gebhart/patrepeval huggingface dataset:
Microfluidic purification and analysis of hematopoietic stem cells from bone marrow (2011)

Hematopoietic stem cells are larger in size than other cells present in bone marrow, with the exception of monocytes. This distinguishing characteristic can be used to separate them from a whole-marrow sample. A microfluidic device was fabricated using an integrated membrane that is porous at defined areas. This allows for simultaneous valving and filtering functionality, which is crucial for preventing irreversible clogging. This device, as well as a separation procedure, was optimized in this work to enrich hematopoietic progenitor cells from diluted bone marrow of leukemia patients without any additional sample preparation. An enrichment of up to 98% was achieved with this method and the process was scaled up to 17.2 μL min(-1) of processed sample. Additionally, stem cells were stained with specific antibodies for further analysis. Using a custom-made computer program, the filter was scanned to characterize and quantify cells based on fluorescence. The results were evaluated by comparing them against the results obtained from flow cytometry, confocal microscopy, and Coulter counting.
Using Ion Mobility Data to Improve Peptide Identification: Intrinsic Amino Acid Size Parameters (2011)

A new method for enhancing peptide ion identification in proteomics analyses using ion mobility data is presented. Ideally, direct comparisons of experimental drift times (t(D)) with a standard mobility database could be used to rank candidate peptide sequence assignments. Such a database would represent only a fraction of sequences in protein databases and significant difficulties associated with the verification of data for constituent peptide ions would exist. A method that employs intrinsic amino acid size parameters to obtain ion mobility predictions that can be used to rank candidate peptide ion assignments is proposed. Intrinsic amino acid size parameters have been determined for doubly charged peptide ions from an annotated yeast proteome. Predictions of ion mobilities using the intrinsic size parameters are more accurate than those obtained from a polynomial fit to t(D) versus molecular weight data. More than a 2-fold improvement in prediction accuracy has been observed for a group of arginine-terminated peptide ions 12 residues in length. The use of this predictive enhancement as a means to aid peptide ion identification is discussed, and a simple peptide ion scoring scheme is presented.
Y-Ba-Cu-O film deposition by metal organic chemical vapor deposition on buffered metal substrates (1999)

YBa/sub 2/Cu/sub 3/O/sub x/ (YBCO) films have been deposited on buffered metal substrates by metal organic chemical vapor deposition (MOCVD). Cube-textured nickel substrates were fabricated by a thermomechanical process, epitaxial CeO/sub 2/ films were deposited on these substrates by thermal evaporation. Nickel alloy substrates with biaxially-textured Yttria-Stabilized Zirconia (YSZ) buffer layers deposited by ion beam assisted deposition were also prepared. Highly biaxially textured YBCO films were deposited by MOCVD on both types of metal substrates. A critical current density greater than 105 A/cm/sup 2/ at 77 K has been achieved in YBCO films on metal substrates.
T-cell activation-associated antigen expression by neoplastic T-cells. (1992)

In this study, a clinicopathologically and immunophenotypically diverse group of T-cell neoplasms were evaluated by one- and two-color flow cytometry and/or immunohistochemistry for the presence of eight antigens (T10, T9, IL2-R, EMA, HLA-DR, LeuM1, Ki-1, and LeuM5) which are expressed in a hierarchical manner by phytohemagglutinin (PHA)-activated benign T cells. We found that 70 of the 72 T-cell neoplasms (97%) expressed at least one of these eight T-cell activation-associated antigens (T-AAgs) and that the number and type of T-AAgs expressed by the neoplastic T cells varied according to the clinicopathologic category of T-cell neoplasia. All 5 T-cell lymphoblastic malignancies expressed T10 and T9; 2 also expressed LeuM1. Twelve of 14 (86%) T cell chronic lymphocytic leukemias (T-CLL) expressed two to four T-AAgs, most frequently T10 (86%) and HLA-DR (79%). The 26 cutaneous T-cell lymphomas (CTCL) expressed between 2 and 5 T-AAgs, most commonly T9 (92%) and HLA-DR (92%), and least often T10 (12%) and EMA (15%). Twenty-six of 27 (96%) peripheral T-cell lymphomas (PTCL) expressed more than 4 T-AAgs. Each of the T-AAgs were expressed by between 22% (LeuM5) and 85% (T9) of the PTCLs. Some T-AAgs were preferentially expressed by the PTCLs in association with other T-AAgs, such as EMA in association with IL2-R and Ki-1. In addition, LeuM5 was preferentially expressed by CD4- CD8+ T-cell neoplasms. However, only 19 of the 72 (26%) T-cell neoplasms (3/5 lymphoblastic malignancies, 3/14 CLLs, 0/26 CTCLs, 13/27 PTCLs) expressed T-AAg immunophenotypic profiles paralleling those expressed by normal peripheral blood T cells activated in vitro with PHA. These results suggest that T-AAg expression by neoplastic T cells does not often mirror the hierarchical order of expression by activated benign T cells, implying that neoplastic T cells do not usually represent the precise malignant counterpart of activated benign, normal T cells.
N-octanoyl dopamine treatment exerts renoprotective properties in acute kidney injury but not in renal allograft recipients (2015)

