gebhart/patrepeval huggingface dataset:
Temporal self-action and compression of intense ultrashort laser pulses in hollow photonic-crystal waveguides (2005)

Hollow-core waveguides with a periodic (photonic-crystal) cladding are shown to allow efficient temporal compression of high-intensity ultrashort laser pulses and formation of megawatt soliton-like features in the regime of robust isolated guided modes. We numerically analyze the temporal envelope evolution and spectral transformation of the light field in air-guided modes of gas-filled hollow coaxial periodic Bragg waveguides. Based on this analysis, we define optimal compression regimes, permitting high compression ratios (of about six) and high compression efficiencies (up to 73%) to be achieved for microjoule laser pulses with an initial pulse length of 80–400 fs.
Bridging the gap between real printouts and digital whiteboard (2008)

In this paper, we describe a paper-based interface, which combines the physical (real) with the digital world: while interacting with real paper printouts, users can seamlessly work with a digital whiteboard at the same time. Users are able to send data from a real paper to the digital world by picking up the content (e.g. images) from real printouts and drop it on the digital surface. The reverse direction for transferring data from the whiteboard to the real paper is supported through printouts of the whiteboard page that are enhanced with integrated Anoto patterns. We present four different interaction techniques that show the potential of this paper and digital world combination. Moreover, we describe the workflow of our system that bridges the gap between the two worlds in detail.
Electrically controlled variation of receptor affinity (2016)

A concept of virtual sensor array based on electrically controlled variation of affinity properties of the receptor layer is described. It was realized on the base of integrated electrochemical chemotransistor containing polyaniline as the receptor layer. Electrical control of the redox state of polyaniline was performed in five-electrode configuration containing four electrodes for conductivity measurements and one Ag/AgCl reference electrode. All the electrodes were integrated on the same glass chip. A room-temperature ionic liquid was used for the electrical connection between the reference electrode and chemosensitive material. Conductivity measurements demonstrated effective potential-controlled electrochemical conversions of the receptor material between different redox states. Binding of trimethylamine at three different potentials, corresponding to the different states of the receptor material, was studied. Concentration dependencies and binding kinetics were analyzed. The results demonstrated that the kinetic as well as the equilibrium binding properties of the receptor layer can be controlled by electrical potential, thus providing a possibility to form a virtual sensor array using only a single sensing element. Graphical abstract Single sensing element with electrical control of its affinity can operate as a virtual sensor array.
Effect of Efavirenz, Nevirapine, Etravirine, and Raltegravir Administration on the Pharmacokinetics of Ritonavir-Boosted Darunavir in a Population of HIV-Infected Patients (2012)

Abstract The influence of efavirenz, etravirine, raltegravir, and nevirapine administration on the pharmacokinetics of ritonavir-boosted darunavir was investigated using population pharmacokinetics analysis. The population was composed of 142 patients infected with HIV: darunavir plus nucleoside/nucleotide reverse transcriptase inhibitors (NRTI), 54 patients (group A); darunavir plus efavirenz±NRTI, 4 patients (group B); darunavir plus etravirine±NRTI, 5 patients (group C); darunavir plus nevirapine±NRTI, 21 patients (group D); darunavir plus raltegravir±NRTI, 38 patients (group E); and darunavir plus raltegravir and etravirine±NRTI, 20 patients (group F). A significant increase in darunavir clearance in combination with nevirapine (+66%) and efavirenz (+235%) was observed. A significant decrease (p<0.05) in trough plasma concentration was observed in groups B and D compared with the other groups. Our study indicates that the combination of ritonavir-boosted darunavir and etravirine or raltegravir has no significant influence on the pharmacokinetics of darunavir in contrast to the combination of ritonavir-boosted darunavir and nevirapine or efavirenz, which involves an increase in darunavir clearance and a decrease in the plasma concentration of darunavir.
Intermediate-band dynamics of quantum dots solar cell in concentrator photovoltaic modules (2014)

