gebhart/patrepeval huggingface dataset:
[Projects to accelerate the practical use of innovative medical devices to collaborate with TWIns, Center for Advanced Biomedical Sciences, Waseda University and School of Engineering, The University of Tokyo]. (2014)

Division of Medical Devices has been conducting the projects to accelerate the practical use of innovative medical devices to collaborate with TWIns, Center for Advanced Biomedical Sciences, Waseda University and School of Engineering, The University of Tokyo. The TWIns has been studying to aim at establishment of preclinical evaluation methods by "Engineering Based Medicine", and established Regulatory Science Institute for Medical Devices. School of Engineering, The University of Tokyo has been studying to aim at establishment of assessment methodology for innovative minimally invasive therapeutic devices, materials, and nanobio diagnostic devices. This report reviews the exchanges of personnel, the implement systems and the research progress of these projects.
Rhodium(I)-Mediated Synthesis of Benzo[2,1-b:3,4-b':5,6-c'']trithiophenes and Naphtho[2,1-b:3,4-b']dithiophenes (1997)

The syntheses of carbonylated benzo[2,1-b:3,4-b':5,6-c'']trithiophenes 2 and naphtho[2,1-b:3,4-b']dithiophenes 3 are described. The treatment of 5,5'-dicarbonylated 3,3'-bis(phenylethynyl)-2,2'-bithiophenes 6 [readily available via Pd(II)-catalyzed alkynylation of the corresponding 3,3'-dibromo-2,2'-bithiophenes 5 in the presence of Cu(I) in (i-Pr)2NH] with chlorotris(triphenylphosphine)rhodium(I) yields the cyclic rhodium complexes 7 which smoothly react with sulfur and acetylenes to give 2 and 3 in good yields.
Early prediction of response to tyrosine kinase inhibitors by quantification of EGFR mutations in plasma of non-small cell lung cancer patients. (2015)

8079 Background: Several studies have investigated the feasibility of detecting EGFR mutations in liquid biopsies of Non-Small Cell Lung Cancer (NSCLC) patients. However, the potential to accurately quantify EGFR mutations in plasma for clinical purposes is largely unexplored. Methods: Plasma samples were obtained from 79 subjects: (a) 42 NSCLC patients with EGFR mutations in primary tumors tissue, from a prospective trial, where blood samples were collected at baseline prior to first-line erlotinib therapy and immediately after progression; (b) 15 previously untreated stage IIIB-IV NSCLC patients, with EGFR mutation positive tumor specimens, where plasma samples were collected at baseline and serially at 4-60 days during TKI therapy; (c) 22 negative control cases. EGFR mutation analysis in plasma was conducted by the cobas EGFR Mutation Test (EGFR test, under development, RMS, Pleasanton, CA) and ultra-deep next generation sequencing (UDNGS) by Roche 454-GS Junior and Illumina MiSeq. A semi-quantitative index (SQI) was derived from a dilution series of known mutation copy numbers. Clinical response, expressed as percent tumor shrinkage (PTS), was evaluated according to RECIST criteria. Results: The sensitivity and specificity of the EGFR test and UDNGS assay in plasma versus tissue was 72% and 100%, and 74% and 100%, respectively. Quantitative indices by the EGFR test and UDNGS showed a significant positive correlation (p < 0.0001). Serial testing of EGFR mutations revealed a progressive decrease in the EGFR semi-quantitative index (SQI) during therapy in all of the patients, starting from the 4thday of treatment in 90% of cases. The rate of SQI decrease was more than 50% at 15 days in 73% of patients (rapid responders) and less than 50% at 15 days in 27% of patients (slow responders) and was correlated with PTS at 2 months. Conclusions: Quantification of EGFR mutations with the cobas test in plasma is feasible. The variation of EGFR SQI during therapy could be useful for early prediction of response and diagnosis of relapse, with further implications for patient management. A prospective trial has been planned to confirm these results. Clinical trial information: EudraCT Number: 2010-023892-24.
Cluster Compounds Bearing both High- and Low-Valent Transition Metal Fragments:  The Reactions of Imido Carbonyl Cluster Ru3(CO)10(μ3-NPh) with Dioxo Acetylide Complexes (C5Me5)W(O)2(CCR), R = Ph and CMeCH2 (1998)

