gebhart/patrepeval huggingface dataset:
Tailor-Making a Protein A-Derived Domain for Efficient Site-Specific Photocoupling to Fc of Mouse IgG1 (2013)

Affinity proteins binding to antibody constant regions have proved to be invaluable tools in biotechnology. Here, protein engineering was used to expand the repertoire of available immunoglobulin binding proteins via improvement of the binding strength between the widely used staphylococcal protein A-derived Z domain and the important immunoglobulin isotype mouse IgG₁ (mIgG₁). Addressing seven positions in the 58-residue three-helix bundle Z domain by single or double amino acid substitutions, a total of 170 variants were individually constructed, produced in E. coli and tested for binding to a set of mouse IgG₁ monoclonal antibodies (mAbs). The best variant, denoted Z(F5I) corresponding to a Phe to Ile substitution at position 5, showed a typical ten-fold higher affinity than the wild-type as determined by biosensor technology. Eight amino acid positions in the Z(F5I) variant were separately mutated to cysteine for incorporation of a photoactivable maleimide-benzophenone (MBP) group as a probe for site-specific photoconjugation to Fc of mIgG₁, The best photocoupling efficiency to mIgG₁ Fc was seen when the MBP group was coupled to Cys at position 32, resulting in adduct formation to more than 60% of all heavy chains, with no observable non-selective conjugation to the light chains. A similar coupling yield was obtained for a panel of 19 different mIgG₁ mAbs, indicating a general characteristic. To exemplify functionalization of a mIgG₁ antibody via site-specific biotinylation, the Z(F5I-Q32C-MBP) protein was first biotinylated using an amine reactive reagent and subsequently photoconjugated to an anti-human interferon-gamma mIgG₁ mAb. When comparing the specific antigen binding ability of the probe-biotinylated mAb to that of the directly biotinylated mAb, a significantly higher bioactivity was observed for the sample biotinylated using the Z(F5I-Q32C-MBP) probe. This result indicates that the use of a site-specific and affinity probe-mediated conjugation strategy can result in antibody reagents with increased assay sensitivity.
An estimate of the total number of true human miRNAs (2019)

While the number of human miRNA candidates continuously increases, only a few of them are completely characterized and experimentally validated. Toward determining the total number of true miRNAs, we employed a combined in silico high- and experimental low-throughput validation strategy. We collected 28 866 human small RNA sequencing data sets containing 363.7 billion sequencing reads and excluded falsely annotated and low quality data. Our high-throughput analysis identified 65% of 24 127 mature miRNA candidates as likely false-positives. Using northern blotting, we experimentally validated miRBase entries and novel miRNA candidates. By exogenous overexpression of 108 precursors that encode 205 mature miRNAs, we confirmed 68.5% of the miRBase entries with the confirmation rate going up to 94.4% for the high-confidence entries and 18.3% of the novel miRNA candidates. Analyzing endogenous miRNAs, we verified the expression of 8 miRNAs in 12 different human cell lines. In total, we extrapolated 2300 true human mature miRNAs, 1115 of which are currently annotated in miRBase V22. The experimentally validated miRNAs will contribute to revising targetomes hypothesized by utilizing falsely annotated miRNAs.
Spatial Sensing in Fibroblasts Mediated by 3′ Phosphoinositides (2000)

The directed movement of fibroblasts towards locally released platelet-derived growth factor (PDGF) is a critical event in wound healing. Although recent studies have implicated polarized activation of phosphoinositide (PI) 3-kinase in G protein-mediated chemotaxis, the role of 3' PI lipids in tyrosine kinase-triggered chemotaxis is not well understood. Using evanescent wave microscopy and green fluorescent protein-tagged Akt pleckstrin homology domain (GFP-AktPH) as a molecular sensor, we show that application of a shallow PDGF gradient triggers a markedly steeper gradient in 3' PI lipids in the adhesion zone of fibroblasts. Polar GFP-AktPH gradients, as well as a new type of radial gradient, were measured from front to rear and from the periphery to the center of the adhesion zone, respectively. A strong spatial correlation between polarized 3' PI production and rapid membrane spreading implicates 3' PI lipids as a direct mediator of polarized migration. Analysis of the temporal changes of 3' PI gradients in the adhesion zone revealed a fast diffusion coefficient (0.5 microm(2)/s) and short lifetime of 3' PIs of <1 min. Together, this study suggests that the tyrosine kinase-coupled directional movement of fibroblasts and their radial membrane activity are controlled by local generation and rapid degradation of 3' PI second messengers.
Prognostic Value of the Preoperative CEA, CA15-3 and TPS Serum Levels in Patients with Breast Cancer (2007)

