gebhart/patrepeval huggingface dataset:
Surface-Enhanced Hyper-Raman Scattering (SEHRS) on Ag Film over Nanosphere (FON) Electrodes:  Surface Symmetry of Centrosymmetric Adsorbates (2006)

Electrochemical surface-enhanced hyper-Raman scattering (SEHRS) and surface-enhanced Raman scattering (SERS) of centrosymmetric molecules on Ag film over nanosphere (AgFON) electrodes are presented. The SEHR spectra of trans-1,2-bis(4-pyridyl)ethylene (BPE) at different potentials (vs Ag/AgCl) are presented for the first time, and a reversible potential tuning of the SEHR spectra of BPE is demonstrated. The SEHRS and SERS techniques were used to determine to what extent either site symmetry reduction or field gradient effects dictate the origin of the observed vibrational spectra. It is found that the SEHR and SER spectra for the molecules studied were distinctly different at all frequency regions at a fixed voltage, suggesting that centrosymmetry is largely retained upon adsorption to the AgFON surface and that field gradient effects are negligible. This work also shows that the SEHR spectra clearly depend on potential, whereas the SER spectra are essentially independent of potenial. It is determined that the combination of changes in deltaGads and the presence of coadsorbed counterions are responsible for altering the local symmetry of the adsorbate and only SEHRS has the sensitivity to detect these changes in the surface environment. Thus, SEHRS is a uniquely useful spectroscopic tool that is much more sensitive to the local adsorption environment than is SERS.
Stabilizers for Osmium Isotopes in Microwave-Irradiated Acid Digestion and Inductively Coupled Plasma Mass Spectrometry Analysis (2021)

Osmium is defined in the international council for harmonization (ICH-Q3D) guidelines as an element whose concentration can be determined by validated methods including microwave-assisted nitric acid digestion and inductively coupled plasma mass spectrometry. However, microwave digestion using nitric acid is known to result in osmium recoveries higher than the theoretical values in spiked tests because of the formation of highly volatile osmium tetroxide in an oxidation reaction. To stabilize osmium, the addition of thiourea as a complexing agent has been tested and proved its utility. It remains unclear whether other compounds can prevent the over-recovery of osmium. In this study, we investigated four compounds, thiourea, ascorbic acid, sodium sulfite, and potassium metabisulfite, that could reduce the overestimation of osmium isotopes. The minimum amounts of thiourea, ascorbic acid, sodium sulfite, and potassium metabisulfite required to stabilize 10 ng/mL osmium in blank matrix were 1.0, 1.0, 2.5, and 2.5 g/L, respectively. The relative standard deviations obtained from 12 analyses for each stabilization solution were less than 3.3% in thiourea, 12.7% in ascorbic acid, 9.0% in sodium sulfite, and 10.6% in potassium metabisulfite. The stabilization solutions were investigated in a digested tablet matrix and were found to be effective. The impact of adding stabilization solutions on the determination of all ICH-Q3D element concentrations was also evaluated. As stabilization solutions had a small or significant impact on the determination of some elements, it was concluded that osmium determination should be conducted independently.
SLAP widgets (2009)

We present Silicone iLluminated Active Peripherals (SLAP), a system of tangible, transparent widgets for use on vision-based multi-touch tabletops. SLAP Widgets are cast from silicone or made of acrylic and include sliders, knobs, keyboards, and keypads. They add tactile feedback to multi-touch tables and can be dynamically relabeled with rear projection. They are inexpensive, battery-free, and untethered widgets combining the flexibility of virtual objects with tangible affordances of physical objects. Our demonstration shows how SLAP Widgets can augment input on multi-touch tabletops with modest infrastructure costs.
Low attentional engagement makes attention network activity susceptible to emotional interference (2014)

The aim of this study was to investigate whether emotion-attention interaction depends on attentional engagement. To investigate emotional modulation of attention network activation, we used a functional MRI paradigm consisting of a visuospatial attention task with either frequent (high-engagement) or infrequent (low-engagement) targets and intermittent emotional or neutral distractors. The attention task recruited a bilateral frontoparietal network with no emotional interference on network activation when the attentional engagement was high. In contrast, when the attentional engagement was low, the unpleasant stimuli interfered with the activation of the frontoparietal attention network, especially in the right hemisphere. This study provides novel evidence for low attentional engagement making attention control network activation susceptible to emotional interference.
Use of Weak Stability Boundry Trajectories for Planetary Capture (2003)

