gebhart/patrepeval huggingface dataset:
Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names (2014)

Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information's (NCBI's) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [<virus name> (<strain>)/<isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation>], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.
Carbon-Containing Nanocomposite Materials for Energy Storage (2012)

Gleb Yushin presented a lecture at the Nano@Tech Meeting on February 14, 2012 at 12 noon in room 1116 of the Marcus Nanotechnology Building.
Understanding and Manipulating Helical Nanofilaments in Binary Systems with Achiral Dopants (2022)

Here, we report the relationship between helical pitch of the helical nanofilament (HNF) phase formed by bent-core molecule NOBOW and the concentration of achiral dopants 5CB and octane, using linearly polarized resonant soft X-ray scattering (RSoXS). Utilizing theory-based simulation, which fits well with the experiments, the molecular helices in the filament were probed and the superstructure of helical 5CB directed by groove of HNFs was observed. Quantitative pitch determination with RSoXS reveals that helical pitch variation is related to 5CB concentration with no temperature dependence. Doping rodlike immiscible 5CB led to a pitch shortening of up to 30%, which was attributed to a change in interfacial tension. By shedding light not only on phase behavior of binary systems but also enabling control over pitch length, our work may benefit various applications of HNF-containing binary systems, including optical rotation devices, circularly polarized light emitters, and chirality transfer agents.
Multimodal Affect Recognition Using Temporal Convolutional Neural Networks (2022)

The field of affective computing has gained significant attention from researchers in the last decade due to the wide variety of applications that can benefit from the technology. Nonetheless, recognizing spontaneous and subtle emotions remains a challenging problem for computers. In this work, we present a model for automatically recognizing human emotions using audio and video features. As opposed to most of the recent work that employs Recurrent Neural Network (RNN) models for emotion recognition from audio and video, we applied a Temporal Convolutional Network (TCN) to model the time-series information. To compare the RNN- and TCN-based networks, we configured the hyperparameters of the models using Gaussian processes and Bayesian analysis to achieve a fair evaluation. Our experimental results show that our TCN-based model outperforms all tested RNN-based models, yielding a concordance correlation coefficient of 0.7440 (vs. 0.7269) on valence and 0.7557 (vs. 0.7255) on arousal for the SEWA dataset.
Transverse mode selection in laser resonators using volume Bragg gratings (2014)

Power scaling of high power laser resonators is limited due to several nonlinear effects. Scaling to larger mode areas can offset these effects at the cost of decreased beam quality, limiting the brightness that can be achieved from the multi-mode system. In order to improve the brightness from such multi-mode systems, we present a method of transverse mode selection utilizing volume Bragg gratings (VBGs) as an angular filter, allowing for high beam quality from large mode area laser resonators. An overview of transverse mode selection using VBGs is given, with theoretical models showing the effect of the angular selectivity of transmitting VBGs on the resonator modes. Applications of this ideology to the design of laser resonators, with cavity designs and experimental results presented for three types of multimode solid state lasers: a Nd:YVO4 laser with 1 cm cavity length and 0.8 mm diameter beam with an M<sup>2</sup> of 1.1, a multimode diode with diffraction limited far field divergence in the slow axis, and a ribbon fiber laser with 13 cores showing M<sup>2</sup> improved from 11.3 to 1.5.
Genotoxicity of different nanocarriers: possible modifications for the delivery of nucleic acids. (2013)

The prevention of cyto- and genotoxicity of nanocarriers is an important task in nanomedicine. In the present investigation, we, at the first time using similar experimental conditions, compared genotoxicity of nanocarriers with different composition, architecture, size, molecular weight and charge. Poly(ethylene glycol) polymers, neutral and cationic liposomes, micelles, poly(amindo amine) and poly(propyleneimine) dendrimers, quantum dots, mesoporous silica, and supermagnetic iron oxide (SPIO) nanoparticles were studied. All nanoparticles were used in non-cytotoxic concentrations. However, even in these concentrations, positively charged cationic liposomes, dendrimers, and SPIO nanoparticles induced genotoxicity leading to the significant formation of micronuclei in cells. Negatively charged and neutral nanocarriers were not genotoxic. A strong positive correlation was found between the number of formed micronuclei and the positive charge of nanocarriers. We proposed modifications of both types of dendrimers and SPIO nanoparticles that substantially decreased their genotoxicity and allowed for an efficient intracellular delivery of nucleic acids.
Recombination Behaviour of Stacking Faults in SiC p-i-n Diodes (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Management of Primary Immune Thrombocytopenia in Pregnancy (2023)