Purpose: Tumor markers are often used to monitor the response to therapy and to detect recurrences in patients with resected breast cancer. Here we evaluated the prognostic value of the preoperative serum concentrations of tumor markers in patients with breast cancer. Methods: The preoperative serum concentrations of tumor markers (CEA, CA15-3 and TPS) were measured in 670 patients who were treated via potentially curative surgical resection for breast cancer from 2001 to 2004. We investigated the association of the serum concentrations of tumor markers with the disease-free survival and overall survival at the time of the primary diagnosis in relation to the established prognostic factors such as tumor size, lymph node status, hormonal receptor status, age and menopausal status. Results: The established prognostic factors and the elevated preoperative serum tumor marker values were correlated with disease-free survival (CEA: P=0.014, CA15-3: P=0.002 and TPS: P＜0.001) and overall survival (CEA: P=0.045, CA15-3: P=0.002 and TPS: P＜0.001) on univariate analysis. On multivariate analysis, tumor size, lymph node status, hormone receptor status and TPS (P=0.03) were independent prognostic factors for recurrence and the lymph node status, hormone receptor status and TPS serum level (P＜0.001) were independent prognostic factors for overall survival. Conclusion: The preoperative serum concentrations of tumor makers (CEA, CA15-3 and TPS) are strong independent prognostic factors for recurrence and survival in patients with breast cancer. The tests for the preoperativeserum concentrations of tumor markers have convenient and reproducible advantages while the others require tumor tissue. Patients with elevated preoperative serum tumor marker values need appropriate adjuvant therapy, careful monitoring and detection of recurrences during the follow-up period. (J Korean Surg Soc 2007;73:21-26)
A novel focus monitoring method using double side chrome mask (2005)

In order to measure the focus control performance on exposure tools with high accuracy, we developed a novel focus monitoring method, entitled Z-SPIN. The features of this Z-SPIN method are the high resolution focus measurement accuracy of < 1nm and process robustness. We therefore began by quantitatively analyzing the issues exposure tools were having through the use of the Z-SPIN method. From this examination result, we demonstrate a robust focus control solution with Z-SPIN mask. In parallel, through the determination of the focus budget with the new focus control technique, a significant improvement of the focus performance on exposure tools is shown. Finally, by tightening focus control, we examined the viability of extending the lifetime of exposure tools as well as enabling device shrinking.
A 20-Mb/s Pulse Harmonic Modulation Transceiver for Wideband Near-Field Data Transmission (2013)

This brief presents a fully integrated low-power transceiver for wideband near-field data transmission across inductive telemetry links based on pulse harmonic modulation (PHM). This PHM transceiver uses two narrow pulses with specific amplitudes and timing at the transmitter (Tx) to suppress intersymbol interference (ISI) at the receiver (Rx) high-Q LC tank to achieve high data rates (DRs) without reducing the inductive link quality factor to extend its bandwidth. This method significantly improves the range and selectivity of the link. The PHM Rx architecture is based on noncoherent energy detection utilizing a novel pulse-based automatic gain control circuit, which significantly reduces the power consumption (46%) and ISI at short coupling distances. The PHM transceiver was fabricated in a 0.35- μm standard CMOS process and achieved a measured DR of 20 Mb/s with a bit error rate of 8.7×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-8</sup> at a 10-mm distance using planar figure-8 coils. The PHM Tx and Rx power consumptions were 180 and 12.15 pJ/bit, respectively, at a 1.8-V supply voltage.
Synthesis of Fragments of the Capsular Polysaccharide of<i>Haemophilus Influenzae</i>type b on Soluble Polymeric Support (1992)

An efficient method for the synthesis of fragments of the capsular polysaccharide of H. influenzae type b containing an aminoheptyl group by the phosphoramidite chemistry using polyethylene glycol monomethyl ether (PEG) as soluble polymeric support is described. The method is suitable for the preparation of pure oligomeric compounds on a relatively large scale.
Multi-objective evolution of the Pareto optimal set of neural network classifier ensembles (2009)

