gebhart/patrepeval huggingface dataset:
Amyloid-β42 Interacts Mainly with Insoluble Prion Protein in the Alzheimer Brain (2011)

The prion protein (PrP) is best known for its association with prion diseases. However, a controversial new role for PrP in Alzheimer disease (AD) has recently emerged. In vitro studies and mouse models of AD suggest that PrP may be involved in AD pathogenesis through a highly specific interaction with amyloid-β (Aβ42) oligomers. Immobilized recombinant human PrP (huPrP) also exhibited high affinity and specificity for Aβ42 oligomers. Here we report the novel finding that aggregated forms of huPrP and Aβ42 are co-purified from AD brain extracts. Moreover, an anti-PrP antibody and an agent that specifically binds to insoluble PrP (iPrP) co-precipitate insoluble Aβ from human AD brain. Finally, using peptide membrane arrays of 99 13-mer peptides that span the entire sequence of mature huPrP, two distinct types of Aβ binding sites on huPrP are identified in vitro. One specifically binds to Aβ42 and the other binds to both Aβ42 and Aβ40. Notably, Aβ42-specific binding sites are localized predominantly in the octapeptide repeat region, whereas sites that bind both Aβ40 and Aβ42 are mainly in the extreme N-terminal or C-terminal domains of PrP. Our study suggests that iPrP is the major PrP species that interacts with insoluble Aβ42 in vivo. Although this work indicated the interaction of Aβ42 with huPrP in the AD brain, the pathophysiological relevance of the iPrP/Aβ42 interaction remains to be established.
Structure, Conductance and Strength of Iridium Wires of Single Atom Width (2006)

The formation of iridium (Ir) wires of single-atom width during the contact and subsequent retraction of two nanometer-sized Ir tips was observed by in situ transmission electron microscopy with simultaneous measurements of conductance and force. The Ir wires, composed of a few atoms, grew straight along the retraction direction with an interatomic distance of 0.21–0.30 nm. The mechanical properties, i.e., elastic limit, Young's modulus and strength, of individual Ir wires were analyzed on the basis of the mechanics of materials on an atomic scale. It was found that in contrast to coarse-grained Ir crystals, the strength and elastic limit of the single-atom-width Ir wires increased to 25±17 GPa and 0.21±0.04, respectively, while Young's modulus decreased to 90±55 GPa. The conductance of the Ir wires at room temperature ranged from 0.2–3.0 G 0 ( G 0 =2 e 2 / h , where e is the charge of an electron and h is Planck's constant), even for the same width, a single atom.
Rickettsia conorii O antigen is the target of bactericidal Weil–Felix antibodies (2019)

Rickettsial diseases have long been diagnosed with serum antibodies cross-reactive against <i>Proteus vulgaris</i> (Weil-Felix reaction). Although Weil-Felix antibodies are associated with the development of immunity, their rickettsial target and contribution to disease pathogenesis are not established. Here, we developed a transposon for insertional mutagenesis of <i>Rickettsia conorii</i>, isolating variants defective for replication in cultured cells and in spotted fever pathogenesis. Mutations in the <i>polysaccharide synthesis operon</i> (<i>pso</i>) abolish lipopolysaccharide O-antigen synthesis and Weil-Felix serology and alter outer-membrane protein assembly. Unlike wild-type <i>R. conorii</i>, <i>pso</i> mutants cannot elicit bactericidal antibodies that bind O antigen. The <i>pso</i> operon is conserved among rickettsial pathogens, suggesting that bactericidal antibodies targeting O antigen may generate universal immunity that could be exploited to develop vaccines against rickettsial diseases.
Seamless integration of fiber optic networks and millimeter-wave wireless access using nonlinear photo-detection scheme (2002)

