gebhart/patrepeval huggingface dataset:
Modeling the Kinetics of Cooking and Precooking Potatoes (1988)

ABSTRACT This research investigated the kinetics of cooking potatoes over the temperature range in which starch gelatinizes. A back extrusion texture test was used to measure cookedness. By correlating the data with that of other researchers using different texture tests and potato varieties, we present a unified model of cooking which is first order, independent of variety, and applies to both cooking and gelatinization over the temperature range of 74°C to 100°C.
Determination of cellular rate distributions in microbial cell populations: Feeding rates of ciliated protozoa (1993)

A novel procedure is proposed for determining distributions of rate properties and correlations of rate with state properties of microbial cell populations. The procedure is novel in that it uses transient data, and thus, it does not require that the population be in balanced growth, although it requires that the population structure does not change during the short transient experiment. The procedure is applied to populations of the ciliated protozoan Tetrahymena to determine ingestion rate variability. The number of ingested microspheres per cell and the single-cell protein content-an indicator of cell size-were directly determined with dual-color flow cytometry. The proposed technique revealed the correlation pattern of the particle ingestion rate with cell size. In particular, ingestion rate was found to be positively correlated with cell size for the smaller feeding cells and to be uncorrelated with size for the larger cells. Using the fact that particle uptake from dilute particle suspensions is a Poisson random process, we determined that the coefficient of variation of the distribution of ingestion rates within the feeding population is about 50%. It was concluded that the dynamics of particle ingestion can be accurately described only if it is realized that particle ingestion rates are distributed.
Reactions of Water Radiolysis Intermediates with Pyrimidine and Purine Bases in Aqueous BeF 2 Glasses: An EPR Study (1993)

Free radical formation by reaction of water radiolysis intermediates produced by X-irradiation in aqueous glasses containing 7 M BeF2 at 77 K with pyrimidine and purine constituents of DNA (10 mM) was studied by electron paramagnetic resonance (EPR) spectroscopy. Reactions of electrons and .OH radicals were observed; H. form a minority and their contribution was difficult to establish. The electrons form substrate radicals at 77 K, while .OH radicals, stabilized in the matrix at 77 K, become mobile at about 140K and in part react with solute molecules. The radicals formed by both reactions were characterized after isolation of the corresponding components by thermal annealing up to about 190 K and spectra simulation using literature parameters whenever possible. The spectra from cytosine gave strong evidence for heteroatom protonation following electron addition while those from adenine were somewhat less clear. The spectra of uracil and all methylated pyrimidines gave no evidence for the protonation state of the electron adduct. For the .OH radical, the reaction with uracil and cytosine was found to be addition to the 5,6-double bond, in line with studies using aqueous solutions. For all methylated pyrimidines, however, H-abstraction from the methyl group was dominant. .OH addition to adenine was found to take place at C2.
Two Cases of Subcutaneous Rupture of the Pectoralis Major Muscle (1974)

Rupture of the pectoralis major muscle is not common. This was first described in 1822 by Patissier. This was not yet described in Japanese literature, We would like to add our two cases to the previously reported thirty two cases and discuss etiology, location of rupture, treatment etc.
Functional Evolution of Mammalian Odorant Receptors (2012)

The mammalian odorant receptor (OR) repertoire is an attractive model to study evolution, because ORs have been subjected to rapid evolution between species, presumably caused by changes of the olfactory system to adapt to the environment. However, functional assessment of ORs in related species remains largely untested. Here we investigated the functional properties of primate and rodent ORs to determine how well evolutionary distance predicts functional characteristics. Using human and mouse ORs with previously identified ligands, we cloned 18 OR orthologs from chimpanzee and rhesus macaque and 17 mouse-rat orthologous pairs that are broadly representative of the OR repertoire. We functionally characterized the in vitro responses of ORs to a wide panel of odors and found similar ligand selectivity but dramatic differences in response magnitude. 87% of human-primate orthologs and 94% of mouse-rat orthologs showed differences in receptor potency (EC50) and/or efficacy (dynamic range) to an individual ligand. Notably dN/dS ratio, an indication of selective pressure during evolution, does not predict functional similarities between orthologs. Additionally, we found that orthologs responded to a common ligand 82% of the time, while human OR paralogs of the same subfamily responded to the common ligand only 33% of the time. Our results suggest that, while OR orthologs tend to show conserved ligand selectivity, their potency and/or efficacy dynamically change during evolution, even in closely related species. These functional changes in orthologs provide a platform for examining how the evolution of ORs can meet species-specific demands.
The Nuclear Membrane and Mechanotransduction: Impaired Nuclear Mechanics and Mechanotransduction in Lamin A/C Deficient Cells (2005)

