gebhart/patrepeval huggingface dataset:
Surface marker abnormalities in myelodysplastic syndromes. (1998)

Several surface antigens in MDS have shown abnormal expression either in the intensity of fluorescence or the percentage of positive cells. These abnormalities include increased, decreased or lineage-aberrant expression. Abnormalities of several surface markers have prognostic significance. MDS patients with a low percentage of bone marrow cells expressing CD11b had a higher risk of evolution to acute myeloid leukemia and shorter survival compared to patients with more than 53% of marrow cells expressing CD11b (29 weeks versus 160 weeks). On the other hand, an increased percentage of bone marrow cells expressing early or immature markers, such as CD 13, CD33, CD34 and HLA-DR, has been associated with a worse outcome and with progression to a higher risk MDS or to acute myeloid leukemia. However, there are numerous discrepancies and inconsistencies in the literature when reviewing surface marker changes in MDS. These discrepancies may be related, at least in part, to the presence of an intracellular storage compartment of numerous surface antigens in the granulocytes and monocytes. Because of these storage pools, the techniques of preparing more mature granulocytes and monocytes, such as density gradient separation, and the interpretation of results must be carefully evaluated. Furthermore, various methods have been used to express abnormal results including percentage of positive or negative cells, fluorescent intensity (FI) of individual patients or a group of patients using a mean fluorescent channel (256 or 1024 channel mode), and finally the expression of FI as molecules of equivalent soluble fluorochromes or antibody binding capacities. Several mechanisms may be involved in the abnormal expression of surface antigens in MDS including defective granulopoiesis, defective intracellular storage pool, abnormal membrane of cytoplasmic granules, and the effect of high levels of marrow cytokines such as tumor necrosis factor alpha and transforming growth factor-beta. Standardization of the methods of preparing and studying mature and maturing granulocytes and monocytes in MDS has to be achieved in order to produce comparable results, thus allowing surface marker studies to be utilized as diagnostic and prognostic tools in MDS.
Hormone replacement therapy and endometrial cancer risk: A meta-analysis (1995)

Endometrial cancer risk increases substantially with long duration of unopposed estrogen use, and this increased risk persists for several years after discontinuation of estrogen. Although not statistically significant, the risk of death from endometrial cancer among unopposed estrogen users is increased, similar to the increased risk of developing the disease. Data regarding risk for endometrial cancer among estrogen plus progestin users are limited and conflicting.
The Acidic Region of the Factor VIII Light Chain and the C2 Domain Together Form the High Affinity Binding Site for von Willebrand Factor (1997)

A binding site for von Willebrand factor (vWf) was previously localized to the carboxyl terminus of the C2 domain of the light chain (LCh) of factor VIII (fVIII). The acidic region of the LCh, residues 1649-1689, also controls fVIII.vWf binding by an unknown mechanism. Although anti-acidic region monoclonal antibodies prevent formation of the fVIII.vWf complex, the direct involvement of the acidic region in this binding has not been demonstrated. By limited proteolysis of LCh with Staphylococcus aureus V8 protease, we prepared 14- and 63-kDa LCh fragments, which begin with fVIII residues 1672 and 1795, respectively. Using surface plasmon resonance to measure binding interactions, we demonstrated that the 14-kDa fragment binds to vWf, but its affinity for vWf (Kd 72 nM) was 19-fold lower than that of LCh. This was not due to an altered conformation of the acidic region within the 14-kDa fragment, since its affinity for an anti-acidic region monoclonal antibody was similar to that of LCh. All LCh derivatives lacking the acidic region (thrombin-cleaved LCh, recombinant C2, and 63-kDa fragment) had also greatly reduced affinities for vWf (Kd 564-660 nM) compared with LCh (Kd 3.8 nM). In addition, the similar affinities of these derivatives for vWf indicated that apart from its acidic region, the LCh contains no vWf binding site other than the one within C2. The reduced affinities of the LCh derivatives lacking the acidic region for monoclonal antibody NMC-VIII/5 (epitope, C2 residues 2170-2327) indicated that removal of the acidic region leads to a conformational change within C2. This change is likely to affect the conformation of the vWf binding site in C2, which overlaps the epitope of NMC-VIII/5; therefore, the acidic region also appears to be required to maintain the optimal conformation of this vWf binding site. Our results demonstrate that the acidic region and the C2 domain are both directly involved in forming a high affinity binding site for vWf.
PYK2 is an adhesion kinase in macrophages, localized in podosomes and activated by ?2-integrin ligation (2000)