Heterobimetallic compounds (C5Me5)W(O)(μ-O)Ru3(μ3-NPh)(CCR)(CO)8, R = Ph and CMeCH2 (1a and 1b), which contain the high oxidation state dioxo tungsten fragment and the low-valent ruthenium carbonyl unit, were obtained from the reaction of Ru3(μ3-NPh)(CO)10 with (C5Me5)W(O)2(CCR), R = Ph and CMeCH2. These complexes consist of an open triangular Ru3 core with the dioxo tungsten unit coordinated to the central Ru atom via a WO→Ru dative interaction. Conversion to the pentametallic complex (C5Me5)W(O)(μ-O)Ru4(μ3-PPh)(CCPh)(CO)10 (2) was realized by treatment of 1a with Ru3(CO)12 in refluxing toluene, while heating a solution of 1b led to the isolation of (C5Me5)W(μ-O)2Ru3(μ3-NPh)(CCCMeCH2)(CO)6 (4) through the removal of two CO ligands. Reaction of 4 with PMe2Ph was examined, giving the monosubstituted (C5Me5)W(μ-O)2Ru3(CCCMeCH2)(μ3-NPh)(CO)5(PMe2Ph) (5) in moderate yield, of which the X-ray diffraction study lends support to the identification of its precursor 4. The reactivity of complex 4 with CO was then established, affording (C5Me5)W(μ-O)2Ru3(μ3-NPh)(CCCMeCH2)(CO)7 (6) and (C5Me5)W(O)2Ru3(μ3-NPh)(CCCMeCH2)(CO)8 (7), which are generated by removal of the vinyl or the dioxo tungsten fragment from the coordination sphere of ruthenium metal, respectively. In addition, upon exposure to pressurized CO atmosphere, complex 7 slowly converts to Ru3(CO)9[C6H5O(CONHPh)] (8), which has been crystallographically shown to possess a Ru3 skeleton with the vinylacetylide linked with one bridging CO and a carboxamido fragment; the latter is derived from the coupling of CO with the imido group. A possible reaction mechanism leading to the formation of 8 is discussed.
Photoactivatable Mussel‐Based Underwater Adhesive Proteins by an Expanded Genetic Code (2017)

Marine mussels exhibit potent underwater adhesion abilities under hostile conditions by employing 3,4-dihydroxyphenylalanine (DOPA)-rich mussel adhesive proteins (MAPs). However, their recombinant production is a major biotechnological challenge. Herein, a novel strategy based on genetic code expansion has been developed by engineering efficient aminoacyl-transfer RNA synthetases (aaRSs) for the photocaged noncanonical amino acid ortho-nitrobenzyl DOPA (ONB-DOPA). The engineered ONB-DOPARS enables in vivo production of MAP type 5 site-specifically equipped with multiple instances of ONB-DOPA to yield photocaged, spatiotemporally controlled underwater adhesives. Upon exposure to UV light, these proteins feature elevated wet adhesion properties. This concept offers new perspectives for the production of recombinant bioadhesives.
Coping with imbalanced training data for improved terrain prediction in autonomous outdoor robot navigation (2010)

Autonomous robot navigation in unstructured outdoor environments is a challenging and largely unsolved area of active research. The navigation task requires identifying safe, traversable paths that allow the robot to progress towards a goal while avoiding obstacles. Machine learning techniques are well adapted to this task, accomplishing near-to-far learning by training appearance-based models using near-field stereo readings in order to predict safe terrain and obstacles in the far field. However, these methods are subject to degraded performance when training data sets exhibit class imbalance, or skew, where data instances of one class outnumber those in another. In such scenarios, classifiers can be overwhelmed by the majority class, and will tend to ignore the minority class. In this paper, we show that typical outdoor terrain scenarios are associated with training data imbalance, and examine the impact of using undersampling, oversampling, SMOTE, and biased penalties techniques to correct for imbalance in stereo-derived training data. We conduct a statistically significant, repeated measures empirical evaluation and demonstrate improved far-field terrain prediction performance when using such methods for handling class imbalance versus taking no corrective action at all.
Beamforming Design for Full-Duplex MIMO Interference Channels–QoS and Energy-Efficiency Considerations (2016)

