gebhart/patrepeval huggingface dataset:
Epigenetic and therapeutic implications of dnmt3b in temporomandibular joint osteoarthritis. (2019)

Temporomandibular joint (TMJ) arthritis causes severe debilitation and has few treatment options. Here, we found a small molecule, DNA methyltransferase 3B (Dnmt3b), as a putative therapeutic target, partially rescued osteoarthritic phenotype. Dnmt3b was detected differentially expressed in cell zones of mandibular condylar cartilage and the expression of Dnmt3b decreased in the progression of TMJ osteoarthritis. Dnmt3b deficiency using conditional knockout mice led to the onset of osteoarthritis-like conditions including cartilage clefts, cartilage matrix loss and premature chondrocyte hypertrophy, which suggested that Dnmt3b functioned as a osteoarthritis suppressor. Dnmt3b gain-of-function in TMJ stem/progenitor cells showed increases in collagen type II but decreases in collagen type X, whereas Dnmt3b knockdown had opposite effects with attenuated collagen type II but increased collagen type X. Dnmt3b acted via Wnt/β-catenin signaling and Dnmt3b regulated TMJ stem/progenitor cells differentiation by inducing their premature progression towards hypertrophic chondrocytes through β-catenin transnucleation and activation. Finally, local Dnmt3b delivery partially rescued cartilage degradation in experimentally induced osteoarthritis. Thus, novel molecules in articular cartilage, such as Dnmt3b, may have therapeutic effects for TMJ osteoarthritis.
Gas‐phase acidity of bis[(perfluoroalkyl)sulfonyl]imides. Effects of the perfluoroalkyl group on the acidity (2014)

The gas‐phase acidity (GA) values were determined for a number of perfluoroalkyl‐substituted sulfonylimides by measuring proton‐transfer equilibria using a Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometer. The GA scale below 286.5 kcal mol −1 for (CF 3 SO 2 ) 2 NH was extended and partially revised. The GA value of (C 4 F 9 SO 2 ) 2 NH which is currently the strongest acid was revised from 284.1 to 278.6 kcal mol −1 . The effect of fluorine atoms on the acidity of perfluoroalkyl‐substituted sulfonylimides was described with the following model urn:x-wiley:08943230:media:poc3317:poc3317-math-0001 where N (α) , N (β) , N (γ) , and N (δ) are the numbers of fluorine atoms at α, β, γ, and δ position in R f SO 2 (R f = perfluoroalkyl group), respectively. This correlation indicates that the electron‐withdrawing ability of the R f SO 2 group can be described in terms of the number of fluorine atoms in the perfluoroalkyl group corrected by taking into account their positions. Copyright © 2014 John Wiley &amp; Sons, Ltd.
Quantum Hamiltonian learning using imperfect quantum resources (2014)

Identifying an accurate model for the dynamics of a quantum system is a vexing problem that underlies a range of problems in experimental physics and quantum information theory. Recently, a method called quantum Hamiltonian learning has been proposed by the present authors that uses quantum simulation as a resource for modeling an unknown quantum system. This approach can, under certain circumstances, allow such models to be efficiently identified. A major caveat of that work is the assumption of that all elements of the protocol are noise free. Here we show that quantum Hamiltonian learning can tolerate substantial amounts of depolarizing noise and show numerical evidence that it can tolerate noise drawn from other realistic models. We further provide evidence that the learning algorithm will find a model that is maximally close to the true model in cases where the hypothetical model lacks terms present in the true model. Finally, we also provide numerical evidence that the algorithm works for noncommuting models. This work illustrates that quantum Hamiltonian learning can be performed using realistic resources and suggests that even imperfect quantum resources may be valuable for characterizing quantum systems.
Printed FLCDs on plastic substrates (2000)

Abstract We report on the requirements of Ferroelectric Liquid Crystal Displays (FLCDs) for Smart Card applications and on the switching behaviour of FLCs with different spontaneous polarization. Furthermore a flexographic printing technique of FLCs on plastic substrates is presented. Experiments show that the phase of the FLC during the printing process has a big influence on the switching voltage of the FLCD. After printing the FLC the substrates are laminated to a display. This technique allows a vacuum free and in consequence economic mass production process of bistable FLC-Displays on flexible plastic substrates.
Self-assembled graphitic nanotubes with one-handed helical arrays of a chiral amphiphilic molecular graphene (2005)

