gebhart/patrepeval huggingface dataset:
Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis (2009)

Plants are exposed to continual changes in the environment. The daily alternation between light and darkness results in massive recurring changes in the carbon budget, and leads to widespread changes in transcript levels. These diurnal changes are superimposed on slower changes in the environment. Quantitative molecular information about the numbers of ribosomes, of transcripts for 35 enzymes in central metabolism and their loading into polysomes is used to estimate translation rates in Arabidopsis rosettes, and explore the consequences for important sub-processes in plant growth. Translation rates for individual enzyme are compared with their abundance in the rosette to predict which enzymes are subject to rapid turnover every day, and which are synthesized at rates that would allow only slow adjustments to sustained changes of the environment, or resemble those needed to support the observed rate of growth. Global translation rates are used to estimate the energy costs of protein synthesis and relate them to the plant carbon budget, in particular the rates of starch degradation and respiration at night.
Office Practice of Neurology (1997)

Office Practice of Neurology edited by Martin A. Samuels, MD, and Steven Feske, MD , 1,280 pp., New York, Churchill Livingstone, 1996, $199.00

A practicing neurologist dives into a major new textbook of neurology with a mixture of anticipation and dread-anticipation of clinical pearls for use with patients, and dread of turgid prose, out-of-date information, and sticker shock. This new book delights in its clinical utility, but does not fail in its price. In the interest of disclosure, I have been trained by many of …
Identification of single amino acid differences in uniformly charged homopolymeric peptides with aerolysin nanopore (2018)

There are still unmet needs in finding new technologies for biomedical diagnostic and industrial applications. A technology allowing the analysis of size and sequence of short peptide molecules of only few molecular copies is still challenging. The fast, low-cost and label-free single-molecule nanopore technology could be an alternative for addressing these critical issues. Here, we demonstrate that the wild-type aerolysin nanopore enables the size-discrimination of several short uniformly charged homopeptides, mixed in solution, with a single amino acid resolution. Our system is very sensitive, allowing detecting and characterizing a few dozens of peptide impurities in a high purity commercial peptide sample, while conventional analysis techniques fail to do so.
Cisplatin-Induced CD95 Redistribution into Membrane Lipid Rafts of HT29 Human Colon Cancer Cells (2004)

We have shown previously that the death receptor CD95 could contribute to anticancer drug-induced apoptosis of colon cancer cells. In addition, anticancer drugs cooperate with CD95 cognate ligand or agonistic antibodies to trigger cancer cell apoptosis. In the present study, we show that the anticancer drug cisplatin induces clustering of CD95 at the surface of the human colon cancer cell line HT29, an event inhibited by the inhibitor of acid sphingomyelinase (aSMase) imipramine. The cholesterol sequestering agent nystatin also prevents cisplatin-induced CD95 clustering and decreases HT29 cell sensitivity to cisplatin-induced apoptosis and the synergy between cisplatin and anti-CD95 agonistic antibodies. CD95, together with the adaptor molecule Fas-associated death domain and procaspase-8, is redistributed into cholesterol- and sphingolipid-enriched cell fractions after cisplatin treatment, suggesting plasma membrane raft involvement. Interestingly, nystatin prevents the translocation of the aSMase to the extracellular surface of plasma membrane and the production of ceramide, suggesting that these early events require raft integrity. In addition, nystatin prevents cisplatin-induced transient increase in plasma membrane fluidity that could be required for CD95 translocation. Together, these results demonstrate that cisplatin activates aSMase and induces ceramide production, which triggers the redistribution of CD95 into the plasma membrane rafts. Such redistribution contributes to cell death and sensitizes tumor cells to CD95-mediated apoptosis.
Universal Scaling of Plasmon Coupling in Metal Nanostructures:  Extension from Particle Pairs to Nanoshells (2007)

