gebhart/patrepeval huggingface dataset:
Unusual Symbiotic Cyanobacteria Association in the Genetically Diverse Intertidal Marine Sponge Hymeniacidon perlevis (Demospongiae, Halichondrida) (2012)

Cyanobacteria represent one of the most common members of the sponge-associated bacterial community and are abundant symbionts of coral reef ecosystems. In this study we used Transmission Electron Microscopy (TEM) and molecular techniques (16S rRNA gene marker) to characterize the spatial distribution of cyanobionts in the widely dispersed marine intertidal sponge Hymeniacidon perlevis along the coast of Portugal (Atlantic Ocean). We described new sponge associated cyanobacterial morphotypes (Xenococcus-like) and we further observed Acaryochloris sp. as a sponge symbiont, previously only reported in association with ascidians. Besides these two unique cyanobacteria, H. perlevis predominantly harbored Synechococcus sp. and uncultured marine cyanobacteria. Our study supports the hypothesis that the community of sponge cyanobionts varies irrespective of the geographical location and is likely influenced by seasonal fluctuations. The observed multiple cyanobacterial association among sponges of the same host species over a large distance may be attributed to horizontal transfer of symbionts. This may explain the absence of a co-evolutionary pattern between the sponge host and its symbionts. Finally, in spite of the short geographic sampling distance covered, we observed an unexpected high intra-specific genetic diversity in H. perlevis using the mitochondrial genes ATP6 (π = 0.00177), COI (π = 0.00241) and intergenic spacer SP1 (π = 0.00277) relative to the levels of genetic variation of marine sponges elsewhere. Our study suggests that genotypic variation among the sponge host H. perlevis and the associated symbiotic cyanobacteria diversity may be larger than previously recognized.
Protein Folding Intermediates and Pathways Studied by Hydrogen Exchange (2000)

In order to solve the immensely difficult protein-folding problem, it will be necessary to characterize the barriers that slow folding and the intermediate structures that promote it. Although protein-folding intermediates are not accessible to the usual structural studies, hydrogen exchange (HX) methods have been able to detect and characterize intermediates in both kinetic and equilibrium modes--as transient kinetic folding intermediates on a subsecond time scale, as labile equilibrium molten globule intermediates under destabilizing conditions, and as infinitesimally populated intermediates in the high free-energy folding landscape under native conditions. Available results consistently indicate that protein-folding landscapes are dominated by a small number of discrete, metastable, native-like partially unfolded forms (PUFs). The PUFs appear to be produced, one from another, by the unfolding and refolding of the protein's intrinsically cooperative secondary structural elements, which can spontaneously create stepwise unfolding and refolding pathways. Kinetic experiments identify three kinds of barrier processes: (a) an initial intrinsic search-nucleation-collapse process that prepares the chain for intermediate formation by pinning it into a condensed coarsely native-like topology; (b) smaller search-dependent barriers that put the secondary structural units into place; and (c) optional error-dependent misfold-reorganization barriers that can cause slow folding, intermediate accumulation, and folding heterogeneity. These conclusions provide a coherent explanation for the grossly disparate folding behavior of different globular proteins in terms of distinct folding pathways.
Biomarkers and Surrogate End Points for Fit-for-Purpose Development and Regulatory Evaluation of New Drugs (2006)

A consistent framework for the acceptance and qualification of biomarkers for regulatory use is needed to facilitate innovative and efficient research and subsequent application of biomarkers in drug development. One key activity is biomarker qualification, a graded, "fit-for-purpose" evidentiary process linking a biomarker with biology and clinical end points. A biomarker consortium model will distribute cost and risk, and drive efficient execution of research and ultimately regulatory acceptance of biomarkers for specific indications.
A 2-bit, 3.1 GS/s, band-pass DSM receiver with 53.7 dB SNDR in 35 MHz bandwidth A single-chip RF-digitizing receiver for cellular active antenna systems (2012)