We consider a K link multiple-input multiple-output interference channel where each link consists of two full-duplex (FD) nodes. Two transmit beamforming design problems are solved: 1) sum-power minimization problem subject to rate constraints and 2) energy-efficiency maximization problem subject to individual power constraints. To tackle the sum-power minimization problem, we first generalize the well-known relationship between weighted-sum-rate (WSR) and weighted minimum-mean-squared-error (WMMSE) problems, originally used to solve the sum-rate maximization problems, and then propose a low complexity centralized algorithm, which converges to a stationary point. To decrease the exchange of a huge amount of data and excessive signaling traffic among the nodes, a distributed algorithm is also proposed. For the energy-efficiency maximization problem, the original fractional form optimization problem is first transformed into an equivalent subtractive-form optimization problem by exploiting the properties of fractional programming, and then performs a dual-layer optimization scheme. In the outer layer, the energy-efficiency parameter is searched using a simple 1-D search, and in the inner layer, the relationship between WSR and WMMSE is exploited to solve the subtractive form optimization problem. Since the proposed algorithms require perfect channel-state-information, which is difficult to acquire in practice, we also propose a robust design, by taking the imperfect channel knowledge into consideration. It is shown in the simulations that the sum-power achieved in FD mode depends heavily on the transmitter/receiver distortion. Also the energy-efficiency of FD systems is lower than that of half-duplex systems, as FD nodes need to overcome self-interference and increased inter-user interference, which leads to high power consumption.
Characterization of white light emitting diodes based ZnO nano structures grown on p-Si (2007)

In this paper ZnO nanorods and nanodots (with and without a SiO2 buffer layer) were grown on p-Si, forming p-n heterojunctions. The nanorods devices showed no electroluminescence (EL) emission but a rectifying behavior with a breakdown voltage around -4V. The nanodot devices showed EL emission under forward bias conditions. The buffer layer increased both the stability and efficiency of the devices. With the buffer layer EL emission was also observed under reverse bias.
Pulsed-light imaging for fluorescence guided surgery under normal room lighting (2013)

Fluorescence guided surgery (FGS) is an emerging technology that has demonstrated improved surgical outcomes. However, dim lighting conditions required by current FGS systems are disruptive to standard surgical workflow. We present a novel FGS system capable of imaging fluorescence under normal room light by using pulsed excitation and gated acquisition. Images from tissue-simulating phantoms confirm visual detection down to 0.25 μM of protoporphyrin IX under 125 μW/cm2 of ambient light, more than an order of magnitude lower than that measured with the Zeiss Pentero in the dark. Resection of orthotopic brain tumors in mice also suggests that the pulsed-light system provides superior sensitivity in vivo.
Vapor sensor realized in an ultracompact polarization interferometer built of a freestanding porous-silicon form birefringent film (2003)

A novel vapor sensor that uses polarization interferometry in a form birefringent porous-silicon film is introduced, analyzed, and experimentally characterized. Simulations and analysis of accuracy, versatility, stability, and control of dynamic range of the device are provided. The simulation accurately predicts the polarization interference signal, which is used to estimate the effective refractive indexes characterizing the form birefringence of a porous-silicon film with 0.001 accuracy. The device was tested for the detection of heptane concentration in a range of 342-20 000 ppm (=2.0%).
Single Diastereomer of a Macrolactam Core Binds Specifically to Myeloid Cell Leukemia 1 (MCL1) (2014)

A direct binding screen of 100 000 sp(3)-rich molecules identified a single diastereomer of a macrolactam core that binds specifically to myeloid cell leukemia 1 (MCL1). A comprehensive toolbox of biophysical methods was applied to validate the original hit and subsequent analogues and also established a binding mode competitive with NOXA BH3 peptide. X-ray crystallography of ligand bound to MCL1 reveals a remarkable ligand/protein shape complementarity that diverges from previously disclosed MCL1 inhibitor costructures.
In vivo synergism of recombinant human interleukin-3 and recombinant human interleukin-6 on thrombopoiesis in primates (1992)

