gebhart/patrepeval huggingface dataset:
Characterization and expression of the unique calmodulin gene of Aspergillus nidulans. (1990)

Complete cDNA and genomic clones for the unique calmodulin (CaM) gene of the filamentous fungus Aspergillus nidulans have been isolated and characterized. The gene contains five introns, of which three are at unique positions relative to other CaM genes. The A. nidulans CaM gene is transcribed as a single, 0.85-kilobase mRNA species that encodes a predicted protein 84% identical (93% similar if conservative changes are considered) to vertebrate CaM. The complete cDNA was ligated into a lambda PL promoter-regulated bacterial expression vector to allow expression of A. nidulans CaM in Escherichia coli. The expressed protein was purified from bacterial lysates by phenyl-Sepharose chromatography and migrated as a single species on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. In the presence of Ca2+, A. nidulans CaM exhibited a shift in apparent Mr identical to vertebrate CaM. The bacterially synthesized protein activated vertebrate CaM-dependent phosphodiesterase, CaM-dependent protein kinase II, and myosin light chain kinase with kinetics similar to vertebrate CaM. Isolated conidia (G0 spores) were germinated to induce synchronous cell cycle re-entry and the levels of CaM mRNA and protein determined. Both CaM and its mRNA were regulated during cell cycle re-entry. Calmodulin mRNA levels increased 20-fold as germlings progressed through the G1 phase, while CaM levels increased 2-fold prior to the initiation of DNA synthesis. Messenger RNA levels decreased during S-phase while protein levels increased an additional 2-fold, peaking at the onset of mitosis followed by a subsequent decrease as cells completed mitosis. Disruption of the CaM gene by site-specific homologous recombination was lethal, indicating that CaM is essential for cell cycle progression.
Band gap engineering and stimulated emission of ZnMgO nanowires (2006)

We report a simple method for fabricating heterostructured ZnMgO nanowires by annealing the preformed ZnO∕MgO core-shell structure. Photoluminescence from the alloy nanowires shows strong near-band-edge (NBE) emission, reflecting good material quality. A blueshift of the NBE emission at room temperature after the annealing treatment is attributed to the diffusion of Mg from the shell into the core ZnO of the nanowires to form a ternary ZnMgO alloy. Band gap engineering and stimulated emissions of ZnMgO nanowires with different Mg doping concentrations are also demonstrated.
Coverage optimized planning: Probabilistic treatment planning based on dose coverage histogram criteria (2010)

This work (i) proposes a probabilistic treatment planning framework, termed coverage optimized planning (COP), based on dose coverage histogram (DCH) criteria; (ii) describes a concrete proof-of-concept implementation of COP within the PINNACLE treatment planning system; and (iii) for a set of 28 prostate anatomies, compares COP plans generated with this implementation to traditional PTV-based plans generated with planning criteria approximating those in the high dose arm of the Radiation Therapy Oncology Group 0126 protocol. Let Dv denote the dose delivered to fractional volume v of a structure. In conventional intensity modulated radiation therapy planning, Dv has a unique value derived from the static (planned) dose distribution. In the presence of geometric uncertainties (e.g., setup errors) Dv assumes a range of values. The DCH is the complementary cumulative distribution function of D(v+). DCHs are similar to dose volume histograms (DVHs). Whereas a DVH plots volume v versus dose D, a DCH plots coverage probability Q versus D. For a given patient, Q is the probability (i.e., percentage of geometric uncertainties) for which the realized value of Dv exceeds D. PTV-based treatment plans can be converted to COP plans by replacing DVH optimization criteria with corresponding DCH criteria. In this approach, PTVs and planning organ at risk volumes are discarded, and DCH criteria are instead applied directly to clinical target volumes (CTVs) or organs at risk (OARs). Plans are optimized using a similar strategy as for DVH criteria. The specific implementation is described. COP was found to produce better plans than standard PTV-based plans, in the following sense. While target OAR dose tradeoff curves were equivalent to those for PTV-based plans, COP plans were able to exploit slack in OAR doses, i.e., cases where OAR doses were below their optimization limits, to increase target coverage. Specifically, because COP plans were not constrained by a predefined PTV, they were able to provide wider dosimetric margins around the CTV, by pushing OAR doses up to, but not beyond, their optimization limits. COP plans demonstrated improved target coverage when averaged over all 28 prostate anatomies, indicating that the COP approach can provide benefits for many patients. However, the degree to which slack OAR doses can be exploited to increase target coverage will vary according to the individual patient anatomy. The proof-of-concept COP implementation investigated here utilized a probabilistic DCH criteria only for the CTV minimum dose criterion. All other optimization criteria were conventional DVH criteria. In a mature COP implementation, all optimization criteria will be DCH criteria, enabling direct planning control over probabilistic dose distributions. Further research is necessary to determine the benefits of COP planning, in terms of tumor control probability and/or normal tissue complication probabilities.
Active learning system for object fingerprinting (2005)

