gebhart/patrepeval huggingface dataset:
Identification of mesenchymal stromal cell survival responses to antimicrobial silver ion concentrations released from orthopaedic implants (2020)

Antimicrobial silver (Ag<sup>+</sup>) coatings on orthopaedic implants may reduce infection rates, but should not be to the detriment of regenerative cell populations, primarily mesenchymal stem/stromal cells (MSCs). We determined intramedullary silver release profiles in vivo, which were used to test relevant Ag<sup>+</sup> concentrations on MSC function in vitro. We measured a rapid elution of Ag<sup>+</sup> from intramedullary pins in a rat femoral implantation model, delivering a maximum potential concentration of 7.8 µM, which was below toxic levels determined for MSCs in vitro (EC<sub>50</sub>, 33 µM). Additionally, we present in vitro data of the reduced colonisation of implants by Staphylococcus aureus. MSCs exposed to Ag<sup>+</sup> prior to/during osteogenic differentiation were not statistically affected. Notably, at clonal density, the colony-forming capacity of MSCs was significantly reduced in the presence of 10 µM Ag<sup>+</sup>, suggesting that a subpopulation of clonal MSCs was sensitive to Ag<sup>+</sup> exposure. At a molecular level, surviving colony-forming MSCs treated with Ag<sup>+</sup> demonstrated a significant upregulation of components of the peroxiredoxin/thioredoxin pathway and processes involved in glutathione metabolism compared to untreated controls. Inhibition of glutathione synthesis using L-buthionine sulfoxamine eliminated MSC clonogenicity in the presence of Ag<sup>+</sup>, which was rescued by exogenous glutathione.
Context Virtualizer: A Cloud Service for Automated Large-scale Mobile App Testing under Real-World Conditions (2013)

Scalable and comprehensive testing of mobile apps is extremely challenging. Every test input needs to be run with a variety of contexts, such as: device heterogeneity, wireless network speeds, locations, and unpredictable sensor inputs. The range of values for each context, e.g. location, can be very large. In this paper we present a one of a kind cloud service, called ConVirt, to which app developers can submit their apps for testing. It leverages two key techniques to make app testing more tractable: (i) pruning the input space into representative contexts, and (ii) prioritizing the context test space to quickly discover failure scenarios for each app. We have implemented ConVirt as a cluster of VMs that can each emulate various combinations of contexts for tablet and phone apps. We evaluate ConVirt by testing 230 commercially available mobile apps based on a comprehensive library of real-world conditions. Our results show that ConVirt leads to an 11.4x improvement in the number of crashes discovered during testing compared to conventional UI automation (i.e., monkey-testing.)
Sensory Testing in a Rat Sciatic Nerve Model (1993)

Grant, Gilbert J. MD; Vermeulen, Kristien MD; Langerman, Lev MD; Turndorf, Herman MD Author Information
ChemInform Abstract: PYRROLIZIDINE ALKALOID SYNTHESIS. (.+‐.)‐SUPINIDINE (1983)

Abstract Alkaloide von Supinidin‐Typ sind wegen antineoplastischer Wirkung von Interesse.
Generation and Cross-Coupling of Organozinc Reagents in Flow (2018)

A versatile flow synthesis method for in situ formation of organozinc reagents and subsequent cross-coupling with aryl halides and activated carboxylic acids is reported. Formation of organozinc reagents is achieved by pumping organic halides, in the presence of ZnCl<sub>2</sub> and LiCl, through an activated Mg-packed column under flow conditions. This method provides efficient in situ formation of aryl, primary, secondary, and tertiary alkyl organozinc reagents, which are subsequently telescoped downstream to a Negishi or decarboxylative Negishi cross-coupling reaction. The described method offers access to a variety of C-C bond formations with organozinc reagents that are otherwise commercially unavailable or difficult to prepare under traditional batch reaction conditions.
Antiviral In vitro activity of Hypericum perforatum l. extract on the human cytomegalovirus (HCMV) (1998)

The total methanol extract and chromatographic fractions of the extract of the aerial parts of Hypericum perforatum L. were investigated for their antiviral activity against human cytomegalovirus (HCMV) AD-169 laboratory strain by modification of the widely used diagnostic method ‘shell-vial’ culture. The plant selection was based on its traditional use against viruses of the Herpes family in Greece. The results showed extract fraction III had the most potent antiviral activity against HCMV which was also superior to that of ganciclovir. Copyright © 1998 John Wiley & Sons, Ltd.
Design Flexibility of a Modular Low-Loss High-Frequency Inductor Structure (2021)

