gebhart/patrepeval huggingface dataset:
In situ localization of manganese peroxidase production in mycelial pellets of Phanerochaete chrysosporium (2003)

The ultrastructure of Phanerochaete chrysosporium hyphae from pellets in submerged liquid cultures was investigated in order to learn more about the interrelation between fungal architecture and manganese peroxidase (MnP) production. At day 2 of cultivation, some subapical regions of hyphae in the outer and middle zones of the pellet initiated differentiation into intercalary thick-walled chlamydospore-like cells of about 10 micro m diameter. At the periphery of the cytoplasm of these cells, a large number of mitochondria and Golgi-like vesicles were observed. The sites of MnP production were localized at different stages of cultivation by an immunolabelling procedure. The immunomarker of MnP was mainly concentrated in the chlamydospore-like cells and principally distributed in Golgi-like vesicles located at the periphery of the cytoplasm. The apices of hyphae in the outer layer of the pellets were apparently minor sites of MnP production. Maximal MnP release into the culture supernatant coincided with apparent autolysis of the chlamydospore-like cells. Production of extracellular autolytic chitinase and protease coincided with the disappearance of these structures from the pellets. The chlamydospore-like cells observed in the mycelial pellets of P. chrysosporium could be metabolically active entities operating as an enzyme reservoir, delivering their content into the surrounding medium possibly by an enzyme-mediated autolytic process.
Supplementary Table 7 from Multilevel Whole-Genome Analysis Reveals Candidate Biomarkers in Clear Cell Renal Cell Carcinoma (2023)

&lt;p&gt;PDF file - 34K, microRNAs expressed concordantly with copy-number aberrations&lt;/p&gt;
Common Symbols (2011)

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Ultrasound-Enhanced Distribution and Treatment Efficacy of Dox-Loaded Intratumoral In Situ Forming Implants in Murine HCT-15 Tumors (2018)

Local drug delivery systems, such as in situ forming implants (ISFIs), allow for sustained elevated drug concentration directly at the tumor site. However, these systems have been challenging to translate into clinical practice due to poor drug penetration through the implant/tumor boundary. Ultrasound (US) has emerged as a popular approach to enhance drug release and cellular drug uptake from nanoparticles, but little work has been done with its use in combination with ISFIs. In this study, ISFIs were intratumorally injected and treated with therapeutic ultrasound (TUS). A significant (p <;0.05) increase was seen in Doxorubicin (Dox) distribution with ISFIs treated with TUS as compared to ISFIs not treated with TUS. Additionally, the combination of Dox ISFIs with TUS showed a significant (p <;0.01) reduction in tumor growth at 20 days, compared to all other treatment groups. While the mechanism of increased drug distribution and enhanced therapeutic efficacy is not yet clear, hyperthermia was seen with all groups that involved application of TUS for these US exposure parameters. This could be attributed to elevated drug penetration and synergy with the chemotherapy, but additional experiments need to confirm this hypothesis. This study demonstrates, for the first time, US-enhanced drug distribution from ISFIs. The combination of US with local chemotherapy could eventually facilitate translation of local drug delivery systems into clinical practice.
Achievement Status toward Goal Blood Pressure Levels and Healthy Lifestyles among Japanese Hypertensive Patients; Cross-sectional Survey Results from Fukushima Research of Hypertension (FRESH) (2011)

The study revealed low achievement rates toward treatment goals, especially non-elderly patients without diabetes mellitus or chronic kidney disease, and patients with these diseases or those who had myocardial infarction. Our data indicated the necessity to improve physicians' awareness of the management of hypertension according to treatment guidelines and the importance of a healthy lifestyle to maintain goal blood pressure levels.
ALVEOLAR DEPOSITION OF MONODISPERSE AEROSOL PARTICLES IN THE LUNG OF PATIENTS WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE (2002)

