gebhart/patrepeval huggingface dataset:
Extracellular DNA, cell surface proteins and c-di-GMP promote biofilm formation in Clostridioides difficile (2021)

Clostridioides difficile is the leading cause of nosocomial antibiotic-associated diarrhoea worldwide, yet there is little insight into intestinal tract colonisation and relapse. In many bacterial species, the secondary messenger cyclic-di-GMP mediates switching between planktonic phase, sessile growth and biofilm formation. We demonstrate that c-di-GMP promotes early biofilm formation in C. difficile and that four cell surface proteins contribute to biofilm formation, including two c-di-GMP regulated; CD2831 and CD3246, and two c-di-GMP-independent; CD3392 and CD0183. We demonstrate that C. difficile biofilms are composed of extracellular DNA (eDNA), cell surface and intracellular proteins, which form a protective matrix around C. difficile vegetative cells and spores, as shown by a protective effect against the antibiotic vancomycin. We demonstrate a positive correlation between biofilm biomass, sporulation frequency and eDNA abundance in all five C. difficile lineages. Strains 630 (RT012), CD305 (RT023) and M120 (RT078) contain significantly more eDNA in their biofilm matrix than strains R20291 (RT027) and M68 (RT017). DNase has a profound effect on biofilm integrity, resulting in complete disassembly of the biofilm matrix, inhibition of biofilm formation and reduced spore germination. The addition of exogenous DNase could be exploited in treatment of C. difficile infection and relapse, to improve antibiotic efficacy.
Further Analysis of Outlier Detection with Deep Generative Models (2020)

The recent, counter-intuitive discovery that deep generative models (DGMs) can frequently assign a higher likelihood to outliers has implications for both outlier detection applications as well as our overall understanding of generative modeling. In this work, we present a possible explanation for this phenomenon, starting from the observation that a model's typical set and high-density region may not conincide. From this vantage point we propose a novel outlier test, the empirical success of which suggests that the failure of existing likelihood-based outlier tests does not necessarily imply that the corresponding generative model is uncalibrated. We also conduct additional experiments to help disentangle the impact of low-level texture versus high-level semantics in differentiating outliers. In aggregate, these results suggest that modifications to the standard evaluation practices and benchmarks commonly applied in the literature are needed.
Differential Beamforming From the Beampattern Factorization Perspective (2020)

Differential beamformers have demonstrated a great potential in forming frequency-invariant beampatterns and achieving high directivity factors. Most conventional approaches design differential beamformers in such a way that their beampatterns resemble a desired or target beampattern. In this paper, we show how to design differential beamformers by simply taking advantage of the fact that the beampattern is actually a particular form of an exponential polynomial. Thanks to this quite obvious formulation, a target beampattern is not really needed while the zeros of the exponential polynomial and/or its factorization are fully exploited. The advantage of this factorization is twofold. First, it gives the relation between the beamformer and the roots of the polynomial, so the former can be directly determined from the latter, which seems natural and convenient. Second, based on this factorization, we propose a new formulation of the beamforming filter, which decomposes the filter into shorter ones with the Kronecker product. This formulation is very general, and many well-known beamformers such as the differential and delay-and-sum (DS) ones can be derived from it. Furthermore, the new formulation allows one to combine different kinds of beamformers together, which gives a great flexibility in forming different beampatterns and achieving a compromise among the directivity factor (DF), white noise gain (WNG), and frequency invariance.
Toward nanorobotics platforms for high-throughput biomedical applications at the nanometer-scale (2002)

A new nanorobotics platform under development and which could be used for high-throughput biomedical applications at the nanometer-scale is briefly described. Each platform is based on a fleet of approximately 100 miniature autonomous instrumented robots, each capable of nanometer-scale operations. A central computer coordinates the operations of each miniature robot based on instructions received previously.
A modular sensornet architecture (2007)