Object fingerprinting and identification is a critical part of effective visual surveillance systems. In this paper, we present an approach to actively learn the object models in order to fingerprint the objects. Our approach uses a view-based classifier cascade that actively learns to recognize the generic class of the object. Salient features unique to the specific instance of the selected class of objects are modeled using fuzzy attribute relational graphs. These graphs are also adapted to represent object information gathered from multiple views. Preliminary results are quite promising and extensive studies are underway to ascertain the use of the system in more complicated scenarios.
DAQ (2015)

Many modern applications deal with exponentially increasing data volumes and aid business-critical decisions in near real-time. Particularly in exploratory data analysis, the focus is on interactive querying and some degree of error in estimated results is tolerable. A common response to this challenge is approximate query processing, where the user is presented with a quick confidence interval estimate based on a sample of the data. In this work, we highlight some of the problems that are associated with this probabilistic approach when extended to more complex queries, both in semantic interpretation and the lack of a formal algebra. As an alternative, we propose deterministic approximate querying (DAQ) schemes, formalize a closed deterministic approximation algebra, and outline some design principles for DAQ schemes. We also illustrate the utility of this approach with an example deterministic online approximation scheme which uses a bitsliced index representation and computes the most significant bits of the result first. Our prototype scheme delivers speedups over exact aggregation and predicate evaluation, and outperforms sampling-based schemes for extreme value aggregations.
Enoyl‐CoA Hydratase: Reaction, Mechanism, and Inhibition (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
The Effect of Glucocorticoids on Joint Destruction in Rheumatoid Arthritis (1995)

In patients with early, active rheumatoid arthritis, prednisolone (7.5 mg daily) given for two years in addition to other treatments substantially reduced the rate of radiologically detected progression of disease.
An Analysis of Polyethylene Thickness in Modular Total Knee Components (1991)

Polyethylene wear has become an important consideration in total knee arthroplasty. The actual polyethylene thickness of modular tibial components is not widely known and may be critical to long-term survival of implants. The actual polyethylene thickness of eight widely used tibial components was measured and found to vary significantly among manufacturers, even though the combined thickness of metal tray and polyethylene was similar. No component met current recommendations for minimum polyethylene thickness.
Adolescent Psychology Around the World (2012)

This book paints a portrait of adolescent psychology in 4 major regions: Africa/the Middle East, Asia, the Americas, and Europe. Featuring 24 revised and updated chapters from the International Encyclopedia of Adolescence (2007), readers are introduced to the way the majority of the world's adolescents actually live. Most contributors are indigenous to the country they review. As a whole the book paints an engaging panorama of adolescent life around the world, broadening students' cultural perspective.
Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry (2013)

This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N'H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.
An iron-regulated sortase anchors a class of surface protein during Staphylococcus aureus pathogenesis (2002)

Sortase (SrtA), an enzyme that anchors surface proteins to the cell wall of Gram-positive bacteria, cleaves sorting signals at the LPXTG motif. We have identified a second sortase (SrtB) in the Gram-positive pathogen Staphylococcus aureus that is required for anchoring of a surface protein with a NPQTN motif. Purified SrtB cleaves NPQTN-bearing peptides in vitro, and a srtB mutant is defective in the persistence of animal infections. srtB is part of an iron-regulated locus called iron-responsive surface determinants (isd), which also contains a ferrichrome transporter and surface proteins with NPQTN and LPXTG motifs. Cell wall-anchored surface proteins and the isd locus seem involved in a novel mechanism of iron acquisition that is important for bacterial pathogenesis.
Fusion Splicing Photonic Crystal Fibers and Conventional Single-Mode Fibers: Microhole Collapse Effect (2007)

We investigate the microhole collapse property of different photonic crystal fibers (PCFs) and its effect on the splice loss using an electric arc fusion splicer. The physical mechanism of the splice loss for different kinds of PCFs is studied, and a guideline for splicing these PCFs and conventional single-mode fibers (SMFs) is proposed. We demonstrate a low-loss fusion splicing of five different PCFs with SMFs, including large-mode PCF, hollow-core PCF, nonlinear PCFs, and polarization-maintaining PCF.
Conformation of Factor VIIa Stabilized by a Labile Disulfide Bond (Cys-310–Cys-329) in the Protease Domain Is Essential for Interaction with Tissue Factor (1997)

