gebhart/patrepeval huggingface dataset:
Frontispiece: Lighting Up the Plasma Membrane: Development and Applications of Fluorescent Ligands for Transmembrane Proteins (2021)

Receptorflix would ideally enable researchers to visualize any already-targeted transmembrane receptor at the cell's surface. Tailor-made fluorescent ligands accessed by coupling pharmacophores to organic fluorescent dyes are successfully employed to image GPCRs, LGICs, and VGICs. Recent advances in fluorescence microscopy and progress in dye synthesis enable their use in distinct techniques and model organisms. Read more about the literature of the last 25 years on the topic, including fluorescent ligand design and subsequent use in fluorescence imaging techniques to study the three most common classes of transmembrane receptors in the Review by S. Munck and E. Ismalaj et al. on 8605 ff.
Alpha-crystallin B chains in trastuzumab-resistant breast cancer cells promote endothelial cell tube formation through activating mTOR (2021)

The specific human epidermal growth factor receptor 2 (HER2)-targeting monoclonal antibody trastuzumab shows considerable clinical efficacy in patients with HER2-overexpressing breast cancer. However, about 20% of patients who receive trastuzumab in the adjuvant setting relapse, and approximately half of patients with metastatic HER2-positive breast cancer develop resistance to trastuzumab within 1 year. Although the mechanism of trastuzumab resistance has been explored broadly, whether and how angiogenesis participates in trastuzumab resistance is unclear. Here, we examined the association between angiogenesis and trastuzumab resistance by using a trastuzumab-resistant cell line (SKBR3-TR). Compared with that from the parental trastuzumab-sensitive SKBR3 cells, the culture supernatant from SKBR3-TR cells significantly increased the sprouting of endothelial cells. To identify intercellular features that contribute to the induction of endothelial tube formation, proteomics revealed that α-crystallin B chain (αB-crystallin) was upregulated in SKBR3-TR cells. Moreover, silencing of αB-crystallin significantly repressed SKBR3-TR-induced tube formation, and knockdown of αB-crystallin in SKBR3-TR cells suppressed the activation of mechanistic target of rapamycin (mTOR) in endothelial cells. In addition, treatment with rapamycin, an inhibitor of mTOR, reversed the SKBR3-TR-induced promotion of tube formation. In summary, αB-crystallin enhanced the ability of SKBR3-TR cells to activate mTOR in endothelial cells and thus promote angiogenesis.
Cooperative Hybrid Networks with Active Relays and RISs for B5G: Applications, Challenges, and Research Directions (2022)

Among the recent advances and innovations in wireless technologies, reconfigurable intelligent surfaces (RISs) have received much attention. RISs are envisioned to be one of the enabling technologies for beyond 5G (B5G) networks. On the other hand, active (or classical) cooperative relays have played a key role in providing reliable and power-efficient communications in previous wireless generations. In this article, we focus on hybrid network architectures that amalgamate both active relays and RISs. First, we discuss each technology's operations concepts and protocols. Subsequently, we present multiple use cases of cooperative hybrid networks, where both active relays and RISs can coexist harmoniously for enhanced rate performances. In addition, we provide a case study demonstrating a communications network's achievable rate performance, assisted by either an active relay, an RIS, or both - and with different relaying protocols. Finally, we present the reader with challenges and key research directions in this area.
Two Diastereomeric Oxalatobis(S-butane-1,3-diamine)cobalt(III) Complexes (1972)

A study of the oxalatobis(S-butane-1,3-diamine)cobalt(III) system shows that the dissymmetric ligand imposes uniquely related geometric and configurational selectivity. The selectivity is in agreement with conformational prediction and the magnitudes of the Cotton effects lend some support to recently developed sector rules.
Nanofibers Resulting from Cooperative Electrostatic and Hydrophobic Interactions between Peptides and Polyelectrolytes of Opposite Charge (2011)