Miniaturization and efficiency of power electronics are limited by magnetic components, which are difficult to scale to small size and high frequency (HF). Inductor structures using field shaping, quasi-distributed gaps, and modular construction can achieve low loss at HF (3-30 MHz) without litz wire. For widespread adoption though, these structures must be shown to remain effective across a wide design range and be economical to manufacture. This article investigates the design flexibility of one such previously proposed inductor structure with a modified pot core and demonstrates that this structure can provide excellent performance for a wide range of inductance and power handling requirements using only a few sets of manufactured core pieces. The core pieces used in the modified pot core structure can be scaled by 4× in volume, compared to roughly 2× for conventional core families, and still achieve high performance over a wide design space. Moreover, this approach can achieve about half the loss of conventional designs at HF and, unlike conventional core sets, can provide a range of low-loss form factors with a single family of components. The proposed inductor structure and design approaches, thus, offer new opportunities in the practical production of low-loss HF inductors.
BYOL for Audio: Exploring Pre-Trained General-Purpose Audio Representations (2022)

Pre-trained models are essential as feature extractors in modern machine learning systems in various domains. In this study, we hypothesize that representations effective for general audio tasks should provide multiple aspects of robust features of the input sound. For recognizing sounds regardless of perturbations such as varying pitch or timbre, features should be robust to these perturbations. For serving the diverse needs of tasks such as recognition of emotions or music genres, representations should provide multiple aspects of information, such as local and global features. To implement our principle, we propose a self-supervised learning method: Bootstrap Your Own Latent (BYOL) for Audio (BYOL-A, pronounced “viola”). BYOL-A pre-trains representations of the input sound invariant to audio data augmentations, which makes the learned representations robust to the perturbations of sounds. Whereas the BYOL-A encoder combines local and global features and calculates their statistics to make the representation provide multi-aspect information. As a result, the learned representations should provide robust and multi-aspect information to serve various needs of diverse tasks. We evaluated the general audio task performance of BYOL-A compared to previous state-of-the-art methods, and BYOL-A demonstrated generalizability with the best average result of 72.4% and the best VoxCeleb1 result of 57.6%. Extensive ablation experiments revealed that the BYOL-A encoder architecture contributes to most performance, and the final critical portion resorts to the BYOL framework and BYOL-A augmentations. Our code is available online for future studies.
A Method for Optimally Localizing Power Quality Monitoring Devices in Power Systems (2007)

This paper presents a method for optimally localizing power quality monitoring devices in power systems. The method is based on calculating the load flow in the frequency domain. The computation algorithm also obtains the Jacobi matrix that reflects the working point of a power system. Singular value decomposition enables obtaining information about nodes sensitive to harmonic. These nodes are where the power quality monitoring systems should be installed.
One-Minute Joule Annealing Enhances the Thermoelectric Properties of Carbon Nanotube Yarns via the Formation of Graphene at the Interface (2019)

Interfaces in nanocarbon materials are highly important, as they determine the properties of carbon-based devices. In terms of carrier and thermal transport properties, the interfacial features are often more important than the intrinsic characteristics. Herein, we describe how 1 min Joule annealing of carbon nanotube (CNT) yarns can convert the interfacial amorphous carbon into graphene fragments. After 1 min Joule annealing, we have obtained multiwalled CNT yarns with extremely high Seebeck coefficients (±100 μV/K) and high thermoelectric power factor (400 and 1000 μW/mK2) at room temperature, both with or without polyethylenimine doping. Theoretical simulations and experimental measurements helped to determine the optimal annealing conditions in terms of a rapid transformation of the interfacial amorphous carbon between the bundled CNTs in the yarn into graphene fragments at ∼2000 K. The present approach represents significant progress in energy materials science, as it provides a guiding principle for the design of interfaces in nanocarbon materials with potential applications in energy-harvesting systems.
Precision Targeting of Tumor Macrophages with a CD206 Binding Peptide (2017)