The consideration of transfers to the Weak Stability Boundary region represents one of the most advanced concepts when trying to reduce the propellant requirements to obtain an interplanetary goal. Deimos Space, under ESA contract, has developed a tool to simulate such transfers to inner planets, giant planets and natural moons of giant planets. The method is based on a three-step approach consisting on: selection of strategy, generation of initial solutions and numerical optimisation. The feasibility of building WSB transfer trajectories to Mercury, Venus and Mars has been proven. Instead of ∆V saving, the greatest advantage results from the increased flexibility in the selection of the final orbit with no ∆V penalty in most cases. The use of the Sun/Planet WSB region for the problem of giant planets capture does not introduce significant profit since the penalty in transfer time makes the mission unrealistic. Feasible missions to Jupiter and Saturn are obtained when using a double flyby strategy in Ganymede and Titan respectively. The capture by a natural moon of a giant planet incorporates a phase of energy reduction by moon flybys using resonant orbits linking at the end with the WSB region of the moon to achieve a ballistic capture.
Redox-Activating Dip-Pen Nanolithography (RA-DPN) (2009)

Dip pen nanolithography (DPN) involves the direct transfer of an ink from a coated atomic force microscope (AFM) tip to a substrate of interest and uses as many as 55,000 pens to form arbitrary patterns of alkanethiols, oligonucleotides, proteins, and viruses. Two limitations of DPN are the difficulty in transporting high molecular weight inks and the need to optimize individually the transport rates and tip inking methods of each molecule. As an alternative strategy that circumvents these two challenges, a method termed redox activating DPN (RA-DPN) is reported. In this strategy, an electrochemically active, quinone functionalized surface is toggled from the reduced hydroquinone form to the oxidized benzoquinone form by the delivery of an oxidant by DPN. While the benzoquinone form is susceptible to nucleophilic attack in Michael-type additions, hydroquinone is not and acts as a passivating agent. Because both forms of the quinone are kinetically stable, the patterned surface can be immersed in a solution of a target containing any strong nucleophile, which will react only where the benzoquinone form persists on the surface. For proof-of-concept demonstrations, quinone surfaces were patterned by the delivery of the oxidant cerric ammonium nitrate and were immersed in solutions of AF549 labeled cholera toxin beta subunit or oligonucleotides modified at the 5' end with an amine and the 3' end with a fluorophore. Fluorescent patterns of both the proteins and oligonucleotides were observed by epifluorescence microscopy. Additionally, RA-DPN maintains the advantageous ability of DPN to control feature size by varying the dwell time of the tip on the surface, and variation of this parameter has resulted in feature sizes as small as 165 nm. With this resolution, patterns of 50,000 spots could be made in a 100 x 100 microm(2) grid.
1.3 µm Mode-Locked Disk Laser with Wafer Fused Gain Chip and SESAM (2010)

We demonstrate a wafer fused mode-locked optically-pumped semiconductor disk laser operating at 1.3 µm spectral range. Both the gain mirror and the SESAM incorporate InP-based active region wafer fused with GaAs/AlGaAs distributed Bragg reflector. ©2010 Optical Society of America
Mipad: a next generation PDA prototype (2000)

MiPad is one of the application prototypes in a project codenamed Dr Who. As a wireless Personal Digital Assistant (PDA), MiPad fully integrates continuous speech recognition (CSR) and spoken language understanding (SLU) to enable users to accomplish many common tasks using a multimodal interface and wireless technologies. It tries to solve the problem of pecking with tiny styluses or typing on minuscule keyboards in today’s PDAs or smart phones. It also avoids the problem of being a cellular telephone that depends on speech-only interaction. MiPad incorporates a built-in microphone that activates whenever a field is selected. As a user taps the screen or uses a built-in roller to navigate, the tapping action narrows the number of possible instructions for spoken language processing. MiPad currently runs on a Windows CE Pocket PC with a Windows 2000 Server where speech recognition is performed. The Dr Who CSR engine has a 64k word vocabulary with a unified context-free grammar and ngram language model. The Dr Who SLU engine is based on a robust chart parser and a plan-based dialog manager. This paper discusses MiPad’s design, implementation work in progress, and preliminary user study in comparison to the existing pen-based PDA interface.
45 dB Single-Stage Single-Frequency Cr:ZnSe Amplifier for 2.2-2.6 μm Spectral Range (2021)

