gebhart/patrepeval huggingface dataset:
A novel approach for trapezoid geometry small animal DOI PET detector using SSLE technique (2019)

528 Objectives: Trapezoid geometry crystal could improve the sensitivity significantly as compared to the conventional box geometry crystal. However, the manufacturing of trapezoid shape crystal is costly and difficult due to the complex geometry. In this study, we present a novel approach for the development of a cost-effective trapezoid crystal based small animal DOI PET detector using sub-surface laser engraving (SSLE) technique. Methods: A 19.3 mm long monolithic trapezoid LYSO plate (Top: 15.3 mm, bottom: 25.6 mm, thickness = 0.9 mm) was pixelized in 15 × 1 array by using SSLE to yield a top crystal pitch of 1.02 mm, a bottom crystal pitch of 1.71 mm, respectively. The three SSLE processed LYSO crystal plates were assembled each other to make 15 × 3 array. The LYSO plates were optically isolated by using enhanced specular reflector (ESR). A 7×6 array SiPM (Hamamatsu, S13360-2050VE) with a pixel pitch of 2.4 mm and 8×4 array SiPM (Hamamatsu, S13361-3050NE-04) with a pixel pitch of 3.2 mm were coupled to the top and bottom surfaces of the trapezoid LYSO array, respectively. For an optical coupling, room temperature vulcanizing (RTV) light guides with a thickness of 1 mm were inserted between the LYSO and SiPM array. In order to evaluate the DOI resolution, a collimated 511 keV photon was irradiated to the detector with different DOI positions (2, 6, 10, 14, and 18 mm). The DOI resolution was calculated by using the signal amplitude ratio of the two SiPMs (top and bottom). The SiPM output signals were multiplexed by using a resistive network, and then digitized by CAMAC DAQ. Results: All the 15 × 3 LYSO pixels segmented by the SSLE could be resolved clearly on the 2D flood histogram. The energy resolution of 25.0%, and the DOI resolution of 3.5 mm were obtained. Conclusions: The feasibility of SSLE based trapezoid PET detector was demonstrated successfully. In future, a prototype trapezoid geometry small animal DOI PET scanner will be developed by using the SSLE technique.
Linear Theory for Self-Localization: Convexity, Barycentric Coordinates, and Cayley–Menger Determinants (2015)

Localization, finding the coordinates of an object with respect to other objects with known coordinates-hereinafter, referred to as anchors, is a nonlinear problem, as it involves solving circle equations when relating distances to Cartesian coordinates, or, computing Cartesian coordinates from angles using the law of sines. This nonlinear problem has been a focus of significant attention over the past two centuries and the progress follows closely with the advances in instrumentation as well as applied mathematics, geometry, statistics, and signal processing. The Internet-of-Things (IoT), with massive deployment of wireless tagged things, has renewed the interest and activity in finding novel, expert, and accurate indoor self-localization methods, where a particular emphasis is on distributed approaches. This paper is dedicated to reviewing a notable alternative to the nonlinear localization problem, i.e., a linear-convex method, based on Khan et al.'s work. This linear solution utilizes relatively unknown geometric concepts in the context of localization problems, i.e., the barycentric coordinates and the Cayley-Menger determinants. Specifically, in an m-dimensional Euclidean space, a set of m+1 anchors, objects with known locations, is sufficient (and necessary) to localize an arbitrary collection of objects with unknown locations-hereinafter, referred to as sensors, with a linear-iterative algorithm. To ease the presentation, we discuss the solution under a structural convexity condition, namely, the sensors lie inside the convex hull of at least m+1 anchors. Although rigorous results are included, several remarks and discussion throughout this paper provide the intuition behind the solution and are primarily aimed toward researchers and practitioners interested in learning about this challenging field of research. Additional figures and demos have been added as auxiliary material to support this aim.
Arg-78 of Nprl2 catalyzes GATOR1-stimulated GTP hydrolysis by the Rag GTPases (2019)