Existing research demonstrates that classifier ensembles can improve on the performance of the single ‘best’ classifier. However, for some problems, although the ensemble may obtain a lower classification error than any of the base classifiers, it may not provide the desired trade-off among the classification rates of different classes. In many applications, classes are not of equal importance, but the preferred trade-off may be hard to quantify a priori. In this paper, we adopt multi-objective techniques to create Pareto optimal sets of classifiers and ensembles, offering the user the choice of preferred trade-off. We also demonstrate that the common practice of developing a single ensemble from an arbitrary (diverse) selection of base classifiers will be inferior to a large proportion of those classifiers.
Materials Degradation Caused by Acid Rain (1986)

The acid rain studies which started with the OECD project 1972-77 have since become a major issue in both North America and Europe. The main cause is sulphuric and nitric acid from the use of fossil fuels. The resulting fish kills in acidified rivers and lakes depend on the soil composition and the release of toxic aluminium ions. This may also be a contributing factor to the forest damage in central Europe., but photochemical oxidants are now believed to be more important. Generally the acidification and the increasing oxidation potential of the atmosphere is slowly changing our chemical environment, and it is not known to what extent the resulting ecological changes will be reversed if the emissions are reduced.
A line sweep thinning algorithm (2002)

We propose a new thinning algorithm based on line sweep procedures. A line sweep is a process where the plane is divided into parallel slabs by lines passing through certain "events" and then items are processed according to an order of the slabs. Assuming that the contours of the object that are to be thinned have been approximated by polygons, the "events" are then the vertices of the polygons and the line sweep algorithm looks for pairs of polygon sides that lie within each slab. Since the procedure is applied in both horizontal and vertical direction, possible conflicts may exist among the pairs of polygon sides. A subsequent effort is to resolve the conflicts according to a few generic types into which they can be classified. After the conflict resolution, the object can be decomposed into the regions that can be represented by the skeletons computed from the pairs of polygon sides, and the regions that are the singular parts of the object. Both types of regions can be used as features for subsequent pattern recognition operations.
Glomerular T cells in Heymann nephritis (2001)

Summary Active Heymann nephritis (HN) is a rat model of human membranous nephropathy. The appearance of T cells within the glomeruli of HN rats suggests a role for these cells in the pathogenesis of the disease. The aims of this study were to investigate T cells infiltrating the glomerulus in HN in Lewis rats by polymerase chain reaction (PCR) of their Vβ chains, CDR3 spectratyping and sequencing. HN was induced in Lewis rats by immunization with renal tubular antigen (Fx1A) in CFA. Kidneys were collected between 4 and 10 weeks. The glomeruli were separated, homogenized and RNA extracted. RT-PCR, CDR3 spectratyping and sequencing were used to further characterize the infiltrating T cells. Multiple Vβ families showed restriction of their CDR3 spectratypes in each animal. Several TCR Vβ families had identical-sized restricted spectratypes across several different animals. Four Vβ families were sequenced. In three of those four families, the dominant clones showed identical sized CDR3 regions and a striking over-expression of Jβ2.6. Further analysis of the CDR3 regions of the Jβ2.6 clones showed a significant restriction of the amino acids at four of the six CDR3 positions. Glomerular T cells bearing similar CDR3 sequences, using Jβ2.6 and expressing at least two, and possibly more, Vβ genes are involved in the pathogenesis of HN.
Comparison of three TCC calculation algorithms for partially coherent imaging simulation (2010)

Three kinds of TCC (transmission cross coefficient) calculation algorithms used for partially coherent imaging simulation, including the integration algorithm, the analytical algorithm, and the matrix-based fast algorithm, are reviewed for their rigorous formulations and numerical implementations. The accuracy and speed achievable using these algorithms are compared by simulations conducted on several mainstream illumination sources commonly used in current lithographic tools. Simulation results demonstrate that the integration algorithm is quite accurate but time consuming, while the matrix-based fast algorithm is efficient but its accuracy is heavily dependent on simulation resolution. The analytical algorithm is both efficient and accurate but not suitable for arbitrary optical systems. It is therefore concluded that each TCC calculation algorithm has its pros and cons with a compromise necessary to achieve a balance between accuracy and speed. The observations are useful in fast lithographic simulation for aerial image modeling, optical proximity correction (OPC), source mask optimization (SMO), and critical dimension (CD) prediction.
Surface corrugation for broadband matching of windows in powerful microwave generators (1991)

