gebhart/patrepeval huggingface dataset:
Human Primary T Cells: A Practical Guide v6 (2018)

Human primary T cells are invaluable and feasible model systems to study the characteristics of the human immune cells in various contexts, including but not limited to cancer immunotherapy. Following isolation of T cells from fresh human blood samples, it is possible to culture, expand, and manipulate these cells, which allows extensive investigation for research purposes. Techniques for isolation and handling of T cells are well-established but parts of the protocols can highly vary across different labs. These differences in the protocols are, often, there due to historical reasons and are only supported by anecdotal evidence. We systematically modified basic components of the T cell culturing protocols and collected data on how they altered the final yield. Here, based on these data, we provide practical hints and tips on basic cellular and molecular techniques for handling primary human T cells. We hope that this guide will serve as a reference point to allow evaluate, discuss, and improve current practices in T cell culturing and manipulation.
ChemInform Abstract: Jacobus Henricus van′t Hoff; Hundred Years of Impact on Stereochemistry in the Netherlands. (2002)

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.
Magnetic Structure ofLaCrO3Perovskite under High Pressure fromIn SituNeutron Diffraction (2011)

The temperature-pressure phase diagram for both the crystal and magnetic structures of LaCrO(3) perovskite has been mapped out by in situ neutron-diffraction experiments under pressure. The system offers the opportunity to study the evolution of magnetic order, spin direction, and magnetic moment on crossing the orthorhombic-rhombohedral phase boundary. Moreover, a microscopic model of the superexchange interaction has been developed on the basis of the crystal structure obtained in this work to account for the behavior of T(N) under high pressure.
Post-transcriptional Up-regulation of Tsc-22 by Ybx1, a Target of miR-216a, Mediates TGF-β-induced Collagen Expression in Kidney Cells* (2010)

Increased accumulation of extracellular matrix proteins and hypertrophy induced by transforming growth factor-β1 (TGF-β) in renal mesangial cells (MC) are hallmark features of diabetic nephropathy. Although the post-transcriptional regulation of key genes has been implicated in these events, details are not fully understood. Here we show that TGF-β increased microRNA-216a (miR-216a) levels in mouse MC, with parallel down-regulation of Ybx1, a miR-216a target and RNA-binding protein. TGF-β also enhanced protein levels of Tsc-22 (TGF-β-stimulated clone 22) and collagen type I α-2 (Col1a2) expression in MC through far upstream enhancer E-boxes by interaction of Tsc-22 with an E-box regulator, Tfe3. Ybx1 colocalized with processing bodies in MC and formed a ribonucleoprotein complex with Tsc-22 mRNA, and this complex formation was reduced by TGF-β, miR-216a mimics, or Ybx1 shRNA to increase Tsc-22 protein levels but enhanced by miR-216a inhibitor oligonucleotides. Chromatin immunoprecipitation (ChIP) assays revealed that TGF-β could increase the occupancies of Tsc-22 and Tfe3 on enhancer E-boxes of Col1a2. Co-immunoprecipitation assays revealed that TGF-β promoted the interaction of Tsc-22 with Tfe3. These results demonstrate that post-transcriptional regulation of Tsc-22 mediated through Ybx1, a miR-216a target, plays a key role in TGF-β-induced Col1a2 in MC related to the pathogenesis of diabetic nephropathy.
Learning Nonlinear Dynamic Models (2009)

We present a novel approach for learning nonlinear dynamic models, which leads to a new set of tools capable of solving problems that are otherwise difficult. We provide theory showing this new approach is consistent for models with long range structure, and apply the approach to motion capture and high-dimensional video data, yielding results superior to standard alternatives.
NetPath: a public resource of curated signal transduction pathways (2010)

Abstract We have developed NetPath as a resource of curated human signaling pathways. As an initial step, NetPath provides detailed maps of a number of immune signaling pathways, which include approximately 1,600 reactions annotated from the literature and more than 2,800 instances of transcriptionally regulated genes - all linked to over 5,500 published articles. We anticipate NetPath to become a consolidated resource for human signaling pathways that should enable systems biology approaches.
The Oncoprotein LMO2 Is Expressed in a Germinal Center B-Cell-Associated Pattern and Predicts Survival in Patients with Diffuse Large B-Cell Lymphoma. (2006)