We report 45 dB single stage Cr:ZnSe amplifier operating over 2.2-2.6 μ m spectral range seeded by CW Cr:ZnSe single frequency laser. The maximum output energy of 1.6 mJ was demonstrated in 25 ns pulses at 1000 Hz repetition rate.
Experimental and theoretical characterization of electrical contact in anisotropically conductive adhesive (2000)

Electrical conduction through anisotropically conductive adhesive (ACA) is caused by deformation of metal fillers under pressure and heat. In this work, the hardness of the electrical particles under various deformation degrees was determined by nano-indentor measurements and the electrical resistance of the electrical contacts was measured under various deformation degrees. Theoretical model and simulation have been developed for the microscopic mechanism of the electrical conduction through metal fillers in the anisotropically conductive adhesive. By comparing with experimental data it is concluded that the deformation of the metal filler in our ACA is plastic even at rather low external load. Further theoretical simulation reveals two important aspects of the conductance characteristics. The conductance is improved by increasing the external load but the dependence of the conductance on the spatial position of the metal filler becomes stronger. Design and optimization of the ACA with respect to the absolute value of the electric conductance and its dependence on the spatial position of the metal filler are of essential importance for the electronics packaging application of the anisotropically conductive adhesives.
RNA Processing in an Escherichia coli Strain Deficient in Both RNase P and RNase III (1980)

It is now evident that primary transcripts of most prokaryotic and eukaryotic RNAs contain extra regions of unknown function interspersed among regions destined to occur in mature molecules. The role of RNA processing enzymes is the correct removal of the extra regions leading to the formation of functional mature RNAs. The most intensively studied RNA processing reactions are those carried out by Escherichia coli RNase III (Robertson et al. 1968; Robertson and Dunn 1975; Dunn 1976), E. coli RNase P (Robertson et al. 1972; Stark et al. 1978), and Bacillus subtilis RNase M5 (Sogin et al. 1977; Meyhack et al. 1978). All three of these enzymes retain the ability to cleave their natural substrates properly in vitro, even following extensive purification of both the enzyme and the RNA precursor molecule. It is difficult to identify and study the mechanism of various E. coli RNA processing enzymes without adopting a comprehensive approach that includes both the genetic and the biochemical definitions of a proposed RNA processing activity. This complication is evident in two of the approaches that have been recently employed to study this problem: several additional enzymatic activities that have been characterized biochemically from E. coli and tested on various RNA precursor substrates (Sakano and Shimura 1975; Schedl et al. 1976; Ghosh and Deutscher 1978) require further identification; in addition, mutations in well-characterized E. coli mutant strains lacking RNase III or RNase P and the resulting changes in RNA metabolism have been correlated with potential new RNA processing activities (Seidman...
Aberration correction using moving particles speckle noise for ultrafast ultrasonic imaging (2010)

The correction of sound speed heterogeneities is an important problem in trans-skull and deep organs imaging. Among all the proposed adaptive focusing methods, time reversal is an elegant one that enables to know the Green's function between the ultrasonic array and a punctual scatterer. However, in the absence of strong well resolved scatterers, time reversal is not useful. In this work we propose to use the echoes coming from moving particles in a flow to generate a virtual point-like scatterer and focus on it by iterative time reversal. This method enables to focus adaptively anywhere a flow is present. Then we use the Green's function to correct the ultrasound images. First, we apply this technique using focused wave then to improve it, we use the ultrafast plane wave imaging and synthetic focusing.
Developmentally regulated nuclear transport of transcription factors in Drosophila embryos enable the heat shock response (1998)