NOD treatment reduces renal injury in warm ischaemia, but is not effective in renal transplant in our experimental animal models. The salutary effect of NOD appears to be TPRV1-dependent, not involving large changes in renal perfusion.
Synthesis and characterization of a poly(acrylic acid)‐graft‐methoxy poly(ethylene oxide) comblike copolymer (2008)

Abstract A methoxy poly(ethylene oxide) (MPEO) grafted poly(acrylic acid) (PAA) comblike copolymer was synthesized by the direct condensation of MPEO onto the PAA backbone in the presence of dicyclohexyl dimethylcarbodiimide (DCC) and 4‐dimethylaminopyridine (DMAP). Its chemical structure was characterized by Fourier transform infrared and 1 H‐NMR spectroscopies. The effects of different catalysts, solvents, reaction temperatures, and reaction times on the grafting degree of the PAA‐ g ‐MPEO comblike copolymer were investigated. Compared to p ‐toluene sulfonic acid, DMAP/DCC as a catalyst markedly increased the grafting degree. The optimum reaction conditions were a tetrahydrofuran/water mixture solvent, a reaction temperature of 50°C, and a reaction time of 168 h. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Abstract 16601: APD811, a Novel and Highly Selective Non-prostanoid IP Receptor Agonist in Smooth Muscle Cells From Patients With Pulmonary Hypertension (2016)

Introduction: APD811 is an oral, non-prostanoid IP receptor agonist with a long plasma half-life (~ 24 hr) in development by Arena Pharmaceuticals Inc for pulmonary arterial hypertension (PAH). Lit...
Rapid Quantification of Digitoxin and Its Metabolites Using Differential Ion Mobility Spectrometry-Tandem Mass Spectrometry (2015)

This study focuses on the quantitative analysis of the cardiac glycoside drug digitoxin and its three main metabolites digitoxigenin-bisdigitoxose, digitoxigenin-monodigitoxose, and digitoxigenin using electrospray ionization-differential ion mobility spectrometry-tandem mass spectrometry (ESI-DMS-MS/MS). Despite large molecular weight differences, gas-phase separation of the four compounds in the DMS drift cell was not possible, even by utilizing additional volatile chemical modifiers. Baseline separation was achieved after adduct formation with alkali metal ions, however, and efficiency was shown to improve with increasing size of the alkali ion, reaching optimum conditions for the largest cesium ion. Subsequently, an assay was developed for quantification of digitoxin and its metabolites from human serum samples and its analytical performance assessed in a series of proof-of-concept experiments. The method was applied to spiked human serum pools with concentration levels between 2 and 80 ng/mL. After a short reversed-phase chromatographic step for desalting the sample, rapid DMS separation of the analytes was carried out, resulting in a total run time of less than 1.5 min. The instrumental method showed good repeatability; the calculated coefficients of variation ranged from 2% to 13%.
Direct Strain Measurement of Polypyrrole Actuators Controlled by the Polymer/Gold Interface (2003)

Electrochemically induced strain and actuation in a polypyrrole/Au/polyimide laminate was measured using a sensitive strain gage during oxidation and reduction (redox) of polypyrrole−ClO4-. The polyimide formed the top layer of the strain gage, allowing direct measurement of strain during redox switching in various electrolytes and potential windows. Strain increased in the order NaCl < NaNO3 < NaClO4. In the NaClO4 solution for oxidizing potentials between 0.1 and 0.5 V vs Ag/AgCl, strain and charge were linearly proportional to voltage. Lower polypyrrole deposition potentials also increased strain. The surface roughness of the Au was varied by electrochemically depositing Au (which we designate EcAu) on top of thermally evaporated Au (EvAu)/polyimide. Greater EcAu deposition times led to greater Au roughness. Strain increased with polypyrrole thickness and Au roughness, which correlated with better adhesion between the polypyrrole and the Au. Au roughness also improved the cycling stability of the actuators.
Adsorption of Crystal Violet to the Silica−Water Interface Monitored by Evanescent Wave Cavity Ring-Down Spectroscopy (2003)