Tumor-associated macrophages (TAMs) expressing the multi-ligand endocytic receptor mannose receptor (CD206/MRC1) contribute to tumor immunosuppression, angiogenesis, metastasis, and relapse. Here, we describe a peptide that selectively targets MRC1-expressing TAMs (MEMs). We performed in vivo peptide phage display screens in mice bearing 4T1 metastatic breast tumors to identify peptides that target peritoneal macrophages. Deep sequencing of the peptide-encoding inserts in the selected phage pool revealed enrichment of the peptide CSPGAKVRC (codenamed "UNO"). Intravenously injected FAM-labeled UNO (FAM-UNO) homed to tumor and sentinel lymph node MEMs in different cancer models: 4T1 and MCF-7 breast carcinoma, B16F10 melanoma, WT-GBM glioma and MKN45-P gastric carcinoma. Fluorescence anisotropy assay showed that FAM-UNO interacts with recombinant CD206 when subjected to reducing conditions. Interestingly, the GSPGAK motif is present in all CD206-binding collagens. FAM-UNO was able to transport drug-loaded nanoparticles into MEMs, whereas particles without the peptide were not taken up by MEMs. In ex vivo organ imaging, FAM-UNO showed significantly higher accumulation in sentinel lymph nodes than a control peptide. This study suggests applications for UNO peptide in diagnostic imaging and therapeutic targeting of MEMs in solid tumors.
Label-free observation of individual solution phase molecules (2023)

The vast majority of chemistry and biology occurs in solution, and new label-free analytical techniques that can help resolve solution-phase complexity at the single-molecule level can provide new microscopic perspectives of unprecedented detail. Here, we use the increased light-molecule interactions in high-finesse fiber Fabry-Pérot microcavities to detect individual biomolecules as small as 1.2 kDa with signal-to-noise ratios >100, even as the molecules are freely diffusing in solution. Our method delivers 2D intensity and temporal profiles, enabling the distinction of sub-populations in mixed samples. Strikingly, we observe a linear relationship between passage time and molecular radius, unlocking the potential to gather crucial information about diffusion and solution-phase conformation. Furthermore, mixtures of biomolecule isomers of the same molecular weight can also be resolved. Detection is based on a novel molecular velocity filtering and dynamic thermal priming mechanism leveraging both photo-thermal bistability and Pound-Drever-Hall cavity locking. This technology holds broad potential for applications in life and chemical sciences and represents a major advancement in label-free <i>in vitro</i> single-molecule techniques.
Active Interference Cancelation for user coexistence in the presence of I/Q imbalance (2010)

Secondary wide-band users have to guarantee that they will not disturb the in-band narrow-band primary users with allocated spectrum. There are techniques proposed to limit the leakage power of secondary wide-band users in the specified in-band narrow bands. Active Interference Cancelation (AIC) can flexibly solve this problem in the digital domain and hence remove the need for extra analog hardware. The main challenge is that the final depth of a nulled band is severely degraded by RF impairments such as PA non-linearity, phase noise, and I/Q mismatch. In this paper, we investigate the effect of I/Q imbalance on the performance of active interference cancelation techniques. Our analysis shows that for a transmitter with 3° phase imbalance and 0.1dB gain imbalance, the null depth will decrease from 40dB (provided in the digital domain) to 28.7dB (at the out of the radio transmitter). Then we introduce a compensation techniques and demonstrate an improvement of 5 - 10dB in the null depth depending on the severity of I/Q imbalance.
IscR‐dependent gene expression links iron‐sulphur cluster assembly to the control of O 2 ‐regulated genes in Escherichia coli (2006)

IscR is an iron-sulphur (Fe-S) cluster-containing transcription factor that represses transcription of the operon containing its own gene and the iscSUA-hscBA-fdx genes, whose products are involved in Fe-S cluster biogenesis. In this study, global transcriptional profiling of Escherichia coli IscR(+) and IscR(-) strains grown under aerobic and anaerobic conditions indicated that 40 genes in 20 predicted operons were regulated by IscR. DNase I footprinting and/or in vitro transcription reactions identified seven new promoters under direct IscR control. Among these were genes encoding known or proposed functions in Fe-S cluster biogenesis (sufABCDSE, yadR and yhgI) and Fe-S cluster-containing anaerobic respiratory enzymes (hyaABCDEF, hybOABCDEFG and napFDAGHBC). The finding that IscR repressed expression of the hyaA, hybO and napF promoters specifically under aerobic growth conditions suggests a new mechanism to explain their upregulation under anaerobic growth conditions. Phylogenetic footprinting of the DNase I protected regions of seven promoters implies that there are at least two different classes of IscR binding sites conserved among many bacteria. The findings presented here indicate a more general role of IscR in the regulation of Fe-S cluster biogenesis and that IscR contributes to the O(2) regulation of several promoters controlling the expression of anaerobic Fe-S proteins.
Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope (2021)