Using a primate model, we examined the effect of recombinant human interleukin-3 (rhIL-3) and rhIL-6 on thrombopoiesis in vivo. Administration of 33 micrograms/kg/d of rhIL-3 for 11 to 14 days increased levels of circulating colony-forming units megakaryocyte (CFU- Mk) by approximately 15-fold in five rhesus monkeys without raising their platelet counts. In contrast, administration of 30 micrograms/kg/d of rhIL-6 for 10 days in four animals did not increase CFU-Mk levels but significantly raised platelet counts from a mean pretreatment value of 460 x 10(3)/microL (range 360 to 610) to a mean maximum of 746 x 10(3)/microL (665 to 790) on day 8. If monkeys were pretreated with rhIL-3 (33 or 100 micrograms/kg/d for 11 days) to expand their CFU-Mk compartment, the thrombopoietic effect of rhIL-6 was synergistically enhanced leading to platelet counts above 1,000 x 10(3)/microL (mean maximum value 1,247) in all three primates studied. The sequential administration of rhIL-3 and rhIL-6 might represent a powerful strategy to stimulate thrombopoiesis in vivo.
PV-Battery Sizing for Stand-Alone Lighting Applications (2013)

This paper presents a follow-up and addition to a system sizing spreadsheet, detailed in [1], with a focus on sizing or verifying the employability of an off-grid PV-battery system for night lighting. A dimensionless criterion, the Battery Usable Fraction UFbatt is defined, which aids both the calculations of systems and allows an approximate comparison of batteries, regardless of the employed battery chemistry. The outputs from the calculations allow users to rapidly identify whether a chosen or designed system will perform as desired. Further, as it provides a basic temperature-dependent battery capacity model, the influence of ambient conditions can be taken into account. This influence of the ambient conditions is shown to be very important, particularly in cases where the system is designed with little room for error with regards to climatological conditions. Measurements performed indicate that a good approximation for the battery temperature in a PV-battery lighting system is the average of the ambient temperature and the integrated PV module backsheet temperature.
Band Assignment in Dual Band Systems: A Learning-Based Approach (2018)

We consider the band assignment problem in dual band systems, where the base-station (BS) chooses one of the two available frequency bands (centimeter-wave and millimeterwave bands) to communicate data to the mobile station (MS). While the millimeter-wave band offers higher data rate when it is available, there is a significant probability of outage during which the communication should be carried on the centimeter-wave band. In this work, we use a machine learning framework to provide an efficient and practical solution to the band assignment problem. In particular, the BS trains a Neural Network (NN) to predict the right band assignment decision using observed channel information. We study the performance of the NN in two environments: (i) A stochastic channel model with correlated bands, and (ii) microcellular outdoor channels obtained by simulations with a commercial ray-tracer. For the former case, for sake of comparison we also develop a threshold based band assignment that relies on the optimal mean square error estimator of the best band. In addition, we study the performance of the NN-based solution with different NN structures and different observed parameters (position, field strength, etc.). We compare the achieved performance to linear and logistic regression based solutions as well as the threshold based solution. Under practical constraints, the learning based band assignment shows competitive or superior performance in both environments.
Supplementary Materials and Methods from Preclinical Development of the Anti-LAG-3 Antibody REGN3767: Characterization and Activity in Combination with the Anti-PD-1 Antibody Cemiplimab in Human <i>PD-1xLAG-3</i>–Knockin Mice (2023)

&lt;p&gt;Supplementary materials and methods&lt;/p&gt;
Millimeter-wave multi-Gigabit WLAN: Challenges and feasibility (2008)

The wide harmonized spectrum in the unlicensed 60 GHz band has been considered for WPAN standardizations. Recently there is also growing interest in the industry to use the same band for multi-Gigabit WLAN usages and standardization. In this paper, we describe the unique challenges and analyze the feasibility of realizing a multi-Gigabit WLAN in this band. We present analysis and simulation findings on the transmission range and spatial reuse opportunity with beamforming. We also explore options for range extension and multi-band integration.
Electrodeposition of Single‐Metal Nanoparticles on Stable Protein 1 Membranes: Application of Plasmonic Sensing by Single Nanoparticles (2011)

Light in the dark: Metal nanoparticles (M=Ag0, Au0, or Cu0) were electrodeposited onto ion-channel pores of a stable protein 1 membrane (see picture). The metal nanoparticles were implemented for detection of antigen–antibody binding events at the single-particle level using dark field microscopy and plasmon resonance Rayleigh scattering. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A Retinoic Acid—Rich Tumor Microenvironment Provides Clonal Survival Cues for Tumor-Specific CD8+ T Cells (2012)

