gebhart/patrepeval huggingface dataset:
An Expanded Multilocus Sequence Typing Scheme for Propionibacterium acnes: Investigation of ‘Pathogenic’, ‘Commensal’ and Antibiotic Resistant Strains (2012)

The Gram-positive bacterium Propionibacterium acnes is a member of the normal human skin microbiota and is associated with various infections and clinical conditions. There is tentative evidence to suggest that certain lineages may be associated with disease and others with health. We recently described a multilocus sequence typing scheme (MLST) for P. acnes based on seven housekeeping genes (http://pubmlst.org/pacnes). We now describe an expanded eight gene version based on six housekeeping genes and two 'putative virulence' genes (eMLST) that provides improved high resolution typing (91eSTs from 285 isolates), and generates phylogenies congruent with those based on whole genome analysis. When compared with the nine gene MLST scheme developed at the University of Bath, UK, and utilised by researchers at Aarhus University, Denmark, the eMLST method offers greater resolution. Using the scheme, we examined 208 isolates from disparate clinical sources, and 77 isolates from healthy skin. Acne was predominately associated with type IA(1) clonal complexes CC1, CC3 and CC4; with eST1 and eST3 lineages being highly represented. In contrast, type IA(2) strains were recovered at a rate similar to type IB and II organisms. Ophthalmic infections were predominately associated with type IA(1) and IA(2) strains, while type IB and II were more frequently recovered from soft tissue and retrieved medical devices. Strains with rRNA mutations conferring resistance to antibiotics used in acne treatment were dominated by eST3, with some evidence for intercontinental spread. In contrast, despite its high association with acne, only a small number of resistant CC1 eSTs were identified. A number of eSTs were only recovered from healthy skin, particularly eSTs representing CC72 (type II) and CC77 (type III). Collectively our data lends support to the view that pathogenic versus truly commensal lineages of P. acnes may exist. This is likely to have important therapeutic and diagnostic implications.
Molecular cloning and characterization of PKC iota, an atypical isoform of protein kinase C derived from insulin-secreting cells. (1993)

The protein kinase C (PKC) family of serine-threonine kinases comprises at least eight members. These are differentially expressed, show varying affinities for activators such as Ca2+ and lipid species, and are therefore thought to play wide-ranging roles in the regulation of such cellular processes as differentiation, growth, and secretion. The aim of this study was to identify new PKC isoforms in the insulin-secreting cell line RINm5F that might be activated by the alterations in lipid metabolism that accompany nutrient-stimulated insulin release. Fragments of cDNA, derived from RINm5F cell mRNA, were amplified by the polymerase chain reaction using degenerate oligonucleotide primers corresponding to highly conserved regions in the catalytic domains of all known PKCs. A novel sequence generated by this approach was subsequently used to screen cDNA libraries. The entire 587-amino acid coding region of a new PKC isoform, PKC iota, was deduced from two overlapping clones isolated from a human kidney cDNA library. The amino acid sequence of PKC iota showed greatest homology to PKC zeta, with 72% identity overall rising to 84% in the catalytic domain. In contrast, the homology of PKC iota to the other isoforms was less pronounced, with < 53% identity even in the highly conserved catalytic region. Further similarities between PKC zeta and PKC iota included a highly conserved pseudosubstrate sequence, the absence of an apparent Ca(2+)-binding region, and the presence of only one cysteine-rich, zinc finger-like domain. Northern blot analysis, using the full-length PKC iota clone as a probe, revealed a single 4.6-kilobase transcript present predominantly in lung and brain, but also expressed at lower levels in many tissues including pancreatic islets. In CHO-K1 cells stably expressing the PKC iota cDNA under the human beta-actin promoter, the protein was detected as a 65-kDa band by Western blotting using an antibody to the COOH terminus of PKC zeta (conserved in PKC iota). Extracts of transfected CHO-K1 cells also displayed a significantly increased kinase activity using myelin basic protein as a substrate. The results suggest that PKC iota should be included in the atypical subgroup of PKCs whose definitive member is PKC zeta. As such, PKC iota is unlikely to be activated by the diacylglycerol that is derived from phosphoinositide hydrolysis, but might be a target for novel lipid activators that are elevated during nutrient-stimulated insulin secretion.
Hematopoietic stem cell gene therapy in Hurler syndrome, globoid cell leukodystrophy, metachromatic leukodystrophy and X-adrenoleukodystrophy. (2008)