Platelet counts often fall during pregnancy; decreases below 50×103 per cubic millimeter may be due to an autoimmune cause. Detection and management of immune thrombocytopenia may be lifesaving.
2021 ESC Guidelines on cardiac pacing and cardiac resynchronization therapy (2021)

The ESC Guidelines represent the views of the ESC and were produced after careful consideration of the scientific and medical knowledge and the evidence available at the time of their publication. The ESC is not responsible in the event of any contradiction, discrepancy, and/or ambiguity between the ESC Guidelines and any other official recommendations or guidelines issued by the relevant public health authorities, in particular in relation to good use of healthcare or therapeutic strategies. Health professionals are encouraged to take the ESC Guidelines fully into account when exercising their clinical judgement, as well as in the determination and the implementation of preventive, diagnostic, or therapeutic medical strategies; however, the ESC Guidelines do not override, in any way whatsoever, the individual responsibility of health professionals to make appropriate and accurate decisions in consideration of each patient's health condition and in consultation with that patient and, where appropriate and/or necessary, the patient's caregiver. Nor do the ESC Guidelines exempt health professionals from taking into full and careful consideration the relevant official updated recommendations or guidelines issued by the competent public health authorities, in order to manage each patient's case in light of the scientifically accepted data pursuant to their respective ethical and professional obligations. It is also the health professional's responsibility to verify the applicable rules and regulations relating to drugs and medical devices at the time of prescription.
Radio Wave Propagation in Perpendicular Streets of Urban Street Grid for Microcellular Communications. Part I: Channel Modeling (2003)

This paper proposes a spatial variant wideband propagation model for perpendicular street of urban street grid. Analytical expression of the spatial variant multi-ray channel transfer function is derived. The model provides characteristics of each ray in explicit expressions. The ray characteristics are given in terms of complex amplitude for both vertical and horizontal polarizations, path length, angle of arrival and departure. A set membership criteria is proposed to determine the coupling radio paths. The proposed model is not only capable in providing macroscopic quantities like mean field values and mean delay spread, but also the full wideband channel information, i.e., space dependent complex channel responses with a high time dispersion resolution. The proposed model can be used for studying different propagation problems in urban street grid for microcellular communications with applications e.g., antenna diversity techniques, multi-input multi-output (MIMO) channel capacity analysis, etc.
Heteromerization of Innexin Gap Junction Proteins Regulates Epithelial Tissue Organization inDrosophila (2006)

Gap junctions consist of clusters of intercellular channels, which enable direct cell-to-cell communication and adhesion in animals. Whereas deuterostomes, including all vertebrates, use members of the connexin and pannexin multiprotein families to assemble gap junction channels, protostomes such as Drosophila and Caenorhabditis elegans use members of the innexin protein family. The molecular composition of innexin-containing gap junctions and the functional significance of innexin oligomerization for development are largely unknown. Here, we report that heteromerization of Drosophila innexins 2 and 3 is crucial for epithelial organization and polarity of the embryonic epidermis. Both innexins colocalize in epithelial cell membranes. Innexin3 is mislocalized to the cytoplasm in innexin2 mutants and is recruited into ectopic expression domains defined by innexin2 misexpression. Conversely, RNA interference (RNAi) knockdown of innexin3 causes mislocalization of innexin2 and of DE-cadherin, causing cell polarity defects in the epidermis. Biochemical interaction studies, surface plasmon resonance analysis, transgenesis, and biochemical fractionation experiments demonstrate that both innexins interact via their C-terminal cytoplasmic domains during the assembly of heteromeric channels. Our data provide the first molecular and functional demonstration that innexin heteromerization occurs in vivo and reveal insight into a molecular mechanism by which innexins may oligomerize into heteromeric gap junction channels.
Homocysteine in relation to cognitive performance in pathological and non-pathological conditions (2005)

