gebhart/patrepeval huggingface dataset:
Activation of the p38 Signaling Pathway by Heat Shock Involves the Dissociation of Glutathione S-Transferase Mu from Ask1 (2002)

Despite the importance of the stress-activated protein kinase pathways in cell death and survival, it is unclear how stressful stimuli lead to their activation. In the case of heat shock, the existence of a specific mechanism of activation has been evidenced, but the molecular nature of this pathway is undefined. Here, we found that Ask1 (apoptosis signal-regulating kinase 1), an upstream activator of the stress-activated protein kinase p38 during exposure to oxidative stress and other stressful stimuli, was also activated by heat shock. Ask1 activity was required for p38 activation since overexpression of a kinase dead mutant of Ask1, Ask1(K709M), inhibited heat shock-induced p38 activation. The activation of Ask1 by oxidative stress involves the oxidation of thioredoxin, an endogenous inhibitor of Ask1. A different activation mechanism takes place during heat shock. In contrast to p38 induction by H(2)O(2), induction by heat shock was not antagonized by pretreatment with the antioxidant N-acetyl-l-cysteine or by overexpressing thioredoxin and was not accompanied by the dissociation of thioredoxin from Ask1. Instead, heat shock caused the dissociation of glutathione S-transferase Mu1-1 (GSTM1-1) from Ask1 and overexpression of GSTM1-1-inhibited induction of p38 by heat shock. We concluded that because of an alternative regulation by the two distinct repressors thioredoxin and GSTM1-1, Ask1 constitutes the converging point of the heat shock and oxidative stress-sensing pathways that lead to p38 activation.
Thermally induced nonreciprocity in the fiber-optic interferometer (1980)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text D. M. Shupe, "Thermally induced nonreciprocity in the fiber-optic interferometer," Appl. Opt. 19, 654-655 (1980) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Cloning of the Nocardia corallina polyhydroxyalkanoate synthase gene and production of poly-(3-hydroxybutyrate-co-3-hydroxyhexanoate) and poly-(3-hydroxyvalerate-co-3-hydroxyheptanoate) (1998)

The polyhydroxyalkanoate (PHA) synthase gene (phaC Nc ) from Nocardia corallina was identified in a lambda library on a 6-kb BamHI fragment. A 2.8-kb XhoII subfragment was found to contain the ntact PHA synthase. This 2.8-kb fragment was subjected to DNA sequencing and was found to contain the coding region for the PHA synthase and a small downstream open reading frame of unknown function. On the basis of DNA sequence, phaC Nc is closest in homology to the PHA synthases (phaC PaI and phaC PaII ) of Pseudomonas aeruginosa (approximately 41% identity and 55% similarity). The 2.8-kb XhoII fragment containing phaC Nc was subcloned into broad host range mobilizable plasmids and transferred into Escherichia coli, Klebsiella aerogenes (both containing a plasmid bearing phaA and phaB from Ralstonia eutropha), and PHA-negative strains of R. eutropha and Pseudomonas putida. The recombinant strains were grown on various carbon sources and the resulting polymers were analyzed. In these strains, the PHA synthase from N. corallina was able to mediate the production of poly(3-hydroxybutyrate-co-3-hydroxy-hexanoate) containing high levels of 3-hydroxyhexanoate when grown on hexanoate and larger even-chain fatty acids and poly(3-hydroxyvalerate-co-3-hydroxyheptanoate) containing high levels of 3-hydroxyheptanoate when grown on heptanoate or larger odd-chain fatty acids. Key words: polyhydroxyalkanoates (PHAs), Nocardia corallina, biodegradable, polyester.
Capillary electrophoresis‐mass spectrometry for glycoscreening in biomedical research (2004)

