gebhart/patrepeval huggingface dataset:
Holographic detection of nanoparticles using acoustically actuated nanolenses (2020)

The optical detection of nanoparticles, including viruses and bacteria, underpins many of the biological, physical and engineering sciences. However, due to their low inherent scattering, detection of these particles remains challenging, requiring complex instrumentation involving extensive sample preparation methods, especially when sensing is performed in liquid media. Here we present an easy-to-use, high-throughput, label-free and cost-effective method for detecting nanoparticles in low volumes of liquids (25 nL) on a disposable chip, using an acoustically actuated lens-free holographic system. By creating an ultrasonic standing wave in the liquid sample, placed on a low-cost glass chip, we cause deformations in a thin liquid layer (850 nm) containing the target nanoparticles (≥140 nm), resulting in the creation of localized lens-like liquid menisci. We also show that the same acoustic waves, used to create the nanolenses, can mitigate against non-specific, adventitious nanoparticle binding, without the need for complex surface chemistries acting as blocking agents.
<title>Consideration of correlativity between litho and etching shape</title> (2012)

We developed an effective method for evaluating the correlation of shape of Litho and Etching pattern. The purpose of this method, makes the relations of the shape after that is the etching pattern an index in wafer same as a pattern shape on wafer made by a lithography process. Therefore, this method measures the characteristic of the shape of the wafer pattern by the lithography process and can predict the hotspot pattern shape by the etching process. The method adopts a metrology management system based on DBM (Design Based Metrology). This is the high accurate contouring created by an edge detection algorithm used wafer CD-SEM. Currently, as semiconductor manufacture moves towards even smaller feature size, this necessitates more aggressive optical proximity correction (OPC) to drive the super-resolution technology (RET). In other words, there is a trade-off between highly precise RET and lithography management, and this has a big impact on the semiconductor market that centers on the semiconductor business. 2-dimensional shape of wafer quantification is important as optimal solution over these problems. Although 1-dimensional shape measurement has been performed by the conventional technique, 2-dimensional shape management is needed in the mass production line under the influence of RET. We developed the technique of analyzing distribution of shape edge performance as the shape management technique. In this study, we conducted experiments for correlation method of the pattern (Measurement Based Contouring) as two-dimensional litho and etch evaluation technique. That is, observation of the identical position of a litho and etch was considered. It is possible to analyze variability of the edge of the same position with high precision.
Ultra-wide-band radio signal generation using optical frequency-shift-keying technique (2005)

We proposed a novel technique for generation of micro- or millimeter-wave pulses using optical frequency-shift-keying (FSK) modulation. FSK signals were obtained by an integrated four optical phase modulators. The pulses can be obtained as an optical beat of two spectral components, during transient FSK state which is shorter than 100 ps.
Research Guides: Wagner College Archive: Photo Collection (2012)

The Wagner Archive is dedicated to collecting and preserving materials documenting the history and legacy of Wagner College.
Pregnancy After Cerebral Bypass for Moyamoya Disease (2019)

INTRODUCTION: Moyamoya disease (MMD) disproportionately affects young to middle age women. Vascular neurosurgeons are often needed to counsel women regarding pregnancy following bypass for MMD, but there is a paucity of data. We set out to examine neurological and obstetric outcomes in an extensive cohort of MMD patients who had pregnancies following cerebral revascularization at the Stanford Medical Center. METHODS: We identified all patients who underwent cerebral bypass for MMD and later became pregnant from 1990 through 2018. Some of these patients also had pregnancies prior to bypass, and we examined these pregnancies as well. We performed a chart review and a brief telephone survey to identify obstetric complications, transient ischemic attack (TIA), and stroke. Neurological and obstetric outcomes were compared to published rates. We also compared pre- and postbypass pregnancy complication rates using logistic regression techniques. RESULTS: There were 71 pregnancies among 56 women with mean age 30.5. Among 59 postbypass pregnancies, there were 5 (8%) perinatal TIAs. There were no magnetic resonance imaging (MRI) confirmed strokes or strokes with residual deficits. Among 12 prebypass pregnancies, there were 3 (25%) TIAs and 2 (17%) MRI-confirmed strokes. There were no hemorrhagic complications in either group. In the multivariable logistic regression analysis, performing cerebral revascularization prior to pregnancy versus postpregnancy was associated with lower odds of perinatal stroke or TIA (OR 0.13, P = .007). The overall rate of cesarean delivery was 39%. CONCLUSION: We present neurological and obstetric outcomes in a large cohort of MMD patients. These data indicate that postbypass pregnancy is accompanied by low complication rates. There were no ischemic or hemorrhagic strokes among postbypass, pregnant MMD patients. Obstetric complications were low overall. We recommend a close collaboration between the vascular neurosurgeon and the obstetrician regarding medical management, including blood pressure goals and continuation of aspirin.
Partial Loss of Function of the GHRH Receptor Leads to Mild Growth Hormone Deficiency (2016)

