gebhart/patrepeval huggingface dataset:
Relationship between structural and dynamic properties of Al-rich Al-Cu melts: Beyond the Stokes-Einstein relation (2016)

We perform ab initio molecular dynamics simulations to study structural and transport properties in liquid $\mathrm{A}{\mathrm{l}}_{1\ensuremath{-}x}\mathrm{C}{\mathrm{u}}_{x}$ alloys, with copper composition $x\ensuremath{\le}0.4$, in relation to the applicability of the Stokes-Einstein (SE) equation in these melts. To begin, we find that self-diffusion coefficients and viscosity are composition dependent, while their temperature dependence follows an Arrhenius-type behavior, except for $x=0.4$ at low temperature. Then, we find that the applicability of the SE equation is also composition dependent, and its breakdown in the liquid regime above the liquidus temperature can be related to different local ordering around each species. In this case, we emphasize the difficulty of extracting effective atomic radii from interatomic distances found in liquid phases, but we see a clear correlation between transport properties and local ordering described through the structural entropy approximated by the two-body contribution. We use these findings to reformulate the SE equation within the framework of Rosenfeld's scaling law in terms of partial structural entropies, and we demonstrate that the breakdown of the SE relation can be related to their temperature dependence. Finally, we also use this framework to derive a simple relation between the ratio of the self-diffusivities of the components and the ratio of their partial structural entropies.
Treatment of Scleroderma (2002)

The treatment of systemic sclerosis (scleroderma) is difficult and remains a great challenge to the clinician. Because the cause is unknown, therapies are directed to improve peripheral blood circulation with vasodilators and antiplatelet aggregation drugs, to prevent the synthesis and release of harmful cytokines with immunosuppressant drugs, and to inhibit or reduce fibrosis with agents that reduce collagen synthesis or enhance collagenase production. The purpose of this review is to critically analyze conventional and new treatments of systemic sclerosis and localized scleroderma. The therapeutic options discussed for the treatment of systemic sclerosis include the use of (1) vasodilators (calcium channel blockers [nifedipine], angiotensin-converting enzyme inhibitors [captopril, losartan potassium], and prostaglandins [iloprost, epoprostenol]), (2) immunosuppressant drugs (methotrexate, cyclosporine, cyclophosphamide, and extracorporeal photopheresis), and (3) antifibrotic agents (D-penicillamine, colchicine, interferon gamma, and relaxin). The treatment options reviewed for localized scleroderma include the use of corticosteroids, vitamin D analogues (calcitriol, calcipotriene), UV-A, and methotrexate. Preliminary reports on new therapies for systemic sclerosis are also considered. These include the use of minocycline, psoralen-UV-A, lung transplantation, autologous stem cell transplantation, etanercept, and thalidomide.
Synergistic Interactions between Aβ, Tau, and α-Synuclein: Acceleration of Neuropathology and Cognitive Decline (2010)

Alzheimer's disease (AD), the most prevalent age-related neurodegenerative disorder, is characterized pathologically by the accumulation of beta-amyloid (Abeta) plaques and tau-laden neurofibrillary tangles. Interestingly, up to 50% of AD cases exhibit a third prevalent neuropathology: the aggregation of alpha-synuclein into Lewy bodies. Importantly, the presence of Lewy body pathology in AD is associated with a more aggressive disease course and accelerated cognitive dysfunction. Thus, Abeta, tau, and alpha-synuclein may interact synergistically to promote the accumulation of each other. In this study, we used a genetic approach to generate a model that exhibits the combined pathologies of AD and dementia with Lewy bodies (DLB). To achieve this goal, we introduced a mutant human alpha-synuclein transgene into 3xTg-AD mice. As occurs in human disease, transgenic mice that develop both DLB and AD pathologies (DLB-AD mice) exhibit accelerated cognitive decline associated with a dramatic enhancement of Abeta, tau, and alpha-synuclein pathologies. Our findings also provide additional evidence that the accumulation of alpha-synuclein alone can significantly disrupt cognition. Together, our data support the notion that Abeta, tau, and alpha-synuclein interact in vivo to promote the aggregation and accumulation of each other and accelerate cognitive dysfunction.
An offline foundation for online accountable pseudonyms (2008)

