gebhart/patrepeval huggingface dataset:
Transcript Expression in Saccharomyces cerevisiae at High Salinity (2001)

Transcript expression of Saccharomyces cerevisiae at high salinity was determined by microarray analysis of 6144 open reading frames (ORFs). From cells grown in 1 m NaCl for 10, 30, and 90 min, changes in transcript abundance >2-fold were classified. Salinity-induced ORFs increased over time: 107 (10 min), 243 (30 min), and 354 (90 min). Up-regulated, functionally unknown ORFs increased from 17 to 149 over this period. Expression patterns were similar early, with 67% of up-regulated transcripts after 10 min identical to those at 30 min. The expression profile after 90 min revealed different up-regulated transcripts (identities of 13% and 22%, respectively). Nucleotide and amino acid metabolism exemplified the earliest responses to salinity, followed by ORFs related to intracellular transport, protein synthesis, and destination. Transcripts related to energy production were up-regulated throughout the time course with respiration-associated transcripts strongly induced at 30 min. Highly expressed at 90 min were known salinity stress-induced genes, detoxification-related responses, transporters of the major facilitator superfamily, metabolism of energy reserves, nitrogen and sulfur compounds, and lipid, fatty acid/isoprenoid biosynthesis. We chose severe stress conditions to monitor responses in essential biochemical mechanisms. In the mutant, Deltagpd1/gpd2, lacking glycerol biosynthesis, the stress response was magnified with a partially different set of up-regulated ORFs.
Inside Cover: Tailoring Small Molecules for an Allosteric Site on Procaspase‐6 (ChemMedChem 1/2014) (2013)

The inside cover picture shows small molecules tailored for an allosteric site in procaspase-6. The combination of biophysical fragment screening, structure- and computation-aided design, and chemical synthesis enabled the discovery of multiple nanomolar-affinity ligands for this new site. The compounds significantly stabilize the protein, suggesting new avenues for controlling caspase activity and/or activation by allosteric mechanisms. For more details, see the Communication by Jeremy Murray, Adam R. Renslo et al. on p. 73 ff.
Structure-to-Property Relationships in Non-Platinum Group Fuel Cell Catalysts: Examination of Length Scale Correlations (2013)

Abstract not Available.
Performance Comparison of IP and CCN as a Communication Infrastructure for Smart Grid. (2015)

The infrastructure for smart grid is classified into three categories: infrastructure for electric power generation, delivery, and consumption, infrastructure for information measurement, surveillance, and management, and infrastructure for information communication. In this paper, we derive the total amount of traffic in the network, average end-to-end communication delay, and availability when using IP and CCN (Content-Centric Networking) as the communication infrastructure for a smart grid, respectively. Through several numerical examples, we clarify under what conditions either IP or CCN is suitable for the communication infrastructure of a smart grid. We found that, in terms of the total amount of traffic and the average end-to-end communication delay, CCN is effective compared with IP except when cache hit rates in RGCC (Remote Grid Control Center) and LGCC (Local Grid Control Center) are very low. We also found that, in terms of availability, the performance advantage of CCN over IP is marginal.
Projection onto the Manifold of Elongated Structures for Accurate Extraction (2015)

Detection of elongated structures in 2D images and 3D image stacks is a critical prerequisite in many applications and Machine Learning-based approaches have recently been shown to deliver superior performance. However, these methods essentially classify individual locations and do not explicitly model the strong relationship that exists between neighboring ones. As a result, isolated erroneous responses, discontinuities, and topological errors are present in the resulting score maps. We solve this problem by projecting patches of the score map to their nearest neighbors in a set of ground truth training patches. Our algorithm induces global spatial consistency on the classifier score map and returns results that are provably geometrically consistent. We apply our algorithm to challenging datasets in four different domains and show that it compares favorably to state-of-the-art methods.
Competitive Substrate Biodegradation during Surfactant-Enhanced Remediation (1999)

