gebhart/patrepeval huggingface dataset:
Facile synthesis of single-phase spherical α″-Fe16N2/Al2O3 core-shell nanoparticles via a gas-phase method (2013)

When nitrogen was inserted into the spherical α-Fe/Al2O3 core shell of 45 nm nanoparticles, the XRD pattern showed a clear change in the crystal modification from a body-centered cubic crystal to that of a single-phase α″-Fe16N2 structure. SEM, TEM, and energy-dispersive X-ray spectroscopy mapping analysis gave the particle size distributions, the shell thickness, and the Fe and Al elements. An examination of the total electron yield (surface sensitive) and fluorescence yield (bulk sensitive) of X-ray absorption fine structure on Fe and N atoms of these core shell nanoparticles confirmed the nitriding of the core iron and showed iron oxide formations on the core surface, indicating stability and resistivity performance. The nitriding process also changed the magnetic properties from paramagnetic to ferromagnetic with a coercivity above 3000 Oe, indicating a promising material for a “rear-earth-free” giant magnet.
Comprehension of grammatical and emotional prosody is impaired in Alzheimer's disease. (2008)

Previous research has demonstrated impairment in comprehension of emotional prosody in individuals diagnosed with Alzheimer's disease (AD). The present pilot study further explored the prosodic processing impairment in AD, aiming to extend our knowledge to encompass both grammatical and emotional prosody processing. As expected, impairments were seen in emotional prosody. AD individuals were also found to be impaired in detecting sentence modality, suggesting that impairments in affective prosody processing in AD may be ascribed to a more general prosodic processing impairment, specifically in comprehending prosodic information signaled across the sentence level. AD participants were at a very mild stage of the disease, suggesting that prosody impairments occur early in the disease course.
Interfacial polarization of disseminated conductive minerals in absence of redox-active species — Part 1: Mechanistic model and validation (2016)

ABSTRACT Electrically conductive mineral inclusions are commonly present in organic-rich mudrock and source-rock formations such as veins, laminations, rods, grains, flakes, and beds. Laboratory and subsurface electromagnetic (EM) measurements performed on geomaterials containing electrically conductive inclusions generally exhibit frequency dispersion due to interfacial polarization phenomena at host-inclusion interfaces. In the absence of redox-active species, surfaces of electrically conductive mineral inclusions are impermeable to the transport of charge carriers, inhibit the exchange of charges and behave as perfectly polarized (PP) interfaces under the influence of an externally applied EM field. Interfacial polarization phenomena involving charge separation, migration, accumulation/depletion, and relaxation around PP interfaces is referred to as PP interfacial polarization; it influences the magnitude and direction of the electric field and charge carrier migration in the geomaterial. We have developed a mechanistic model to quantify the complex-valued electrical conductivity response of geomaterials containing electrically conductive mineral inclusions, such as pyrite and magnetite, uniformly distributed in a fluid-filled, porous matrix made of nonconductive grains possessing surface conductance, such as silica and clay grains. The model first uses a linear approximation of the Poisson-Nernst-Planck equations of dilute solution theory to determine the induced dipole moment of a single isolated conductive inclusion and that of a single isolated nonconductive grain surrounded by an electrolyte. A consistent effective-medium formulation was then implemented to determine the effective complex-valued electrical conductivity of the geomaterial. Model predictions were in good agreement with laboratory measurements of multifrequency complex-valued electrical conductivity, relaxation time, and chargeability of mixtures containing electrically conductive inclusions.
N-Alkylated 6′-Aminoluciferins Are Bioluminescent Substrates for Ultra-Glo and QuantiLum Luciferase: New Potential Scaffolds for Bioluminescent Assays (2008)

