gebhart/patrepeval huggingface dataset:
Surface subwavelength structure and photonic device fabrication with temporally tailored multiple femtosecond laser pulses (2005)

We have demonstrated the nanostructure fabrication on the Si surface by a 150 fs, 800 nm femtosecond laser pulse. The nanohole size of about 100 nm can be formed presumably by a near-field optical enhancement effect induced by the particle illumination. The nanohole size is nearly independent of the irradiated pulse number. It is found that the optical enhancement factor was about 7 in this experiment. The hexagonally arrayed nanoholes were fabricated. The diameter of the fabricated nanohole was about 90 nm and the depth was about 9 nm. In addition, using the double pulse fs laser, we demonstrated a low-loss waveguide fabrication in fused silica. A low-optical-loss waveguide is fabricated under the conditions that the first pulse energy and teh second pulse energy in the double pulse mode are 30 jJ and 160 jJ, respectively, nad the pulse time interval is 3 ps. The weak first pulse would act as a pre-conditioner of the fused silica and then the second subsequent pulse effectively induces the uniform refractive index change. This new femtosecond double pulse fabrication technique will be very promising for low-loss photonic device fabrication for photonic networks.
A variable-rate CELP coder for fast remote voicemail retrieval using a notebook computer (2002)

Remote retrieval of compressed voicemail data over a telephone line is one of several emerging applications of speech coding. Using a notebook computer equipped with a modem, a user can remotely access a networked desktop unit located at their office or home to retrieve various types of information such as email, FAX, electronic documents as well as voicemail. By compressing the speech data, we reduce the amount of time needed for the transfer of voice data over the telephone line. We have developed a high-quality variable-rate CELP (code-excited linear prediction) coder which can be used in such an application. The coder operates at an average rate of 3 kb/s assuming 80% speech activity and uses several new techniques including a mode decision mechanism based on the use of a peakiness measure and a novel excitation search method called gain-matched analysis-by-synthesis. The coder gives quality comparable to the Microsoft GSM 6.10 Audio Codec at 13 kb/s.
The full genome sequence of three strains of Jamestown Canyon virus and their pathogenesis in mice or monkeys (2011)

The first complete sequence of JCV is reported for three separate isolates, and a relatively high level of amino acid sequence conservation was observed even for viruses isolated 57 years apart indicating that the virus is in relative evolutionary stasis. JCV is highly infectious for mice and monkeys, and these animals, especially mice, represent useful experimental hosts for further study.
Total-Body Irradiation Exacerbates Dissemination of Cutaneous Candida Albicans Infection (2016)

Exposure to radiation, particularly a large or total-body dose, weakens the immune system through loss of bone marrow precursor cells, as well as diminished populations of circulating and tissue-resident immune cells. One such population is the skin-resident immune cells. Changes in the skin environment can be of particular importance as the skin is also host to a number of commensal organisms, including Candida albicans , a species of fungus that causes opportunistic infections in immunocompromised patients. In a previous study, we found that a 6 Gy sublethal dose of radiation in mice caused a reduction of cutaneous dendritic cells, indicating that the skin may have a poorer response to infection after irradiation. In this study, the same 6 Gy sublethal radiation dose led to a weakened response to a C. ablicans cutaneous infection, which resulted in systemic dissemination from the ear skin to the kidneys. However, this impaired response was mitigated through the use of interleukin-12 (IL-12) administered to the skin after irradiation. Concomitantly with this loss of local control of infection, we also observed a reduction of CD4<sup>+</sup> and CD8<sup>+</sup> T cells in the skin, as well as the reduced expression of IFN-γ, CXCL9 and IL-9, which influence T-cell infiltration and function in infected skin. These changes suggest a mechanism by which an impaired immune environment in the skin after a sublethal dose of radiation increases susceptibility to an opportunistic fungal infection. Thus, in the event of radiation exposure, it is important to include antifungal agents, or possibly IL-12, in the treatment regimen, particularly if wounds are involved that result in loss of the skin's physical barrier function.
ChemInform Abstract: Palladium‐Catalyzed Silylation of Aryl Chlorides with Hexamethyldisilane. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Interocular contrast difference drives illusory 3D percept (2017)