The impact of synthetic surfactants on the aqueous phase biodegradation of benzene, toluene, and p-xylene (BTpX) was studied using two anionic surfactants, sodium dodecyl sulfate (SDS) and sodium dodecyl benzene sulfonate (SDBS), and two nonionic surfactants, POE(20) sorbitan monooleate (T-maz-80) and octylphenolpoly(ethyleneoxy) ethanol (CA-620). Batch biodegradation experiments were performed to evaluate surfactant biodegradability using two different microbial cultures. Of the four surfactants used in this study, SDS and T-maz-80 were readily degraded by a microbial consortium obtained from an activated sludge treatment system, whereas only SDS was degraded by a microbial culture that was acclimated to BTpX. Biodegradation kinetic parameters associated with SDS and T-maz-80 degradation by the activated sludge consortium were estimated using respirometric data in conjunction with a nonlinear parameter estimation technique as μmax = 0.93 h−1, Ks = 96.18 mg/L and μmax = 0.41 h−1, Ks = 31.92 mg/L, respectively. When both BTpX and surfactant were present in the reactor along with BTpX-acclimated microorganisms, two distinct biodegradation patterns were seen. SDS was preferentially utilized inhibiting hydrocarbon biodegradation, whereas the other three surfactants had no impact on BTpX biodegradation. None of the four surfactants were toxic to the microbial cultures used in this study. Readily biodegradable surfactants are not very effective for subsurface remediation applications as they are rapidly consumed, and also because of their potential inhibitory effects on intrinsic hydrocarbon biodegradation. This greatly increases treatment costs as surfactant recovery and reuse are adversely affected.
Determining the phase transition of condensate formed by heterogeneous nucleation of condensable vapors onto a cold substrate. (1994)

The heterogeneous phase transition of four organic vapors and water vapor on a cold substrate was studied by either slowly cooling a substrate or by accumulating vapor under reduced-pressure conditions. At low vapor pressures a solid condensate formed directly on the substrate. At higher vapor pressures, liquid condensate usually appeared first, followed either by1) subsequent formation of solid crystals independently from the liquid phase (subsequent solidification) or 2) rapid freezing of the liquid condensate (subsequent freezing). Subsequent freezing occurred in a wider temperature range than did the subsequent solidification. A new phase transition model is proposed, based on the equilibrium phase diagram and the measured relationship between critical vapor pressure and temperature for solid condensate formation. The proposed model explains the experimental results quite well. Liquid condensate always forms at critical supersaturation ratios close to unity. The critical vapor pressure and temperature at the boundary separating the formation of the solid condensate from formation of the liquid condensate, as determined by the proposed model, agrees well with the experimentally determined values.
Acidic Fibroblast Growth Factor Induces an Antifibrogenic Phenotype in Human Lung Fibroblasts (1999)

Acidic fibroblast growth factor (FGF-1), a prototype member of the heparin-binding growth factor family, influences proliferation, differentiation, and protein synthesis in different cell types. However, its possible role on lung extracellular matrix (ECM) metabolism has not been evaluated. In this study we examined the effects of FGF-1 and FGF-1 plus heparin on type I collagen, collagen-binding stress protein HSP47, interstitial collagenase (matrix metalloproteinase [MMP]-1), gelatinase A, and tissue inhibitor of metalloproteinase (TIMP)-1 and TIMP-2 expression by normal human lung fibroblasts. Heparin was used because it enhances the biologic activities of FGF-1. Fibroblasts were exposed either to 20 ng/ml FGF-1 plus 100 micrograms/ml heparin for 48 h or to FGF-1 or heparin alone. Messenger RNA (mRNA) expression was analyzed by Northern blot. Collagen synthesis was evaluated by digestion of [3H]collagen with bacterial collagenase, MMP-1 by Western blot, and gelatinolytic activities by zymography. Our results show that FGF-1 induced collagenase mRNA expression, which was strongly enhanced when FGF-1 was used with heparin. Likewise, both FGF-1 and FGF-1 plus heparin reduced by 70 to 80% the expression of type I collagen transcript, in part through effect on pro-alpha1(I) collagen mRNA stability. A downregulation of HSP47 gene expression was also observed. Synthesis of collagen and collagenase proteins paralleled gene expression results. FGF-1 activities were abolished with genistein, a tyrosine kinase inhibitor. Neither FGF-1 nor FGF-1 plus heparin affected the expression of TIMP-1, TIMP-2, and gelatinase A. These findings demonstrate that FGF-1, mostly in the presence of heparin, upregulates collagenase and downregulates type I collagen expression that might have a protective role in avoiding collagen accumulation during lung ECM remodeling.
Dimensional Control of Line Gratings by Small Angle X-Ray Scattering: Shape and Roughness Extraction (2020)