Elevated serum homocysteine has been associated with increased risk of Alzheimer's disease. Furthermore, elevated homocysteine levels are related to cognitive dysfunction in the elderly. The aim of the present study was to explore the disease specificity of the relation between serum total homocysteine levels and cognitive function. For this, we summarize data from several studies on homocysteine levels in both normal and pathological conditions performed in our laboratories and evaluate possible mechanisms of effects of elevated homocysteine levels in the central nervous system. Total homocysteine levels were measured in serum of: 1) healthy aging individuals; 2) patients with Alzheimer's and Parkinson's disease and patients with other cognitive disorders; and 3) patients with multiple sclerosis. Increased serum homocysteine concentration was related to worse cognitive performance over a 6-year period in the normal aging population (r=-0.36 to -0.14, p<0.01 for the Word learning tests; r=0.76, p<0.05 for the Stroop Colored Word test). Homocysteine was only increased in patients with Parkinson's disease on L-Dopa therapy (18.9 vs. 16.5 micromol/L in healthy controls), and not in dementia patients. Homocysteine was elevated in patients with progressive multiple sclerosis (15.0 micromol/L, n=39, compared to 12.0 micromol/L in 45 controls) and correlated to both cognitive and motor function (r=-0.33 and -0.33, p<0.05, respectively). The relationship between homocysteine and cognitive function in non-pathological and pathological situations indicates that changes in its levels may play a role in cognitive functioning in a broad spectrum of conditions.
Novel therapeutics for systemic lupus erythematosus (2006)

Purpose of review This review provides an update on recently explored therapies in systemic lupus erythematosus and introduces novel therapeutic approaches under consideration. Recent advances in our understanding of systemic lupus are highlighted as well, as these must now inform consideration of therapeutics. Recent findings Many therapeutic strategies have been shown to be beneficial in murine models of lupus. Compounds that inhibit cellular signaling in response to autoantigens or other triggers and protocols that reconstitute the immune repertoire to diminish autoreactivity are now entering clinical trials. Summary Requirements for novel approaches in lupus include improved efficacy and lower toxicity than current therapies, with the goal to reduce tissue damage while preserving immunocompetence.
An Auctioning Reputation System Based on Anomaly Detection (2005)

Existing reputation systems used by online auction houses do not address the concern of a buyer shopping for commodities—find ing a good bargain. These systems do not provide information on the practices adopted by sellers to ensure profitable auctions. These practices may be legitimate, like imposing a minimum starting bid on an auction, or fraudulent, like using colluding bidders t o inflate the final price in a practice known as shilling. We develop a reputation system to help buyers identify sellers whose auctions seem price-inflated. Our reputation system i s based upon models that characterize sellers according to statist ical metrics related to price inflation. We combine the statistical m odels with anomaly detection techniques to identify the set of suspicious sellers. The output of our reputation system is a set of value s for each seller representing the confidence with which the syste m can say that the auctions of the seller are price-inflated. We evaluate our reputation system on 604 high-volume sellers who posted 37,525 auctions on eBay. Our system automatically pinpoints sellers whose auctions contain potential shill b idders. When we manually analyze these sellers’ auctions, we find that man y winning bids are at about the items’ market values, thus undercu tting a buyer’s ability to find a bargain and demonstrating the effec tiveness of our reputation system.
Data Supplement from Neuronal Pentraxin 2 Supports Clear Cell Renal Cell Carcinoma by Activating the AMPA-Selective Glutamate Receptor-4 (2023)

&lt;p&gt;Supplementary Figure 3. (A) QPCR for GluR4 mRNA in A498 cells infected with one of four lentiviral constructs against GluR4 (sh925, sh1676, sh2145, sh2285) as compared to NT control. (B) Western blot analysis for GluR4 expression in all four A498 GluR4 shRNA clones compared to NT control. Protein expression level quantitation is normalized to β-actin. (C) Proliferation of A498 GluR4 shRNA clones compared to NT control.&lt;/p&gt;
Development of Proteolysis Targeting Chimeras as a Target for Hepatocellular Carcinoma (2020)