We investigated whether cationic peptides that contain hydrophobic side chains were able to stabilize themselves via hydrophobic interactions between neighboring peptide molecules upon electrostatic binding to oppositely charged polyelectrolytes. The interaction mechanism was examined through a model system consisting of the anionic polyelectrolyte alginate and the cationic decapeptide ozarelix. The interaction resulted in the formation of highly ordered complexes that were noticeable upon visual inspection. These complexes were then investigated by microscopic techniques and shown to exhibit a branched network structure. Cryogenic-temperature transmission electron microscopy (cryo-TEM) and negative staining TEM revealed that the molecular interactions between alginate and ozarelix led to the formation of nanofibers. The rodlike nanofibers had a diameter distribution of 4-8 nm. Isothermal titration calorimetry was used to determine the thermodynamic parameters of the alginate-ozarelix interaction. The binding constant was found to be on the order of 10(6) M(-1), indicating a high binding affinity. The interaction of the peptide with the polyelectrolyte triggered profound changes in the conformation of ozarelix, which was confirmed by UV spectroscopy and circular dichroism. On the basis of these experimental results, a theoretical modeling study of the alginate-ozarelix interaction was conducted to gain a better molecular-level understanding of the complex structure. It revealed that, upon binding of ozarelix to alginate, new intermolecular and intramolecular aromatic interactions between the ozarelix molecules occurred. These interactions changed the conformation of the peptide, a modification in which the aromatic side chains played a major role. Our results indicate that the cationic peptides interact with the polyanions via electrostatic interactions, but are additionally stabilized via hydrophobic interactions. This binding mode may serve as a powerful tool to extend the duration of drug release in hydrogel drug delivery systems.
Estimating tissue permeability and other bioelectrical parameters using membrane voltage and short-circuit current. (1991)

Evaluating the acute toxic effects of drugs or toxins is based mainly on studies which require the use of light microscopy. Recently, the effects of such substances on biological membranes, such as the nasal membrane, has been studied using the traditional Ussing chambers, which make it possible to study the transepithelial flux of drugs across membranes and to measure some bioelectrical parameters. A model is described, with which the changes in the membrane permeability, for sodium, potassium and chlorine, can be calculated directly, based on values obtained from the Ussing chamber system. Also, an experiment is described for evaluating the toxic effects of the cholera toxin B subunit, by measuring these changes in isolated rabbit nasal mucosa.
Improved Therapeutic Antibody Delivery to Xenograft Tumors Using Cavitation Nucleated by Gas-Entrapping Nanoparticles (2021)

<b>Aims:</b> Testing ultrasound-mediated cavitation for enhanced delivery of the therapeutic antibody cetuximab to tumors in a mouse model. <b>Methods:</b> Tumors with strong EGF receptor expression were grown bilaterally. Cetuximab was coadministered intravenously with cavitation nuclei, consisting of either the ultrasound contrast agent Sonovue or gas-stabilizing nanoscale SonoTran Particles. One of the two tumors was exposed to focused ultrasound. Passive acoustic mapping localized and monitored cavitation activity. Both tumors were then excised and cetuximab concentration was quantified. <b>Results:</b> Cavitation increased tumoral cetuximab concentration. When nucleated by Sonovue, a 2.1-fold increase (95% CI 1.3- to 3.4-fold) was measured, whereas SonoTran Particles gave a 3.6-fold increase (95% CI 2.3- to 5.8-fold). <b>Conclusions:</b> Ultrasound-mediated cavitation, especially when nucleated by nanoscale gas-entrapping particles, can noninvasively increase site-specific delivery of therapeutic antibodies to solid tumors.
On Locating Byzantine Attackers (2008)

We examine networks that employ network coding and are subject to Byzantine attacks. We assume that an appropriate network error correcting scheme is employed that is able to correct (up to a certain number of) Byzantine errors. Given this setup, we formulate the problem of locating these malicious nodes that insert errors. We utilize the sub- space properties of (randomized) network coding to develop algorithms to locate the Byzantine attackers.
Glutathione Induced Immune-Stimulatory Activity by Promoting M1-Like Macrophages Polarization via Potential ROS Scavenging Capacity (2019)