Hurler syndrome, metachromatic leukodystrophy, globoid-cell leukodystrophy (Krabbe's disease) and X-linked adrenoleukodystrophy are inherited diseases of the CNS that can be cured or arrested by allogeneic hematopoietic stem-cell transplantation (HSCT). Despite significant progress in medical procedures and the availability of banked umbilical cord blood, HSCT is still associated with significant risks of graft failure or GVHD that can lead to death. Transplantation of autologous hematopoietic stem cells genetically modified to express the missing protein may circumvent the majority of the problems associated with allogeneic HSCT. Promising in concept, these strategies are now at a stage to be tested in phase I/II clinical trials to assess safety and potential efficacy.
Characterization of surface channel CCD image arrays at low light levels (1974)

The characterization of surface channel charge-coupled device line imagers with front-surface imaging, interline transfer, and 2-phase stepped oxide, silicon-gate CCD registers is presented. The analysis, design, and evaluation of 1/spl times/64 CCD line arrays are described in terms of their performance at low light levels. The authors describe the responsivity, resolution, spectral, and noise measurements on silicon-gate CCD sensors and CCD interline shift-registers. The influence of transfer inefficiency and electrical fat-zero insertion on resolution and noise is described at low light levels.
Albumin. 2. Guidelines for clinical use (1977)

PARTLY on the basis of the physiologic information given in part 1 and partly on the basis of empiric observations derived from uncontrolled clinical administration, it is believed pertinent to propose guidelines for the contemporary therapeutic use of albumin, an important plasma protein. The guidelines for this biologic are designed to assure appropriate use. Certain principles were followed in preparation of the recommendations. (1) It was believed that the selection of proper clinical circumstances for the therapeutic use of albumin should not be dictated by arbitrary or pragmatic restrictions but rather by the education of physicians in its normal physiologic function. (2) Although only a few specific disorders regularly require the use of albumin, a broad diversity of pathologic complications may justify its occasional use. (3) Many clinical disorders exist in which there is incomplete or conflicting data on the effectiveness of albumin therapy. (4) Still other disorders exist in
Structural features of the antibody-A chain linkage that influence the activity and stability of ricin A chain immunotoxins (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructural features of the antibody-A chain linkage that influence the activity and stability of ricin A chain immunotoxinsAlan J. Cumber, John H. Westwood, Raymond V. Henry, Geoffrey D. Parnell, Brian F. Coles, and Edward J. WawrzynczakCite this: Bioconjugate Chem. 1992, 3, 5, 397–401Publication Date (Print):September 1, 1992Publication History Published online1 May 2002Published inissue 1 September 1992https://pubs.acs.org/doi/10.1021/bc00017a007https://doi.org/10.1021/bc00017a007research-articleACS PublicationsRequest reuse permissionsArticle Views162Altmetric-Citations2LEARN 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
Nanoscale Morphological and Chemical Changes of High Voltage Lithium–Manganese Rich NMC Composite Cathodes with Cycling (2014)

Understanding the evolution of chemical composition and morphology of battery materials during electrochemical cycling is fundamental to extending battery cycle life and ensuring safety. This is particularly true for the much debated high energy density (high voltage) lithium-manganese rich cathode material of composition Li(1 + x)M(1 - x)O2 (M = Mn, Co, Ni). In this study we combine full-field transmission X-ray microscopy (TXM) with X-ray absorption near edge structure (XANES) to spatially resolve changes in chemical phase, oxidation state, and morphology within a high voltage cathode having nominal composition Li1.2Mn0.525Ni0.175Co0.1O2. Nanoscale microscopy with chemical/elemental sensitivity provides direct quantitative visualization of the cathode, and insights into failure. Single-pixel (∼ 30 nm) TXM XANES revealed changes in Mn chemistry with cycling, possibly to a spinel conformation and likely including some Mn(II), starting at the particle surface and proceeding inward. Morphological analysis of the particles revealed, with high resolution and statistical sampling, that the majority of particles adopted nonspherical shapes after 200 cycles. Multiple-energy tomography showed a more homogeneous association of transition metals in the pristine particle, which segregate significantly with cycling. Depletion of transition metals at the cathode surface occurs after just one cycle, likely driven by electrochemical reactions at the surface.
Structures of prokaryotic ribosomal proteins: implications for RNA binding and evolution (1995)