We report for the first time a successful fabrication and operation of an InAs/GaAs quantum dot based intermediate band solar cell concentrator photovoltaic (QD-IBSC-CPV) module to the IEC62108 standard with recorded power conversion efficiency of 15.3%. Combining the measured experimental results at Underwriters Laboratory (UL®) licensed testing laboratory with theoretical simulations, we confirmed that the operational characteristics of the QD-IBSC-CPV module are a consequence of the carrier dynamics via the intermediate-band at room temperature.
Reproducible Mouse Sciatic Nerve Crush and Subsequent Assessment of Regeneration by Whole Mount Muscle Analysis (2012)

Regeneration in the peripheral nervous system (PNS) is widely studied both for its relevance to human disease and to understand the robust regenerative response mounted by PNS neurons thereby possibly illuminating the failures of CNS regeneration(1). Sciatic nerve crush (axonotmesis) is one of the most common models of peripheral nerve injury in rodents(2). Crushing interrupts all axons but Schwann cell basal laminae are preserved so that regeneration is optimal(3,4). This allows the investigator to study precisely the ability of a growing axon to interact with both the Schwann cell and basal laminae(4). Rats have generally been the preferred animal models for experimental nerve crush. They are widely available and their lesioned sciatic nerve provides a reasonable approximation of human nerve lesions(5,4). Though smaller in size than rat nerve, the mouse nerve has many similar qualities. Most importantly though, mouse models are increasingly valuable because of the wide availability of transgenic lines now allows for a detailed dissection of the individual molecules critical for nerve regeneration(6, 7). Prior investigators have used multiple methods to produce a nerve crush or injury including simple angled forceps, chilled forceps, hemostatic forceps, vascular clamps, and investigator-designed clamps(8,9,10,11,12). Investigators have also used various methods of marking the injury site including suture, carbon particles and fluorescent beads(13,14,1). We describe our method to obtain a reproducibly complete sciatic nerve crush with accurate and persistent marking of the crush-site using a fine hemostatic forceps and subsequent carbon crush-site marking. As part of our description of the sciatic nerve crush procedure we have also included a relatively simple method of muscle whole mount we use to subsequently quantify regeneration.
Inflammatory Myofibroblastic Tumour Of The Trachea (2005)

We present a case of inflammatory myofibroblastic tumour (IMT) of the trachea arising in a young woman. The patient presented with acute upper airway obstruction, dyspnoea and cough. At videobronchoscopy, the lesion appeared as a smooth, pink, polipoid mass of 1,5 cm obstructing the 70% of the tracheal lumen. The mass was endoscopically removed. &#13;\nHistopathologic examination revealed a lesion composed of spindle shaped cells admixed with a prominent inflammatory infiltrate, which included hystiocytes, plasma cells and lymphocytes. Immunohistochemical studies revealed that the spindle cells were reactive with anti-vimentin, while cytokeratin, S-100, smooth muscle actin, CD21, CD23, CD34 and CD31 were all consistently negative. The proliferative index, shown by Ki67 antibody, was about 7% . Two years after diagnosis , the patient is well without evidence of disease. IMT of the respiratory tract occurs more frequently in the lung. To the best of our knowledge there are only 2 previously reported cases of tracheal IMT. This type of lesion, has to be differentiated from malignant neoplasms such as spindle cell carcinoma and fibrosarcoma
Monte Carlo Device Simulations (2017)

This chapter focuses on Monte Carlo methods for the solution of the Boltzmann transport equation. The ensemble Monte Carlo techniques have been used for well over 40 years as a numerical method to simulate nonequilibrium transport in semiconductor materials and devices and have been the subject of numerous books and reviews. The Monte Carlo algorithm consists of generating random free-flight times for each particle, choosing the type of scattering occurring at the end of the free flight, changing the final energy and momentum of the particle after scattering, and then repeating the procedure for the next free flight. In the bulk Monte Carlo method, particle motion is assumed to consist of free flights terminated by instantaneous scattering events, which change the momentum and energy of the particle after scattering. As in the case of solving the drift-diffusion, hydrodynamic, for a stable Monte Carlo device simulation, one has to choose the appropriate time step, and the spatial mesh size.
Collaborative Augmented Reality Ping-Pong Via Markerless Real Rackets (2011)

