gebhart/patrepeval huggingface dataset:
Southern blot analysis of ALL-1 rearrangements at chromosome 11q23 in acute leukemia. (1993)

The chromosome 11q23 band is a genetic region frequently involved in nonrandom karyotypic abnormalities of acute leukemia. A genomic locus named ALL-1 or MLL, where 11q23 breakpoints are clustered, has been recently cloned and characterized. We have made use of an ALL-1-specific probe in Southern blot experiments to analyze the configuration of this gene in a large series of acute leukemia patients, representative of all different myeloid and lymphoid subtypes. Nine of 145 cases (6.2%) showed abnormal ALL-1 restriction fragments in leukemic DNAs. Of these nine cases, five patients in whom karyotypic data were available displayed chromosome 11q23 aberrations, including t(4;11) (three cases) and t(9;11) (two cases). Immunophenotypic and morphocytochemical characterization of ALL-1-rearranged acute leukemia revealed prevalence of poorly differentiated B lymphoid and/or monoblastic features. Considering the whole series, ALL-1 rearrangements were significantly associated with female sex, higher white blood cell counts at presentation, and very poor clinical outcome. The presence of residual disease was molecularly documented in one case at the time of clinical remission after induction treatment and was followed by early relapse. We conclude that ALL-1 rearrangements are new molecular markers of human leukemia with considerable diagnostic and prognostic relevance.
Antioxidant Activities of Natural Vitamin E Formulations (2003)

The antioxidant activities of natural d-alpha-tocopherol, mixed tocopherols and tocotrienols, and formulations comprising all forms of vitamin E, providing 400 IU, were determined employing an improved oxygen radical absorbance capacity (ORAC) assay using fluorescein (FL) as the fluorescent probe, randomly methylated beta-cyclodextrin (RMCD), 2,2'-azobis(2-amidino-propane)dihydrochloride (AAPH) as the peroxyl radical generator, and Trolox as the standard in 75 mM phosphate buffer. The antioxidant activities, expressed in micromol Trolox equivalent per gram, of d-alpha-tocopherol (87%), mixed tocopherols (70%), and tocotrienols (30%) were found to be 1,293, 1,948, and 1,229, respectively. Some of the vitamin E formulations showed antioxidant activities superior to d-alpha-tocopherol.
MicroRNAs in Metabolism and Metabolic Diseases (2011)

Aberrant cholesterol/lipid homeostasis is linked to a number of diseases prevalent in the developed world, including metabolic syndrome, type II diabetes, and cardiovascular disease. We have previously uncovered gene regulatory mechanisms of the sterol regulatory element-binding protein (SREBP) family of transcription factors, which control the expression of genes involved in cholesterol and lipid biosynthesis and uptake. Intriguingly, we recently discovered conserved microRNAs (miR-33a/b) embedded within intronic sequences of the human SREBF genes that act in a concerted manner with their host gene products to regulate cholesterol/lipid homeostasis. Indeed, miR-33a/b control the levels of ATP-binding cassette (ABC) transporter ABCA1, a cholesterol efflux pump critical for high-density lipoprotein (HDL) synthesis and reverse cholesterol transport from peripheral tissues. Importantly, antisense inhibition of miR-33 in mice results in elevated HDL and decreased atherosclerosis. Interestingly, miR-33a/b also act in the fatty acid/lipid homeostasis pathway by controlling the fatty acid β-oxidation genes carnitine O-octanoyltransferase (CROT), hydroxyacyl-coenzyme A-dehydrogenase (HADHB), and carnitine palmitoyltransferase 1A (CPT1A), as well as the energy sensor AMP-activated protein kinase (AMPKα1), the NAD(+)-dependent sirtuin SIRT6, and the insulin signaling intermediate IRS2, key regulators of glucose and lipid metabolism. These results have revealed a highly integrated microRNA (miRNA)-host gene circuit governing cholesterol/lipid metabolism and energy homeostasis in mammals that may have important therapeutic implications for the treatment of cardiometabolic disorders.
<i>TMPRSS2:ERG</i> Fusion-Associated Deletions Provide Insight into the Heterogeneity of Prostate Cancer (2006)