mTOR complex 1 (mTORC1) is a major regulator of cell growth and proliferation that coordinates nutrient inputs with anabolic and catabolic processes. Amino acid signals are transmitted to mTORC1 through the Rag GTPases, which directly recruit mTORC1 onto the lysosomal surface, its site of activation. The Rag GTPase heterodimer has a unique architecture that consists of two GTPase subunits, RagA or RagB bound to RagC or RagD. Their nucleotide-loading states are strictly controlled by several lysosomal or cytosolic protein complexes that directly detect and transmit the amino acid signals. GATOR1 (GTPase-activating protein (GAP) activity toward Rags-1), a negative regulator of the cytosolic branch of the nutrient-sensing pathway, comprises three subunits, Depdc5 (DEP domain-containing protein 5), Nprl2 (NPR2-like GATOR1 complex subunit), and Nprl3 (NPR3-like GATOR1 complex subunit), and is a GAP for RagA. GATOR1 binds the Rag GTPases via two modes: an inhibitory mode that holds the Rag GTPase heterodimer and has previously been captured by structural determination, and a GAP mode that stimulates GTP hydrolysis by RagA but remains structurally elusive. Here, using site-directed mutagenesis, GTP hydrolysis assays, coimmunoprecipitation experiments, and structural analysis, we probed the GAP mode and found that a critical residue on Nprl2, Arg-78, is the arginine finger that carries out GATOR1's GAP function. Substitutions of this arginine residue rendered mTORC1 signaling insensitive to amino acid starvation and are found frequently in cancers such as glioblastoma. Our results reveal the biochemical bases of mTORC1 inactivation through the GATOR1 complex.
Trial of therapy with monoclonal antibody 17-1A in pancreatic carcinoma: preliminary results. (1986)

Monoclonal antibody 17-1A was administered to 25 patients with advanced unresectable carcinoma of the pancreas. Ten patients received 17-1A alone in 400 mg doses delivered intravenously, while 15 patients received 400 mg 17-1A absorbed on to autologous peripheral blood mononuclear cells collected by leukapheresis (usual yield greater than 10(9) cells). No toxicity was observed. Twenty-three patients developed circulating anti-murine immunoglobulin within three weeks of treatment, and 11 patients developed circulating anti-idiotypic immunoglobulin. Four out of 19 clinically evaluable patients (21%) showed objective regressions of tumor. Response did not correlate with the presence or absence of anti-idiotypic antibody and did not correlate with the method of treatment with 17-1A alone or 17-1A and mononuclear cells, at the time of current analysis.
Chromatic dispersion monitoring and automated compensation for NRZ and RZ data using clock regeneration and fading without adding signaling (2001)

We show that the clock signal can be extracted from both NRZ and RZ data, and that this extracted signal power represents the total accumulated dispersion. We also demonstrate dynamic dispersion compensation at 10 Gbit/s using the extracted power as a control signal.
Erratum: POEGMA‐b‐PAA comb‐like polymer dispersant for Al2 suspensions (2016)

Article First Published online: 9 March 2016 DOI: 10.1002/app.43577 [Article in J. Appl. Polym. Sci. 2016, 133, DOI: 10.1002/app.43352] In the published article cited above, the title was incorrectly given as “POEGMA-b-PAA comb-like polymer dispersant for Al2 suspensions”. The correct title is “POEGMA-b-PAA comb-like polymer dispersant for Al2O3 suspensions”. The publisher regrets any inconvenience this may have caused.
Serum Cohn fraction IV-1 supports the growth of Giardia lamblia in vitro (1994)

Bovine serum Cohn fractions were substituted for whole bovine serum in TYI-S-33 medium. Only fraction IV-1 supported attachment, cysteine uptake, and growth of Giardia lamblia. Among the mammalian sources tested, only goat and horse fractions showed activities comparable to that of the bovine fraction. Agglutinating immunoglobulins were identified as deleterious agents in human, rat, rabbit, and dog fractions.
The 1:1 co-crystal of triphenyl(2,3,5,6-tetrafluorobenzyl)phosphonium bromide and 1,1,2,2-tetrafluoro-1,2-diiodoethane (2013)

The title compound, C25H18F4P(+)·Br(-)·C2F4I2, is a 1:1 co-crystal of triphen-yl(2,3,5,6-tetra-fluoro-benz-yl)phospho-nium (TTPB) bromide and 1,1,2,2-tetra-fluoro-1,2-di-iodo-ethane (TFDIE). The crystal structure consists of a framework of TTPB cations held together by C-H⋯Br inter-actions. In this framework, infinite channels along [100] are filled by TFDIE mol-ecules held together in infinite ribbons by short F⋯F [2.863 (2)-2.901 (2)Å] inter-actions. The structure contains halogen bonds (XB) and hydrogen bonds (HB) in the bromide coordination sphere. TFDIE functions as a monodentate XB donor as only one I atom is linked to the Br(-) anion and forms a short and directional inter-action [I⋯Br(-) 3.1798 (7) Å and C-I⋯Br(-) 177.76 (5)°]. The coordination sphere of the bromide anion is completed by two short HBs of about 2.8 Å (for H⋯Br) with the acidic methyl-ene H atoms and two longer HBs of about 3.0 Å with H atoms of the phenyl rings. Surprisingly neither the second iodine atom of TFDIE nor the H atom on the tetra-fluoro-phenyl group make any short contacts.
Optical characterization of Nd3+:LiCaAlF<inf>6</inf> in the vacuum ultraviolet region at low temperature (2017)