Proteasomes are novel targets for cancer treatments and can be used for targeted protein degradation. Proteolysis-Targeting Chimeras, or PROTACs, contain a region that binds to a target protein linked to a hydrophobic tag which binds to E3 ligase. PROTACs are designed to degrade specific proteins of interest by binding to the target protein, resulting in poly-ubiquitination and flagging of the protein for degradation. Hepatocellular carcinoma is one of the most common types of liver cancers in adults and is the third leading cause of cancer death in the world. Androgen receptors have been studied as potential targets for the treatment of hepatocellular carcinoma. Studies have shown that AR agonists can be incorporated into PROTACs to recruit the receptor for degradation. Proteasome inhibitors can also be used in the treatment of cancer, but they cause an accumulation of pro-apoptotic proteins which leads to cell death, rather than causing the degradation of proteins. These molecules were studied when designing PROTACs as a different mechanism to target the proteasome. PROTACs can be synthesized using CLICK chemistry, which is a method that can be used for conjugation reactions to rapidly create these chimeras while generating byproducts that can be easily removed. Research indicates that changes to the linker region and the linker attachment site of the PROTAC can affect the biological activity of these molecules. A review of the current literature on PROTAC development has aided in the design of novel degraders. The application of these design principles will be discussed for a variety of androgen receptor agonists.
A Game Theoretic Solution for Exploiting Multiuser Diversity in Cooperative Slotted Aloha (2007)

In multiuser systems, multiuser diversity gains can be achieved by assigning channels to users with higher channel quality. To avoid the extensive information exchange required for centralized approaches, we propose a distributed fair pricing strategy for a slotted ALOHA system in which users act selfishly to improve their own utilities. Based on a game theoretic framework, we show that multiuser diversity gains can be achieved by appropriately designing the Nash equilibrium thresholds for the selfish users, such as to preserve the throughput and revenue achieved in the centralized schemes. The network enforces fairness among different users by employing a pricing policy that favors equal access probabilities. Our simulation results show significant multiuser diversity gains achieved in terms of energy consumption and/or spectral efficiency.
16‐2: Distinguished Student Paper: Characterization of Electronic Displays using Advanced CMOS Single Photon Avalanche Diode Image Sensors (2018)

Advanced CMOS Single Photon Avalanche Diode Arrays have the potential to reveal characteristics of electronic display panels that have, until now, been extremely challenging or impossible to measure routinely. We demonstrate the use of a CMOS SPAD array to make optical measurements of pixels of an OLED microdisplay at very high sampling rates, very low light levels and over a very wide dynamic range.
Focal adhesion membrane is dotted with protein islands and partitioned for molecular hop diffusion (2021)

Abstract Using the ultrafast camera system and new theories for hop diffusion described in the companion paper, we for the first time demonstrated that membrane molecules undergo hop diffusion among the compartments in the bulk basal plasma membrane (PM), with virtually the same compartment sizes (108 nm) as those in the bulk apical PM and the same dwell lifetimes within a compartment (10 and 24 ms for the phospholipid and transferrin receptor, respectively), suggesting that the basic structures and molecular dynamics are very similar in the bulk regions of the apical and basal PMs. Ultrafast PALM and single-molecule imaging revealed that the focal adhesion (FA) is mostly a fluid membrane, partitioned into ∼74-nm compartments where transferrin receptor and β3 integrin undergo hop diffusion, and that the FA membrane is sparsely dotted with 51-nm diameter paxillin islands, where many other FA proteins probably assemble (compartmentalized archipelago model). β3 integrin intermittently associates with the paxillin islands, dynamically linking them to the extracellular matrix. Summary An ultrafast camera with single fluorescent-molecule sensitivities developed by Fujiwara et al. reveals that the focal adhesion membrane is dotted with protein islands and partitioned for molecular hop diffusion, and integrin β3 molecules become temporarily immobilized at the islands.
Mild and Selective Sodium Azide Mediated Cleavage of p-Nitrobenzoic Esters (2001)

A mild and selective cleavage of p-nitrobenzoic esters by sodium azide in methanol is reported. This new methodology is mild enough for use with acid- or base-sensitive compounds. No elimination byproducts are formed. Fmoc- and trifluoroacetyl-amino protecting groups, benzyl esters, and ethyl esters remain unaffected. Less reactive compounds are discussed in terms of steric factors, and yields are increased by altering the azide solvation.
From the molecule to an expanded I-VII semiconductor quantum superlattice: silver, sodium halo-sodalites (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFrom the molecule to an expanded I-VII semiconductor quantum superlattice: silver, sodium halo-sodalitesAndreas Stein, Geoffrey A. Ozin, and Galen D. StuckyCite this: J. Am. Chem. Soc. 1990, 112, 2, 904–905Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://pubs.acs.org/doi/10.1021/ja00158a080https://doi.org/10.1021/ja00158a080research-articleACS PublicationsRequest reuse permissionsArticle Views154Altmetric-Citations35LEARN 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 optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts