gebhart/patrepeval huggingface dataset:
P1‐282: ANALYTICAL PERFORMANCE OF A FULLY AUTOMATED CHEMILUMINESCENT PTAU 181 ASSAY ON THE LUMIPULSE G SERIES (2018)

Today levels of amyloid peptides (β-amyloid 1-42 and 1-40) and tau proteins (total Tau and Tau hyperphosphorylated at threonine 181) in cerebrospinal fluid (CSF) are well-accepted biomarkers representing Alzheimer's disease (AD) from the earliest stages on. CSF phospho-Tau181 provides added value in discriminating AD from other dementias. Widespread use of these biomarkers in AD diagnosis requires reliable, highly precise, and accurate measurements. The analytical performance of a novel fully automated Lumipulse G pTau 181 assay (under development) for the quantification of phospho-Tau181 was evaluated. The LUMIPULSE G instrument series use single, ready-to-use immunoreaction cartridges with a throughput of 60 and 120 tests/hour for the G600II and the G1200 instrument, respectively. Each cartridge generates quantitative results within approximately 30 minutes. The Lumipulse G pTau 181 assay under development uses established monoclonal antibodies. Analytical assay performance was characterized according to CLSI guidelines. Using a panel of CSF and control samples, assay variability was determined and resulted in total CV ≤ 6 % and ≤ 5%, respectively. The LoD was shown to be < 0.5 pg/mL and the LoQ < 5 pg/mL. No high dose hook effect was observed for samples containing up to 30000 pg/mL of phospho-Tau181. Linearity was shown across the clinical relevant range. A method comparison study with the INNOTEST® PHOSPHO-TAU-(181P) assay demonstrated a good correlation (r>0.90). Automation, the mono test cartridge principle, short throughput times, and instrument flexibility are key attributes of the LUMIPULSE G instrument series making it the ideal platform to fulfill today's needs for rapid and accurate quantification of CSF biomarkers. The novel Lumipulse G pTau 181 assay (under development) shows good sensitivity and precision, correlates well with the INNOTEST assay and completes the routine CSF biomarker panel for AD on LUMIPULSE.
Exploiting the properties of line-shape singularities in orientationally selected electron spin echo envelope modulation spectra of Cu2+−(15N-imidazole)4 for the determination of hyperfine coupling with the remote imidazole nitrogen (1994)

Orientationally selected two-, three-, and four-pulse electron spin echo envelope modulation (ESEEM) spectra from remote 15N nuclei in a Cu2+-(15N–imidazole)4 complex have been obtained in the microwave frequency region 9.12–9.82 GHz. This range of frequencies has allowed us to reach the conditions corresponding to S and ν⊥ singularities of the lineform of basic transitions. The development of these lineform singularities in orientationally selected spectra is discussed. The knowledge of the magnetic fields corresponding to the singularities was used to find the hyperfine coupling parameters for the remote nitrogen as a=2.44 MHz and T⊥=−0.39 MHz as well as to determine the angle between the axis of the complex and the direction of the largest principal hyperfine tensor element as 40°. Additional geometrical information about the ligand orientation has been obtained from the analysis of shifts of the sum combination harmonic in proton four-pulse ESEEM spectra.
Rapid biocompatible macrocyclization of peptides with decafluoro-diphenylsulfone (2016)

