gebhart/patrepeval huggingface dataset:
Design of a Companion Bioinformatic Tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants (2020)

Abstract Background Tracking the genetic variability of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is a crucial challenge. Mainly to identify target sequences in order to generate robust vaccines and neutralizing monoclonal antibodies, but also to track viral genetic temporal and geographic evolution and to mine for variants associated with reduced or increased disease severity. Several online tools and bioinformatic phylogenetic analyses have been released, but the main interest lies in the Spike protein, which is the pivotal element of current vaccine design, and in the Receptor Binding Domain, that accounts for most of the neutralizing the antibody activity. Methods Here, we present an open-source bioinformatic protocol, and a web portal focused on SARS-CoV-2 single mutations and minimal consensus sequence building as a companion vaccine design tool. Furthermore, we provide immunogenomic analyses to understand the impact of the most frequent RBD variations. Results Results on the whole GISAID sequence dataset at the time of the writing (October 2020) reveals an emerging mutation, S477N, located on the central part of the Spike protein Receptor Binding Domain, the Receptor Binding Motif. Immunogenomic analyses revealed some variation in mutated epitope MHC compatibility, T-cell recognition, and B-cell epitope probability for most frequent human HLAs. Conclusions This work provides a framework able to track down SARS-CoV-2 genomic variability.
Bioabsorbable polymer optical waveguides for deep-tissue photomedicine (2016)

Advances in photonics have stimulated significant progress in medicine, with many techniques now in routine clinical use. However, the finite depth of light penetration in tissue is a serious constraint to clinical utility. Here we show implantable light-delivery devices made of bio-derived or biocompatible, and biodegradable polymers. In contrast to conventional optical fibres, which must be removed from the body soon after use, the biodegradable and biocompatible waveguides may be used for long-term light delivery and need not be removed as they are gradually resorbed by the tissue. As proof of concept, we demonstrate this paradigm-shifting approach for photochemical tissue bonding (PTB). Using comb-shaped planar waveguides, we achieve a full thickness (>10 mm) wound closure of porcine skin, which represents ∼ 10-fold extension of the tissue area achieved with conventional PTB. The results point to a new direction in photomedicine for using light in deep tissues.
TIPPING THE BALANCE WITH DIELECTRO- PHORETIC FORCES - AN ELECTRIC DETERMI- NISTIC LATERAL DISPLACEMENT DEVICE (2008)

We present experimental results and simulations on a simple method for tunable particle separation based on a combination of Deterministic Lateral Displacement (DLD) and Insulator Based Dielectrophoresis (I-DEP). Rather than deriving its tunability from its elastic properties[1], our present device uses an applied AC field to perturb the particle trajectories in the pressure-driven flow and is thereby capable of scanning the critical size over a range of factor two. Potential benefits include: extended dynamic range, facilitated fabrication and less clogging for given particle sizes, and combination of the precision afforded by DLD with the versatility of DEP.
Statistical physics methods for sparse graph codes (2009)

This thesis deals with the asymptotic analysis of coding systems based on sparse graph codes. The goal of this work is to analyze the decoder performance when transmitting over a general binary-input memoryless symmetric-output (BMS) channel. We consider the two most fundamental decoders, the optimal maximum a posteriori (MAP) decoder and the sub-optimal belief propagation (BP) decoder. The BP decoder has low-complexity and its performance analysis is, hence, of great interest. The MAP decoder, on the other hand, is computationally expensive. However, the MAP decoder analysis provides fundamental limits on the code performance. As a result, the MAP-decoding analysis is important in designing codes which achieve the ultimate Shannon limit. It would be fair to say that, over the binary erasure channel (BEC), the performance of the MAP and BP decoder has been thoroughly understood. However, much less is known in the case of transmission over general BMS channels. The combinatorial methods used for analyzing the case of BEC do not extend easily to the general case. The main goal of this thesis is to advance the analysis in the case of transmission over general BMS channels. To do this, we use the recent convergence of statistical physics and coding theory. Sparse graph codes can be mapped into appropriate statistical physics spin-glass models. This allows us to use sophisticated methods from rigorous statistical mechanics like the correlation inequalities, interpolation method and cluster expansions for the purpose of our analysis. One of the main results of this thesis is that in some regimes of noise, the BP decoder is optimal for a typical code in an ensemble of codes. This result is a pleasing extension of the same result for the case of BEC. An important consequence of our results is that the heuristic predictions of the replica and cavity methods of spin-glass theory are correct in the realm of sparse graph codes.
Heterogenized Gold Complexes: Recoverable Catalysts for Multicomponent Reactions of Aldehydes, Terminal Alkynes, and Amines (2012)

A series of gold complexes were tested as catalysts in the synthesis of propargylamines by the three component coupling reaction of amines, aldehydes, and alkynes. These complexes are efficient catalysts for the three-component coupling reaction (yields up to 97%). In homogeneous solution, the conversions to the respective propargylamine were higher than under heterogeneous conditions. Heterogenized complexes were stable and recoverable for at least six cycles. Ligands, gold(I) or gold(III), homogeneous or heterogenized systems have pronounced effects on the catalytic activity of the corresponding gold complexes.
Data from: Structural instability and divergence from conserved residues underlie intracellular retention of mammalian odorant receptors (2019)

Mammalian odorant receptors are a diverse and rapidly evolving set of G protein-coupled receptors expressed in olfactory cilia membranes. Most odorant receptors show little to no cell surface expression in non-olfactory cells due to endoplasmic reticulum retention, which has slowed down biochemical studies. Here, we provide evidence that structural instability and divergence from conserved residues of individual odorant receptors underlie intracellular retention using a combination of large-scale screening of odorant receptors cell surface expression in heterologous cells, point mutations, structural modeling, and machine learning techniques. We demonstrate the importance of conserved residues by synthesizing "consensus" odorant receptors that show high levels of cell surface expression similar to conventional G protein-coupled receptors. Furthermore, we associate in silico structural instability with poor cell surface expression using molecular dynamics simulations. We propose an enhanced evolutionary capacitance of olfactory sensory neurons that enable the functional expression of odorant receptors with cryptic mutations.
Anterior pituitary adenomas: inherited syndromes, novel genes and molecular pathways (2010)

Pituitary adenomas are common tumors. Although rarely malignant, pituitary adenomas cause significant morbidity due to mass effects and/or hormonal hypo- and/or hyper-secretion. Molecular understanding of pituitary adenoma formation is essential for the development of medical therapies and the treatment of post-operative recurrences. In general, mutations in genes involved in genetic syndromes associated with pituitary tumors are not a common finding in sporadic lesions. By contrast, multiple endocrine neoplasia type 1 (MEN-1) and aryl hydrocarbon receptor-interacting protein (AIP) mutations may be more frequent among specific subgroups of patients, such as children and young adults, with growth hormone-producing adenomas. In this article, we present the most recent data on the molecular pathogenesis of pituitary adenomas and discuss some of the most recent findings from our laboratory. Guidelines for genetic screening and clinical counseling of patients with pituitary tumors are provided.
An Enantioselective Synthesis of N-Methylfucosamine via Tandem C-C/C-O Bond Formation (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn Enantioselective Synthesis of N-Methylfucosamine via Tandem C-C/C-O Bond FormationDalibor Sames and Robin PoltCite this: J. Org. Chem. 1994, 59, 16, 4596–4601Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/jo00095a039https://doi.org/10.1021/jo00095a039research-articleACS PublicationsRequest reuse permissionsArticle Views349Altmetric-Citations44LEARN 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
Investigation of Al/sub 2/O/sub 3/ and TiO/sub 2/ as gate insulators for 4H-SiC pulsed power devices (2004)

Achieving high quality and high electric breakdown of oxide on 4H-SiC substrates is still a major research challenge. 500 /spl Aring/ Al/sub 2/O/sub 3/ and TiO/sub 2/ were deposited on 4H-SiC by high vacuum and low-temperature e-beam evaporation. AFM (atomic force microscopy) results show that a surface mean height of 4-7 /spl Aring/ of Al/sub 2/O/sub 3/ was found on Si substrate and 74 /spl Aring/ of Al/sub 2/O/sub 3/ was found on SiC substrate. MIS capacitors were fabricated using one mask to evaluate the quality of these gate materials. C-V measurements at 10 kHz show that Al/sub 2/O/sub 3/ and TiO/sub 2/ have dielectric constants of more than 9 and 20, respectively. The leakage current of an Al/sub 2/O/sub 3/ MIS capacitor is about 10/sup -9/ A on a capacitor area of 150 /spl mu/m /spl times/ 150/spl mu/m at a gate voltage of /spl plusmn/10 V. An Al/sub 2/O/sub 3/ MIS capacitor has a lower leakage current than a TiO/sub 2/ MIS capacitor due to its large band gap offsets. Its breakdown electric field strength is more than 8 MV/cm. This research indicates that e-beam deposited Al/sub 2/O/sub 3/ may be a promising dielectric material for the pulsed power SiC devices.
Severe Acute Respiratory Syndrome Coronavirus Infection of Golden Syrian Hamsters (2004)

Small animal models are needed in order to evaluate the efficacy of candidate vaccines and antivirals directed against the severe acute respiratory syndrome coronavirus (SARS CoV). We investigated the ability of SARS CoV to infect 5-week-old Golden Syrian hamsters. When administered intranasally, SARS CoV replicates to high titers in the lungs and nasal turbinates. Peak replication in the lower respiratory tract was noted on day 2 postinfection (p.i.) and was cleared by day 7 p.i. Low levels of virus were present in the nasal turbinates of a few hamsters at 14 days p.i. Viral replication in epithelial cells of the respiratory tract was accompanied by cellular necrosis early in infection, followed by an inflammatory response coincident with viral clearance, focal consolidation in pulmonary tissue, and eventual pulmonary tissue repair. Despite high levels of virus replication and associated pathology in the respiratory tract, the hamsters showed no evidence of disease. Neutralizing antibodies were detected in sera at day 7 p.i., and mean titers at day 28 p.i. exceeded 1:400. Hamsters challenged with SARS CoV at day 28 p.i. were completely protected from virus replication and accompanying pathology in the respiratory tract. Comparing these data to the mouse model, SARS CoV replicates to a higher titer and for a longer duration in the respiratory tract of hamsters and is accompanied by significant pathology that is absent in mice. Viremia and extrapulmonary spread of SARS CoV to liver and spleen, which are seen in hamsters, were not detected in mice. The hamster, therefore, is superior to the mouse as a model for the evaluation of antiviral agents and candidate vaccines against SARS CoV replication.
Shielding gas brazing of martensitic stainless steel with copper free silver based filler metals (2007)

In the present work, the applicability of the copper free silver based alloys Ag–15Mn and Ag–5Pd as filler metals for shielding gas brazing of the martensitic stainless steel X3CrNiMo13-4 was investigated. The joints were examined with respect to their microstructure, their corrosion behaviour in aequous NaCl solution as well as – in the case of the specimens brazed with AgPd5 – their mechanical performance under tensile and torsion loading. Specimens brazed with Ag– 15Mn showed pronounced oxidation in the Ar/H 2 shielding gas atmosphere as well as a low corrosion resistance in 0 ? 5M NaCl solution. The filler metal Ag–5Pd showed very good brazing results. With this filler metal, defect free and corrosion resistant joints with an ultimate tensile strength of 800 MPa and a low cycle fatigue strength of 490 MPa could be produced.
Payments for Outsourced Computations (2011)

With the recent advent of cloud computing, the concept of outsourcing computations, initiated by volunteer computing efforts, is being revamped. While the two paradigms differ in several dimensions, they also share challenges, stemming from the lack of trust between outsourcers and workers. In this work, we propose a unifying trust framework, where correct participation is financially rewarded: neither participant is trusted, yet outsourced computations are efficiently verified and validly remunerated. We propose three solutions for this problem, relying on an offline bank to generate and redeem payments; the bank is oblivious to interactions between outsourcers and workers. We propose several attacks that can be launched against our framework and study the effectiveness of our solutions. We implemented our most secure solution and our experiments show that it is efficient: the bank can perform hundreds of payment transactions per second and the overheads imposed on outsourcers and workers are negligible.
SIX TAX LAWS LATER: HOW INDIVIDUALS' MARGINAL FEDERAL INCOME TAX RATES CHANGED BETWEEN 1980 AND 1995 (1998)

We examine the evolution of marginal federal income tax rates from 1980 to 1995 using panel and crosssectional data. Marginal rates fell dramatically for most taxpayers. Whereas in 1980 three-quarters of taxpayers faced statutory tax rates above 15 percent less than one-quarter of taxpayers were in that situation in 1995. Individuals' tax rates also rose and fell due to life-cycle changes in income. Young people (age 30 to 44) were twice as likely to experience tax rate increases as older taxpayers. Nonetheless, the majority of taxpayers in every age group experienced rate reductions. The large marginal tax rate cuts in 1981 and 1986 clearly dominate life-cycle effects.
Design and Verification of Shielding for the Advanced Spent Fuel Conditioning Process Facility (2008)

An Advanced spent fuel Conditioning Process Facility (ACPF) has recently been constructed by a modification of previously unused cells. ACPF is a hot cell with two rooms located in the basement of the Irradiated Materials Experiment Facility (IMEF) at the Korea Atomic Energy Research Institute. This is for demonstrating the advanced spent fuel conditioning process being proposed in Korea, which is an electrolytic reduction process of spent oxide fuels into a metallic form. The ACPF was designed with a more than 90 cm thick high density concrete shield wall to handle 1.38 PBq (37,430 Ci) of radioactive materials with dose rates lower than 10 muSv h in the operational areas (7,000 zone) and 150 muSv h in the service areas (8,000 zone). In Monte Carlo calculations with a design basis source inventory, the results for the bounding wall showed a maximum of 3 muSv h dose rate at an exterior surface of the ACPF for gamma radiation and 0.76 muSv h for neutrons. All the bounding structures of the ACPF were investigated to check on the shielding performance of the facility to ensure the radiation safety of the facility. A test was performed with a 2.96 TBq (80 Ci) 60Co source unit and the test results were compared with the calculation results. A few failure points were discovered and carefully fixed to meet the design criteria. After fixing the problems, the failure points were rechecked and the safety of the shielding structures was confirmed. In conclusion, it was confirmed that all the investigated parts of the ACPF passed the shielding safety limits by using this program and the ACPF is ready to fulfill its tasks for the advanced spent fuel conditioning process.
Preparation and optimization of a diverse workload for a large-scale heterogeneous system (2019)

Productivity from day one on supercomputers that leverage new technologies requires significant preparation. An institution that procures a novel system architecture often lacks sufficient institutional knowledge and skills to prepare for it. Thus, the "Center of Excellence" (CoE) concept has emerged to prepare for systems such as Summit and Sierra, currently the top two systems in the Top 500. This paper documents CoE experiences that prepared a workload of diverse applications and math libraries for a heterogeneous system.
Serial Concatenated TCM With an Inner Accumulate Code—Part I: Maximum-Likelihood Analysis (2005)

We propose a serial concatenated trellis-coded modulation system using one or more inner rate-1 accumulate codes and a mapping to a higher order, Gray-labeled signal constellation. As outer codes, we consider repeat codes, single parity-check codes, and convolutional codes. We show that under maximum-likelihood decoding, there exists a signal-to-noise ratio threshold beyond which the bit-error probability goes to zero as the blocklength goes to infinity. We then evaluate the performance for finite blocklengths using a modified union bound. Computer simulations demonstrate that the proposed system, despite its use of a simple rate-1 inner code, achieves performance in additive white Gaussian noise and Rayleigh fading that is comparable to, or better than, that of more complex systems suggested in the literature.
Supplementary Figures 1 and 2 from Targeting Integrin-Linked Kinase Suppresses Invasion and Metastasis through Downregulation of Epithelial-to-Mesenchymal Transition in Renal Cell Carcinoma (2023)

&lt;p&gt;Figure S1. Expression and localization of ILK protein and EMT-related molecular markers in normal renal epithelial cells and RCC cells. Figure S2. Anti-angiogenic effects of in vivo knockdown of ILK in orthotopic RCC xenografts.&lt;/p&gt;
Targeting the tumor microenvironment (2013)

Persistent JAK-STAT3 signaling is implicated in many aspects of tumorigenesis. Apart from its tumor-intrinsic effects, STAT3 also exerts tumor-extrinsic effects, supporting tumor survival and metastasis. These involve the regulation of paracrine cytokine signaling, alterations in metastatic sites rendering these permissive for the growth of cancer cells and subversion of host immune responses to create an immunosuppressive environment. Targeting this signaling pathway is considered a novel promising therapeutic approach, especially in the context of tumor immunity. In this article, we will review to what extent JAK-STAT3-targeted therapies affect the tumor microenvironment and whether the observed effects underlie responsiveness to therapy.
Mechanical loss and magnetoelectric response in magnetostrictive/interdigitated-electrode/piezoelectric laminated resonators (2013)

The mechanical quality factor and the resonant magnetoelectric (ME) response of multi-push-pull mode Metglas/interdigitated (ID)-electrode/Pb(Zr,Ti)O3 (PZT) ME resonators have been studied as a function of ID-electrode geometry for both sandwich and bimorph configurations. The results show that the mechanical quality factor of the PZT core composite and the effective mechanical quality factor of the ME resonator are increased with increasing ID-electrode spacing. The sandwich resonator was found to exhibit a higher effective mechanical quality factor than the bimorph one.
Advantage of Plasma Doping for Source/Drain Extension in Bulk Fin Field Effect Transistor (2011)

The impact of plasma doping (PD) on the formation of source/drain extension (SDE) is demonstrated for a p-type bulk fin field effect transistor (FinFET). The impurity distribution in a narrow fin (15 nm) was analyzed with atom probe tomography (APT) and secondary ion mass spectroscopy (SIMS). The lateral distribution of boron in the Si fin by the PD is similar to the case with conventional beam-line ion implantation (BL). However, the vertical distribution of boron by the PD is much steeper than that by the conventional BL. TCAD simulations show that the driving current of the FinFET fabricated by the PD is 34% higher than that of the FinFET fabricated by the BL under the same off-leakage current. Therefore, the PD is a key technology for fabricating the SDE of narrow bulk-FinFETs in the future.
Antibacterial Properties of Metallocenyl-7-ADCA Derivatives and Structure in Complex with CTX-M β-Lactamase (2017)

A series of six novel metallocenyl-7-ADCA (metallocenyl = ferrocenyl or ruthenocenyl; 7-ADCA = 7-aminodesacetoxycephalosporanic acid) conjugates were synthesized and their antibacterial properties evaluated by biochemical and microbiological assays. The ruthenocene derivatives showed a higher level of inhibition of DD-carboxypeptidase 64-575, a Penicillin Binding Protein (PBP), than the ferrocene derivatives and the reference compound penicillin G. Protein X-ray crystallographic analysis revealed a covalent acyl-enzyme complex of a ruthenocenyl compound with CTX-M β-lactamase E166A mutant, corresponding to a similar complex with PBPs responsible for the bactericidal activities of these compounds. Most interestingly, an intact compound was captured at the crystal-packing interface, elucidating for the first time the structure of a metallocenyl β-lactam compound that previously eluded small molecule crystallography. We propose that protein crystals, even from biologically unrelated molecules, can be utilized to determine structures of small molecules.
Short Course: Introduction to electric machine design for manufacturing (2014)

This article consists of a collection of slides from the author's conference presentation. Some of the specific areas/topics discussed include: Fundamentals of theory and design; Manufacturing methods, robust design, and six sigma concepts; Multi-physics analysis, vibration, and noise; and Automated design optimization.