Any processing delay between the two eyes can result in illusory 3D percepts for moving objects because of either changes in the pure disparities over time for disparity sensors or by changes to sensors that encode motion/disparity conjointly. This is demonstrated by viewing a fronto-parallel pendulum through a neutral density (ND) filter placed over one eye, resulting in the illusory 3D percept of the pendulum following an elliptical orbit in depth, the so-called Pulfrich phenomenon. Here we use a paradigm where a cylinder rotating in depth, defined by moving Gabor patches is presented at different interocular phases, generating strong to ambiguous depth percepts. This paradigm allows one to manipulate independently the contrast and the luminance of the patches to determine their influence on perceived motion-in-depth. Thus we show psychophysically that an interocular contrast difference can itself result in a similar illusory 3D percept of motion-in-depth. We argue that contrast, like luminance (ND filter) can modify the dynamics of visual neurons resulting in an interocular processing delay or an interocular velocity difference.
Retinoic Acid-Loaded Poly(lactic-co-glycolic acid) Nanoparticle Formulation of ApoB-100-Derived Peptide 210 Attenuates Atherosclerosis (2020)

We developed a vaccine formulation containing ApoB derived P210 peptides as autoantigens, retinoic acid (RA) as an immune enhancer, both of which were delivered using PLGA nanoparticles. The formula was used to induce an immune response in 12-week-old male <i>Apoe</i><sup>-/-</sup> mice with pre-existing atherosclerotic lesions. The nanotechnology platform PRINT<sup>®</sup> was used to fabricate PLGA nanoparticles that encapsulated RA inside and adsorbed the P210 onto the particle surface. In this study, we demonstrated that immunization of <i>Apoe</i><sup>-/-</sup> mice with the formulation was able to considerably attenuate atherosclerotic lesions, accompanied by increased P210 specific IgM and another oxidized lipid derived autoantigen, M2AA, specific IgG autoantibodies, and decreased the inflammatory response, as compared to the P210 group with Freund's adjuvant. Our formulation represents an exciting technology to enhance the efficacy of the P210 vaccine.
Intravitreal Sustained Release of VEGF Causes Rentinal Neovascularization in Rabbits and Breakdown of the Blood-Retinal Barrier in Rabbits and Primates. (1998)

Ozaki, H; Hayashi, H; Vinores, S A; Moromizato, Y; Campochiaro, P A; Oshima, K Author Information
Development of a decision making algorithm for airbag control (2002)

The method for airbag control developed uses two different parameters to predict the severity of the crash. The first parameter is the change in vehicle velocity, which is used to discriminate between barrier crashes. The second parameter is the length of the filtered accelerometer signal curve, which is used to discriminate between all other cases. The authors tested the algorithm on crash data and found that the results were very close to the requirement.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression profile of the entire detoxification gene inventory of the western honeybee, Apis mellifera across life stages (2023)

