gebhart/patrepeval huggingface dataset:
Production in Escherichia coli and one‐step purification of bifunctional hybrid proteins which bind maltose (1988)

Two enzymes, the secreted Staphylococcus aureus nuclease A and the Klenow fragment of the cytoplasmic Escherichia coli DNA polymerase I, were fused, at the genetic level, to MalE, the periplasmic maltose-binding protein of E. coli, or to a signal-sequence mutant. The hybrid proteins were synthesized in large amounts by E. coli under control of promoter malEp. The synthesis was repressed with glucose and could be totally switched off in a malT mutant strain. The hybrid between MalE and the nuclease was exported into the periplasmic space. Several criteria demonstrated that a fraction of the hybrid chains with the Klenow polymerase was exported to the periplasm in a signal-sequence-specific manner and ruled out the possibility of a membrane leakage. The hybrid with the Klenow polymerase was not exported and remained in the cytoplasm when carrying a tight signal-sequence mutation in its MalE portion. The hybrid proteins were purified in one step by affinity chromatography on cross-linked amylose. Most of the hybrid chains in the periplasm but only a fraction of those in the other cell compartments had their MalE portion correctly folded. The nuclease and the Klenow polymerase had their full specific activities in the purified hybrids. The potential of MalE as a vector for the production, export and purification of desirable proteins in E. coli is discussed.
Inhibition of Bid-induced Apoptosis by Bcl-2 (2003)

Bcl-2 family proteins are important regulators of apoptosis. They can be pro-apoptotic (e.g. Bid, Bax, and Bak) or anti-apoptotic (e.g. Bcl-2 and Bcl-x(L)). The current study examined Bid-induced apoptosis and its inhibition by Bcl-2. Transfection of Bid led to apoptosis in HeLa cells. In these cells, Bid was processed into active forms of truncated Bid or tBid. Following processing, tBid translocated to the membrane-bound organellar fraction. Bcl-2 co-transfection inhibited Bid-induced apoptosis but did not prevent Bid processing or tBid translocation. On the other hand, Bcl-2 blocked the release of mitochondrial cytochrome c in Bid-transfected cells, suggesting actions at the mitochondrial level. Alkaline treatment stripped off tBid from the membrane-bound organellar fraction of Bid plus Bcl-2-co-transfected cells, but not from cells transfected with only Bid, suggesting inhibition of tBid insertion into mitochondrial membranes by Bcl-2. Bcl-2 also prevented Bid-induced Bax translocation from cytosol to the membrane-bound organellar fraction. Finally, Bcl-2 diminished Bid-induced oligomerization of Bax and Bak within the membrane-bound organellar fraction, shown by cross-linking experiments. In conclusion, Bcl-2 inhibited Bid-induced apoptosis at the mitochondrial level by blocking cytochrome c release, without suppressing Bid processing or activation. Critical steps blocked by Bcl-2 included tBid insertion, Bax translocation, and Bax/Bak oligomerization in the mitochondrial membranes.
Rituximab in patients with rheumatoid arthritis in routine practice (GERINIS): six-year results from a prospective, multicentre, non-interventional study in 2,484 patients (2014)

Prolonged RTX treatment in routine care is associated with good efficacy and tolerability, as measured by conventional parameters and by physicians' and patients' global assessments. Rheumatoid factor status served as a distinct and quantitative biomarker of RTX responsiveness. With growing experience, physicians repeated treatments earlier in patients with less severe disease activity.
Hybrid routing in clustered DTNs with message ferrying (2007)

