gebhart/patrepeval huggingface dataset:
One-Dimensional Pattern Formation of Adsorbed Molecules on the Ge(100)-2 × 1 Surface Driven by Nearest-Neighbor Effects (2012)

Formations of distinct one-dimensional patterns along the dimer row have been reported in methanol and ethylene adsorption on the germanium(100)-2 × 1 surface. A theoretical investigation is carried out in this study to provide a unified explanation of the pattern formation. Density functional theory calculation results show that an existing adsorbate affects the adsorption kinetics of the adjacent dimer, an effect that is mostly confined to the nearest neighbor. Kinetic Monte Carlo simulations are performed with the calculated kinetic parameters. The simulation results agree well with the experimental observations of ethylene and methanol adsorption on Ge(100), showing that the nearest-neighbor effect leads to longer-range pattern formation. The modeling is extended to the Si(100) surface where a similar pattern as on Ge(100) was formed with ethylene but not with methanol, and it can be further applied to spontaneous adsorbate patterning on ordered surfaces.
An Open Architecture for Embedding VR-Based Mechanical Tools Into CAD Applications (2008)

Virtual Reality (VR)-based assembly and disassembly analysis systems have been in use for several years. There have also been various efforts at creating bi-directional integration between CAD systems and VR-based assembly systems. The next step in this integration is to provide the capabilities of CAD and the immersive systems under one umbrella. This paper presents an open/extensible architecture for embedding VR-based mechanical tools within CAD systems to assist in assembly and disassembly analyses. The goal is to allow the user to perform immersive assembly/disassembly evaluations entirely within the CAD system. The architecture discussed in this paper is designed to leverage the inherent visualization and modeling capabilities provided by any commercial CAD system, while allowing the user to use any level of immersion ranging from simple tracking and stereo visualization to complete haptics devices. The focus is on providing assembly and disassembly capabilities using mechanical tools (e.g. wrenches, screwdrivers, etc.). The architecture is designed to be open (generic) for easy adaptation with any CAD system (through the API of the CAD system) and any haptic device (through the API of the haptic device). It provides a template consisting of modules and classes, which are relevant irrespective of the choice of the CAD system or the haptics system. The architecture is also designed to be extensible to include advanced interactions and simulations beyond the basic capabilities implemented in the system described in this paper. The CAD model library structure is leveraged for managing virtual tools and fasteners available to the user. The proposed architecture has been implemented to provide virtual assembly functionality within CATIA V5 using the VirtualHand™ Toolkit from Immersion Corporation. Examples of this implementation using threaded fasteners and tools are also presented. The extensibility of the architecture was tested by implementing a different suite of mechanical tools for a different simulation purpose.
The receptor tyrosine kinase p185HER2 is expressed on a subset of B- lymphoid blasts from patients with acute lymphoblastic leukemia and chronic myelogenous leukemia (1995)

The class I receptor tyrosine kinase (RTK) HER2 is an oncoprotein that is frequently involved in the pathogenesis of tumors of epithelial origin. Here we report mRNA expression in peripheral blood and bone marrow cells from healthy donors in hematopoietic cell lines and leukemic blasts from patients with acute lymphoblastic leukemia (ALL), acute myeloblastic leukemia (AML), chronic lymphoblastic leukemia (CLL), and chronic myeloid leukemia (CML). However, cell surface expression of HER2 protein (p185HER2) was found exclusively on a subset of leukemic cells of the B-lymphoblastic lineage. p185HER2 expression was found on blasts in 2 of 15 samples from infants, 9 of 19 samples from adult patients with C-ALL (CD19+CD10+), and 1 of 2 samples from patients with pro-B ALL (CD19+CD10-), whereas none of the leukemic cells from patients with AML (0/30), T-ALL (0/7), CLL (0/5) (CD19+CD5+), or CML in chronic and accelerated phase (0/5) or in blast crisis with myeloid differentiation (0/14) were positive for p185HER2. However, cells from 3 of 4 patients with CML in B-lymphoid blast crisis (CD19+CD10+) expressed high levels of p185HER2, which was also found on the surface of the CML-derived B-cell lines BV-173 and Nalm-1. Our study shows p185HER2 expression on malignant cells of hematopoietic origin for the first time. Aberrant expression of this oncogenic receptor tyrosine kinase in hematopoietic cell types may be an oncogenic event contributing to the development of a subset of B-lymphoblastic leukemias.
Acoustical behavior of an elastomer-coated submerged steel plate with one unconstrained surface (1979)

The results of a computer evaluation of the theoretical equations that describe the acoustic field either radiated or reflected by a 5-cm-thick steel plate, to which is bonded an elastomer coating, are reported. The equations that describe the acoustical behavior of the coated plate were derived by applying Timoshenko-Mindlin thick-plate theory to both the plate and the coating layer. The coated plate has water on one side and is unconstrained on the other. The computations treat elastomeric coating layers of various thicknesses. Two different elastomeric coating materials are also considered, a relatively soft, low-loss nitrile rubber and a stiffer high-loss neoprene. The computations demonstrate that the presence of an elastomeric coating, whatever the elastic properties of the coating material might be, does not significantly affect the acoustical characteristics of the steel plate, even when the coating thickness becomes equal to the thickness of the plate. The reason why elastomer-coated plates exhibit this behavior is discussed.
Reconfigurable Spin-Wave Nonreciprocity Induced by Dipolar Interaction in a Coupled Ferromagnetic Bilayer (2019)

In the growing field of $m\phantom{\rule{0}{0ex}}a\phantom{\rule{0}{0ex}}g\phantom{\rule{0}{0ex}}n\phantom{\rule{0}{0ex}}o\phantom{\rule{0}{0ex}}n\phantom{\rule{0}{0ex}}i\phantom{\rule{0}{0ex}}c\phantom{\rule{0}{0ex}}s$, spin waves (magnons) are manipulated as information carriers, particularly for data processing. Thus controlling the propagation of spin waves is of paramount interest here. This investigation considers a ferromagnetic bilayer with dipolar coupling as a potential nonreciprocal magnonic device, in which frequency dispersion is reciprocal for parallel yet nonreciprocal for antiparallel orientation of layer magnetizations. This is progress in the technological implementation of magnonic devices with asymmetric transmission properties, since reconfigurability can be easily achieved just by switching, without any rotation of the applied magnetic field.
The Epithelial–Mesenchymal Transcription Factor SNAI1 Represses Transcription of the Tumor Suppressor miRNA let-7 in Cancer (2021)

We aimed to determine the mechanism of epithelial-mesenchymal transition (EMT)-induced stemness in cancer cells. Cancer relapse and metastasis are caused by rare stem-like cells within tumors. Studies of stem cell reprogramming have linked <i>let-7</i> repression and acquisition of stemness with the EMT factor, <i>SNAI1</i>. The mechanisms for the loss of <i>let-7</i> in cancer cells are incompletely understood. In four carcinoma cell lines from breast cancer, pancreatic cancer, and ovarian cancer and in ovarian cancer patient-derived cells, we analyzed stem cell phenotype and tumor growth via mRNA, miRNA, and protein expression, spheroid formation, and growth in patient-derived xenografts. We show that treatment with EMT-promoting growth factors or <i>SNAI1</i> overexpression increased stemness and reduced <i>let-7</i> expression, while <i>SNAI1</i> knockdown reduced stemness and restored <i>let-7</i> expression. Rescue experiments demonstrate that the pro-stemness effects of <i>SNAI1</i> are mediated via <i>let-7</i>. In vivo, nanoparticle-delivered siRNA successfully knocked down <i>SNAI1</i> in orthotopic patient-derived xenografts, accompanied by reduced stemness and increased <i>let-7</i> expression, and reduced tumor burden. Chromatin immunoprecipitation demonstrated that <i>SNAI1</i> binds the promoters of various <i>let-</i>7 family members, and luciferase assays revealed that <i>SNAI1</i> represses <i>let-7</i> transcription. In conclusion, the <i>SNAI1</i>/<i>let-7</i> axis is an important component of stemness pathways in cancer cells, and this study provides a rationale for future work examining this axis as a potential target for cancer stem cell-specific therapies.
Laser Ablation with Vacuum Capture for MALDI Mass Spectrometry of Tissue (2015)

We have developed a laser ablation sampling technique for matrix-assisted laser desorption ionization (MALDI) mass spectrometry and tandem mass spectrometry (MS/MS) analyses of in-situ digested tissue proteins. Infrared laser ablation was used to remove biomolecules from tissue sections for collection by vacuum capture and analysis by MALDI. Ablation and transfer of compounds from tissue removes biomolecules from the tissue and allows further analysis of the collected material to facilitate their identification. Laser ablated material was captured in a vacuum aspirated pipette-tip packed with C18 stationary phase and the captured material was dissolved, eluted, and analyzed by MALDI. Rat brain and lung tissue sections 10 μm thick were processed by in-situ trypsin digestion after lipid and salt removal. The tryptic peptides were ablated with a focused mid-infrared laser, vacuum captured, and eluted with an acetonitrile/water mixture. Eluted components were deposited on a MALDI target and mixed with matrix for mass spectrometry analysis. Initial experiments were conducted with peptide and protein standards for evaluation of transfer efficiency: a transfer efficiency of 16% was obtained using seven different standards. Laser ablation vacuum capture was applied to freshly digested tissue sections and compared with sections processed with conventional MALDI imaging. A greater signal intensity and lower background was observed in comparison with the conventional MALDI analysis. Tandem time-of-flight MALDI mass spectrometry was used for compound identification in the tissue.
Engineering adeno-associated viral vectors to evade innate immune and inflammatory responses (2021)

Nucleic acids are used in many therapeutic modalities, including gene therapy, but their ability to trigger host immune responses in vivo can lead to decreased safety and efficacy. In the case of adeno-associated viral (AAV) vectors, studies have shown that the genome of the vector activates Toll-like receptor 9 (TLR9), a pattern recognition receptor that senses foreign DNA. Here, we engineered AAV vectors to be intrinsically less immunogenic by incorporating short DNA oligonucleotides that antagonize TLR9 activation directly into the vector genome. The engineered vectors elicited markedly reduced innate immune and T cell responses and enhanced gene expression in clinically relevant mouse and pig models across different tissues, including liver, muscle, and retina. Subretinal administration of higher-dose AAV in pigs resulted in photoreceptor pathology with microglia and T cell infiltration. These adverse findings were avoided in the contralateral eyes of the same animals that were injected with the engineered vectors. However, intravitreal injection of higher-dose AAV in macaques, a more immunogenic route of administration, showed that the engineered vector delayed but did not prevent clinical uveitis, suggesting that other immune factors in addition to TLR9 may contribute to intraocular inflammation in this model. Our results demonstrate that linking specific immunomodulatory noncoding sequences to much longer therapeutic nucleic acids can "cloak" the vector from inducing unwanted immune responses in multiple, but not all, models. This "coupled immunomodulation" strategy may widen the therapeutic window for AAV therapies as well as other DNA-based gene transfer methods.
Ethanol Content Estimation in Flex Fuel Direct Injection Engines Using In-Cylinder Pressure Measurements (2010)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Flexible fuel vehicles (FFVs) are able to operate on a blend of ethanol and gasoline in any volumetric concentration of up to 85% ethanol (93% in Brazil). The estimation of ethanol content is crucial for optimized and robust performance in such vehicles. Even if an ethanol sensor is utilized, an estimation scheme independent of the ethanol sensor measurement retains advantages in enhancing the reliability of ethanol estimation and allowing on-board diagnostics. It is well-known that an exhaust gas oxygen (EGO) sensor could be utilized to estimate the ethanol content, which exploits the difference in stoichiometric air-to-fuel ratio (SAFR) between ethanol (9.0) and gasoline (14.6). The SAFR-based ethanol estimation has been shown to be prone to large errors with mass air flow sensor bias and/or fuel injector shift. In this paper, an ethanol estimation scheme is proposed by additionally using measurement of in-cylinder pressure, which essentially exploits the difference in latent heat of vaporization (LHV) between ethanol and gasoline, and hence detects the charge cooling effects of ethanol. Due to the additional and independent information introduced by the new algorithm, the proposed ethanol content estimation is more tolerant to air flow sensor drifts and injector shifts.&lt;/div&gt;&lt;/div&gt;
A Single Slow-Light Element for Independent Delay Control and Synchronization on Multiple Gb/s Data Channels (2007)

Independent delay control and bit-level synchronization of multiple data channels are demonstrated through a single stimulated Brillouin scattering (SBS)-based slow-light element. Multiple, independently tunable SBS gain resonances are generated in a single piece of highly nonlinear fiber from multiple SBS pumps. Each pump is broadened by noise modulating the laser current so that the bandwidth is compatible with high-speed gigabit-per-second data signals. Bit-level synchronization on three 2.5-Gb/s nonreturn-to-zero on-off keying channels shows independent and continuous delay control of up to 112ps. Bit-error-rate measurement on the synchronized channels shows 3.5-dB power penalty. Effect of one channel on the other channel's delay is also investigated and the reason is attributed to the nonlinear crosstalk.
How adaptation, training, and customization contribute to benefits from exoskeleton assistance (2021)

Exoskeletons can enhance human mobility, but we still know little about why they are effective. For example, we do not know the relative importance of training, how much is required, or what type is most effective; how people adapt with the device; or the relative benefits of customizing assistance. We conducted experiments in which naïve users learned to walk with ankle exoskeletons under one of three training regimens characterized by different levels of variation in device behavior. Assistance was also customized for one group. After moderate-variation training, the benefits of customized assistance were large; metabolic rate was reduced by 39% compared with walking with the exoskeleton turned off. Training contributed about half of this benefit and customization about one-quarter; a generic controller reduced energy cost by 10% before training and 31% afterward. Training required much more exposure than typical of exoskeleton studies, about 109 minutes of assisted walking. Type of training also had a strong effect; the low-variation group required twice as long as the moderate-variation group to become expert, and the high-variation group never acquired this level of expertise. Curiously, all users adapted in a way that resulted in less mechanical power from the exoskeleton as they gained expertise. Customizing assistance required less time than training for all parameters except peak torque magnitude, which grew slowly over the study, suggesting a longer time scale adaptation in the person. These results underscore the importance of training to the benefits of exoskeleton assistance and suggest the topic deserves more attention.
Robustness of mutual information based intra-operative registration (2006)

We investigated the robustness of the registration of intra-operative 3D rotational angiography (3DRA) data with pre-operative anatomical data, such as CT and MR. The analysis has been done in the context of interventional treatment of vascular pathologies and endovascular treatment of the neoplastic tissue. We used Mutual Information as similarity measure, and the Powell algorithm as optimizer. The robustness was measured as function of translation in different directions and rotation around different axes, for 11 patients.
Calmodulin priming: Nuclear translocation of a calmodulin complex and the memory of prior neuronal activity (2001)

The neuronal nucleus plays a vital role in information processing, but whether it supports computational functions such as paired-pulse facilitation, comparable to synapses, is unclear. Ca(2+)-dependent movement of calmodulin (CaM) to the nucleus is highly responsive to Ca(2+) entry through L-type channels and promotes activation of the transcription factor CREB (cAMP-responsive element binding protein) through phosphorylation by CaM-sensitive kinases. We characterized key features of this CaM translocation and its possible role in facilitation of nuclear signaling. Nuclear CaM was elevated within 15 s of stimulus onset, preceding the first signs of CREB phosphorylation in hippocampal pyramidal neurons. Depolarization-induced elevation of nuclear CaM also was observed in cerebellar granule cells, neocortical neurons, and dentate gyrus granule cells. Nuclear translocation of CaM was not blocked by disruption of actin filaments or microtubules, or by emptying endoplasmic reticulum Ca(2+) stores with thapsigargin. Translocation of fluorescently tagged CaM was prevented by fusing it with the Ca(2+)/CaM binding peptide M13, suggesting that nuclear CaM accumulation depends on association with endogenous Ca(2+)/CaM binding proteins. To determine whether increased nuclear [CaM] might influence subsequent nuclear signal processing, we compared responses to two consecutive depolarizing stimuli. After a weak "priming" stimulus that caused CaM translocation, CREB phosphorylation caused by a subsequent stimulus was significantly faster, more sensitive to Ca(2+) elevation, and less specifically dependent on Ca(2+) influx through L-type channels. CaM translocation not only supports rapid signaling to the nucleus, but also could provide a "memory" for facilitatory effects of repeated neural activity, seen in altered phosphorylated CREB dynamics and Ca(2+) channel dependence.
Self-Organizing Resource Management Framework in OFDMA Femtocells (2014)

Next generation wireless networks (i.e., WiMAX, LTE) provide higher bandwidth and spectrum efficiency leveraging smaller (femto) cells with orthogonal frequency division multiple access (OFDMA). The uncoordinated, dense deployments of femtocells however, pose several unique challenges relating to interference and resource management in OFDMA femtocell networks. Towards addressing these challenges, we propose RADION, a distributed resource management framework that effectively manages interference across femtocells. RADION's core building blocks enable femtocells to opportunistically determine the available resources in a completely distributed and efficient manner. Further, RADION's modular nature paves the way for different resource management solutions to be incorporated in the framework. We implement RADION on a real WiMAX femtocell testbed deployed in a typical indoor setting. Two distributed solutions are enabled through RADION and their performance is studied to highlight their quick self-organization into efficient resource allocations.
Performance Analysis of Space-Time Coded Modulation Techniques using GBSB-MIMO Channel Models (2002)

Wireless systems are rapidly developing to provide high speed voice, text and multimedia messaging services which were traditionally offered by wire line networks. To support these services, channels with large capacities are required. Information theoretic investigations have shown that Multiple Input Multiple Output (MIMO) channels can achieve very high capacities. Space-Time Block Coding (STBC) and Bell Labs Layered Space-Time Architecture (BLAST) are two potential schemes which utilize the diversity offered by MIMO channels to provide reliable high date rate wireless communication. This work studies the sensitivity of these two schemes to spatial correlation in MIMO channels. The first part of the thesis studies the effect of spatial correlation on the performance of STBC by using Geometrically Based Single Bounce MIMO (GBSB-MIMO) channel models. Performance is analyzed for two scenarios: one without scatterers in the vicinity of the transmitter and other with scatterers. In the second part of the thesis, the sensitivity of BLAST to spatial correlation is analyzed. Later, schemes which use the principles of Multilayered Space-Time Coded Modulation to combine the benefits of BLAST and STBC are introduced and their performance is investigated in correlated and uncorrelated Rayleigh fading. Results indicate that schemes using orthogonal design space-time block codes are reasonably robust to spatial correlation while schemes like BLAST are very sensitive as they depend on array processing to separate signals from various transmit antennas.
Domain Adaptation for Microscopy Imaging (2014)

Electron and light microscopy imaging can now deliver high-quality image stacks of neural structures. However, the amount of human annotation effort required to analyze them remains a major bottleneck. While machine learning algorithms can be used to help automate this process, they require training data, which is time-consuming to obtain manually, especially in image stacks. Furthermore, due to changing experimental conditions, successive stacks often exhibit differences that are severe enough to make it difficult to use a classifier trained for a specific one on another. This means that this tedious annotation process has to be repeated for each new stack. In this paper, we present a domain adaptation algorithm that addresses this issue by effectively leveraging labeled examples across different acquisitions and significantly reducing the annotation requirements. Our approach can handle complex, nonlinear image feature transformations and scales to large microscopy datasets that often involve high-dimensional feature spaces and large 3D data volumes. We evaluate our approach on four challenging electron and light microscopy applications that exhibit very different image modalities and where annotation is very costly. Across all applications we achieve a significant improvement over the state-of-the-art machine learning methods and demonstrate our ability to greatly reduce human annotation effort.
Q-switched operation of microchip lasers: erratum (1991)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text J. J. Zayhowski, "Q-switched operation of microchip lasers: erratum," Opt. Lett. 16, 1287-1287 (1991) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article