The capabilities of Small Angle X-ray Scattering (SAXS) for dimensional control of line gratings are reviewed. We first introduce different experimental methodologies used to extract the pitch, the critical dimension (CD) and the side-wall angle (SWA) of line gratings. A special focus is done on line roughness extraction. We already demonstrated that the SAXS technique has the sensitivity to measure line roughness amplitude below 1 nm on a set of line gratings designed with a controlled line roughness [1]. Fast Fourier Transforms (FFT) simulations revealed that the Line Width Roughness (LWR) defined as a Power Spectral Density (PSD) can be measured in a SAXS pattern at some specific positions in the reciprocal space [2]. In the present study, a comparison of the LWR PSD extracted by SAXS and by Scanning Electron Microscope (SEM) on one set of samples was done.
Practical data-centric storage (2006)

Most data retrieval mechanisms in wireless sensor networks adopt a data-centric approach, in which data is identified directly by name rather than through the location of the node on which it is stored. Initial data-centric methods, such as directed diffusion and TinyDB/TAG, focused on the conveyance of data. One of the advantages of these algorithms is that they do not require pointto-point routing, which has proved to be difficult and costly to implement in wireless sensor networks, and instead require only the simpler and more robust treeconstruction primitives. Some recent data retrieval proposals have extended the data-centric paradigm to storage. Data-centric storage uses in-network placement of data to increase the efficiency of data retrieval in certain circumstances. Unfortunately, all such proposals have been based on pointto-point routing, and therefore have faced a significant deployment barrier. In this paper we hope to make data-centric storage more practical by removing the need for point-to-point routing. To that end, we propose pathDCS, an approach to data-centric storage that requires only standard tree construction algorithms, a primitive already available in many real-world deployments. We describe the design and implementation of pathDCS and evaluate its performance through both high-level and packet-level simulations, as well as through experiments on a sensor testbed. 1
Optimal Subhourly Electricity Resource Dispatch Under Multiple Price\n Signals With High Renewable Generation Availability (2017)

This paper proposes a system-wide optimal resource dispatch strategy that\nenables a shift from a primarily energy cost-based approach, to a strategy\nusing simultaneous price signals for energy, power and ramping behavior. A\nformal method to compute the optimal sub-hourly power trajectory is derived for\na system when the price of energy and ramping are both significant. Optimal\ncontrol functions are obtained in both time and frequency domains, and a\ndiscrete-time solution suitable for periodic feedback control systems is\npresented. The method is applied to North America Western Interconnection for\nthe planning year 2024, and it is shown that an optimal dispatch strategy that\nsimultaneously considers both the cost of energy and the cost of ramping leads\nto significant cost savings in systems with high levels of renewable\ngeneration: the savings exceed 25% of the total system operating cost for a 50%\nrenewables scenario.\n
Potent and Broad Neutralization of SARS-CoV-2 Variants of Concern (VOCs) including Omicron Sub-lineages BA.1 and BA.2 by Biparatopic Human VH Domains (2022)

The emergence of SARS-CoV-2 variants of concern (VOCs) requires the development of next-generation biologics with high neutralization breadth. Here, we characterized a human VH domain, F6, which we generated by sequentially panning large phage displayed VH libraries against receptor binding domains (RBDs) containing VOC mutations. Cryo-EM analyses reveal that F6 has a unique binding mode that spans a broad surface of the RBD and involves the antibody framework region. Attachment of a Fc region to a fusion of F6 and ab8, a previously characterized VH domain, resulted in a construct (F6-ab8-Fc) that broadly and potently neutralized VOCs including Omicron. Additionally, prophylactic treatment using F6-ab8-Fc reduced live Beta (B.1.351) variant viral titers in the lungs of a mouse model. Our results provide a new potential therapeutic against SARS-CoV-2 variants including Omicron and highlight a vulnerable epitope within the spike that may be exploited to achieve broad protection against circulating variants.
Gene Therapy for Mucopolysaccharidosis Type VI Is Effective in Cats Without Pre-Existing Immunity to AAV8 (2012)