This paper presents a radio frequency (RF) continuous-time band-pass delta sigma modulator (CT BP DSM) receiver realized in a 180 nm SiGe BiCMOS technology. The internal quantizer and feedback DAC resolution is 2 bit. Without applying DAC linearization techniques such as trimming or dynamic element matching, measured performance parameters include an SNR and SNDR in 35 MHz of 56.7 dB and 53.7 dB, respectively. Image rejection across the notch center at a quarter of the clock frequency is at least 76 dB. IIP3 and noise figure are -6.6 dBm and 10 dB, respectively.
Generation and Characterization of a Diabody Targeting the αvβ6 Integrin (2013)

The αvβ6 integrin is up-regulated in cancer and wound healing but it is not generally expressed in healthy adult tissue. There is increasing evidence that it has a role in cancer progression and will be a useful target for antibody-directed cancer therapies. We report a novel recombinant diabody antibody fragment that targets specifically αvβ6 and blocks its function. The diabody was engineered with a C-terminal hexahistidine tag (His tag), expressed in Pichia pastoris and purified by IMAC. Surface plasmon resonance (SPR) analysis of the purified diabody showed affinity in the nanomolar range. Pre-treatment of αvβ6-expressing cells with the diabody resulted in a reduction of cell migration and adhesion to LAP, demonstrating biological function-blocking activity. After radio-labeling, using the His-tag for site-specific attachment of (99m)Tc, the diabody retained affinity and targeted specifically to αvβ6-expressing tumors in mice bearing isogenic αvβ6 +/- xenografts. Furthermore, the diabody was specifically internalized into αvβ6-expressing cells, indicating warhead targeting potential. Our results indicate that the new αvβ6 diabody has a range of potential applications in imaging, function blocking or targeted delivery/internalization of therapeutic agents.
Effects of Endothelin-1 on bacterial clearance (1998)

ANESTHESIOLOGY is the highest-impact, peer-reviewed medical journal that publishes trusted evidence that transforms the practice of perioperative, critical care, and pain medicine along with clinical reviews, editorials, podcasts, infographics, and videos.
Structural Phase Diagram of Mn–Fe Cyanide against Cation Concentration (2011)

Cyano-bridged transition metal compounds, represented as Na x Mn[Fe(CN) 6 ] y · z H 2 O, are promising cathode materials for Li ion secondary batteries. Here, we systematically investigated their structure against temperature ( T ) and cation concentration ( x ). We observed successive changes in their structure from cubic ( F m \bar3 m ; Z = 4 in the hexagonal setting) to trigonal ( R \bar3 m ; Z = 12), to monoclinic ( P 2/ m ; Z = 2) ones with decreasing T and increasing x . The trigonal–monoclinic structural phase transition was discussed in terms of the interaction between the host framework and the guest cation.
Motion understanding from qualitative visual dynamics (2002)

In many situations, motion is naturally grasped as an ordered sequence of poses, expressing stages in a general development. Capturing the underlying dynamics is an important first step for gaining insight and constructing a representation that has expressive power. The authors compute a pose function for a motion that qualitatively characterizes it in terms of dynamics. The study is based in dynamic systems analysis, constructing the function in phase space-a geometric depiction of the observed behaviour. The analysis itself is geometrical, but yields a representation of the visual dynamics. The global component of the pose function is an expression of external forces, and the local component and expression of deformation. The computation is simple, making only few general assumptions. The function captures all the relevant parameters of the motion in the sense that a qualitative simulation of the behavior is made possible, thus, facilitating subsequent reasoning about observed events.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Duplication models for biological networks (2006)

Are biological networks different from other large complex networks? Both large biological and non-biological networks exhibit power-law graphs (number of nodes with degree k, N(k) ~ k-b) yet the exponents, b, fall into different ranges. This may be because duplication of the information in the genome is a dominant evolutionary force in shaping biological networks (like gene regulatory networks and protein-protein interaction networks), and is fundamentally different from the mechanisms thought to dominate the growth of most non-biological networks (such as the internet [1-4]). The preferential choice models non-biological networks like web graphs can only produce power-law graphs with exponents greater than 2 [1-4,8]. We use combinatorial probabilistic methods to examine the evolution of graphs by duplication processes and derive exact analytical relationships between the exponent of the power law and the parameters of the model. Both full duplication of nodes (with all their connections) as well as partial duplication (with only some connections) are analyzed. We demonstrate that partial duplication can produce power-law graphs with exponents less than 2, consistent with current data on biological networks. The power-law exponent for large graphs depends only on the growth process, not on the starting graph.
Improved healing of small-caliber polytetrafluoroethylene prostheses by induction of a clot layer: a review of experimental studies in rats. (1992)