A set of 6'-alkylated aminoluciferins are shown to be bioluminescent substrates for Ultra-Glo and QuantiLum luciferases. These studies demonstrate that both the engineered and wild-type firefly luciferases tolerate much greater steric bulk at the 6' position of luciferin than has been previously reported. The nature of the alkyl substituent strongly affects the strength of the bioluminescent signal, which varies widely based on size, shape, and charge. Several compounds were observed to generate more light than the corresponding unsubstituted 6'-aminoluciferin. Determination of Michaelis-Menten constants for the substrates with Ultra-Glo indicated that the variation arises primarily from differences in V max, ranging from 1.33 x 10 (4) to 332 x 10 (4) relative light units, but in some cases K m (0.73-10.8 microM) also plays a role. Molecular modeling results suggest that interactions of the side chain with a hydrogen-bonding network at the base of the luciferin binding pocket may influence substrate-enzyme binding.
Nitazoxanide Inhibits Biofilm Formation by Staphylococcus epidermidis by Blocking Accumulation on Surfaces (2010)

Coagulase-negative species of Staphylococcus are often associated with opportunistic hospital-acquired infections that arise from the colonization of indwelling catheters. Here we show that the antiparasitic drug nitazoxanide (NTZ) and its active metabolite, tizoxanide (TIZ), are inhibitory to the growth of Staphylococcus epidermidis and other staphylococci, including methicillin-resistant Staphylococcus aureus strains, under aerobic and microaerobic conditions (MICs, 8 to 16 microg/ml). At sub-MIC levels, NTZ and TIZ also inhibited biofilm production under static conditions by strains of S. epidermidis and Staphylococcus haemolyticus with a 50% inhibitory concentration of approximately 2.5 microg/ml (8 microM). The 5-nitro group was required for biological activity, and a hydrophilic derivative of NTZ (AMIX) also inhibited biofilm formation. NTZ did not disperse the existing biofilm but did block further accumulation. Sub-MICs of NTZ had no effect on primary attachment to surfaces at either 4 or 37 degrees C. The inhibitory action of NTZ and TIZ, but not vancomycin, on biofilm production could be reversed by the addition of zinc salts (2.5 to 40 microM) but not other metals, suggesting that NTZ might target the zinc-dependent accumulation-associated protein (Aap) that mediates accumulation on surfaces. However, neither NTZ nor TIZ formed chelation complexes with zinc salts, based on spectrophotometric and nuclear magnetic resonance analyses, and addition of excess zinc to NTZ-grown bacteria (apo-Aap) did not restore the accumulation phenotype. Our studies suggest that sub-MIC levels of NTZ may affect the assembly or function of cell structures associated with the biofilm phenotype.
Decentralized planning for dynamic motion generation of multi-link robotic systems (2009)

This paper presents a decentralized planning method for generating dynamic whole body motions of multilink robots including humanoids. First, a robotic system will be modeled as a general multi-body dynamical system. The planning problem of a multi-body system will then be formulated as a constraint resolution problem. The problem will be solved by means of an extended Gauss-Seidel method, which is capable of handling multiple constraint groups with different priorities. The method will be demonstrated in whole-body motion generation tasks of a humanoid, both in numerical simulations and in experiments using a real humanoid robot.
Directed mutagenesis of the redox-active disulfide in the flavoenzyme mercuric ion reductase (1985)

Mercuric ion reductase, a flavoenzyme with an active site redox-active cystine, Cys135-Cys140, is an unusual enzyme that reduces Hg(II) to Hg(0) with stoichiometric NADPH oxidation. To probe the catalytic mechanism, we have constructed two active site Cys to Ser mutations by oligonucleotide-directed mutagenesis. The native and the Cys135, Ser140 and Ser135, Cys140 mutant enzymes are expressed on an overproducing plasmid and purified to homogeneity by a one-step procedure in high yield. The optical spectra of the mutant proteins are distinct, with the Ser135, Cys140 mutant displaying a thiolate-flavin charge-transfer band (Cys140 pKa = 5.2), confirming that Cys140, not Cys135, is in charge-transfer distance both in this mutant and in two electron reduced native enzyme. The native and both mutant proteins are dimers and are precipitated by antibody to native enzyme. Thiol titrations with 5,5'-dithiobis(2-nitrobenzoate) (DTNB) indicate that both mutants contain three kinetically accessible thiols in both oxidized and reduced states. The native enzyme has two titratable thiols when oxidized and four in the two electron reduced state. The native and two Cys to Ser mutant enzymes show differentiable NADPH-dependent catalytic behavior with Hg(SR)2 (R = CH2CH2OH), Hg(CN)2, DTNB, thio-NADP+, and O2, the most striking of which are the activities toward the Hg(II) complexes and DTNB. Only native enzyme reduces Hg(SR)2. The Ser135, Cys140 enzyme alone shows sustained Hg(CN)2 reduction, whereas the native and Cys135, Ser140 enzymes are rapidly inactivated. DTNB reduction is catalyzed by the native and Cys135, Ser140 enzymes, but not by the Ser135, Cys140 enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)
Bleomycin therapy in advanced Hodgkin's disease and epidermoid cancers (1972)

