gebhart/patrepeval huggingface dataset:
Synaptic tau and synaptogyrin‐3 are promising targets to tackle tauopathies (2021)

Background Different pathogenic conditions (Alzheimer's disease and other tauopathies) induce detachment of Tau protein from microtubules. Detached Tau accumulates at synapses and binds to synaptic vesicle-associated protein Synaptogyrin-3, hampering vesicle mobility and neurotransmitter release (Zhou et al., Nature Communications 2017). Lowering the levels of Synaptogyrin-3 alleviates synaptic dysfunction in fruit flies and mouse primary neurons McInnes et al., Neuron 2018). Method We pursued two strategies to lower Synaptogyrin-3 expression in a tauopathy mouse model (human P301S Tau-expressing mice; "PS19 mouse line"). We generated a synaptogyrin-3 knockout mouse usign CRISPR/Cas9 and crossed it with Tau P301S mice. In paralel, we designed several antisense oligonucleotides (ASOs) against common sequences of mouse and human Synaptogyrin-3. Result We showed that lowering expression of Synaptogyrin-3 is benign in mice, but strongly rescues mutant Tau-induced defects in long-term synaptic plasticity and working memory. We screened several anti-Synaptogyrin-3 ASOs in vitro and selected the most effective one to further study its effects in vivo. Conclusion Lowering Synaptogyrin-3 is safe and sufficient to prevent cognitive decline in Tau P301S mice. Further research will determine the therapeutic potential of interfering with the interaction of Tau and Synaptogyrin-3 in the context of tauopathies.
Sparse relational data sets: issues and an application (2008)

This dissertation comprises three parts. The first part presents a relational approach to building a workbench that supports extracting and processing structured data from unstructured data for querying, and that allows users to query using as much structured data as is currently available. The workbench provides basic operations that can be combined to process data in a pay as you go fashion, and a wide table to store the resulting sparse data set, in which most attributes are null for most documents. As a proof of concept, we conducted a case study on applying this relational workbench approach to support structured queries over Wikipedia. We present examples of incremental data processing with a series of operations and show that users can pose increasingly sophisticated queries over the results of these operations. Our conclusion from the case study is that while the relational workbench approach is promising and worth investigating, its success heavily relies on good relational database support for sparse data. 
Unfortunately, most relational database systems are not good at handling sparse data sets. The second part of the dissertation addresses some challenges presented when managing sparse data in relational database systems. With recent work showing that we can store sparse data efficiently by using interpreted storage, we show that storing a sparse data set in a single, wide table is an effective approach. For querying, we show that keyword search often provides focused results because most terms appear in few rows and columns. As for query evaluation, we show that sparse B-tree indexes allow a much broader index coverage over a sparse data set than the more common full B-tree indexes; moreover, we describe how to automatically infer from a sparse data set a hidden schema, which we could use as a reference for building materialized views, a browsing directory, or query forms over the wide table. 
The last part of the dissertation addresses the problem of building structured queries over a relational database system without knowing SQL and the database schema. We propose to combine keyword search and query forms to try to provide the best of both. We present a systematic approach to generate forms, and propose techniques to handle keyword queries having a mix of database constants and terms that appear on the forms. We consider grouping similar forms returned by keyword search to help users more easily find the right form. Our real-life user study shows that our keyword search implementations are efficient and generally effective, and that grouping forms is an important post-processing step of keyword search to lead users to the right forms.
Development of quartz resonant sensors using FEM (1994)

The design of vibrating quartz sensors for force or pressure measurement is a problem that can only be solved by computer simulation. One possibility is the use of finite element analysis, but the multitude and variety of the effects that must be considered make the analysis difficult. The FEM program must be able to compute the piezoelectric coupling between the electric stimulation and the mechanical vibration in anisotropic bodies, a dynamic problem. The determination of the force vs. frequency characteristic requires the implementation of the acoustoelastic effect, which describes the change of the elastic wave velocity as a function of mechanical stress. The expansion of the standard FEM program ANSYS with special user routines makes the investigation, design and optimisation of quartz resonant sensors possible.
In-band full duplex cellular operation with reconfigurable uplink antennas at base station (2016)

In this paper, we propose an in-band full duplex (IBFD) cellular operation with reconfigurable uplink (UL) antennas at base station (BS). For handling mobile station (MS)-to-MS interference in an IBFD cellular system, a repetition coding of UL MSs is considered. While the repetition coding of UL MSs is applied, downlink (DL) MSs can cancel MS-to-MS interference by using one silent symbol to measure MS-to-MS interference. To avoid UL system throughput loss due to the repetition coding of UL MSs, we propose using reconfigurable antennas to enable to serve more UL users simultaneously than the number of UL antennas. The proposed scheme does not require any MS-to-MS channel estimation or channel information feedback, as well as any interference cancellation receiver at the DL MSs. We analyze the degrees of freedom (DoF) gain of the proposed scheme. It is shown that the proposed scheme achieves the double DoF gain compared with half duplex scheme when the number of UL MSs and the preset modes of reconfigurable antennas go infinity. Numerical results show that the proposed scheme has a significant sum rate performance gain even though the number of UL MSs and the number of preset modes of reconfigurable antennas do not go infinity.
Repolarization of polarization-scrambled optical signals due to polarization dependent loss (1997)