Knowledge about the regional deposition of aerosol particles is essential in order to perform efficient inhalation therapy or to minimize health risks due to environmental or occupational aerosol particles. In this study, 2 techniques were used to measure thoracic deposition and to differentiate between bronchial and alveolar deposition. The first technique was the clearance-derived regional deposition (CRD) technique and the second the single-breath regional deposition (SBRD) technique. Deposition was measured in 12 patients with alpha1-antitrypsin deficiency and symptoms of moderate to severe chronic obstructive pulmonary disease (COPD) using monodisperse test particles with aerodynamic diameters of 2, 3, and 4 microm. In CRD, the kinetic of particle clearance within the first 24 hours after inhalation was used to determine bronchial and alveolar deposition. In SBRD, the longitudinal distribution of deposited inert test particles was used to calculate the particle fraction deposited within and distal to the dead space. Both techniques delivered very similar mean values for total and alveolar deposition. Due to controlled slow and deep inhalations, alveolar deposition was as much as 50%. Therefore, SBRD can be considered as an easy tool to study alveolar deposition in patients.
New Methodology for Robust-Optimal Design with Acceptable Risks: An Application to Blended/Wing/Body Aircraft (2022)

In this paper, a new design methodology guaranteeing optimal performance and constraint satisfaction with acceptable risks is presented. This methodology is particularly tailored to conceptual design, wherein variability stemming from modifications that will inevitably occur in downstream design phases must be taken into account. Based on second-order Taylor expansions, a new method allowing the transformation of this robust-optimal design problem with acceptable risks into an equivalent deterministic quadratically constrained quadratic programming (QCQP) problem is provided and then applied to an example problem for validation. Hence, all the available QCQP optimizers can be used to find a robust-optimal solution. The proposed methodology is applied to the blended-wing/body (BWB) at the conceptual design phase, where robust drag minimization is sought under a pitching moment constraint. Numerical results show the impacts on both the BWB optimal planform parameters and guaranteed drag as a function of the acceptable risk levels taken. The study shows that two of the six planform shape variables are significantly affected by the risk level, namely, the kink parameter and the outer wing span. Variations of almost 20% are obtained on these two variables for a risk level of 0.1% as compared to a standard deterministic optimization.
Coordination of dual robot arms using kinematic redundancy (1987)

http://deepblue.lib.umich.edu/bitstream/2027.42/7819/5/bad2440.0001.001.pdf
Optical design of a color-corrected 2.75 g visual loupe (2013)

The key contribution is the optical design of a 2.75 g 2.5× magnification visual loupe developed within the Defense Advanced Research Projects Agency Manufacturable Gradient Index (M-GRIN) phase 2 program. We present a visual loupe (i.e., a Galilean telescope) that is constructed by a positive optical power objective lens that makes use of a spherical gradient index profile and a negative optical power eye lens that collimates the light for visual use. The optical materials and the preform thickness in the design are judiciously designed to be manufacturable within the spherical gradient index design rules available today. A comparison of the M-GRIN design to an all-plastic homogeneous baseline design shows that the M-GRIN design reduces the weight from 4.15 to 2.75 g while maintaining equivalent optical performance of the baseline.
Melanoma-associated fibroblasts decrease tumor cell susceptibility to NK cell-mediated killing through matrix-metalloproteinases secretion (2017)

Cancer-associated fibroblasts (CAFs) play a central role in the complex process of tumor-stroma interaction and promote tumor growth. Emerging evidences also suggest that these fibroblasts are involved in the alteration of the anti-tumor immune response by impacting several immune cell populations, especially through their secretion of pro-inflammatory and immunosuppressive factors in the tumor microenvironment. However, the underlying immuno-modulating mechanisms triggered by these fibroblasts are still only partially defined. In this study, we provide evidence that melanoma-associated fibroblasts decrease the susceptibility of melanoma tumor cells to NK-mediated lysis through the secretion of active matrix metalloproteinases. This secretion reduces the expression of the two NKG2D ligands, MICA/B, at the surface of tumor cells and consequently decreases the NKG2D-dependent cytotoxic activity of NK cells against melanoma tumor cells. Together, our data demonstrate that the modification of tumor cell susceptibility to killer cells is an important determinant of the anti-tumor immune response alteration triggered by CAFs.
WebPerf (2016)