We report the first coexistence of two novel compound homozygous GHRHR variants in two unrelated pedigrees associated with a partial loss of function. Surprisingly, the patients have a relatively mild IGHD phenotype. Analysis revealed that the pP79L mutation is associated with the compromise in function, with the residual partial activity explaining the mild phenotype.
A 56GS/S 6b DAC in 65nm CMOS with 256&#x00D7;6b memory (2011)

This paper demonstrates more than one order of magnitude improvement in 6b CMOS DAC design with a test circuit operating at 56Gs/s, achieving SFDR >;30dBc and EI\IOB>;4.3b up to the output frequency of 26.9GHz. Total power dissipation is less than 750mW and the core DAC die area is less than 0.6x0.4 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Component based modeling of routing protocols for Mobile Ad Hoc Networks (2015)

Routing protocols perform several functionalities and can be considered as complex software systems. The design and performance analysis of these protocols is difficult and complex and most of them are not adaptable to changes of the environment. In this paper, we present a component based methodology for modeling mobile ad hoc routing protocols. Componentization is used for modeling and analysis of complex systems, because it introduces modularity in protocol design and reusability of designed components across protocols of the same class. We define the fundamental components of the routing protocols based on their functionalities and investigate their interactions. More specifically, we present an initial investigation of the influence of the separate components on the performance metrics of the protocol, such as delay, packet delivery ratio and routing overhead. Proactive routing protocols are being examined and we consider OLSR and DSDV as use cases for our methodology. In addition, we propose an adaptive reusable modification in the Routing Metrics component of OLSR that lead to better overall performance in energy constrained environments.
10 × 224-Gb/s WDM Transmission of 28-Gbaud PDM 16-QAM on a 50-GHz Grid over 1,200 km of Fiber (2010)

We demonstrate ten-channel wavelength-division-multiplexed long-haul optical networking of 28-Gbaud PDM 16-QAM signals on a 50-GHz grid (spectral efficiency of 4 b/s/Hz). We achieve transmission over 1,200 km of ultra-large-area fiber, including three wavelength-selective-switch passes.
ChemInform Abstract: Purification of Large Peptides Using Chemoselective Tags (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Municipal Wastewater (2020)

SARS-CoV-2 has recently been detected in feces, which indicates that wastewater may be used to monitor viral prevalence in the community. Here, we use RT-qPCR to monitor wastewater for SARS-CoV-2 RNA over a 74-day time course. We show that changes in SARS-CoV-2 RNA concentrations follow symptom onset gathered by retrospective interview of patients but precedes clinical test results. In addition, we determine a nearly complete (98.5%) SARS-CoV-2 genome sequence from wastewater and use phylogenetic analysis to infer viral ancestry. Collectively, this work demonstrates how wastewater can be used as a proxy to monitor viral prevalence in the community and how genome sequencing can be used for genotyping viral strains circulating in a community.
Pulmonary lobe segmentation using the thin plate spline (TPS) with the help of the fissure localization areas (2013)