In this manuscript, we describe modification of Cys-residues in peptides and proteins in aqueous solvents <i>via</i> aromatic nucleophilic substitution (S<sub>N</sub>Ar) with perfluoroarenes (fAr). Biocompatibility of this reaction makes it attractive for derivatization of proteins and peptide libraries comprised of 20 natural amino acids. Measurement of the reaction rates for fAr derivatives by <sup>19</sup>F NMR with a model thiol donor (β-mercaptoethanol) in aqueous buffers identified decafluoro-diphenylsulfone (<b>DFS</b>) as the most reactive S<sub>N</sub>Ar electrophile. Reaction of <b>DFS</b> with thiol nucleophiles is >100 000 faster than analogous reaction of perfluorobenzene; this increase in reactivity enables application of <b>DFS</b> at low concentrations in aqueous solutions compatible with biomolecules and protein complexes irreversibly degraded by organic solvents (<i>e.g.</i>, bacteriophages). <b>DFS</b> forms macrocycles when reacted with peptides of the general structure X <sub><i>n</i></sub> -Cys-X <sub><i>m</i></sub> -Cys-X <sub><i>l</i></sub> , where X is any amino acid and <i>m</i> = 1-15. It formed cyclic peptides with 6 peptide hormones-oxytocin, urotensin II, salmon calcitonin, melanin-concentrating hormone, somatostatin-14, and atrial natriuretic factor (1-28) as well as peptides displayed on M13 phage. Rates up to 180 M<sup>-1</sup> s<sup>-1</sup> make this reaction one of the fastest Cys-modifications to-date. Long-term stability of macrocycles derived from <b>DFS</b> and their stability toward oxidation further supports <b>DFS</b> as a promising method for modification of peptide-based ligands, cyclization of genetically-encoded peptide libraries, and discovery of bioactive macrocyclic peptides.
Nucleic acid binding drugs. VIII. Structures of 1-[2-(diethylamino)ethylamino]anthracene-9,10-dione, C20H22N2O2 (I) and 1,5-bis[2-(diethylamino)ethylamino]anthracene-9,10-dione, C26H36N4O2 (II), models for antitumour drugs (1983)

(I) M r = 322.41, P21/n, a = 7.118 (1), b = 26.873(2), c=8.886(1)A, fl=97.74(1)°, ~ V= 1684.3 (6) A 3, Z = 4, D m = 1.27, D x = 1.271 Mg m -3, 2 (Cu Ka) = 1.54178 A,/~ = 6.67 cm -1, F(000) = 688, T= 298 K, R w= 0.049 for 981 unique significant reflections. (II) Mr=436.61, P21/c, a= 15.360 (2), b = 5.245 (1), c= 15.483 (1)A, fl= 94.23 (1) °, V= 1244.0 (5)/~3, Z = 2, D m -- 1.17, D x = 1.165 Mg m -s, 2(Cu Kt~) = 1.54178/k, /t = 5.98 cm -1, F(000) = 472, T= 298 K, R w = 0.090 for 457 unique significant reflections. The chromophore is highly planar in both compounds.
The LAPACK for clusters project: an example of self adapting numerical software (2004)

This article describes the context, design, and recent development of the LAPACK for clusters (LFC) project (LAPACK stands for Linear Algebra PACKage). It has been developed in the framework of self-adapting numerical software (SANS) since we believe such an approach can deliver the convenience and ease of use of existing sequential environments bundled with the power and versatility of highly-tuned parallel codes that execute on clusters. Accomplishing this task is far from trivial as we argue in the paper by presenting pertinent case studies and possible usage scenarios.
Optimization and resource management in NOMA wireless networks supporting real and non-real time service bundling (2017)

In this paper, the problem of joint users' uplink transmission power and rate allocation in NOMA wireless networks is studied, under the scenario that each user is simultaneously requesting multiple services. Each user is associated with a two-variable utility function that represents his satisfaction from his allocated resources (i.e., power and rate). In order to appropriately reflect the combined needs of the user for bundling different types of services under the same common umbrella, user's utility function consists of two parts while different percentages are adopted by each user for each part in order to express his need for real and non-real time services. The joint resource allocation problem is directly confronted as a two-variable optimization problem and formulated as a non-cooperative game. The theory of S-modular multivariable games is adopted towards determining the Nash equilibrium point of the game. A distributed, iterative and low complexity algorithm for computing game's Nash equilibrium is introduced, while updating user's uplink transmission power and rate at the same step. Detailed numerical results exhibit the ability of the proposed framework to simultaneously satisfy diverse multiple services requested by the same user.
Investigation of Potential Antioxidant, Thrombolytic and Neuropharmacological Activities of Homalomena aromatica Leaves Using Experimental and In Silico Approaches (2021)