Application of capillary electrophoresis (CE) in combination with mass spectrometry (MS) and tandem MS to glycoscreening in biomedical projects is highlighted. In the first part recent CE-MS experiments by sheath liquid CE and multiple stage MS are reported. Neutral and negatively charged N-glycan mixtures from ribonuclease B and fetuin, high-mannose type N-glycoforms, oligosaccharides from lipopolysaccharides (LPS) of Haemophilus influenzae, polysaccharides of Pseudomonas aeruginosa and Staphylococcus aureus were analyzed. A particular emphasis is devoted to the applicability of novel off- and on-line CE-MS and tandem MS methods for screening of proteoglycan-derived oligosaccharides, glycosaminoglycans (GAGs), such as hyaluronates from Streptococcus agalactiae, chondroitin/dermatan sulfates (CS/DS) from bovine aorta and human skin fibroblast decorin, and heparin/heparan sulfate (HS) from porcine and bovine mucosa. The performance of CE-MS/MS for identification of glycoforms in glycopeptides and glycoproteins is illustrated by experiments performed on complex mixtures from urine of patients suffering from a hereditary N-acetylhexosaminidase deficiency (Schindler's disease) and urine of patients suffering from cancer cachexia. For determination of glycosylation patterns in glycoproteins like enzymes and antibodies by CE/MS, both CE-matrix assisted laser desorption/ionization (MALDI) and CE-electrospray ionization (ESI)-MS were functional. Finally, the potential of CE-ESI-MS strategy in glycolipid analysis is demonstrated for gangliosides from bovine brain for which particular CE buffer conditions are required.
Identification of new members of hydrophobin family using primary structure analysis (2006)

Abstract Background Hydrophobins are fungal proteins that can turn into amphipathic membranes at hydrophilic/hydrophobic interfaces by self-assembly. The assemblages by Class I hydrophobins are extremely stable and possess the remarkable ability to change the polarity of the surface. One of its most important industrial applications is its usage as paint. Without detailed knowledge of the 3D structure and self-assembly principles of hydrophobins, it is difficult to make significant progress in furthering its research. Results In order to provide useful information to hydrophobin researchers, we analyzed primary structure of hydrophobins to gain more insight about these proteins. In this paper, we presented an in-depth primary sequence analysis using batch BLAST search of the database, sequence filtering by programming and motif finding by MEME. We used batch BLAST to find similar sequences in the NCBI nr database. Then we used MEME to find out motifs. Based on the newly found motifs and the well-known C-CC-C-C-CC-C pattern we used MAST to search the entire nr database. At the end, domain search and phylogenetic analysis were conducted to confirm the result. After searching the nr database with the new PSSM-format motifs identified by MEME, many sequences from various species were found by MAST. Filtering process by pattern, domain and length left 9 qualified candidates. Conclusion All of 9 newly identified potential hydrophobins possess the common pattern and hydrophobin domain. From the multiple sequence alignment result, we can see that some of them are grouped very close to other known hydrophobins, which means their phylogenetic relationship is very close and it is highly plausible that they are indeed hydrophobin proteins.
Vitreoretinal influences on lens function and cataract (2011)

The lens is composed of a thin metabolically active outer layer, consisting of epithelial and superficial fibre cells. Lying within this outer shell are terminally differentiated, metabolically inactive fibre cells, which are divided into an outer cortex and central nucleus. Mature fibre cells contain a very high protein concentration, which is important for the transparency and refractive power of the lens. These proteins are protected from oxidation by reducing substances, like glutathione, and by the low-oxygen environment around the lens. Glutathione reaches the mature fibre cells by diffusing from the metabolically active cells at the lens surface. With age, the cytoplasm of the nucleus becomes stiffer, reducing the rate of diffusion and making nuclear proteins more susceptible to oxidation. Low pO(2) is maintained at the posterior surface of the lens by the physical and physiological properties of the vitreous body, the gel filling the space between the lens and the retina. Destruction or degeneration of the vitreous body increases exposure of the lens to oxygen from the retina. Oxygen reaches the lens nucleus, increasing protein oxidation and aggregation and leading to nuclear cataract. We suggest that maintaining low pO(2) around the lens should prevent the formation of nuclear cataracts.
Carcinoembryonic antigen (CEA)-related cell adhesion molecules are co-expressed in the human lung and their expression can be modulated in bronchial epithelial cells by non-typable Haemophilus influenzae, Moraxella catarrhalis, TLR3, and type I and II interferons (2013)