High-affinity MHC I-peptide interactions are considered essential for immunogenicity. However, some neo-epitopes with low affinity for MHC I have been reported to elicit CD8 T cell dependent tumor rejection in immunization-challenge studies. Here we show in a mouse model that a neo-epitope that poorly binds to MHC I is able to enhance the immunogenicity of a tumor in the absence of immunization. Fibrosarcoma cells with a naturally occurring mutation are edited to their wild type counterpart; the mutation is then re-introduced in order to obtain a cell line that is genetically identical to the wild type except for the neo-epitope-encoding mutation. Upon transplantation into syngeneic mice, all three cell lines form tumors that are infiltrated with activated T cells. However, lymphocytes from the two tumors that harbor the mutation show significantly stronger transcriptional signatures of cytotoxicity and TCR engagement, and induce greater breadth of TCR reactivity than those of the wild type tumors. Structural modeling of the neo-epitope peptide/MHC I pairs suggests increased hydrophobicity of the neo-epitope surface, consistent with higher TCR reactivity. These results confirm the in vivo immunogenicity of low affinity or 'non-binding' epitopes that do not follow the canonical concept of MHC I-peptide recognition.
Fiber span failure protection in mesh optical networks (2001)

A major challenge of optical network design is deciding where spare capacity is needed and how much, so that interrupted traffic may be rerouted in the event of a failure. Given the optical network topology and traffic forecast, the network design needs to map the traffic forecast into optical connection demands. For each optical connection demand, two paths need to be computed, i.e., a service path and a restoration path. In most cases, optical network design mainly considers single failure. If two service paths do not share any single failure, their restoration paths can share the same capacity on any links that they have in common. In this way, the total spare capacity needed for restoration can be dramatically reduced. However, due to the layered architecture in optical networks, a pair of diverse paths in a particular layer won't necessarily be diverse when the lower layer topology is considered. For example, optical networks are typically built on top of a network of fiber spans. A single span cut in the fiber network can cause multiple link failures in the optical layer. In this paper, we investigate fiber span failure protection scenarios in mesh optical networks. Specifically, we provide an algorithm to find two fiber span disjoint paths for each demand, such that the total spare capacity allocated in the network is minimized. Another problem that arises in restoration path computation is the existence of a trap topology. In a trap topology, the pre- selected service path may not have a diverse restoration path even though two diverse paths exist in the network. For simple link-disjoint protection, the min-cost max-flow algorithm can be used to avoid this problem. For fiber span failure protection, the trap topology problem becomes complicated. We show that it is NP-hard problem to find the maximum number of fiber-span disjoint paths between two nodes. We provide two heuristic algorithms to solve this trap topology problem. We have implemented fiber span failure protection in our restoration capacity planning toolkit Cplan. We describe an application of fiber span failure protection at the end of the paper.
Characterization of the Binding Site for Inhibitors of the HPV11 E1−E2 Protein Interaction on the E2 Transactivation Domain by Photoaffinity Labeling and Mass Spectrometry (2004)

An indandione-containing class of inhibitors abrogates DNA replication of human papillomavirus (HPV) types 6 and 11 by binding reversibly to the transactivation domain (TAD) of the viral E2 protein and inhibiting its interaction with the viral E1 helicase. To locate the binding site of this class of protein-protein interaction inhibitors, a benzophenone derivative was used to generate an irreversibly labeled E2-TAD polypeptide. The single site of covalent modification of the E2-TAD was identified by proteolytic digestions using trypsin, LysC, and V8 proteases and characterization of the resulting peptides by LC-MS procedures. Through this methodology, the benzophenone attachment point was located at the terminal methyl of residue Met101. Evidence further pinpointed the site of photoaffinity attachment to the terminal carbon atom, which is significant in providing a definitive example of the ability to locate photoinduced cross-linking to a polypeptide with atomic resolution using solely mass spectrometric detection. The location of the inhibitor binding site vis-à-vis the Glu39 and Glu100 residues sensitive to mutation for HPV 11 E2-TAD is discussed in relation to the crystal structure of the E2-TAD from the related HPV type 16.
Fully Integrated Chip Platform for Electrically Pumped Frequency Comb Generation (2018)

