gebhart/patrepeval huggingface dataset:
Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade (2006)

We report herein the application of a set of algorithms to identify a large number (2869) of single-copy orthologs (COSII), which are shared by most, if not all, euasterid plant species as well as the model species Arabidopsis. Alignments of the orthologous sequences across multiple species enabled the design of "universal PCR primers," which can be used to amplify the corresponding orthologs from a broad range of taxa, including those lacking any sequence databases. Functional annotation revealed that these conserved, single-copy orthologs encode a higher-than-expected frequency of proteins transported and utilized in organelles and a paucity of proteins associated with cell walls, protein kinases, transcription factors, and signal transduction. The enabling power of this new ortholog resource was demonstrated in phylogenetic studies, as well as in comparative mapping across the plant families tomato (family Solanaceae) and coffee (family Rubiaceae). The combined results of these studies provide compelling evidence that (1) the ancestral species that gave rise to the core euasterid families Solanaceae and Rubiaceae had a basic chromosome number of x=11 or 12.2) No whole-genome duplication event (i.e., polyploidization) occurred immediately prior to or after the radiation of either Solanaceae or Rubiaceae as has been recently suggested.
BRAFMutations Are Not a Major Event in Post-Chernobyl Childhood Thyroid Carcinomas (2004)

The BRAF gene has been shown to be a major target for mutations in papillary thyroid carcinoma (PTC) (36-69%), which forms almost all of the over 2000 cases of thyroid carcinoma that have occurred in Chernobyl. BRAF is activated by point mutation, and were it to occur at a high frequency in Chernobyl-related tumors, it would challenge the dominant role of double-strand breaks in radiation-induced PTC. In a previous study, we detected the BRAF V600E mutation in 46% (23 of 50) of sporadic adult PTC. Using the same methodology, we have analyzed 34 post-Chernobyl PTC and detected RET/PTC rearrangements in 14 (41%) and BRAF mutations (V600E) in four (12%). These two alterations did not coexist in any PTCs. The mean age at exposure of patients with PTC showing BRAF mutation was higher than that of patients with tumors without BRAF mutation irrespective of their RET status. We have also analyzed 17 sporadic cases of childhood PTC and found that only one (6%) harbored the BRAF V600E mutation. We conclude that the frequency of BRAF mutations is significantly lower (P = 0.0008) in post-Chernobyl PTC than in adult sporadic PTC, whereas no significant difference was found between post-Chernobyl and sporadic childhood PTCs.
Correction to Targeting Metalloenzymes for Therapeutic Intervention (2019)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to Targeting Metalloenzymes for Therapeutic InterventionAllie Y. ChenAllie Y. ChenMore by Allie Y. Chen, Rebecca N. AdamekRebecca N. AdamekMore by Rebecca N. Adamek, Benjamin L. DickBenjamin L. DickMore by Benjamin L. Dick, Cy V. CredilleCy V. CredilleMore by Cy V. Credille, Christine N. MorrisonChristine N. MorrisonMore by Christine N. Morrison, and Seth M. Cohen*Seth M. Cohen*E-mail: [email protected]More by Seth M. Cohenhttp://orcid.org/0000-0002-5233-2280Cite this: Chem. Rev. 2019, 119, 12, 7719Publication Date (Web):June 11, 2019Publication History Published online11 June 2019Published inissue 26 June 2019https://pubs.acs.org/doi/10.1021/acs.chemrev.9b00322https://doi.org/10.1021/acs.chemrev.9b00322correctionACS PublicationsCopyright © 2019 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 Views2161Altmetric-Citations2LEARN 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 (209 KB) Get e-Alertsclose Get e-Alerts
An optical tomography PSF almost insensitive to aberrations: the benefit of a spatial incoherent illumination(Conference Presentation) (2016)

An aberrated imaging system PSF is broadened; this broadening is responsible of the blurring of the images. A lot of effort has been carried out to correct the effects of aberrations on OCT images for eye examination or biological samples. We have worked on quantifying the effect of geometrical aberrations on Full-Field OCT images and found that there is mostly no loss of resolution but a decrease of the signal level. This is obviously why we use these signals as metric to correct the wavefront distortion. Moreover we found that this absence of blurring, which is due to the fact that we record the dot product of a diffraction limited reference signal and the distorted sample signal, is specific to the use of an incoherent illumination and did not show up with OCT approaches that use spatially coherent sources. More precisely the loss in signal is roughly proportional to the square root of the Strehl ratio: for example, a Strehl ratio of 1/9, which is considered to give a low quality image, would only be 1/3 in Full-Field OCT while keeping the sharpness of the image. Using both an USAF resolution target and a transmissive SLM we have demonstrated this unique feature of sharpness conservation. It was also confirmed by using biological samples. We think that we can thus restrict the aberration corrections in eye examination to the main aberrations (e.g. focus and astigmatism) that will increase the speed of the correction.
Intuitive Human Interfaces for an Audio-database. (1994)

Database technology can now host multimedia applications through the representation of sounds and images, but such new applications also require extensions to HCI technology. This paper examines the problems of querying and manipulating audio information. We argue that no single “style” of user interface can provide a complete solution, and propose two novel types of interface to complement conventional database languages. The first is gestural, and allows users literally to reach into spaces of sounds and to “grab” the required objects. The second involves retrieval by mimicry. The main part of this paper describes our research into the viability of the gestural interface. We have experimented using the ISEE (Intuitive Sound Editing Environment) interface, a four-dimensional perceptually-based space of sounds. Our experiments have involved a user population and a range of multidimensional input devices, and have provided strong evidence that the approach is viable, but that the choice of input devices has a significant impact on the usability of the system. The second proposed interface, which we are currently researching, involves the use of neural networks within the data model to derive perceptually-based attributes. The neural networks can be trained on expertly created sound spaces, together with vocal imitations of the sounds, and subsequently used to retrieve on the basis of vocal imitations of the required sounds.
Mimic: In-Situ Recording and Re-Use of Demonstrations to Support Robot Teleoperation (2022)

Remote teleoperation is an important robot control method when they cannot operate fully autonomously. Yet, teleoperation presents challenges to effective and full robot utilization: controls are cumbersome, inefficient, and the teleoperator needs to actively attend to the robot and its environment. Inspired by end-user programming, we propose a new interaction paradigm to support robot teleoperation for combinations of repetitive and complex movements. We introduce Mimic, a system that allows teleoperators to demonstrate and save robot trajectories as templates, and re-use them to execute the same action in new situations. Templates can be re-used through (1) macros—parametrized templates assigned to and activated by buttons on the controller, and (2) programs—sequences of parametrized templates that operate autonomously. A user study in a simulated environment showed that after initial set up time, participants completed manipulation tasks faster and more easily compared to traditional direct control.
Data from First-in-Human Study of Utomilumab, a 4-1BB/CD137 Agonist, in Combination with Rituximab in Patients with Follicular and Other CD20<sup>+</sup> Non-Hodgkin Lymphomas (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;In this phase I study (NCT01307267), we evaluated safety, pharmacokinetics, clinical activity, and pharmacodynamics of treatment with utomilumab plus rituximab in patients with relapsed/refractory follicular lymphoma (FL) and other CD20&lt;sup&gt;+&lt;/sup&gt; non-Hodgkin lymphomas (NHL).&lt;/p&gt;Patients and Methods:&lt;p&gt;Primary objectives were to assess treatment safety and tolerability for estimating the MTD, using a modified time-to-event continual reassessment method, and selecting the recommended phase II dose (RP2D).&lt;/p&gt;Results:&lt;p&gt;Sixty-seven patients received utomilumab (0.03–10.0 mg/kg every 4 weeks) and rituximab (375 mg/m&lt;sup&gt;2&lt;/sup&gt; weekly) in the dose-escalation groups or utomilumab (1.2 mg/kg every 4 weeks) plus rituximab in the dose-expansion cohort. No patient experienced dose-limiting toxicity. The MTD for utomilumab in combination with rituximab was not reached and estimated to be ≥10 mg/kg every 4 weeks. The majority of the utomilumab treatment-related adverse events (AE) were grade 1 to 2; the most common AE was fatigue (16.4%). The pharmacokinetics of utomilumab in combination with rituximab was linear in the 0.03 to 10 mg/kg dose range. A low incidence (1.5%) of treatment-induced antidrug antibodies against utomilumab was observed. The objective response rate was 21.2% (95% CI, 12.1%–33.0%) in all patients with NHL, including four complete and 10 partial responses. Analysis of paired biopsies from a relapsed/refractory FL patient with complete response showed increased T-cell infiltration and cytotoxic activity in tumors. Biomarker correlations with outcomes suggested that clinical benefit may be contingent on patient immune function.&lt;/p&gt;Conclusions:&lt;p&gt;Utomilumab in combination with rituximab demonstrated clinical activity and a favorable safety profile in patients with CD20&lt;sup&gt;+&lt;/sup&gt; NHLs.&lt;/p&gt;&lt;/div&gt;
Crystallographic Characterization of 12-Helical Secondary Structure in β-Peptides Containing Side Chain Groups (2010)

Helices are the most extensively studied secondary structures formed by β-peptide foldamers. Among the five known β-peptide helices, the 12-helix is particularly interesting because the internal hydrogen bond orientation and macrodipole are analogous to those of α-peptide helices (α-helix and 3&lt;sub&gt;10&lt;/sub&gt;-helix). The β-peptide 12-helix is defined by &lt;i&gt;i&lt;/i&gt;, &lt;i&gt;i&lt;/i&gt;+3 CO···H−N backbone hydrogen bonds and promoted by β-residues with a five-membered ring constraint. The 12-helical scaffold has been used to generate β-peptides with specific biological functions, for which diverse side chains must be properly placed along the backbone and, upon folding, properly arranged in space. Only two crystal structures of 12-helical β-peptides have previously been reported, both for homooligomers of &lt;i&gt;trans&lt;/i&gt;-2-aminocyclopentanecarboxylic acid (ACPC). Here we report five additional crystal structures of 12-helical β-peptides, all containing residues that bear side chains. Four of the crystallized β-peptides include &lt;i&gt;trans&lt;/i&gt;-4,4-dimethyl-2-aminocyclopentanecarboxylic acid (&lt;i&gt;dm&lt;/i&gt;-ACPC) residues, and the fifth contains a β&lt;sup&gt;3&lt;/sup&gt;-hPhe residue. These five β-peptides adopt fully folded 12-helical conformations in the solid state. The new crystal structures, along with previously reported data, allow a detailed characterization of the 12-helical conformation; average backbone torsion angles of β-residues and helical parameters are derived. These structural parameters are found to be similar to those for &lt;i&gt;i&lt;/i&gt;, &lt;i&gt;i&lt;/i&gt;+3 CO···H−N hydrogen-bonded helices formed by other peptide backbones generated from α- and/or β-amino acids. The similarity between the conformational behavior of &lt;i&gt;dm&lt;/i&gt;-ACPC and ACPC is consistent with previous NMR-based conclusions that 4,4-disubstituted ACPC derivatives are compatible with 12-helical folding. In addition, our data show how a β&lt;sup&gt;3&lt;/sup&gt;-residue is accommodated in the 12-helix, thus enhancing understanding of the diverse conformational behavior of this flexible class of β-amino acids.
Deuterium-induced volume expansion inFe0.5V0.5/Vsuperlattices (2010)

Neutron reflectometry was used to investigate the deuterium uptake in a thin metal superlattice that displays an anisotropic elastic response [${\text{Fe}}_{0.5}{\text{V}}_{0.5}/\text{V}$ (6/21 monolayers)]. We see evidence of the presence of a coexistence region which has never before been seen in vanadium-based superlattices. The loading process is completely reversible from which we conclude that the phases must be coherent, in stark contrast to bulk ${\text{VD}}_{x}$, where the two-phase region displays hysteresis. The deuterium-induced volume expansion exhibits changes in slope that correlate with the plateau region and the expansion is comparable and even larger than in the bulk. The spectacular cooperation between the elastic fields seems to be found only in one-dimensionally confined structures with biaxial compressive strain states.
Inhibition of endoplasmic reticulum chaperone protein glucose-regulated protein 78 potentiates anti-angiogenic therapy in renal cell carcinoma through inactivation of the PERK/eIF2α pathway (2015)

Tumor microenvironments are characterized by decreased oxygen and nutrition due to the rapid and progressive nature of tumors and also stresses induced by several anti-tumor therapies. These intense cell stressors trigger a protective cell survival mechanism heralded by the unfolded protein response (UPR). The UPR is induced by an accumulation of unfolded proteins in the endoplasmic reticulum (ER) following cell starvation. Although the ER stress response is implicated in cytoprotection, its precise role during anti-angiogenic therapy remains unclear. One of the major proteins involved in ER stress is glucose-regulated protein 78 (GRP78), which binds to unfolded proteins and dissociates from membrane-bound ER stress sensors. To determine the role of ER stress responses during anti-angiogenic therapy and the potential role of GRP78 in combined therapy in renal cell carcinoma (RCC), we used GRP78 overexpressing or knockdown RCC cells under hypoxic or hypoglycemic conditions in vitro and in animal models treated with sunitinib. Here, we report that GRP78 plays a crucial role in protecting RCC cells from hypoxic and hypoglycemic stress induced by anti-angiogenic therapy. Knockdown of GRP78 using siRNA inhibited cancer cell survival and induced apoptosis in RCC cells in vitro and also resulted in ER stress-induced apoptosis and hypoxic/hypoglycemic stress-induced apoptosis by inactivating the PERK/eIF-2α pathway. Finally, GRP78 knockdown showed potent suppression of tumor growth and enhanced the antitumor effect of sunitinib in RCC xenografts. Our findings suggest that GRP78 may serve as a novel therapeutic target in combination with anti-angiogenic therapy for the management of RCC.
Numerical analysis of ac loss in bifilar stacks and coils of ion beam assisted deposition YBCO coated conductors (2009)

In this paper we present a finite element model using the commercial COMSOL® software package for calculating the ac loss in bifilar stacks of high temperature superconducting tape. In the model, the current-voltage relationship characterizing the superconducting properties is assumed to follow a power law. The calculations were performed for infinite bifilar stacks with different values of layer-to-layer separation D. With appropriate settings for the boundary conditions, the numerical results agree well with the analytical data obtained from a recently proposed model [J. R. Clem, Phys. Rev. B 77, 134506 (2008)]. The numerical approach was also used to investigate the end effects in a bifilar stack to answer the following question: how many layers away from the end of a stack are required before the environment of a given layer is identical to that in an infinite stack? We find that the answer to this question depends strongly on the value of D. Based on this study, a model for calculating the ac loss in bifilar noninductively wound coils with a finite number of turns is proposed.
Data from An Adenoviral Vaccine Encoding Full-Length Inactivated Human Her2 Exhibits Potent Immunogenicty and Enhanced Therapeutic Efficacy without Oncogenicity (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Overexpression of the breast cancer oncogene &lt;i&gt;HER2&lt;/i&gt; correlates with poor survival. Current &lt;i&gt;HER2&lt;/i&gt;-directed therapies confer limited clinical benefits and most patients experience progressive disease. Because refractory tumors remain strongly &lt;i&gt;HER2&lt;/i&gt;+, vaccine approaches targeting &lt;i&gt;HER2&lt;/i&gt; have therapeutic potential, but wild type (wt) &lt;i&gt;HER2&lt;/i&gt; cannot safely be delivered in imunogenic viral vectors because it is a potent oncogene. We designed and tested several HER2 vaccines devoid of oncogenic activity to develop a safe vaccine for clinical use.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We created recombinant adenoviral vectors expressing the extracellular domain of HER2 (Ad-HER2-ECD), ECD plus the transmembrane domain (Ad-HER2-ECD-TM), and full-length HER2 inactivated for kinase function (Ad-HER2-ki), and determined their immunogenicity and antitumor effect in wild type (WT) and HER2-tolerant mice. To assess their safety, we compared their effect on the cellular transcriptome, cell proliferation, anchorage-dependent growth, and transformation potential &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Ad-HER2-ki was the most immunogenic vector in WT animals, retained immunogenicity in HER2-transgenic tolerant animals, and showed strong therapeutic efficacy in treatment models. Despite being highly expressed, HER2-ki protein was not phosphorylated and did not produce an oncogenic gene signature in primary human cells. Moreover, in contrast to HER2-wt, cells overexpressing HER2-ki were less proliferative, displayed less anchorage-independent growth, and were not transformed &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Vaccination with mutationally inactivated, nononcogenic Ad-HER2-ki results in robust polyclonal immune responses to HER2 in tolerant models, which translates into strong and effective antitumor responses &lt;i&gt;in vivo&lt;/i&gt;. Ad-HER2-ki is thus a safe and promising vaccine for evaluation in clinical trials. Clin Cancer Res; 16(5); 1466–77&lt;/p&gt;&lt;/div&gt;
Organic Thin‐Film Transistors: Flexible Low‐Voltage Organic Complementary Circuits: Finding the Optimum Combination of Semiconductors and Monolayer Gate Dielectrics (Adv. Mater. 2/2015) (2015)

The observation that n-channel organic semiconductors perform better when deposited onto fluoroalkyl self–assembled monolayers (SAMs) while p-channel semiconductors perform better on alkyl SAMs raises the question as to which SAM to employ in complementary circuits. As U. Kraft and co-workers describe on page 207, the answer depends on the transistor's contact resistance and hence the channel length. Here, a signal delay of 3.1 μs is measured in -circuits based on transistors with a channel length of 1 μm.
Miniature Electrodynamic Wireless Power Transmission Receiver Using a Micromachined Silicon Suspension (2021)

We present the design, modeling, fabrication, and experimental characterization of an electrodynamic wireless power transmission (EWPT) receiver for low-frequency (<; 1 kHz), near-field wireless power transmission. The device utilizes a bulk-micromachined silicon serpentine suspension, two NdFeB magnets and two precision-manufactured coils. The architecture of the transducer is designed to maximize the electrodynamic coupling coefficient while maintaining a low mechanical resonant frequency in order to maximize the power density for low-frequency wireless power transmission. An equivalent lumped-element circuit model is established to parameterize the system and to predict the output performance of the proposed system. A prototype device is fabricated, assembled and tested, and the results are compared with the model prediction. The 0.31 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> device generates 2.46 mW average power (7.9 mW·cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> power density) at 4 cm distance from a transmitter coil operating at 821 Hz and safely within allowable human exposure limits. This data corresponds to a normalized power density of 21.9 mW·cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> ·mT <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> , which is 44% higher than similar reported devices. Based on these results, this device shows great suitability for wirelessly charging mobile, wearable and bio-implantable devices. [2020-0161]
Space robotics-driver for a new mechatronic generation of light-weight arms and multifingered hands (2002)

Based on the long term goal "robonauts for space", the paper describes design and development efforts in DLR's robotics lab towards a new generation of "mechatronic" ultra-light weight robots with articulated hands. The design of fully sensorized joints with complete state feedback and the underlying mechanisms are outlined. The second light-weight arm generation is available now; in the same way the second generation a most highly integrated 4 finger-hand is near completion. Thus it is hoped that big steps towards a new generation of space as well as service and personal robots have been achieved.
Field-deployable Ultra-low-noise Clockwork for Precision Optical Clocks (2020)

We report the development of a field-deployable frequency comb operated as clockwork for transportable Sr-clocks. While referencing it at ~194.4THz, we characterize spectral lines at ~214.6THz. Prospects on complete Sr-lattice laser systems will be outlined.
Aberration correction in multiscale lenses (2009)

Multiscale lens design splits the field into subregions and attempts to correct the local wavefront error in each subfield rather than the global error. We review the aberration theory underlying the approach.
Experimental analysis on the relaxation of macromodeling methods (2007)

Abstract — Relaxed Vector Fitting is known to be a reliable tool for the macromodeling of noisy frequency reponses. The strength of this method originates from the introduction of a “relaxed ” non-triviality condition. In this paper, some alternative, generalized formulations are proposed and compared to the classical scheme.