Bleomycin was used to treat 31 patients with a variety of advanced, previously treated malignancies, with particular emphasis on Hodgkin's disease and epidermoid cancers. Bleomycin was administered either twice weekly, 15 mg per dose, or in 5-day courses, 105 mg total dose per course. Three of 10 patients with Hodgkin's disease had good responses, lasting 6, 10, and 12 weeks. Three other patients with Hodgkin's disease had transient responses. There was a suggestion, in Hodgkin's disease, of the superiority of the twice weekly to daily drug administration. One patient with an epidermoid cancer of the skin had a good response lasting 9 weeks. No responses were seen in epidermoid cancer of the head and neck (five patients), or epidermoid cancer of the cervix and vagina (five patients). Eleven of 14 patients followed with serial pulmonary function tests developed 20-50% decreases in either diffusion capacity or forced vital capacity as compared to pretreatment determinations. Only one, however, developed clinical pulmonary toxicity. This patient died from probable bleomycin pneumonia, at a total dose of 255 mg. Skin changes were seen in 75% of patients and mucosal toxicity in 30%. Seven additional patients with epidermoid cancers received a combination of bleomycin and methotrexate, sequentially. They developed severe skin and mucosal toxicity. However, six of seven had tumor responses, and further studies of less toxic combinations of these drugs are warranted.
Discovery of Selective Menaquinone Biosynthesis Inhibitors against Mycobacterium tuberculosis (2012)

Aurachin RE (1) is a strong antibiotic that was recently found to possess 1,4-dihydroxy-2-naphthoate prenyltransferase (MenA) and bacterial electron transport inhibitory activities. Aurachin RE is the only molecule in a series of aurachin natural products that has the chiral center in the alkyl side chain at C9'-position. To identify selective MenA inhibitors against Mycobacterium tuberculosis , a series of chiral molecules were designed based on the structures of previously identified MenA inhibitors and 1. The synthesized molecules were evaluated in in vitro assays, including MenA enzyme and bacterial growth inhibitory assays. We could identify novel MenA inhibitors that showed significant increase in potency of killing nonreplicating M. tuberculosis in the low oxygen recovery assay (LORA) without inhibiting other Gram-positive bacterial growth even at high concentrations. The MenA inhibitors reported here are useful new pharmacophores for the development of selective antimycobacterial agents with strong activity against nonreplicating M. tuberculosis.
Chemisorption of Organic Triols on Ge(100)-2 × 1 Surface: Effect of Backbone Structure on Adsorption of Trifunctional Molecules (2017)

The effect of backbone on the adsorption mechanism of homo-trifunctional molecules on Ge(100)-2 × 1 has been studied. The chemisorption of the triols 1,3,5-benzenetriol and 2-hydroxymethyl-1,3-propanediol on Ge(100)-2 × 1 was investigated by means of Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and density functional theory calculations. Both triol molecules undergo an O–H dissociation reaction with the Ge dimers, with experiments showing that the fraction of O–H groups that dissociates per molecule is the same for 2-hydroxymethyl-1,3-propanediol and 1,3,5-benzenetriol. Experimental results suggest that for both molecules there is a mix of products formed at saturation, with evidence of trifold adsorbates. The flexibility of the backbone is shown to influence surface coverage and dimer occupancy, with the flexible backbone able to pack the surface more easily. DFT calculations support these results by showing favorable pathways for all reactions through single, double, and triple O–H dissociative products for both molecules along the reaction coordinate. DFT results also show differences in adsorbate-induced strain between both molecular backbones.
On Achievable Rate Regions for Half-Duplex Causal Cognitive Radio Channels (2010)