Hsp70 is a broadly conserved thermotolerance factor, but inhibits growth at normal temperatures and cannot be induced in early embryos. We report that in Drosophila embryos the temporal and spatial patterns of Hsp70 inducibility were unexpectedly complex, with striking differences between the soma and the germline. In both, regulation occurred at the level of transcription. During the refractory period for Hsp70 induction, HSF (heat-shock transcription factor) exhibited specific DNA-binding activity characteristic of activation in extracts of heated embryos. Remarkably, however, HSF was restricted to the cytoplasm in intact embryos even after heat shock. HSF moved from the cytoplasm to the nucleus in the absence of heat precisely when the capacity to induce Hsp70 was acquired (cycle 12 of the germline, cycle 13 in the soma). During oogenesis, Hsp70 inducibility was lost in nurse cells around stage 10, in a posterior-to-anterior gradient and HSF redistributed from nucleus to cytoplasm in the same spatiotemporal pattern. In a highly inbred derivative of the Samarkind strain, HSF moved into embryonic nuclei earlier than in our standard wild-type strain. Correspondingly, Hsp70 was inducible earlier, confirming that nuclear transport of HSF controls the inducibility of Hsp70 in early embryos. We also report for the first time the nuclear import patterns of two general transcription factors, RNA polymerase subunit Ilc and TATA binding protein (TBP). Both enter nuclei in a highly synchronous manner, independently of each other and of HSF. The import of TBP coincides with the first reported appearance of transcripts in the embryo. We suggest that the potentiation of general and heat shock-specific transcription in Drosophila embryos is controlled by the developmentally programmed relocalization of general and heat shock-specific transcription factors. Restricted nuclear entry of HSF represents a newly described mechanism for regulating the heat-shock response.
Elimination of -mannose glycan structures in Pichia pastoris (2011)

The methylotrophic yeast, Pichia pastoris, is an important organism used for the production of therapeutic proteins. However, the presence of fungal-like glycans, such as those containing β-mannose (Man) linkages, can elicit an immune response or bind to Man receptors, thus reducing their efficacy. Recent studies have confirmed that P. pastoris has four genes from the β-mannosyl transferase (BMT) family and that Bmt2p is responsible for the majority of β-Man linkages on glycans. While expressing recombinant human erythropoietin (rhEPO) in a developmental glycoengineered strain devoid of BMT2 gene expression, cross-reactivity was observed with an antibody raised against host cell antigens. Treatment of the rhEPO with protein N-glycosidase F eliminated cross-reactivity, indicating that the antigen was associated with the glycan. Thorough analysis of the glycan profile of rhEPO demonstrated the presence of low amounts of α-1,2-mannosidase resistant high-Man glycoforms. In an attempt to eliminate the α-mannosidase resistant glycoforms, we used a systemic approach to genetically knock-out the remaining members of the BMT family culminating in a quadruple bmt2,4,1,3 knock-out strain. Data presented here conclude that the additive elimination of Bmt2p, Bmt3p and Bmt1p activities are required for total abolition of β-Man-associated glycans and their related antigenicity. Taken together, the elimination of β-Man containing glycoforms represents an important step forward for the Pichia production platform as a suitable system for the production of therapeutic glycoproteins.
Bacterial Detection and Differentiation via Direct Volatile Organic Compound Sensing with Surface Enhanced Raman Spectroscopy (2017)

Abstract Current methods for detecting bacterial infections, such as culture and morphological analysis of bacterial colonies, are time and labor intensive. Through the direct detection of bacterial volatile organic compounds (VOCs), via surface enhanced Raman spectroscopy (SERS), we report here a reconfigurable assay for the identification and monitoring of bacteria. We demonstrate differentiation between highly clinically relevant organisms: Escherichia coli , Enterobacter cloacae , and Serratia marcescens . This is the first differentiation of bacteria via SERS of bacterial VOC signatures. The assay also detected as few as 10 CFU/ml of E. coli in under 12 hrs, and detected E. coli from whole human blood and human urine in 16 hrs at clinically relevant concentrations of 10 3 CFU/ml and 10 4 CFU/ml, respectively. In addition, the recent emergence of portable Raman spectrometers uniquely allows SERS to bring VOC detection to point‐of‐care settings for diagnosing bacterial infections.
Data from Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-cell Persistence Following Adoptive Cell Therapy (2023)