Liver gene transfer with adeno-associated viral (AAV) 2/8 vectors is being considered for therapy of systemic diseases like mucopolysaccharidosis type VI (MPS VI), a lysosomal storage disease due to deficiency of arylsulfatase B (ARSB). We have previously reported that liver gene transfer with AAV2/8 results in sustained yet variable expression of ARSB. We hypothesized that the variability we observed could be due to pre-existing immunity to wild-type AAV8. To test this, we compared the levels of AAV2/8-mediated transduction in MPS VI cats with and without pre-existing immunity to AAV8. In addition, since levels of lysosomal enzymes as low as 5% of normal are expected to be therapeutic, we evaluated the impact of pre-existing immunity on MPS VI phenotypic rescue. AAV2/8 administration to MPS VI cats without pre-existing neutralizing antibodies to AAV8 resulted in consistent and dose-dependent expression of ARSB, urinary glycosaminoglycan (GAG) reduction, and femur length amelioration. Conversely, animals with pre-existing immunity to AAV8 showed low levels of ARSB expression and limited phenotypic improvement. Our data support the use of AAV2/8-mediated gene transfer for MPS VI and other systemic diseases, and highlight that pre-existing immunity to AAV8 should be considered in determining subject eligibility for therapy.
Electroosmotic Pumps Fabricated From Porous Silicon Membranes (2006)

N-type porous silicon can be used to realize electroosmotic pumps with high flow rates per applied potential difference. The porosity and pore size of porous silicon membranes can be tuned, the pore geometry has near-unity tortuosity, and membranes can be made thin and with integrated support structures. The size of hexagonally packed pores is modified by low-pressure chemical vapor deposition (LPCVD) polysilicon deposition, followed by wet oxidation of the polysilicon layer, resulting in a pore radius varying from 1 to 3 /spl mu/m. Pumping performance of these devices is experimentally studied as a function of pore size and compared with theory. These 350-/spl mu/m-thick silicon membranes exhibit a maximum flow rate per applied field of 0.13 ml/min/cm/sup 2//V. This figure of merit is five times larger than previously demonstrated porous glass EO pumps.
DICTIONARY OF THE ECONOMIC PRODUCTS OF INDIA pages 542 to 545 (2014)

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Supplementary Table from The PD-L1/4-1BB Bispecific Antibody–Anticalin Fusion Protein PRS-344/S095012 Elicits Strong T-Cell Stimulation in a Tumor-Localized Manner (2023)

Supplementary Table from The PD-L1/4-1BB Bispecific Antibody–Anticalin Fusion Protein PRS-344/S095012 Elicits Strong T-Cell Stimulation in a Tumor-Localized Manner
A Review on the ESD Robustness of Drain-Extended MOS Devices (2012)

This paper reviews electrostatic discharge (ESD) investigations on laterally diffused MOS (LDMOS) and drain-extended MOS (DeMOS) devices. The limits of the safe operating area of LDMOS/DeMOS devices and device physics under ESD stress are discussed under various biasing conditions and layout schemes. Specifically, the root cause of early filament formation is highlighted. Differences in filamentary nature among various LDMOS/DeMOS devices are shown. Based on the physical understanding, device optimization guidelines are given. Finally, an outlook on technology scaling is presented.
Electronic structure of BaSn1−xSbxO3studied by photoemission spectroscopy (1993)

We have studied the electronic structure of BaSn${}_{1}$${}_{\mathrm{\ensuremath{-}}}$${}_{\mathit{x}}$Sb${}_{\mathit{x}}$O${}_{3}$ by photoemission and bremsstrahlung isochromat spectroscopy. The Sb 3d core-level spectra show the presence of only Sb${}^{5}$${}^{+}$ ions and give no evidence for charge disproportionation into Sb${}^{3}$${}^{+}$ and Sb${}^{5}$${}^{+}$. The combined valence- and conduction-band spectra are found to be in good agreement with band theory and indicate that, upon doping, the Fermi level is placed at the bottom of the conduction band. We discuss the spectroscopic results in relation to earlier Mo\ifmmode\ddot\else\textasciidieresis\fi{}ssbauer and transport data and propose a model of the electronic structure in which the electrons introduced by the Sb doping occupy the lowest-lying Sn-5s--derived conduction-band states. This scenario can be obtained by a static oxygen displacement, which would stabilize the Sb${}^{5}$${}^{+}$ valence state by lifting the Sb 5s states well above the conduction-band minimum.
Toso, a Functional IgM Receptor, Is Regulated by IL-2 in T and NK Cells (2012)