Lung lobe segmentation is clinically important for disease classification, treatment and follow-up of pulmonary diseases. Diseases such as tuberculosis and silicolis typically present in specific lobes i.e. almost exclusively the upper ones. However, the fissures separating different lobes are often difficult to detect because of their variable shape, appearance and low contrast in computed tomography images. In addition, a substantial fraction of patients have missing or incomplete fissures. To solve this problem, several methods have been employed to interpolate incomplete or missed fissures. For example, Pu et al. used an implicit surface fitting with different radial basis functions; Ukil et al. apply fast marching methods; and Ross et al. used an interactive thin plate spline (TPS) interpolation where the user selects the points that will be used to compute the fissure interpolation via TPS. In our study, results of an automated fissure detection method based on a plate-filter as well points derived from vessels were fed into an a robust TPS interpolation that ultimately defined the lobes. To improve the selection of detected points, we statistically determined the areas where fissures are localized from 19 data-sets. These areas were also used to constrain TPS fitting so it reflected the expected shape and orientation of the fissures, hence improving result accuracy. Regions where the detection step provided low response were replaced by points derived from a distance-to-vessels map. The error, defined as the Euclidian mean distance between ground truth points and the TPS fitted fissures, was computed for each dataset to validate our results. Ground truth points were defined for both exact fissure locations and approximate fissure locations (when the fissures were not clearly visible). The mean error was 5.64&plusmn;4.83 mm for the exact ground truth points, and 10.01 &plusmn; 8.23 mm for the approximate ground truth points.
Regulation of HAX-1 Anti-apoptotic Protein by Omi/HtrA2 Protease during Cell Death (2004)

Omi/HtrA2 is a nuclear-encoded mitochondrial serine protease that has a pro-apoptotic function in mammalian cells. Upon induction of apoptosis, Omi translocates to the cytoplasm and participates in caspase-dependent apoptosis by binding and degrading inhibitor of apoptosis proteins. Omi can also initiate caspase-independent apoptosis in a process that relies entirely on its ability to function as an active protease. To investigate the mechanism of Omi-induced apoptosis, we set out to isolate novel substrates that are cleaved by this protease. We identified HS1-associated protein X-1 (HAX-1), a mitochondrial anti-apoptotic protein, as a specific Omi interactor that is cleaved by Omi both in vitro and in vivo. HAX-1 degradation follows Omi activation in cells treated with various apoptotic stimuli. Using a specific inhibitor of Omi, HAX-1 degradation is prevented and cell death is reduced. Cleavage of HAX-1 was not observed in a cell line derived from motor neuron degeneration 2 mice that carry a mutated form of Omi that affects its proteolytic activity. Degradation of HAX-1 is an early event in the apoptotic process and occurs while Omi is still confined in the mitochondria. Our results suggest that Omi has a unique pro-apoptotic function in mitochondria that involves removal of the HAX-1 anti-apoptotic protein. This function is distinct from its ability to activate caspase-dependent apoptosis in the cytoplasm by degrading inhibitor of apoptosis proteins.
Chirped Return-to-Zero Modulation by Imbalanced Pulse Carver Driving Signals (2004)

We demonstrate a simple way of generating chirped and alternate-chirp return-to-zero signals of various duty cycles by means of a sinusoidally driven dual-drive Mach-Zehnder modulator. The amount of inherently bit-synchronized chirp is tuned by varying the imbalance of the drive signals' amplitudes or their relative delay. High temporal resolution measurements of the intensity and phase of the modulated optical field are obtained at 20 and 40 Gb/s using the spectrogram technique.
A study on surface treatments of woods for prevention from water penetration (2007)

木材は軽くて強く,断熱性に優れ,調湿性があり,工作しやすい特徴を有している。これらの特徴を活かして木材は古来より建材,家具,道具などに広く用いられてきた。しかし,木材は水が浸透しやすいという性質を有する。そこで本研究では吸水性ポリマーを含むゾル・ゲル反応液を用いて木材の表面処理を行って木材への水の浸透を防止する検討を行った。吸水性ポリマーを含むゾル・ゲル反応液で表面処理した木材は未表面処理木材と比較して水の浸透性が小さく,水を滴下した際の接触角が大きいことが認められた。また,吸水性ポリマーと酸化チタン微粒子とを含むゾル・ゲル反応液で表面処理した木材は湿度上昇に伴う重量増加率が未処理木材とほぼ同等であることが明らかとなった。SEM-EDX分析の結果から,表面処理木材には少なくとも表面から深さ0.5mmまでゾル・ゲル反応液が浸入してシロキサン重合体が形成されているものと推測した。形成されたシロキサン重合体には疎水性の部分が存在し,それが表面処理木材の水浸透防止性などの特性発現に結びついているものと推測した。
A high sensitivity photonic frequency discriminator for low phase noise tunable micro/mm wave synthesis (2018)