Developers deploying web applications in the cloud often need to determine how changes such as service tiers or runtime loads may affect user-perceived page load time. We devise and evaluate a systematic methodology for exploring such "what-if" questions at the time a web application is deployed. Given a website, a web request, and “whatif” scenario, with a hypothetical configuration and runtime condition, our methodology, embedded in a system called WebPerf, can estimate a distribution of end-to-end response times for the request under the “what-if” scenario. WebPerf makes three contributions: (1) automated instrumentation of web sites written with increasingly popular task parallel libraries, to capture causal call dependencies of various computation and asynchronous I/O calls; (2) an algorithm to use the call dependencies, together with online- and offlineprofiled models of various I/O calls to estimate a distribution of end-to-end latency of the request; and (3) an algorithm to optimize modeling errors by deciding how many measurements to take within a limited time. We have implemented WebPerf for Microsoft Azure. Our experiments with five real websites and seven scenarios show that the median error of WebPerf’s estimation is within 7% for all applications and scenarios.
Photoactivation process observed around the reaction center of photoreactive nitrile hydratase (2002)

The RecA proteins of E. coli form a filamentous complex around a singlestranded (ss) DNA prior to homology search in homologous recombination. The filament pitches are 95 and 65 in the presence of ATP and ADP, respectively. NMR studies revealed recently a novel RecA/Rad51-induced extended ssDNA structure including deoxyribose-base stacking (PNAS, 95 (1997), 6623) and the authors propose two models of deoxyribose for the ATP (C3' endo) and ADP (C2' endo) forms with alternative puckers. X-ray crystal analysis of RecA protein shows a filament of 83 pitch with a 61 screw symmetry (Nature, 355 (1992), 318). We succeeded in the present study to crystallize the RecA protein in a different pitch of 72 and analyzed at 2.8 resolution using BL44B2 of SPring-8. Its crystal parameters were very similar to those previously reported except the c-axis. The overall monomer structures also resemble each other except two DNA-binding loops highly ordered in the current crystals. The loops protruded from monomers toward the filament axis and constructed two continuous side-walls of a spiral gutter. The gutter was expected as the ssDNA-binding site. Comparing the filament structures in crystals, we found a small rotation of monomer around a hinge point near the N-terminal helix. Since the differences on monomer structures were small, we rotated the monomer further so as to realize a putative filament structure of 95 pitch for the ATP form. The DNA-binding loops thus rearranged seem to fit very well with the ssDNA proposed from the NMR studies.
The Impact of Functionality and Porous System of Nanostructured Carriers Based on Metal–Organic Frameworks of UiO-66-Type on Catalytic Performance of Embedded Au Nanoparticles in Hydroamination Reaction (2023)

New methods for the preparation of metal–organic frameworks UiO-66 and NH2-UiO-66 with a hierarchical porous structure were developed using the MW-assisted technique under atmospheric pressure. The synthesized nanostructured meso-UiO-66 and meso-NH2-UiO-66 matrices were utilized as Au nanoparticle carriers. The resulting Au@meso-UiO-66 and Au@NH2-UiO-66 nanohybrids were studied in the reaction of phenylacetylene hydroamination with aniline into imine ([phenyl-(1-phenylethylydene)amine]) for the first time. Their catalytic behavior is significantly determined by a combination of factors, such as a small crystal size, micro–mesoporous structure, and functionality of the UiO-66 and NH2-UiO-66 carriers, as well as a high dispersion of embedded gold nanoparticles. The Au@meso-UiO-66 and Au@NH2-UiO-66 nanocatalysts demonstrate high activities (TOF), with conversion and selectivity values over 90. This excellent catalytic performance is comparable or even better than that demonstrated by heterogeneous systems based on conventional inorganic and inorganic supports known from the literature.
Single-cycle infrared waveform control (2022)

