micros. The switch has a very simple construction and so has the potential to be low in cost.
Renin-Angiotensin Activation and Oxidative Stress in Early Heart Failure with Preserved Ejection Fraction (2015)

Animal models have suggested a role of renin-angiotensin system (RAS) activation and subsequent cardiac oxidation in heart failure with preserved ejection fraction (HFpEF). Nevertheless, RAS blockade has failed to show efficacy in treatment of HFpEF. We evaluated the role of RAS activation and subsequent systemic oxidation in HFpEF. Oxidative stress markers were compared in 50 subjects with and without early HFpEF. Derivatives of reactive oxidative metabolites (DROMs), F2-isoprostanes (IsoPs), and ratios of oxidized to reduced glutathione (E h GSH) and cysteine (E h CyS) were measured. Angiotensin converting enzyme (ACE) levels and activity were measured. On univariate analysis, HFpEF was associated with male sex (p = 0.04), higher body mass index (BMI) (p = 0.003), less oxidized E h CyS (p = 0.001), lower DROMs (p = 0.02), and lower IsoP (p = 0.03). Higher BMI (OR: 1.3; 95% CI: 1.1-1.6) and less oxidized E h CyS (OR: 1.2; 95% CI: 1.1-1.4) maintained associations with HFpEF on multivariate analysis. Though ACE levels were higher in early HFpEF (OR: 1.09; 95% CI: 1.01-1.05), ACE activity was similar to that in controls. HFpEF is not associated with significant systemic RAS activation or oxidative stress. This may explain the failure of RAS inhibitors to alter outcomes in HFpEF.
A Survey of Social Network Forensics (2016)

Social networks in any form, specifically online social networks (OSNs), are becoming a part of our everyday life in this new millennium especially with the advanced and simple communication technologies through easily accessible devices such as smartphones and tablets. The data generated through the use of these technologies need to be analyzed for forensic purposes when criminal and terrorist activities are involved. In order to deal with the forensic implications of social networks, current research on both digital forensics and social networks need to be incorporated and understood. This will help digital forensics investigators to predict, detect and even prevent any criminal activities in different forms. It will also help researchers to develop new models / techniques in the future. This paper provides literature review of the social network forensics methods, models, and techniques in order to provide an overview to the researchers for their future works as well as the law enforcement investigators for their investigations when crimes are committed in the cyber space. It also provides awareness and defense methods for OSN users in order to protect them against to social attacks.
Modeling Teacher-Student Techniques in Deep Neural Networks for Knowledge Distillation (2020)

Knowledge distillation (KD) is a new method for transferring knowledge of a structure under training to another one. The conventional application of KD is in the form of learning a small model (named as a student) by soft labels produced by a complex model (named as a teacher). Due to the novel idea introduced in KD, recently, its notion is used in different methods such as compression and processes that are going to enhance the model accuracy. Although different techniques are proposed in the area of KD, there is a lack of a model to generalize KD techniques. In this paper, various studies in the scope of KD are investigated and analyzed to build a general model for KD. All the methods and techniques in KD can be summarized through the proposed model. By utilizing the proposed model, different methods in KD are better investigated and explored. The advantages and disadvantages of different approaches in KD can be better understood and developing a new strategy for KD can be possible. Using the proposed model, different KD methods are represented in an abstract view.
Lipid-catalyzed transport of copper(II) through liquid membranes (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLipid-catalyzed transport of copper(II) through liquid membranesF. M. Menger and Jeng Jong LeeCite this: J. Org. Chem. 1993, 58, 7, 1909–1916Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/jo00059a050https://doi.org/10.1021/jo00059a050research-articleACS PublicationsRequest reuse permissionsArticle Views279Altmetric-Citations24LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Imaging Angiogenesis: Applications and Potential for Drug Development (2005)

Recognition of the importance of angiogenesis to tumor growth and metastasis has led to efforts to develop new drugs that are targeted to angiogenic vasculature. Clinical trials of these agents are challenging, both because there is no agreed upon method of establishing the correct dosage for drugs whose mechanism of action is not primarily cytotoxic and because of the long time it takes to determine whether such drugs have a clinical effect. Therefore, there is a need for rapid and effective biomarkers to establish drug dosage and monitor clinical response. This review addresses the potential of imaging as a way to accurately and reliably assess changes in angiogenic vasculature in response to therapy. We describe the advantages and disadvantages of several imaging modalities, including positron emission tomography, x-ray computed tomography, magnetic resonance imaging, ultrasound, and optical imaging, for imaging angiogenic vasculature. We also discuss the analytic methods used to derive blood flow, blood volume, empirical semiquantitative hemodynamic parameters, and quantitative hemodynamic parameters from pharmacokinetic modeling. We examine the validity of these methods, citing studies that test correlations between data derived from imaging and data derived from other established methods, their reproducibility, and correlations between imaging-derived hemodynamic parameters and other pathologic indicators, such as microvessel density, pathology score, and disease outcome. Finally, we discuss which imaging methods are most likely to have the sensitivity and reliability required for monitoring responses to cancer therapy and describe ways in which imaging has been used in clinical trials to date.