Abstract Profiles and orientations of corrugated surfaces are described, which can be used to eliminate the reflection of microwaves from single-disc windows. The use of linear grooves which are perpendicular to each other on the two sides of the window allows easier manufacturing while not influencing the polarization of the transmitted waves.
IL-12 secreting tumor-targeted chimeric antigen receptor T cells eradicate ovarian tumors <i>in vivo</i> (2015)

A novel approach for the treatment of ovarian cancer includes immunotherapy with genetically engineered T cells targeted to ovarian cancer cell antigens. Using retroviral transduction, T cells can be created that express an artificial T cell receptor (TCR) termed a chimeric antigen receptor (CAR). We have generated a CAR, 4H11-28z, specific to MUC-16<sup>ecto</sup> antigen, which is the over-expressed on a majority of ovarian tumor cells and is the retained portion of MUC-16 after cleavage of CA-125. We previously demonstrated that T cells modified to express the 4H11-28z CAR eradicate orthotopic human ovarian cancer xenografts in SCID-Beige mice. However, despite the ability of CAR T cells to localize to tumors, their activation in the clinical setting can be inhibited by the tumor microenvironment, as is commonly seen for endogenous antitumor immune response. To potentially overcome this limitation, we have recently developed a construct that co-expresses both MUC16<sup>ecto</sup> CAR and IL-12 (4H11-28z/IL-12). <i>In vitro</i>, 4H11-28z/IL-12 CAR T cells show enhanced proliferation and robust IFNγ secretion compared to 4H11-28z CAR T cells. In SCID-Beige mice with human ovarian cancer xenografts, IL-12 secreting CAR T cells exhibit enhanced antitumor efficacy as determined by increased survival, prolonged persistence of T cells, and higher systemic IFNγ. Furthermore, in anticipation of translating these results into a phase I clinical trial which will be the first to study IL-12 secreting CAR T cells in ovarian cancer, an elimination gene has been included to allow for deletion of CAR T cells in the context of unforeseen or off-tumor on-target toxicity.
Staphylococcal enterotoxin B and toxic shock syndrome toxin-1 bind to distinct sites on HLA-DR and HLA-DQ molecules. (1989)

Staphylococcal enterotoxins (SE) activate human T cells in vitro. This requires the presence of Ia+ accessory cells but does not require processing of the toxin by the accessory cell. We and others have recently demonstrated direct binding of SE to human MHC class II molecules. In this study, we have compared in detail the ability of class II molecules to bind two SE, toxic shock syndrome toxin-1 (TSST-1) and SEB. Scatchard analysis of equilibrium binding data indicate that SEB binds to Ia+ human cell lines with a 10-fold lower affinity than TSST-1. Likewise, SEB precipitates HLA-DR alpha- and beta-chains from detergent lysates of Ia+ cells less efficiently than TSST-1. The binding of TSST-1 and SEB to transfected L cells expressing HLA-DR and HLA-DQ gene products was differentially inhibited by anti-HLA-DR mAb. There was virtually no cross-inhibition of TSST-1 and SEB in competitive binding assays. We conclude that TSST-1 and SEB bind to two MHC class II sites which can be distinguished by their relative accessibility to blocking by anti-class II mAb and heterologous toxin.
Temperature, modulation and reliability characteristics of 1.3 μm-VCSELs on InP with AlGaInAs/InP lattice matched DBR (2005)

Lasing operation up to 125 /spl deg/C of 1.3 /spl mu/m InP-based VCSELs with AlGaInAs/InP DBR has been demonstrated. A single mode power of 0.6 mW at 85 /spl deg/C, 10 Gbit/s transmission through 10 km and >2500 hours lifetime have been achieved.
Nanoparticles Biosynthesized by Fungi and Yeast: A Review of Their Preparation, Properties, and Medical Applications (2015)

In the field of nanotechnology, the use of various biological units instead of toxic chemicals for the reduction and stabilization of nanoparticles, has received extensive attention. Among the many possible bio resources, biologically active products from fungi and yeast represent excellent scaffolds for this purpose. Since fungi and yeast are very effective secretors of extracellular enzymes and number of species grow fast and therefore culturing and keeping them in the laboratory are very simple. They are able to produce metal nanoparticles and nanostructure via reducing enzyme intracellularly or extracellularly. The focus of this review is the application of fungi and yeast in the green synthesis of inorganic nanoparticles. Meanwhile the domain of biosynthesized nanoparticles is somewhat novel; the innovative uses in nano medicine in different areas including the delivery of drug, cancer therapy, antibacterial, biosensors, and MRI and medical imaging are reviewed. The proposed signaling pathways of nanoparticles induced apoptosis in cancerous cells and anti-angiogenesis effects also are reviewed. In this article, we provide a short summary of the present study universally on the utilization of eukaryotes like yeast and fungi in the biosynthesis of nanoparticles (NPs) and their uses.
High precision fluidic alignment of carbon nanotubes using magnetic attraction on a metal catalyst (2008)