Self-assembly of a Gemini-shaped, chiral amphiphilic hexa-peri-hexabenzocoronene having two chiral oxyalkylene side chains, along with two lipophilic side chains, yields graphitic nanotubes with one-handed helical chirality. The nanotubes are characterized by an extremely high aspect ratio of >1,000 and have a uniform diameter of 20 nm and a wall thickness of 3 nm. The nanotubes with right- and left-handed helical senses were obtained from the (S)- and (R)-enantiomers of the amphiphile, respectively, due to an efficient translation of point chirality into supramolecular helical chirality. The (S)- and (R)-enantiomers coassemble at varying mole ratios to give nanotubes, whose circular dichroism profiles are almost unchanged over a wide range of the enantiomeric excess of the amphiphile (100-20%). The high level of chirality amplification thus observed indicates a long-range cooperativity in the self-assembling process. In sharp contrast, a hexabenzocoronene amphiphile with chiral lipophilic side chains did not form nanotubular assemblies. The present work demonstrates the majority rule in noncovalent systems and also may provide a synthetic strategy toward realization of molecular solenoids.
Investigation and Improvement of a Bouncing Torsional Vibration in Automotive Dual Mass Flywheel by Combining Testing and 1D CAE Modeling Approach (2019)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Dual mass flywheel (DMF) is a well-known isolation system for vehicle drivetrain. DMF has two typical elastic energy storage systems: long travel arc springs and in-series spring units (including two or more springs) and sliding shoes connected in series. DMF has such complex nonlinear characteristics as torque-dependent torsional stiffness and rotational speed-dependent hysteresis friction due to its dependency of centrifugal force that is applied to components and radial force of springs. Because of this complexity, sub-harmonic vibration (SHV) may occur under certain circumstances, such as under light-load and high-rotational conditions. In general, since SHV’s frequency is 1/2 or 1/3 of the engine’s combustion frequency and may cause human discomfort, DMF must be designed robust against such nonlinear vibration. In this paper to reduce the SHV occurrence and to show a more robust design indicator, the SHV causing the mechanism is researched by testing and 1D CAE modeling. In detail, DMF interior behavior in high-speed rotation is clarified with high-speed cinematography on a test bench, and high-resolution relative torsional angle of DMF is obtained by evaluating the actual vehicle with a conventional four-cylinder gasoline engine, which is equipped with in-series spring unit type DMF. As a result, bouncing torsional vibration (BTV) might occur when sliding shoe and secondary-side driven flange contact each other, and that is triggering the SHV excitation. 1D CAE model, whose development is based on the tested mechanism, is verified since the substantially same BTV and SHV occur between tests and simulation results. According to 1D CAE, highly sensitive parameters and ideas for reducing SHV can be found with sensitivity analysis of the physical DMF parameters. The effect of those parameters was confirmed with vehicle tests.&lt;/div&gt;&lt;/div&gt;
Fighting Cancer with Corroles (2016)

Corroles are exceptionally promising platforms for the development of agents for simultaneous cancer-targeting imaging and therapy. Depending on the element chelated by the corrole, these theranostic agents may be tuned primarily for diagnostic or therapeutic function. Versatile synthetic methodologies allow for the preparation of amphipolar derivatives, which form stable noncovalent conjugates with targeting biomolecules. These conjugates can be engineered for imaging and targeting as well as therapeutic function within one theranostic assembly. In this review, we begin with a brief outline of corrole chemistry that has been uniquely useful in designing corrole-based anticancer agents. Then we turn attention to the early literature regarding corrole anticancer activity, which commenced one year after the first scalable synthesis was reported (1999-2000). In 2001, a major advance was made with the introduction of negatively charged corroles, as these molecules, being amphipolar, form stable conjugates with many proteins. More recently, both cellular uptake and intracellular trafficking of metallocorroles have been documented in experimental investigations employing advanced optical spectroscopic as well as magnetic resonance imaging techniques. Key results from work on both cellular and animal models are reviewed, with emphasis on those that have shed new light on the mechanisms associated with anticancer activity. In closing, we predict a very bright future for corrole anticancer research, as it is experiencing exponential growth, taking full advantage of recently developed imaging and therapeutic modalities.
Nearest-neighbour nanocrystal bonding dictates framework stability or collapse in colloidal nanocrystal frameworks (2017)

Block copolymers serve as architecture-directing agents for the assembly of colloidal nanocrystals into a variety of mesoporous solids. Here we report the fundamental order-disorder transition in such assemblies, which yield, on one hand, ordered colloidal nanocrystals frameworks or, alternatively, disordered mesoporous nanocrystal films. Our determination of the order-disorder transition is based on extensive image analysis of films after thermal processing. The number of nearest-nanocrystal neighbours emerges as a critical parameter dictating assembly outcomes, which is in turn determined by the nanocrystal volume fraction (f<sub>NC</sub>). We also identify the minimum f<sub>NC</sub> needed to support the structure against collapse.
Enantioselective Hydrogenation with Racemic and Enantiopure Binap in the Presence of a Chiral Ionic Liquid (2008)

Racemic but enantioselective: rac-Binap and a chiral ionic liquid (cIL) used for the asymmetric hydrogenation of dimethyl itaconate led to identical ee values as enantiopure binap. The enantiodifferentiation results primarily from a diastereomeric interaction of the binap–Rh unit and the proline ester moiety. For other substrates, enhanced enantioselectivity with inverted absolute configuration was obtained with the enantiopure ligand in the cIL relative to organic solvents.
Cowpea mosaic virus : effects on host cell processes (2002)

SUMMARY Taxonomy: Cowpea mosaic virus (CPMV) is the type member of the Comoviridae and bears a strong resemblance to animal picornaviruses, both in gene organization and in the amino acid sequence of replication proteins. Little systematic work has been done to compare isolates of the virus from different parts of the world. Physical properties: Purified preparations of virus contain three centrifugal components; empty protein shells without RNA (T) and two nucleoprotein components (M and B), containing 24% and 34% RNA, respectively. The icosahedral particles have with a diameter of 28 nm, consist of 60 copies of two coat proteins, and are heat stable. Hosts: CPMV causes one of the most commonly reported virus diseases of cowpea (Vigna unguiculata), in which it produces chlorotic spots with diffuse borders in inoculated primary leaves. Trifoliate leaves develop a bright yellow or light green mosaic of increasing severity in younger leaves. The host range is rather limited, and few hosts are known outside the Leguminosae. The virus is transmitted by various beetles with biting mouthparts. Reported in Africa, the Philippines and Iran. Is apparently absent from North and South America. Useful website: http://mmtsb.scripps.edu/viper/1cpmv.html (structure); http://image.fs.uidaho.edu/vide/descr254.htm (general information).
Common genetic determinants of breast-cancer risk in East Asian women: a collaborative study of 23 637 breast cancer cases and 25 579 controls (2013)

In a consortium including 23 637 breast cancer patients and 25 579 controls of East Asian ancestry, we investigated 70 single-nucleotide polymorphisms (SNPs) in 67 independent breast cancer susceptibility loci recently identified by genome-wide association studies (GWASs) conducted primarily in European-ancestry populations. SNPs in 31 loci showed an association with breast cancer risk at P < 0.05 in a direction consistent with that reported previously. Twenty-one of them remained statistically significant after adjusting for multiple comparisons with the Bonferroni-corrected significance level of <0.0015. Eight of the 70 SNPs showed a significantly different association with breast cancer risk by estrogen receptor (ER) status at P < 0.05. With the exception of rs2046210 at 6q25.1, the seven other SNPs showed a stronger association with ER-positive than ER-negative cancer. This study replicated all five genetic risk variants initially identified in Asians and provided evidence for associations of breast cancer risk in the East Asian population with nearly half of the genetic risk variants initially reported in GWASs conducted in European descendants. Taken together, these common genetic risk variants explain ~10% of excess familial risk of breast cancer in Asian populations.
Ultrafast Optical Parametric Oscillator Pumped by an All Normal Dispersion (ANDi) Yb: Fiber Oscillator (2012)

We describe a 13 nJ, 100 fs, 60 MHz Yb:Fiber ANDi oscillator that pumps a MgO2:PPLN optical parametric oscillator (OPO), producing up to 300 mW (signal+idler) of total output, and overall efficiency of 37%.
Cloning and Expression of cDNA Encoding a Protein That Binds a Palindromic Promoter Element Essential for Induction of Fungal Cutinase by Plant Cutin (1995)

Previous studies showed that a palindromic sequence located at -159 base pairs is essential for induction of cutinase gene in Fusarium solani f. sp. pisi (Nectria haematococca mating type VI) by the hydroxy fatty acids from plant cutin and that a 50-kDa nuclear protein binds to a promoter that contains this element. Screening of a phage lambda gt11 expression library with the concatenated palindromic sequence as the probe identified a cDNA encoding a palindrome-binding protein (PBP). Nucleotide sequence of this cDNA revealed an open reading frame that would code for PBP with a calculated molecular weight of 49,847. This PBP contains a putative nuclear localization signal and a zinc finger motif sharing homology with the zinc finger DNA binding domains of transcription factors from mammals, Saccharomyces cerevisiae, Neurospora crassa, and Ustilago maydis. A highly basic region immediately adjacent to the carboxyl side of the zinc finger was also observed. PBP expressed in Escherichia coli showed specific binding to the palindromic DNA fragment.
Tyrosine kinase fusion genes in pediatric BCR-ABL1-like acute lymphoblastic leukemia (2016)

Approximately 15% of pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL) is characterized by gene expression similar to that of BCR-ABL1-positive disease and unfavorable prognosis. This BCR-ABL1-like subtype shows a high frequency of B-cell development gene aberrations and tyrosine kinase-activating lesions. To evaluate the clinical significance of tyrosine kinase gene fusions in children with BCP-ALL, we studied the frequency of recently identified tyrosine kinase fusions, associated genetic features, and prognosis in a representative Dutch/German cohort. We identified 14 tyrosine kinase fusions among 77 BCR-ABL1-like cases (18%) and none among 76 non-BCR-ABL1-like B-other cases. Novel exon fusions were identified for RCSD1-ABL2 and TERF2-JAK2. JAK2 mutation was mutually exclusive with tyrosine kinase fusions and only occurred in cases with high CRLF2 expression. The non/late response rate and levels of minimal residual disease in the fusion-positive BCR-ABL1-like group were higher than in the non-BCR-ABL1-like B-others (p<0.01), and also higher, albeit not statistically significant, compared with the fusion-negative BCR-ABL1-like group. The 8-year cumulative incidence of relapse in the fusion-positive BCR-ABL1-like group (35%) was comparable with that in the fusion-negative BCR-ABL1-like group (35%), and worse than in the non-BCR-ABL1-like B-other group (17%, p=0.07). IKZF1 deletions, predominantly other than the dominant-negative isoform and full deletion, co-occurred with tyrosine kinase fusions. This study shows that tyrosine kinase fusion-positive cases are a high-risk subtype of BCP-ALL, which warrants further studies with specific kinase inhibitors to improve outcome.
Tensor networks and graphical calculus for open quantum systems (2015)

We describe a graphical calculus for completely positive maps and in doing so review the theory of open quantum systems and other fundamental primitives of quantum information theory using the language of tensor networks. In particular we demonstrate the construction of tensor networks to pictographically represent the Liouville-superoperator, Choi-matrix, process-matrix, Kraus, and system-environment representations for the evolution of quantum states, review how these representations interrelate, and illustrate how graphical manipulations of the tensor networks may be used to concisely transform between them. To further demonstrate the utility of the presented graphical calculus we include several examples where we provide arguably simpler graphical proofs of several useful quantities in quantum information theory including the composition and contraction of multipartite channels, a condition for whether an arbitrary bipartite state may be used for ancilla assisted process tomography, and the derivation of expressions for the average gate fidelity and entanglement fidelity of a channel in terms of each of the different representations of the channel.
Matrix-immobilized yeast for large-scale production of recombinant human lactoferrin (2015)

An improved method of recombinant human lactoferrin (hLF) expression in rich culture medium is demonstrated using macroporous microencapsulation.
Effect of sodium chloride, sucrose, and xanthan gum on pasting properties and gel syneresis of hairless canary seed starch (2019)

Abstract Background and objectives Hairless (glabrous) canary seed is a novel food and promising source of starch, protein, and oil that recently received food approval from Health Canada and GRAS status from US FDA. This study is designed to investigate effects of sodium chloride, sucrose, and xanthan gum on pasting properties of starch from two hairless canary seed varieties and their gel stability during refrigerated storage and freeze–thaw treatment in comparison with wheat starch. Findings The DSC data showed differences in gelatinization transition temperatures and enthalpies indicating differences in starch structure between canary seed and wheat. The addition of sodium chloride lowered breakdown and setback viscosities of canary seed and wheat starch pastes but in a different way as indicated by opposite effects on peak viscosity. Sucrose increased peak, trough, and final viscosities of canary seed and wheat starches especially at 1.0%. Xanthan gum improved stability of starch paste against heat and shear force. The current study demonstrates better stability for hairless canary seed starch gels over wheat starch gels during refrigerated storage and freeze–thaw treatment. Conclusions The results demonstrate the ability of sodium chloride, sucrose, or xanthan gum at small concentrations to modulate pasting properties and gel stability of canary seed starch. Significance and novelty Use of sodium chloride, sucrose, or xanthan gum to modify canary seed starch pastes and improve gel stability could promote its utilization in food and nonfood industries.
Multiplicity of Generation, Selection, and Classification Procedures for Jammed Hard-Particle Packings (2001)

Hard-particle packings have served as useful starting points to study the structure of diverse systems such as liquids, living cells, granular media, glasses, and amorphous solids. Howard Reiss has played a major role in helping to illuminate our understanding of hard-particle systems, which still offer scientists many interesting conundrums. Jammed configurations of hard particles are of great fundamental and practical interest. What one precisely means by a "jammed" configuration is quite subtle and considerable ambiguity remains in the literature on this question. We will show that there is a multiplicity of generation, selection, and classification procedures for jammed configurations of identical d-dimensional spheres. We categorize common ordered lattices according to our definitions and discuss implications for random disk and sphere packings. We also show how the concept of rigidity percolation (which has been used to understand the mechanical properties of network glasses) can be generalized to further characterize hard-sphere packings.
Serum total IgE and specific IgE to Dermatophagoides pteronyssinus, but not eosinophil cationic protein, are more likely to be elevated in elderly asthmatic patients. (2005)

Serum IgE (total and five specific) and eosinophil cationic protein (ECP) levels were compared in elderly physician-diagnosed patients with asthma with non-asthmatic controls matched by age and gender to ascertain whether elevated levels are indicators of asthma in the elderly. All subjects and controls were non-smokers. The subjects were participants in the Florida Geriatric Research Program (FGRP), a longitudinal aging study that tracks the health status of people 65 years and older. Frozen sera from 33 randomly selected asthmatic patients and 21 controls, none of whom had any other chronic respiratory disease, such as chronic obstructive pulmonary disease (COPD), all between the ages of 65 and 90, were assessed for total IgE; five specific IgE concentrations (for cat, ragweed, German cockroach, Dermatophagoides pteronyssinus (Dp) and live oak); and ECP levels using the Pharmacia Unicap System. The odds of an elderly asthmatic patient having a total IgE of > 100 KU/L were higher than that for a non-asthmatic patient (odds ratio (OR) = 13.0; Mantel-Haenszel (MH) p = 0.005). The odds of elderly asthmatic patients having at least one positive serum specific IgE compared to elderly age-matched non-asthmatic patients were higher (OR = 21.2; MH p = 0.001). Among the five specific IgE concentrations, only IgE for Dp was higher in asthmatic than in non-asthmatic patients (OR = 13.00; MH p = 0.005). The ECP level was not significantly different between elderly asthmatic and non-asthmatic patients (asthmatic mean = 20.7 microg/L, SE = 0.48; control mean = 19.5 microg/L. SE = 0.76) (mean for younger adults 4.4 microg/L, Pharmacia Diagnostics). The serum of elderly asthmatic patients is more likely to have elevated total IgE and a positive specific IgE to Dp. ECP is elevated in elderly subjects but is not an indicator of asthma.