gebhart/patrepeval huggingface dataset:
DNA-Functionalized, Bivalent Proteins* (2020)

Bivalent DNA conjugates of beta-galactosidase, having pairs of oligonucleotides positioned closely on opposing faces of the protein, have been synthesized and characterized. These structures, due to their directional bonding characteristics, allow for the programmable access of one-dimensional protein materials. This chapter explores the assembly of isotropically, or highly functionalized proteins; however, realizing directional interactions with small numbers of oligonucleotides strategically placed on the periphery of a protein building block remains unexplored, but could represent a powerful, and general strategy to realize nanoscale building blocks with programmed valency. It demonstrates that only two surface-conjugated oligonucleotides are sufficient to achieve directional DNA bonding, which is important for generalizing this assembly approach to proteins with small edge lengths that cannot accommodate large numbers of DNA modifications. The chapter explains a new platform to synthesize nanoscale building blocks where both valency and directionality can be defined in a manner entirely controlled through exploiting the addressable and tunable chemical topologies of protein surfaces.
Correction for absorption distortion of dual-tracer fluorescence imaging of receptor binding potential (2015)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text S. C. Kanick, K. M. Tichauer, J. Gunn, K. S. Samkoe, and B. W. Pogue, "Correction for absorption distortion of dual-tracer fluorescence imaging of receptor binding potential," in Optics in the Life Sciences, OSA Technical Digest (online) (Optica Publishing Group, 2015), paper OW1D.5. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
PSIII-21 Optimum SID Threonine to Lysine Ratio in Nursery Pigs (2021)

Abstract A total of 270 pigs (PIC 1050 x DNA 600, 6.0 kg) were used in a 42-d nursery trial to determine the optimum SID threonine to SID lysine (SID Thr/Lys) ratio for young pigs. Pigs were sorted by sex and initial BW, and were allotted to each pen (3 barrows, 3 gilts). Pens were then randomly assigned to diets containing incremental levels of SID Thr/Lys ratio (0.55, 0.60, 0.65, 0.70, 0.75), achieved using THRPRO 80 (CJ America, CA) as the source of L-threonine. Each treatment consisted of 45 piglets and 9 replicates per treatment. There were 3 dietary phases (2 weeks each) and the same levels of SID Thr/Lys were tested for each phase. All performance data (ADG, ADFI, and Gain to Feed (G:F)) were analyzed using Proc Mixed in a RCBD model with SID Thr/Lys ratio as fixed effect and weight block as random effect. Orthogonal contrasts were performed to test for linear and quadratic effects of SID Thr/Lys ratio on all performance parameters. Final BW averaged around 20.8 kg (±0.6) and was not influenced by SID Thr/Lys ratio (P&amp;gt;0.20). It was however lower than previously observed from previous nursery batches and might be due to pig infection with Lawsonia intracellularis and Streptococcus suis. A linear trend on ADG was observed during the last phase of nursery (P=0.10) but this response was not significant for the overall study (P&amp;gt;0.15). SID Thr/Lys ratio had no significant effect on ADFI during any phase or overall experimental period (P&amp;gt;0.20). Increasing SID Thr/Lys ratio, however, linearly increase G:F of nursery pigs overall (P&amp;lt; 0.05). The results of this study suggest that there is value in terms of increasing efficiency of gain with higher level of SID Thr/Lys as compared to current NRC recommendation (0.59), especially under disease challenge conditions.
Use of support vector machines for disease risk prediction in genome-wide association studies: Concerns and opportunities (2012)