The mobile wireless research community has invested in the development of routing algorithms and protocols for two distinct environments. The mobile ad-hoc network (MANET) environment is generally assumed to contain relatively dense nodes connected by multi-hop paths, where disconnection is rare. The disruption tolerant network (DTN) environment is generally assumed to contain relatively sparse nodes that are frequently disconnected. We are interested in a different environment in which clusters of nodes have MANET-like dense connectivity, while there is DTN-like sparse connectivity between clusters. We focus in this paper on the case of stationary clusters, where message ferrying provides inter-cluster connectivity. Our routing approach combines message ferry routing with MANET routing through the use of gateway nodes. To best utilize gateway nodes, we develop various algorithms for data aggregation at gateways and transmission scheduling between gateways and the ferry. To further improve performance, we design algorithms to customize ferry routes according to node location and traffic condition. Our hybrid routing schemes are evaluated via extensive simulations.
3D Cell Culture: A Review of Current Approaches and Techniques (2010)

Cell culture in two dimensions has been routinely and diligently undertaken in thousands of laboratories worldwide for the past four decades. However, the culture of cells in two dimensions is arguably primitive and does not reproduce the anatomy or physiology of a tissue for informative or useful study. Creating a third dimension for cell culture is clearly more relevant, but requires a multidisciplinary approach and multidisciplinary expertise. When entering the third dimension, investigators need to consider the design of scaffolds for supporting the organisation of cells or the use of bioreactors for controlling nutrient and waste product exchange. As 3D culture systems become more mature and relevant to human and animal physiology, the ability to design and develop co-cultures becomes possible as does the ability to integrate stem cells. The primary objectives for developing 3D cell culture systems vary widely - and range from engineering tissues for clinical delivery through to the development of models for drug screening. The intention of this review is to provide a general overview of the common approaches and techniques for designing 3D culture models.
Area selective atomic layer deposition of titanium dioxide: Effect of precursor chemistry (2006)

Area selective atomic layer deposition (ALD) of titanium dioxide using polymer films as masking layers has been investigated. A number of factors which must be considered while designing a successful area selective ALD process have been determined and are briefly discussed. Reactivity of the polymer with the ALD precursor species, diffusion of ALD precursors through the polymer mask, and remnant precursor content in the masking film during ALD cycling are key factors. This article investigates the effect of different precursor chemistries in view of the above mentioned factors. Titanium tetrachloride and titanium isopropoxide have been used as two different metal precursors in conjunction with poly(methyl methacrylate) films as photodefinable masking layers. Processing problems arising from factors such as diffusion of precursors through the masking layer can be solved through careful choice of ALD precursors.
Regulating Bone Formation via Controlled Scaffold Degradation (2003)

It is widely assumed that coupling the degradation rate of polymers used as cell transplantation carriers to the growth rate of the developing tissue will improve its quantity or quality. To test this hypothesis, we developed alginate hydrogels with a range of degradation rates by gamma-irradiating high-molecular-weight alginate to yield polymers of various molecular weights and structures. Decreasing the size of the polymer chains increased the degradation rate in vivo, as measured by implant retrieval rates, masses, and elastic moduli. Rapidly and slowly degrading alginates, covalently modified with RGD-containing peptides to control cell behavior, were then used to investigate the effect of biodegradation rate on bone tissue development in vivo. The more rapidly degrading gels led to dramatic increases in the extent and quality of bone formation. These results indicate that biomaterial degradability is a critical design criterion for achieving optimal tissue regeneration with cell transplantation.
Fabrication of ultrathin film containing bienzyme of glucose oxidase and glucoamylase based on electrostatic interaction and its potential application as a maltose sensor (1996)

Abstract An enzyme multilayer film composed of glucose oxidase and glucoamylase alternating with a bipolar quaternary ammonium salt was achieved on the surface of a quartz slide or a gold electrode and its application as a bienzyme maltose sensor was studied.
Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber (2010)