This report reviews our experiments that have been undertaken to test the hypothesis whether the induction of a clot layer on the graft surface of small-caliber polytetrafluoroethylene (PTFE) prostheses might improve their healing. PTFE prostheses with a fibril length of 30 microns, PTFE prostheses with a fibril length of 30 microns and either impregnated with Chitosan, or pretreated with alcohol or mechanically roughened, and PTFE prostheses with a fibril length of 60 microns (all prostheses: length 1 cm, ID 1.5 mm) were implanted into the abdominal aorta of rats and were evaluated from 1 day up till 6 weeks after implantation with regard to the presence or absence of a clot layer and with regard to the amount of graft healing. All untreated PTFE prostheses were never found to be covered with a clot layer and showed poor neoendothelial healing: even at 6 weeks after implantation, there were only endothelial cells near the anastomotic sides, directly on the graft surface. In contrast, all other PTFE prostheses were completely covered with a clot layer upon implantation and demonstrated almost complete neoendothelial healing after 6 weeks. Moreover, in these prostheses, the endothelial cells were present on a matrix of smooth muscle cells. These results confirm our hypothesis that the induction of a clot layer on the graft surface of PTFE prostheses improves their healing: the clot probably functions as a provisional matrix for the regeneration of arterial wall tissue, just as occurs in normal arterial wall repair.
Compressive Sensing for Indoor THz Channel Estimation (2018)

Terahertz (THz) communication is a new emerging technology which has the potential to satisfy the steadily growing demands for high data rates. However, transmission over the THz channel is a difficult task since perfect channel state information (CSI) is not available in real systems. Due to the high transmission rate and a high molecular absorption, spreading loss and reflection loss, the discrete-time channel impulse response (CIR) of the THz channel is very long and exhibits an approximately sparse characteristic. Conventional least-squares (LS) channel estimation does not incorporate the sparsity assumption into the estimation process. Therefore, in this work, sparse channel estimation for an indoor THz transmission example scenario using compressive sensing (CS) techniques is analyzed. A CS method based on solving a convex program by using the Dantzig selector (DS) and a CS approach using a greedy pursuit method called compressive sampling matching pursuit (CoSaMP) are investigated. All methods are analyzed with respect to mean squared error (MSE) performance, computational efficiency and numbers of observations needed. The numerical results show that significant advantages over LS estimation are achievable in all categories.
One-Pot Synthesis of Elastomeric Monoliths Filled with Individually Encapsulated Liquid Droplets (2012)

The ability to encapsulate and store liquids within discrete, micrometer-scale containers is essential for living organisms and is used by water-storage cells to keep plants healthy, even during a prolonged drought. This paper describes the one-pot synthesis of liquid droplet elastomers (LDEs), a novel materials system with advantageous properties. LDEs are tissue-like elastomeric monoliths that contain around 85% water in the form of individually encapsulated micrometer-scale droplets. The LDE structure is templated within high internal phase Pickering emulsions, emulsions stabilized by nanoparticles that also function as cross-linking centers. The polyhedral shapes of the droplets, which accommodate the high volume fraction of water, are “locked-in” to the LDE during polymerization. The water retention in these unique materials is exceedingly high, and as seen for living systems, the presence of the encapsulated water droplets enhances the resistance to compressive deformation and to ignition upon direct exposure to a flame.
Complex Formation in Oligonucleotides and Its Application to the Separation of Polynucleotides (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComplex Formation in Oligonucleotides and Its Application to the Separation of PolynucleotidesP. T. GilhamCite this: J. Am. Chem. Soc. 1962, 84, 7, 1311–1312Publication Date (Print):April 1, 1962Publication History Published online1 May 2002Published inissue 1 April 1962https://pubs.acs.org/doi/10.1021/ja00866a055https://doi.org/10.1021/ja00866a055research-articleACS PublicationsRequest reuse permissionsArticle Views100Altmetric-Citations30LEARN 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
Active hypertext for distributed Web applications (2003)