The leaves of <i>Homalomena aromatica</i> are traditionally used in Bangladesh for the treatment of different chronic ailments. The purpose of this study was to explore in vitro antioxidant, thrombolytic activities, and in vivo neuropharmacological effects of methanolic extract of <i>Homalomena aromatica</i> (MEHA) leaves. Antioxidant activity of MEHA was assessed by a DPPH free radical scavenging assay and total phenolics content, total flavonoids content were also measured. The thrombolytic activity was determined by percentage of clot lysis and neuropharmacological activities by hole board, tail suspension, forced swimming and elevated plus maze tests. The results showed that the IC<sub>50</sub> value of the extract against DPPH was 199.51 μg/mL. Quantitative analysis displayed higher contents of phenolics and flavonoids (147.71 mg gallic acid equivalent/g & 66.65 mg quercetin equivalent/g dried extract, respectively). The extract also showed a significant clot lysis (33.31%) activity. In case of anxiolytic activity, the elevate plus maze (EPM) test demonstrated an increase in time spent in open arms, and in case of hole board test, the number of head dipping was also significantly increased (<i>p</i> < 0.05). All the test compared with control (1% Tween in water) and standard (diazepam 1 mg/kg), significant dose (200 & 400 mg/kg) dependent anxiolytic activity was found. In antidepressant activity, there was a significant decrease in period of immobility in both test models (tail suspension and forced swimming) (<i>p</i> < 0.05). Moreover, 13 compounds were identified as bioactive, showed good binding affinities to xanthine oxidoreductase, tissue plasminogen activator receptor, potassium channel receptor, human serotonin receptor targets in molecular docking experiments. Furthermore, ADME/T analysis revealed their drug-likeness, likely pharmacological actions and non-toxic upon consumption. Taken together, our finding support the traditional medicinal use of this plant, which may provide a potential source for future drug discovery.
Apolipoprotein A-IV inhibits experimental colitis (2004)

The antiatherogenic properties of apoA-IV suggest that this protein may act as an anti-inflammatory agent. We examined this possibility in a mouse model of acute colitis. Mice consumed 3% dextran sulfate sodium (DSS) in their drinking water for 7 days, with or without daily intraperitoneal injections of recombinant human apoA-IV. apoA-IV significantly and specifically delayed the onset, and reduced the severity and extent of, DSS-induced inflammation, as assessed by clinical disease activity score, macroscopic appearance and histology of the colon, and tissue myeloperoxidase activity. Intravital fluorescence microscopy of colonic microvasculature revealed that apoA-IV significantly inhibited DSS-induced leukocyte and platelet adhesive interactions. Furthermore, apoA-IV dramatically reduced the upregulation of P-selectin on colonic endothelium during DSS-colitis. apoA-IV knockout mice exhibited a significantly greater inflammatory response to DSS than did their WT littermates; this greater susceptibility to DSS-induced inflammation was reversed upon exogenous administration of apoA-IV to knockout mice. These results provide the first direct support for the hypothesis that apoA-IV is an endogenous anti-inflammatory protein. This anti-inflammatory effect likely involves the inhibition of P-selectin-mediated leukocyte and platelet adhesive interactions.
Model-based integrated HRR object tracking and classification (2009)

Radar target classification based on 2D stochastic object model matching is studied in this paper. A network of High Range Resolution (HRR) radars provides range measurements at multiple time steps, while the extended object is moving in the surveillance area. Alignment of the multi-aspect HRR data in a common 2D coordinate system is required. For this reason, tracking of the extended object is integrated in the classification algorithm. The novelty of this work is the estimation of the object state, conditioned on the object class, by applying the HRR data on a particle filter. A coarse-to-fine multi-resolution data processing scheme is introduced in the filter update step. The reason is the experienced filter degeneracy, when working with HRR data. The proposed processing scheme achieves accurate auto-alignment of the HRR data. The classification system successfully distinguishes between very similar objects, by applying 2D object model matching.
‘Knock-down’ of spinal CB1 receptors produces abnormal pain and elevates spinal dynorphin content in mice (2002)