We find that the cell surface receptor Toso is dramatically downregulated by in vitro stimulation of human T and NK cells with IL-2 in a STAT5-dependent manner. The fact that IL-2 is known to prime NK and T cells for Fas/TNF-mediated activation-induced cell death (AICD) fits nicely with the original and recent descriptions of Toso as an inhibitor of Fas/TNF-induced apoptosis. In support of this possibility, effector memory T cells express markedly lower levels of Toso than those of naive T cells, indicating that activation in vivo correlates with the downregulation of Toso. Moreover, in vitro activation of memory T cells through TCR dramatically downregulates Toso expression compared with that of naive CD4 T cells. However, overexpression of Toso in human NK cells and Jurkat T cells does not inhibit Fas-mediated apoptosis, and, in agreement with other recent reports, Toso clearly functions as an IgM receptor. Unlike CD16, Toso expression by NK cells does not convey cytotoxic potential, but its ligation does trigger intracellular signaling in NK cells. In summary, our data indicate that Toso is a functional IgM receptor that is capable of activating signaling molecules, is regulated by IL-2, and is not inherently an antiapoptotic molecule.
H2O: Two Hands Manipulating Objects for First Person Interaction\n Recognition (2021)

We present a comprehensive framework for egocentric interaction recognition\nusing markerless 3D annotations of two hands manipulating objects. To this end,\nwe propose a method to create a unified dataset for egocentric 3D interaction\nrecognition. Our method produces annotations of the 3D pose of two hands and\nthe 6D pose of the manipulated objects, along with their interaction labels for\neach frame. Our dataset, called H2O (2 Hands and Objects), provides\nsynchronized multi-view RGB-D images, interaction labels, object classes,\nground-truth 3D poses for left &amp; right hands, 6D object poses, ground-truth\ncamera poses, object meshes and scene point clouds. To the best of our\nknowledge, this is the first benchmark that enables the study of first-person\nactions with the use of the pose of both left and right hands manipulating\nobjects and presents an unprecedented level of detail for egocentric 3D\ninteraction recognition. We further propose the method to predict interaction\nclasses by estimating the 3D pose of two hands and the 6D pose of the\nmanipulated objects, jointly from RGB images. Our method models both inter- and\nintra-dependencies between both hands and objects by learning the topology of a\ngraph convolutional network that predicts interactions. We show that our method\nfacilitated by this dataset establishes a strong baseline for joint hand-object\npose estimation and achieves state-of-the-art accuracy for first person\ninteraction recognition.\n
Potentiation of the Cytotoxicity of the Anticancer Agent Tirapazamine by BenzotriazineN-oxides:  The Role of Redox Equilibria (2005)

Tirapazamine (3-amino-1,2,4-benzotriazine 1,4-dioxide), the lead bioreductive drug with selective toxicity for hypoxic cells in tumors, is thought to act by forming an active oxidizing radical of high one-electron reduction potential, E(1), when reduced by reductases. It has a dual mechanism of action, both generating DNA radicals, following its one-electron reduction and subsequently oxidizing these DNA radicals to form labile cations or hydrolyzable lactones through transferring an O atom, resulting in DNA strand breaks. These parallel secondary reactions have been proposed to be also initiated by its two-electron reduced metabolite, the 1-oxide. We have used pulse radiolysis to show that the benzotriazinyl radical of a highly soluble analogue of tirapazamine, the 3-(N,N-dimethyl-1,2-ethanediamine) analogue, is able to oxidize tirapazamine itself. We have found that both tirapazamine and the 1-oxides are in equilibrium with their respective benzotriazinyl radicals, with high concentrations of the more soluble 1-oxide maintaining a high concentration of the more reactive oxidizing radical of tirapazamine. The one-electron reduction potentials, E(1), of the 1-oxides and related compounds have been measured and, together with the E(1) values of tirapazamine and the 2-nitroimidazole radiosensitizer, misonidazole, are shown to predict the published percentages of electron transfer. This radical chemistry study gives an insight into the mechanisms of the potentiation of radical damage, reported for DNA, that underlies the hypoxic cytotoxicity of electron affinic compounds. The E(1) values of the benzotriazinyl radicals of the benzotriazine compounds govern the position of the redox equilibria, which determine the amount of initial radical damage. The E(1) values of the 1,4-dioxides and 1-oxide compounds govern the degree of potentiation of the initial radical damage once formed.