Abstract Diffuse large B-cell lymphoma (DLBCL) is clinically and molecularly heterogeneous and portends a poor prognosis in more than half the affected patients. We developed a multivariate model based on the RNA expression of six genes – LMO2, BCL6, FN1, CCND2, SCYA3 and BCL2 – that independently predicts survival in DLBCL patients treated with anthracycline-containing regimens (Lossos et al, NEJM 2004). Since the transcription factor LMO2 emerged as the strongest predictor of superior outcome, we generated a monoclonal anti-LMO2 antibody in order to document the tissue expression pattern of LMO2 protein and to establish its prognostic significance. Immunohistological analysis of 1200 normal tissues and hematolymphoid neoplasms showed that LMO2 protein is expressed as a nuclear marker in normal germinal center (GC) B-cells and in a subset of B-cell lymphomas. It is rarely expressed in mature T, NK and plasma cell neoplasms. Immature precursors of all bone marrow hematopoietic lineages and a significant proportion of acute lymphomphoblastic and myeloid leukemias express LMO2 protein. Apart from endothelial cells, no other non-hematolymphoid tissues we tested showed LMO2 protein expression. Hierarchical cluster analysis of immunohistologic data in DLBCL demonstrated that the expression profile of LMO2 protein is similar to that of other GC-associated proteins (HGAL, BCL6 and CD10) but different from that of non-GC proteins (MUM1/IRF4 and BCL2). LMO2 protein expression paralleled its RNA expression in B-cell lymphoma cell lines and was found in GC B, but not in non-GC, B-cell lines. To test the prognostic significance of LMO2 protein we analyzed an independent cohort of 203 DLBCL patients (mean age 63, range 18–93), uniformly treated with anthracycline-containing chemotherapy not containing rituximab, from four medical centers. No significant difference in response to therapy (CR and CRu) was observed between patients with LMO2-positive and LMO2-negative lymphomas (77% and 59%, respectively, p 0.05). However, Kaplan- Meier curves demonstrated a statistically significant difference in overall survival (OS) between LMO2-positive and LMO2-negative cases (p 0.035; median OS of 74 and 20 months, respectively). Similarly, event-free survival (EFS) was also significantly longer in patients with LMO2-positive compared to LMO2-negative lymphomas (p 0.01, median EFS of 48 and 12 months, respectively). The predictive power of LMO2 expression was IPI-independent. Multivariate analyses with protein expression profiles of HGAL, BCL6, CD10, JAW1, MUM1/IRF4 and BCL2 on this cohort of patients are underway to construct a clinically applicable immunohistologic algorithm for predicting survival. The capacity of LMO2 protein to identify DLBCL patients with improved outcome in an IPI-independent manner indicates its important role in risk stratification in this disease.
The Cognitive Radio paradigm for Ultra-Wideband systems: The European Project EUWB (2008)

In this paper we will discuss the research activity in Cognitive Radio (CR) for Ultra-Wideband (UWB) systems within the FP7 European Project EUWB. We cover the issues related to the interference and coexistence between narrowband (NB) and UWB communication systems in a realistic scenario. We show the great potential of the UWB technology in adapting the transmitted spectrum to counteract NB interference and at the same time to guarantee low spectral emissions over existing narrowband communications. We also discuss the role of location capable radios on cognitive UWB nodes.
Isoflurane-Induced Hypotension and Vital Organ Blood Flow (1994)

Department of Anesthesiology, ZA-14 Hurborview Medical Center University of Washington School of Medicine Seattle, WA 98104
Mild Organic Ammonium Tribromide–Mediated Regioselective Ring Opening of Epoxides with Alcohols, Water, Acetic Anhydride, and Amines Under Solvent-Free Reaction Conditions (2011)

Abstract Organic ammonium tribromide (OATB), N-methylpyrrolidine-2-one hydrotribromide (MPHT) was found to be an efficient catalyst for the regioselective ring opening of epoxides with various nucleophiles under solvent free conditions. This procedure occurs under neutral and mild reaction conditions with out adding any additive and afforded high yields of products.
Diethoxymethyl Protected Pyrroles: Synthesis and Regioselective Transformations (2001)