After a long hiatus, the pace of determination of the structures of ribosomal proteins has accelerated dramatically. We discuss here the structures of five ribosomal proteins from Bacillus stearothermophilus: S5, S17, L6, L9, and L14. These structures represent several new motifs. Each of these structures has revealed new insights, and we have developed criteria for recognizing RNA-binding regions of each protein and correlating the structures with such properties as antibiotic resistance. The information here should also prove invaluable in an eventual high-resolution picture of the intact ribosome.
PCR engineering of viral quasispecies: a new method to preserve and manipulate genetic diversity of RNA virus populations (1996)

A PCR-based method for the controlled manipulation of individual genomic sites of poliovirus with concomitant preservation of the sequence heterogeneity of the rest of the genome is proposed. The new approach can be used for the creation of stable DNA repositories of populations of extremely heterogenous RNA viruses and may have implications for live vaccine technology.
Megakaryocyte morphogenesis stimulated in vitro by whole and partially fractionated thrombocytopenic plasma: a model system for the study of platelet formation (1987)

Isolated guinea pig megakaryocytes were cultured in the presence of plasma from normal or thrombocytopenic rabbits. Thrombocytopenic but not normal plasma stimulated formation of long cytoplasmic processes and cytoplasmic fragmentation. Activity was found in the 60% to 80% ammonium sulfate fraction of thrombocytopenic plasma but not in the 0% to 60% fraction. The 60% to 80% fraction of normal plasma contained a small amount of activity. Both colchicine and vincristine inhibited the morphogenesis stimulated by thrombocytopenic plasma. Cytochalasin B and D both mimicked the thrombocytopenic plasma-induced morphological change and affected more megakaryocytes than did the thrombocytopenic plasma. Cytochalasin and thrombocytopenic plasma together had a synergistic effect, causing many megakaryocytes to form processes and break into cytoplasmic fragments 3 to 6 microns in diameter. Immunofluorescence staining with antitubulin antiserum showed that cytoplasmic processes formed in the presence of thrombocytopenic plasma contain microtubules and that fragments released by the megakaryocytes contain microtubule rings. A model for the cytoskeletal basis of platelet formation is proposed.
Ultrasound Assessment of Subcutaneous Abdominal Fat Thickness After Treatments With a High-Intensity Focused Electromagnetic Field Device: A Multicenter Study (2019)

Based on the ultrasonographic and photographic observations, the authors conclude that the application of an HIFEM field is an effective option for the noninvasive treatment of subcutaneous fat.
Applications of Game Theory in Ad Hoc Networks (2003)

Ad hoc networks are an emerging networking technology, in which the terminals form a network without any fixed infrastructure. The operation of the network is based on cooperation. Each node forwards traffic of the others. While real life applications have not become common, ad hoc networks are predicted to be applied for example in emergency and rescue operations and military environment. Game theory deals with multiperson decision making, in which each decision maker tries to maximize his utility. Game theory originates from economics, but it has been applied in various fields. In this thesis, we introduce the basic concepts of game theory and its applications in telecommunications. The cooperation of the users is crucial to the operation of ad hoc networks, hence game theory provides a good basis to analyze the networks. We analyze the relationship between a node and the rest of the network from the energy efficiency perspective using game theory. We study how much forwarding effort the network can demand from the node, while it is still beneficial for the node to join the network. We study a situation in which the node either connects to the network or not and a situation in which the node can join the network without participating in the routing in order to save energy. We simulate networks in order to study the characteristics of the nodes that lose energy when joining the network. We examine the number and locations of the nodes losing energy.
Non-data aided timing acquisition of ultra-wideband transmissions using cyclostationarity (2004)