We calculate the distribution function of the degree of polarization of an initially polarization scrambled signal propagating long distances in an optical fiber.We show that a significant repolarization can occur for modern-day parameters.We estimate how far the polarization dependent loss must be reduced before repolarization becomes negligible.
864. Adsorption of Adeno-Associated Virus to Commonly Used Catheter Materials (2005)

Published literature has suggested that various materials that are commonly used in injection catheters (e.g., stainless steel, nitinol) inactivate adenovirus (Adv), a viral vector that is widely used in the field of gene therapy. No such information is available for recombinant adeno-associated virus (rAAV). rAAV has a number of advantages over Adv, most notably, that rAAV is associated with more sustained gene expression. Therefore, we specifically investigated the stability of rAAV when exposed to stainless steel or nitinol catheters.
In Vivo Evaluation of an Adenoviral Vector Encoding Canine Factor VIII: High-Level, Sustained Expression in Hemophiliac Mice (1999)

Hemophilia A is the most common severe hereditary coagulation disorder and is caused by a deficiency in blood clotting factor VIII (FVIII). Canine hemophilia A represents an excellent large animal model that closely mimicks the human disease. In previous studies, treatment of hemophiliac dogs with an adenoviral vector encoding human FVIII resulted in complete correction of the coagulation defect and high-level FVIII expression [Connelly et al. (1996). Blood 88, 3846]. However, FVIII expression was short term, limited by a strong antibody response directed against the human protein. Human FVIII is highly immunogenic in dogs, whereas the canine protein is significantly less immunogenic. Therefore, sustained phenotypic correction of canine hemophilia A may require the expression of the canine protein. In this work, we have isolated the canine FVIII cDNA and generated an adenoviral vector encoding canine FVIII. We demonstrate expression of canine FVIII in hemophiliac mice at levels 10-fold higher than those of the human protein expressed from an analogous vector. Canine FVIII expression was sustained above human therapeutic levels (50 mU/ml) for at least 1 year in hemophiliac mice.
Physics-based Models, Machine Learning, and Experiment: Towards Understanding Complex Electrode Degradation (2022)

Degradation phenomena in Li-ion batteries are highly complex, coupled, and sensitive to use history and operating conditions. In this study, we show how tracking model parameters in continuum-level physics-based models, expedited by machine learning, can be useful in testing hypotheses for degradation mechanisms. An exemplary analysis using this approach is presented for a set of lithium trivanadate ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mi>L</mml:mi> <mml:msub> <mml:mrow> <mml:mi>i</mml:mi> </mml:mrow> <mml:mrow> <mml:mi>x</mml:mi> </mml:mrow> </mml:msub> <mml:msub> <mml:mrow> <mml:mi>V</mml:mi> </mml:mrow> <mml:mrow> <mml:mn>3</mml:mn> </mml:mrow> </mml:msub> <mml:msub> <mml:mrow> <mml:mi>O</mml:mi> </mml:mrow> <mml:mrow> <mml:mn>8</mml:mn> </mml:mrow> </mml:msub> </mml:math> ) cathodes cycled over a range of current rates. A simple cell revival process is combined with the parameter estimates over the course of cycling to extract valuable insights into cathode evolution and eliminate hypothesized degradation mechanisms for these cathodes. The presented approach is expected to be broadly applicable for degradation analysis of other electrodes.
Systematic Analysis of Anti-NY-ESO-1 T Cell Responses Reveals Striking HLA-Dependent Immunodominance (2005)

s: Abstracts for the 20th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer (Primary Authors are Italicized): IMMUNE MONITORING
Measurement of flow harmonics correlations with mean transverse momentum in lead–lead and proton–lead collisions at $$\sqrt{s_{\mathrm{NN}}} = 5.02~\hbox {TeV}$$ with the ATLAS detector (2019)