article Share on A modular sensornet architecture: past, present, and future directions Authors: Arsalan Tavakoli UC Berkeley EECS Dept., Berkeley, California UC Berkeley EECS Dept., Berkeley, CaliforniaView Profile , Prabal Dutta UC Berkeley EECS Dept., Berkeley, California UC Berkeley EECS Dept., Berkeley, CaliforniaView Profile , Jaein Jeong UC Berkeley EECS Dept., Berkeley, California UC Berkeley EECS Dept., Berkeley, CaliforniaView Profile , Sukun Kim UC Berkeley EECS Dept., Berkeley, California UC Berkeley EECS Dept., Berkeley, CaliforniaView Profile , Jorge Ortiz UC Berkeley EECS Dept., Berkeley, California UC Berkeley EECS Dept., Berkeley, CaliforniaView Profile , David Culler UC Berkeley EECS Dept., Berkeley, California UC Berkeley EECS Dept., Berkeley, CaliforniaView Profile , Phillip Levis Stanford CS Dept., Stanford, California Stanford CS Dept., Stanford, CaliforniaView Profile , Scott Shenker UC Berkeley EECS Dept., Berkeley, California UC Berkeley EECS Dept., Berkeley, CaliforniaView Profile Authors Info & Claims ACM SIGBED ReviewVolume 4Issue 3July 2007 pp 49–54https://doi.org/10.1145/1317103.1317112Online:01 July 2007Publication History 10citation357DownloadsMetricsTotal Citations10Total Downloads357Last 12 Months7Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
A Novel and Scalable Spatio-Temporal Technique for Ocean Eddy Monitoring (2021)

Swirls of ocean currents known as ocean eddies are a crucial component of the ocean's dynamics. In addition to dominating the ocean's kinetic energy, eddies play a significant role in the transport of water, salt, heat, and nutrients. Therefore, understanding current and future eddy patterns is a central climate challenge to address future sustainability of marine ecosystems. The emergence of sea surface height observations from satellite radar altimeter has recently enabled researchers to track eddies at a global scale. The majority of studies that identify eddies from observational data employ highly parametrized connected component algorithms using expert filtered data, effectively making reproducibility and scalability challenging. In this paper, we frame the challenge of monitoring ocean eddies as an unsupervised learning problem. We present a novel change detection algorithm that automatically identifies and monitors eddies in sea surface height data based on heuristics derived from basic eddy properties. Our method is accurate, efficient, and scalable. To demonstrate its performance we analyze eddy activity in the Nordic Sea (60-80N and 20W-20E), an area that has received limited attention and has proven to be difficult to analyze using other methods.
Transition-metal complexes of superstructured cyclidene macrobicycles: structural features and their chemical consequences. 1. Complexes of the unbridged cyclidene ligands and of precursor ligands (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTransition-metal complexes of superstructured cyclidene macrobicycles: structural features and their chemical consequences. 1. Complexes of the unbridged cyclidene ligands and of precursor ligandsNathaniel W. Alcock, Wang Kan Lin, Alan Jircitano, James D. Mokren, P. W. R. Corfield, Gordon Johnson, George Novotnak, Colin Cairns, and Daryle H. BuschCite this: Inorg. Chem. 1987, 26, 3, 440–452Publication Date (Print):February 1, 1987Publication History Published online1 May 2002Published inissue 1 February 1987https://doi.org/10.1021/ic00250a018Request reuse permissionsArticle Views113Altmetric-Citations39LEARN 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 InReddit PDF (1 MB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Shape Complexity and Process Energy Consumption in Electron Beam Melting: A Case of Something for Nothing in Additive Manufacturing? (2016)

Summary Additive manufacturing (AM) technology is capable of building up component geometry in a layer‐by‐layer process, entirely without tools, molds, or dies. One advantage of the approach is that it is capable of efficiently creating complex product geometry. Using experimental data collected during the manufacture of a titanium test part on a variant of AM technology, electron beam melting (EBM), this research studies the effect of a variation in product shape complexity on process energy consumption. This is done by applying a computationally quantifiable convexity‐based characteristic associated with shape complexity to the test part and correlating this quantity with per‐layer process energy consumption on the EBM system. Only a weak correlation is found between the complexity metric and energy consumption (ρ = .35), suggesting that process energy consumption is indeed not driven by shape complexity. This result is discussed in the context of the energy consumption of computer‐controlled machining technology, which forms an important substitute to EBM. This article further discusses the impact of available additional shape complexity at the manufacturing process level on the incentives toward minimization of energy inputs, additional benefits arising later within the product's life cycle, and its implications for value creation possibilities.
Kinetic studies on four-coordinate chelate complexes of copper(II): isotopic ligand exchange of bis(salicylaldiminato)copper(II) in toluene (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetic studies on four-coordinate chelate complexes of copper(II): isotopic ligand exchange of bis(salicylaldiminato)copper(II) in tolueneH. Voss, K. J. Wannowius, and H. EliasCite this: Inorg. Chem. 1979, 18, 6, 1454–1459Publication Date (Print):June 1, 1979Publication History Published online1 May 2002Published inissue 1 June 1979https://pubs.acs.org/doi/10.1021/ic50196a010https://doi.org/10.1021/ic50196a010research-articleACS PublicationsRequest reuse permissionsArticle Views135Altmetric-Citations8LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
[P73: a kin to the p52 tumor suppressor gene]. (1997)