A novel high sensitivity photonic frequency discriminator is implemented for a low phase noise tunable micro/mm wave synthesizer. In a proof-of-concept demonstration, a low phase noise tunable opto-electronic oscillator (6 - 18 GHz) and a low phase noise tunable heterodyne beat from two independent cw lasers (10 - 30 GHz) are demonstrated via locking to the photonic frequency discriminator.
Effect of Interaction among Magnesium Ions, Anion, and Solvent on Kinetics of the Magnesium Deposition Process (2020)

To clarify the effects of anion species and solvents on the Coulombic efficiency and polarization of magnesium deposition/dissolution reactions, the anode/electrolyte interfacial behavior of magnesium tetrakis(hexafluoroisopropyloxy) borate (Mg[B(HFIP)4]2) and magnesium bis(trifluoromethanesulfonyl)amide (Mg(TFSA)2) was investigated and compared in triglyme and 2-methlytetrahydrofuran (2-MeTHF). When using triglyme, which has strong interaction with magnesium ions, decomposition of [B(HFIP)4]− in Mg[B(HFIP)4]2/triglyme was hard to occur because of the high reduction stability of the uncoordinated [B(HFIP)4]− anion, resulting in significantly higher Coulombic efficiency and smaller polarization than Mg(TFSA)2/triglyme. When 2-MeTHF was used as the solvent, magnesium deposition/dissolution reactions occurred in the Mg[B(HFIP)4]2/2-MeTHF electrolyte but not in the Mg[TFSA]2/2-MeTHF electrolyte. This is because the coordinated [B(HFIP)4]− anion in Mg[B(HFIP)4]2/2-MeTHF is stable at the magnesium deposition potential. However, the reductive stability of the coordinated [B(HFIP)4]− anion is inferior to that of the uncoordinated [B(HFIP)4]− anion, resulting in the Mg[B(HFIP)4]2/2-MeTHF Coulombic efficiency being lower than that of Mg[B(HFIP)4]2/triglyme. Our results indicate that solvents that could not be used with Mg(TFSA)2 are suitable in weakly coordinating anion electrolytes, such as Mg[B(HFIP)4]2. Controlling the interaction between magnesium ions and anions by selecting suitable anions and solvents is essential for designing new electrolytes for magnesium rechargeable batteries.
Robust dual control MPC with application to soft-landing control (2015)

Dual control frameworks for systems subject to uncertainties aim at simultaneously learning the unknown parameters while controlling the system dynamics. We propose a robust dual model predictive control algorithm for systems with bounded uncertainty with application to soft landing control. The algorithm exploits a robust control invariant set to guarantee constraint enforcement in spite of the uncertainty, and a constrained estimation algorithm to guarantee admissible parameter estimates. The impact of the control input on parameter learning is accounted for by including in the cost function a reference input, which is designed online to provide persistent excitation. The reference input design problem is non-convex, and here is solved by a sequence of relaxed convex problems. The results of the proposed method in a soft-landing control application in transportation systems are shown.
Nonlinear Geometric Effects in Mechanical Bistable Morphing Structures (2012)

Bistable structures associated with nonlinear deformation behavior, exemplified by the Venus flytrap and slap bracelet, can switch between different functional shapes upon actuation. Despite numerous efforts in modeling such large deformation behavior of shells, the roles of mechanical and nonlinear geometric effects on bistability remain elusive. We demonstrate, through both theoretical analysis and tabletop experiments, that two dimensionless parameters control bistability. Our work classifies the conditions for bistability, and extends the large deformation theory of plates and shells.
Streamed wireless video for low-end consumer digital cameras (2003)

The latest models of low-end consumer digital cameras have begun to support A/V streaming directly to the memory card. This greatly enhances the utility of the camera to an end user. We investigate techniques to provide a similar streaming service from camera directly to a wireless network server.
Erratum: Coupling-induced oscillations in overdamped bistable systems [Phys. Rev. E68, 045102 (2003)] (2009)

Received 10 November 2009DOI:https://doi.org/10.1103/PhysRevE.80.069902©2009 American Physical Society
Structural and Antiviral Studies of the Human Norovirus GII.4 Protease (2019)