It has been recently shown that the strength of plasmon coupling between a pair of plasmonic metal nanoparticles falls as a function of the interparticle gap scaled by the particle size with a near-exponential decay trend that is universally independent of nanoparticle size, shape, metal type, or medium dielectric constant. In this letter, we extend this universal scaling behavior to the dielectric core-metal shell nanostructure. By using extended Mie theory simulations of silica core-metal nanoshells, we show that when the shift of the nanoshell plasmon resonance wavelength scaled by the solid nanosphere resonance wavelength is plotted against the shell thickness scaled by the core radius, nanoshells with different dimensions (radii) exhibit the same near-exponential decay. Thus, the nanoshell system becomes physically analogous to the particle-pair system, i.e., the nanoshell plasmon resonance results from the coupling of the inner shell surface (cavity) and the outer shell surface (sphere) plasmons over a separation distance essentially given by the metal shell thickness, which is consistent with the plasmon hybridization model of Prodan, Halas, and Nordlander. By using the universal scaling behavior in the nanoshell system, we propose a simple expression for predicting the dipolar plasmon resonance of a silica-gold nanoshell of given dimensions.
Photo-and electroluminescence in the 1.3-µm wavelength range from quantum-dot structures grown on GaAs substrates (1999)

A method is proposed to increase the emission wavelength from structures grown on GaAs substrates by inserting a strained InAs quantum dot array into an external InGaAs quantum well. The dependence of the luminescence peak position on the active region design was investigated for structures grown by this method. Room-temperature photo-and electroluminescence spectra in the 1.3-µm wavelength range are compared.
MobiLenin combining a multi-track music video, personal mobile phones and a public display into multi-user interactive entertainment (2005)

This paper introduces a novel and creative approach for coupling multimedia art with a non-conventional distributed human-computer interface for multi-user interactive entertainment. The proposed MobiLenin system allows a group of people to interact simultaneously with a multi-track music video shown on a large public display using their personal mobile phones, effectively empowering the group with the joint authorship of the video. The system is realized with a client-server architecture which includes server-driven real-time control of the client UI to guarantee ease of use and a lottery mechanism as an incentive for interaction. Our analysis of the findings of an empirical user evaluation conducted in a true environment of use shows that the MobiLenin system is successful, addressing many of the challenges identified in the literature. The proposed system offers a new form of interactive entertainment for pubs and other public places, and the underlying architecture provides a framework for realizing similar installations with different types of multimedia content.
Reflections on Smart Antennas for MAC Protocols in Multihop Ad Hoc Networks (2002)

Colloque avec actes et comité de lecture. internationale.
Bushfire, storms and soil erosion (2003)

Fire and storm events have had a significant influence on the type, structure and conservation of soils in eastern Australia. Fire of anthropogenic and natural origins has been the cause of great changes in the flora and soil fauna of the region. Storm events are related to seasons and vary in terms of intensity on a quasi-seasonal basis in some sub-regions. They are also influenced by the La Nina/El Nino cycle. The interaction of fire and storm events is examined in this paper. The intensity of storm events of high or low precipitation intensity will have markedly different effects on the soils, where the storm is immediately preceded by fire. Where fire has occurred in close time sequence with storm (precipitation) events erosion can be enhanced and hence soil profiles permanently altered. Fire management includes control burning as a tool. Fire management that uses control burning should also take into account the soil condition of the areas designated to be burnt, the immediate storm and precipitation history, and the likely (expected) meteorological conditions for the season. Control burning should be minimised where severe storm events are likely and where they occur without low-level precipitation being a likely precursor. The condition of the underlying soil in an area to be burnt should be taken into account before burning is undertaken. The effect of having to consider soil condition and the probability of extreme storm events, subsequent to controlled burning, will reduce the window of opportunity for controlled burning. This will have the effect of requiring additional and more flexible resources for controlled burning and other fuel reduction procedures, being made available.
Functional analysis of fibrin γ-chain cross-linking by activated factor XIII: determination of a cross-linking pattern that maximizes clot stiffness (2007)