The present study investigated the immunomodulatory activity of reduced glutathione (GSH) by assessment of the macrophage polarization (MP)-mediated immune response in RAW 264.7 cells. Furthermore, we identified the signal pathway associated with immune regulation by GSH. The expressions of MP-associated cytokines and chemokines were assessed using cytokine array, nCounter Sprit platform, ELISA and immunoblotting. Phagocytosis activity and intracellular reactive oxygen species (ROS) generation were measured using fluorescence-activated cell sorter. As results of the cytokine array and nCounter gene array, GSH not only up-regulated pro-inflammatory cytokines, including interleukins and tumor necrosis factor-α, but also overexpressed neutrophil-attracting chemokines. Furthermore, GSH significantly stimulated the production of immune mediators, including nitric oxide and PGE<sub>2</sub>, as well as phagocytosis activity through nuclear factor kappa B activation. In addition, GSH significantly decreased LPS-induced ROS generation, which was associated with an activation of nuclear factor erythroid-derived 2-related factor 2 (Nrf2)/ heme oxygenease-1 (HO-1) signaling pathway. Our results suggest that GSH has potential ROS scavenging capacity via the induction of Nrf2-mediated HO-1, and immune-enhancing activity by regulation of M1-like macrophage polarization, indicating that GSH may be a useful strategy to increase the human defense system.
Mechanics of Nanowires (2002)

Journal Article Mechanics of Nanowires Get access Rodney S Ruoff, Rodney S Ruoff Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 Search for other works by this author on: Oxford Academic Google Scholar Xinqi Chen, Xinqi Chen Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 Search for other works by this author on: Oxford Academic Google Scholar Dmitriy Dikin, Dmitriy Dikin Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 Search for other works by this author on: Oxford Academic Google Scholar Weiqiang Ding, Weiqiang Ding Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 Search for other works by this author on: Oxford Academic Google Scholar Ming-Feng Yu, Ming-Feng Yu Zyvex Corporation, Advanced Technologies Group, 1321 North Plano Road, Richardson, TX 75081 Search for other works by this author on: Oxford Academic Google Scholar Gregory J Wagner Gregory J Wagner Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 8, Issue S02, 1 August 2002, Pages 304–305, https://doi.org/10.1017/S1431927602100845 Published: 01 November 2002
Polarisation and modal behaviour of low thresholdoxide and airgap confined vertical cavity lasers (1995)

Polarisation and modal behaviour are compared for very low threshold oxide confined and airgap confined vertical cavity lasers. Although both structures have nearly identical optical models leading to the same stable fundamental mode emission up to many times threshold, they show very different polarisation behaviours. Predetermined polarisation up to 18 times threshold is achieved for the oxide confined vertical cavity lasers.
Acid‐Catalyzed Synthesis and Deprotection of Dimethyl Acetals in a Miniaturized Electroosmotic Flow Reactor. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Digital Low Level RF Systems for Diamond Light Source (2017)

Analogue low level RF (LLRF) systems have been used to date for both Diamond storage ring and booster RF cavities. They have been in operation for nearly ten years without a major problem. However, digital LLRF can offer new desirable functionalities such as fast data logging, 'probe blip' blockage and automation of routine tasks. Better performance is also envisaged with up to date hardware. A digital LLRF system has been developed with Alba Synchrotron as a common platform for the storage ring and booster, including superconducting and normal conducting RF cavities. The new digital LLRF is based on Virtex6 FPGA and fast ADCs and DACs. One system has been built and verified in the Diamond booster with beam. The design will be implemented for all other Diamond RF cavities.
CONSORT Extension for Chinese Herbal Medicine Formulas 2017: Recommendations, Explanation, and Elaboration (Traditional Chinese Version) (2017)

Editors' Note: This article is the traditional Chinese version of the CONSORT Extension for Chinese Herbal Medicine Formulas 2017: Recommendations, Explanation, and Elaboration. (Cheng C, Wu T, Shang H, Li, Y, Altman D, Moher D; CONSORT-CHM Formulas 2017 Group. CONSORT Extension for Chinese Herbal Medicine Formulas 2017: Recommendations, Explanation, and Elaboration. Ann Intern Med. 2017;167:112-21. [Epub 27 June 2017]. doi:10.7326/M16-2977).
Erratum: Bloch Oscillations of Path-Entangled Photons [Phys. Rev. Lett.105, 263604 (2010)] (2011)