Treatment of the acceptor-substituted pyrroles 1a-k with neat triethyl orthoformate gives access to the diethoxymethyl (DEM) protected derivatives 2a-k in high yield. Convenient and mild cleavage was achieved by subsequent treatment of the DEM-pyrroles 2a-k with trifluoroacetic acid in acetonitrile and aqueous NaOH at room temperature. DEM protection proved suitable for a variety of regioselective transformations involving directed ortho-metalation and iodine-magnesium exchange processes. Furthermore, electrophilic halogenations and Pd-catalyzed coupling reactions were also carried out.
ChemInform Abstract: Mesomorphic Molecular Materials. Dielectric and Nonlinear Optical Properties of Donor‐Acceptor Azomethine Nematogens. (1992)

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.
Vascular endothelial growth factor (VEGF) is expressed by neurons in the hippocampus. (2015)

&lt;p&gt;Figure shows immunoreactivity of VEGF, NeuN and merged in the granule cell layer (GCL) and hilus (Hi) of the dentate gyrus. In both controls and Flk-1 OE mice, neurons in the hippocampus express VEGF. Scale bar is set to 20 µm.&lt;/p&gt;
Acute myocardial ischemia: magnetic resonance contrast enhancement with gadolinium-DTPA. (1984)

Gadolinium-DTPA (Gd-DTPA) was used to improve the diagnostic utility of magnetic resonance (MR) in detecting early ischemia, before the onset of infarction. Following one minute of left anterior descending coronary artery occlusion, 9 dogs were intravenously injected with either 0.5 mM/kg of Gd-DTPA (6 dogs) or normal saline (3 dogs). One more minute was allowed for perfusion of injectate prior to cardiectomy and MR imaging of the ex situ heart. There was no visible difference in intensity or alterations in magnetic relaxation times between normal and ischemic myocardium in the control (saline-injected) animals. The Gd-DTPA-injected dogs had a well-defined segment of high intensity representing the ischemic myocardium in the anterior wall of the left ventricle, due to significant T2 relaxation rate enhancement in the adjacent normal myocardium. Both T1 and T2 were significantly (p less than 0.01) shortened in the normal myocardium of the Gd-DTPA animals, but relatively greater T2 relaxation rate enhancement resulted in reduced intensity of normal myocardium, thus increasing contrast with ischemic myocardium. As a result of the significant shortening of T1 and T2 in the normal myocardium relative to the ischemic myocardium, improved delineation of the ischemic segment could be obtained using calculated T1 and T2 images. It is concluded that Gd-DTPA has the potential to expand the sensitivity and diagnostic utility of MR in the study of occlusive coronary artery disease.
Making Better Batteries with Metal Oxide & Graphene Composites (2017)

Learn how PNNL and Princeton scientists create better materials for batteries, materials that assemble on their own into durable nanocomposites.
Model of the Origin of a Ciguatoxic Grouper (Plectropomus leopardus) (2023)

Published data were used to model the transfer of ciguatoxins (CTX) across three trophic levels of a marine food chain on the Great Barrier Reef (GBR), Australia, to produce a mildly toxic common coral trout (<i>Plectropomus leopardus</i>), one of the most targeted food fishes on the GBR. Our model generated a 1.6 kg grouper with a flesh concentration of 0.1 µg/kg of Pacific-ciguatoxin-1 (P-CTX-1 = CTX1B) from 1.1 to 4.3 µg of P-CTX-1 equivalents (eq.) entering the food chain from 0.7 to 2.7 million benthic dinoflagellates (<i>Gambierdiscus</i> sp.) producing 1.6 pg/cell of the P-CTX-1 precursor, P-CTX-4B (CTX4B). We simulated the food chain transfer of ciguatoxins via surgeonfishes by modelling <i>Ctenochaetus striatus</i> feeding on turf algae. A <i>C. striatus</i> feeding on ≥1000 <i>Gambierdiscus</i>/cm<sup>2</sup> of turf algae accumulates sufficient toxin in <2 days that when preyed on, produces a 1.6 kg common coral trout with a flesh concentration of 0.1 µg/kg P-CTX-1. Our model shows that even transient blooms of highly ciguatoxic <i>Gambierdiscus</i> can generate ciguateric fishes. In contrast, sparse cell densities of ≤10 <i>Gambierdiscus</i>/cm<sup>2</sup> are unlikely to pose a significant risk, at least in areas where the P-CTX-1 family of ciguatoxins predominate. The ciguatera risk from intermediate <i>Gambierdiscus</i> densities (~100 cells/cm<sup>2</sup>) is more difficult to assess, as it requires feeding times for surgeonfish (~4-14 days) that overlap with turnover rates of turf algae that are grazed by herbivorous fishes, at least in regions such as the GBR, where stocks of herbivorous fishes are not impacted by fishing. We use our model to explore how the duration of ciguatoxic <i>Gambierdiscus</i> blooms, the type of ciguatoxins they produce, and fish feeding behaviours can produce differences in relative toxicities between trophic levels. Our simple model indicates thresholds for the design of risk and mitigation strategies for ciguatera and the variables that can be manipulated to explore alternate scenarios for the accumulation and transfer of P-CTX-1 analogues through marine food chains and, potentially, for other ciguatoxins in other regions, as more data become available.
Localization and Properties of Nad-Dependent 15 Hydroxyprostaglandin Dehydrogenase Activity in Spontaneously Hypertensive Rat Kidney (1986)