The success of genome-wide association studies (GWAS) in deciphering the genetic architecture of complex diseases has fueled the expectations whether the individual risk can also be quantified based on the genetic architecture. So far, disease risk prediction based on top-validated single-nucleotide polymorphisms (SNPs) showed little predictive value. Here, we applied a support vector machine (SVM) to Parkinson disease (PD) and type 1 diabetes (T1D), to show that apart from magnitude of effect size of risk variants, heritability of the disease also plays an important role in disease risk prediction. Furthermore, we performed a simulation study to show the role of uncommon (frequency 1-5%) as well as rare variants (frequency <1%) in disease etiology of complex diseases. Using a cross-validation model, we were able to achieve predictions with an area under the receiver operating characteristic curve (AUC) of ~0.88 for T1D, highlighting the strong heritable component (∼90%). This is in contrast to PD, where we were unable to achieve a satisfactory prediction (AUC ~0.56; heritability ~38%). Our simulations showed that simultaneous inclusion of uncommon and rare variants in GWAS would eventually lead to feasible disease risk prediction for complex diseases such as PD. The used software is available at http://www.ra.cs.uni-tuebingen.de/software/MACLEAPS/.
A flexible 2.1‐in. active‐matrix electrophoretic display with high resolution and a thickness of 100 μm (2007)

Abstract— A paper‐thin QVGA, flexible 2.1‐in. active‐matrix electrophoretic display (AMEPD) that features 100‐μm thick and a 192‐ppi resolution has been developed. An LTPS‐TFT backplane with integrated peripheral driver circuits was first fabricated on a glass substrate and then transferred to a very thin (30‐μm) plastic film by employing surface‐free technology by laser ablation/annealing (SUFTLA®). A micro‐encapsulated electrophoretic imaging sheet was laminated on the backplane. A supporting substrate was used to support the LTPS‐TFT backplane. Fine images were successfully displayed on the rollable AM‐EPD. The integrated driver circuits dramatically reduce the number of external connection terminals, thus easily boosting the reliability of electrical connections even on such a thin plastic film.
The association of statins plus LDL receptor‐targeted liposome‐encapsulated doxorubicin increases in vitro drug delivery across blood–brain barrier cells (2012)

We suggest that our 'Trojan horse' approach, based on the administration of statins plus a LDL receptor-targeted liposomal drug, might have potential applications in the pharmacological therapy of different brain diseases for which the BBB represents an obstacle.
Multiplicity dependence of charged pion, kaon, and (anti)proton production at large transverse momentum in p–Pb collisions at sNN=5.02 TeV (2016)

The production of charged pions, kaons and (anti)protons has been measured at mid-rapidity (−0.5<y<0) in p–Pb collisions at sNN=5.02 TeV using the ALICE detector at the LHC. Exploiting particle identification capabilities at high transverse momentum (pT), the previously published pT spectra have been extended to include measurements up to 20 GeV/c for seven event multiplicity classes. The pT spectra for pp collisions at s=7 TeV, needed to interpolate a pp reference spectrum, have also been extended up to 20 GeV/c to measure the nuclear modification factor (RpPb) in non-single diffractive p–Pb collisions. At intermediate transverse momentum (2<pT<10 GeV/c) the proton-to-pion ratio increases with multiplicity in p–Pb collisions, a similar effect is not present in the kaon-to-pion ratio. The pT dependent structure of such increase is qualitatively similar to those observed in pp and heavy-ion collisions. At high pT (>10 GeV/c), the particle ratios are consistent with those reported for pp and Pb–Pb collisions at the LHC energies. At intermediate pT the (anti)proton RpPb shows a Cronin-like enhancement, while pions and kaons show little or no nuclear modification. At high pT the charged pion, kaon and (anti)proton RpPb are consistent with unity within statistical and systematic uncertainties.
Correction: Publisher Correction: Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation (2018)

