gebhart/patrepeval huggingface dataset:
Adoptive Transfer of MART-1 T-Cell Receptor Transgenic Lymphocytes and Dendritic Cell Vaccination in Patients with Metastatic Melanoma (2014)

Double cell therapy with ACT of TCR-engineered T cells with a very short ex vivo manipulation and DC vaccines is feasible and results in antitumor activity, but improvements are needed to maintain tumor responses.
Lipocalin-2 Is an Autocrine Mediator of Reactive Astrocytosis (2009)

Astrocytes, the most abundant glial cell type in the brain, provide metabolic and trophic support to neurons and modulate synaptic activity. In response to a brain injury, astrocytes proliferate and become hypertrophic with an increased expression of intermediate filament proteins. This process is collectively referred to as reactive astrocytosis. Lipocalin 2 (lcn2) is a member of the lipocalin family that binds to small hydrophobic molecules. We propose that lcn2 is an autocrine mediator of reactive astrocytosis based on the multiple roles of lcn2 in the regulation of cell death, morphology, and migration of astrocytes. lcn2 expression and secretion increased after inflammatory stimulation in cultured astrocytes. Forced expression of lcn2 or treatment with LCN2 protein increased the sensitivity of astrocytes to cytotoxic stimuli. Iron and BIM (Bcl-2-interacting mediator of cell death) proteins were involved in the cytotoxic sensitization process. LCN2 protein induced upregulation of glial fibrillary acidic protein (GFAP), cell migration, and morphological changes similar to characteristic phenotypic changes termed reactive astrocytosis. The lcn2-induced phenotypic changes of astrocytes occurred through a Rho-ROCK (Rho kinase)-GFAP pathway, which was positively regulated by nitric oxide and cGMP. In zebrafishes, forced expression of rat lcn2 gene increased the number and thickness of cellular processes in GFAP-expressing radial glia cells, suggesting that lcn2 expression in glia cells plays an important role in vivo. Our results suggest that lcn2 acts in an autocrine manner to induce cell death sensitization and morphological changes in astrocytes under inflammatory conditions and that these phenotypic changes may be the basis of reactive astrocytosis in vivo.
CRISPR/Cas9‐mediated tetra‐allelic mutation of the ‘Green Revolution’ SEMIDWARF‐1 (SD‐1) gene confers lodging resistance in tef (Eragrostis tef) (2022)

Tef is a staple food and a valuable cash crop for millions of people in Ethiopia. Lodging is a major limitation to tef production, and for decades, the development of lodging resistant varieties proved difficult with conventional breeding approaches. We used CRISPR/Cas9 to introduce knockout mutations in the tef orthologue of the rice SEMIDWARF-1 (SD-1) gene to confer semidwarfism and ultimately lodging resistance. High frequency recovery of transgenic and SD-1 edited tef lines was achieved in two tef cultivars by Agrobacterium-mediated delivery into young leaf explants of gene editing reagents along with transformation and regeneration enhancing morphogenic genes, BABY BOOM (BBM) and WUSCHEL2 (WUS2). All of the 23 lines analyzed by next-generation sequencing had at least two or more alleles of SD-1 mutated. Of these, 83% had tetra-allelic frameshift mutations in the SD-1 gene in primary tef regenerants, which were inherited in subsequent generations. Phenotypic data generated on T<sub>1</sub> and T<sub>2</sub> generations revealed that the sd-1 lines have reduced culm and internode lengths with no reduction in either panicle or peduncle lengths. These characteristics are comparable with rice sd-1 plants. Measurements of lodging, in greenhouse-grown plants, showed that sd-1 lines have significantly higher resistance to lodging at the heading stage compared with the controls. This is the first demonstration of the feasibility of high frequency genetic transformation and CRISPR/Cas9-mediated genome editing in this highly valuable but neglected crop. The findings reported here highlight the potential of genome editing for the improvement of lodging resistance and other important traits in tef.
Two‐dimensional electrophoresis of prostate‐specific antigen in sera of men with prostate cancer or benign prostate hyperplasia (1999)

This chapter contains sections titled: Introduction Materials and methods Results and discussion Concluding remarks References
Moderate intrinsic phenotypic alterations in C9orf72 ALS/FTD iPSC-microglia despite the presence of C9orf72 pathological features (2023)

While motor and cortical neurons are affected in <i>C9orf72</i> amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD), it remains largely unknown if and how non-neuronal cells induce or exacerbate neuronal damage. We differentiated <i>C9orf72</i> ALS/FTD patient-derived induced pluripotent stem cells into microglia (iPSC-MG) and examined their intrinsic phenotypes. Similar to iPSC motor neurons, <i>C9orf72</i> ALS/FTD iPSC-MG mono-cultures form G<sub>4</sub>C<sub>2</sub> repeat RNA foci, exhibit reduced C9orf72 protein levels, and generate dipeptide repeat proteins. Healthy control and <i>C9orf72</i> ALS/FTD iPSC-MG equally express microglial specific genes and perform microglial functions, including inflammatory cytokine release and phagocytosis of extracellular cargos, such as synthetic amyloid beta peptides and healthy human brain synaptoneurosomes. RNA sequencing analysis revealed select transcriptional changes of genes associated with neuroinflammation or neurodegeneration in diseased microglia yet no significant differentially expressed microglial-enriched genes. Moderate molecular and functional differences were observed in <i>C9orf72</i> iPSC-MG mono-cultures despite the presence of C9orf72 pathological features suggesting that a diseased microenvironment may be required to induce phenotypic changes in microglial cells and the associated neuronal dysfunction seen in C9orf72 ALS/FTD neurodegeneration.
Protein phosphatase AP2C1 negatively regulates basal resistance and defense responses toPseudomonas syringae (2016)

Mitogen-activated protein kinases (MAPKs) mediate plant immune responses to pathogenic bacteria. However, less is known about the cell autonomous negative regulatory mechanism controlling basal plant immunity. We report the biological role of Arabidopsis thaliana MAPK phosphatase AP2C1 as a negative regulator of plant basal resistance and defense responses to Pseudomonas syringae. AP2C2, a closely related MAPK phosphatase, also negatively controls plant resistance. Loss of AP2C1 leads to enhanced pathogen-induced MAPK activities, increased callose deposition in response to pathogen-associated molecular patterns or to P. syringae pv. tomato (Pto) DC3000, and enhanced resistance to bacterial infection with Pto. We also reveal the impact of AP2C1 on the global transcriptional reprogramming of transcription factors during Pto infection. Importantly, ap2c1 plants show salicylic acid-independent transcriptional reprogramming of several defense genes and enhanced ethylene production in response to Pto. This study pinpoints the specificity of MAPK regulation by the different MAPK phosphatases AP2C1 and MKP1, which control the same MAPK substrates, nevertheless leading to different downstream events. We suggest that precise and specific control of defined MAPKs by MAPK phosphatases during plant challenge with pathogenic bacteria can strongly influence plant resistance.
Binarisation of photographed documents image quality and processing time assessment (2021)

Smartphones with cameras are omnipresent in today's world and are very often used to photograph documents. Document binarization is a key process in many document processing platforms. This competition on binarizing photographed documents assessed the quality and time performance of 13 new algorithms and 50 existing algorithms. The evaluation dataset is composed of offset, laser, and deskjet printed documents, photographed using four widely-used mobile devices with the strobe flash on and off, under two different angles and places of capture.
Probe based confocal microendoscopy and its use for in-vivo microimaging of the distal lungs (2015)

International audience
Active Viremia in Rotavirus-Infected Mice (2006)

Rotavirus circulates extraintestinally in animals used as models for rotavirus infection and in children. Rotavirus infection in mice was used to define host or viral factors that affect rotavirus viremia. Antigenemia was observed with homologous and heterologous rotaviruses, and neither age nor mouse strain genetics altered the occurrence of rotavirus antigenemia or viremia. Rotavirus RNA and infectious virus were present in sera and associated with the plasma fraction of blood in all infected mice. These findings indicate that antigenemia/viremia occurs routinely in rotavirus infections and imply that infectious rotavirus has access to any extraintestinal cell within contact of blood.
Inactivation of γ-Aminobutyric Acid Aminotransferase by Various Amine Buffers (1992)

It is hypothesized that buffers capable of forming a Schiff base with the PLP of gamma-aminobutyric acid aminotransferase (GABA-AT) may lead to denaturation and inactivation of the enzyme. On the basis of this hypothesis three new methods for the selective destruction of GABA-AT in GABAse (a commercial bacterial source of a mixture of GABA-AT and succinic semialdehyde dehydrogenase [SSDH]) and from pig brain are described: (1) dialysis against a primary or secondary amine buffer; (2) gel filtration with a primary or secondary amine buffer as eluent; (3) inactivation with gabaculine followed by dialysis or gel filtration with pyrophosphate buffer. The SSDH activity in GABAse, which remains unchanged by all of these methods, may then be used in a coupled assay to measure the activity of GABA-AT from different sources. These results also suggest that the use of primary and secondary amine buffers should be avoided when inhibitors are being tested with GABA-AT.
Near-field coupling and readout of nano recording marks (Conference Presentation) (2017)

Near-field optical disk (NFOD) is a novel and demanded developments of optical storage technology. The nonlinear plasmonic coupling effect of the complete nano recording unit is important for increasing the near and far field optical readout contrast. Here, we present a simple plasmonic near-field coupling optical disk system. The near-field coupling effect between two nano-recording marks with various thickness of the dielectric spacer layer are investigated.
GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser (2021)

Abstract Access to web-based platforms has enabled scientists to perform research remotely. A critical aspect of mass spectrometry data analysis is the inspection, analysis, and visualization of the raw data to validate data quality and confirm statistical observations. We developed the GNPS Dashboard, a web-based data visualization tool, to facilitate synchronous collaborative inspection, visualization, and analysis of private and public mass spectrometry data remotely.
Short‐term suppression of the xeno‐immune response with mCTLA4‐Fc treatment (1997)

Abstract: A murine CTLA4‐Fc chimeric fusion protein was used to determine if inhibition of the CD28‐B7 pathway for T‐cell activation could result in prolonged or indefinite survival of pancreatic islet xenografts in mice. B6AF1 recipients of Wistar rat pancreatic islet xenografts that received short‐term mCTLA4‐Fc treatment had prolonged graft survival (28 days vs. 9 days) but all animals rejected their grafts. This survival advantage was similar to that achieved with short‐term depletion of CD3+ or CD4+ T cells with 145.2C11 (median graft survival 21 days) or GK1.5 mAb (median graft survival 33 days), respectively. Combined GK1.5, 145.2C11, and mCTLA4‐Fc treatment for the first 2 weeks post‐transplant and maintenance therapy with GK1.5 and mCTLA4‐Fc for the next 4 weeks produced the best results (median survival 63 days). However, islet xenografts were rapidly rejected upon cessation of treatment. Unlike in allografts, short‐term inhibition of the CD28‐B7 pathway with mCTLA4‐Fc did not result in long‐term rat xenograft survival. This suggests that the conditions necessary for quenching xenograft rejection and inducing tolerance differ significantly from those found in allotransplantation and acquired xenograft tolerance may be difficult to achieve.
The effect of Ti conduit on the critical current in (NbTi)/sub 3/ Sn cable-in-conduit conductors (1993)

The authors investigated the effect of Ti conduit on the critical current in (NbTi)/sub 3/Sn cable-in-conduit conductors in comparison with stainless steel and copper-nickel alloy conduits. Ti has a coefficient of thermal expansion closely matching (NbTi)/sub 3/Sn and is expected to prevent the compressive thermal prestrain introduced in (NbTi)/sub 3/Sn filaments. As samples, two kinds of conductors were prepared, one consisting of seven (NbTi)/sub 3/Sn strands and the other of 36 (NbTi)/sub 3/Sn strands. The (NbTi)/sub 3/Sn strands produced by a bronze process had a diameter of 1.0 mm and a copper ratio of 2. The experimental results indicated that the critical current density in conductors with a Ti conduit and void fraction in the range of 5-46% nearly matched that of a single strand. From these results, Ti appears to be attractive as a practical conduit material for (NbTi)/sub 3/Sn cable-in-conduit conductors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fractionation of the Three Stable Oxygen Isotopes by Oxygen-Producing and Oxygen-Consuming Reactions in Photosynthetic Organisms (2005)

The triple isotope composition (delta17O and delta18O) of dissolved O2 in the ocean and in ice cores was recently used to assess the primary productivity over broad spatial and temporal scales. However, assessment of the productivity with the aid of this method must rely on accurate measurements of the 17O/16O versus 18O/16O relationship in each of the main oxygen-producing and -consuming reactions. Data obtained here showed that cleavage of water in photosystem II did not fractionate oxygen isotopes; the delta18O and delta17O of the O2 evolved were essentially identical to those of the substrate water. The fractionation slopes for the oxygenase reaction of Rubisco and respiration were identical (0.518 +/- 0.001) and that of glycolate oxidation was 0.503 +/- 0.002. There was a considerable difference in the slopes of O2 photoreduction (the Mehler reaction) in the cyanobacterium Synechocystis sp. strain PCC 6803 (0.497 +/- 0.004) and that of pea (Pisum sativum) thylakoids (0.526 +/- 0.001). These values provided clear and independent evidence that the mechanism of O2 photoreduction differs between higher plants and cyanobacteria. We used our method to assess the magnitude of O2 photoreduction in cyanobacterial cells maintained under conditions where photorespiration was negligible. It was found that electron flow to O2 can be as high as 40% that leaving photosystem II, whereas respiratory activity in the light is only 6%. The implications of our findings to the evaluation of specific O2-producing or -consuming reactions, in vivo, are discussed.
Metabolism of Pyrene by the Basidiomycete Crinipellis stipitaria and Identification of Pyrenequinones and Their Hydroxylated Precursors in Strain JK375 (1994)

The metabolism of pyrene, a polycyclic aromatic hydrocarbon, by submerged cultures of the basidiomycete Crinipellis stipitaria was studied. After incubation for 68 h at 25 degrees C in a 20-liter fermentor with complex medium and 20 mg of pyrene per liter, five metabolites were detected. The compounds were isolated by preparative high-performance liquid chromatography on RP18 and DIOL gels. By UV, infrared, and H nuclear magnetic resonance spectroscopy and mass spectrometry, 1-hydroxypyrene, 1,6-dihydroxypyrene, 1,8-dihydroxypyrene, 1,6-pyrenequinone, and 1,8-pyrenequinone were identified. 1,6- and 1,8-dihydroxypyrene were obtained from fungal cultures for the first time. The formation of these metabolites was confirmed by investigations with [4,5,9,10-C]pyrene.
Correction method for high-precision CD measurements on electrostatically charged wafers (2002)

A correction method for automatic, high-precision CD-measurements on electrostatically charged wafers has been developed and installed in the Hitachi CD-SEM S-9260 to evaluate its performance. There are two types of charging: global and local. Global charging is stable and spreads all over a wafer while the local charging area is limited within the beam scanning area. A conventional CD-SEM has two weak points with respect to those charged wafers: one is failure at the positioning and autofocusing procedure which interferes with the fully automatic measurement sequence, and the other is disturbance of optical magnification which degrades the precision of CD-measurement values. By probing the global charging voltage with an electrostatic voltmeter prior to the CD-measurements, we subtract the voltage from a retarding voltage and then apply it to the wafer holder. The beam-focusing condition can stay within the fully automatically tunable range. And by generating numerical functions to represent the relationship between the global charging voltage, wafer height, excitation current of the objective lens and optical magnification, with the help of electron optical simulations, we can calculate the true optical magnification and the correct CD-measurement values. The local charging voltage is derived from the voltage shift of S-curves of secondary electron yield between conductive and insulated wafers measured with an energy filter. We correct the CD-measurement values using the simulated proportional relationship between magnifications of the electrostatic micro-lens and the local charging voltage. The coefficient is almost constant when the charging area is smaller than an equivalent circle of 100mm radius. We demonstrate that the CD-measurement values are successfully corrected within 0.1 percent in deviation for both charging types.
ChemInform Abstract: Fluorous Chemistry in Pittsburgh: 1996—2008 (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Some Novel Applications of Explanation-Based Learning to Parsing Lexicalized Tree-Adjoining Grammars (1995)

In this paper we present some novel applications of Explanation-Based Learning (EBL) technique to parsing Lexicalized Tree-Adjoining grammars. The novel aspects are (a) immediate generalization of parses in the training set, (b) generalization over recursive structures and (c) representation of generalized parses as Finite State Transducers. A highly impoverished parser called a ``stapler'' has also been introduced. We present experimental results using EBL for different corpora and architectures to show the effectiveness of our approach.
Analysis and reduction method of conducted noise in GaN HEMTs based totem-pole bridgeless PFC converter (2016)

Totem-pole bridgeless PFC converter is proposed to pursuit better efficiency as it reduces the loss added by the diode bridge. However, the conducted noise performance of totem-pole bridgeless PFC converter is unsatisfactory as the spike current occurs at input voltage zero-crossing and causes severe common mode noise. In this paper, the noise mechanism at zero-crossing of the converter is discussed and a noise reduction method is proposed. Finally, the experiments have been achieved under the condition: 230V ac input, 390V dc output and 50kHz switching frequency, and the effectiveness of the proposed noise reduction method is verified.
Analysis of the Power Outage Effects in RFID (2016)

During RFID inventories, transmission losses due to fading may cause power outage events to the tags, which loose their state and abandon the ongoing identification round. We develop an analytical model, which includes this effect and allows us to accurately characterize RFID anti-collision protocol performance. We show that power outage events produce deviations from ideal performance, leading to new criteria to set the optimal operation parameters in RFID.
Engineering of technetium‐99m‐binding artificial receptors for imaging gene expression (2003)

(1) Both types of engineered 'artificial receptors' were expressed on the surface of eukaryotic cells; (2) marker proteins were functional in binding (99m)TcOT; and (3) type II membrane proteins were more efficient in binding (99m)TcOT than type I proteins. We anticipate that the developed approach could be useful for 'tagging' transfected cells with (99m)TcOT enabling imaging of tracking in vivo transduced cells or cell therapies.
Retinoic Acid in the Immune System (2008)

On occasion, emerging scientific fields intersect and great discoveries result. In the last decade, the discovery of regulatory T cells (T(reg)) in immunity has revolutionized our understanding of how the immune system is controlled. Intersecting the rapidly emerging field of T(reg) function, has been the discovery that retinoic acid (RA) controls both the homing and differentiation of T(reg). Instantly, the wealth and breadth of knowledge of the molecular basis for RA action, its receptors, and how it controls cellular differentiation can and will be exploited to understand its profound effects on T(reg). Historically, vitamin A deprivation and repletion and RA agonists have been shown to profoundly affect immunity. Now these findings can be interpreted in light of the revelations that RA controls leukocyte homing and T(reg) function.
Boric Acid‐Catalyzed Direct Condensation of Carboxylic Acids with Benzene‐1,2‐diamine into Benzimidazoles (2011)

Abstract The applicability of boric acid catalysis for the direct condensation of carboxylic acids with benzene‐1,2‐diamine to give 2‐substituted benzimidazoles was investigated. It was found that catalytic amounts (5–10 mol‐%) of boric acid efficiently promote the cyclocondensation of aliphatic carboxylic acids in refluxing toluene. In addition, the relatively neutral conditions allow the use of acid‐sensitive substrates and give rise to specific transformations and selectivities that are not observed with some classical methods. Benzoic acids were found to be less reactive than aliphatic acids and thus require refluxing xylene for better efficiency. Phenylboronic acid was found to be inactive as a catalyst due to its rapid consumption by condensation with benzene‐1,2‐diamine to give a 2‐phenylbenzodiazaborole.
Modified cine inversion recovery pulse sequence for the quantification of myocardial T1 and gadolinium partition coefficient (2012)

It was feasible to measure T1 and λ(Gd) with MCine-IR and the results were in good agreement with the literature.