Low-complexity rapid timing acquisition constitutes a major challenge in realizing the high potential that ultra-wideband (UWB) wireless technology promises for indoor communications. We derive and test two such timing acquisition algorithms which capitalize on the cyclostationarity that is naturally present in UWB transmissions. Our novel schemes are blind, they do not require multiple antennas or oversampling, and rely on frame-rate sampling which reduces complexity and acquisition delay considerably.
Importance of mycoloyltransferases on the physiology of Corynebacterium glutamicum (2003)

Mycoloyltransferases (Myts) play an essential role in the biogenesis of the cell envelope of members of the Corynebacterineae, a group of bacteria that includes the mycobacteria and corynebacteria. While the existence of several functional myt genes has been demonstrated in both mycobacteria and corynebacteria (cmyt), the disruption of any of these genes has at best generated cell-wall-defective but always viable strains. To investigate the importance of Myts on the physiology of members of the Corynebacterineae, a double mutant of Corynebacterium glutamicum was constructed by deleting cmytA and cmytB, and the consequences of the deletion on the viability of the mutant, the transfer of corynomycoloyl residues onto its cell-wall arabinogalactan and trehalose derivatives, and on its cell envelope ultrastructure were determined. The double mutant strain failed to grow at 34 degrees C and exhibited a growth defect and formed segmentation-defective cells at 30 degrees C. Biochemical analyses showed that the double mutant elaborated 60 % less cell-wall-bound corynomycolates and produced less crystalline surface layer proteins associated with the cell surface than the parent and cmytA-inactivated mutant strains. Freeze-fracture electron microscopy showed that the DeltacmytA DeltacmytB double mutant, unlike the wild-type and cmytA-inactivated single mutant strains, frequently exhibited an additional fracture plane that propagated within the plasma membrane and rarely exposed the S-layer protein. Ultra-thin sectioning of the double mutant cells showed that they were totally devoid of the outermost layer. Complementation of the double mutant with the wild-type cmytA or cmytB gene restored completely or partially this phenotype. The data indicate that Myts are important for the physiology of C. glutamicum and reinforce the concept that these enzymes would represent good targets for the discovery of new drugs against the pathogenic members of the Corynebacterineae.
Adapting Fluorescence Resonance Energy Transfer with Quantum Dot Donors for Solid-Phase Hybridization Assays in Microtiter Plate Format (2013)

Methods have been developed for the solid-phase detection of nucleic acids using mixed films of quantum dots (QDs) and oligonucleotide probes in microtiter plates. Polystyrene microwells were functionalized with multidentate imidazole ligands to immobilize QDs. Oligonucleotide hybridization was transduced using QDs as donors in fluorescence resonance energy transfer (FRET). One detection channel paired green-emitting QD donors with Cy3 acceptors and served as an internal standard. A second detection channel paired red-emitting QDs with Alexa Fluor 647 acceptors and served as the primary detection channel. A selective assay for multiple targets was demonstrated using a 96-well plate format, which combined the advantages of two-plex QD-FRET with the high-throughput capability and convenience of microtiter plates. The assay had excellent resistance to the nonspecific adsorption of DNA and discriminated between fully complementary and single base-pair mismatched sequences with a contrast ratio >2. Under optimal conditions for a single color (green QD) assay format, the limit of detection (LOD) was 4 nM, and the dynamic range was from 20 to 300 nM. In a two-color assay, the detection channel (red QD) exhibited linear response between 4 and 100 nM and a LOD of 4 nM.
Development of a stress response therapy targeting aggressive prostate cancer (2018)