This article proposes a method of constructing a ping-pong system via markerless real rackets in collaborative augmented reality. Except a pair of video cameras, without any other sensors or artificial markers, users can use real rackets to hit virtual ping-pong ball on a virtual table and interact with remote partners in augmented reality scene just as they were playing ping-pong in the same place. First, the real racket can be detected and tracked in real-time in the video captured by a single camera in each site. By 3D registration, the real racket can seamlessly interact with the virtual ping-pong ball and table. Then, a communication scheme is designed for the consistent perception between users in collaborative augmented reality ping-pong system. To achieve real-time interaction, the whole method is implemented in a parallel computing environment through multi-core processors. Experimental results demonstrate that our system can provide consistent perception and natural user interaction with low latency and high precision.
Silicon carbide deformable mirror with 37 actuators for adaptive optics (2015)

We present a prototype of a silicon carbide (SiC) deformable mirror (DM) for high power laser applications. The DM has a continuous SiC faceplate, the diameter and the thickness of which are 100 mm and 2 mm, respectively, and 37 stack-type piezoelectric actuators arranged in a rectangular grid. Compared with the glass faceplates used for conventional DMs, SiC has a high thermal diffusivity that effectively minimizes mirror distortions due to thermal gradients. The faceplate is thick enough for possible integration with monolithic cooling channels inside the faceplate. The faceplate without cooling channels presented in this paper has a high bending stiffness compared with glass DMs, but the proposed actuator configuration has flexure supports to reduce the shear stress at the adhesive while preserving optical performances. To examine the characteristics of the SiC DM, we simulated influence functions (IFs) by using a finite element analysis and then compared these results with the IF measured by using an optical interferometer. The optical performance of the DM was verified by generating Zernike polynomial modes based on the measured IF.
A Silicon-Rhodamine Chemical-Genetic Hybrid for Far Red Voltage Imaging from Defined Neurons in Brain Slice (2020)

We describe the design, synthesis, and application of voltage-sensitive silicon rhodamines. Based on the Berkeley Red Sensor of Transmembrane potential, or BeRST, scaffold, the new dyes possess an isomeric molecular wire for improved alignment in the plasma membrane and contain 2' carboxylic acids for ready functionalization. Conjugation with secondary amines affords tertiary amides that localize to cellular membranes and respond to voltage changes with a 24% ΔF/F per 100 mV. When combined with a flexible polyethyleneglycol (PEG) linker and a chloroalkane HaloTag ligand, the new indicators, or isoBeRST dyes, enable voltage imaging from genetically defined cells and neurons. Covalent ligation of isoBeRST to cell surface-expressed HaloTag enzymes provides up to 3-fold improved labeling over previous, rhodamine-based hybrid strategies. We show that isoBeRST-Halo hybrid indicators achieve single-trial voltage imaging of membrane potential dynamics from dissociated rat hippocampal neurons or mouse cortical neurons in brain slices. With far-red/near infrared excitation and emission, turn-on response to action potentials, effective cell labeling in thick tissue, and excellent photostability, the new isoBeRST-Halo derivatives provide an important complement to voltage imaging in neurobiology.
Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element (2021)