While we did not find a direct correlation between CEACAM1 expression and COPD, the COPD-associated bacteria NTHi and M. catarrhalis were able to increase the expression of their own receptor on host cells. Further, the data suggest a role for CEACAM1 and CEACAM5 in the phenomenon of increased host susceptibility to bacterial infection upon viral challenge in the human respiratory tract.
Axonal damage markers in cerebrospinal fluid are increased in ALS (2006)

The authors propose that axonal damage markers in CSF may discriminate between subtypes of ALS and that they could be used as markers for therapeutic trials. CSF NfH was superior to tau in these discriminations.
Bioconjugation – using selective chemistry to enhance the properties of proteins and peptides as therapeutics and carriers (2016)

The pharmaceutical market has largely been dominated by small molecule drugs; however, larger biomolecules have recently become important contenders. Of these biomolecules, protein and peptide therapeutics are proving useful due to their often improved pharmacokinetic properties. In many circumstances, functionalisation of the protein or peptide therapeutics results in performance enhancement, and various methodologies are applied. In addition, introducing unnatural amino acids for structural reinforcement via chemical modification is also common. These strategies are discussed in this review.
Core cross-linked star polymers via controlled radical polymerisation (2008)

Star polymers are comprised of multiple arms or branches radiating from a central point or core and have been of huge scientific interest since they were first prepared sixty years ago, as a result of their unique physical properties. Star polymers are not just an academic curiosity, but are currently employed or under investigation in a wide range of industries and commercial materials ranging from engine oils and coating technologies to contact lenses and biomedical devices. Although there are many different types of star polymers and methods for their synthesis, recent advances in the field of controlled radical polymerisation have enabled the facile production of complex star polymer architectures from a large range of monomer families, without the requirement of highly stringent reaction conditions. In particular, well-defined, nanometre scale core cross-linked star (CCS) polymers, which are readily accessible by controlled radical polymerisation techniques, have been increasingly prominent in the scientific literature. As a result, this feature article provides a comprehensive review covering the development, functionalisation, physical properties and application of core cross-linked star polymers prepared by controlled radical polymerisation and the arm-first approach.
Critique of the Treatment of Tense in Focus on Grammar: A High-intermediate Course for Reference and Practice (2006)

Grammar is a tool in language learning and it should be taught communicatively. In teaching grammar, it is very important to teach students how to use tense accurately, meaningfully and appropriately in communication. This paper discusses the ways how tense is taught in the book and makes some suggestions where the use of target tense isn't fully explained.
The HOX11 gene encodes a DNA-binding nuclear transcription factor belonging to a distinct family of homeobox genes. (1993)

A translocation involving human chromosome 10, band q24, in a subset of T-cell acute leukemias disrupts a region surrounding the putative oncogene HOX11, which encodes a protein with a homeodomain. The HOX11 protein binds to a specific DNA sequence, it localizes to the cell nucleus, and it transactivates transcription of a reporter gene linked to a cis-regulatory element, suggesting that HOX11 functions in vivo as a positive transcription activator. PCR analysis shows that the HOX11 homeodomain is a member of a distinct class of homeodomains, representatives of which occur in murine and Drosophila genomes. These all contain a threonine residue in place of the more common isoleucine or valine in helix 3 of the homeodomain. HOX11 therefore appears to belong to a family of DNA-binding transactivators of transcription.
Bottom-Up Abstractive Summarization (2018)

Neural network-based methods for abstractive summarization produce outputs that are more fluent than other techniques, but which can be poor at content selection. This work proposes a simple technique for addressing this issue: use a data-efficient content selector to overdetermine phrases in a source document that should be part of the summary. We use this selector as a bottom-up attention step to constrain the model to likely phrases. We show that this approach improves the ability to compress text, while still generating fluent summaries. This two-step process is both simpler and higher performing than other end-to-end content selection models, leading to significant improvements on ROUGE for both the CNN-DM and NYT corpus. Furthermore, the content selector can be trained with as little as 1,000 sentences, making it easy to transfer a trained summarizer to a new domain.
Surgical Treatment of Femoroacetabular Impingement: Evaluation of the Effect of the Size of the Resection (2006)