Activated coagulation factor XIII (FXIIIa) cross-links the gamma-chains of fibrin early in clot formation. Cross-linking of the alpha-chains occurs more slowly, leading to high molecular weight multimer formations that can also contain gamma-chains. To study the contribution of FXIIIa-induced gamma-chain cross-linking on fibrin structure and function, we created 2 recombinant fibrinogens (gammaQ398N/Q399N/K406R and gammaK406R) that modify the gamma-chain cross-linking process. In gammaK406R, gamma-dimer cross-links were absent, but FXIIIa produced a cross-linking pattern similar to that observed in tissue transglutaminase cross-linked fibrin(ogen) with mainly alpha-gamma cross-links. In Q398N/Q399N/K406R, cross-links with any gamma-chain involvement were completely absent, and only alpha-chain cross-linking occurred. Upon cross-linking, recombinant normal fibrin yielded a 3.5-fold increase in stiffness, compared with a 2.5-fold increase by alpha-chain cross-linking alone (gammaQ398N/Q399N/K406R). gammaK406R fibrin showed a 1.5-fold increase in stiffness after cross-linking. No major differences in clot morphology, polymerization, and lysis rates were observed, although fiber diameter was slightly lower in cross-linked normal fibrin relative to the variants. Our results show that gamma-chain cross-linking contributes significantly to clot stiffness, in particular through gamma-dimer formation; alpha-gamma hybrid cross-links had the smallest impact on clot stiffness.
ICNet for Real-Time Semantic Segmentation on High-Resolution Images (2017)

We focus on the challenging task of real-time semantic segmentation in this paper. It finds many practical applications and yet is with fundamental difficulty of reducing a large portion of computation for pixel-wise label inference. We propose an image cascade network (ICNet) that incorporates multi-resolution branches under proper label guidance to address this challenge. We provide in-depth analysis of our framework and introduce the cascade feature fusion unit to quickly achieve high-quality segmentation. Our system yields real-time inference on a single GPU card with decent quality results evaluated on challenging datasets like Cityscapes, CamVid and COCO-Stuff.
Estrogen Receptor Binding to DNA Is Not Required for Its Activity through the Nonclassical AP1 Pathway (2001)

In the classical signaling pathway, the estrogen receptor (ER) binds directly to estrogen response elements (EREs) to regulate gene transcription. To test the hypothesis that the nonclassical pathway involves ER interactions with other proteins rather than direct binding to DNA, mutations were introduced into the DNA binding domain (DBD) of the mouse ERalpha. The effects of these DBD mutations were examined in DNA binding assays using reporter constructs containing either EREs (classical) or AP1 (nonclassical) response elements. Using the AP1 reporter, there was a reversal of ER action relative to that seen with the ERE reporter. Estradiol induced suppression, and the antiestrogen ICI 182,780 stimulated transcription of the AP1 reporter. DBD mutations in the proximal (P-box) of the first zinc finger of the ER (E207A/G208A and E207G/G208S) eliminated ERE binding. These mutants were inactive using the ERE reporter but retained partial or full activity with the AP1 reporter. The DBD mutant ERs interacted with Jun when tested in mammalian cell two-hybrid assays. Two mutations (K366D and I362R) in the ER ligand binding domain known to alter coactivator interactions impaired transcriptional responses using either the ERE or AP1 reporters. We concluded that ER action through the AP1 response element involves interactions with other promoter-bound proteins instead of, or in addition to, direct binding to DNA. Interactions with coactivators were required for both pathways. These data supported a model in which ER-mediated transcriptional activation or repression is dependent on the ligand and the nature of the response element in the target gene.
Lipopolysaccharide is a frequent contaminant of plasmid DNA preparations and can be toxic to primary human cells in the presence of adenovirus. (1994)

Endotoxin (lipopolysaccharide, LPS) is commonly found as a contaminant in plasmid DNA preparations. We demonstrate here that the quantities of LPS typically contaminating DNA preparations can generate a toxicity to primary cells (primary human skin fibroblasts, primary human melanoma cells) in the presence of entry-competent adenovirus particles. Toxicity can be observed with as little as 100 ng/ml free LPS or 100 pg/ml LPS when the LPS is assembled into polylysine/adenovirus complexes. Simple and effective methods of removing the contaminating LPS using either a polymyxin B resin or Triton X-114 extraction are described. Treatment of DNA samples to remove LPS eliminates the toxicity to primary cells.
Volume Change Characteristics of Partially Saturated Soils (1968)