Unlike other trypsin-type serine proteases, zymogento-enzyme transition of conformation of factor VII apparently requires not only conversion of the zymogen to active form factor VIIa (VIIa) but also interaction of VIIa with tissue factor (TF). To determine the region of interaction that correlates with maturation of the VIIa active site, we modified intramolecular disulfide bonds in VIIa and examined the interaction of the modified VIIa with soluble TF (sTF). We found that partial reduction and S-carboxamidomethylation of disulfide bonds in VIIa led to losses of amidolytic activity and the binding ability to sTF. To determine the sites of modification that associate with the loss of functions, partially S-carboxamidomethylated VIIa was separated on a column of immobilized sTF. Each of the sTF-bound and sTF-unbound fractions and native VIIa was then digested by trypsin, and the digest was analyzed by reversed-phase high performance liquid chromatography. We found that reduction and S-carboxamidomethylation of a disulfide bond between Cys-310 and Cys-329 in the protease domain of VIIa led to loss of the binding ability with sTF, and the modification of a disulfide bond between Cys-340 and Cys-368 of VIIa led to loss of the amidolytic activity. In the three-dimensional structures of trypsinogen and trypsin, the disulfide bonds corresponding to Cys-340-Cys-368 and Cys-310-Cys-329 of VIIa are, respectively, in and adjacent to the activation domain, which has flexible conformation in trypsinogen but not in trypsin. Furthermore, the crystal structure of human VIIa.TF complex indicates that the region next to Cys-310-Cys-329 is in contact with sTF. We speculate that a regional flexibility, reflected by the labile nature of disulfide bonds of Cys-310-Cys-329 and Cys-340-Cys-368 in the protease domain, contributes to the inability of VIIa to attain the active conformation. Interaction of TF with this flexible region may stabilize the structure in a conformation similar to that of the active state of VIIa.
Effect of Age on Directional Microphone Hearing Aid Benefit and Preference (2010)

These results indicate that although listeners of different ages may obtain and perceive comparable benefit from DMHAs in laboratory testing, older users tend to perceive less benefit than do younger users in the real world. The implications of these findings are discussed.
Semiconductor Nanowires for Energy Conversion (2009)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTSemiconductor Nanowires for Energy ConversionAllon I. Hochbaum*† and Peidong Yang*View Author Information Department of Chemistry, University of California, Berkeley, California 94720 and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720* To whom correspondence should be addressed. E-mail: [email protected] (A.H.), [email protected] (P.Y.).†Current address: School of Engineering and Applied Sciences and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138.Cite this: Chem. Rev. 2010, 110, 1, 527–546Publication Date (Web):October 9, 2009Publication History Received26 February 2009Published online9 October 2009Published inissue 13 January 2010https://pubs.acs.org/doi/10.1021/cr900075vhttps://doi.org/10.1021/cr900075vreview-articleACS PublicationsCopyright © 2009 American Chemical SocietyRequest reuse permissionsArticle Views26050Altmetric-Citations1283LEARN 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 SUBJECTS:Electrodes,Nanoparticles,Nanowires,Silicon,Solar cells Get e-Alerts
The C‐Terminal Domain V of Perlecan Promotes β1 Integrin‐Mediated Cell Adhesion, Binds Heparin, Nidogen and Fibulin‐2 and Can be Modified by Glycosaminoglycans (1997)

Domain V of the major basement-membrane proteoglycan perlecan, a domain which consists of three laminin type G (LG) and four epidermal-growth-factor-like (EG) modules, was obtained in recombinant form by transfecting embryonic kidney cells with an episomal expression vector. A major 90-kDa fragment V was obtained together with fragments Va (74 kDa) and Vb (26 kDa) which were generated by endogenous proteolysis in front of the most C-terminal LG module. All three fragments bound to a heparin affinity column and could be displaced at a moderate (0.2 M) NaCl concentration. Rotary-shadowing electron microscopy demonstrated a three-globule structure for fragment V. Fragment V also showed a strong immunological cross-reaction with tissue-derived perlecan, indicating that it was folded into a native structure. A further, larger fragment, Vc, was apparently substituted with heparan sulphate and/or chondroitin sulphate chains and failed to bind to heparin. Fragment V but not fragment Vc promoted a distinct adhesion of several cell lines and this could be blocked by antibodies against the integrin beta1 chain. This domain may, however, represent only one of several cell-adhesive sites of perlecan. The recombinant perlecan fragment V bound in surface plasmon resonance assays to fibulin-2, laminin-nidogen complex, nidogen and two nidogen fragments. This indicated two different nidogen-binding epitopes on perlecan domain V with about a 10-fold difference in their affinities (Kd = 0.05-0.2 microM and about 2 microM). Perlecan domain V therefore seems to participate in the supramolecular assembly and cell connections of basement membranes.
TRM-IoT: A trust management model based on fuzzy reputation for internet of things (2011)

