gebhart/patrepeval huggingface dataset:
EEG-Based Brain-Computer Interaction: Improved Accuracy by Automatic Single-Trial Error Detection (2007)

Brain-computer interfaces (BCIs), as any other interaction modality based on physiological signals and body channels (e.g., muscular activity, speech and gestures), are prone to errors in the recognition of subject's intent. An elegant approach to improve the accuracy of BCIs consists in a verification procedure directly based on the presence of error-related potentials (ErrP) in the EEG recorded right after the occurrence of an error. Six healthy volunteer subjects with no prior BCI experience participated in a new human-robot interaction experiment where they were asked to mentally move a cursor towards a target that can be reached within a few steps using motor imagination. This experiment confirms the previously reported presence of a new kind of ErrP. These Interaction ErrP exhibit a first sharp negative peak followed by a positive peak and a second broader negative peak (~290, ~350 and ~470 ms after the feedback, respectively). But in order to exploit these ErrP we need to detect them in each single trial using a short window following the feedback associated to the response of the classifier embedded in the BCI. We have achieved an average recognition rate of correct and erroneous single trials of 81.8% and 76.2%, respectively. Furthermore, we have achieved an average recognition rate of the subject's intent while trying to mentally drive the cursor of 73.1%. These results show that it's possible to simultaneously extract useful information for mental control to operate a brain-actuated device as well as cognitive states such as error potentials to improve the quality of the brain-computer interaction. Finally, using a well-known inverse model (sLORETA), we show that the main focus of activity at the occurrence of the ErrP are, as expected, in the pre-supplementary motor area and in the anterior cingulate cortex.
Computer program to predict likelihood of finding and HLA-matched donor: methodology, validation, and application. (1996)

Approximately 65% of the patients requiring bone marrow transplantation do not have an HLA-A, -B, -DR identical sibling and therefore need to find a phenotypically matched unrelated donor. As of June 30, 1996, the National Marrow Donor Program maintains a registry of 2.31 million volunteer donors, 35% of whom are fully typed for HLA-A, -B, -DR loci. Because a majority of the donors has not been DR typed, a patient who does not find a complete match at the time of the preliminary search may elect to prospectively DR type A, B matched and A, B one-antigen mismatched donors. An efficient strategy is therefore needed for determining the likelihood that an appropriate donor exists and for deciding which of the donors that have not yet been DR typed should be tested for DR matching with the candidate. We developed a mathematical algorithm and computer program to facilitate the search for a suitable donor by donor race and phenotype. The program provides information on the likelihood of 1) finding at least one HLA-A, -B, -DR phenotypically matched donor, 2) the likelihood of finding at least one DR match among m A, B matched donors who have not yet been DR typed, and 3) the likelihood of an A, B one antigen mismatched donor of a specific phenotype being a DR match with the patient. The mathematical models underlying the program are based on basic population genetics theory and utilize HLA-A, -B, DR haplotype frequencies derived from the NMDP registry. The results of the validation study show that the prediction is highly accurate at the level of broad antigens. The algorithm and program have the potential to assist patients and physicians in optimizing their decisions regarding clinical management and resource allocation on the process of searching for a suitable unrelated bone marrow donor.
Role of sphingosine 1-phosphate receptor type 1 in lymphocyte egress from secondary lymphoid tissues and thymus. (2006)

Circulation of mature lymphocytes between blood and secondary lymphoid tissues plays a central role in the immune system. Homing of lymphocytes from blood into secondary lymphoid tissues beyond high endothelial venules is highly dependent on the interaction between the chemokines CCL19, CCL21, CXCL12, and CXCL13, and their receptors CCR7, CXCR4 and CXCR5. However, the molecular mechanism(s) of lymphocyte egress from secondary lymphoid tissues to lymph remained unclear. We have found a new class of immunomodulator, FTY720 by chemical modification of vegetative wasp-derived natural product, ISP-I (myriocin). FTY720 has been shown to be highly effective in experimental allograft and autoimmune disease models. A striking feature of FTY720 is the induction of a marked decrease in peripheral blood lymphocytes at doses that show immunomodulating activity in these models. The reduction of circulating lymphocytes by FTY720 is caused by sequestration of lymphocytes into secondary lymphoid tissues and thymus. FTY720 is rapidly converted to (S)-enantiomer of FTY720-phosphate [(S)-FTY720-P] by sphingosine kinase 2 in vivo. (S)-FTY720-P acting as a potent agonist of S1P receptor type 1 (S1P1), induces long-term down-regulation of S1P1 on lymphocytes, and thereby inhibits the migration of lymphocytes toward S1P. Thus, it is presumed that FTY720-induced lymphocyte sequestration is due to the inhibition of S1P/S1P1-dependent lymphocyte egress from secondary lymphoid tissues and thymus by its active metabolite (S)-FTY720-P. Throughout the analysis of the mechanism of action of FTY720, it is clarified that S1P/S1P1 interaction plays an important role for lymphocyte egress from secondary lymphoid tissues and thymus.
Metastatic Breast Cancer With ESR1 Mutation: Clinical Management Considerations From the Molecular and Precision Medicine (MAP) Tumor Board at Massachusetts General Hospital (2016)