A combination of genetic and functional approaches has identified three independent breast cancer risk loci at 2q35. A recent fine-scale mapping analysis to refine these associations resulted in 1 (signal 1), 5 (signal 2), and 42 (signal 3) credible causal variants at these loci. We used publicly available in silico DNase I and ChIP-seq data with in vitro reporter gene and CRISPR assays to annotate signals 2 and 3. We identified putative regulatory elements that enhanced cell-type-specific transcription from the IGFBP5 promoter at both signals (30- to 40-fold increased expression by the putative regulatory element at signal 2, 2- to 3-fold by the putative regulatory element at signal 3). We further identified one of the five credible causal variants at signal 2, a 1.4 kb deletion (esv3594306), as the likely causal variant; the deletion allele of this variant was associated with an average additional increase in IGFBP5 expression of 1.3-fold (MCF-7) and 2.2-fold (T-47D). We propose a model in which the deletion allele of esv3594306 juxtaposes two transcription factor binding regions (annotated by estrogen receptor alpha ChIP-seq peaks) to generate a single extended regulatory element. This regulatory element increases cell-type-specific expression of the tumor suppressor gene IGFBP5 and, thereby, reduces risk of estrogen receptor-positive breast cancer (odds ratio = 0.77, 95% CI 0.74-0.81, p = 3.1 × 10<sup>-31</sup>).
Disrupted auto-regulation of the spliceosomal gene SNRPB causes cerebro–costo–mandibular syndrome (2014)

Elucidating the function of highly conserved regulatory sequences is a significant challenge in genomics today. Certain intragenic highly conserved elements have been associated with regulating levels of core components of the spliceosome and alternative splicing of downstream genes. Here we identify mutations in one such element, a regulatory alternative exon of SNRPB as the cause of cerebro-costo-mandibular syndrome. This exon contains a premature termination codon that triggers nonsense-mediated mRNA decay when included in the transcript. These mutations cause increased inclusion of the alternative exon and decreased overall expression of SNRPB. We provide evidence for the functional importance of this conserved intragenic element in the regulation of alternative splicing and development, and suggest that the evolution of such a regulatory mechanism has contributed to the complexity of mammalian development.
First-Principles Prediction of New Electrides with Nontrivial Band Topology Based on One-Dimensional Building Blocks (2018)

We introduce a new class of electrides with nontrivial band topology by coupling materials database searches and first-principles-calculations-based analysis. Cs_{3}O and Ba_{3}N are for the first time identified as a new class of electrides, consisting of one-dimensional (1D) nanorod building blocks. Their crystal structures mimic β-TiCl_{3} with the position of anions and cations exchanged. Unlike the weakly coupled nanorods of β-TiCl_{3}, Cs_{3}O and Ba_{3}N retain 1D anionic electrons along the hollow interrod sites; additionally, a strong interrod interaction in C_{3}O and Ba_{3}N induces band inversion in a 2D superatomic triangular lattice, resulting in Dirac-node lines. The new class of electrides can serve as a prototype for new electrides with a large cavity space that can be utilized for various applications such as gas storage, ion transport, and metal intercalation.
Regulated and unregulated exhaust gas components from LD vehicles on petrol, diesel, LPG and CNG (1993)

Four fuels (petrol, LPG, CNG and diesel) are compared on passenger cars and lighter vans. The comparisons are made for the usual regulated components, but also for a number of unregulated components. The project was financed by the Dutch government, the association of gas suppliers, a number of LPG/CNG equipment manufacturers, and TNO. The measurements were performed by IW-TNO and IMW-TNO.
Finding Unknown Interests Utilizing the Wisdom of Crowds in a Social Bookmark Service (2006)

In this paper, we develop an information recommendation system based on information edited by various users. This system targets a social bookmark service. Our method for finding appropriate information is to gather each user's bookmark data on the Web and develop a system that analyzes the user's association. Assuming that users that have similar interests also have information associated to those interests, we describe user co-citation relationships as a network. We extract the sub-graph as the community in which each user centers from this network. And we develop a Web service designed to automatically recommend new information regarding these interests. That service has a list of users who share similar preferences with the specified user and a system to present recommended information to the user
Identification of bacteria and bacteria-associated chemical cues that mediate oviposition site preferences byAedes aegypti (2008)