Online anonymity often appears to undermine accountability, offering little incentive for civil behavior, but accountability failures usually result not from anonymity itself but from the disposability of virtual identities. A user banned for misbehavior---e.g., spamming from a free E-mail account or stuffing an online ballot box---can simply open other accounts or connect from other IP addresses. Instead of curtailing freedom of expression by giving up anonymity, online services and communities should support accountable pseudonyms: virtual personas that can provide both anonymity and accountability. We propose Pseudonym parties, a scheme for creating accountable pseudonyms, which combine inperson social occasions (parties) with technical infrastructure (a pseudonymous sign-on service) to enforce the rule that one real person gets one virtual persona on any participating online service. Pseudonym parties enable the user to adopt different personas in different online spaces without revealing the connection between them, while ensuring that each user has only one accountable pseudonym in each space. Pseudonym parties can be started incrementally in a fully decentralized fashion, can run on volunteer labor with minimal funds, and may even be fun.
Fetal morbidity and mortality after acute human parvovirus B19 infection in pregnancy: prospective evaluation of 1018 cases (2004)

Our data demonstrate a relevant B19-associated risk of fetal death, which is largely confined to maternal B19 infection in the first 20 WG. Timely intrauterine transfusion of fetuses with severe hydrops fetalis reduces the risk of fetal death. Parvovirus B19-associated stillbirth without hydropic presentation is not a common finding.
3D-PRNN: Generating Shape Primitives with Recurrent Neural Networks (2017)

The success of various applications including robotics, digital content creation, and visualization demand a structured and abstract representation of the 3D world from limited sensor data. Inspired by the nature of human perception of 3D shapes as a collection of simple parts, we explore such an abstract shape representation based on primitives. Given a single depth image of an object, we present 3D-PRNN, a generative recurrent neural network that synthesizes multiple plausible shapes composed of a set of primitives. Our generative model encodes symmetry characteristics of common man-made objects, preserves long-range structural coherence, and describes objects of varying complexity with a compact representation. We also propose a method based on Gaussian Fields to generate a large scale dataset of primitive-based shape representations to train our network. We evaluate our approach on a wide range of examples and show that it outperforms nearest-neighbor based shape retrieval methods and is on-par with voxel-based generative models while using a significantly reduced parameter space.
Role of Epidermal Growth Factor Receptor Degradation in Cisplatin-Induced Cytotoxicity in Head and Neck Cancer (2010)

Cisplatin and its analogues are the most commonly used agents in the treatment of head and neck squamous cell carcinoma. In this study, we investigated a possible role of epidermal growth factor (EGF) receptor (EGFR) phosphorylation and degradation in cisplatin-induced cytotoxicity. Cisplatin treatment led to an increase in initial EGFR phosphorylation at Y1045, the binding site of ubiquitin ligase, Casitas B-lineage lymphoma (c-Cbl), followed by ubiquitination in the relatively cisplatin-sensitive cell lines. However, cisplatin-resistant cell lines underwent minimal EGFR phosphorylation at the Y1045 site and minimal ubiquitination. We found that EGFR degradation in response to cisplatin was highly correlated with cytotoxicity in seven head and neck cancer cell lines. Pretreatment with EGF enhanced cisplatin-induced EGFR degradation and cytotoxicity, whereas erlotinib pretreatment blocked EGFR phosphorylation, degradation, and cisplatin-induced cytotoxicity. Expression of a mutant Y1045F EGFR, which is relatively resistant to c-Cbl-mediated degradation, in Chinese hamster ovary cells and the UMSCC11B human head and neck cancer cell line protected EGFR from cisplatin-induced degradation and enhanced cell survival compared with wild-type (WT) EGFR. Transfection of WT c-Cbl enhanced EGFR degradation and cisplatin-induced cytotoxicity compared with control vector. These results show that cisplatin-induced EGFR phosphorylation and subsequent ubiquitination and degradation is an important determinant of cisplatin sensitivity. Our findings suggest that treatment with an EGFR inhibitor before cisplatin would be antagonistic, as EGFR inhibition would protect EGFR from cisplatin-mediated phosphorylation and subsequent ubiquitination and degradation, which may explain the negative results of several recent clinical trials. Furthermore, they suggest that EGFR degradation is worth exploring as an early biomarker of response and as a target to improve outcome.
Integrated multi-electrode fluidic nitric-oxide sensor and VLSI potentiostat array (2004)