While vitamin A has been implicated in host resistance to infectious disease, little is known about the role of vitamin A and its active metabolite, retinoic acid (RA) in host defenses against cancer. Here, we show that local RA production within the tumor microenvironment (TME) is increased up to 5-fold as compared with naïve surrounding tissue, with a commensurate increase in RA signaling to regionally infiltrating tumor-reactive T cells. Conditional disruption of RA signaling in CD8(+) T cells using a dominant negative retinoic acid receptor α (dnRARα) established that RA signaling is required for tumor-specific CD8(+) T-cell expansion/accumulation and protective antitumor immunity. In vivo analysis of antigen-specific CD8(+) T-cell responses revealed that early T-cell expansion was RA-independent; however, late T-cell expansion and clonal accumulation was suppressed strongly in the absence of RA signaling. Our findings indicate that RA function is essential for the survival of tumor-reactive CD8(+) T cells within the TME.
Night Vision Goggles Objectives Lens Focusing Methodology (2000)

Before performing an airborne mission that uses night vision goggles (NVGs) , aircrew must properly set the NVGOs various adjustments: interpupillary distance, tilt, eye relief, height, eyepiece and objective lens focus. Currently, aircrew use a Hoffman 20/20 test unit to pre-focus their NVG objective lenses at optical infinity before boarding their aircraft. They may also refocus their objective lenses while in the cockpit and during the course of the mission. This paper examines observersO abilities to resolve targets of different sizes, viewed through NVGs, as a function of different pre-focused distances corresponding to focusing errors.
OCD enhanced: implementation and validation of spectral interferometry for nanosheet inner spacer indentation (2021)

In this work, the novel enhancement to multichannel scatterometry data collection, Spectral Interferometry, is introduced and discussed. The Spectral Interferometry technology adds unique spectroscopic data by providing absolute phase information. This enhances metrology performance by improving sensitivity to weak target parameters and reducing parameter correlations. Spectral Interferometry enhanced OCD capabilities were demonstrated for one of the most critical and challenging applications of gate-all-around nanosheet device manufacturing: lateral etching of SiGe nanosheet layers to form inner spacer indentations. The inner spacer protects the channel from the source/drain regions during channel release and defines the gate length of the device. Additionally, a methodology is presented, which enables reliable and reproducible manufacturing of reference samples with engineered sheet-specific indent variations at nominal etch processing. Such samples are ideal candidates for evaluating metrology solutions with minimal destructive reference metrology costs. Two strategies, single parameter and sheet-specific indent monitoring are discussed, and it was found that the addition of spectroscopic information acquired by Spectral Interferometry improved both optical metrology solutions. In addition to improving the match to references for single parameter indent monitoring, excellent sheet-specific indent results can be delivered
RecombinantMycobacterium bovisBCG Expressing Pertussis Toxin Subunit S1 Induces Protection against an Intracerebral Challenge with LiveBordetella pertussisin Mice (2000)

The recent development of acellular pertussis vaccines has been a significant improvement in the conventional whole-cell diphtheria-pertussis-tetanus toxoid vaccines, but high production costs will limit its widespread use in developing countries. Since Mycobacterium bovis BCG vaccination against tuberculosis is used in most developing countries, a recombinant BCG-pertussis vaccine could be a more viable alternative. We have constructed recombinant BCG (rBCG) strains expressing the genetically detoxified S1 subunit of pertussis toxin 9K/129G (S1PT) in fusion with either the beta-lactamase signal sequence or the whole beta-lactamase protein, under control of the upregulated M. fortuitum beta-lactamase promoter, pBlaF*. Expression levels were higher in the fusion with the whole beta-lactamase protein, and both were localized to the mycobacterial cell wall. The expression vectors were relatively stable in vivo, since at two months 85% of the BCG recovered from the spleens of vaccinated mice maintained kanamycin resistance. Spleen cells from rBCG-S1PT-vaccinated mice showed elevated gamma interferon (IFN-gamma) and low interleukin-4 (IL-4) production, as well as increased proliferation, upon pertussis toxin (PT) stimulation, characterizing a strong antigen-specific Th1-dominant cellular response. The rBCG-S1PT strains induced a low humoral response against PT after 2 months. Mice immunized with rBCG-S1PT strains displayed high-level protection against an intracerebral challenge with live Bordetella pertussis, which correlated with the induction of a PT-specific cellular immune response, reinforcing the importance of cell-mediated immunity in the protection against B. pertussis infection. Our results suggest that rBCG-expressing pertussis antigens could constitute an effective, low-cost combined vaccine against tuberculosis and pertussis.