Coding for the causal cognitive radio channel, with the cognitive source subjected to a half-duplex constraint, is studied. A discrete memoryless channel model incorporating the half-duplex constraint is presented, and a new achievable rate region is derived for this channel. It is proved that this rate region contains the previously known causal achievable rate region of \cite{Devroye06} for Gaussian channels.
ChemInform Abstract: Design, Synthesis, and Characterization of Polyintercalating Ligands. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
First principles study of pyrophosphate defects and dopant–defect interactions in stronium-doped lanthanum orthophosphate (2013)

LaPO4 has been actively studied for proton conductor applications, due to its stability and proton uptake in humid atmospheres over intermediate temperature ranges. An important process underlying the application of this and related materials for proton-conductor applications is the hydrolysis of pyrophosphate defects. In this work we undertake density-functional-theory (DFT) calculations of the relative energetics of pyrophosphate defects and protons in LaPO4, including their binding with divalent dopant cations. Due to the low symmetry of the monazite crystal structure for LaPO4, there exists four symmetry-distinct pyrophosphate defect configurations; DFT calculations are used to identify the most stable configuration, which is 0.24 eV lower in energy than all others. Further, from supercell calculations with 1.85 mol% Sr doping, we investigate the dopant-binding energies for pyrophosphate defects to be 0.37 eV, which is comparable to the value of 0.34 eV calculated for proton–dopant binding energies in the same system. These results establish that dopant–defect interactions further stabilize proton incorporation, with the hydration enthalpies when the dopants are nearest and furthest from the protons and pyrophosphate defects being −1.66 eV and −1.37 eV, respectively. Even though our calculations show that dopant binding enhances the enthalpic favorability of proton incorporation, they also suggest that such binding is likely to substantially lower the kinetic rate of hydrolysis of pyrophosphate defects.
Intravenous Nicorandil in Conjunction With Coronary Reperfusion Therapy is Associated With Better Clinical and Functional Outcomes in Patients With Acute Myocardial Infarction. (2003)

The aim of this retrospective study was to assess whether intravenous nicorandil, a hybrid of NO and a KATP channel opener, in conjunction with percutaneous coronary intervention (PCI) improves the long-term prognosis in patients with acute myocardial infarction (AMI). Intravenous nicorandil has already been shown to improve the in-hospital prognosis of patients with anterior AMI. The study population consisted of 272 patients with a reperfused AMI who were admitted during a similar time interval, before (control; n=114) and after nicorandil treatment (n=158). In the nicorandil group, a 4 mg bolus injection was given, followed by 6 mg/h infusion for 24 h and then oral nicorandil at 15 mg/day for at least 1 month. In the patients with an anterior AMI, left ventricular (LV) function was better and the frequency of LV remodeling was lower after 3 months in the nicorandil group; however, in those with a non-anterior AMI, there were no differences in functional outcome and the frequency of LV remodeling between the 2 groups. The frequency of cardiac events was significantly lower in the nicorandil group, and the use of nicorandil was derived as a potential factor related to freedom from cardiac events (p<0.01, odds ratio = 0.27). Nicorandil treatment was associated with better myocardial perfusion and a better functional and clinical outcome than PCI alone, and this beneficial effect was maintained for a long time, particularly in patients with anterior AMI.
Dissecting Cis Regulation of Gene Expression in Human Metabolic Tissues (2011)