Mutations in the lamin A/C gene cause a variety of human diseases including Emery-Dreifuss muscular dystrophy, dilated cardiomyopathy and Hutchinson-Gilford progeria syndrome. The tissue specific effects of lamin mutations are unclear, in part because the function of lamin A/C is incompletely defined, but the many muscle specific phenotypes suggest that defective lamin A/C could increase cellular mechanical sensitivity. Lamin A/C deficient fibroblasts were subjected to mechanical strain to measure nuclear mechanical properties and strain-induced signalling. We found that lamin A/C deficient fibroblasts are characterized by impaired nuclear mechanics and mechanotransduction, reflected by increased nuclear deformations, increased nuclear fragility, attenuated expression of mechanosensitive genes, and impaired transcriptional activation, leading to impaired viability of mechanically strained cells. Lamins and other nuclear envelope proteins can thus affect several levels of the mechanotransduction cascade, altering nuclear and cytoskeletal mechanics as well as playing an important role in mechanically activated gene regulation. Individual mutations in the lamin A/C gene could potentially selectively interfere with any of these functions, explaining the tissue-specific effects observed in the laminopathies.
Development of Highly-sensitive Fructosyl-valine Enzyme Sensor Employing Recombinant Fructosyl Amine Oxidase (2003)

We recently isolated a novel fructosyl-amine oxidase (FAOD) from the soil bacterium Arthrobacter sp. FV 1-1, cloned the gene encoding FAOD and succeeded in the recombinant production. This bacterial FAOD showed high specificity towards fructosyl valine (FV), a proteolytic product of hemoglobin A1c (HbA1c), but was almost completely inactive towards ε-fructosyl-lysine (ε-FK), a proteolytic product of glycated albumin. By utilizing recombinant FAOD expressed in E. coli, an FAOD sensor based on hydrogen peroxide detection was constructed. The sensor showed FV specificity, with a minimum detectable concentration of 1 μM. The sensitivity was 7.1 mAM-1cm-2, which is 17 times higher than that of the previously reported FAOD-based enzyme sensors. Because the bacterial FAOD-based sensor could detect FV concentration and discriminate FV in the presence of ε-FK, it has the great potential for use in the measurement of HbA1c in whole blood samples.
Developmental Potential for Endomorphin Opioidmimetic Drugs (2012)

Morphine, which is agonist for μ-opioid receptors, has been used as an anti-pain drug for millennia. The opiate antagonists, naloxone and naltrexone, derived from morphine, were employed for drug addiction and alcohol abuse. However, these exogenous agonists and antagonists exhibit numerous and unacceptable side effects. Of the endogenous opioid peptides, endomorphin(EM)-1 and endomorphin(EM)-2 with their high μ-receptor affinity and exceptionally high selectivity relative to δ- and κ-receptors in vitro and in vivo provided a sufficiently sequence-flexible entity in order to prepare opioid-based drugs. We took advantage of this unique feature of the endomorphins by exchanging the N-terminal residue Tyr(1) with 2',6'-dimethyl-l-tyrosine (Dmt) to increase their stability and the spectrum of bioactivity. We systematically altered specific residues of [Dmt(1)]EM-1 and [Dmt(1)]EM-2 to produce various analogues. Of these analogues, [N-allyl-Dmt(1)]EM-1 (47) and [N-allyl-Dmt(1)]EM-2 (48) exhibited potent and selective antagonism to μ-receptors: they completely inhibited naloxone- and naltrexone-induced withdrawal from following acute morphine dependency in mice and reversed the alcohol-induced changes observed in sIPSC in hippocampal slices. Overall, we developed novel and efficacious opioid drugs without deleterious side effects that were able to resist enzymatic degradation and were readily transported intact through epithelial membranes in the gastrointestinal tract and the blood-brain-barrier.
Femtosecond laser patterning of plasmonic and nonlinear optical properties in silver-doped (2015)