Prostate cancer is a common and clinically heterogeneous disease with marked variability in progression. The recent identification of gene fusions of the 5'-untranslated region of TMPRSS2 (21q22.3) with the ETS transcription factor family members, either ERG (21q22.2), ETV1 (7p21.2), or ETV4 (17q21), suggests a mechanism for overexpression of the ETS genes in the majority of prostate cancers. In the current study using fluorescence in situ hybridization (FISH), we identified the TMPRSS2:ERG rearrangements in 49.2% of 118 primary prostate cancers and 41.2% of 18 hormone-naive lymph node metastases. The FISH assay detected intronic deletions between ERG and TMPRSS2 resulting in TMPRSS2:ERG fusion in 60.3% (35 of 58) of the primary TMPRSS2:ERG prostate cancers and 42.9% (3 of 7) of the TMPRSS2:ERG hormone-naive lymph node metastases. A significant association was observed between TMPRSS2:ERG rearranged tumors through deletions and higher tumor stage and the presence of metastatic disease involving pelvic lymph nodes. Using 100K oligonucleotide single nucleotide polymorphism arrays, a homogeneous deletion site between ERG and TMPRSS2 on chromosome 21q22.2-3 was identified with two distinct subclasses distinguished by the start point of the deletion at either 38.765 or 38.911 Mb. This study confirms that TMPRSS2:ERG is fused in approximately half of the prostate cancers through deletion of genomic DNA between ERG and TMPRSS2. The deletion as cause of TMPRSS2:ERG fusion is associated with clinical features for prostate cancer progression compared with tumors that lack the TMPRSS2:ERG rearrangement.
High‐luminance 1‐m‐long plasma tubes for wall displays (2004)

Abstract— The plasma‐tube array is expected to realize a wall‐sized display. This method will realize an emissive‐type display with a flexible screen shape and an expandable screen size. The shape of the plasma tube was investigated to realize high luminance, high luminance efficacy, and high flexural strength. As the result, a cylindroid tube is proposed to satisfy these demands. An experimental display of 1 m × 128 mm has been developed with these cylindroid tubes and it demonstrated a high luminous efficacy of 3.1 lm/W.
Mitigating measurement errors in multiqubit experiments (2021)

Reducing measurement errors in multiqubit quantum devices is critical for performing any quantum algorithm. Here we show how to mitigate measurement errors by a classical postprocessing of the measured outcomes. Our techniques apply to any experiment where measurement outcomes are used for computing expected values of observables. Two error-mitigation schemes are presented based on tensor product and correlated Markovian noise models. Error rates parametrizing these noise models can be extracted from the measurement calibration data using a simple formula. Error mitigation is achieved by applying the inverse noise matrix to a probability vector that represents the outcomes of a noisy measurement. The error-mitigation overhead, including the number of measurements and the cost of the classical postprocessing, is exponential in $\ensuremath{\epsilon}n$, where $\ensuremath{\epsilon}$ is the maximum error rate and $n$ is the number of qubits. We report experimental demonstration of our error-mitigation methods on IBM Quantum devices using stabilizer measurements for graph states with $n\ensuremath{\le}12$ qubits and entangled 20-qubit states generated by low-depth random Clifford circuits.
The human digestive tract has proteases capable of gluten hydrolysis (2017)

The digestive tracts of patients with CD and healthy subjects have enzymatic machinery needed for gluten degradation. Patients with CD showed more gluten hydrolysis than did healthy individuals, although, in both cases, a fraction of 33-mer peptide remained intact. Gliadin peptides derived from gastrointestinal digestion, especially the 33-mer, can potentially be used by commensal microbiota from both CD-positive and CD-negative individuals, and differences in bacterial hydrolysis can modify its immunogenic capacity.
Extraction of Lipids from Aqueous Protein‐Rich Streams using Near‐Critical Dimethylether (2007)

Abstract An extraction process for obtaining lipids from aqueous protein/lipid mixtures has been developed using near‐critical dimethylether (DME) as the solvent. The process has been demonstrated on fresh and reconstituted egg yolks, and on selected dairy by‐product streams. The lipid yield is dependent on the processing temperature, solids content and feed ratio of solvent to liquid. The extent of protein denaturation is also dependent on these parameters. The phase equilibria of DME‐water‐phospholipid mixtures are presented with modeling of the DME‐water system using the Peng‐Robinson equation of state.
Computerized characterization of the yarn snarling distribution (2006)

2006-2007 > Academic research: refereed > Publication in refereed journal
Dynamics and Performance of Tailless Micro Aerial Vehicle with Flexible Articulated Wings (2012)