Abstract Tailoring the electric-field waveform of ultrashort light pulses forms the basis for controlling nonlinear optical phenomena on their genuine, attosecond timescale. Here we extend waveform control from the visible and near-infrared—where it was previously demonstrated—to the mid-infrared spectral range. Our approach yields single-cycle infrared pulses over several octaves for the first time. Sub-10-fs pulses from a carrier-envelope-phase-stabilized, Kerr-lens-mode-locked, diode-pumped Cr:ZnS laser drive cascaded intrapulse difference-frequency generation and control the electric-field evolution of the resulting coherent emission over 0.9–12.0 μm. Sub-cycle field control in this wavelength range will be instrumental for launching and steering few-femtosecond electron/hole wavepackets in low-gap materials, extending the bandwidth of electronic signal processing to multi-terahertz frequencies, as well as for electric-field-resolved molecular fingerprinting of biological systems.
A low smear structure for 2 M-pixel CCD image sensors (1991)

The authors have developed a novel smear suppression cell structure, built with a second Al shunt process, for 1-inch optical format FIT-CCD (frame interline transfer charge-coupled device) image sensors with 2 million pixels. The first Al layer works as a photo-shield and the second one is used for V-register drive pulse wiring. With this structure, one can reduce smear levels to less than -110 dB. Moreover, one can achieve levels below -120 dB with an on-chip microlens.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
SYSTEMS AND METHODS FOR ACTUATINGSOFT ROBOTIC ACTUATORS (2018)

Systems and methods for providing a soft robot is provided. In one system , a robotic device includes a flexible body having a fluid chamber, where a portion of the flexible body includes an elastically extensible material and a portion of the flexible body is strain limiting relative to the elastically extensible material. The robotic device can further include a pressurizing inlet in fluid communication with the fluid chamber, and a pressurizing device in fluid communication with the pressurizing inlet, the pressurizing device including a reaction chamber configured to accommodate a gas producing chemical reaction for providing pressurized gas to the pressurizing inlet.
Broadband optical comb generation using a MZM-based flat comb generator and a dispersion-shifted fiber for high accurate terahertz wave generation (2014)

We report on broadband optical comb generation with high frequency accuracy using a Mach-Zehnder-modulator-based flat comb generator and a high-nonlinear dispersion-shifted fiber. Broadband comb signals with a bandwidth of over 40 nm were successfully generated.
Pattern-integrated interference [Invited] (2012)

Pattern-integrated interference (PII) is described as a logical progression starting from the primary precursors of interference and holography. PII produces, in a single-exposure step, a periodic interference pattern with preselected periods absent. These blocked periods, for example, can form the nonperiodic functional elements of a photonic-crystal device or the circuit elements in a periodic-layout-design semiconductor chip. Various possible system configurations for PII are presented and compared. Example PII-produced intensity patterns for a photonic-crystal microresonator filter and an optical switch are simulated and discussed.
Spect image reconstruction under imaging time constraints (2017)

Single photon emission computed tomography (SPECT) is a nuclear imaging modality used by, among others, oncologists in the imaging of tumors. At its core, SPECT is an underdetermined signal recovery problem. The degree of difficulty in recovering the underlying image increases as the imaging time decreases. To make the image reconstruction problem well-posed, it is advantageous to introduce a signal prior, such as the total variation. Such priors can dramatically improve reconstruction performance and allow for faster scans. The issue with the adoption of such priors in practice is the lack of an automated method for selecting the regularization strength. The purpose of this work is to review the SPECT problem, discuss the role of regularizers in SPECT, and propose a method for estimating the regularization strength.
Improved trap-related characteristics on SiNx/AlGaN/GaN MISHEMTs with surface treatment (2014)

In this paper, the reliable SiN <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> /AlGaN/GaN MISHEMTs on silicon substrate with improved trap-related characteristics have been well demonstrated. The devices with our proposed treatment method showed less deep-level traps and more Si surface donors at SiN <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> -AlGaN interface. The trap related device characteristics are also improved by using our optimized treatment method. The devices with proposed treatment method exhibit less current collapse and better positive bias temperature stability of threshold voltage. All the results suggest that the proposed treatment method is very effective to improve the slow-trap related device reliability.
What Factors Influence the Success of Medial Gastrocnemius Flaps in the Treatment of Infected TKAs? (2015)

Level IV, therapeutic study.
The Distribution of Type 1 Chain ABH and Related Histo-Blood Group Antigens in Normal Cycling Human Endometrium (1993)