Summary form only given. Solid-state vacuum ultraviolet (VUV) lasers are currently being developed because these are more robust, easier to maintain, and more cost-efficient compared to conventional light sources such as excimer lasers, synchrotron radiation, and free electron lasers. Fluorides are excellent solid-state laser host materials for this purpose because of their wide bandgaps, making them transparent down to nearly 100 nm. Moreover, interconfigurational 4f <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n-1</sup> to 4f <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> transitions in rare-earth-doped fluorides result to broad fluorescence bandwidths. Previous work has shown that LiCaAlF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> is an excellent laser host when doped with Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> + ions [1]. However, emission from Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> activator ions cannot extend below 265 nm. In this work, we investigate the optical properties of Nd <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> -doped LiCaAlFe (Nd:LiCAF). Nd <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> -doping results to emissions in the VUV region.
Ga/HZSM-5 Catalysed Acetic Acid Ketonisation for Upgrading of Biomass Pyrolysis Vapours (2019)

Pyrolysis bio-oils contain significant amounts of carboxylic acids which limit their utility as biofuels. Ketonisation of carboxylic acids within biomass pyrolysis vapours is a potential route to upgrade the energy content and stability of the resulting bio-oil condensate, but requires active, selective and coke-resistant solid acid catalysts. Here we explore the vapour phase ketonisation of acetic acid over Ga-doped HZSM-5. Weak Lewis acid sites were identified as the active species responsible for acetic acid ketonisation to acetone at 350 °C and 400 °C. Turnover frequencies were proportional to Ga loading, reaching ~6 min−1 at 400 °C for 10Ga/HZSM-5. Selectivity to the desired acetone product correlated with the weak:strong acid site ratio, being favoured over weak Lewis acid sites and reaching 30% for 10Ga/HZSM-5. Strong Brønsted acidity promoted competing unselective reactions and carbon laydown. 10Ga/HZSM-5 exhibited good stability for over 5 h on-stream acetic acid ketonisation.
Cyclic linear binary locally repairable codes (2015)

Locally repairable codes (LRCs) are a class of codes designed for the local correction of erasures. They have received considerable attention in recent years due to their applications in distributed storage. Most existing results on LRCs do not explicitly take into consideration the field size q, i.e., the size of the code alphabet. In particular, for the binary case, only a few specific results are known by Goparaju and Calderbank. Recently, however, an upper bound on the dimension k of LRCs was presented by Cadambe and Mazumdar. The bound takes into account the length n, minimum distance d, locality r, and field size q, and it is applicable to both non-linear and linear codes. In this work, we first develop an improved version of the bound mentioned above for linear codes. We then focus on cyclic linear binary codes. By leveraging the cyclic structure, we notice that the locality of such a code is determined by the minimum distance of its dual code. Using this result, we investigate the locality of a variety of well known cyclic linear binary codes, e.g., Hamming codes and Simplex codes, and also prove their optimality with our improved bound for linear codes. We also discuss the locality of codes which are obtained by applying the operations of Extend, Shorten, Expurgate, Augment, and Lengthen to cyclic linear binary codes. Several families of such modified codes are considered and their optimality is addressed. Finally, we investigate the locality of Reed-Muller codes. Even though they are not cyclic, it is shown that some of the locality results for cyclic codes still apply.
Sofosbuvir (Sovaldi): The First‐in‐Class HCV NS5B Nucleotide Polymerase Inhibitor (2015)

Chronic hepatitis C virus (HCV) infection is a global health problem. This chapter describes the pharmacological profile and chemical syntheses of sofosbuvir. HCV specifically infects hepatocytes, entering the cells through endocytosis. NS5B RNA-dependent RNA polymerase (RdRp) inhibitors can be divided into two subclasses: nucleoside/nucleotide polymerase inhibitor (NPI) and nonnucleoside polymerase inhibitors (NNPI). Sofosbuvir once metabolized to the 5'-triphosphate is an inhibitor of the HCV NS5B RNA-dependent RNA polymerase. Given sofosbuvir's superior efficacy across all genotypes, high genetic barrier to resistance, overall safety, tolerability, and minimal drug-drug interaction profile, sofosbuvir-based regimens provide an excellent opportunity to cure chronic hepatitis C. Based on all the encouraging results from the studies with sofosbuvir as the backbone therapy, HCV may be the first chronic viral infection to be eradicated worldwide with combinations of direct-acting antivirals (DAAs) through a treatment-as-prevention approach.
In Vitro and In Vivo Evaluation of a Cyclic LyP-1-Modified Nanosystem for Targeted Endostatin Delivery in a KYSE-30 Cell Xenograft Athymic Nude Mice Model (2022)