Abstract To assess the properties of the quark–gluon plasma formed in ultrarelativistic ion collisions, the ATLAS experiment at the LHC measures a correlation between the mean transverse momentum and the flow harmonics. The analysis uses data samples of lead–lead and proton–lead collisions obtained at the centre-of-mass energy per nucleon pair of 5.02 TeV, corresponding to total integrated luminosities of $$22~\upmu \text {b}^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>22</mml:mn><mml:mspace/><mml:mi>μ</mml:mi><mml:msup><mml:mtext>b</mml:mtext><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math> and $$28~\text {nb}^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>28</mml:mn><mml:mspace/><mml:msup><mml:mtext>nb</mml:mtext><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math> , respectively. The measurement is performed using a modified Pearson correlation coefficient with the charged-particle tracks on an event-by-event basis. The modified Pearson correlation coefficients for the 2nd-, 3rd-, and 4th-order flow harmonics are measured in the lead–lead collisions as a function of event centrality quantified as the number of charged particles or the number of nucleons participating in the collision. The measurements are performed for several intervals of the charged-particle transverse momentum. The correlation coefficients for all studied harmonics exhibit a strong centrality evolution, which only weakly depends on the charged-particle momentum range. In the proton–lead collisions, the modified Pearson correlation coefficient measured for the 2nd-order flow harmonics shows only weak centrality dependence. The lead-lead data is qualitatively described by the predictions based on the hydrodynamical model.
ChemInform Abstract: Tetrazole is an Effective Sn‐3 Phosphate Replacement in Substrate Analogue Inhibitors of 14 kDa Phospholipase A2. (1997)

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.
Characterisation of the dynamic behaviour of lipid droplets in the early mouse embryo using adaptive harmonic generation microscopy (2010)

LD in pre-implantation mouse embryos show a previously unappreciated complexity of behaviour that is dependent not only on microtubules, but also microfilaments. Unlike LD in other systems, LD in the mouse embryo do not fuse but form aggregates. This study establishes HGM with adaptive optics as a powerful tool for the study of LD biology and provides insights into the photo-toxic effects of imaging embryos.
The Synthesis of Stable, Complex Organocesium Tetramic Acids through the Ugi Reaction and Cesium‐Carbonate‐Promoted Cascades (2015)

Abstract Two structurally unique organocesium carbanionic tetramic acids have been synthesized through expeditious and novel cascade reactions of strategically functionalized Ugi skeletons delivering products with two points of potential diversification. This is the first report of the use of multicomponent reactions and subsequent cascades to access complex, unprecedented organocesium architectures. Moreover, this article also highlights the first use of mild cesium carbonate as a cesium source for the construction of cesium organometallic scaffolds. Relativistic DFT calculations provide an insight into the electronic structure of the reported compounds.
Absorption of supersonically expanded cyclopentadiene in the vacuum-ultraviolet region (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAbsorption of supersonically expanded cyclopentadiene in the vacuum-ultraviolet regionE. Sominska, V. Kelner, and A. GedankenCite this: J. Phys. Chem. 1992, 96, 25, 10240–10242Publication Date (Print):December 1, 1992Publication History Published online1 May 2002Published inissue 1 December 1992https://pubs.acs.org/doi/10.1021/j100204a027https://doi.org/10.1021/j100204a027research-articleACS PublicationsRequest reuse permissionsArticle Views41Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Implementation of platform for long‐term evolution cell perspective resource utilization analysis (2020)

As wireless communication continues to develop in limited frequency resource environments, it is becoming important to identify the state of spectrum utilization and predict the amount needed in future. It is essential to collect reliable information for data analysis. This paper introduces a platform that enables the gathering of the scheduling information of a long-term evolution (LTE) cellular system without connecting to the network. A typical LTE terminal can confirm its assigned resource information using the configuration parameters delivered from a network. However, our platform receives and captures only the LTE signal over the air and then enables the estimation of the data relevant to scheduling for all terminals within an LTE cell. After extracting the control channel signal without loss from all LTE subframes, it detects valid downlink control information using the proposed algorithm, which is based on the error vector magnitude of depatterned symbols. We verify the reliability of the developed platform by comparing it with real data from mobile phones and service operators. The average difference in resource block utilization is only 0.28%.
Gaze Direction Modulates Finger Movement Activation Patterns in Human Cerebral Cortex (1999)

We investigated whether gaze direction modified the pattern of finger movement activation in human cerebral cortex using functional magnetic resonance imaging (MRI). Participants performed a sequential finger-tapping task or made no finger movements while maintaining gaze in the direction of the moving hand (aligned conditions) or away from the location of the moving hand. Functional MR signals, measured in the hemisphere contralateral to the moving hand, revealed finger movement-related activation in primary motor cortex, lateral and medial premotor cortex, and a wide extent of the lateral superior and inferior parietal lobules. In each area, the extent of the finger movement activation increased when static gaze was more aligned with the moving hand compared to when gaze was directed away from the moving hand. These data suggest the existence of large-scale cortical networks related to finger actions and indicate that skeletomotor processing in the cerebral cortex is consistently modified by gaze direction signals.
Uncertainty quantification of a thrombosis model considering the clotting assay PFA-100 (2021)