Resection of up to 30% of the anterolateral quadrant of the head-neck junction did not significantly alter the load-bearing capacity of the proximal part of the femur. However, a 30% resection significantly decreased the amount of energy required to produce a fracture. Thirty percent should be considered to be the greatest feasible amount of resection because of the change in the pattern of the femoral head-neck response to axial loads that we observed.
Psychological Perspectives of Organizational Learning (2001)

Abstract In recent years the term ‘organizational learning’ has appeared increasingly in scientific and nonscientific publications alike. It stems from an analogy, namely, the idea that a goaloriented social structure, such as an organization, is able to learn like an organism. This interest in organizational learning is fueled by social and economic challenges confronting many organizations: the globalization of markets and ever keener worldwide competition, the shortening of development cycles for individual products, demographic shifts in the world’s industrialized countries, and reduction in the half-life of knowledge, among others (e.g. Prange 1999).
Binary-counting true time delay generator using a white cell design and deformable mirror devices (2002)

We have shown a modified version of the binary white cell-based true time delay (TTD) generator architecture to allow the use of a deformable mirror device (DMD). If 10 bits of delay are required, then each beam will make 20 bounces and use 20 pixels on the DMD. A commercial DMD with 500,000 elements can thus in principle provide 10 bits of delay for 50,000 antenna elements.
Recent developments in the surgical management of perianal fistula for Crohn's disease. (2014)

Perianal manifestations of Crohn's disease (CD) are common and, of them, fistulas are the most common. Perianal fistulas can be extremely debilitating for patients and are often very challenging for clinicians to treat. CD perianal fistulas usually require multidisciplinary and multimodality treatment, including both medical and surgical approaches. The majority of patients require multiple surgical interventions. CD patients with perianal fistulas have a high rate of primary non-healing, surgical morbidity, and high recurrence rates. This has led to constant efforts to improve surgical management of this disease process.
Irreversible electroporation for the treatment of cardiac arrhythmias (2018)

Cardiac ablation is an established treatment modality for the management of patients with cardiac arrhythmias. Current approaches to cardiac ablation employ thermal based energy to achieve lesions (damage) within the heart. There are many shortcomings and limitations of thermal based approaches. Electroporation (DC energy) is a non-thermal alternative approach to ablation that has shown significant promise in animal studies. Areas covered: An extensive review of the literature on the application of electroporation for ablation (both cardiac and collateral cardiac tissue) was undertaken. This review explores irreversible electroporation as a cardiac ablation modality. Specifically, it focuses and explains the biophysics of electroporation, the limitations of current thermal based approaches and examines the current data published on electroporation cardiac ablation. Expert commentary: Electroporation is a fast-growing novel ablation modality that has many advantages over current thermal based approaches. Current research in animal models shows its can be safely and efficaciously applied to the heart. Although further research is required, electroporation represents an appealing option for the ablation cardiac arrhythmias.
Kinetic model of pectin demethylation (2003)

−− −− −− Pectins are polysaccharides that act as a cellular binder in the peel of many different fruits and vegetables. An important feature of pectins is the esterification of the galacturonic acid residues with methanol. The degree of methylation is defined as the number of moles of methanol per 100 moles of galacturonic acid. The objective of the present work was to study the acid demethylation of apple pectin at different temperatures, by following changes in the degree of methylation. A solution of high methoxyl apple pectin was demethylated with concentrated HCl (pH = 0.5). The processes were carried out for 120 min at T = 80°C and 400 min at T = 65°C and T = 50°C. Anhydrogalacturonic acid content, degree of methylation and intrinsic viscosity as a function of reaction time were determined. Results showed pectin demethylation followed a second order kinetics and demethylation rate increased exponentially with temperature. Results also showed pectin “purity”, as anhydrogalacturonic acid content, increased with demethylation. However, intrinsic viscosity reduced with reaction time. This behavior was associated with the hydrolysis of non-polyuronic material during the acid treatment, lowering in that way the average molecular weight.
Microstructured Shape Memory Polymer Surfaces with Reversible Dry Adhesion (2013)