ER+ breast tumors are known to undergo genomic evolution during treatment with the acquisition of new mutations that confer resistance to treatment.ESR1 mutations in the ligand-binding domain of ER can lead to a ligand-independent, constitutively active form of ER and mediate resistance to aromatase inhibitors.ESR1 mutations may be detected by genomic sequencing of tissue biopsies of the metastatic tumor or by sequencing the circulating tumor cells or tumor DNA (ctDNA).Sequencing results may lead to a therapeutic "match" with an existing FDA-approved drug or match with an experimental agent that fits the clinical setting.
Laser-fiber-optic "optrode" for real time in vivo blood carbon dioxide level monitoring (1987)

A fiber-optic sensor has been developed to measure and monitor the partial pressure of carbon dioxide in blood via fluorescence or phosphorescence changes in sensing dyes. The pCO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> optrode uses a nanoliter size droplet of a concentrated fluorescein derivative in a buffered sodium ascorbate solution as a pH indicator. The pH of the droplet equilibrates with the volatile constituents of blood across an air bubble trapped at the tip of the capillary surrounding the fiber. Ascorbic acid is used to reduce photobleaching, which is further minimized by working on the right portion of the concentration quenching curve. Signal levels of 300 000 counts per second are obtained at 0.5 μW using the 488-nm line of an argon ion laser. A response range of 25 percent was obtained when the sensor was evaluated from 1.97 to 7.40 percent CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> in air at controlled humidity and temperature.
A human cDNA sequence with homology to non-mammalian lysophosphatidic acid acyltransferases (1997)

A novel human homologue of Escherichia coli, yeast and plant 1-acylglycerol-3-phosphate acyltransferase has been isolated from U937 cell cDNA. Expression of the cloned sequence in 1-acylglycerol-3-phosphate acyltransferase-deficient E. coli resulted in increased incorporation of oleic acid into cellular phospholipids. Membranes made from COS7 cells transfected with the cDNA exhibited higher acyltransferase activity towards a range of donor fatty acyl-CoAs and lysophosphatidic acid. Northern-blot analysis of the cDNA sequence indicated high levels of expression in immune cells and epithelium. Rapid amplification of cDNA ends revealed differentially expressed splice variants, which suggests regulation of the enzyme by alternative splicing. This cDNA therefore represents the first described sequence of a mammalian gene homologous to non-mammalian lysophosphatidic acid acyltransferases.
Transforming growth factor β (TGF-β) and atherosclerosis -activation of latent TGF-β at the vascular wall- (1994)