Precise self-assembly of carbon nanotubes (CNTs) by magnetic attraction on a catalyst and alignment by fluidic shear forces is reported in this work. The solution containing dispersed nanotubes was flowed in a microchannel and external magnetic field was applied by a permanent magnet for attracting a metal catalyst located at the end of the CNT. The assembly procedure and electrical characterization of the assembled nanotubes are presented and results are discussed. This work can provide a potential breakthrough for creating massively parallel CNT circuits for high performance nano electronic devices or nano biosensors.
Anhydrobiosis in nematodes: Carbohydrate and lipid metabolism during dehydration (1975)

Abstract 1. Changes in the chemical composition of pellets of the nematode Aphelenchus avenae were studied as the worms experienced evaporative water loss during 72 hours at 97% RH. 2. Lipid content declines rapidly during the first 24 hours, and decreases to about 60% of the original by the end of 72 hours. 3. Glycogen content declines to about 50% of original by the end of 24 hours, and to 10% of original by 72 hours. 4. Glucose content remains constant. 5. Glycerol and trehalose contents both increase rapidly, reaching about 700% of the 24‐hour content by the end of 72 hours, in each case. 6. Strong correlations between survival in dry air and glycerol and trehalose contents were observed.
Ableitung der Hauptaufgaben (1990)

Das gegenwärtige Steuersystem ist durch eine große materielle Gewichtigkeit der aus ihm resultierenden Konsequenzen gekennzeichnet. Diese beruht auf der in aller Regel beträchtlichen Höhe der Steuerbelastung , die jede einzelne Steuerart verursacht , auf der Vielzahl der Steuerarten , die an die (oft komplexen) betriebswirtschaftlichen Dispositionen anknüpfen , sowie auf den Dependenzen und Interdependenzen zwischen den Steuerarten.
CEU Introduction: Treatment of the “A's”— Alexia, Agraphia, Apraxia, Agnosia, Acalculia (2002)

No AccessPerspectives on Neurophysiology and Neurogenic Speech and Language DisordersSIG News1 Apr 2002CEU Introduction: Treatment of the “A's”— Alexia, Agraphia, Apraxia, Agnosia, Acalculia Margaret Greenwald Margaret Greenwald Google Scholar More articles by this author https://doi.org/10.1044/nnsld12.1.3 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationTrack Citations ShareFacebookTwitterLinked In "CEU Introduction: Treatment of the “A's”— Alexia, Agraphia, Apraxia, Agnosia, Acalculia." Perspectives on Neurophysiology and Neurogenic Speech and Language Disorders, 12(1), p. 3 Additional Resources FiguresReferencesRelatedDetails Volume 12Issue 1April 2002Pages: 3-3 Get Permissions Add to your Mendeley library History Published in issue: Apr 1, 2002 Metrics Downloaded 77 times Topicsasha-topicsleader-topicsasha-article-typesasha-sigsCopyright & Permissions© 2002 American Speech-Language-Hearing AssociationLoading ...
Measurement of Pyrimidine (6-4) Photoproducts in DNA by a Mild Acidic Hydrolysis-HPLC Fluorescence Detection Assay (1995)

Pyrimidine (6-4) pyrimidone photoproducts constitute one of the major classes of DNA lesions induced by far-UV irradiation. However, their biological role remains difficult to assess partly because of the lack of a specific and sensitive assay for monitoring their formation in DNA. Here is presented a measurement method based on the release of the (6-4) base adducts from DNA followed by an HPLC separation associated with a sensitive and specific fluorescence detection. The quantitative and mechanistic aspects of the chemical hydrolysis, based on the use of hydrogen fluoride stabilized in pyridine, were investigated, using dinucleoside monophosphate (6-4) photoproducts as model compounds. The final hydrolysis products were isolated and characterized by UV, fluorescence, mass, and 1H NMR spectroscopies. Application of the assay to far-UV irradiated calf thymus DNA provided information on the sequence effect on the rate of formation of three of the four possible bipyrimidine (6-4) photoproducts.