This work investigated the use of LyP-1 as a homing peptide for p32 receptor targeting on the surface of an endostatin (ENT)-loaded chitosan-grafted nanosystem intended for intracellular delivery of ENT and mitochondrial targeting in a squamous cell carcinoma (SCC) cell line (KYSE-30) model. The angiogenic factors for VEGF-C and MMP2 were assessed with in vivo evaluation of the nanosystem upon ENT release and tumor necrosis in nude mice with a KYSE-30 cell xenograft. The LyP-1-modified nanosystem revealed a three-fold decrease in proliferation at 1000 µg/mL compared with the control and facilitated receptor-mediated cellular uptake and internalization. In addition, targeting of the Lyp-1-functionalized nanosystem to mitochondrial and nuclear proteins in vitro and in vivo was achieved. Up to 60% inhibition of KYSE-30 cell migration was observed and the expressions of VEGF-C and MMP-2 as angiogenic markers were reduced 3- and 2-fold, respectively. A marked reduction in tumor mass was recorded (43.25%) with the control, a 41.36% decrease with the nanoparticles and a 61.01% reduction with the LyP-1-modified nanosystem following treatment in mice. The LyP-1-functionalized nanosystem targeted tumor lymphatics, instigated nuclear rupture and mitochondrial distortion, and decreased cell proliferation and migration with inhibition of VEGF-C and MMP2 expression.
Pyrene Metabolism in Crinipellis stipitaria : Identification of trans -4,5-Dihydro-4,5-Dihydroxypyrene and 1-Pyrenylsulfate in Strain JK364 (1994)

The isolation and identification of two novel metabolites in the fungal metabolism of pyrene are described. The plant-inhabiting basidiomycete Crinipellis stipitaria JK364 metabolized pyrene, a polycyclic aromatic hydrocarbon containing four rings, when grown in submerged cultures in a medium containing malt extract, glucose, and yeast extract. In experiments with [C] pyrene, after 7 days of incubation 40% of the labeled substrate was converted into organic solvent-extractable metabolites. Metabolites isolated from cultures grown with pyrene were identified as 1-pyrenylsulfate and trans-4,5-dihydro-4,5-dihydroxypyrene. 1-Hydroxypyrene, the precursor of 1-pyrenylsulfate, was also detected. 1-Pyrenylsulfate was isolated from mycelial extracts, whereas trans-4,5-dihydro-4,5-dihydroxypyrene was recovered from the culture filtrate. Identification of the compounds was based on their UV spectra, mass spectra, and nuclear magnetic resonance spectra. This is the first report on the detoxification of a polycyclic aromatic hydrocarbon by a plant-inhabiting basidiomycete. The occurrence of 1-pyrenylsulfate and trans-4,5-dihydro-4,5-dihydroxypyrene among fungal metabolites of pyrene is also new.
The effect of alginates on deoxycholic-acid-induced changes in oesophageal mucosal biology at pH 4 (2007)

Long-standing gastro-oesophageal reflux disease (GORD) can give rise to Barrett's oesophagus (BM), a metaplastic condition and precursor to oesophageal adenocarcinoma (AC). Oesophageal cancer was once rare but is now the 5th biggest cancer killer in the U.K. Reflux of bile acids into the oesophagus is implicated in the progression to BM as bile acids at pH 4 have been shown to induce c-myc expression, an oncogene upregulated in BM and AC. In the present study we investigated the role of the biopolymer alginate on bile acid induced molecular changes in oesophageal cell lines. OE21, OE33 and TE-7 oesophageal cell lines were exposed to 100 microM deoxycholic acid at pH 4 in the presence or absence of alginates. Levels of c-myc, E-cadherin, beta-catenin and Tcf signalling were determined by Real-Time PCR, Western blotting, immunofluoresence and reporter assays. All alginates tested were able to prevent the induction of c-myc by acidified deoxycholic acid in vitro. The upstream effects of acidified deoxycholic acid on E-cadherin, beta-catenin and Tcf signalling were also suppressed by alginate. Therefore, we have demonstrated that reflux of bile acids into the oesophagus initiates a potentially damaging molecular cascade of events using an in vitro model and that a biopolymer, alginate, can protect against these effects.
Helicobacter pylori adherence to gastric epithelial cells: a role for non-adhesin virulence genes (2002)