The western honeybee, Apis mellifera, is a managed pollinator of many crops and potentially exposed to a wide range of foreign compounds, including pesticides throughout its life cycle. Honeybees as well as other insects recruit molecular defense mechanisms to facilitate the detoxification of xenobiotic compounds. The inventory of detoxification genes (DETOXome) is comprised of five protein superfamilies: cytochrome P450 monooxygenases (P450), carboxylesterases, glutathione S-transferases (GST), UDP-glycosyl transferases (UGT) and ATP-binding cassette (ABC) transporters. Here we characterized the gene expression profile of the entire honeybee DETOXome by analyzing 47 transcriptomes across the honeybee life cycle, including different larval instars, pupae, and adults. All life stages were well separated by principal component analysis, and K-means clustering revealed distinct temporal patterns of gene expression. Indeed, >50% of the honeybee detoxification gene inventory is found in one cluster and follows strikingly similar expression profiles, i.e., increased expression during larval development, followed by a sharp decline after pupation and a steep increase again in adults. This cluster includes 29 P450 genes dominated by CYP3 and CYP4 clan members, 15 ABC transporter genes mostly belonging to the ABCC subfamily and 13 carboxylesterase genes including almost all members involved in dietary/detox and hormone/semiochemical processing. RT-qPCR analysis of selected detoxification genes from all families revealed high expression levels in various tissues, especially Malpighian tubules, fatbody and midgut, supporting the view that these tissues are essential for metabolic clearance of environmental toxins and pollutants in honeybees. Our study is meant to spark further research on the molecular basis of detoxification in this critical pollinator to better understand and evaluate negative impacts from potentially toxic substances. Additionally, the entire gene set of 47 transcriptomes collected and analyzed provides a valuable resource for future honeybee research across different disciplines.
Genetic analysis of obstructive sleep apnoea discovers a strong association with cardiometabolic health (2020)

Abstract There is currently only limited understanding of the genetic aetiology of obstructive sleep apnoea (OSA). The aim of our study is to identify genetic loci associated with OSA risk and to test if OSA and its comorbidities share a common genetic background. We conducted the first large-scale genome-wide association study of OSA using FinnGen Study (217,955 individuals) with 16,761 OSA patients identified using nationwide health registries. We estimated 8.3% [0.06-0.11] heritability and identified five loci associated with OSA (P &lt; 5.0 × 10 −8 ): rs4837016 near GTPase activating protein and VPS9 domains 1 ( GAPVD1 ), rs10928560 near C-X-C motif chemokine receptor 4 ( CXCR4 ), rs185932673 near Calcium/calmodulin-dependent protein kinase ID ( CAMK1D ) and rs9937053 near Fat mass and obesity-associated protein ( FTO ) - a variant previously associated with body mass index (BMI). In a BMI-adjusted analysis, an association was observed for rs10507084 near Rhabdomyosarcoma 2 associated transcript ( RMST )/NEDD1 gamma-tubulin ring complex targeting factor ( NEDD1 ). We found genetic correlations between OSA and BMI (rg=0.72 [0.62-0.83]) and with comorbidities including hypertension, type 2 diabetes (T2D), coronary heart disease (CHD), stroke, depression, hypothyroidism, asthma and inflammatory rheumatic diseases (IRD) (rg &gt; 0.30). Polygenic risk score (PRS) for BMI showed 1.98-fold increased OSA risk between the highest and the lowest quintile and Mendelian randomization supported a causal relationship between BMI and OSA. Our findings support the causal link between obesity and OSA and joint genetic basis between OSA and comorbidities.
Mode-Resolved Gain Analysis of a 7-Core Fiber Laser Based on Multi-Supermode Interference (2014)

A supermode interference monolithic fiber laser utilizing optical gain from several supermodes amplified in an Yb-doped 7-core fiber is investigated. In addition, we present moderesolved gain measurements providing insight on the laser dynamics. © 2014 OSA.
Synthetic anthracyclines: Regiospecific total synthesis of a D-ring indole analogue of daunomycin. (1990)

The 4-methoxy-5-methylpyrano[4,3-b]indole-1,3(4H,5H)-dione (9), prepared from methyl 3-methoxycarbonyl-1-methylindol-2-yl acetate (6), underwent a strong base-induced cycloaddition reaction with 2-chloro-6,6-ethylenedioxy-5,6,7,8-tetrahydro-1,4-naphthoquinone (11) to give the tetrahydronaphtho[2,3-b]carbazole-7,12-dione (10), regioselectively. The cycloadduct (10) was successfully converted to a D-ring indole analogue of daunomycin (1a).
Hybrid inverter concept for extreme bandwidth high‐power AC source (2017)