The purpose of this paper is to analyze and discuss the performance and stability of a tailless micro aerial vehicle\nwith flexible articulated wings. The dihedral angles can be varied symmetrically on both wings to control the aircraft\nspeed independently of the angle of attack and flight-path angle, while an asymmetric dihedral setting can be used to\ncontrol yaw in the absence of a vertical tail.Anonlinear aero-elastic model is derived, and it is used to study the steady-state performance and flight stability of the micro aerial vehicle. The concept of the effective dihedral is introduced, which allows for a unified treatment of rigid and flexible wing aircraft. It also identifies the amount of elasticity that is necessary to obtain tangible performance benefits over a rigid wing. The feasibility of using axial tension to stiffen the wing is discussed, and, at least in the context of a linear model, it is shown that adding axial tension is effective but undesirable. The turning performance of an micro aerial vehicle with flexible wings is compared to an otherwise identical micro aerial vehicle with rigid wings. The wing dihedral alone can be varied asymmetrically to perform rapid turns and regulate sideslip. The maximum attainable turn rate for a given elevator setting, however, does not increase unless antisymmetric wing twisting is employed.
Microbeam radiation therapy (1992)

It is proposed to carry out radiotherapy and radiosurgery for brain lesions by crossfiring an array of parallel, closely spaced microbeams of synchrotron-generated x rays several times through an isocentric target, each microbeam in the array having an approximately 25-microns-wide adjustable-height rectangular cross section. The following inferences from the known tissue sparing of 22-MeV deuteron microbeams in the mouse brain and the following exemplary Monte Carlo computations indicate that endothelial cells in the brain that are lethally irradiated by any microbeam in an array of adequately spaced microbeams outside an isocentric target will be replaced by endothelial cells regenerated from microscopically contiguous, minimally irradiated endothelium in intermicrobeam segments of brain vasculature. Endothelial regeneration will prevent necrosis of the nontargeted parenchymal tissue. However, neoplastic and/or nonneoplastic targeted tissues at the isocenter will be so severely depleted of potentially mitotic endothelial and parenchymal cells by multiple overlapping microbeams that necrosis will ensue. The Monte Carlo computations simulate microbeam irradiations of a 16-cm diameter, 16-cm-long cylindrical human head phantom using 50-, 100-, and 150-keV monochromatic x rays.
Development and Validation of a Biomarker for Diarrhea-Predominant Irritable Bowel Syndrome in Human Subjects (2015)

Diarrhea-predominant irritable bowel syndrome (IBS) is diagnosed through clinical criteria after excluding "organic" conditions, and can be precipitated by acute gastroenteritis. Cytolethal distending toxin B (CdtB) is produced by bacteria that cause acute gastroenteritis, and a post-infectious animal model demonstrates that host antibodies to CdtB cross-react with vinculin in the host gut, producing an IBS-like phenotype. Therefore, we assessed circulating anti-CdtB and anti-vinculin antibodies as biomarkers for D-IBS in human subjects. Subjects with D-IBS based on Rome criteria (n=2375) were recruited from a large-scale multicenter clinical trial for D-IBS (TARGET 3). Subjects with inflammatory bowel disease (IBD) (n=142), subjects with celiac disease (n=121), and healthy controls (n=43) were obtained for comparison. Subjects with IBD and celiac disease were recruited based on the presence of intestinal complaints and histologic confirmation of chronic inflammatory changes in the colon or small intestine. Subjects with celiac disease were also required to have an elevated tTG and biopsy. All subjects were aged between 18 and 65 years. Plasma levels of anti-CdtB and anti-vinculin antibodies were determined by ELISA, and compared between groups. Anti-CdtB titers were significantly higher in D-IBS subjects compared to IBD, healthy controls and celiac disease (P<0.001). Anti-vinculin titers were also significantly higher in IBS (P<0.001) compared to the other groups. The area-under-the-receiver operating curves (AUCs) were 0.81 and 0.62 for diagnosis of D-IBS against IBD for anti-CdtB and anti-vinculin, respectively. Both tests were less specific in differentiating IBS from celiac disease. Optimization demonstrated that for anti-CdtB (optical density≥2.80) the specificity, sensitivity and likelihood ratio were 91.6%, 43.7 and 5.2, respectively, and for anti-vinculin (OD≥1.68) were 83.8%, 32.6 and 2.0, respectively. These results confirm that anti-CdtB and anti-vinculin antibodies are elevated in D-IBS compared to non-IBS subjects. These biomarkers may be especially helpful in distinguishing D-IBS from IBD in the workup of chronic diarrhea.
Analysis of SSR signals by super resolution algorithms (2005)