Norovirus is the leading cause of acute gastroenteritis worldwide with a yearly reported 700 million cases driving a $60 billion global socioeconomic burden. With no United States Food and Drug Administration approved therapeutics and the chance for severe chronic infection and life-threatening complications, researchers have identified the protease as a potential target. However, drug development has focused on the norovirus GI.1 strain despite its accounting for less than 5% of all outbreaks. Our lab aims to change focus for norovirus drug design from GI.1 to the highly infective GII.4, responsible for more than 50% of all outbreaks worldwide. With the first published crystal structure of the norovirus GII.4 protease, we have identified several significant differences in the structure and active site that have hindered development of a potent inhibitor targeting the norovirus GII.4 protease. With these new insights, we have begun designing compounds that demonstrate increased inhibition of the clinically most relevant norovirus GII.4 strain.
Ion-Exchanging Graphenic Nanochannels for Macroscopic Osmotic Energy Harvesting (2022)

The Gibbs free energy difference between seawater and river water can be tapped by selective ion transport across charged nanochannels, referred to as reverse electrodialysis (RED). However, existing single pore and micro/nanofluidic RED systems have shown poor prospects for scalability and practical implementation. Herein, we present a macroscopic RED system, utilizing a cation-selective membrane or an anion-selective membrane. The membranes comprise reduced graphene oxide (rGO) nanosheets decorated uniformly with TiO2 nanoparticles. The nanosheets are covalently functionalized with polystyrene (PS) and subsequently linked to sulfonate or quaternary amine functional groups to obtain cation and anion selectivity, respectively. The membranes show excellent ion transport properties along with high power densities demonstrated under artificial salinity gradients. The cation-exchange membrane (CEM) delivered a power density of 448.7 mW m–2 under a 500-fold concentration gradient, while the anion-exchange membrane (AEM) produced a substantial power output of 177.8 mW m–2 under a similar gradient. The efficiencies ranged from 10.6% to 42.3% for CEM and from 9.7% to 46.1% in the case of AEM. Testing under varying pH conditions revealed higher power output under acidic conditions and substantial power output across the entire pH range, rendering them practically viable for sustainable energy harvesting in acidic and alkaline wastewaters.
A Multiscale Adaptive Network Model of Motion Computation in Primates (1990)

We demonstrate a multiscale adaptive network model of motion computation in primate area MT. The model consists of two stages: (1) local velocities are measured across multiple spatio-temporal channels, and (2) the optical flow field is computed by a network of direction-selective neurons at multiple spatial resolutions. This model embeds the computational efficiency of Multigrid algorithms within a parallel network as well as adaptively computes the most reliable estimate of the flow field across different spatial scales. Our model neurons show the same nonclassical receptive field properties as Allman's type I MT neurons. Since local velocities are measured across multiple channels, various channels often provide conflicting measurements to the network. We have incorporated a veto scheme for conflict resolution. This mechanism provides a novel explanation for the spatial frequency dependency of the psychophysical phenomenon called Motion Capture.
Antibody elicited by HIV-1 immunogen vaccination in macaques displaces Env fusion peptide and destroys a neutralizing epitope (2021)

Abstract HIV-1 vaccine design aims to develop an immunogen that elicits broadly neutralizing antibodies against a desired epitope, while eliminating responses to off-target regions of HIV-1 Env. Here we report isolation and characterization of Ab1245, an off-target antibody against the Env gp120-gp41 interface, from V3-glycan patch immunogen-primed and boosted macaques. A 3.7Å cryo-EM structure of an Ab1245-Env complex reveals one Ab1245 Fab binding asymmetrically to Env trimer at the gp120-gp41 interface using its long CDRH3 to mimic regions of gp41. The mimicry includes positioning of a CDRH3 methionine into the gp41 tryptophan clasp, resulting in displacement of the fusion peptide and fusion peptide-proximal region. Despite fusion peptide displacement, Ab1245 is non-neutralizing even at high concentrations, implying that only two fusion peptides per trimer are required for viral–host membrane fusion. These structural analyses facilitate immunogen design to prevent elicitation of Ab1245-like antibodies that block neutralizing antibodies against the fusion peptide.