A gene with remarkable sequence homology with the tumour suppressor gene p53 is located at the tip of the short arm of human chromosome 1 which is often found to be deleted in neuroblastomas, melanomas and breast cancers. Despite their structural and functional similarities, p53 and p73 may have distinct roles in cell grow regulation.
Micromagnetic study of CoPt–SiO2 granular films by spin-wave Brillouin scattering (2000)

A spin-wave Brillouin scattering study of a CoPt–SiO2 granular magnetic recording medium was made. This film contains ferromagnetic CoPt particles in a SiO2 matrix, and has an extremely low medium noise property due to little exchange coupling between magnetic grains. Spin waves of both the propagating surface mode and standing wave mode were found to be excited in granular magnetic films with various microstructures. A possible origin of the spin wave is a magnetostatic coupling between regularly ordered CoPt grains, as reported for artificially patterned magnetic thin films. This result shows two promising features of the CoPt–SiO2 granular film for high density recording medium: It is an ordered media obtained in a self-organizing manner, and it is less influenced by the thermal fluctuation effect, which is a serious problem for current high density magnetic recording.
38‐1: Invited Paper : Ink‐Jet‐Printed OLEDs for Display Applications (2016)

We report performance of red, green and blue inkjet printed organic light emitting diodes with common blue device architecture. Device efficiency, voltage, color and lifetime are reported, and emission profile discussed. We demonstrate that inkjet printed OLED performance metrics are rapidly approaching commercial requirements for display applications, and discuss strong potential for further progress.
Ribosomal protein L29/HIP deficiency delays osteogenesis and increases fragility of adult bone in mice (2008)

Mice lacking HIP/RPL29, a ribosomal modulator of protein synthesis rate, display a short stature phenotype. To understand the contribution of HIP/RPL29 to bone formation and adult whole bone mechanical properties, we examined both developing and adult bone in our knockout mice. Results indicated that bone shortening in HIP/RPL29-null mice is due to delayed entry of chondro-osteoprogenitors into the cell cycle. Structural properties of adult null bones were analyzed by micro-computed tomography. Interestingly, partial preservation of cortical thickness was observed in null males indicating a gender-specific effect of the genotype on cortical bone parameters. Null males, and to a lower extent null females, displayed increased bone material toughness to counteract decreased bone size. This elevation in a bone material property was associated with increased bone mineral density only in null males. Neither male nor female null animals could withstand the same maximum load as gender-matched controls in three-point bending tests, and smaller post-yield displacements (and thus increased bone brittleness) were found for null animals. These results suggest that HIP/RPL29-deficient mice exhibit increased bone fragility due to altered matrix protein synthesis rates as a consequence of ribosomal insufficiency. Thus, sub-efficient protein translation increased fracture risk in HIP/RPL29-null animals. Taken together, these studies provide strong genetic evidence that the ability to regulate and amplify protein synthesis rates, including those proteins that regulate the cell cycle entry during skeletal development, are important determinants for establishment of normal bone mass and quality.
Preparation of low-spin trans-polyacetylene (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of low-spin trans-polyacetyleneG. L. Baker, J. A. Shelburne, and F. S. BatesCite this: J. Am. Chem. Soc. 1986, 108, 23, 7377–7380Publication Date (Print):November 1, 1986Publication History Published online1 May 2002Published inissue 1 November 1986https://pubs.acs.org/doi/10.1021/ja00283a037https://doi.org/10.1021/ja00283a037research-articleACS PublicationsRequest reuse permissionsArticle Views136Altmetric-Citations11LEARN 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
The combined actions of NK and T lymphocytes are necessary to reject an EGFP+ mesenchymal tumor through mechanisms dependent on NKG2D and IFNγ (2007)