A hybrid inverter concept for switch‐mode power amplifiers as used, e.g. in power‐hardware‐in‐the‐loop testing is proposed. A main converter operating from the supplying DC voltage generates a multilevel output voltage by means of parallel‐interleaved operation of several bridge legs and combination of the bridge leg output voltages with coupled inductors into a multilevel waveform. A second, series‐connected inverter features a floating DC bus with only a fraction of the main converter's DC voltage, which enables a significantly higher switching frequency. The series inverter compensates the deviation of the main inverter's multilevel output voltage from the reference voltage, whereby pulse‐width modulation with sawtooth carriers is employed, and hence defines the effective switching frequency of the hybrid inverter's overall output voltage. This allows for a higher output filter cutoff frequency and ultimately features a significant increase of the full‐range system bandwidth, which improves by more than an order of magnitude for the considered 100 kVA example system compared with a conventional approach. Finally, closed‐loop circuit simulations verify the high performance of the proposed system.
Repair for Distributed Storage Systems With Packet Erasure Channels and Dedicated Nodes for Repair (2016)

We study the repair problem in distributed storage systems where storage nodes are connected through packet erasure channels and some nodes are dedicated to repair [termed as dedicated-for-repair (DR) storage nodes]. We first investigate the minimum required repair-bandwidth in an asymptotic setup, in which the stored file is assumed to have an infinite size. The result shows that the asymptotic repair-bandwidth over packet erasure channels with a fixed erasure probability has a closed-form relation to the repair-bandwidth in lossless networks. Next, we show the benefits of DR storage nodes in reducing the repair bandwidth, and then we derive the necessary minimal storage space of DR storage nodes. Finally, we study the repair in a nonasymptotic setup, where the stored file size is finite. We study the minimum practical-repair-bandwidth, i.e., the repair-bandwidth for achieving a given probability of successful repair. A combinatorial optimization problem is formulated to provide the optimal practical-repair-bandwidth for a given packet erasure probability. We show the gain of our proposed approaches in reducing the repair-bandwidth.
Periodic Transmissions in Random Access Networks: Stressed Period and Delay (2023)

Most IoT systems use random access protocols for wireless communication. This paper considers an IoT node that generates periodic traffic to be delivered to a destination over a random access network; each packet of the node is expected to be delivered before its deadline. We say that the node is in a stressed period if, within a time interval, its successive packets miss their deadlines. In many systems, the worst-case performance is significantly affected by stressed periods. Characterizing the stochastic properties of stressed periods is thus of fundamental importance. In this paper, we use a fluid flow model to approximate the evolution of the buffer occupancy (i.e., backlog) at the transmitting node. We derive a relationship between buffer occupancy and delay and formally define a stressed period via a time interval in which the buffer occupancy exceeds a certain threshold. With this model, we analyze the dynamics of the buffer occupancy evolution and obtain the probability distributions of stressed period duration and delay. Real network experiments show that our model can well approximate the distributions of stressed period duration and delay in practical WiFi networks. The theoretical results of this paper can be used to analyze the robustness and worst-case performance of IoT monitoring and control systems built on random access networks.
Protein-based molecular contrast optical coherence tomography (2004)

We describe a novel technique for contrast enhancement in optical coherence tomography (OCT) which uses optically switchable protein based chromophores. Photosensitive proteins, such as bacteriorhodopsin and phytochrome, are promising OCT molecular contrast agents by reason of their remarkably low transition activation intensities compatible with in vivo imaging, and their potential for use as genetically expressible markers for molecular imaging. This study details the use of a novel optical switch suppression scheme which uses the absorption change between the two state groups of phytochrome to extract concentration and distribution information of the contrast agent within a target sample.
The application of SMASH alignment system for 65-55-nm logic devices (2007)