A new method for SSR (secondary surveillance radar) signal analysis, in particular SSR Mode S replies, can be obtained exploiting the super resolution algorithms capability to discriminate signals in the frequency domain. This work summarises the results obtained by the application of Tufts-Kumaresan, Music, Esprit and Unitary Esprit algorithms to decode Mode S replies and squitters acquired in a live environment. Hence, we propose 16 possible processing schemes which, compared to conventional schemes, have shown sensible improvements. It results that the main limit is represented by the quality of the on board transponder local oscillator which causes a too small spectral separation between two overlapped signals.
Repurposing therapies for the personalised treatment of cystic fibrosis (2018)

Introduction: Cystic Fibrosis (CF) is an inherited, lethal and expensive rare disease affecting more than 85,000 people worldwide. CF is caused by more than 2000 loss-of-function mutations in the gene coding for the cystic fibrosis transmembrane conductance regulator (CFTR). Personalized interventions on individual CF patients probably constitute the future of CF management.Areas covered: The molecular genetics exploration of CF has led in the last years to the development of mutation-specific therapies that aim at directly targeting the mutant CFTR to reverse disease phenotype. Here, we will summarize the strategies of drug repositioning, i.e. the use of ‘old drugs’ for ‘new purposes’ in the perspective of a personalized approach to CF treatment.Expert opinion: Rare diseases like CF may well enter the era of precision medicine. A personalized/repositioning medicine in CF could help to provide the right drug to the right patient and potentially reduce the costs of developing disease-modifying drugs.
Novel Conformationally Constrained Tropane Analogues by 6-<i>e</i><i>ndo-trig</i> Radical Cyclization and Stille Coupling − Switch of Activity toward the Serotonin and/or Norepinephrine Transporter (2000)

A novel class of tricyclic tropane analogues has been synthesized by making use of radical cyclization technology in combination with the Stille coupling reaction. As hybrids between tropanes and quinuclidines, these tropaquinuclidines represent a significant structural departure from many of the other classes of tropane ligands synthesized to date. This structure class is characterized by the boat conformation of the tropane ring and the orientation of the additional bridge (and therefore of the nitrogen lone pair) together with the unusual placement of the aromatic moiety. All compounds were tested for their ability to inhibit monoamine reuptake under identical conditions. The ability to inhibit reuptake of dopamine in comparison to cocaine is generally decreased in this series but for one compound. (1S,3R, 6S)-(Z)-9-(thienylmethylene)-7-azatricyclo[4.3.1.0(3, 7)]decane-2beta-carboxylic acid methyl ester (5h) exhibits reasonable activity at the dopamine transporter (DAT) (K(i) = 268 nM) and good activity at the norepinephrine transporter (NET) (K(i) = 26 nM). The potency and selectivity shown by some of these ligands for the NET, serotonine transporter (SERT), or NET/SERT is striking, particularly in view of the displacement of the aromatic ring in this series from its usual position at C-3 in the WIN analogues. Thus, (1S,3R,6S)-(Z)-9-(4-biphenylylmethylene)-7-azatricyclo[4.3.1 . 0(3,7)]decane-2beta-carboxylic acid methyl ester (5a) is a selective inhibitor of norepinephrine reuptake (K(i) = 12 nM). Its p-methoxy analogue 5c is a mixed inhibitor of norepinephrine and serotonin reuptake (K(i) = 187 nM at the NET and 56 nM at the SERT). The most active and selective compound we found in the present series is compound 8b [(1S,3R,6S)-2-(acetoxymethyl)-(Z)-9-(3, 4-dichlorophenylmethylene)-7-azatricyclo[4.3.1.0(3,7)]decane ]. This compound is a potent (K(i) = 1.6 nM) and selective inhibitor of serotonin reuptake into rat midbrain synaptosomes. Its selectivity is about 400-fold over the NET and about 1000-fold over the DAT. The results of this study further demonstrate the possibility of tuning the selectivity of tropane analogues toward the SERT or NET binding site. The ligands disclosed herein provide additional pharmacological tools of use in attempting to correlate structure and transporter selectivity with in vivo studies of behavioral outcomes.
Specific reduction of wheat storage proteins by thioredoxin h. (1992)