Evanescent wave cavity ring-down spectroscopy (EW-CRDS) has been used to investigate the adsorption of crystal violet (CV+) to a charged silica−water interface as a function of bulk pH by the direct measurement of the absorbance of the CV+ chromophore. Absolute absorbances of order 10-4 have been routinely detected, showing significant variation in the structure of the silica−water interface. At low ionic strength, the interfacial absorbance of CV+ shows a monotonic increase with increasing pH. A simple competitive Langmuir adsorption model, which provides values for the silica surface parameters that are in broad agreement with the existing literature values, has been fit to the data. In addition, interfacial absorbance has been monitored as a function of pH for CV+ solutions maintained at high ionic strength with NaCl, KCl, and CaCl2. As pH increases, the CV+ interfacial absorbance exhibits a pronounced maximum, which occurs at pH 8.7 for Na+ and K+ and at pH 7.9 for Ca2+, followed by a sharp decrease. This trend is attributed to competitive binding between the metal cations and CV+ to the silica surface binding site, and it has not been observed in previous measurements using second-harmonic generation. The simple Langmuir model, however, does not accurately describe the high ionic strength behavior.
Self-assembly of a homopolymer mixture via phase separation (1994)

We propose a mechanism for creating lateral order in thin films of a homopolymer mixture via spinodal decomposition in the presence of a laterally structured substrate surface. The system under consideration is a mixture of deuterated polystyrene and partially brominated polystyrene (PBrxS, x=0.5) spuncast onto different substrates from toluene solution. We demonstrate that periodic stripe-like domain structures can be observed in the polymer films after spinodal decomposition on a periodic array of Cr lines on a H-terminated Si surface. The effect vanishes when the chemistry of the underlying structure is changed, strongly indicating an interface-driven ordering of the polymer film.
Core Set of Radiographic Parameters for Shoulder Arthroplasty Monitoring (2019)

This represents a major step toward the standardization of shoulder arthroplasty radiographic monitoring for routine quality controls and research investigations.
A phase 2 biomarker-driven study of ruxolitinib demonstrates effectiveness of JAK/STAT targeting in T-cell lymphomas (2021)

Signaling through JAK1 and/or JAK2 is common among tumor and nontumor cells within peripheral T-cell lymphoma (PTCL). No oral therapies are approved for PTCL, and better treatments for relapsed/refractory disease are urgently needed. We conducted a phase 2 study of the JAK1/2 inhibitor ruxolitinib for patients with relapsed/refractory PTCL (n = 45) or mycosis fungoides (MF) (n = 7). Patients enrolled onto 1 of 3 biomarker-defined cohorts: (1) activating JAK and/or STAT mutations, (2) ≥30% pSTAT3 expression among tumor cells by immunohistochemistry, or (3) neither or insufficient tissue to assess. Patients received ruxolitinib 20 mg PO twice daily until progression and were assessed for response after cycles 2 and 5 and every 3 cycles thereafter. The primary endpoint was clinical benefit rate (CBR), defined as the combination of complete response, partial response (PR), and stable disease lasting at least 6 months. Only 1 of 7 patients with MF had CBR (ongoing PR > 18 months). CBR among the PTCL cases (n = 45) in cohorts 1, 2, and 3 were 53%, 45%, and 13% (cohorts 1 & 2 vs 3, P = .02), respectively. Eight patients had CBR > 12 months (5 ongoing), including 4 of 5 patients with T-cell large granular lymphocytic leukemia. In an exploratory analysis using multiplex immunofluorescence, expression of phosphorylated S6, a marker of PI3 kinase or mitogen-activated protein kinase activation, in <25% of tumor cells was associated with response to ruxolitinib (P = .05). Our findings indicate that ruxolitinib is active across various PTCL subtypes and support a precision therapy approach to JAK/STAT inhibition in patients with PTCL. This trial was registered at www.clincialtrials.gov as #NCT02974647.
Apparent conductivity for borehole electromagnetic propagation measurements (2020)