The yellow fever mosquito, Aedes aegypti, the global vector of dengue and yellow fever, is inexorably linked to water-filled human-made containers for egg laying and production of progeny. Oviposition is stimulated by cues from water containers, but the nature and origin of these cues have not been elucidated. We showed that mosquito females directed most of their eggs to bamboo and white-oak leaf infusions, and only a small fraction of the eggs were laid in plain water containers. In binary choice assays, we demonstrated that microorganisms in leaf infusions produced oviposition-stimulating kairomones, and using a combination of bacterial culturing approaches, bioassay-guided fractionation of bacterial extracts, and chemical analyses, we now demonstrate that specific bacteria-associated carboxylic acids and methyl esters serve as potent oviposition stimulants for gravid Ae. aegypti. Elucidation of these compounds will improve understanding of the chemical basis of egg laying behavior of Ae. aegypti, and the kairomones will likely enhance the efficacy of surveillance and control programs for this disease vector of substantial global public health importance.
A Metathesis Model for the Dehydrogenative Coupling of Amines with Alcohols and Esters into Carboxamides by Milstein’s [Ru(PNN)(CO)(H)] Catalysts (2014)

Milstein's [Ru(PNN)(CO)(H)] catalyst (1-Ru) is known to mediate the dehydrogenative coupling of alcohols into esters. When it is used in alcohol-amine mixtures it catalyzes carboxamide formation selectively over esters and imines. The given chemistry is generally accepted to follow metal-ligand cooperation (MLC) mechanisms involving hemiacetals and hemiaminals as intermediates. Using electronic structure DFT methods we investigate alternative, more direct OR/H and NHR/H metal/acyl metathesis routes to coupling that circumvent the intermediacy of the hemiacetal and the hemiaminal. The newly proposed mechanism involves formation of hemiacetaloxide and hemiaminaloxide ion-pairs by addition of an aldehyde (from metal-catalyzed alcohol dehydrogenation) to an octahedral ruthenium-alkoxide or ruthenium-amide intermediate (from alcohol or amine addition to 1-Ru), followed by simple rearrangement (slippage) within the intact ion-pairs to transfer a hydride from the hemiacetaloxide or hemiaminaloxide to the metal. We show that the computed potential energy surfaces that are sometimes invoked to support the MLC mechanism correspond to indirect routes to metathesis. Both the ion-pair and the MLC routes predict the dehydrogenative coupling of ethanol and methanol into methyl acetate to be kinetically much more favored than the kinetics of formation of N-methylacetamide from ethanol and methylamine. However, the calculations provide evidence for the accessibility of a low energy NHR/OR metathesis path that would amidate the ester into the experimentally observed thermodynamically more favored carboxamide product. In fact, 1-Ru is known to be a catalyst for ester amidation.
Mosapride citrate improves nonalcoholic steatohepatitis with increased fecal lactic acid bacteria and plasma glucagon-like peptide-1 level in a rodent model (2014)

Several lines of evidence have suggested a role of gut microbiota in the etiology of nonalcoholic steatohepatitis (NASH). NASH subjects reportedly showed a prolonged orocecal transit time coexistent with small intestinal bacterial overgrowth. We considered the possibility that enhanced gastrointestinal motility would influence gut microbiota and thus investigated the effects of the gastroprokinetic agent mosapride citrate (MC) on gut microbiota and the development of NASH using a methionine-choline deficient (MCD) diet-fed rodent model. Mice were divided into three groups, given the normal chow diet (NCD), the MCD diet, or the MCD diet containing 10 mg·kg(-1)·day(-1) of MC (MCD plus MC) for 6 wk. NASH development was evaluated based on hepatic histochemical findings, serum parameters and various mRNA and/or protein expression levels. MC treatment suppressed MCD diet-induced NASH development, with reduced serum lipopolysaccharide and increased plasma glucagon-like peptide-1 (GLP-1) concentrations. Calculation of the relative abundance of each strain based on gut microbiota analyses indicated lactic acid bacteria specifically, such as Bifidobacterium and Lactobacillus, in feces to be decreased in the MCD, compared with the NCD group. Interestingly, the reduction in lactic acid bacteria in the MCD diet group was reversed in the MCD plus MC group. In addition, colon inflammation observed in the MCD diet group was reduced in the MCD plus MC group. Therefore, MC showed a protective effect against MCD diet-induced NASH development in our rodent model, with possible involvements of increased fecal lactic acid bacteria, protection against colon inflammation and elevated plasma GLP-1.