Spider dragline silk is a remarkably strong fiber that makes it attractive for numerous applications. Much has thus been done to make similar fibers by biomimic spinning of recombinant dragline silk proteins. However, success is limited in part due to the inability to successfully express native-sized recombinant silk proteins (250-320 kDa). Here we show that a 284.9 kDa recombinant protein of the spider Nephila clavipes is produced and spun into a fiber displaying mechanical properties comparable to those of the native silk. The native-sized protein, predominantly rich in glycine (44.9%), was favorably expressed in metabolically engineered Escherichia coli within which the glycyl-tRNA pool was elevated. We also found that the recombinant proteins of lower molecular weight versions yielded inferior fiber properties. The results provide insight into evolution of silk protein size related to mechanical performance, and also clarify why spinning lower molecular weight proteins does not recapitulate the properties of native fibers. Furthermore, the silk expression, purification, and spinning platform established here should be useful for sustainable production of natural quality dragline silk, potentially enabling broader applications.
Dose-Dependent Contribution of CD34-Positive Cell Transplantation to Concurrent Vasculogenesis and Cardiomyogenesis for Functional Regenerative Recovery After Myocardial Infarction (2006)

Human CD34+ cell transplantation may have significant and dose-dependent potential for vasculogenesis and cardiomyogenesis with functional recovery from MI.
An intelligent system for information retrieval over the internet through spoken dialogue (1997)

For the purpose of coping with the affluence of information available over the Internet, an efficient, accurate and user-friendly system for information retrieval is mandatory. This paper presents an intelligent system based on the use of spoken dialogue as the main channel for usersystem interface, use of key concepts, processing of unknown words, automatic acquisition of various kinds of knowledge for improving the performance, and agent technologies for system realization. Details of functions required for the agents are also described.
A novel human IL-2 mutein with minimal systemic toxicity exerts greater antitumor efficacy than wild-type IL-2 (2018)

IL-2 is critical to the activation, growth, and survival of T cells and NK cells, and maintains the delicate balance between auto-immunity and anti-neoplasm surveillance. High IL-2 doses have clear antitumor capabilities, but also have severe side effects that limit its clinical use. Side effects include the vascular leak syndrome (VLS), which results in lung edema and liver damage. Therefore, a new version of IL-2 that does not induce organ toxicity would improve IL-2-based immunotherapy. We conducted a systematic screening by changing one amino acid at a time at the interaction area of IL-2 with its receptor IL-2R to select one particular mutant IL-2, FSD13, in which the proline at position 65 was substituted by lysine (P65L). FSD13 had a greater ability than wild-type IL-2 in stimulating CD4<sup>+</sup> T, CD8<sup>+</sup> T, and NK cell proliferation, enhancing the expression of CD69, CD183, CD44, and CD54 in these cells, and triggering cancer cell apoptosis. FSD13 had three-time lower than wild-type IL-2 in inducing CD4<sup>+</sup> T to Tregs. Compared with wild-type IL-2, FSD13 greatly limited the growth, invasion into adjacent tissues, and metastasis of melanoma metastatic into the lung. In contrast to wild-type IL-2, high dose of FSD3 did not alter structures and induce any pathogenic changes in the liver and lung. Thus, we generated a novel the IL-2 mutant, FSD13, by targeting a different area than previously reported. FSD13 surpasses the wild-type IL-2's ability in stimulating the antitumor immune cell functions, but exerts much less systemic toxicity.
Characterization of Ca2+/calmodulin-dependent protein kinase IV. Role in transcriptional regulation. (1994)

We have characterized Ca2+/calmodulin-dependent protein kinase IV (CaM kinase IV), expressed using the baculovirus/Sf9 cell system, to assess its potential role in Ca2+-dependent transcriptional regulation. CaM kinase IV was strongly inhibited in vitro by KN-62, a specific CaM kinase inhibitor which suppresses Ca2+-dependent transcription of several genes, so we tested whether CaM kinase IV could stimulate transcription. Co-transfection of COS-1 cells by cDNA for CaM kinase IV gave 3-fold stimulation of a reporter gene expression, whereas co-transfection with CaM kinase II gave no transcriptional stimulation. Since this transcriptional response was mediated by phosphorylation of cAMP responsive element-binding protein (CREB), we determined the kinetics and site specificities of CaM kinases IV and II for phosphorylating CREB in vitro. CaM kinases IV and II and cAMP kinase (protein kinase A) all had similar Km values for CREB (1-5 microns), but the Vmax of CaM kinase IV was 40-fold lower than those of CaM kinase II and protein kinase A. Although all three kinases phosphorylated Ser133 in CREB, CaM kinase II also gave equal phosphorylation of a second site which was not Ser98. The two CREB phosphorylation sites were separately 32P-labeled, and the abilities of protein phosphatases 1, 2A, and 2B (calcineurin) to dephosphorylate them were tested. Our results show that all three phosphatases could dephosphorylate both sites, and calcineurin was a stronger catalyst for dephosphorylating site 1 (Ser133) than for site 2. These results indicate that CaM kinase IV may be important in Ca2+-dependent transcriptional regulation through phosphorylation of Ser133 in CREB. The fact that CaM kinase II phosphorylates another site in addition to Ser133 in CREB raises the possibility that this second phosphorylation site may account for the suppressed phosphorylation site may account for the suppressed ability of CaM kinase II to enhance transcription through the CRE/CREB system. In addition multiple protein phosphatases, including calcineurin, may exert a modulatory effect on transcription depending on which site they dephosphorylate.
Azidocytidine is incorporated into RNA of 3T6 mouse fibroblasts (1985)

Earlier work has shown that azidocytidine inhibits the growth and DNA synthesis of 3T6 mouse fibroblasts by inactivation of the enzyme ribonucleotide reductase. RNA synthesis, as measured by incorporation of [3H]cytidine was not affected. Here I show that azidocytidine is incorporated into RNA, but not into DNA. Incorporation of the analogue into RNA may under special circumstances contribute to the biological effect of the nucleoside.
New synthetic route for preparing rattle-type silica particles with metal cores (2004)

Rattle-type silica particles with metal cores, applicable to catalysts and metal/inorganic composite coating materials, were prepared by the pre-shell/post-core method that can control the size of metal cores inside silica capsules and exchange from metal cores into different ones with a metal displacement reaction.
1 The Treasure Under the Right Stone (1993)

When the reverse transcriptase was first discovered back in 1970, the Central Dogma of DNA→RNA→protein so completely dominated thinking that the notion of RNA-dependent DNA synthesis came as a great surprise. That surprise grew out of consideration of how RNA tumor viruses are able to transform cells stably. It was the general feeling then, and time has reinforced it, that RNA is a transient molecule in cells. There were already known and well-understood classes of lytic viruses that used RNA as their genetic material, but the stability of their heredity was not a contradiction to RNA’s lability because they grew only transiently in any one cell and continually required new cells for their propagation. These viruses stayed one step ahead of the grim reaper. The existence of a group of RNA-containing viruses that could permanently alter the heredity of cells —a situation that was particularly obvious because these viruses made the cells tumorigenic — required either that they make a uniquely stable RNA, one that can equal the permanence of DNA, or that they transmute their information into a stable condition. Howard Temin had long argued that the likely solution was that they encode a DNA able to integrate itself into the cell’s chromosomes, a provirus, but the community of molecular biologists found this hard to accept given the sway of the Central Dogma. Looked at in retrospect, it was a comfortably conservative viewpoint because the chemistry was so easy to imagine. DNA→RNA or RNA→DNA makes very little chemical difference, and...
ChemInform Abstract: Lysine 2,3‐Aminomutase: Role of S‐Adenosyl‐L‐methionine in the Mechanism. Demonstration of Tritium Transfer from (2RS,3RS)‐(3‐3H) Lysine to S‐Adenosyl‐L‐methionine. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Integrated Proteomic Profiling of Cell Line Conditioned Media and Pancreatic Juice for the Identification of Pancreatic Cancer Biomarkers (2011)