Gliadins and glutenins, the major storage proteins of wheat endosperm (Triticum durum, Desf. cv Monroe), were reduced in vitro by the NADP/thioredoxin system (NADPH, NADP-thioredoxin reductase and thioredoxin; in plants, the h type) from either the same source or the bacterium Escherichia coli. A more limited reduction of certain members of these protein groups was achieved with the reduced form of glutathione or glutaredoxin, a protein known to replace thioredoxin in certain bacterial and mammalian enzyme systems but not known to occur in higher plants. Endosperm extracts contained the enzymes necessary to reduce NADP by the oxidative pentose phosphate pathway (hexokinase, glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase). The gliadins and glutenins were also reduced in vivo during germination--an event that accompanied their proteolytic breakdown. The results suggest that thioredoxin, reduced by NADPH generated via the oxidative pentose phosphate pathway, functions as a signal in germination to enhance metabolic processes such as the mobilization of storage proteins and, as found earlier, the activation of enzymes.
Generation of the rotationally symmetric TE&lt;inf&gt;01&lt;/inf&gt;and TM&lt;inf&gt;01&lt;/inf&gt;modes from a wavelength-tunable laser (1974)

A nitrogen-laser-pumped dye laser has been made to operate in the rotationally symmetric TE <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01</sub> or TM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01</sub> modes. The modes are preserved as the laser wavelength is varied. The mode selector allows convenient switching from one mode to the other. The theory of the operation of the mode selector is described.
A Processor-Based OCR System (1983)

A low-cost optical character recognition (OCR) system can be realized by means of a document scanner connected to a CPU through an interface. The interface performs elementary image processing functions, such as noise filtering and thresholding of the video image from the scanner. The processor receives a binary image of the document, formats the image into individual character patterns, and classifies the patterns one-by-one. A CPU implementation is highly flexible and avoids much of the development and manufacturing costs for special-purpose, parallel circuitry typically used in commercial OCR. A processor-based recognition system has been investigated for reading documents printed in fixed-pitch conventional type fonts, such as occur in routine office typing. Novel, efficient methods for tracking a print line, resolving it into individual character patterns, detecting underscores, and eliminating noise have been devised. A previously developed classification technique, based on decision trees, has been extended in order to improve reading accuracy in an environment of considerable character variation, including the possibility that documents in the same font style may be produced using quite different print technologies. The system has been tested on typical office documents, and also on artificial stress documents, obtained from a variety of typewriters.
Antimalarial, Antiproliferative, and Antitumor Activities of Artemisinin-Derived, Chemically Robust, Trioxane Dimers (1999)

Nine C-10 non-acetal derivatives of the natural trioxane artemisinin (1) were prepared as dimers using some novel chemistry. As designed, each dimer was stable chemically. C-10 Olefinic dimers 7 and C-10 saturated dimers 8-13 all showed good to excellent antimalarial and antiproliferative activities in vitro. Dimers 8, 10, and 12 were especially potent and selective at inhibiting growth of some human cancer cell lines in the NCI in vitro 60-cell line assay.
IRF5 hyper-activation is a driver of systemic lupus erythematosus (SLE) onset and severity (2018)

Abstract The transcription factor interferon regulatory factor 5 (IRF5) is a central mediator of innate and adaptive immunity. Genetic variations within IRF5 associate with risk for systemic lupus erythematosus (SLE) and mice lacking Irf5 are protected from lupus onset and severity. Here we show that IRF5 genetic variants confer risk by increasing basal IRF5 activation in plasmacytoid dendritic cells resulting in elevated IFNα production. IRF5 hyperactivation in SLE immune cells correlates with SLEDAI and dsDNA titers. Upon characterization of immune cells from NZB/W F1 lupus-prone mice, we found that Irf5 was hyperactivated at 19 weeks-old, which precedes clinical onset. To test whether IRF5 hyperactivation is a driver of SLE, we developed novel therapeutics targeting IRF5 activation. Inhibitors are cell permeable, non-toxic and selectively bind to full-length inactive IRF5 monomer. In vivo analysis revealed functional mimicry with Irf5 knockout mice and treatment of NZB/W F1 mice for a two-week period prior to clinical onset gave significantly reduced dsDNA titers, anti-nuclear antibody (ANA) staining, and improved survival. The IRF5 inhibitor also blocked ex vivo SLE serum-induced IRF5 activation and reversed IRF5 hyperactivation detected in SLE immune cells. Results implicate IRF5 hyperactivation as a risk factor that drives SLE and provide the first pre-clinical support for treating SLE patients or those at risk of SLE with IRF5 inhibitors.