Recent studies demonstrate the possible existence of tonic modulatory control of nociceptive input mediated by spinal cannabinoid receptors (CB1). Accordingly, it is predicted that a reduction in the spinal CB1 receptors may enhance sensitivity to sensory stimuli and a decrease in spinal antinociceptive potency to cannabinoid agonists. An antisense oligodeoxynucleotide (ODN) specific to the CB1 receptor was used to 'knock-down' CB1 receptors in the lumbar spinal cord and dorsal root ganglia by the local, repeated intrathecal (i.th.) administration of the ODN. This treatment resulted in a decrease in lumbar spinal CB1 receptor expression accompanied by a decrease in the response thresholds to both innocuous tactile and noxious thermal stimuli. The antinociceptive action of the CB1 agonist, WIN 55,212-2, by i.th. administration was also significantly attenuated after treatment with the antisense ODN. Similar treatment using a mismatch control ODN had no effect on receptor protein or on sensory thresholds. The effects of the antisense ODN treatment on sensory thresholds were fully reversed after discontinuation of the ODN injection. The antisense ODN treated rats also showed a significant increase in lumbar spinal dynorphin A. Acute i.th. injection of MK-801 or an antidynorphin antiserum blocked the antisense ODN-induced tactile and thermal hypersensitivity. These data support the possibility of endogenous inhibitory cannabinoid tone to limit spinal afferent input of thermal and tactile stimuli. Lifting of this inhibitory tone through a 'knock-down' of spinal CB1 receptors apparently lowers the thresholds for sensory input, as reflected by the actions of MK-801 to block tactile and thermal hypersensitivity. The increased spinal dynorphin may act to further promote afferent outflow and abnormal pain because sequestration of spinal dynorphin with antiserum also reverses the manifestations of abnormal pain following knock-down of CB1 receptors.
P834 Proteus is a key candidate in the pathogenesis of Crohn’s disease: mucosa, stool genomics and functional analysis: the ENIGMA study (2019)

Proteus, Gram-negative facultative anaerobic bacilli, has recently been identified as a key genus in Crohn’s disease (CD) recurrence after intestinal resection. In this study, we investigated the role of Proteus as a gut pathogen in mediating inflammation in Crohn’s disease. 54 pairs of faecal samples and 80 colonic samples (61 CD patients; 19 healthy controls) were collected. The abundance of Proteus were determined by quantitative PCR. Proteus was isolated from faeces and biopsies of CD patients by selection culture in conditional agar and confirmed by Proteus specific target sequencing. To study effects of isolated Proteus, we established an in vitro microbe-enterocyte co-culture system by using two normal epithelial cells INT407, NCM460 and two CRC cell lines CaCo2 and HT29. Pathogenic function of Proteus was determined by in vivo mouse models and in vitro cell assays. Bacterial invasion ability was measured by fluorescence staining and confocal microscopy. Intracellular gene expression profiles and regulated pathways in normal cells treated with or without Proteus were analysed by RNA seq and KEGG analysis. We confirmed the presence of Proteus in the gut and stool. The prevalence of Proteus in faecal samples was higher in CD patients compared with healthy controls (p < 0.05). Levels of Proteus were significantly increased in CD biopsies compared with control tissue. Amongst 24 Proteus-monoclones isolated from faeces and biopsy of CD patients, all of them belonged to members of P. mirabilis lineages. Proteus gavaged mice showed a shortened colon length compared with mice treated with E. coli 1655 (5.97 cm vs. 7.15 cm; p < 0.05). Mice depleted of bacteria and exposed to Proteus and DSS showed significantly higher severity of inflammation on HE staining. Compared with the cells co-cultured with E. coli 1655 or cultured in medium only (showed normal phenomenon), 70–80% of cells co-cultured with Proteus were unhealthy (rounded and detached) or dead. Increased necrotic cells were found in four cell lines co-cultured with Proteus due to bacterial invasion. Moreover, Proteus stimulated the production of pro-inflammatory cytokines including IL-18 (p < 0.001) and IL-1α (p < 0.01) in co-cultured cells (INT407 and NCM460). In keeping with this, Proteus induced key pro-inflammatory pathways including NOD-like receptor signalling (p < 0.001), Jak-STAT signalling (p < 0.01) and MAPK signalling pathways (p < 0.01) identified by RNA sequencing. Our results show P. mirabilis, a urease producing organism in the gut, is associated with CD and can induce inflammation in cell lines and animal models of colitis. We contend that P. mirabilis and related species may act as a pathobiont and thereby play a critical role in the pathogenesis of CD.
Upsettability of SiCp/6061 aluminum matrix composite and its mechanical properties. (1993)