Since a large scale Wireless Sensor Network (WSN) is to be completely integrated into Internet as a core part of Internet of Things (IoT) or Cyber Physical System (CPS), it is necessary to consider various security challenges that come with IoT/CPS, such as the detection of malicious attacks. Sensors or sensor embedded things may establish direct communication between each other using 6LoWPAN protocol. A trust and reputation model is recognized as an important approach to defend a large distributed sensor networks in IoT/CPS against malicious node attacks, since trust establishment mechanisms can stimulate collaboration among distributed computing and communication entities, facilitate the detection of untrustworthy entities, and assist decision-making process of various protocols. In this paper, based on in-depth understanding of trust establishment process and quantitative comparison among trust establishment methods, we present a trust and reputation model TRM-IoT to enforce the cooperation between things in a network of IoT/CPS based on their behaviors. The accuracy, robustness and lightness of the proposed model is validated through a wide set of simulations.
The Relationship between the Myelodysplastic Syndromes and the Myeloproliferative Disorders (1999)

As a result of clonal evolution typical cases of one of the myelodysplastic syndromes may develop myeloproliferative features. Similarly, typical cases of one of the myeloproliferative disorders may develop dysplastic features, either as part of the natural history of the disease or as a result of exposure to mutagenic drugs or isotopes. There is also an important group of "overlap syndromes" in which cases, at presentation, have both dysplastic and proliferative features. Chronic myelomonocytic leukaemia and many cases of atypical chronic myeloid leukaemia, juvenile chronic myeloid leukaemia and the childhood monosomy 7 syndrome are "overlap syndromes". In addition, a significant minority of cases which fit the generally agreed criteria for a diagnosis of one of the myelodysplastic syndromes (refractory anaemia, refractory anaemia with ring sideroblasts or refractory anaemia with excess of blasts) also have thrombocytosis, neutrophilia, monocytosis, eosinophilia or basophilia.
Controlled Extracellular Matrix Degradation in Breast Cancer Tumors Improves Therapy by Trastuzumab (2010)

Extracellular matrix (ECM) in solid tumors affects the effectiveness of therapeutics through blocking of intratumoral diffusion and/or physical masking of target receptors on malignant cells. In immunohistochemical studies of tumor sections from breast cancer patients and xenografts, we observed colocalization of ECM proteins and Her2/neu, a tumor-associated antigen that is the target for the widely used monoclonal antibody trastuzumab (Herceptin). We tested whether intratumoral expression of the peptide hormone relaxin (Rlx) would result in ECM degradation and the improvement of trastuzumab therapy. As viral gene delivery into epithelial tumors with extensive tumor ECM is inefficient, we used a hematopoietic stem cell (HSC)-based approach to deliver the Rlx gene to the tumor. In mouse models with syngeneic breast cancer tumors, HSC-mediated intratumoral Rlx expression resulted in a decrease of ECM proteins and enabled control of tumor growth. Moreover, in a model with Her2/neu-positive BT474-M1 tumors and more treatment-refractory tumors derived from HCC1954 cells, we observed a significant delay of tumor growth when trastuzumab therapy was combined with Rlx expression. Our results have implications for antibody therapy of cancer as well as for other anticancer treatment approaches that are based on T-cells or encapsulated chemotherapy drugs.
Functional and biochemical characterizations of avian T lymphocyte antigens identified by monoclonal antibodies (1988)

Seven monoclonal antibodies (mAb) were used to characterize antigens present on chicken T lymphocytes and on natural killer cells by flow cytometry, radioimmunoprecipitation and by effects on cell-mediated cytotoxicity and mitogen-induced proliferation. mAb CTLA8 and 5 stained 73% of thymus, 44% of spleen and 51% of peripheral blood lymphocytes (PBL), respectively, and immunoprecipitated 65- and 45-kDa proteins from detergent extracts of 125I surface-labeled thymocytes. Pretreatment of splenic lymphocytes with mAb CTLA5 and 8 in the presence of rabbit complement (C) eliminated the concanavalin A (Con A)-induced T cell proliferative responses. mAb CTLA3, 4 and 9 stained 43% of thymus, 36% of spleen and 18% of PBL, and immunoprecipitated 33-35-kDa proteins. Pretreatment of spleen cells with mAb 4 or 9 plus C reduced, but did not eliminate, the Con A-induced proliferative response and significantly reduced both major histocompatibility complex (MHC)-restricted and non-MHC-restricted cellular cytotoxicity. mAb CTLA1 and 6 stained 58% of thymus, 13% of spleen and 19% of PBL. mAb CTLA1 and 6 immunoprecipitated a 65-kDa protein. mAb CTLA1 and 6 had no effect on the Con A-induced blastogenesis and CTLA6 caused no decrease in virus-specific cytotoxic T lymphocyte and natural killer activity. These results indicate that (a) mAb CTLA5 and 8 identify antigens on mature T lymphocytes that are similar in tissue distribution, molecular mass and function to the mammalian CD5 antigen; (b) mAb CTLA3, 4 and 9 detect the avian homologue of CD8 antigen; and (c) mAb CTLA1 and 6 identify the avian homologue of CD4 antigen.