Received 9 March 2011DOI:https://doi.org/10.1103/PhysRevLett.106.149902© 2011 American Physical Society
Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids (2008)

In addition to the genomes of Arabidopsis (Arabidopsis thaliana) and poplar (Populus trichocarpa), two near-complete rosid genome sequences, grape (Vitis vinifera) and papaya (Carica papaya), have been recently released. The phylogenetic relationship among these four genomes and the placement of their three independent, fractionated tetraploidies sum to a powerful comparative genomic system. CoGe, a platform of multiple whole or near-complete genome sequences, provides an integrative Web-based system to find and align syntenic chromosomal regions and visualize the output in an intuitive and interactive manner. CoGe has been customized to specifically support comparisons among the rosids. Crucial facts and definitions are presented to clearly describe the sorts of biological questions that might be answered in part using CoGe, including patterns of DNA conservation, accuracy of annotation, transposability of individual genes, subfunctionalization and/or fractionation of syntenic gene sets, and conserved noncoding sequence content. This précis of an online tutorial, CoGe with Rosids (http://tinyurl.com/4a23pk), presents sample results graphically.
Simultaneous formation of a metallic Mn layer and a MnOx / MnSixOy barrier layer by chemical vapor deposition at 250°C (2012)

A metallic Mn layer was successfully formed on tetraethylorthosilicate (TEOS)?SiO2 substrate at the deposition temperature of 250 ?C by chemical vapor deposition (CVD) using a newly developed Mn precursor, bis[1-(tert-butylamide)-2-dimethylaminoethane-N,N ']manganese. A thin and uniform Mn oxide layer was simultaneously formed at a CVD-Mn/TEOS?SiO2 interface, and was partially embedded in the TEOS?SiO2. This Mn oxide layer was composed of a bilayer of MnOx and MnSixOy. After annealing at 400 ?C in vacuum for 10 h, the interface Mn oxide layer showed a good barrier property and thermal stability.
Angle-Resolved Surface-Enhanced Raman Scattering on Metallic Nanostructured Plasmonic Crystals (2005)

Surface-enhanced Raman scattering is an ideal tool for identifying molecules from the "fingerprint" of their molecular bonds; unfortunately, this process lacks a full microscopic understanding and, practically, is plagued with irreproducibility. Using nanostructured metal surfaces, we demonstrate strong correlations between plasmon resonances and Raman enhancements. Evidence for simultaneous ingoing and outgoing resonances in wavelength and angle sheds new light on the Raman enhancement process, allowing optimization of a new generation of reproducible Raman substrates.
A Voltage-Controlled, Oscillation-Based ADC Design for Computation-in-Memory Architectures Using Emerging ReRAMs (2022)

Conventional von Neumann architectures cannot successfully meet the demands of emerging computation and data-intensive applications. These shortcomings can be improved by embracing new architectural paradigms using emerging technologies. In particular, Computation-In-Memory (CiM) using emerging technologies such as Resistive Random Access Memory (ReRAM) is a promising approach to meet the computational demands of data-intensive applications such as neural networks and database queries. In CiM, computation is done in an analog manner; digitization of the results is costly in several aspects, such as area, energy, and performance, which hinders the potential of CiM. In this article, we propose an efficient Voltage-Controlled-Oscillator (VCO)–based analog-to-digital converter (ADC) design to improve the performance and energy efficiency of the CiM architecture. Due to its efficiency, the proposed ADC can be assigned in a per-column manner instead of sharing one ADC among multiple columns. This will boost the parallel execution and overall efficiency of the CiM crossbar array. The proposed ADC is evaluated using a Multiplication and Accumulation (MAC) operation implemented in ReRAM-based CiM crossbar arrays. Simulations results show that our proposed ADC can distinguish up to 32 levels within 10 ns while consuming less than 5.2 pJ of energy. In addition, our proposed ADC can tolerate ≈30% variability with a negligible impact on the performance of the ADC.
InfoFlo: a novel communication infrastructure for personal digital assistants (2002)