Nowadays the optical properties and structural arrangements of several inorganic materials can be modified using ultrafast and intense laser sources. Among several lithographic techniques, Direct Laser Writing (DLW) considered as a maskless patterning process, presents numerous advantages over usual techniques. DLW offers rapid patterning at sub-micrometer resolutions, with flexibility and scalability. At last, true three-dimensional structuration is allowed thanks to non-linear interaction in optical transparent materials. In this context, DLW of materials containing photosensitive agents can initiate photochemical processes,[1,2] opening routes toward the design of nanocomposites. DLW techniques can modify the size, the shape, and the arrangement of the metal clusters. It is a powerful and flexible tool to control and optimize the linear and nonlinear properties of metallo-dielectric composites. Many groups have shown interest in patterning metals in three dimensions in transparent media such as glasses [3] or polymers [4]. This becomes particularly challenging when structures much smaller than the diffraction limit need to be patterned for infrared or optical applications.
Method to improve spatial uniformity with lightpipes (2008)

A heuristic method to obtain lightpipes that provide both collimation and good spatial uniformity is proposed. The change in shape that is likely to improve spatial uniformity, with minimal efficiency loss, can be predicted. Several case studies where this technique has been used are presented.
Molecular Mechanism of Selective Al2O3 Atomic Layer Deposition on Self-Assembled Monolayers (2023)

Area-selective atomic layer deposition (AS-ALD) of insulating metallic oxide layers could be a useful nanopatterning technique for making increasingly complex semiconductor circuits. Although the alkanethiol self-assembled monolayer (SAM) has been considered promising as an ALD inhibitor, the low inhibition efficiency of the SAM during ALD processes makes its wide application difficult. We investigated the deposition mechanism of Al<sub>2</sub>O<sub>3</sub> on alkanethiol-SAMs using temperature-dependent vibrational sum-frequency-generation spectroscopy. We found that the thermally induced formation of gauche defects in the SAMs is the main causative factor deteriorating the inhibition efficiency. Here, we demonstrate that a discontinuously temperature-controlled ALD technique involving self-healing and dissipation of thermally induced stress on the structure of SAM substantially enhances the SAM's inhibition efficiency and enables us to achieve 60 ALD cycles (6.6 nm). We anticipate that the present experimental results on the ALD mechanism on the SAM surface and the proposed ALD method will provide clues to improve the efficiency of AS-ALD, a promising nanoscale patterning and manufacturing technique.
Supplementary Fig. 2 from Clinical Importance of the lncRNA <i>NEAT1</i> in Cancer Patients Treated with Immune Checkpoint Inhibitors (2023)

&lt;p&gt;Supplementary Fig. 2 NEAT1 expression is associated with the interferon-gamma response in melanoma.&lt;/p&gt;
A rationally designed oral vaccine induces Immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants (2019)

Introductory paragraph The ability of gut bacterial pathogens to escape immunity by antigenic variation, particularly via changes to surface-exposed antigens, is a major barrier to immune clearance 1 . However, not all variants are equally fit in all environments 2, 3 . It should therefore be possible to exploit such immune escape mechanisms to direct an evolutionary trade-off. Here we demonstrated this phenomenon using Salmonella enterica subspecies enterica serovar Typhimurium ( S. Tm). A dominant surface antigen of S. Tm is its O-antigen: A long, repetitive glycan that can be rapidly varied by mutations in biosynthetic pathways or by phase-variation 4, 5 . We quantified the selective advantage of O-antigen variants in the presence and absence of O-antigen specific IgA and identified a set of evolutionary trajectories allowing immune escape without an associated fitness cost in naïve mice. Through the use of oral vaccines, we rationally induced IgA responses blocking all of these trajectories, which selected for Salmonella mutants carrying deletions of the O-antigen polymerase wzyB. Due to their short O-antigen, these evolved mutants were more susceptible to environmental stressors (detergents, complement), predation (bacteriophages), and were impaired in gut colonization and virulence in mice. Therefore, a rationally induced cocktail of intestinal antibodies can direct an evolutionary trade-off in S. Tm. This lays the foundations for the exploration of mucosal vaccines capable of setting evolutionary traps as a prophylactic strategy.
A 2.0-/spl mu/m pixel pitch MOS image sensor with 1.5 transistor/pixel and an amorphous Si color filter (2006)