This corrects the article DOI: 10.1038/ncomms5999.
Connecting Together Nanocenters around the World (2017)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTConnecting Together Nanocenters around the WorldMinghua Liu, Chunli Bai, Markus Antonietti, Iseult Lynch, Chad A. Mirkin, Ali Khademhosseini, Shuit-Tong Lee, Helmuth Möhwald, Andrey L. Rogach, Andrew T. S. Wee, and Paul S. WeissView Author Information National Centre for Nano Science and Technology Chinese Academy of Sciences Max-Planck Institute of Colloids & Interfaces University of Birmingham Northwestern UniversityCite this: ACS Nano 2017, 11, 9, 8531–8532Publication Date (Web):September 26, 2017Publication History Published online26 September 2017Published inissue 26 September 2017https://pubs.acs.org/doi/10.1021/acsnano.7b06550https://doi.org/10.1021/acsnano.7b06550editorialACS PublicationsCopyright © 2017 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 Views2407Altmetric-Citations8LEARN 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 (2 MB) Get e-AlertscloseSUBJECTS:Nanoscience,Nanotechnology Get e-Alerts
TRPV1 Agonist, Capsaicin, Induces Axon Outgrowth after Injury via Ca2+/PKA Signaling (2018)

Preconditioning nerve injuries activate a pro-regenerative program that enhances axon regeneration for most classes of sensory neurons. However, nociceptive sensory neurons and central nervous system neurons regenerate poorly. In hopes of identifying novel mechanisms that promote regeneration, we screened for drugs that mimicked the preconditioning response and identified a nociceptive ligand that activates a preconditioning-like response to promote axon outgrowth. We show that activating the ion channel TRPV1 with capsaicin induces axon outgrowth of cultured dorsal root ganglion (DRG) sensory neurons, and that this effect is blocked in TRPV1 knockout neurons. Regeneration occurs only in NF200-negative nociceptive neurons, consistent with a cell-autonomous mechanism. Moreover, we identify a signaling pathway in which TRPV1 activation leads to calcium influx and protein kinase A (PKA) activation to induce a preconditioning-like response. Finally, capsaicin administration to the mouse sciatic nerve activates a similar preconditioning-like response and induces enhanced axonal outgrowth, indicating that this pathway can be induced <i>in vivo</i>. These findings highlight the use of local ligands to induce regeneration and suggest that it may be possible to target selective neuronal populations for repair, including cell types that often fail to regenerate.
Proteasome Activator Enhances Survival of Huntington's Disease Neuronal Model Cells (2007)

In patients with Huntington's disease (HD), the proteolytic activity of the ubiquitin proteasome system (UPS) is reduced in the brain and other tissues. The pathological hallmark of HD is the intraneuronal nuclear protein aggregates of mutant huntingtin. We determined how to enhance UPS function and influence catalytic protein degradation and cell survival in HD. Proteasome activators involved in either the ubiquitinated or the non-ubiquitinated proteolysis were overexpressed in HD patients' skin fibroblasts or mutant huntingtin-expressing striatal neurons. Following compromise of the UPS, overexpression of the proteasome activator subunit PA28gamma, but not subunit S5a, recovered proteasome function in the HD cells. PA28gamma also improved cell viability in mutant huntingtin-expressing striatal neurons exposed to pathological stressors, such as the excitotoxin quinolinic acid and the reversible proteasome inhibitor MG132. These results demonstrate the specific functional enhancements of the UPS that can provide neuroprotection in HD cells.
Residual Stress and Structural Anisotropy of Cortical Bone (2013)

The concept of residual stress and strain does not have long history for biological tissues. In the case of cortical bone, during remodeling process the old tissue is replaced by the new tissue with construction of osteons. Since the new tissue is generated under in vivo loadings as a non-deformed state, an indeterminate structure may be generated as a result of difference between the deformations of the old and new phases. Further, the mechanical properties (e.g. elastic modulus) are also different in these phases. Because of such non-uniform structures in cortical bone, residual stress/strain will remain in the replaced region even without external loading being applied. Tadano and co-workers initiated efforts to estimate residual stress/strain in cortical bone. In a very few applications with bone, the authors have successfully applied X-ray diffraction to quantify residual stresses at the bone surface. In this work, site-specific residual strain characteristics in relation with the mineral crystal orientation were studied and the sin2 ψ method was applied to measure residual stresses in bovine and rabbit extremities. The relationship between residual stress and osteon population density on the respective sites has also been obtained. Thus the knowledge about residual stress/strain in cortical bone, related with mineral crystal distribution and osteon population density, might play an important role in the biomechanical aspects of bone healing and remodeling.
Table S1 from Microbiota-Centered Interventions: The Next Breakthrough in Immuno-Oncology? (2023)