It would be attractive if the functionality of millimeter-wave (mm-wave) wireless transmitters could be integrated in an existing fiber optic access network for signal transmission of baseband and/or intermediate frequencies. It would be further desired if one were able to utilize the optical signals in the network without any O/E or E/O conversions. We have pointed out that such seamless integration of mm-wave wireless accessibility to a fiber optic system can be implemented by the mm-wave photonic methods such as the optical feeding technique of mm-wave signals from distant local oscillators and the optoelectronic mixing technique at the photo-detection stage in an antenna base station. Furthermore, we have proposed and demonstrated experimentally that the requirement on the base station components for the seamless integration can be drastically relaxed by employing a novel optoelectronic mixing technique called nonlinear photo-detection.
Engineering microaerobic metabolism of E. coli for 1,2-propanediol production (2015)

Establishment of novel metabolic pathways for biosynthesis of chemicals, fuels and pharmaceuticals has been demonstrated in Escherichia coli due to its ease of genetic manipulation and adaptability to varying oxygen levels. E. coli growing under microaerobic condition is known to exhibit features of both aerobic and anaerobic metabolism. In this work, we attempt to engineer this metabolism for production of 1,2-propanediol. We first redirect the carbon flux by disrupting carbon-competing pathways to increase the production of 1,2-propanediol microaerobically from 0.25 to 0.85 g/L. We then disrupt the first committed step of E. coli's ubiquinone biosynthesis pathway (ubiC) to prevent the oxidation of NADH in microaerobic conditions. Coupling this strategy with carbon flux redirection leads to enhanced production of 1,2-propanediol at 1.2 g/L. This work demonstrates the production of non-native reduced chemicals in E. coli by engineering its microaerobic metabolism.
Applying Laplacian Magic Mirror in Freeform Illumination Optics Tolerancing (2021)

Tolerance analysis is an integral part of the design process that saves time and money while improving the product quality. Nevertheless, tolerancing of illumination optics is often glossed over by the current industry. Consequently, there is a need to understand and establish tolerancing in illumination optics. This research focuses on single surface deformation. In the process referred to as surface perturbation, the surface is perturbed by a known amount. Then, the changes on the irradiance target are evaluated. A localized surface perturbation, like a bump or hole, results in either a local increase in irradiance with an annulus dip around the elevated irradiance or a local decrease in irradiance with an annulus increase around the decreased irradiance. Such an outcome is a result of flux conservation. The ratio between the height and the surface area (referred to as the size) of the localized surface perturbation has an approximately linear relationship to the largest irradiance change. Once the linearity of the relationship is understood for the localized surface perturbation of a particular size, the tolerance range can be estimated for other localized surface perturbations sizes. Within the optics’ tolerancing range, the Laplacian of the surface perturbation predicts the irradiance change. As long as the ray-mapping between the surface and the target is known, the Laplacian of the surface change can be mapped onto the target. The surface change also perturbs the ray-mapping. Thus, taking the perturbed ray-mapping into account enables prediction with greater accuracy. Using this method, expected surface deformation from the manufacturing process can guide estimating irradiance changes, providing a first-order method to tolerance illumination optics.
Blind Bin Picking of Small Screws Through In-finger Manipulation With Compliant Robotic Fingers (2020)

Although picking up objects a few centimeters in size is a common task, achieving such ability in a robot manipulator remains challenging. We take a step toward solving this problem by focusing on the task of picking a 1.0-cm screw from a bulk bin using only tactile information to achieve the task. Inspired by how humans pick up small objects from a bin, we propose a "grasp-separate" strategy for robotic picking, which involves grasping many objects first and then separating a single object through manipulation in the fingers, for robotic picking. Based on this strategy, we developed a tactile-based screw bin-picking system. We trained a convolution neural network to estimate the number of screws in the fingers first and built a controller that generates manipulation behaviors to separate a screw using reinforcement learning. To compensate for the low resolution of off-the-shelf tactile sensor arrays, we adopted active sensing, which uses observations obtained during a predefined simple movement. We show that this approach enhances the estimation accuracy and manipulation performance. Furthermore, to enable flexible finger motion, such as between the thumb and the index finger in a human hand, we propose a soft robot finger structure that leverages compliant materials. A soft actor-critic algorithm successfully found dexterous screw separation behaviors in compliant soft robotic fingers. In the evaluation, the system obtained an average success rate of 80%, which was difficult to achieve without the grasp-separate manipulation technique.
Optimal Receive Antenna Selection in Time-Varying Fading Channels with Practical Training Constraints (2010)