The prevailing architecture for Web-based applications relies on HTML, HTTP and loosely integrated functional elements, propagating a strong distinction between client and server. The proposed approach for active hypertext documents however realizes applications through hypertext documents with embedded application logic. Furthermore, the need for separating the approach into a model, a development method and supporting tools is identified. The core model is based on open standards such as XML and CSS. It is extended by idioms which describe important concepts and reusable constructs. Examples for the application of the model are given.
Atmospheric chemistry of (Z)- and (E)-1,2-dichloroethene: kinetics and mechanisms of the reactions with Cl atoms, OH radicals, and O3 (2022)

Smog chambers interfaced with <i>in situ</i> FT-IR detection were used to investigate the kinetics and mechanisms of the Cl atom, OH radical, and O<sub>3</sub> initiated oxidation of (<i>Z</i>)- and (<i>E</i>)-1,2-dichloroethene (CHClCHCl) under atmospheric conditions. Relative and absolute rate methods were used to measure <i>k</i>(Cl + (<i>Z</i>)-CHClCHCl) = (8.80 ± 1.75) × 10<sup>-11</sup>, <i>k</i>(Cl + (<i>E</i>)-CHClCHCl) = (8.51 ± 1.69) × 10<sup>-11</sup>, <i>k</i>(OH + (<i>Z</i>)-CHClCHCl) = (2.02 ± 0.43) × 10<sup>-12</sup>, <i>k</i>(OH + (<i>E</i>)-CHClCHCl) = (1.94 ± 0.43) × 10<sup>-12</sup>, <i>k</i>(O<sub>3</sub> + (<i>Z</i>)-CHClCHCl) = (4.50 ± 0.45) × 10<sup>-21</sup>, and <i>k</i>(O<sub>3</sub> + (<i>E</i>)-CHClCHCl) = (1.02 ± 0.10) × 10<sup>-19</sup> cm<sup>3</sup> molecule<sup>-1</sup> s<sup>-1</sup> in 700 Torr of N<sub>2</sub>/air diluent at 298 ± 2 K. Pressure dependencies for the Cl atom reaction kinetics were observed for both isomers, consistent with isomerization occurring <i>via</i> Cl atom elimination from the chemically activated CHCl-CHCl-Cl adduct. The observed products from Cl initiated oxidation were HC(O)Cl (117-133%), CHCl<sub>2</sub>CHO (29-30%), and the corresponding CHClCHCl isomer (11-20%). OH radical initiated oxidation gives HC(O)Cl as a major product. For reaction of OH with (<i>E</i>)-CHClCHCl, (<i>Z</i>)-CHClCHCl was also observed as a product. A significant chlorine atom elimination channel was observed experimentally (HCl yield) and supported by computational results. Photochemical ozone creation potentials of 12 and 11 were estimated for (<i>Z</i>)- and (<i>E</i>)-CHClCHCl, respectively. Finally, an empirical kinetic relationship is explored for the addition of OH radicals or Cl atoms to small alkenes. The results are discussed in the context of the atmospheric chemistry of (<i>Z</i>)- and (<i>E</i>)-CHClCHCl.
High-resolution Imaging using Scattered Light (2013)

Wavefront shaping and speckle correlation methods have spurred recent advances in focusing and imaging with scattered light. We show speckle correlation imaging at speckle scale resolution without the need of a reference particle or beam.
ADA-AT/DT: An Adversarial Approach for Cross-Domain and Cross-Task Knowledge Transfer (2021)