Cycling endometrial tissue was examined immunohistochemically for blood group antigens using a panel of monoclonal antibodies with specificity to type 1 chain carbohydrates. Staining was evaluated against the genetic background (ABO, Lewis, and saliva-secretor status) and the subphase of the menstrual cycle. Expression of type 1 chain antigens in most cases correlated with the genetic background; however, Le(a) and Le(b) antigens were in a few cases demonstrated in endometria with the erythrocyte Le(a-b-) phenotype and Le(b) antigen in erythrocyte Le(a + b-) endometria also. In addition, Le(b) antigen was preferentially expressed in endometria from blood group O individuals. Type 1 chain antigens were, in general, maximally demonstrated in the surface epithelium. Chain 1 A, H, ALe(b), Le(a), and disialosyl-Le(a) (dsLe(a)) determinants were demonstrated only sporadically in functionalis and basalis glands of cycling endometria. Staining for most type 1 chain antigens showed variations that were related to the histomorphology (layer and menstrual phase), and monosialosyl-Le(a) (msLe(a)) seemed to be a marker of secretory differentiation in the endometrium. Our results support the view that synthesis and expression of type 1 chain antigens in human endometrium is influenced by the genetic background and is modulated by the hormonal environment.
Tailored Uniaxial Alignment of Nanowires Based on Off-Center Spin-Coating for Flexible and Transparent Field-Effect Transistors (2022)

The alignment of nanowires (NWs) has been actively pursued for the production of electrical devices with high-operating performances. Among the generally available alignment processes, spin-coating is the simplest and fastest method for uniformly patterning the NWs. During spinning, the morphology of the aligned NWs is sensitively influenced by the resultant external drag and inertial forces. Herein, the assembly of highly and uniaxially aligned silicon nanowires (Si NWs) is achieved by introducing an off-center spin-coating method in which the applied external forces are modulated by positioning the target substrate away from the center of rotation. In addition, various influencing factors, such as the type of solvent, the spin acceleration time, the distance between the substrate and the center of rotation, and the surface energy of the substrate, are adjusted in order to optimize the alignment of the NWs. Next, a field-effect transistor (FET) incorporating the highly aligned Si NWs exhibits a high effective mobility of up to 85.7 cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup>, and an on-current of 0.58 µA. Finally, the single device is enlarged and developed in order to obtain an ultrathin and flexible Si NW FET array. The resulting device has the potential to be widely expanded into applications such as wearable electronics and robotic systems.
Discovery of (3S,3aR)-2-(3-Chloro-4-cyanophenyl)-3-cyclopentyl-3,3a,4,5-tetrahydro-2H-benzo[g]indazole-7-carboxylic Acid (PF-3882845), an Orally Efficacious Mineralocorticoid Receptor (MR) Antagonist for Hypertension and Nephropathy (2010)

We have discovered a novel class of nonsteroidal pyrazoline antagonists of the mineralocorticoid receptor (MR) that show excellent potency and selectivity against other nuclear receptors. Early analogues were poorly soluble and had a propensity to inhibit the hERG channel. Remarkably, both of these challenges were overcome by incorporation of a single carboxylate moiety. Structural modification of carboxylate-containing lead R-4g with a wide range of substituents at each position of the pyrazoline ring resulted in R-12o, which shows excellent activity against MR and reasonable pharmacokinetic profile. Introduction of conformational restriction led to a novel series characterized by exquisite potency and favorable steroid receptor selectivity and pharmacokinetic profile. Oral dosing of 3S,3aR-27d (PF-3882845) in the Dahl salt sensitive preclinical model of salt-induced hypertension and nephropathy showed blood pressure attenuation significantly greater than that with eplerenone, reduction in urinary albumin, and renal protection. As a result of these findings, 3S,3aR-27d was advanced to clinical studies.
III-V on-silicon sources for optical interconnect applications (2014)

Optical interconnects require efficient and flexible optical sources. This paper presents results on two technology platforms being developed for realizing these. Integration using wafer bonding technologies is well established now and the focus is on new device types including tunable lasers, multi-wavelength lasers and switching. As an alternative, we also started work on monolithic integration using heteroepitaxy directly on silicon. We here report recent results on low threshold nanowire lasers.