Pyk2 is a member of the focal adhesion kinase (FAK) family, highly expressed in the central nervous system and haemopoietic cells. Although Pyk2 is homologous to FAK, its role in signaling pathways was shown to be distinct from that of FAK. We show here that Pyk2 is highly expressed in peritoneal IC-21 macrophage and is tyrosine phosphorylated in response to cell attachment to fibronectin and fibrinogen. Upon IC-21 cell adhesion, Pyk2 tyrosine phosphorylation is inhibited by blocking antibodies to the integrin subunits alpha(M) and beta(2). Furthermore, Pyk2 is rapidly tyrosine phosphorylated in response to ligation of beta(2) integrins by antibodies. In migrating macrophages, Pyk2 localizes to perinuclear regions and to podosomes, where it is clustered with tyrosine phosphorylated proteins. Furthermore, in the podosomal ring structure, which surrounds the central actin core, Pyk2 co-localizes with vinculin, talin, and paxillin. In the podosomes, Pyk2 also co-localizes with the integrin alpha(M)beta(2). Lastly, reduction of Pyk2 expression in macrophages leads to inhibition of cell migration. We propose that Pyk2 is functionally linked to the formation of podosomes where it mediates the integrin-cytoskeleton interface and regulates cell spreading and migration.
Optimized enzymatic synthesis of geranyl butyrate with lipase AY from candida rugosa (1996)

Response surface methodology (RSM) and five-level, five-variable central composite rotatable design (CCRD) were used to evaluate the effects of synthetic variables, such as reaction time (1-9 h), temperature (25-65 degrees C), enzyme amount (10-50%), substrate molar ratio of geraniol to tributyrin (1:0.33-1:1), and added water amount (0-20%) on molar percent yield of geranyl butyrate, using lipase AY from Candida rugosa. Reaction time and temperature were the most important variables and substrate molar ratio had no effect on percent molar conversion. Based on contour plots, optimum conditions were: reaction time 9 h, temperature 35 degrees C, enzyme amount 50%, substrate molar ratio 1:0.33, and added water 10%. The predicted value was 100% and actual experimental value was 96.8% molar conversion. (c) 1996 John Wiley & Sons, Inc.
A FLEX Switch Targets Channelrhodopsin-2 to Multiple Cell Types for Imaging and Long-Range Circuit Mapping (2008)

### Introduction Genetic approaches have yielded progress toward characterizing the relationship of molecularly defined neuronal cell types to behavior. However, relatively little is known about the functional properties of the connections between these molecularly defined cell types. This
Bioorthogonal Turn‐On Probes for Imaging Small Molecules inside Living Cells (2010)

Glowing tags: a series of activatable ("turn-on") tetrazine-conjugated fluorescent probes was developed, which react rapidly in an inverse-electron-demand [4+2] cycloaddition with strained dienophiles such as trans-cyclooctene, thereby strongly increasing the fluorescence intensity. The novel turn-on probes were applied for intracellular live-cell imaging of a microtubuli-binding trans-cyclooctene modified taxol.
Targeting factor D of the alternative complement pathway reduces geographic atrophy progression secondary to age-related macular degeneration (2017)

The phase 2 MAHALO clinical trial shows that lampalizumab reduces geographic atrophy secondary to age-related macular degeneration and implicates complement dysregulation in disease pathogenesis.
RNA: A Laboratory Manual (2010)