&lt;p&gt;Supplementary Table S1&lt;/p&gt;
ChemInform Abstract: Solid and Solution Phase Synthesis of α‐Keto Amides via Azetidinone Ring‐Opening: Application to the Synthesis of Poststatin. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
3D Reconstruction of Whole Stomach from Endoscope Video Using Structure-from-Motion (2019)

Gastric endoscopy is a common clinical practice that enables medical doctors to diagnose the stomach inside a body. In order to identify a gastric lesion's location such as early gastric cancer within the stomach, this work addressed to reconstruct the 3D shape of a whole stomach with color texture information generated from a standard monocular endoscope video. Previous works have tried to reconstruct the 3D structures of various organs from endoscope images. However, they are mainly focused on a partial surface. In this work, we investigated how to enable structure-from-motion (SfM) to reconstruct the whole shape of a stomach from a standard endoscope video. We specifically investigated the combined effect of chromo-endoscopy and color channel selection on SfM. Our study found that 3D reconstruction of the whole stomach can be achieved by using red channel images captured under chromo-endoscopy by spreading indigo carmine (IC) dye on the stomach surface.
Maximum Power Estimation of Lithium-Ion Batteries Accounting for Thermal and Electrical Constraints (2013)

Enforcement of constraints on the maximum deliverable power is essential to protect lithium-ion batteries from over-charge/discharge and overheating. This paper develops an algorithm to address the often overlooked temperature constraint in determining the power capability of battery systems. A prior knowledge of power capability provides dynamic constraints on currents and affords an additional control authority on the temperature of batteries. Power capability is estimated using a lumped electro-thermal model for cylindrical cells that has been validated over a wide range of operating conditions. The time scale separation between electrical and thermal systems is exploited in addressing the temperature constraint independent of voltage and state-of-charge (SOC) limits. Limiting currents and hence power capability are determined by a model-inversion technique, termed Algebraic Propagation (AP). Simulations are performed using realistic depleting currents to demonstrate the effectiveness of the proposed method.
Design considerations for a medium frequency transformer in a line side power conversion system (2004)

Design considerations are presented for a medium frequency transformer in a line side power conversion system for electric railway traction. The system employs soft commutation in order to reduce switching losses and allow for high operating frequency of the transformer. Two different designs are evaluated; The first one is dry insulated and the second one is liquid-immersed. Calculations indicate that a 1 MVA transformer operating at 4 kHz could be realized with an active weight of below 150 kg for both dry and liquid-immersed transformer concepts. The transformers are modeled magnetically, electrically and thermally, and a geometric optimization procedure based on a cost function is applied to achieve an optimum design.
267 Promoting Early-Life Immune Development by Perinatal Administration of Probiotics to Pregnant/Lactating Mice: Optimal time Window for Intervention (2012)