In order to assess the possibility of a forging process of aluminum matrix composites, the upsettability and flow stress of a SiC/6061 aluminum alloy composite and the tensile strength of the upset composite were investigated. The composite was prepared with a powder extruding method. The upsetting test and the compressive test were carried out to measure a critical reduction in height and a flow stress. After some upsetting processes and those followed by a heat treatment, the strength and ductility are measured using a small tensile specimen machined from the upset material. At temperature higher than 300°C, the upsettability of the composite is as high as that of conventional alloy. Both at room and elevated temperatures, upset composite is weaker but more ductile than unupset one. The low strength and the high ductility are maintained after subsequent heat treating process.
Study on Power Fluctuation Dispatch and Capacity Design of Short Period Power Fluctuation Compensation System in Consideration of Power Loss (2013)

Since output of photovoltaic generation (PV) includes power fluctuation caused by natural conditions, installation of PV on a large scale is supposed to affect Load Frequency Control (LFC) of the power grid. One method to compensate power fluctuation is the use of energy storage (ES), such as batteries and capacitors. A power fluctuation compensation system composed of an electrical double layer capacitor energy storage system (EDLC ESS) and a Li-ion battery energy storage system (Li-ion BESS) is considered. Power loss characteristics of both ESSs during power fluctuation compensation are modeled by equivalent circuits based on ES impedance spectra. The models are validated through experiments simulating power fluctuation compensation. Using these ES models, simulations were carried out to determine power fluctuation dispatch method between both ESSs and ESSs' capacity in consideration of power loss minimization.
NMD Microarray Analysis for Rapid Genome‐Wide Screen of Mutated Genes in Cancer (2005)

Gene mutations play a critical role in cancer development and progression, and their identification offers possibilities for accurate diagnostics and therapeutic targeting. Finding genes undergoing mutations is challenging and slow, even in the post-genomic era. A new approach was recently developed by Noensie and Dietz to prioritize and focus the search, making use of nonsense-mediated mRNA decay (NMD) inhibition and microarray analysis (NMD microarrays) in the identification of transcripts containing nonsense mutations. We combined NMD microarrays with array-based CGH (comparative genomic hybridization) in order to identify inactivation of tumor suppressor genes in cancer. Such a "mutatomics" screening of prostate cancer cell lines led to the identification of inactivating mutations in the EPHB2 gene. Up to 8% of metastatic uncultured prostate cancers also showed mutations of this gene whose loss of function may confer loss of tissue architecture. NMD microarray analysis could turn out to be a powerful research method to identify novel mutated genes in cancer cell lines, providing targets that could then be further investigated for their clinical relevance and therapeutic potential.
Indirect CO2 emissions caused by the fuel demand switch in international shipping (2021)

In 2020 the fuel sulphur limit in international shipping was reduced from 3.5 to 0.5 wt%. Three adaptive measures dominate: (i) increased exhaust gas cleaning in the maritime industry enabling continued use of high-sulphur fuel oil, (ii) increased refining output ratio of low-sulphur fuels, and iii) increased use of blended fuels. As (i) and (ii) are insufficient to comply with the new demand, refiners will resort to (iii), which requires increased crude oil throughput. Extracted crude oil will typically oxidize completely over longer time periods, so increased crude oil throughput is synonymous with increased CO2 emissions of up to 323 Mton in 2020, corresponding to ∼1% of the total global CO2 emissions from fossil fuels. Transferring demand from low-value to high-value oil products cause indirect CO2 emissions, and vice versa. CO2 emissions can be mitigated by prioritizing demand reduction according to oil product value starting with the most valuable products.
Towards gaze-based prediction of the intent to interact in virtual reality (2021)

With the increasing frequency of eye tracking in consumer products, including head-mounted augmented and virtual reality displays, gaze-based models have the potential to predict user intent and unlock intuitive new interaction schemes. In the present work, we explored whether gaze dynamics can predict when a user intends to interact with the real or digital world, which could be used to develop predictive interfaces for low-effort input. Eye-tracking data were collected from 15 participants performing an item-selection task in virtual reality. Using logistic regression, we demonstrated successful prediction of the onset of item selection. The most prevalent predictive features in the model were gaze velocity, ambient/focal attention, and saccade dynamics, demonstrating that gaze features typically used to characterize visual attention can be applied to model interaction intent. In the future, these types of models can be used to infer user’s near-term interaction goals and drive ultra-low-friction predictive interfaces.