In this paper, an ultrafine pixel size (2.0/spl times/2.0 /spl mu/m/sup 2/) MOS image sensor with very high sensitivity is developed. The key technologies that realize the MOS image sensor are a newly developed pixel circuit configuration (1.5 transistor/pixel), a fine 0.15-/spl mu/m design rule, and an amorphous Si color filter (Si-CF). In the new pixel circuit configuration, a unit pixel consists of one photodiode, one transfer transistor, and an amplifier circuit with two transistors that are shared by four neighboring pixels. Thus, the unit pixel has only 1.5 transistors. The fine design rule of 0.15 /spl mu/m enables reduction of wiring area by 40%. As a result, a high aperture ratio of 30% is achieved. A newly developed Si-CF realizes the 1/10 thickness of that of the conventional organic-pigment CF, giving rise to high light-collection efficiency. With these three technologies combined, a high sensitivity of 3400 electrons/lx/spl middot/s is achieved even with a pixel size of 2.0/spl times/2.0 /spl mu/m/sup 2/.
Road anomaly estimation: Model based pothole detection (2015)

This paper describes a model-based pothole detection algorithm that exploits a multi-phase dynamic model. The responses of hitting potholes are empirically broken down into three phases governed by three simpler dynamic system sub-models. Each sub-model is based on a rigid-ring tire and quarter-car suspension model. The model is validated by comparing simulation results over various scenarios with FTire, a commercial simulation software for tire-road interaction. Based on the developed model, a pothole detection algorithm with Unscented Kalman Filter (UKF) and Bayesian estimation is developed and demonstrated.
DECAF: detecting and characterizing ad fraud in mobile apps (2014)

Ad networks for mobile apps require inspection of the visual layout of their ads to detect certain types of placement frauds. Doing this manually is error prone, and does not scale to the sizes of today's app stores. In this paper, we design a system called DECAF to automatically discover various placement frauds scalably and effectively. DECAF uses automated app navigation, together with optimizations to scan through a large number of visual elements within a limited time. It also includes a framework for efficiently detecting whether ads within an app violate an extensible set of rules that govern ad placement and display. We have implemented DECAF for Windows-based mobile platforms, and applied it to 1,150 tablet apps and 50,000 phone apps in order to characterize the prevalence of ad frauds. DECAF has been used by the ad fraud team in Microsoft and has helped find many instances of ad frauds.
The Role of Structural Dynamics of Actin in Class-Specific Myosin Motility (2015)

The structural dynamics of actin, including the tilting motion between the small and large domains, are essential for proper interactions with actin-binding proteins. Gly146 is situated at the hinge between the two domains, and we previously showed that a G146V mutation leads to severe motility defects in skeletal myosin but has no effect on motility of myosin V. The present study tested the hypothesis that G146V mutation impaired rotation between the two domains, leading to such functional defects. First, our study showed that depolymerization of G146V filaments was slower than that of wild-type filaments. This result is consistent with the distinction of structural states of G146V filaments from those of the wild type, considering the recent report that stabilization of actin filaments involves rotation of the two domains. Next, we measured intramolecular FRET efficiencies between two fluorophores in the two domains with or without skeletal muscle heavy meromyosin or the heavy meromyosin equivalent of myosin V in the presence of ATP. Single-molecule FRET measurements showed that the conformations of actin subunits of control and G146V actin filaments were different in the presence of skeletal muscle heavy meromyosin. This altered conformation of G146V subunits may lead to motility defects in myosin II. In contrast, distributions of FRET efficiencies of control and G146V subunits were similar in the presence of myosin V, consistent with the lack of motility defects in G146V actin with myosin V. The distribution of FRET efficiencies in the presence of myosin V was different from that in the presence of skeletal muscle heavy meromyosin, implying that the roles of actin conformation in myosin motility depend on the type of myosin.
ChemInform Abstract: SYNTHESIS OF CYCLOSPORINE. I. SYNTHESIS OF ENANTIOMERICALLY PURE (2S,3R,4R,6E)‐3‐HYDROXY‐4‐METHYL‐2‐METHYLAMINO‐6‐OCTENOIC ACID STARTING FROM TARTARIC ACID (1984)