Pancreatic cancer is one of the leading causes of cancer-related deaths, for which serological biomarkers are urgently needed. Most discovery-phase studies focus on the use of one biological source for analysis. The present study details the combined mining of pancreatic cancer-related cell line conditioned media and pancreatic juice for identification of putative diagnostic leads. Using strong cation exchange chromatography, followed by LC-MS/MS on an LTQ-Orbitrap mass spectrometer, we extensively characterized the proteomes of conditioned media from six pancreatic cancer cell lines (BxPc3, MIA-PaCa2, PANC1, CAPAN1, CFPAC1, and SU.86.86), the normal human pancreatic ductal epithelial cell line HPDE, and two pools of six pancreatic juice samples from ductal adenocarcinoma patients. All samples were analyzed in triplicate. Between 1261 and 2171 proteins were identified with two or more peptides in each of the cell lines, and an average of 521 proteins were identified in the pancreatic juice pools. In total, 3479 nonredundant proteins were identified with high confidence, of which ∼ 40% were extracellular or cell membrane-bound based on Genome Ontology classifications. Three strategies were employed for identification of candidate biomarkers: (1) examination of differential protein expression between the cancer and normal cell lines using label-free protein quantification, (2) integrative analysis, focusing on the overlap of proteins among the multiple biological fluids, and (3) tissue specificity analysis through mining of publically available databases. Preliminary verification of anterior gradient homolog 2, syncollin, olfactomedin-4, polymeric immunoglobulin receptor, and collagen alpha-1(VI) chain in plasma samples from pancreatic cancer patients and healthy controls using ELISA, showed a significant increase (p < 0.01) of these proteins in plasma from pancreatic cancer patients. The combination of these five proteins showed an improved area under the receiver operating characteristic curve to CA19.9 alone. Further validation of these proteins is warranted, as is the investigation of the remaining group of candidates.
Palladium-catalyzed coupling of tetraorganotin compounds with aryl and benzyl halides. Synthetic utility and mechanism (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPalladium-catalyzed coupling of tetraorganotin compounds with aryl and benzyl halides. Synthetic utility and mechanismD. Milstein and J. K. StilleCite this: J. Am. Chem. Soc. 1979, 101, 17, 4992–4998Publication Date (Print):August 1, 1979Publication History Published online1 May 2002Published inissue 1 August 1979https://pubs.acs.org/doi/10.1021/ja00511a032https://doi.org/10.1021/ja00511a032research-articleACS PublicationsRequest reuse permissionsArticle Views3591Altmetric-Citations422LEARN 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-Alertsclose Get e-Alerts
Natural Products as Leads for New Pesticides with Reduced Risks (1999)

Although the use of naturally-derived secondary metabolites as pest control agents predates modern agriculture by centuries, technologydriven agricultural practices adapted during the past 50 years curtailed their use in favor of simpler, faster acting and more environmentally stable synthetics. Technological advances are again leading a trend back to naturally-derived materials as the industry learns how to find, optimize, and deliver naturally-derived pest control products. The result will be safer, less environmentally hazardous products for pest control.
Lysyl Oxidases Play a Causal Role in Vascular Remodeling in Clinical and Experimental Pulmonary Arterial Hypertension (2014)

Lysyl oxidases are dysregulated in clinical and experimental PH. Lysyl oxidases play a causal role in experimental PH and represent a candidate therapeutic target. Our proof-of-principle study demonstrated that modulation of lung matrix cross-linking can affect pulmonary vascular remodeling associated with PH.
Phase diversity and continuous-time operation in time stretch A/D converter (2004)

Phase diversity is used to overcome the dispersion penalty leading to 480 Gsample/s conversion. Separately, virtual time gating is employed to demonstrate continuous-time operation.
Efficiency enhancement of microcavity organic light emitting diodes (1996)

We report microcavity efficiency enhancement of organic electroluminescent devices based on the hole transporter bis(triphenyl) diamine and the electron transporter and light emitter tris(8-hydroxyquinoline) aluminum. Microcavity organic light emitting diodes are described that emit four times the light measured in the forward direction (spectrally integrated), or almost twice the total light (spectrally and spatially integrated) of a noncavity organic light-emitting diode for identical electrical drive conditions.