&lt;div&gt;Abstract&lt;p&gt;Adoptive cell therapy (ACT) using tumor-infiltrating lymphocytes (TIL) can mediate responses in some patients with metastatic epithelial cancer. Identifying gene signatures associated with successful ACT might enable the development of improved therapeutic approaches. The persistence of transferred T cells in the peripheral blood is one indication of clinical effectiveness, but many T-cell and host factors may influence T-cell persistence. To limit these variables, we previously studied a patient with metastatic colorectal cancer treated with polyclonal TILs targeting the &lt;i&gt;KRAS&lt;/i&gt;(G12D) hotspot mutation, who experienced a partial response for 9 months. Three dominant clonotypes specifically recognizing KRAS(G12D) epitopes were identified, but we found that only two clonotypes persisted 40 days after ACT. Because of these findings, in this study, we performed the single-cell transcriptome analysis of the infused TILs. The analysis revealed a total of 472 genes that were differentially expressed between clonotypes 9.1-NP and 9.2-P single cells, and 528 genes between 9.1-NP and 10-P. Following these clonotypes in the peripheral blood after ACT, the gene expression patterns changed, but &lt;i&gt;IL7R, ITGB1, KLF2&lt;/i&gt;, and &lt;i&gt;ZNF683&lt;/i&gt; remained expressed in the persistent 9.2-P and 10-P cells, compared with the nonpersistent 9.1-NP cells. In addition, four autologous TILs, which were used for treatment but persisted poorly 1 month after ACT, did not express the gene profiles associated with persistence. These results suggest that certain TIL populations possess a unique gene expression profile that can lead to the persistence of T cells. Thus, this single-patient study provides insight into how to improve ACT for solid cancer.&lt;/p&gt;&lt;/div&gt;
Nicotinamide Promotes Cell Survival and Differentiation as Kinase Inhibitor in Human Pluripotent Stem Cells (2018)

Nicotinamide, the amide form of vitamin B3, is widely used in disease treatments and stem cell applications. However, nicotinamide's impact often cannot be attributed to its nutritional functions. In a vitamin screen, we find that nicotinamide promotes cell survival and differentiation in human pluripotent stem cells. Nicotinamide inhibits the phosphorylation of myosin light chain, suppresses actomyosin contraction, and leads to improved cell survival after individualization. Further analysis demonstrates that nicotinamide is an inhibitor of multiple kinases, including ROCK and casein kinase 1. We demonstrate that nicotinamide affects human embryonic stem cell pluripotency and differentiation as a selective kinase inhibitor. The findings in this report may help researchers design better strategies to develop nicotinamide-related stem cell applications and disease treatments.
A continuum model of docking of synaptic vesicle to plasma membrane (2014)

Neurotransmitter release from neuronal terminals is governed by synaptic vesicle fusion. Vesicles filled with transmitters are docked at the neuronal membrane by means of the SNARE machinery. After a series of events leading up to the fusion pore formation, neurotransmitters are released into the synaptic cleft. In this paper, we study the mechanics of the docking process. A continuum model is used to determine the deformation of a spherical vesicle and a plasma membrane, under the influence of SNARE-machinery forces and electrostatic repulsion. Our analysis provides information on the variation of in-plane stress in the membranes, which is known to affect fusion. Also, a simple model is proposed to study hemifusion.
(Invited) Direct Bonding: A Key Enabler for 3D Monolithic Integration (2014)

By stacking transistor levels on each other sequentially, monolithic 3D integration appears to be an alternative solution to scaling. By taking fully advantages of the vertical dimension, circuit partitioning at the transistor scale is then possible. This papers gives the different opportunities offered by such technology and summarizes the technological challenges that raises from this concept. A general overview of the different techniques to create an active layer above a bottom transistor level is presented. Direct bonding from a SOI wafer clearly appears to be currently the best solution to obtain a defect free monocrystalline active layer with a well-controlled thickness. Finally, the challenge of realizing a top transistor level with a low temperature thermal budget is explained. This thermal budget is quantified by studying the electrical stability of the bottom level. Some electrical results on low temperature activated junctions are also presented.