Hardware constraints, which motivate receive antenna selection, also require that various antenna elements at the receiver be sounded sequentially to obtain estimates required for selecting the 'best' antenna and for coherently demodulating data thereafter. Consequently, the channel state information at different antennas is outdated by different amounts and corrupted by noise. We show that, for this reason, simply selecting the antenna with the highest estimated channel gain is not optimum. Rather, a preferable strategy is to linearly weight the channel estimates of different antennas differently, depending on the training scheme. We derive closed-form expressions for the symbol error probability (SEP) of AS for MPSK and MQAM in time-varying Rayleigh fading channels for arbitrary selection weights, and validate them with simulations. We then characterize explicitly the optimal selection weights that minimize the SEP. We also consider packet reception, in which multiple symbols of a packet are received by the same antenna. New suboptimal, but computationally efficient weighted selection schemes are proposed for reducing the packet error rate. The benefits of weighted selection are also demonstrated using a practical channel code used in third generation cellular systems. Our results show that optimal weighted selection yields a significant performance gain over conventional unweighted selection.
Design of a link-controller architecture for multiple serial link protocols (2010)

This paper introduces a novel Multi-mode Serial Link Controller (MMSLC) for logic physical layer (PHY) and data link layer (DLL) of USB 3.0, PCIe 2.0 and SATA 3.0. Functions defined in these protocols are grouped based on qualifying similarities and workload. The framework consists of a configurable circuit, programmable accelerator and event processor for flexible implementation. This MMSLC can essentially substitute for three individual link-controllers across protocols, thus achieving area reduction. An RTL level implementation is fulfilled and the synthesis results are shown at the end of this paper.
Vaccine adjuvant properties of probiotic bacteria. (2011)

Vaccine-preventable diseases are still responsible for the deaths of more than 1 million children under the age of 5 years annually, mostly in developing countries. A substantial number of these deaths are due to pneumococcal bacteria and infections with rotavirus. Important issues faced by the WHO, governments, vaccine manufacturers, and international organizations such as UNICEF and the Global Alliance for Vaccines and Immunization (GAVI) are the cost-effective introduction of these life-saving vaccines in resource-poor countries where there is a considerable disease burden, and achieving high rates of completion of vaccination schedules remains elusive. Problems with vaccine coverage and vaccine delivery in these regions are significant, as in some cases large proportions of the target population do not receive adequate vaccination. Consequently, there is a need to develop more effective vaccination strategies that can provide adequate protection with reduced schedules. To date, emphasis has been placed on identifying novel vaccine antigens and adjuvants that induce stronger protective immune responses, as well as developing mucosally-administered vaccines. These approaches would have enormous benefits in allowing safe administration of vaccines in remote areas and may overcome the necessity for multiple doses. In this regard, the use of probiotic bacteria as novel mucosal adjuvants to enhance existing vaccine specific-immune responses offers an exciting new approach. In this review, we discuss the evidence for the role of probiotics in enhancing vaccine responses and provide justification for further investigation into their clinical effects and mechanisms of action.
Low-field nuclear magnetic resonance relaxation study of the thermal denaturation of transferrins (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLow-field nuclear magnetic resonance relaxation study of the thermal denaturation of transferrinsP. Lambelet, F. Ducret, J. L. Leuba, and M. GeoffroyCite this: J. Agric. Food Chem. 1991, 39, 2, 287–292Publication Date (Print):February 1, 1991Publication History Published online1 May 2002Published inissue 1 February 1991https://pubs.acs.org/doi/10.1021/jf00002a013https://doi.org/10.1021/jf00002a013research-articleACS PublicationsRequest reuse permissionsArticle Views79Altmetric-Citations6LEARN 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-Alertsclose Get e-Alerts
P326 DNA replication initiator proteins stabilize the kinetochore in the human fungal pathogen Cryptococcus neoformans (2022)