To evaluate the pathophysiological significance of renal NAD-dependent 15 hydroxyprostaglandin dehydrogenase (PGDH) in young spontaneously hypertensive rats (SHR), the intranephron distribution of PGDH was compared with age-matched Wistar Kyoto rats (WKY). With supernatants of kidney homogenates, PGDH activities in 3 week-old SHR were significantly lower than those in WKY, and no difference in PGDH activities was found between male and female in both WKY and SHR. By using microdissected nephron segments of 3 week-old WKY and SHR, PGDH activities in both groups were found to be exclusively distributed in the proximal tubules, within which the activity of the straight portion (PST) was several fold higher than that of the convoluted one (PCT). In 3 week-old SHR, a significant decrease of PGDH activity was observed only in PST, possibly indicating a decrease of enzyme content in PST because of similar Km values in both groups. These results may suggest that intraproximal PG concentration could be regulated by the change of PGDH in PST of young SHR.
Laser-based control of microfluidic droplets (2004)

We have constructed a simple optical system to control small droplets over a wide range of sizes (30 μm −1.5 mm diameter), based on the thermal Marangoni effect. We observed droplet fusion and rapid mixing (&lt;30 ms), and we have performed an absorption-based protein detection assay.
Behavior of Lattice Oxygen in Mixtures of V2O5 and Bi2O3 (1999)

The interaction between V2O5 and Bi2O3 and the evolution processes of lattice oxygen from their physical mixtures and a binary oxide (BiVO4) have been studied by thermal gravimetric analysis. The source of lattice oxygen was Bi2O3, and it was more easily evolved from the physical mixtures especially of a V:Bi = 1:1 mole ratio than respective single metal oxides or the binary oxide. When the physical mixtures of V2O5−Bi2O3 are heated at low temperatures which do not cause phase transformation of oxides, they can evolve or absorb oxygen reversibly. The reoxidation of reduced oxides proceeded much faster than the evolution of oxygen. The effective contact between two oxide phases appeared to be an important factor for the synergy between two phases in the evolution of lattice oxygen.
Supplementary Figures and Legends from PRMT1-Mediated Translation Regulation Is a Crucial Vulnerability of Cancer (2023)

&lt;p&gt;This file contains additional data supporting the role of Prmt1 in human OS maintenance and murine OS tumor initiation, as well as proteomics and RNA-seq data supporting the role of Prmt1 in translation regulation.&lt;/p&gt;
Turbulent water coupling in shock wave lithotripsy (2013)

Previous studies have demonstrated that stone comminution decreases with increased pulse repetition frequency as a result of bubble proliferation in the cavitation field of a shock wave lithotripter (Pishchalnikov et al 2011 J. Acoust. Soc. Am. 130 EL87-93). If cavitation nuclei remain in the propagation path of successive lithotripter pulses, especially in the acoustic coupling cushion of the shock wave source, they will consume part of the incident wave energy, leading to reduced tensile pressure in the focal region and thus lower stone comminution efficiency. We introduce a method to remove cavitation nuclei from the coupling cushion between successive shock exposures using a jet of degassed water. As a result, pre-focal bubble nuclei lifetime quantified by B-mode ultrasound imaging was reduced from 7 to 0.3 s by a jet with an exit velocity of 62 cm s(-1). Stone fragmentation (percent mass <2 mm) after 250 shocks delivered at 1 Hz was enhanced from 22 ± 6% to 33 ± 5% (p = 0.007) in water without interposing tissue mimicking materials. Stone fragmentation after 500 shocks delivered at 2 Hz was increased from 18 ± 6% to 28 ± 8% (p = 0.04) with an interposing tissue phantom of 8 cm thick. These results demonstrate the critical influence of cavitation bubbles in the coupling cushion on stone comminution and suggest a potential strategy to improve the efficacy of contemporary shock wave lithotripters.
Neuropeptide Y and neuron-specific enolase levels in benign and malignant pheochromocytomas (1990)

Neuron-specific enolase (NSE) is the isoform of enolase, a glycolytic enzyme found in the neuroendocrine system. Neuropeptide Y (NPY) is a peptide recently discovered in the peripheral and central nervous systems. Serum NSE and plasma NPY levels have been reported to be increased in some patients with pheochromocytoma. The authors evaluated whether the measurement of these molecules could help to discriminate between benign and malignant forms of pheochromocytoma. The NSE levels were normal in all patients with benign pheochromocytoma (n = 13) and elevated in one half of those with malignant pheochromocytoma (n = 13). Plasma NPY levels were on the average significantly higher in the malignant (177.1 +/- 38.9 pmol/l, n = 16) than in the benign forms of the disease (15.7 +/- 389 pmol/l, n = 24). However, there was no difference in the percentage of patients with elevated NPY levels. These results show that determination of serum NSE may be useful for distinguishing between malignant and benign pheochromocytoma; the measurement of plasma NPY is not useful for differentiating the two kinds of tumors.
Friction Stir Welded “A” Frame for Dual Function Test Fixture (2011)

This chapter contains sections titled: Introduction Pin and Parameter Methodology Pin and Parameter Results with Discussion FSW Fabrication Conclusions Acknowledgements
Active Acoustic Ranging to Locate Two Nearby Wellbores in Deepwater Gulf of Mexico (2017)

Abstract Salt drilling in Deepwater Gulf of Mexico (GOM) presents unique challenges. One of these challenges is the effect salt has on ranging technologies used in contingency relief well designs. A new technique called Active Acoustic Ranging (AAR) addresses the challenge of locating and tracking the target wellbore to the interception phase. This case study details the degree of precision that this new technique provided while locating two nearby wellbores within salt. This study is intended to improve industry awareness and understanding of relief well ranging options available to the industry, specifically wellbore ranging activities conducted within a salt formation. Sonic logging started in the early 1930s to determine rock characteristics by measuring the refracted signals from a combination of transmitters and receivers. The technique evolved by recording acoustic signals beyond the refracted zone, by positioning the transmitters and receivers downhole in the logging tool. AAR utilizes surface seismic processing methods to determine azimuthal direction and distance of compressional and shear acoustic signals, reflected from around the borehole. After processing the reflected signals, the distance and direction of nearby wellbores can be determined. This can be effective in salt formations, where resistivity inhibits use of active electromagnetic ranging tools. This case study presents test results conducted in a GOM Deepwater operation to locate two nearby wellbores, a cased hole and an open hole, using AAR. It shows that AAR signals can be successful in locating offset wellbores within salt formations. The acoustic signals, both compressional and shear, were recorded using a stack of 13 receivers. Each stack had 8 sector azimuthal receivers to determine the distance and direction of the corresponding target wellbores. By utilizing compressional and shear signals generated from the various distances of monopole and dipole transmitters, a redundant process was provided to determine the location of the target wellbores with a high degree of accuracy. In addition, the acoustic images provided estimates of the salt quality, which can be used to select the interception location for hydraulic kills. The maximum ranging distance is dependent on the velocity and attenuation of the transmitted acoustic signals in the traversed formations. Salt typically has higher velocities that will enable ranging at greater distances than other formations. One of the primary benefits of this technique is the ability to provide two different measurements using monopole and dipole sources to locate nearby wellbores. This reduces uncertainties that may arise when ranging with a system using only a single measurement. AAR benefits from the salt formation, whereas other ranging technologies, i.e. electromagnetic, were not optimized for salt. AAR increases the ranging options in salt formations.