Personal digital assistants (PDAs) are becoming commonplace, and feature continually increasing processing and storage capabilities. Distribution of media through wireless means to these devices is becoming less expensive, but is not yet widespread. The authors describe a novel communication infrastructure to provide distribution of information to PDAs utilizing inexpensive methods; our approach is both scalable and flexible. Most PDAs support infrared (IR) communication, and we focus on this; our infrastructure is not restricted to this, however, and is adaptable to the emerging wireless communication technologies.
The experience of pregnancy among women living with HIV in Nordic countries: A qualitative narrative enquiry (2022)

The findings emphasize a sense of normality in pregnancy among women living with HIV. However, pregnancy does come with unique considerations and concerns, which highly influence the women's experience of pregnancy. Healthcare providers should focus on person-centered care, ensuring continuity and that women living with HIV do not feel discriminated against throughout their pregnancy.
Frames: a corpus for adding memory to goal-oriented dialogue systems (2017)

This paper proposes a new dataset, Frames, composed of 1369 human-human dialogues with an average of 15 turns per dialogue.This corpus contains goal-oriented dialogues between users who are given some constraints to book a trip and assistants who search a database to find appropriate trips.The users exhibit complex decision-making behaviour which involve comparing trips, exploring different options, and selecting among the trips that were discussed during the dialogue.To drive research on dialogue systems towards handling such behaviour, we have annotated and released the dataset and we propose in this paper a task called frame tracking.This task consists of keeping track of different semantic frames throughout each dialogue.We propose a rule-based baseline and analyse the frame tracking task through this baseline.
Zn/Cu-vegetative batteries, bioelectrical characterizations, and primary cost analyses (2010)

Developing a cheap, sustainable, and simple to use low power electrical energy source will substantially improve the life quality of 1.6×109 people, comprising 32% of the developing non-Organization for Economic Co-Operation and Development populations currently lacking access to electrical infrastructure (World Energy Outlook, 2006, http://www.worldenergyoutlook.org/2006.asp, 10 September 2009). Such a source will provide important needs as lighting, telecommunication, and information transfer. Our previous studies on Zn/Cu electrolysis in animal tissues revealed a new fundamental bioelectrical property: the galvanic apparent internal impedance (GAII) [A. Golberg, H. D. Rabinowitch, and B. Rubinsky, Biochem. Biophys. Res. Commun. 389, 168 (2009)], with potential use for tissue typing. We now report on new fundamental studies on GAII in vegetative matter and on a simple way for significant performance improvement of Zn/Cu-vegetative battery. We show that boiled or irreversible electroporated potato tissues with disrupted cell membranes generate electric power up to tenfold higher than equal galvanic cell made of untreated potato. The study brought about basic engineering data that make possible a systematic design of a Zn/Cu-potato electrolytic battery. The ability to produce and utilize low power electricity was demonstrated by the construction of a light-emitting diode based system powered by potato cells. Primary cost analyses showed that treated Zn/Cu-potato battery generates portable energy at ∼9 USD/kW h, which is 50-fold cheaper than the currently available 1.5 V AA alkaline cell (retail) or D cells (∼49–84 USD/kW h). Admittedly very simple, the treated potato or similarly treated other plant tissues could provide an immediate, environmental friendly, and inexpensive solution to many of the low power energy needs in areas of the world lacking access to electrical infrastructure.
MEMS liquid metal through-wafer microstrip to microstrip transition (2008)

A novel approach for creating an RF MEMS switch in the form of a microstrip-to-microstrip liquid-metal transition is presented. A slug of non-toxic liquid metal that controllably fills a through-wafer via is the key component of the switch. The large contact area between this slug and the solid microstrip lines renders this design an excellent candidate for high-power switching and particularly for hot-switching applications. With the slug inside the via the switch presents a measured insertion loss of 0.24 and 1.1 dB up to 5 and 10 GHz respectively. When the slug is removed from the via the switch isolation is measured to be more than 20 dB up to 7 GHz. The fabrication technology and critical trade-offs between RF and microfluidic performances are discussed in the paper. The slug movement is controlled by an external micropump. The recent advances in microfluidics have resulted in a large variety of practical micropumps that may be monolithically integrated with such switching designs.