65-55nm Logic-Devices require high performance of not only the resolution, of but also the overlay accuracy (Mean+3sigmas < 20-30nm). Thus, here, overlay performance of several layers in our advanced devices is investigated with using Immersion-exposure-tool. We used the new alignment system called SMASH<sup>TM</sup> which has the phase grating alignment sensor newly installed in our immersion-exposure-tool (XT1400Ei). SMASH supports flexible mark design in terms of size and pitch of the grating so that it can comply for our design requirement. SMASH has much smaller alignment beam size of ~ 40um for it. New mark design for our 65-55nm process will be investigated so as to obtain higher alignment accuracy than that of current marks. The alignment performance becomes more accurate proportionally to data density of the mark and it depends on the diffraction angle and efficiency from the mark. Thus, to obtain acceptable alignment accuracy with smaller mark, it should be designed such as diffraction efficiency is maximized within the required boundary condition in the pitch [diffraction angle] and segmentation of the mark. In this paper, several new marks are designed and evaluated. The evaluation shows that comparable performance could be obtained in the new design mark as in ASML's conventional marks. Finally, we select one from the new smaller marks and apply it to our 65-55nm process, especially, to the five process modules (Gate-to-Active, Contact-to-Gate, Metal1-to-Contact, Via1-to-Metal1, Metal2-to-Via1), and performance within 20nm (Mean+3sigmas) are typically obtained. The overlay accuracy needed for our 65-55nm Logic-Devices is successfully achieved with immersion-exposure-tool. SMASH* (SMart Alignment Sensor Hybrid): the name of alignment system using with phase grating alignment sensor.
Towards Understanding the Structure-Function Relationship of Human Amyloid Disease (2004)

Immunoglobulin light chain (LC) proteins exhibit the greatest sequence variability of all proteins associated with amyloid disease. The hallmark event in amyloidogenesis is a change in the secondary and/or tertiary structure of a normal, soluble protein, that fosters self-aggregation and fibril formation. The structural heterogeneity of light chain proteins has hampered understanding of the precise mechanisms involved in fibril formation. The development of effective therapeutics will be benefited by a fundamental understanding of mechanisms and structural prerequisites which govern amyloidogenesis. This review focuses on light chain (AL) amyloidosis resulting from the aggregation of kappa and lambda LCs. Specifically the thermodynamic and structural data of several WT and mutant amyloidogenic LCs have been carefully examined. Moreover, we discuss the importance of hydrophobic and ionic interactions on amyloidosis by comparing several available three-dimensional structures of amyloidogenic and highly homologous non-amyloidogenic proteins that can be destabilized to become amyloidogenic by site specific mutations.
Quantum dots as contrast agents for endoscopy: mathematical modeling and experimental validation of the optimal excitation wavelength (2007)

Our group is investigating the use of ZnS-capped CdSe quantum dot (QD) bioconjugates combined with fluorescence endoscopy for improved early cancer detection in the esophagus, colon and lung. A major challenge in using fluorescent contrast agents in vivo is to extract the relevant signal from the tissue autofluorescence (AF). Our studies are aimed at maximizing the QD signal to AF background ratio (SBR) to facilitate detection. This work quantitatively evaluates the effect of the excitation wavelength on the SBR, using both experimental measurements and mathematical modeling. Experimental SBR measurements were done by imaging QD solutions placed onto (surface) or embedded in (sub-surface) ex vivo murine tissue samples (brain, kidney, liver, lung), using a polymethylmethacrylate (PMMA) microchannel phantom. The results suggest that the maximum contrast is reached when the excitation wavelength is set at 400±20 &mgr;m for the surface configuration. For the sub-surface configuration, the optimal excitation wavelength varies with the tissue type and QD emission wavelengths. Our mathematical model, based on an approximation to the diffusion equation, successfully predicts the optimal excitation wavelength for the surface configuration, but needs further modifications to be accurate in the sub-surface configuration.