Chapter 1: The Fundamentals Chapter 2: Purification of RNA from Natural Sources Chapter 3: Detection and Sequence Determination of Specific RNAs Chapter 4: Synthesis and Modification of RNA In Vitro Chapter 5: Uses of Synthetic RNAs Chapter 6: Testing RNA Substrates for Activity In Vitro Chapter 7: RNAi-related Techniques Chapter 8: Genomic Approaches Appendices I Reagents II Stock Solutions III Nucleases and What They Do IV Miscellaneous Protocols V Cautions
Inhibition of ice crystal growth by preferential peptide adsorption: a molecular modelling study (1993)

A molecular modelling approach has been used to study the relative binding of a winter flounder antifreeze peptide (AFP) to the faces and the internal planes, in particular the c-face and the 20text-decoration:overline21 plane, of the ice (Ih) crystal. The in vacuo binding energies of the peptide molecule with the two surfaces differ by a factor of more than three, which could account for the suggested higher affinity of the molecule for the 20text-decoration:overline21 plane than for the c-face or the prism face. The propensities of the molecule to hydrogen bond with these surfaces are not so different. The key difference in the mode of attachment of the molecule to the various surfaces appears to stem from their geometrical features: the c-face and the prism face are flat, precluding intimate physical contact to be made with the peptide, but the 20text-decoration:overline21 plane contains ‘ridges’ and ‘valleys’ which produce a near-perfect steric match for the structure of the peptide molecule, so accommodating it in the ‘lock and key’ fashion.
Inhibition of Gammaherpesvirus Replication by RNA Interference (2003)

RNA interference (RNAi) is a conserved mechanism in which double-stranded, small interfering RNAs (siRNAs) trigger a sequence-specific gene-silencing process. Here we describe the inhibition of murine herpesvirus 68 replication by siRNAs targeted to sequences encoding Rta, an immediate-early protein known as an initiator of the lytic viral gene expression program, and open reading frame 45 (ORF 45), a conserved viral protein. Our results suggest that RNAi can block gammaherpesvirus replication and ORF 45 is required for efficient viral production.
Mixing effects in dead end hydrogenation of oils: Sulfite oxidation model (1971)

Abstract Most industrial hydrogenators are of the dead end type where the gas is bubbled at the bottom of the apparatus, builds up a certain pressure on top of the oil, and is not recirculated. The hydrogen needed by the reaction comes partly from the fraction of the bubbles that is absorbed and partly from the gas space. It was found that sodium sulfite oxidation follows the same mixing pattern, i.e., the highest rate of oxidation always occurred in the upper half of the liquid and correlated strongly with the Reynolds number of the turbine. it is shown that for Reynolds numbers above 600 the optimum impeller position is about two thirds the liquid height measured from the bottom of the vessel. Information is given regarding the variations in selectivity, isomerization and hydrogenation of oils when the speed, relative location and dimensions of the turbine are varied.
Floral determination and expression of floral regulatory genes in Arabidopsis (1997)

The expression of the floral regulators LEAFY, APETALA1 and AGAMOUS-LIKE8 was examined during light treatments that induced flowering in Arabidopsis, and was compared to time points at which floral determination occurred. Extension of an 8-hour day by either continuous red- or far-red-enriched light induced LEAFY and AGAMOUS-LIKE8 expression within 4 hours. The 4 hours of additional light was sufficient for floral determination only in the far-red-enriched conditions, while 12-16 hours of additional light was required for floral determination in the red-enriched conditions. These results indicate that the induction of floral regulatory genes and induction of flower formation can be uncoupled under certain circumstances. Expression of LEAFY and AGAMOUS-LIKE8 in the shoot apex at the time of floral determination is also consistent with genetic data indicating that these genes are involved in the first steps of the transition from vegetative to reproductive development. In contrast to LEAFY and AGAMOUS-LIKE8, APETALA1 expression was first observed 16 hours after the start of photoinduction. Since this time point was always after floral determination, APETALA1 is an indicator of floral determination.
Use of Fibrin Sealant for Prosthetic Mesh Fixation in Laparoscopic Extraperitoneal Inguinal Hernia Repair (2001)