Oncogenic lesions up-regulate bioenergetically demanding cellular processes, such as protein synthesis, to drive cancer cell growth and continued proliferation. However, the hijacking of these key processes by oncogenic pathways imposes onerous cell stress that must be mitigated by adaptive responses for cell survival. The mechanism by which these adaptive responses are established, their functional consequences for tumor development, and their implications for therapeutic interventions remain largely unknown. Using murine and humanized models of prostate cancer (PCa), we show that one of the three branches of the unfolded protein response is selectively activated in advanced PCa. This adaptive response activates the phosphorylation of the eukaryotic initiation factor 2-α (P-eIF2α) to reset global protein synthesis to a level that fosters aggressive tumor development and is a marker of poor patient survival upon the acquisition of multiple oncogenic lesions. Using patient-derived xenograft models and an inhibitor of P-eIF2α activity, ISRIB, our data show that targeting this adaptive brake for protein synthesis selectively triggers cytotoxicity against aggressive metastatic PCa, a disease for which presently there is no cure.
A novel role of metalloproteinase in cancer-mediated immunosuppression. (2001)

Depressed immune responses have been observed frequently in cancer patients. In a variety of human malignancies, the expression of interleukin-2 receptor alpha (IL-2R alpha) on activated tumor-infiltrating lymphocytes was down-regulated. Because IL-2R alpha plays a pivotal role in the development and propagation of functional T cells, its depressed expression may result in poor function of tumor-reactive cytotoxic lymphocytes. For elucidating the mechanism responsible for down-regulation of IL-2R alpha, a coculture model of in vitro mixed autologous lymphocytes and tumor cells was established. Kinetic analysis showed that cervical cancer cells down-regulated IL-2R alpha expression on encountered T cells. The amount of IL-2R alpha mRNA in tumor-infiltrating lymphocytes-derived CD8+ T cells was compatible with that in the corresponding activated CD8+ T cells. Additional evidence showed that cervical cancer cells could induce the release of soluble IL-2R alpha expression on encountered T cells. By using protease inhibition assays we demonstrated that tissue inhibitors of metalloproteinase abrogated the cancer-mediated IL-2R alpha proteolytic process and restored the T-cell proliferation function. Immunohistochemical stainings further revealed prominent metalloproteinase (MMP) expressions, including MMP-1, MMP-2, and MMP-9, in cervical cancer tissues. Additional in vitro studies showed that MMP-9 mediates cleavage of IL-2R alpha and down-regulates the proliferative capability of cancer-encountered T cells. Our findings suggest a new role of MMPs in tumor-mediated immunosuppression and provide a possible therapeutic potential for patients with cervical cancer.
Evidence for the Presence of the Ascorbate-Glutathione Cycle in Mitochondria and Peroxisomes of Pea Leaves (1997)

The presence of the enzymes of the ascorbate-glutathione cycle was investigated in mitochondria and peroxisomes purified from pea (Pisum sativum L.) leaves. All four enzymes, ascorbate peroxidase (APX; EC 1.11.1.11), monodehydroascorbate reductase (EC 1.6.5.4), dehydroascorbate reductase (EC 1.8.5.1), and glutathione reductase (EC 1.6.4.2), were present in mitochondria and peroxisomes, as well as in the antioxidants ascorbate and glutathione. The activity of the ascorbate-glutathione cycle enzymes was higher in mitochondria than in peroxisomes, except for APX, which was more active in peroxisomes than in mitochondria. Intact mitochondria and peroxisomes had no latent APX activity, and this remained in the membrane fraction after solubilization assays with 0.2 M KCl. Monodehydroascorbate reductase was highly latent in intact mitochondria and peroxisomes and was membrane-bound, suggesting that the electron acceptor and donor sites of this redox protein are not on the external side of the mitochondrial and peroxisomal membranes. Dehydroascorbate reductase was found mainly in the soluble peroxisomal and mitochondrial fractions. Glutathione reductase had a high latency in mitochondria and peroxisomes and was present in the soluble fractions of both organelles. In intact peroxisomes and mitochondria, the presence of reduced ascorbate and glutathione and the oxidized forms of ascorbate and glutathione were demonstrated by high-performance liquid chromatography analysis. The ascorbate-glutathione cycle of mitochondria and peroxisomes could represent an important antioxidant protection system against H2O2 generated in both plant organelles.