Complex diseases such as obesity and type II diabetes can result from a failure in multiple organ systems including the central nervous system and tissues involved in partitioning and disposal of nutrients. Studying the genetics of gene expression in tissues that are involved in the development of these diseases can provide insights into how these tissues interact within the context of disease. Expression quantitative trait locus (eQTL) studies identify mRNA expression changes linked to proximal genetic signals (cis eQTLs) that have been shown to affect disease. Given the high impact of recent eQTL studies, it is important to understand what role sample size and environment plays in identification of cis eQTLs. Here we show in a genotyped obese human population that the number of cis eQTLs obey precise scaling laws as a function of sample size in three profiled tissues, i.e. omental adipose, subcutaneous adipose and liver. Also, we show that genes (or transcripts) with cis eQTL associations detected in a small population are detected at approximately 90% rate in the largest population available for our study, indicating that genes with strong cis acting regulatory elements can be identified with relatively high confidence in smaller populations. However, by increasing the sample size we allow for better detection of weaker and more distantly located cis-regulatory elements. Yet, we determined that the number of tissue specific cis eQTLs saturates in a modestly sized cohort while the number of cis eQTLs common to all tissues fails to reach a maximum value. Understanding the power laws that govern the number and specificity of eQTLs detected in different tissues, will allow a better utilization of genetics of gene expression to inform the molecular mechanism underlying complex disease traits.
Is it possible to diagnose autism by brain imaging? (2013)

Harvard University Schools of Medicine & Public Health, MA, USA and Neurostatistics Laboratory, McLean Hospital, MA, USA nlange@hms.harvard.edu The root biological causes of autism spectrum disorder – autism – remain a complex mystery despite 70 years of effort to solve the puzzle. A total of 6 years after Leo Kanner first identified ‘early infantile autism’ in 1943 through astute observation of 11 children [1], he retracted his initial biological theory. Since then, no alternative theory has yet been validated by genetics or molecular biology to take its place [2]. Today’s autism research is awash with an abundance of statistically significant brain imaging results that provide little differentiation between individuals with the disorder and typically developing individuals [3], and this body of findings cannot yet be employed as useful diagnostic criteria in clinical practice. As we know, and as the Oxford English Dictionary reminds us, any image is merely “an artificial imitation or representation of the external form”, a “copy,” “likeness,” “similitude,” “semblance,” “appearance” and “shadow.” Some researchers today have exclaimed, “science is imaging”. Regardless of how ‘real’ the everimproving spatiotemporal image resolution, brilliance of color and attraction of animation appear to be, this statement broadcasts a clear misconception. Much of science is measurement, and we continue to have difficulty measuring the same brain structure twice within a short time interval and getting the same number, even after accounting for the ‘regression to the mean’ effect. The reliability of autism imaging is a major present-day limitation of the technology. MR brain images are perhaps the most beautiful of all image types (so beautiful because so mutable?), and these beauties are sometimes subjected to ‘circular analysis’ in attempts to ground their impressions in solid statistics [4]. MR images, these quantized imitations of reality, are indeed measurements amenable to statistical regression and classification analysis, but they cannot yet
Automatic Parallelization to Asynchronous Task-Based Runtimes Through a Generic Runtime Layer (2019)

With the end of Moore's law, asynchronous task-based parallelism has seen growing support as a parallel programming paradigm, with the runtime system offering such advantages as dynamic load balancing, locality, and scalability. However, there has been a proliferation of such programming systems in recent years, each of which presents different performance tradeoffs and runtime semantics. Developing applications on top of these systems thus requires not only application expertise but also deep familiarity with the runtime, exacerbating the perennial problems of programmability and portability. This work makes three main contributions to this growing landscape. First, we extend a polyhedral optimizing compiler with techniques to extract task-based parallelism and data management for a broad class of asynchronous task-based runtimes. Second, we introduce a generic runtime layer for asynchronous task-based systems with representations of data and tasks that are sparse and tiled by default, which serves as an abstract target for the compiler backend. Finally, we implement this generic layer using OpenMP and Legion, demonstrating the flexibility and viability of the generic layer and delivering an end-to-end path for automatic parallelization to asynchronous task-based runtimes. Using a wide range of applications from deep learning to scientific kernels, we obtain geometric mean speedups of 23.0× (OpenMP) and 9.5× (Legion) using 64 threads.