An adequate mesh fixation in the extraperitoneal inguinal area can be accomplished using FS. This method is mechanically equivalent to the fixation achieved by staples and superior to nonfixed grafts. Biologic soft fixation with FS will prevent early graft migration and will avoid the complications associated with staple use.
Secondary structure of the 5′ nontranslated regions of hepatitis C virus and pestivirus genomic RNAs (1992)

The RNA genomes of human hepatitis C virus (HCV) and the animal pestiviruses responsible for bovine viral diarrhea (BVDV) and hog cholera (HChV) have relatively lengthy 5' nontranslated regions (5'NTRs) sharing short segments of conserved primary nucleotide sequence. The functions of these 5'NTRs are poorly understood. By comparative sequence analysis and thermodynamic modeling of the 5'NTRs of multiple BVDV and HChV strains, we developed models of the secondary structures of these RNAs. These pestiviral 5'NTRs are highly conserved structurally, despite substantial differences in their primary nucleotide sequences. The assignment of similar structures to conserved segments of primary nucleotide sequence present in the 5'NTR of HCV resulted in a model of the secondary structure of the HCV 5'NTR which was refined by determining sites at which synthetic HCV RNA was cleaved by double- and single-strand specific RNases. These studies indicate the existence of a large conserved stem-loop structure within the 3' 200 bases of the 5'NTRs of both HCV and pestiviruses which corresponds to the ribosomal landing pad (internal ribosomal entry site) of HCV. This structure shows little relatedness to the ribosomal landing pad of hepatitis A virus, suggesting that these functionally similar structures may have evolved independently.
Angiotensin II, Cell Proliferation and Angiogenesis Regulator: Biologic and Therapeutic Implications in Cancer (2004)

Angiotensin II (ANG II) is the main effector peptide in the renin-angiotensin system. It is generated by the activation of Angiotensin I through the Angiotensin II Converter Enzyme (ACE II). ANG II has multiple physiologic effects that regulate vascular tone, hormone secretion, tissue growth and neural activity. It has systemic (endocrine) and local (paracrine and autocrine) effects, favoring cell growth and differentiation through four types of receptors from which types 1 and 2 (AT(1) and AT(2)) are the most important. Stimulation of AT(1) leads to the activation of intracellular pathways that finally lead to vasoconstriction, inflammation and proliferation. The AT(2) receptor is mainly expressed in fetal tissue and scantly in the cardiovascular system under different circumstances. Its effects are opposite to those of the AT(1). The stimulation of AT(1) activates second messengers that lead to a rapid production of diacylglycerol and 1-4-5-inositol triphosphate, as well as to the activation of C protein. Several reports indicate that ANG II can induce neovascularization in experimental systems due to the expression of different growth factors such as angiopoietin 2, vascular endothelial factor, and its receptor, fibroblast growth factor, platelet derived growth factor, transforming growth factor beta and epidermal growth factor. Other mechanisms associated with ANG II induced angiogenesis are nitric oxide synthase and metalloproteinase expression, as well as inflammation induction. Angiogenesis is a fundamental process to tissue repair and development, and it participates in several pathologic processes. In addition, the AT(1) receptor is expressed in many malignant neoplasms and its blockade through ECA II inhibitors and ANG II antagonists has shown antineoplastic activity as well as angiogenesis inhibition in tumoral experimental models. This review discusses the mechanisms by which ANG II participates in neoplastic and non-neoplastic tissue angiogenesis and its possible therapeutic implications.
An integrated microfluidic biochemical detection system for protein analysis with magnetic bead-based sampling capabilities (2002)