Although tool constants have been used for laterolog and induction logging for a long time to directly determine formation resistivity or conductivity, no tool constants have been presented for propagation logging. In this work, we give the tool constant for propagation measurements in order to determine formation conductivity directly from the measurements. The formation conductivity found in such a way is referred to as apparent conductivity. Two apparent conductivities are introduced accordingly: one associated with phase shift, and the other associated with attenuation. By doing so, propagation measurements are put on equal footing with laterolog and induction measurements. The two apparent conductivities can be used to assist in understanding and interpreting propagation data in a variety of scenarios. The tool constant can be used to understand how the electronic error affects the accuracy of measurements. It can also be used to optimize the tool design by taking advantage of its explicit expression of frequencyand spacing. Presentation Date: Monday, October 12, 2020 Session Start Time: 1:50 PM Presentation Time: 2:15 PM Location: Poster Station 2 Presentation Type: Poster
PEG-Supported Chiral Diamine Ligand for Pd-Catalyzed Allylic Alkylation (2006)

Poly(ethylene glycol)-supported diaminooligothiophene was prepared and used as a chiral ligand in the palladium-catalyzed asymmetric allylic alkylation. The polymer-supported diamino­oligothiophene 3 was prepared by the reaction of the diaminooligothiophene 1 with poly(ethylene glycol) mesylate 2 (eq. 1). The asymmetric allylic alkylation of allyl carbonates with dimethyl malo­nate took place in the presence of allylpalladium(II) chloride dimer and the polymer-supported ligand 3 to give the allylic alkylated adducts in 50-90% yield with 78-95% ee (eq. 2). The polymeric palladium complex is dissolved in CH2Cl2 to provide a homogeneous mixture during the reaction. Ligand 3 was recovered by precipitation and filtration and was reused twice [91% yield, 92% ee (1st reuse), 84 % yield, 92% ee (2nd reuse)].
On the impact of IEEE 802.11 MAC on traffic characteristics (2003)

IEEE 802.11 medium access control (MAC) is gaining widespread popularity as a layer-2 protocol for wireless local-area networks. While efforts have been made previously to evaluate the performance of various protocols in wireless networks and to evaluate the capacity of wireless networks, very little is understood or known about the traffic characteristics of wireless networks. In this paper, we address this issue and first develop an analytic model to characterize the interarrival time distribution of traffic in wireless networks with fixed base stations or ad hoc networks using the 802.11 MAC. Our analytic model and supporting simulation results show that the 802.11 MAC can induce pacing in the traffic and the resulting interarrival times are best characterized by a multimodal distribution. This is a sharp departure from behavior in wired networks and can significantly alter the second order characteristics of the traffic, which forms the second part of our study. Through simulations, we show that while the traffic patterns at the individual sources are more consistent with long-range dependence and self-similarity, in contrast to wired networks, the aggregate traffic is not self-similar. The aggregate traffic is better classified as a multifractal process and we conjecture that the various peaks of the multimodal interarrival time distribution have a direct contribution to the differing scaling exponents at various timescales.
ChemInform Abstract: PMP (p‐Methoxyphenyl), a Versatile N‐Protective Group in the Synthesis of Chiral Amines and Amino Acids (2010)

Abstract Review: 40 refs.
ChemInform Abstract: Synthesis of Heterocyclic β‐Amino Acids. A Convenient Preparation of β‐Amino‐5‐pyrimidinepropanoic Acid and Derivatives. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: ALKYLATION AND ALDOL CONDENSATION REACTIONS OF 1,3‐OXATHIOLANONES (1984)

Abstract Alkylierungsreaktionen und Aldol‐Kondensationen werden an den lß‐Oxathiolanonen (I) untersucht.
Arginase modulates myocardial contractility by a nitric oxide synthase 1-dependent mechanism (2006)