Helicobacter pylori is a major aetiological agent in gastroduodenal disorders and adherence of the bacteria to the gastric mucosa is one of the initial stages of infection. Although a number of specific adhesins has been identified, other H. pylori virulence factors may play a role in adherence to gastric epithelial cells directly or through interaction with other adhesins. This study assessed the effect of 16 H. pylori virulence factors on the adherence of the bacteria to gastric AGS cells and on gastric epithelial cell cycle distribution. Defined isogenic H. pylori SS1 mutants were used. After co-incubation of gastric AGS cells and bacteria, adherence of H. pylori to AGS cells was visualised by immunofluorescence microscopy and quantified by flow cytometry. Cell cycle phase distribution was analysed by flow cytometry with propidium iodide staining. Mutants were tested for their ability to adhere to AGS cells and compared with the wild-type SS1 strain. Mutations in genes in the cag pathogenicity island showed that cagP and cagE mutants adhered less than the wild-type strain to AGS cells, whereas a cagF mutant showed no reduction in adherence. Mutations in genes involved in flagellar biosynthesis showed that the adherence ability of fliQ, fliM and fliS mutants was reduced, but a flhB mutant possessed wild-type levels of adherence. Mutations in genes coding for the urease (ureB) and phospholipase (pldA) enzymes did not affect adherence, but mutation of the tlyA gene encoding an H. pylori haemolysin resulted in a reduced adherence. A fliQ mutant, with reduced adherence to AGS cells, was less able to induce AGS cell apoptosis than SS1. The ability to induce G0G1 cell cycle arrest was also abolished in the fliQ mutant. However, an increased cell number in S phase was observed when AGS cells were exposed to the fliQ mutant compared with SS1, suggesting that unattached bacteria may still be able to stimulate cell proliferation. In addition to known adhesins, other bacterial virulence factors such as CagE, CagP, FliQ, FliM, FliS and TlyA appear to play a role in H. pylori adherence to gastric epithelial cells. Mutations in these genes may affect H. pylori pathogenicity by reducing either the ability of the bacteria to attach to gastric epithelial cells or the intensity of bacteria-host cell interactions.
Supplementary Table 1 from <i>HIST1H2BB</i> and <i>MAGI2</i> Methylation and Somatic Mutations as Precision Medicine Biomarkers for Diagnosis and Prognosis of High-grade Serous Ovarian Cancer (2023)

&lt;p&gt;Survival Genes&lt;/p&gt;
Investigations of output power and beam divergence of slab waveguide rf-pumping CO 2 laser (1996)

Results of experimental investigations of output power and beam divergence for a slab waveguide rf-excited carbon- dioxide laser are presented. Laser output power 150 - 250 W and maximum efficiency 10 - 13% in a beam with near- diffraction-limit divergence has been achieved. In repetitive-rate mode, the pulsed power was more than twice as much as the average one in the cw mode. After beam shaping lens, the sum beam divergence of 2.5 mrad at the 0.8 total power level has been obtained.
A compact, 37% fractional bandwidth millimeter-wave phase shifter using a wideband lange coupler for 60-GHz and E-band systems (2017)

A wideband 57.7-84.2 GHz Phase Shifter is presented using a compact Lange coupler to generate in-phase and quadrature signal. The Lange coupler is followed by two balun transformers that provide the IQ vector modulation with differential I and Q signals. The implemented Phase Shifter demonstrates an average 6-dB insertion loss and 5-dB gain variation. The measured average rms phase and gain errors are 7 degrees and 1 dB, respectively. The phase shifter is implemented in GlobalFoundries 45-nm SOI CMOS technology using a trap-rich substrate. The chip area is 385 μm × 285 μm and the Phase Shifter consumes less than 17 mW. To the best of authors knowledge, this is the first phase shifter that covers both 60 GHz band and E-band frequencies with a fractional bandwidth of 37%.
Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation (2008)

Some of the genes we identified distinguish key transcripts previously seen in array studies, while others are newly defined. Many of the genes identified as overexpressed in ER- tumors were previously identified as expression markers for neoplastic transformation in multiple human cancers. Moreover, our motif analysis identified a collection of specific cis-acting target sites which may collectively play a role in the differential gene expression patterns observed in ER+ versus ER- breast cancer tumors. Importantly, the gene sets and associated DNA motifs provide a starting point with which to explore the mechanistic basis for the observed expression patterns in breast tumors.