We demonstrate the first chip-based microresonator comb source consisting of a semiconductor laser integrated with a silicon nitride microresonator. For electrical powers as low as 130 mW, we generate a single-soliton comb spanning 90 nm.
Antisense oligonucleotides (2019)

There are few disease-modifying therapeutics for neurodegenerative diseases, but successes on the development of antisense oligonucleotide (ASO) therapeutics for spinal muscular atrophy and Duchenne muscular dystrophy predict a robust future for ASOs in medicine. Indeed, existing pipelines for the development of ASO therapies for spinocerebellar ataxias, Huntington disease, Alzheimer disease, amyotrophic lateral sclerosis, Parkinson disease, and others, and increased focus by the pharmaceutical industry on ASO development, strengthen the outlook for using ASOs for neurodegenerative diseases. Perhaps the most significant advantage to ASO therapeutics over other small molecule approaches is that acquisition of the target sequence provides immediate knowledge of putative complementary oligonucleotide therapeutics. In this review, we describe the various types of ASOs, how they are used therapeutically, and the present efforts to develop new ASO therapies that will contribute to a forthcoming toolkit for treating multiple neurodegenerative diseases.
Regioselective C–F Bond Transformations of Silyl Difluoroenolates (2023)

Herein, we report the development of a nickel-catalyzed cross-coupling reaction of silyl difluoroenolates with aryl zinc reagents via C-F bond cleavage. Treatment of a stoichiometric amount of Ni(0)/<i>N</i>-heterocyclic carbene (NHC) with silyl difluoroenolates in the presence of a lithium salt resulted in C-F bond cleavage to selectively afford the corresponding (<i>Z</i>)-alkenyl Ni complexes. On the basis of the observations, we developed a catalytic cross-coupling reaction that selectively delivers a single geometric isomer of a fluoroenolate.
Linearly polarized 120-W output from a diode-pumped Nd:YALO laser (2000)

We present here a compact 120 W, continuous-wave (CW), diode-pumped Nd:YALO laser at 1079 nm. This linearly polarized output from the optically anisotropic Nd:YALO crystal is advantageous for pumping non-linear crystals. The 1 at% doped Nd:YALO laser rod, 4 mm diameter by 97 mm long, is cut along the b-axis, with both ends anti-reflection coated at 1079 nm and 1341 nm. It is water-cooled (16 degree(s)C) and side-pumped by 5 close-coupled CW diode arrays operating at 803 nm. We obtained 121 W output at the maximum diode pump power of 571 W. The optical slope efficiency is 60%. This is, to the best of our knowledge, the highest power obtained from a diode-pumped Nd:YALO laser. We have studied this thermal lensing at different diode pump powers in lasing and non-lasing configurations. The measured thermal lens decreased from 37.5 to 11 cm as the pump power increased from 185 to 542 W in the lasing configuration. In the non-lasing case, the corresponding thermal lens decreased from 35.5 to 9.5 cm. We have also successfully operated our Nd:YALO laser at 1341 nm. We obtained a maximum output of 60 W, to the best of our knowledge, the highest diode-pumped laser output at this wavelength.
Transverse oscillations of a long-pulse electron beam on a laser-formed channel (1991)

An intense relativistic electron beam may be transported in low-pressure gas using an ion channel which focuses and guides the beam. The beam can be unstable to the growth of transverse oscillations caused by the electric force between the beam and channel-the ion hose instability. Beam propagation on channels created by photoionization of gas with an excimer laser is discussed. Ion hose oscillations have been recorded which have a betatron wavelength of approximately 1.5 m. The growth rate of the ion hose instability in the linear regime was measured as 1.67+or-0.45. At this level of growth, the amplitude of beam oscillations equals the channel radius after a period of one-third of an ion oscillation time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>