Abstract Aus dem Diester (I) wird zunächst das Triol (VI) synthetisiert, aus dem dann durch Kettenverlängerung das Diol (X) erhalten wird.
Human CIDEC transgene improves lipid metabolism and protects against high-fat diet–induced glucose intolerance in mice (2022)

Cell death-inducing DNA fragmentation factor-like effector C (CIDEC) expression in adipose tissue positively correlates with insulin sensitivity in obese humans. Further, E186X, a single-nucleotide CIDEC variant is associated with lipodystrophy, hypertriglyceridemia, and insulin resistance. To establish the unknown mechanistic link between CIDEC and maintenance of systemic glucose homeostasis, we generated transgenic mouse models expressing CIDEC (Ad-CIDECtg) and CIDEC E186X variant (Ad-CIDECmut) transgene specifically in the adipose tissue. We found that Ad-CIDECtg but not Ad-CIDECmut mice were protected against high-fat diet-induced glucose intolerance. Furthermore, we revealed the role of CIDEC in lipid metabolism using transcriptomics and lipidomics. Serum triglycerides, cholesterol, and low-density lipoproteins were lower in high-fat diet-fed Ad-CIDECtg mice compared to their littermate controls. Mechanistically, we demonstrated that CIDEC regulates the enzymatic activity of adipose triglyceride lipase via interacting with its activator, CGI-58, to reduce free fatty acid release and lipotoxicity. In addition, we confirmed that CIDEC is indeed a vital regulator of lipolysis in adipose tissue of obese humans, and treatment with recombinant CIDEC decreased triglyceride breakdown in visceral human adipose tissue. Our study unravels a central pathway whereby adipocyte-specific CIDEC plays a pivotal role in regulating adipose lipid metabolism and whole-body glucose homeostasis. In summary, our findings identify human CIDEC as a potential 'drug' or a 'druggable' target to reverse obesity-induced lipotoxicity and glucose intolerance.
Cellular Energetics in the Preconditioned State (2001)

Cell survival is critically dependent on the preservation of cellular bioenergetics. However, the metabolic mechanisms that confer resistance to injury are poorly understood. Phosphotransfer reactions integrate ATP-consuming with ATP-producing processes and could thereby contribute to the generation of a protective phenotype. Here, we used ischemic preconditioning to induce a stress-tolerant state and (18)O-assisted (31)P nuclear magnetic resonance spectroscopy to capture intracellular phosphotransfer dynamics. Preconditioning of isolated perfused hearts triggered a redistribution in phosphotransfer flux with significant increase in creatine kinase and glycolytic rates. High energy phosphoryl fluxes through creatine kinase, adenylate kinase, and glycolysis in preconditioned hearts correlated tightly with post-ischemic functional recovery. This was associated with enhanced metabolite exchange between subcellular compartments, manifested by augmented transfer of inorganic phosphate from cellular ATPases to mitochondrial ATP synthase. Preconditioning-induced energetic remodeling protected cellular ATP synthesis and ATP consumption, improving contractile performance following ischemia-reperfusion insult. Thus, the plasticity of phosphotransfer networks contributes to the effective functioning of the cellular energetic system, providing a mechanism for increased tolerance toward injury.
Transcortical Screw Fixation of the Olecranon Shows Equivalent Strength and Improved Stability Compared With Tension Band Fixation (2013)

In a synthetic bone model of simple transverse olecranon fractures, screw fixation provided equivalent strength and less plastic deformation as compared with tension banding.