Mathematical models of thrombosis are currently used to study clinical scenarios of pathological thrombus formation. Most of these models involve inherent uncertainties that must be assessed to increase the confidence in model predictions and identify avenues of improvement for both thrombosis modeling and anti-platelet therapies. In this work, an uncertainty quantification analysis of a multi-constituent thrombosis model is performed considering a common assay for platelet function (PFA-100). The analysis is performed using a polynomial chaos expansion as a parametric surrogate for the thrombosis model. The polynomial approximation is validated and used to perform a global sensitivity analysis via computation of Sobol' coefficients. Six out of fifteen parameters were found to be influential in the simulation variability considering only individual effects. Nonetheless, parameter interactions are highlighted when considering the total Sobol' indices. In addition to the sensitivity analysis, the surrogate model was used to compute the PFA-100 closure times of 300,000 virtual cases that align well with clinical data. The current methodology could be used including common anti-platelet therapies to identify scenarios that preserve the hematological balance.
Establishment of an Algorithm Using prM/E- and NS1-Specific IgM Antibody-Capture Enzyme-Linked Immunosorbent Assays in Diagnosis of Japanese Encephalitis Virus and West Nile Virus Infections in Humans (2015)

The front-line assay for the presumptive serodiagnosis of acute Japanese encephalitis virus (JEV) and West Nile virus (WNV) infections is the premembrane/envelope (prM/E)-specific IgM antibody-capture enzyme-linked immunosorbent assay (MAC-ELISA). Due to antibody cross-reactivity, MAC-ELISA-positive samples may be confirmed with a time-consuming plaque reduction neutralization test (PRNT). In the present study, we applied a previously developed anti-nonstructural protein 1 (NS1)-specific MAC-ELISA (NS1-MAC-ELISA) on archived acute-phase serum specimens from patients with confirmed JEV and WNV infections and compared the results with prM/E containing virus-like particle-specific MAC-ELISA (VLP-MAC-ELISA). Paired-receiver operating characteristic (ROC) curve analyses revealed no statistical differences in the overall assay performances of the VLP- and NS1-MAC-ELISAs. The two methods had high sensitivities of 100% but slightly lower specificities that ranged between 80% and 100%. When the NS1-MAC-ELISA was used to confirm positive results in the VLP-MAC-ELISA, the specificity of serodiagnosis, especially for JEV infection, was increased to 90% when applied in areas where JEV cocirculates with WNV, or to 100% when applied in areas that were endemic for JEV. The results also showed that using multiple antigens could resolve the cross-reactivity in the assays. Significantly higher positive-to-negative (P/N) values were consistently obtained with the homologous antigens than those with the heterologous antigens. JEV or WNV was reliably identified as the currently infecting flavivirus by a higher ratio of JEV-to-WNV P/N values or vice versa. In summary of the above-described results, the diagnostic algorithm combining the use of multiantigen VLP- and NS1-MAC-ELISAs was developed and can be practically applied to obtain a more specific and reliable result for the serodiagnosis of JEV and WNV infections without the need for PRNT. The developed algorithm should provide great utility in diagnostic and surveillance activities in which test accuracy is of utmost importance for effective disease intervention.
Another Look at Pterygium Surgery with Postoperative Beta Radiation (1994)

Although complications associated with the use of beta radiation after pterygium surgery can occur, the author has found the use of beta radiation to be beneficial in preventing recurrences when used with pterygium surgery. An effective surgical regime of pterygium surgery is presented. A procedure made up of steps that tend to prevent revascularization of the operative site after pterygium surgery will decrease the recurrence rate. The use of strontium 90 and the mechanism of action of beta ray therapy in treatment of the pterygium is discussed. Few complications have occurred in > 200 surgically treated cases of pterygium with postoperative beta radiation administered with a strontium 90 applicator. No cases of radiation cataract have been observed.
Feasibility study of TaSiOx-type Att-PSM for 157-nm lithography (2002)

TaSiOx is expected to be the most effective film material for use in attenuated phase shifting masks (Att-PSMs), in terms of both its durability under irradiation and its lithographic performance in 157-nm lithography. In this study, we optimized the transmittance of 5.5 percent and evaluated the effectiveness of TaSiOx by both aerial image simulation and exposure experiment in order to evaluate the material's potential for 157 nm lithography. Through the aerial image simulation, it was confirmed that aerial image intensity of side lobes was less than half of that needed for resolving patterns by transmittance of 5.5 percent. In an exposure experiment, the resolution, depth of focus (DOF), and mask error enhancement factor (MEEF) were evaluated for hole patterns. The result of this evaluation was that we were able to fabricate a pattern of 100-nm diameter isolated holes without side lobes and obtain a better than 200-nm DOF and MEEF greater than three with a 5.5 percent TaSiOx type Att-PSM. This study has confirmed that TaSiOx type Att-PSMs have strong potential for application in the fabrication of 100-nm hole patterns by 157-nm lithography.