Nitric oxide (NO) serves as an important intercellular messenger in the human body, and is mechanistically involved in vascular disease, stroke, chronic hear failure, and epilepsy. We present a multi-electrode NO measurement sensor with integrated microfluidics. An array of carbon-based electrodes detect the spatial and temporal diffusion profile of NO in a PDMS laminar fluidic channel. The array interfaces to a multichannel potentiostatic VLSI system recording the amperometric output in real time, with five orders of magnitude in dynamic range over four scales down to hundreds of picoamperes. The integrated sensor-fluidic-VLSI system is expected to serve as a powerful tool to study the diffusion mechanism of NO under different fluid flow paradigms.
Salt effects in extraction of ethanol, 1‐butanol and acetone from aqueous solutions (1994)

Abstract Experimental studies were performed to assess the effect of salt addition on the extraction of 1‐butanol, ethanol and acetone from dilute aqueous solutions using cyclopentanol, n ‐valeraldehyde, tert‐amyl alcohol, and Adol 85NF as extractants. The liquid‐liquid partitioning was examined for a few strong electrolytes in a broad range of concentrations. Results demonstrate that the distribution coefficient and selectivity in systems with reduced water activity resulting from salt addition were markedly increased. These observations can be qualitatively explained on the basis of the hydration theory. It was also determined that strong electrolytes added to the aqueous feed reduced extractant solubility in the aqueous phase, thus contributing to lower solvent losses. The results showed that the extraction efficiency was not significantly affected by increasing salt content beyond a level that reduces the water activity to a value of 0.92.
Association of Anti-tumor Necrosis Factor Therapy With the Development of Multiple Sclerosis (2005)

A 35-year-old woman with a history of indeterminate colitis developed symptoms of multiple sclerosis after treatment with infliximab. Neurologic examination confirmed upper and lower extremity motor and sensory deficits. MRI showed multiple enhancing white matter lesions distributed throughout her brain as well as her thoracic spine. There may be a link between inflammatory demyelinating disease of the central nervous system and anti-tumor necrosis-alpha therapy. This case report describes the onset or worsening of a demyelinating process after the initiation of infliximab therapy in a patient with indeterminate colitis.
Mechanically Encoded Cellular Shapes for Synthesis of Anisotropic Mesoporous Particles (2014)

The asymmetry that pervades molecular mechanisms of living systems increasingly informs the aims of synthetic chemistry, particularly in the development of catalysts, particles, nanomaterials, and their assemblies. For particle synthesis, overcoming viscous forces to produce complex, nonspherical shapes is particularly challenging; a problem that is continuously solved in nature when observing dynamic biological entities such as cells. Here we bridge these dynamics to synthetic chemistry and show that the intrinsic asymmetric shapes of erythrocytes can be directed, captured, and translated into composites and inorganic particles using a process of nanoscale silica-bioreplication. We show that crucial aspects in particle design such as particle-particle interactions, pore size, and macromolecular accessibility can be tuned using cellular responses. The durability of resultant particles provides opportunities for shape-preserving transformations into metallic, semiconductive, and ferromagnetic particles and assemblies. The ability to use cellular responses as "structure directing agents" offers an unprecedented toolset to design colloidal-scale materials.
Leucine Metabolism in IDDM: Role of Insulin and Substrate Availability (1990)