This paper presents the development and characterization of an integrated microfluidic biochemical detection system for fast and low-volume immunoassays using magnetic beads, which are used as both immobilization surfaces and bio-molecule carriers. Microfluidic components have been developed and integrated to construct a microfluidic biochemical detection system. Magnetic bead-based immunoassay, as a typical example of biochemical detection and analysis, has been successfully performed on the integrated microfluidic biochemical analysis system that includes a surface-mounted biofilter and electrochemical sensor on a glass microfluidic motherboard. Total time required for an immunoassay was less than 20 min including sample incubation time, and sample volume wasted was less than 50 microl during five repeated assays. Fast and low-volume biochemical analysis has been successfully achieved with the developed biofilter and immunosensor, which is integrated to the microfluidic system. Such a magnetic bead-based biochemical detection system, described in this paper, can be applied to protein analysis systems.
Optical waveguides. Photon plumbing for the chemistry lab: fiber optics, waveguides, and evanescent waves as tools for chemical analysis (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOptical waveguides. Photon plumbing for the chemistry lab: fiber optics, waveguides, and evanescent waves as tools for chemical analysisIlan ChabayCite this: Anal. Chem. 1982, 54, 9, 1071A–1080APublication Date (Print):August 1, 1982Publication History Published online21 September 2008Published inissue 1 August 1982https://doi.org/10.1021/ac00246a004Request reuse permissionsArticle Views160Altmetric-Citations24LEARN 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 InReddit PDF (7 MB) Get e-Alertsclose Get e-Alerts
Using Inertial Sensors for Position and Orientation Estimation (2017)

In recent years, microelectromechanical system (MEMS) inertial sensors (3D accelerometers and 3D gyroscopes) have become widely available due to their small size and low cost. Inertial sensor measurements are obtained at high sampling rates and can be integrated to obtain position and orientation information. These estimates are accurate on a short time scale, but suffer from integration drift over longer time scales. To overcome this issue, inertial sensors are typically combined with additional sensors and models. In this tutorial we focus on the signal processing aspects of position and orientation estimation using inertial sensors.We discuss different modeling choices and a selected number of important algorithms. The algorithms include optimizationbased smoothing and filtering as well as computationally cheaper extended Kalman filter and complementary filter implementations. The quality of their estimates is illustrated using both experimental and simulated data.
Bifunctional Dendrimers: From Robust Synthesis and Accelerated One‐Pot Postfunctionalization Strategy to Potential Applications (2008)

A fourth wheel: Two sets of bifunctional AB(2)C dendrimers having internal acetylene/azides and external hydroxy groups were constructed utilizing benign synthetic protocols. An in situ postfunctionalization strategy was successfully carried out to illustrate the chemoselective nature of these dendrimers. The dendrimers were also transformed into dendritic nanoparticles or utilized as dendritic crosslinkers for the fabrication hydrogels.
Cetalox® and Analogues: Synthesis via Acid‐Mediated Polyene Cyclizations (2008)

Using a novel, acid-mediated cyclization methodology, a direct access to Cetalox ((+/-)-1; a commercially important ambergris-type odorant) and various structurally related didehydro (i.e., 19, 26, and 30) and tetradehydro (i.e., 28 and 37/38) analogues is described. Treatment of either (E,E)-14 or (E)-15 with an excess of FSO(3)H in 2-nitropropane at -90 degrees stereospecifically afforded (+/-)-1 in 40 and 42% yield, respectively. Under similar conditions, cyclization of (E)-18 or 20 furnished 19 in 60 and 64% yield, respectively. Analogously, using an excess of ClSO(3)H in CH(2)Cl(2) at -80 degrees, 26 is formed with high stereoselectivity by cyclization of either (E)-24 or (Z)-25 (52 and 31% yield, resp.); in the same manner, 28 was prepared from 27 (22% yield). The same principle was applied to the synthesis of racemic Superambrox (30), via cyclization of 35, but only with poor selectivity (22%) and low yield (7%). Another approach via cyclization of (E)-40 under solvolysis conditions (excess TFA in CH(2)Cl(2) at -10 degrees) gave a higher yield (15%) with improved selectivity (43%). Finally, cyclization of 34 (1:1 diastereoisomer mixture) afforded 37/38 (10:1) in 27% yield. The qualitative organoleptic properties of 19, 26, 28, 30, and 37/38 (10:1) are briefly discussed.