Abstract Poster session 3, September 23, 2022, 12:30 PM - 1:30 PM Objectives DNA replication licensing ensures maintenance of the ploidy state by limiting DNA replication once per cell cycle. The mini-chromosome maintenance (MCM) complex is an evolutionarily conserved DNA helicase in eukaryotes that aids this process. Upon activation in the S phase by several protein kinases, the MCM complex unwinds the double-stranded DNA and moves away from DNA replication origins preventing re-initiation of replication in the remainder of the cell cycle. Deregulation of MCM function can lead to malignant transformation of proliferating cells as indicated by their upregulated expression in human cancer and pre-cancerous cells. MCMs, therefore, serve as important biomarkers and potential targets for anti-cancer drugs. This study aims to decipher the effect of deregulated expression of the MCM complex on the cell cycle events of the human fungal pathogen, Cryptococcus neoformans, which is more similar to metazoans than other budding yeast. Aneuploidy-mediated drug resistance is a common mechanism in many major human fungal pathogens including Cryptococcus and Candida. Methods We generated conditional mutants of individual subunits of the MCM complex in C. neoformans and assayed the impact of their altered expression on cell cycle events. We also tested the alternative role of MCM subunits in the assembly of the kinetochore, a vital component of the chromosome segregation machinery. Results Our screen with MCM conditional mutants identified two in vivo functional subcomplexes that comprise the MCM complex in C. neoformans. Although upregulated expression of either Mcm2 or Mcm3 does not affect cell cycle progression, overexpression of either Mcm6 or Mcm7 led to the accumulation of cells in the large bud stage with nuclear segregation defects. This work provides evidence for the first time for a mitotic role of pre-replication complex proteins, MCM 2-7 complex in Cryptococcus. Depletion of Mcm2 led to arrest of cells in the S and G2/M stages of the cell cycle with defects in nuclear segregation. Localization and expression of several kinetochore proteins upon depletion of Mcm2 established that Mcm2 is vital for kinetochore assembly/integrity. Although the centromeric histone H3 variant, CENP-A, remains largely clustered, the outer kinetochore did not mature indicating that Mcm2 alone or as part of the MCM complex plays a role in kinetochore assembly/integrity and thereby in chromosome segregation. Conclusion A conserved eukaryotic DNA helicase, MCM 2-7 complex, has an unexplored non-canonical role in kinetochore assembly/integrity and chromosome segregation.
Foundational Issues in Natural Language Processing: Introduction (1991)

Citation Sells, Peter, Stuart M. Shieber, and Thomas Wasow. 1991. Foundational Issues in Natural Language Processing: Introduction. In Foundational Issues in Natural Language Processing: Introduction, ed. Peter Sells, Stuart M. Shieber, and Thomas Wasaw. System Development Foundation Benchmark Series. Cambridge: MIT Press. Introduction reprinted in Carlos P. Otero, ed., Noam Chomsky. 1994. Critical Assessments (2), 81-90, New York: Routledge.
ChemInform Abstract: A New Approch to Prostanoids. (1986)

Abstract Cyclohexenon (I) wird als optisch aktives Acetal zum Cyclopentenon‐aldehyd gespalten und dann mit den Borverbindungen (III) in definierte Addukte (IV) umgewandelt.
PON Deployment of Angle Polished Connectors: Endface Geometry and Connector Reliability in the Outside Plant (2005)