<h3>Background and Aims</h3> Transmission of immune competence from mothers to newborns is crucial for optimal development of neonate immune system. Maternal perinatal probiotics supplementation having been observed to be able to modulate this process, the goal of the present study was to investigate the importance of the time window of probiotics intervention (pregnancy/lactation) on early-life immune maturation and response to immunization. <h3>Methods</h3> Pregnant C57/BL6 mice were supplemented with <i>Bifidobacterium lactis</i> CNCM I-3446, 2.5x10<sup>8</sup> CFU/day, during either end of gestation and lactation, end of gestation only or lactation only. Maltodextrin was given during both periods (placebo) or in replacement of probiotics when not administered. Immune maturation was assessed by measuring natural mucosal IgA production (ELISPOTs) at weaning and 6 weeks later. Pups were mucosally immunized at weaning, and again four weeks later, with live attenuated <i>Salmonella typhimurium</i> ΔaroA. Two weeks after the second immunization, specific antibody responses in serum were analyzed. <h3>Results</h3> All probiotic regimens significantly enhanced natural IgA production in pups in comparison to placebo, an effect observable up to the end of study, 6 weeks post-weaning. Supplementation during end of pregnancy and lactation, or lactation only provided significantly highest values. Specific antibody titers tended to be potentiated by all three regimens in pups responding to immunization, with highest values being obtained after supplementation during both periods. <h3>Conclusions</h3> This study further supports the benefit of maternal perinatal intervention with probiotics on neonatal immune maturation, moreover emphasizing that supplementation during both pregnancy and lactation is needed to achieve overall optimal effects.
A characterization of the power of vector machines (1974)

Random access machines (RAMs) are usually defined to have registers that hold integers. While this captures in part the structure of a commercial computer, it overlooks an implementation-dependent feature of most binary oriented machines, namely their ability to operate bit by bit on the bit vectors used to represent integers. Typical operations are bit-wise Boolean operations (and, or, not, etc.) and shifts by an amount specified in some register. These operations are ideal for certain problems, such as dealing with sets represented as bit vectors, some parsing algorithms [4], propositional calculus theorem proving, and analysis of sorting networks. A RAM so implemented we shall call a vector machine.
Conceptual study of a gearbox fault detection method applied on a 5‐MW spar‐type floating wind turbine (2018)

Abstract In this paper, a model‐based fault detection method for fault detection of gearboxes in offshore wind turbines is presented. The main aim of this paper is to support conceptual studies with more emphasis on early fault detection methods for floating wind turbines. The method is introduced and applied on a 5‐MW reference gearbox installed on a spar‐type floating wind turbine. Faults applied on the main bearing, high and intermediate speed shaft bearings, and the planet bearing are examined with this method. The gearbox is modelled in a multibody simulation environment with high fidelity. The 5‐MW gearbox model used in this study is an offshore reference gearbox that consists of 3 stages, 2 planetary and 1 parallel stages, which is supported in a 4‐point configuration layout. The bearing faults are detected through the angular velocity error function. The angular velocity measurements are performed at input, output shafts, and 2 additional sensors inside the gearbox. The aim of the method is also to detect the fault through the external sensors—input and output shafts—measurements, which can be embedded in the existing control system. The results reveal the possibility of early fault detection by this method for large floating wind turbines.
Large-signal characterization and modeling approach suitable for the design of actively load-modulated amplifiers (2006)

An active load pull based large signal modeling approach suitable for designing and optimizing load modulated amplifiers, such as Doherty or LINC based amplifiers, is proposed. The dynamic loads seen by the amplifier's transistor was optimized using a large signal load pull based behavior model built into a CAD software. The simulation versus measurement results demonstrated the strong ability of the constructed model to predict the nonlinear behavior of actively loaded amplifiers. The developed approach was used to optimize the design of 16 watts peak-envelope power Doherty amplifier in terms of power added efficiency, AM/AM and AM/PM distortions.
A distributed web-based water quality diagnosis and simulation system in lakes and reservoirs (1998)

Over the last few years Connectionistic Networks, also referred to as Parallel Distributed Processing Systems or Neural Networks (NNs), have been in the center of a renewed and increasing interest. Indeed, the application of NNs in different arenas such as forecasting, machine vision or speech recognition are examples of their widely use in problem solving. The advent of environments for creating and using software agents, allowing for cooperation and interactions among such entities, have proved to be and interesting to explore their potential. Combining these technologies, a prototype of a Distributed Web-Based Multi-Agent Water Quality Diagnosis and Simulation System in Lakes and Reservoirs, built up both on symbolic and nouvelle Artificial Intelligence, offering the possibility of web-based links emerged.