Chronic alcohol consumption leads to extracellular matrix hyperplasia and liver fibrosis with a great role of hepatic stellate cell (HSC) activation in this process. The present study was designed to investigate the possible protective effects of diethylcarbamazine (DEC) (50 mg/kg, acting as an anti-inflammatory drug, interferes with the arachidonic acid metabolism) when administrated in combination with hesperidin (HDN) (200 mg/kg, a flavanone glycoside with potent antioxidant and anti-inflammatory activities) against alcoholic liver fibrosis in wistar rats compared to silymarin (Sil) (100 mg/kg). Liver fibrosis was induced in rats using ethanol (EtOH) (1 ml/100 g/day, p.o.) twice a week for seven weeks. Then, tissue and blood samples were collected to assess the protective effect of DEC + HDN combination. Our results indicated that DEC when combined with HDN blunted EtOH-induced necroinflammation and elevation of liver injury parameters in serum. Besides, attenuated EtOH- induced liver fibrosis, as demonstrated by hepatic histopathology scoring and 4-hydroxyproline content. The mechanisms behind these beneficial effects of both DEC and HDN were also elucidated. These include (1) counteracting hepatic oxidative stress and augmenting hepatic antioxidants; (2) inhibiting the activation of NF-κB as indicated by preventing release of hepatic IL6; (3) preventing the activation of hepatic stellate cells (HSCs), as denoted by reducing a-smooth muscle actin (a-SMA) expression in the liver; and (4) inhibiting the fibrogenesis response of HSCs, as indicated by inhibiting serum transforming growth factor-b1 (TGF-b1). Our study indicates a novel hepatoprotective effect when DEC was co-administered with HDN against liver fibrosis.
Down-regulation of p21 WAF1/CIP1 or p27 Kip1 abrogates antiestrogen-mediated cell cycle arrest in human breast cancer cells (2000)

Estrogens and antiestrogens influence the G(1) phase of the cell cycle. In MCF-7 breast cancer cells, estrogen stimulated cell cycle progression through loss of the kinase inhibitor proteins (KIPs) p27 and p21 and through G(1) cyclin-dependent kinase (cdk) activation. Treatment with antiestrogen drugs, Tamoxifen or ICI 182780, caused cell cycle arrest, with up-regulation of both p21 and p27 levels, an increase in their binding to cyclin E-cdk2, and kinase inhibition. The requirement for these KIPs in the arrests induced by estradiol depletion or by antiestrogens was investigated with antisense. Antisense inhibition of p21 or p27 expression in estradiol-depleted or antiestrogenarrested MCF-7 led to abrogation of cell cycle arrest, with loss of cyclin E-associated KIPs, activation of cyclin E-cdk2, and S phase entrance. These data demonstrate that depletion of either p21 or p27 can mimic estrogen-stimulated cell cycle activation and indicate that both of these KIPs are critical mediators of the therapeutic effects of antiestrogens in breast cancer.
HLA‐DRB sequencing‐based typing: an improved protocol which shows complete DRB exon 2 sequences and includes exon 3 of HLA‐DRB4/5 (2007)

Several human leukocyte antigen (HLA)-DRB protocols for sequencing-based typing have been described. In general, the DRB1 amplification is performed using group-specific amplification primers (GSAPs) located in HVR I or intron 1. Only some protocols include amplification of DRB3, DRB4, and DRB5. However, prior knowledge obtained by alternative methods such as PCR-SSP is preferred for some protocols and a large amount of DNA is often required for adequate typing of HLA-DRB1. We describe a new protocol that uses GSAPs located in the introns, includes also sequencing of exon 3 to enable high resolution. This protocol allows DRB typing without prior knowledge of the HLA type.
Differentiation and Immune Regulation of IL-9−Producing CD4+ T Cells in Malignant Pleural Effusion (2012)

Our data revealed that Th9 cells were increased in MPE and that Th9 cells exerted an important immune regulation on lung cancer cells in human tumor environment.
FTY720 Induces Apoptosis in Hepatocellular Carcinoma Cells through Activation of Protein Kinase C δ Signaling (2008)

This study was aimed at elucidating the mechanism by which FTY720, a synthetic sphingosine immunosuppressant, mediated antitumor effects in hepatocellular carcinoma (HCC) cells. The three HCC cell lines examined, Hep3B, Huh7, and PLC5, exhibited differential susceptibility to FTY720-mediated suppression of cell viability, with IC(50) values of 4.5, 6.3, and 11 mumol/L, respectively. Although FTY720 altered the phosphorylation state of protein kinase B and p38, our data refuted the role of these two signaling kinases in FTY720-mediated apoptosis. Evidence indicates that the antitumor effect of FTY720 was attributable to its ability to stimulate reactive oxygen species (ROS) production, which culminated in protein kinase C (PKC)delta activation and subsequent caspase-3-dependent apoptosis. We showed that FTY720 activated PKC delta through two distinct mechanisms: phosphorylation and caspase-3-dependent cleavage. Cotreatment with the caspase-3 inhibitor Z-VAD-FMK abrogated the effect of FTY720 on facilitating PKC delta proteolysis. Equally important, pharmacologic inhibition or shRNA-mediated knockdown of PKC delta protected FTY720-treated Huh7 cells from caspase-3 activation. Moreover, FTY720 induced ROS production to different extents among the three cell lines, in the order of Hep3B > Huh7 >> PLC5, which inversely correlated with the respective glutathione S-transferase pi expression levels. The low level of ROS generation might underlie the resistant phenotype of PLC5 cells to the apoptotic effects of FTY720. Blockade of ROS production by an NADPH oxidase inhibitor protected Huh7 cells from FTY720-induced PKC delta activation and caspase-3-dependent apoptosis. Together, this study provides a rationale to use FTY720 as a scaffold to develop potent PKC delta-activating agents for HCC therapy.
Toward RNA interference‐based therapy for filovirus infections (2009)

Abstract Ebola (EBOV) and Marburg (MARV) viruses, of the family filoviridae, cause severe hemorrhagic fever in humans and nonhuman primates (NHPs) with mortality rates of up to 90%. Infection is thought to occur through mucous membranes or breaks in the skin after contact with infected animal tissue or body fluids of infected individuals. Beyond naturally occurring outbreaks, the potential use of these viruses in acts of bioterrorism remains a public health and national security concern. EBOV and MARV are classified as category A bioterrorism agents by the Centers for Disease Control and Prevention (CDC). To date, there are no licensed vaccines or therapeutics for filovirus infections. Major efforts are now under way to develop anti‐viral therapeutics that use the cellular RNA interference (RNAi) pathway. Small synthetic double‐stranded RNA oligonucleotides (siRNAs), or small hairpin RNAs (shRNAs) enter the RNAi pathway and guide the degradation of target mRNA transcripts with homologous sequence, for experimental or therapeutic benefit. Chemical modifications improve the in vivo stability of siRNAs and various strategies are being investigated to improve delivery. Importantly, siRNAs and shRNAs have been successfully used to inhibit virus replication in vitro, and in animal models. siRNAs as therapy for a variety of ailments have now moved into clinical trials. This review provides an overview of therapeutic siRNAs and details preclinical efforts to use these molecules as therapy for filovirus infections. Drug Dev Res 70:246–254, 2009. Published 2009 Wiley‐Liss, Inc.
Rapid and selective extraction, isolation, preconcentration, and quantitation of small RNAs from cell lysate using on-chip isotachophoresis (2009)

We present a technique which enables the separation of small RNAs-such as microRNAs (miRNAs), short interfering RNAs (siRNAs), and Piwi-interacting RNAs (piRNAs)-from >or=66 nucleotide RNAs and other biomolecules contained in a cell lysate. In particular, the method achieves separation of small RNAs from precursor miRNAs (pre-miRNAs) in less than 3 min. We use on-chip isotachophoresis (ITP) for the simultaneous extraction, isolation, preconcentration and quantitation of small RNAs (approximately 22 nucleotides) and employ the high-efficiency sieving matrix Pluronic F-127; a thermo-responsive triblock copolymer which allows convenient microchannel loading at low temperature. We present the isolation of small RNAs from the lysate of 293A human kidney cells, and quantitate the number of short RNA molecules per cell to be 2.9x10(7). We estimate this quantity is an aggregate of roughly 500 types of short RNA molecules per 293A cell. Currently, the minimal cell number for small RNA extraction and detection with our method is approximately 900 (from a 5 microL sample volume), and we believe that small RNA analysis from tens of cells is realizable. Techniques for rapid and sensitive extraction and isolation of small RNAs from cell lysate are much-needed to further uncover their full range and functionality, including RNA interference studies.
Inverse halftoning via MAP estimation (1997)

There has been a tremendous amount of research in the area of image halftoning, where the goal has been to find the most visually accurate representation given a limited palette of gray levels (often just two, black and white). This paper focuses on the inverse problem, that of finding efficient techniques for reconstructing high-quality continuous-tone images from their halftoned versions. The proposed algorithms are based on a maximum a posteriori (MAP) estimation criteria using a Markov random field (MRF) model for the prior image distribution. Image estimates obtained with the proposed model accurately reconstruct both the smooth regions of the image and the discontinuities along image edges. Algorithms are developed and example gray-level reconstructions are presented generated from both dithered and error-diffused halftone originals. Application of the technique to the problems of rescreening and the processing of halftone images are shown.
Bubbles, Drops, and Particles in Non-Newtonian Fluids (2006)

Bubbles, Drops, and Particles in Non-Newtonian Fluids, Second Edition continues to provide thorough coverage of the scientific foundations and the latest advances in particle motion in non-Newtonian media. The book demonstrates how dynamic behavior of single particles can yield useful information for modeling transport processes in complex multipha
Biochemical and analytical development of the CIME cocktail for drug fate assessment in humans (2010)

Phenotyping based on drug metabolism activity appears to be informative regarding mechanism-based interactions during drug development. We report here the first steps of the development of the innovative CIME cocktail. This cocktail is designed not only for the major cytochrome P450, with caffeine, amodiaquine, tolbutamide, omeprazole, dextromethorphan and midazolam as substrates of CYP1A2, CYP2C8, CYP2C9, CYP2C19, CYP2D6 and CYP3A, respectively, but also phase II enzymes UGT 1A1/6/9 with acetaminophen, P-gp and OATP1B1 with digoxin and rosuvastatin, and renal function with memantine. An assay combining ultra-performance liquid chromatography using a 1.7 microm particle size column with tandem mass spectrometry (UPLC/MS/MS) was set up for the simultaneous quantification of the 20 substrates and metabolites after extraction from human plasma using solid-phase extraction. The method was validated in the spirit of the FDA guidelines. Mean accuracy ranged from 87.7 to 115%, the coefficient of variance (CV%) of intra- and inter-run from 1.7 to 16.4% and from 1.6 to 14.9%, respectively, and for the limit of quantification (LOQ) with ten lots of plasma, accuracy ranged from 84 to 115% and CV% precision was <16%. Short-term stability was evaluated in eluate (4 h, room temperature), plasma (24 h, room temperature), the autosampler (24 h, 4 degrees C) and in three freeze/thaw cycles in plasma. All except three analytes were stable under these conditions. For the three others a specific process can be followed. This robust, fast and sensitive assay in human plasma provides an analytical tool for ten-probe drugs of the CIME cocktail. Clinical samples will be assayed in the near future using this new assay method.
Time Course of Irreversible Electroporation Lesion Development Through Short- and Long-Term Follow-Up in Pulsed-Field Ablation–Treated Hearts (2022)

Pulsed-field ablation for pulmonary vein and superior vena cava isolation with the novel PFA system was feasible, safe with myocardial-specific ablative effect. Durable lesions were observed at the target areas. with inflammation phenomena mainly documented at 7 days.
DNA‐Origami‐Directed Self‐Assembly of Discrete Silver‐Nanoparticle Architectures (2010)

Noble decoration: DNA origami nanostructures (purple) were utilized as spatially addressable templates to organize noble-metal nanoparticles of silver (yellow balls) and gold (red ball) into well-defined discrete architectures (see examples of nanostructure designs and TEM images of the assembled structures).
Reversible Immortalization of Human Primary Cells by Lentivector-Mediated Transfer of Specific Genes (2000)

We exploited the ability of lentiviral vectors to govern the stable transduction of cells irrespective of their cycling status to induce the reversible immortalization of human primary cells. First, bicistronic HIV-derived lentiviral vectors expressing GFP- and the HSV1 thymidine kinase and containing the LoxP sequence in their LTR (HLox) were used to transduce HeLa cells. Cre expression led to efficient proviral deletion, and unexcised cells could be eliminated by ganciclovir treatment. A human liver biopsy was then exposed to a combination of HLox vectors that harbored either the SV40 large T (TAg) or the human telomerase (hTERT) DNAs in place of GFP. This led to the isolation of liver sinusoidal endothelial cell (LSEC) clones that exhibited an immortalized phenotype while retaining most of the features of primary hLSEC. Complete growth arrest of these cells was observed in 2 days of Cre expression, and the resulting stationary culture could be kept for at least 2 weeks. Transduction of human adult pancreatic islets with HLox vectors coding for Tag and Bmi-1 also induced the proliferation of insulin-positive cells. These results indicate that lentivectors can be used to mediate the reversible immortalization of primary nondividing cells and should allow for the production of large supplies of a wide variety of human cells for both therapeutic and research purposes.