Angled physical contact (APC) fiber optic connectors with zirconia ferrules have become the de facto standard in PON networks currently being deployed for FTTH initiatives. The angle on the fiber in APC connectors produces low back reflections when the connector is not mated to another connector: Reflected light is directed into the fiber cladding because the endface angle is greater than the acceptance angle of the fiber. The low reflection of an unmated APC connector provides an advantage for PON networks: A connector in the PON will usually remain unmated until service is required from that circuit. This results in unused connectors emitting their signal into air, which can produce Frensel reflections as high as -14dB for connectors without an angle on the endface. Service providers need to minimize system reflections so it won't interfere with OLT card operation. One solution is to use non-angled connectors and mate all unused connectors to a terminator. This solution adds cost because terminators are an additional component. Using APC connectors provides a cost-effective method to greatly reduce reflection issues caused by unmated connectors in the PON. Using APC connectors eliminates the need for terminators because the reflectance of unmated APC connectors is less than -50dB.
Supplementary Figure 3 from Nonclassical Antigen-Processing Pathways Are Required for MHC Class II–Restricted Direct Tumor Recognition by NY-ESO-1–Specific CD4<sup>+</sup> T Cells (2023)

&lt;p&gt;PDF file - 152K, MHC class II antigen presentation pathway of intracellular NY-ESO-1 by SK-MEL-37.&lt;/p&gt;
Finite element analysis of phased plano-concave multi-layer transducers (2002)

Phased multi-layer transducers offer the potential for yielding very high (multiple octave) usable bandwidth. The null normally encountered at the second harmonic is avoided and replaced with a resonant peak. However, the resulting spectrum exhibits a number of 'bumps' that result in an undesirable 'tail' in the time-domain impulse response. In this paper we present new results obtained using finite element analysis of modified multi-layer transducers in which the elements have diverse thickness so as to smooth out the associated spectral response. In this example we use dual-layer plano-concave elements. 3D finite element analysis is well suited to these complex 3D devices since they can include finite dimension effects in all three directions and properly account for the irregular geometry. Fortunately both the PZFlex finite element analysis technique and the materials of interest (PZT-5H type material) are very well characterized at this time and thereby enable reliable, accurate virtual design and test. In this paper we explore some of the design variables (e.g. maximum ratio of the thickness dimensions along the PZT bar element) and determine the practical extent of achievable bandwidth consistent with a smooth spectral characteristic, relatively uniform thickness vibrational motion and a lack of spurious lateral wave activity.
Multi-Agent Deep Reinforcement Learning Based User Association for Dense mmWave Networks (2019)

Finding the optimal association between users and base stations that maximizes the network sum-rate is a complex task. This problem is combinatorial and non-convex, and is even more challenging in millimeter-wave networks due to beamforming, blockages, and severe path loss. Despite the interest that this problem has gained over the last years, the various solutions proposed so far in the literature still fail at being flexible, computationally effective, and suitable to the dynamic nature of mobile networks. This paper addresses these issues with a novel distributed algorithm based on multi-agent reinforcement learning. More specifically, we model each user as an agent, which, at each time step, maps its observations to an action corresponding to an association request to a base station in its coverage range. Our numerical results show that the proposed solution offers near optimal performance and thanks to its flexibility, provides large sum-rate gain with respect to the state-of-art approaches.
A convenient synthesis of [3‐3H]squalene and [3‐3H]‐2,3‐oxidosqualene (1994)

Abstract [3‐ 3 H]Squalene and [3‐ 3 H]‐2,3‐oxidosqualene, key compounds for studying the biosynthesis of sterols, were synthesized. The main step was a modified Wittig reaction of [1‐ 3 H]trisnorsqualene aldehyde with a phosphorus ylide to give [3‐ 3 H]squalene or with a sulfur ylide to give [3‐ 3 H]‐2,3‐oxidosqualene. These compounds were obtained in high radiochemical yield and high purity under simple conditions.
Supplementary Figure 1 from Temporal Dissection of Tumorigenesis in Primary Cancers (2023)

Supplementary Figure 1 from Temporal Dissection of Tumorigenesis in Primary Cancers