We present a shape memory polymer (SMP) surface with repeatable, very strong (>18 atm), and extremely reversible (strong to weak adhesion ratio of >1 × 10(4)) dry adhesion to a glass substrate. This was achieved by exploiting bulk material properties of SMP and surface microstructuring. Its exceptional dry adhesive performance is attributed to the SMP's rigidity change in response to temperature and its capabilities of temporary shape locking and permanent shape recovery, which when combined with a microtip surface design enables time-independent control of contact area.
Structural proteins of equine arteritis virus (1992)

We have recently shown that the genome of equine arteritis virus (EAV) contains seven open reading frames (ORFs). We now present data on the structural proteins of EAV and the assignment of their respective genes. Virions are composed of a 14-kDa nucleocapsid protein (N) and three membrane proteins designated M, GS, and GL. M is an unglycosylated protein of 16 kDa, and GS and GL are N-glycosylated proteins of 25 and 30 to 42 kDa, respectively. The broad size distribution of GL results from heterogeneous N-acetyllactosamine addition since it is susceptible to digestion by endo-beta-galactosidase. Using monospecific antisera as well as an antivirion serum, and by expression of individual ORFs, the genes for the structural proteins were identified: ORF 7 codes for N, ORF 6 for M, ORF 5 for GL, and ORF 2 for GS. With the exception of GS, the proteins are about equally abundant in EAV virions, being present at a molar ratio of 3 (N):2 (M):3 (GL). The GS protein, which is expressed at a level similar to that of M in infected cells, is strikingly underrepresented in virus particles (1 to 2%). Our data justify a distinct taxonomic position for EAV, together with lactate dehydrogenase-elevating virus and simian hemorrhagic fever virus; although coronavirus- and toroviruslike in features of transcription and translation, the virion architecture of EAV is fundamentally different.
Principles Underlying the Development and Use of Live Attenuated Cold-Adapted Influenza A and B Virus Vaccines (2002)

BIVALENT INFLUENZA A VIRUSES Generation and characterization of the influenza A/AnnArbor(AA)/6/60 ca donor virus.The influenza A/AA/6/60 (H2N2) ca donor virus was generated by adaptation to replication at low temperature as indicated in Figure 2. The multiple passages at progressively lower temperatures in primary chicken kidney cell (PCKC) culture including biological cloning yielded the A/AA/6/60 ca donor virus that exhibited LIVE ATTENUATED COLD-ADAPTED INFLUENZA A AND B VIRUS VACCINES FIG. 2. Attenuation of the influenza A/AA/6/60 (H2N2) ca donor virus by passage in primary chicken kidney cells (PCKC) at successively lower temperatures (53).The influenza A/AA/6/60 (H2N2) ca donor virus exhibits three phenotypes, that is, the ts, ca, and att phenotypes.E indicates a passage in the allantoic cavity of embryonated chicken eggs.FIG. 5. Derivation of the influenza B/AA/1/66 ca virus by passage at progressively lower temperature in primary chicken kidney cells (PCKC) and by amplification in embryonated chicken eggs (E).
Membrane-bound human SCF/KL promotes in vivo human hematopoietic engraftment and myeloid differentiation (2012)

In recent years, advances in the humanized mouse system have led to significantly increased levels of human hematopoietic stem cell (HSC) engraftment. The remaining limitations in human HSC engraftment and function include lymphoid-skewed differentiation and inefficient myeloid development in the recipients. Limited human HSC function may partially be attributed to the inability of the host mouse microenvironment to provide sufficient support to human hematopoiesis. To address this problem, we created membrane-bound human stem cell factor (SCF)/KIT ligand (KL)-expressing NOD/SCID/IL2rgKO (hSCF Tg NSG) mice. hSCF Tg NSG recipients of human HSCs showed higher levels of both human CD45(+) cell engraftment and human CD45(+)CD33(+) myeloid development compared with NSG recipients. Expression of hSCF/hKL accelerated the differentiation of the human granulocyte lineage cells in the recipient bone marrow. Human mast cells were identified in bone marrow, spleen, and gastrointestinal tissues of the hSCF Tg NSG recipients. This novel in vivo humanized mouse model demonstrates the essential role of membrane-bound hSCF in human myeloid development. Moreover, the hSCF Tg NSG humanized recipients may facilitate investigation of in vivo differentiation, migration, function, and pathology of human mast cells.