We deal with the problem of cross-task and cross-domain knowledge transfer in the realm of scene understanding for autonomous vehicles. We consider the scenario where supervision is available for a pair of tasks in a source domain while it is available for only one of the tasks in the target domain. Given that, the goal is to perform inference for the task in the target which is devoid of any training information. We argue that the only reported work in learning across tasks and domains (AT/DT) [26] faces the problem of domain shift between the source and target domains, hindering predictions on the target domain when the transfer of knowledge is learned on a statistically different yet related source domain. As a remedy, we develop a novel framework called ADA-AT/DT based on the adversarial training strategy to ensure that the domain-gaps are minimized for the common cross-domain supervised task. This, in effect, helps in realizing a domain-independent task-transfer function that eventually helps in performing improved inference in the target domain. We demonstrate that our proposed method significantly outperforms [26] by using models with 81% fewer trainable parameters. In addition, we perform experiments on a transformation mapping similar to U-Net to ensure maximum exploitation of features for task transfer. Extensive experiments have been performed on four different domains (Synthia, CityScapes, Carla, and KITTI) for two visual tasks (depth estimation and semantic segmentation) to confirm the superiority of our method.
Cathepsin-mediated Necrosis Controls the Adaptive Immune Response by Th2 (T helper type 2)-associated Adjuvants (2013)

Immunologic adjuvants are critical components of vaccines, but it remains unclear how prototypical adjuvants enhance the adaptive immune response. Recent studies have shown that necrotic cells could trigger an immune response. Although most adjuvants have been shown to be cytotoxic, this activity has traditionally been considered a side effect. We set out to test the role of adjuvant-mediated cell death in immunity and found that alum, the most commonly used adjuvant worldwide, triggers a novel form of cell death in myeloid leukocytes characterized by cathepsin-dependent lysosome-disruption. We demonstrated that direct lysosome-permeabilization with a soluble peptide, Leu-Leu-OMe, mimics the alum-like form of necrotic cell death in terms of cathepsin dependence and cell-type specificity. Using a combination of a haploid genetic screen and cathepsin-deficient cells, we identified specific cathepsins that control lysosome-mediated necrosis. We identified cathepsin C as critical for Leu-Leu-OMe-induced cell death, whereas cathepsins B and S were required for alum-mediated necrosis. Consistent with a role of necrotic cell death in adjuvant effects, Leu-Leu-OMe replicated an alum-like immune response in vivo, characterized by dendritic cell activation, granulocyte recruitment, and production of Th2-associated antibodies. Strikingly, cathepsin C deficiency not only blocked Leu-Leu-OMe-mediated necrosis but also impaired Leu-Leu-OMe-enhanced immunity. Together our findings suggest that necrotic cell death is a powerful mediator of a Th2-associated immune response.
Molecular Design Strategies for Color Tuning of Blue TADF Emitters (2019)

New thermally activated delayed fluorescence (TADF) blue emitter molecules based on the known donor-acceptor-donor (D-A-D)-type TADF molecule, 2,7-bis(9,9-dimethylacridin-10-yl)-9,9-dimethylthioxanthene-<i>S</i>,<i>S</i>-dioxide (DDMA-TXO2), are reported. The motivation for the present investigation is via the use of rational molecular design, based on DDMA-TXO2, to elevate the organic light emitting diode (OLED) performance and obtain deeper blue color coordinates. To achieve this goal, the strength of the donor (D) unit and acceptor (A) units have been tuned with methyl substituents. The methyl functionality on the acceptor was also expected to modulate the D-A torsion angle in order to obtain a blue shift in the electroluminescence. The effect of regioisomeric structures has also been investigated. Herein, we report the photophysical, electrochemical, and single-crystal X-ray crystallography data to assist with the successful OLED design. The methyl substituents on the DDMA-TXO2 framework have profound effects on the photophysics and color coordinates of the emitters. The weak electron-donating methyl groups alter the redox properties of the D and A units and consequently affect the singlet and triplet levels but not the energy gap (Δ<i>E</i><sub>ST</sub>). By systematically manipulating all of the aforementioned factors, devices have been obtained with acceptor-substituted <b>III</b> with a maximum external quantum efficiency of 22.6% and Commission Internationale de l'Éclairage coordinates of (0.15, 0.18) at 1000 cd m<sup>-2</sup>.