Better understanding of the mechanisms that mediate spontaneous immune rejections ought to be important in the quest for improvements in immunotherapy of cancer. A set of intraperitoneal tumors of mesenchymal origin that had been chemically induced in ubiquitously expressing EGFP transgenic mice provided a model in which both T and NK cells were absolutely required for tumor rejection. Tumor cells were traceable because of being fluorescent and readily grafted in RAG1(-/-) immunodeficient mice, whereas they were rejected in a majority of syngeneic C57BL/6 and EGFP-transgenic mice. Tumor-cell clones with the highest EGFP expression tended to be rejected, but a direct involvement of EGFP as the antigen recognized for the immune rejections was ruled out. Rejections were absolutely dependent on NK cells as well as on CD4(+) and CD8(+) T lymphocytes according to selective depletion studies. Furthermore, CD8(+) and CD4(+) T lymphocytes as well as NK cells were detected in the inflammatory infiltrate that mediates tumor rejection along with some DC. The effects of IFN gamma, produced at the tumor site by T and NK lymphocytes, were only required at the malignant cell level and were necessary for tumor eradication. NK recognition of tumor cells was mediated by the NKG2D-activating receptor and blocking its function in vivo partially interfered with rejection. Therefore, complete rejection of these mesenchymal tumors requires a concerted set of activities including direct tumor-cell destruction and IFN gamma production that are mediated by both NK and T cells.
Alpha‐synuclein and its disease‐causing mutants induce ICAM‐1 and IL‐6 in human astrocytes and astrocytoma cells (2006)

Autosomal dominant Parkinson disease (PD) is caused by duplication or triplication of the alpha-synuclein gene as well as by the A30P, E46K, and A53T mutations. The mechanisms are unknown. Reactive astrocytes in the substantia nigra of PD and MPTP-treated monkeys display high levels of the inflammatory mediator intercellular adhesion molecule-1 (ICAM-1), indicating that chronic inflammation contributes to the degeneration. Here we report that alpha-synuclein strongly stimulates human astrocytes as well as human U-373 MG astrocytoma cells to up-regulate both interleukin (IL)-6 and ICAM-1 (ED50=5 microg ml(-1)). The mutated forms are more potent stimulators than wild-type (WT) alpha-synuclein in these assays. We demonstrate by immunoblotting analysis that this up-regulation is associated with activation of the major mitogen-activated protein kinase (MAPK) pathways. It is also attenuated by PD 98059, an inhibitor of the MAPK/extracellular-regulated kinase kinase MEK1/2, SP 600125, an inhibitor of c-Jun N-terminal kinase (JNK), and SB 202190, an inhibitor of p38 MAPK. The inhibitory effects on human astrocytes have IC50 values of 2, 5, and 1.5 microM respectively. We hypothesize that the neuroinflammation stimulated by release of an excess of normal alpha-synuclein or by release of its mutated forms can be involved in the pathobiology of PD.
Hardware/software partitioning of software binaries (2002)

Partitioning an embedded system application among a microprocessor and custom hardware has been shown to improve the performance, power or energy of numerous examples. The advent of single-chip microprocessor/FPGA platforms makes such partitioning even more attractive. Previous partitioning approaches have partitioned sequential program source code, such as C or C++. We introduce a new approach that partitions at the software binary level. Although source code partitioning is preferable from a purely technical viewpoint, binary-level partitioning provides several very practical benefits for commercial acceptance. We demonstrate that binary-level partitioning yields competitive speedup results compared to source-level partitioning, achieving an average speedup of 1.4 compared to 1.5 for eight benchmarks partitioned on a single-chip microprocessor/FPGA device.
Giant Magnetoresistance in Antiferromagnetic Co/Cu Multilayers Grown on Kapton (1992)

Multilayers of Co/Cu, sputter deposited onto thin kapton films, display very large room-temperature magnetoresistance, almost as large as that found in similar structures prepared on silicon wafers. Such flexible structures suggest a number of intriguing technological applications. Plane-view and cross section transmission electron micrographs reveal a high degree of structural order with grains extending over several hundred angstrom with sharp grain boundaries.
Information dissemination in heterogeneous-intent networks (2016)

Many qualitative studies of communication practices on social media have recognized that people's motivation for participating in social networks can vary greatly. Some people participate for fame and fortune, while others simply wish to chat with friends. In this paper, we study the implications of such heterogeneous intent for modeling information diffusion in social networks. We experiment with user-level perception of messages, analyze large-scale information cascades, and model information diffusion in heterogeneous-intent networks. We perform carefully designed user studies to establish the relationship between the intent and language style of a message sender. Style of the user appear to adapt their language to achieve different intents. We perform a large-scale data analysis on Twitter message cascades and confirm that message propagation through a network is correlated with historical representations of individuals' intents. Finally, we posit a simple analytical model of information diffusion in social networks that takes heterogeneous intents into account and find that this model is able to explain empirically observed properties of structural virality that are not explained by current models.