Synopsis It is apparent that the principle of effective stress alone is inadequate to explain volumetric behaviour of partially saturated soils subjected to external stresses. This Paper describes a method which can be adopted to explain the behavior of patially saturated soils subjected mainly to increasing proportional loading (all-round pressure and K 0 loading). By treating applied stress and suction as two independent variables, it is shown that variations in void ratio and degree of saturation are represented by unique surfaces in a stress-void ratio and stress-degree of saturation space respectively. Il est évident que le principe de tension efficace seul ne suffit pas à expliquer le comportement volumétrique de sols partiellement saturés soumis à des tensions externes. Cet expose décrit une méthode que l'on peut adopter pour expliquer le comportement de sols partiellement saturés soumis principalement à des charges proportionnelles croissantes (pression dans toutes les directions et charge K 0 ). En traitant la tension appliquée et la succion en tant que deux variables independantes, on montre que les variations de l'indice de vide et du degré de saturation sont représentées par des surfaces uniques dans un espace tension-indice de vide et tension degré de saturation respectivement.
Filling the gap in LNAantisense oligo gapmers: the effects of unlocked nucleic acid (UNA) and 4′- C -hydroxymethyl-DNA modifications on RNase H recruitment and efficacy of an LNA gapmer (2009)

Stability against nucleases, affinity for the targeted mRNA and the ability to recruit RNase H are prerequisites for antisense oligonucleotide (AON) applications where gene expression knockdown is required. Typically chimeric gapmer AON designs are used with a central continuous stretch of RNase H recruiting nucleotides (e.g. phosphorothioate DNA), flanked by affinity and stability-enhancing modified nucleotides. However, many types of nucleotide modifications in the central DNA gap can disturb RNase H function. Here we present studies into two different types of nucleotide modifications, a flexible acyclic RNA analog named unlocked nucleic acid (UNA) and 4'-C-hydroxymethyl-DNA in the gap of an LNA (locked nucleic acid) flanked gapmer. We compared the efficacy of mRNA degradation by the gap modified LNA antisense gapmers in cell-free assays and cultured cells. This study shows that both UNA and 4'-C-hydroxymethyl-DNA gap insertions are compatible with RNase H activity when used sparingly. However, multiple 4'-C-hydroxymethyl-DNA modifications are better tolerated by RNase H than multiple UNA modifications in the gap. Furthermore, this report shows that LNA gapmer AONs with multiple 4'-C-hydroxymethyl-DNA moieties in the gap can mediate target knockdown in vivo.
Wideband internal folded planar monopole antenna for UMTS/WiMAX folder‐type mobile phone (2005)

Abstract A simple folded planar metal‐plate monopole antenna suitable for operation as a wideband internal antenna for a folder‐type mobile phone is presented. The folder‐type mobile phone is modeled to comprise an upper ground plane and a lower ground plane, and the proposed antenna is employed at the hinge position between the upper and lower ground planes. The antenna has a compact structure and yet generates a wide operating bandwidth of about 4.8 GHz (from about 1.7 to 6.5 GHz), allowing it to easily cover UMTS and WiMAX operations. Details of the proposed antenna are described, and the experimental results of constructed prototypes are presented and discussed. The effects of the various lengths of the upper ground plane on the impedance matching of the antenna are also studied. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 48: 324–327, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.21339
Optical interconnects at the top of the rack for energy-efficient data centers (2015)