Cardiac myocytes contain two constitutive NO synthase (NOS) isoforms with distinct spatial locations, which allows for isoform-specific regulation. One regulatory mechanism for NOS is substrate (l-arginine) bioavailability. We tested the hypothesis that arginase (Arg), which metabolizes l-arginine, constrains NOS activity in the cardiac myocyte in an isoform-specific manner. Arg activity was detected in both rat heart homogenates and isolated myocytes. Although both Arg I and II mRNA and protein were present in whole heart, Arg II alone was found in isolated myocytes. Arg inhibition with S-(2-boronoethyl)-l-cysteine (BEC) augmented Ca(2+)-dependent NOS activity and NO production in myocytes, which did not depend on extracellular l-arginine. Arg II coimmunoprecipited with NOS1 but not NOS3. Isolation of myocyte mitochondrial fractions in combination with immuno-electron microscopy demonstrates that Arg II is confined primarily to the mitochondria. Because NOS1 positively modulates myocardial contractility, we determined whether Arg inhibition would increase basal myocardial contractility. Consistent with our hypothesis, Arg inhibition increased basal contractility in isolated myocytes by a NOS-dependent mechanism. Both the Arg inhibitors N-hydroxy-nor-l-arginine and BEC dose-dependently increased basal contractility in rat myocytes, which was inhibited by both nonspecific and NOS1-specific NOS inhibitors N(G)-nitro-l-arginine methyl ester and S-methyl-l-thiocitrulline, respectively. Also, BEC increased contractility in isolated myocytes from WT and NOS3 but not NOS1 knockout mice. We conclude that mitochondrial Arg II negatively regulates NOS1 activity, most likely by limiting substrate availability in its microdomain. These findings have implications for therapy in pathophysiologic states such as aging and heart failure in which myocardial NO signaling is disrupted.
ChemInform Abstract: N‐METHYLTETRAHYDROCHINOLIN UND N‐METHYLINDOLIN (1970)

Abstract Die intramolekulare radikalische Cyclisierung der aus 1‐Brom‐3‐phenylpropan (I) und Methylamin (II) erhaltenen N‐Chlorverbindung (IV) ergibt glatt N‐Methyltetrahydrochinolin (V) (Ausbeute 81%).
Ruxolitinib reduces JAK2 p.V617F allele burden in patients with polycythemia vera enrolled in the RESPONSE study (2017)

In patients with polycythemia vera (PV), an elevated JAK2 p.V617F allele burden is associated with indicators of more severe disease (e.g., leukocytosis, splenomegaly, and increased thrombosis risk); however, correlations between allele burden reductions and clinical benefit in patients with PV have not been extensively evaluated in a randomized trial. This exploratory analysis from the multicenter, open-label, phase 3 Randomized Study of Efficacy and Safety in Polycythemia Vera With JAK Inhibitor INCB018424 Versus Best Supportive Care trial evaluated the long-term effect of ruxolitinib treatment on JAK2 p.V617F allele burden in patients with PV. Evaluable JAK2 p.V617F-positive patients randomized to ruxolitinib (n = 107) or best available therapy (BAT) who crossed over to ruxolitinib at week 32 (n = 97) had consistent JAK2 p.V617F allele burden reductions throughout the study. At all time points measured (up to weeks 208 [ruxolitinib-randomized] and 176 [ruxolitinib crossover]), mean changes from baseline over time in JAK2 p.V617F allele burden ranged from -12.2 to -40.0% (ruxolitinib-randomized) and -6.3 to -17.8% (ruxolitinib crossover). Complete or partial molecular response was observed in 3 patients (ruxolitinib-randomized, n = 2; ruxolitinib crossover, n = 1) and 54 patients (ruxolitinib-randomized, n = 33; ruxolitinib crossover, n = 20; BAT, n = 1), respectively. Among patients treated with interferon as BAT (n = 13), the mean maximal reduction in allele burden from baseline was 25.6% after crossover to ruxolitinib versus 6.6% before crossover. Collectively, the data from this exploratory analysis suggest that ruxolitinib treatment for up to 4 years provides progressive reductions in JAK2 p.V617F allele burden in patients with PV who are resistant to or intolerant of hydroxyurea. The relationship between allele burden changes and clinical outcomes in patients with PV remains unclear.
Instrument System to Monitor the Dynamic Behavior of a 27-m Sprayer Boom (2003)

The problem was to identify wide boom behavior under field conditions. The objective wasto develop a spray boom instrumentation system to monitor x-y-z accelerations at boom ends, boomcenter, and sprayer vehicle rear; boom end heights; and sprayer position along a track. A pc-baseddata acquisition system was required instead of a data logger, based on required samplingfrequencies. In general, peak amplitudes were measured at frequencies ranging from 4 to 5 Hz.Other characteristic frequency components were identified for bumps and dips placed along thetrack, and for the effect of water load in the sprayer hopper. Data may aide the design of sprayersuspension and boom mount systems to minimize adverse boom movement.