gebhart/patrepeval huggingface dataset:
EBV Protein BNLF2a Exploits Host Tail-Anchored Protein Integration Machinery To Inhibit TAP (2011)

EBV, the prototypic human γ(1)-herpesvirus, persists for life in infected individuals, despite the presence of vigorous antiviral immunity. CTLs play an important role in the protection against viral infections, which they detect through recognition of virus-encoded peptides presented in the context of HLA class I molecules at the cell surface. The viral peptides are generated in the cytosol and are transported into the endoplasmic reticulum (ER) by TAP. The EBV-encoded lytic-phase protein BNLF2a acts as a powerful inhibitor of TAP. Consequently, loading of antigenic peptides onto HLA class I molecules is hampered, and recognition of BNLF2a-expressing cells by cytotoxic T cells is avoided. In this study, we characterize BNLF2a as a tail-anchored (TA) protein and elucidate its mode of action. Its hydrophilic N-terminal domain is located in the cytosol, whereas its hydrophobic C-terminal domain is inserted into membranes posttranslationally. TAP has no role in membrane insertion of BNLF2a. Instead, Asna1 (also named TRC40), a cellular protein involved in posttranslational membrane insertion of TA proteins, is responsible for integration of BNLF2a into the ER membrane. Asna1 is thereby required for efficient BNLF2a-mediated HLA class I downregulation. To optimally accomplish immune evasion, BNLF2a is composed of two specialized domains: its C-terminal tail anchor ensures membrane integration and ER retention, whereas its cytosolic N terminus accomplishes inhibition of TAP function. These results illustrate how EBV exploits a cellular pathway for TA protein biogenesis to achieve immune evasion, and they highlight the exquisite adaptation of this virus to its host.
Mutation Analysis for Heterozygote Detection and the Prenatal Diagnosis of Cystic Fibrosis (1990)

The cystic fibrosis gene was recently cloned, and a three-base deletion removing phenylalanine 508 from the coding region was identified as the mutation on the majority of cystic fibrosis chromosomes. We used the polymerase chain reaction and hybridization with allele-specific oligonucleotides to analyze the presence or absence of this mutation on 439 cystic fibrosis chromosomes and 433 normal chromosomes from non-Ashkenazic white families. This mutation was present on 75.8 percent of the cystic fibrosis chromosomes. Using the DNA markers XV-2c and KM-19, we found that 96 percent of cystic fibrosis chromosomes with the mutation had a single DNA haplotype that occurs frequently with cystic fibrosis chromosomes. This haplotype was also found on 54 percent of the cystic fibrosis chromosomes without the three-base deletion. The three-base deletion was found on only 30.3 percent of cystic fibrosis chromosomes from Ashkenazic families, although the common cystic fibrosis haplotype was present on 97 percent of cystic fibrosis chromosomes from Ashkenazic families. The ability to detect the common mutation causing cystic fibrosis represents a major improvement in prenatal diagnosis and heterozygote detection, particularly in families in which no DNA sample is available from the affected child, and provides an improved method of testing for spouses of carriers of cystic fibrosis. Mutation analysis introduces the possibility of population-based screening programs for carriers, which on the basis of the sample in this study, would currently identify about 57 percent of the non-Ashkenazic white couples at risk.
Corrections to Rational Modification of a Candidate Cancer Drug for Use against Chagas Disease (2009)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrections to Rational Modification of a Candidate Cancer Drug for Use against Chagas DiseaseJames M. Kraus, Christophe L. M. J. Verlinde, Mandana Karimi, Galina I. Lepesheva, Michael H. Gelb*, and Frederick S. Buckner*Cite this: J. Med. Chem. 2009, 52, 14, 4549Publication Date (Web):June 2, 2009Publication History Published online2 June 2009Published inissue 23 July 2009https://pubs.acs.org/doi/10.1021/jm900650shttps://doi.org/10.1021/jm900650scorrectionACS PublicationsCopyright © 2009 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views945Altmetric-Citations1LEARN 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 PDF (540 KB) Get e-AlertscloseSUBJECTS:Cancer,Modification Get e-Alerts
Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative (2022)

Abstract Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p=5.41×10 −7 ). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights. Author Summary COVID-19 clinical outcomes vary immensely, but a patient’s genetic make-up is an important determinant of how they will fare against the virus. While many genetic variants commonly found in the populations were previously found to be contributing to more severe disease by the COVID-19 Host Genetics Initiative, it isn’t clear if more rare variants found in less individuals could also play a role. This is important because genetic variants with the largest impact on COVID-19 severity are expected to be rarely found in the population, and these rare variants require different technologies to be studies (usually whole-exome or whole-genome sequencing). Here, we combined sequencing results from 21 cohorts across 12 countries to perform a rare variant association study. In an analysis comprising 5,085 participants with severe COVID-19 and 571,737 controls, we found that the gene for toll-like receptor 7 ( TLR7 ) on chromosome X was an important determinant of severe COVID-19. Importantly, despite being found on a sex chromosome, this observation was consistent across both sexes.
Neural Coding in Spiking Neural Networks: A Comparative Study for Robust Neuromorphic Systems (2021)

Various hypotheses of information representation in brain, referred to as neural codes, have been proposed to explain the information transmission between neurons. Neural coding plays an essential role in enabling the brain-inspired spiking neural networks (SNNs) to perform different tasks. To search for the best coding scheme, we performed an extensive comparative study on the impact and performance of four important neural coding schemes, namely, rate coding, time-to-first spike (TTFS) coding, phase coding, and burst coding. The comparative study was carried out using a biological 2-layer SNN trained with an unsupervised spike-timing-dependent plasticity (STDP) algorithm. Various aspects of network performance were considered, including classification accuracy, processing latency, synaptic operations (SOPs), hardware implementation, network compression efficacy, input and synaptic noise resilience, and synaptic fault tolerance. The classification tasks on Modified National Institute of Standards and Technology (MNIST) and Fashion-MNIST datasets were applied in our study. For hardware implementation, area and power consumption were estimated for these coding schemes, and the network compression efficacy was analyzed using pruning and quantization techniques. Different types of input noise and noise variations in the datasets were considered and applied. Furthermore, the robustness of each coding scheme to the non-ideality-induced synaptic noise and fault in analog neuromorphic systems was studied and compared. Our results show that TTFS coding is the best choice in achieving the highest computational performance with very low hardware implementation overhead. TTFS coding requires 4x/7.5x lower processing latency and 3.5x/6.5x fewer SOPs than rate coding during the training/inference process. Phase coding is the most resilient scheme to input noise. Burst coding offers the highest network compression efficacy and the best overall robustness to hardware non-idealities for both training and inference processes. The study presented in this paper reveals the design space created by the choice of each coding scheme, allowing designers to frame each scheme in terms of its strength and weakness given a designs' constraints and considerations in neuromorphic systems.
Optimizing Battery Sizing and Vehicle Lightweighting for an Extended Range Electric Vehicle (2011)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;In designing vehicles with significant electric driving range, optimizing vehicle energy efficiency is a key requirement to maximize the limited energy capacity of the onboard electrochemical energy storage system. A critical factor in vehicle energy efficiency is the vehicle mass. Optimizing mass allows for the possibility of either increasing electric driving range with a constant level of electrochemical energy storage or holding the range constant while reducing the level of energy storage, thus reducing storage cost. In this paper, a methodology is outlined to study the tradeoff between the battery cost savings achieved by vehicle mass reduction for a constant electric driving range and the cost associated with lightweighting a vehicle. This methodology enables informed business decisions about the available engineering options for lightweighting early in the vehicle development process.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;The methodology was applied to a compact extended-range electric vehicle (EREV) concept. Detailed design and analysis was carried out to develop a vehicle concept which would achieve substantial vehicle mass reduction over the baseline design. This work resulted in the identification of many mass-reduction enablers and incorporated mass reduction potentials as well as cost estimates for implementing the enablers. In addition, a study was conducted to determine the cost of a battery as a function of vehicle mass for different generations of battery technology. Charts of the cost of lightweighting for all the enablers as well as the battery cost savings as a function of mass reduction were developed with and without the influence of mass decompounding. These charts were used to determine how much lightweighting is practical for various generations of battery technology.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Results from the study indicate that there is generally a point at which the cumulative cost of mass-reduction enablers exceeds the benefit in battery cost savings. For early generations of battery technology where storage costs are relatively high, it makes more sense to spend money on vehicle lightweighting; however, as new battery technologies emerge (with lower cost and higher performance) the more costly vehicle lightweighting measures become uneconomical.&lt;/div&gt;&lt;/div&gt;
In Vivo Fluorescence Lifetime Imaging Monitors Binding of Specific Probes to Cancer Biomarkers (2012)

One of the most important factors in choosing a treatment strategy for cancer is characterization of biomarkers in cancer cells. Particularly, recent advances in Monoclonal Antibodies (MAB) as primary-specific drugs targeting tumor receptors show that their efficacy depends strongly on characterization of tumor biomarkers. Assessment of their status in individual patients would facilitate selection of an optimal treatment strategy, and the continuous monitoring of those biomarkers and their binding process to the therapy would provide a means for early evaluation of the efficacy of therapeutic intervention. In this study we have demonstrated for the first time in live animals that the fluorescence lifetime can be used to detect the binding of targeted optical probes to the extracellular receptors on tumor cells in vivo. The rationale was that fluorescence lifetime of a specific probe is sensitive to local environment and/or affinity to other molecules. We attached Near-InfraRed (NIR) fluorescent probes to Human Epidermal Growth Factor 2 (HER2/neu)-specific Affibody molecules and used our time-resolved optical system to compare the fluorescence lifetime of the optical probes that were bound and unbound to tumor cells in live mice. Our results show that the fluorescence lifetime changes in our model system delineate HER2 receptor bound from the unbound probe in vivo. Thus, this method is useful as a specific marker of the receptor binding process, which can open a new paradigm in the "image and treat" concept, especially for early evaluation of the efficacy of the therapy.
All optical regenerator using a semiconductor laser amplifier in a loop mirror configuration (1993)

All optical repeaters, which retime optical data signals, are essential components for photonic switching systems. In general these regenerators operate as follows. The optical data signal is combined with an optical clock signal (synchronized with the data signal) and both are coupled into a decision gate (AND gate). Decision gates based on a SEED (data rate 5 kbit/s [1]), on a bistable Fabry-Perot amplifier (data rate 140 Mbit/s [2]), on a bistable three electrode DFB laser diode (data rate 200 Mbit/s [3]) and on a nonlinear Sagnac interferometer switch (data rate 3 Gbit/s [4]) have been demonstrated. In this paper we report on a new kind of decision gate based on a semiconductor laser amplifier (SLA) in a loop mirror (SLALOM) configuration. This decision gate was operated at 1 Gbit/s. It exhibits a contrast ratio of better than 20 dB, no polarization dependence for the data signals, and it enables simultaneously all-optical wavelength conversion over a wavelength range of about 60 nm. As compared to the nonlinear Sagnac interferometer switch, it requires optical powers for switching, which are about three orders of magnitude lower. It is very compact and offers the advantage of a possible integration on a chip.
Iterative reweighted algorithms for sparse signal recovery with temporally correlated source vectors (2011)

Iterative reweighted algorithms, as a class of algorithms for sparse signal recovery, have been found to have better performance than their non-reweighted counterparts. However, for solving the problem of multiple measurement vectors (MMVs), all the existing reweighted algorithms do not account for temporal correlations among source vectors and thus their performance degrades significantly in the presence of the correlations. In this work we propose an iterative reweighted sparse Bayesian learning (SBL) algorithm exploiting the temporal correlations, and motivated by it, we propose a strategy to improve existing reweighted ℓ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> algorithms for the MMV problem, i.e. replacing their row norms with Mahalanobis distance measure. Simulations show that the proposed reweighted SBL algorithm has superior performance, and the proposed improvement strategy is effective for existing reweighted ℓ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> algorithms.
Correction to “Evidence of Preformed Lewis Acid–Base and Wheland-Type Complexes Acting as Dopants for p-Type Conjugated Polymers” (2023)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to "Evidence of Preformed Lewis Acid–Base and Wheland-Type Complexes Acting as Dopants for p-Type Conjugated Polymers"Tushita MukhopadhyayaTushita MukhopadhyayaMore by Tushita Mukhopadhyaya, Taein LeeTaein LeeMore by Taein Lee, Connor GanleyConnor GanleyMore by Connor Ganley, Paulette ClancyPaulette ClancyMore by Paulette Clancyhttps://orcid.org/0000-0002-0468-6420, and Howard E. Katz*Howard E. KatzMore by Howard E. Katzhttps://orcid.org/0000-0002-3190-2475Cite this: ACS Appl. Polym. Mater. 2023, 5, 2, 1624Publication Date (Web):January 25, 2023Publication History Received3 January 2023Published online25 January 2023Published inissue 10 February 2023https://pubs.acs.org/doi/10.1021/acsapm.3c00014https://doi.org/10.1021/acsapm.3c00014correctionACS PublicationsCopyright © 2023 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views332Altmetric-Citations-LEARN 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 PDF (876 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Adaptive Kalman Filter-Based Yaw Rate Estimation Using Accelerometers and Wheel Speed Sensors (2009)

This paper presents a kinematic yaw rate estimator which combines measurements obtained from a pair of accelerometers and ABS wheel speed sensors of the non-driven wheels. The Extended Kalman Filter methodology has been used for realization of this sensor fusion-based estimator. The estimator adapts to variations in reliability levels of individual sensors. The estimator performance is validated and corresponding estimation errors are analyzed by computer simulations for different driving maneuvers.
Recent Progress of Patterned Media (2007)

Recent progress in the development of patterned magnetic recording media is presented, focusing on the results of patterned media fabricated by a self-assembled mask process. Several issues such as fabrication process, flyability, and signal processing have been discussed so far. However, recent progress seems to resolve these problems. A fabrication process using nano-imprint lithography is a possible solution in terms of productivity. Good results for flyability have been reported for discrete track recording media. Certain advantages with respect to signal processing have been reported. Although problems remain to be resolved, patterned media is expected to be commercialized following the introduction of the discrete track media, as a high density perpendicular magnetic recording media.
The remarkably invariant interaction energies of lithium first‐row compounds with water and with ammonia (1986)

Abstract Solvation energies of lithium first‐row compounds LiX (X  H, Li, BeH, BH 2 , CH 3 , NH 2 , OH, F) and of the lithium cation with the model solvents, water and ammonia, have been calculated ab inito (MP2/6‐31 + G * //6‐31G * with zero‐point vibrational energy corrections at 3‐21G//3‐21G). The solvation energies are found to be remarkably constant: −18.0 ± 1.2 and −21.5 ± 1.3 kcal/mol for the hydrates and ammonia solvates, respectively. This independence on the nature of X is due largely to the ionic character of the LiX compounds (dipole moments 4.7–6.6 debye). The unexpectedly high solvation energies of the lithium molecule (−14.3 and −17.8 kcal/mol, respectively) are due to the polarizability of Li 2 . At the same level, the lithium cation has interaction energies with H 2 O and NH 3 of −34.1 and −39.7 kcal/mol, respectively. For the hydrates of LiOH and LiF cyclic structures with hydrogen bonds and somewhat increased solvation energies also are described.
An Advanced GNU Radio Receiver of IEEE 802.15.4 OQPSK Physical Layer (2021)

In this article, we present an advanced coherent receiver for the IEEE 802.15.4 offset quadrature phase-shift keying (OQPSK) physical layer and provide an open-source implementation in the GNU Radio framework. Simulation and field test results show that the proposed receiver achieves about 11-dB power gain over an existing GNU Radio receiver, which treats OQPSK as minimum-shift-keying (MSK) for low-complexity processing. While suitable modules can be added to the MSK-based receiver for performance enhancement, the proposed receiver still maintains a 6-dB power gain. The proposed coherent receiver is attractive for IoT applications where a powerful software-defined-radio (SDR)-based gateway is deployed to interact with various sensors.
Renal inner medullary choline dehydrogenase activity: characterization and modulation (1989)

Betaine belongs to the trimethylamine class of osmolytes (osmotically active substances believed to play an important role in cell volume homeostasis) and has recently been identified in the inner medulla of the mammalian kidney. Trimethylamines accumulate in the renal inner medulla during hypertonic stress, and betaine content in the inner medulla has been shown recently to increase during hypernatremia, yet the mechanisms governing the modulation of trimethylamine content and, in particular, of betaine content are not well understood. In this study, we demonstrate the presence of choline dehydrogenase activity in the renal inner medullas of three separate rat strains. Choline dehydrogenase is the enzyme that catalyzes the first of two successive oxidation steps in the biosynthetic conversion of choline to betaine. The presence of choline dehydrogenase activity in the inner medulla suggests that betaine accumulation in the inner medulla may result, at least in part, through in situ synthesis. The Km and Vmax of the reaction in the inner medullas of Long-Evans rats are 4.7 +/- 0.5 mM and 36.9 +/- 5.0 nmol.mg protein-1.min-1, respectively. These values are similar to the characteristics of choline dehydrogenase in mammalian liver. During hypernatremia, when betaine content of the inner medulla has been shown to increase 1.5-fold, choline dehydrogenase activity remains unchanged (or slightly increased), whereas enzyme activity in the cortex increases approximately 50%. Possible mechanisms of inner medullary betaine accumulation are discussed.