The effect of insulin on plasma amino acid concentrations and leucine metabolism was examined in 18 healthy nondiabetic young volunteers and in 7 subjects with insulin-dependent diabetes mellitus (IDDM) with the euglycemic insulin-clamp technique (40 mU.m-2.min-1) in combination with [1-14C]leucine. All diabetic subjects were studied while in poor metabolic control (fasting glucose 13.3 +/- 1.1 mM; HbA1c 10.8 +/- 0.2%) and again after 2 mo of intensified insulin therapy (fasting glucose 7.2 +/- 0.5 mM; HbA1c 8.0 +/- 0.2%). Insulin-mediated total-body glucose uptake in poorly controlled diabetic subjects (3.6 +/- 0.5 mg.kg-1.min-1) was significantly reduced compared with control subjects (7.5 +/- 0.2 mg.kg-1.min-1; P less than .001) and improved slightly after insulin therapy (4.8 +/- 0.3 mg.kg-1.min-1; P less than .05), although it still remained significantly lower than in control subjects (P less than .01). During the insulin-clamp study performed in subjects with poorly controlled IDDM, endogenous leucine flux (ELF), leucine oxidation (LO), and nonoxidative leucine disposal (NOLD) all decreased (50.1 +/- 2.0 to 26.4 +/- 0.4; 9.2 +/- 0.4 to 6.0 +/- 0.3; 40.9 +/- 2.0 to 20.4 +/- 2.0 mumol.m-2.min-1, respectively) to the same extent as in control subjects. After 2 mo of intensified insulin therapy, the effect of acute hyperinsulinemia on ELF, LO, and NOLD was comparable to that of control subjects, whereas insulin-stimulated glucose metabolism was still impaired. To examine the effect of substrate availability on leucine turnover, well-regulated IDDM and control subjects underwent a repeat insulin-clamp study combined with a balanced amino acid infusion designed to increase circulating plasma amino acid levels approximately twofold. Under these conditions, NOLD was equally enhanced above baseline in both control and IDDM subjects (P less than .01), whereas ELF was inhibited to a greater extent (P less than .01) than during the insulin clamp performed without amino acid infusion (control vs. diabetic subjects, NS). In conclusion, insulin-mediated glucose metabolism is severely impaired in subjects with both poorly controlled and well-controlled IDDM, whereas the effect of acute insulin infusion on leucine turnover is normal, and combined hyperaminoacidemia/hyperinsulinemia stimulated NOLD to a similar extent in both IDDM and control subjects.
A Novel Antibody–4-1BBL Fusion Protein for Targeted Costimulation in Cancer Immunotherapy (2008)

Costimulation is an essential step in T-cell activation and hence, represents an important aspect in cancer immunotherapy. 4-1BB, a member of the tumor necrosis factor receptor family, has gained particular interest as a costimulatory molecule. Here, we investigated the potential of a targeted activation of 4-1BB-mediated costimulation at the tumor site by generating a recombinant antibody-cytokine fusion protein composed of a single-chain antibody fragment (scFv36) specific for the tumor stromal antigen fibroblast activation protein (FAP) and the extracellular domain of the 4-1BB ligand (4-1BBL). The scFv36-4-1BBL fusion protein is a homotrimeric molecule that binds specifically to FAP and the receptor 4-1BB. T-cell costimulation was demonstrated by interferon-gamma release of peripheral blood mononuclear cells cocultured with FAP-expressing HT1080 cells upon T-cell receptor triggering by monoclonal anti-CD3 antibody. Costimulatory activity of the scFv36-4-1BBL fusion protein was concentration dependent, ligand-specific, and substantially constrained to FAP-expressing target cell binding. Furthermore, scFv36-4-1BBL enhanced T-cell activation when the bispecific antibody scDb33CD3 (specific for FAP and CD3) was used as primary stimulus. Thus, target cell-dependent costimulation with scFv36-4-1BBL constitutes a new option to enhance T-cell activation by bispecific antibodies or antigen-dependent T-cell receptor triggering and should be useful to improve T cell-mediated antitumor responses.
Homomeric interactions between transmembrane proteins of Moloney murine leukemia virus (1996)

We have studied homomeric interactions between transmembrane proteins (TM) of the Moloney murine leukemia virus envelope using the Saccharomyces cerevisiae two-hybrid system. TM interacts strongly with itself but not with various control proteins. Deletional and mutational analyses indicated that the putative leucine zipper motif in the extracellular domain of TM is essential and sufficient to mediate the binding. The first three repeats of the leucine zipper-like motif are the most important in mediating the interaction. The TM-TM interaction detected in this system may play a role in several stages of viral replication.
1,2,4‐triazines. III. A convenient synthesis of 1,2,4‐triazines and their covalent hydration (1970)

Abstract A general synthesis of 1,2,4‐triazines, from 3‐methylthiotriazines is described. It has been shown that 1,2,4‐triazines undergo covalent hydration across the N 4 ‐C 5 bond.
[In vitro selection and affinity function of the aptamers to Bacillus anthracis spores by SELEX]. (2002)

To obtain oligonucleotide aptamers, specifically binding to Bacillus anthracis spores, and to find the relationship between the structures and the affinities, and to determine whether the aptamers can be used as a novel molecule for spore detection, a synthetic 35 mer random DNA library was subjected to 18 rounds of selection by using SELEX (systematic evolution of ligands by exponential enrichment) protocol against spores of Bacillus anthracis vaccine strain A. 16R. The selected aptamers were cloned and sequenced. Software packages CLUSTALX (1.8) and DNASIS v2.5 were employed to analyze the conserved sequences and second structures of the aptamers, respectively. Affinities of aptamers to the spores were visualized by biotin streptavidin horseradish peroxidase system. DAB was used to visualize signals, as an assay method. A membrane-based hybrid sandwich assay was developed for detecting Bacillus anthracic spores by using a 5'-biotinylated ssDNA aptamers and anti-spore antibodies. PCR amplification band pattern of the first round selection was different from that of the ninth round. The binding assay demonstrated that the affinity of the eighteenth round pool increased thirty-seven folds more than that of the first round pool. The affinities of the aptamers were different: the highest A at 450 nm was 1.20, and the lowest was 0.20. The secondary structure analysis revealed possible stem-loop and hairpin structures for binding to the spores. The colorimetry on the immuno-membrane got the best signal with a ratio of 16 microgram aptamer to 4x10(7) spores. A set of aptamers with considerable binding affinity to Bacillus anthracis spores was successfully selected from the initial random ssDNA pool. The stem-loop and hairpin at 5' end of the aptamers worked as the main motif in the interaction between oligonucleotides and spores, while the neighbor bases of the triple structure might affect the stability. Therefore ssDNA aptamers seem to be a type of potential diagnostic molecule.
Elastic behavior, birefringence, and swelling of amorphous polyethylene networks (1967)

Abstract Polyethylene networks were prepared by γ‐irradiation of linear polyethylene, both molten and crystalline. The elastic and photoelastic properties of the networks were studied at high temperatures, i.e., in the molten state. The equilibrium swelling was also measured in several solvents. Values of the crosslinking efficiency G of γ‐radiation, the molecular, weight M e between entanglements, the optical anisotropy α of the equivalent random link, and the polymer‐solvent interaction parameter μ are deduced. Samples prepared by irradiation in the amorphous state showed markedly non‐Gaussian elastic behavior. The presence of a large non‐Gaussian term in the optical anisotropy is also deduced. The value of α obtained for swollen samples, which showed substantially Gaussian elastic behavior, was 3.9 × 10 −24 cm. 3 , about one‐half of that obtained for dry samples. It corresponds to an equivalent random link of only about 5 CH 2 units, on the basis of Denbigh's values for bond polarizabilities. The samples prepared by irradiation in the crystalline state showed lower values for α, which also depended upon the degree of crosslinking. This is attributed to the nonrandom chain configurations prevailing at the time of crosslinking. The same samples were found to show more nearly Gaussian elastic behavior, which is attributed to the same cause.
Luteolin and Apigenin Attenuate 4-Hydroxy-2-Nonenal-Mediated Cell Death through Modulation of UPR, Nrf2-ARE and MAPK Pathways in PC12 Cells (2015)

Luteolin and apigenin are dietary flavones and exhibit a broad spectrum of biological activities including antioxidant, anti-inflammatory, anti-cancer and neuroprotective effects. The lipid peroxidation product 4-hydroxy-2-nonenal (4-HNE) has been implicated as a causative agent in the development of neurodegenerative disorders. This study investigates the cytoprotective effects of luteolin and apigenin against 4-HNE-mediated cytotoxicity in neuronal-like catecholaminergic PC12 cells. Both flavones restored cell viability and repressed caspase-3 and PARP-1 activation in 4-HNE-treated cells. Luteolin also mitigated 4-HNE-mediated LC3 conversion and reactive oxygen species (ROS) production. Luteolin and apigenin up-regulated 4-HNE-mediated unfolded protein response (UPR), leading to an increase in endoplasmic reticulum chaperone GRP78 and decrease in the expression of UPR-targeted pro-apoptotic genes. They also induced the expression of Nrf2-targeted HO-1 and xCT in the absence of 4-HNE, but counteracted their expression in the presence of 4-HNE. Moreover, we found that JNK and p38 MAPK inhibitors significantly antagonized the increase in cell viability induced by luteolin and apigenin. Consistently, enhanced phosphorylation of JNK and p38 MAPK was observed in luteolin- and apigenin-treated cells. In conclusion, this result shows that luteolin and apigenin activate MAPK and Nrf2 signaling, which elicit adaptive cellular stress response pathways, restore 4-HNE-induced ER homeostasis and inhibit cytotoxicity. Luteolin exerts a stronger cytoprotective effect than apigenin possibly due to its higher MAPK, Nrf2 and UPR activation, and ROS scavenging activity.