The growing popularity of cloud and multimedia services is dramatically increasing the traffic volume that each data center needs to handle. This is driving the demand for highly scalable, flexible, and energy-efficient networks inside data centers, in particular for the edge tier, which requires a large number of interconnects and consumes the dominant part of the overall power. Optical fiber communication is widely recognized as the highest energy- and cost-efficient technique to offer ultra-large capacity for telecommunication networks. It has also been considered as a promising transmission technology for future data center applications. Taking into account the characteristics of the traffic generated by the servers, such as locality, multicast, dynamicity, and burstiness, the emphasis of the research on data center networks has to be put on architectures that leverage optical transport to the greatest possible extent. However, no feasible solution based on optical switching is available so far for handling the data center traffic at the edge tier. Therefore, apart from conventional optical switching, we investigate a completely different paradigm, passive optical interconnects, and aim to explore the possibility for optical interconnects at the top of the rack. In this article, we present three major types of passive optical interconnects and carry out a performance assessment with respect to the ability to host data center traffic, scalability, optical power budget, complexity of the required interface, cost, and energy consumption. Our results have verified that the investigated passive optical interconnects can achieve a significant reduction of power consumption and maintain cost at a similar level compared to its electronic counterpart. Furthermore, several research directions on passive optical interconnects have been pointed out for future green data centers.
The Steroid Receptor Coactivator-1 Regulates Twist Expression and Promotes Breast Cancer Metastasis (2009)

In breast cancer, steroid receptor coactivator-1 (SRC-1) expression positively correlates with HER2 expression and poor prognosis. In mouse mammary tumor virus-polyoma middle T (PyMT) breast cancer mouse model, SRC-1 strongly promotes mammary tumor metastasis. However, the molecular targets and mechanisms that mediate the role of SRC-1 in metastasis are unknown. In this study, SRC-1 wild-type (WT) and knockout (KO) cell lines were developed from the mammary tumors of WT/PyMT and KO/PyMT mice. WT cells exhibited strong migration and invasion capabilities, reduced E-cadherin and beta-catenin epithelial markers, gained N-cadherin and vimentin mesenchymal markers, and formed undifferentiated invasive structures in three-dimensional culture. In contrast, KO cells showed slow migration and invasion, retained E-cadherin, had less N-cadherin and vimentin, and developed partially differentiated three-dimensional structures. Importantly, WT cells expressed Twist, a master regulator of metastasis, at significantly higher levels versus KO cells. SRC-1 knockdown in WT cells reduced Twist expression, whereas SRC-1 restoration in KO cells also rescued Twist expression. Furthermore, SRC-1 was found to coactivate Twist transcription through physical interaction with the transcription factor PEA3 at the proximal Twist promoter. Accordingly, Twist knockdown in WT cells increased E-cadherin and reduced cell invasion and metastasis, and Twist expression in KO cells decreased E-cadherin and increased cell invasion. SRC-1 knockdown in human breast cancer cells also decreased Twist, cell migration, and invasion. Therefore, SRC-1 promotes breast cancer invasiveness and metastasis by coactivating PEA3-mediated Twist expression. Intervention of SRC-1 function may provide new strategies to inhibit breast cancer metastasis.
Evaluation strategies for image understanding and retrieval (2005)

We address evaluation of image understanding and retrieval large scale image data in the context of three evaluation projects. The first project is a comprehensive strategy for evaluating image retrieval algorithms and provides an open reference data set for doing so. The second project develops word prediction as a semantically relevant evaluation strategy, and applies it to the evaluation of of image processing methods for semantic image analysis. The third project evaluates words for suitability of their visual properties for use in an image annotation framework.
Robust, Soluble Pentacene Ethers (2004)

We report the synthesis and characterization of a series of alkoxy-substituted silylethynylated pentacene derivatives (R = CH(2)CH(2), CHCH, CH(2)). All three compounds are easily prepared, soluble in common organic solvents, and stable both as solids and in solution. Two of the derivatives possess significant pi-face interactions in the crystal. Values for lambda(max) for these new pentacene derivatives range from 621 to 674 nm, and oxidation potentials lie between 109 and 301 mV versus ferrocene.
Efficient generation of the binary reflected gray code and its applications (1976)

Algorithms are presented to generate the n-bit binary reflected Gray code and codewords of fixed weight in that code. Both algorithms are efficient in that the time required to generate the next element from the current one is constant. Applications to the generation of the combinations of n things taken k at a time, the compositions of integers, and the permutations of a multiset are discussed.
Gene Expression Profile Associated with Response to Doxorubicin-Based Therapy in Breast Cancer (2005)

A trio of genes might potentially distinguish doxorubicin-responsive from nonresponsive tumors, but further validation by a larger number of samples is still needed.