gebhart/patrepeval huggingface dataset:
Survival and Injury of Splittail and Chinook Salmon Passed through a Large Hidrostal Pump (2001)

The passage survival, descaling, and injury rates of marked splittail Pogonichthys macrolepidotus and juvenile chinook salmon Oncorhynchus tshawytscha that were inserted into the entrance (suction side) of a Hidrostal pump were compared with those of control fish inserted at the exit (pressure side) in 130 paired trials conducted from December 1998 to July 1999. The Hidrostal pump had no significant effect (P < 0.001) on immediate or latent (96-h) mortality, descaling, or body injury rates for all flow rates and sizes and densities of fish tested, except for the 96-h mortality of splittail in June. The immediate survival rates for splittail and chinook salmon averaged 99%, and the cumulative (96-h) survival for these species averaged 93% and 96%, respectively. Average scale loss on splittail and chinook salmon usually was low (1.9% and 2.4%, respectively), and the frequency of injury to head, eyes, skin, and fins typically was low and not significantly different among quality control, control, and treatment fish. Observations on wild fish (26 species; 7,197 fish) entrained from the Sacramento–San Joaquin River Delta during the pumping trials indicated high immediate survival (99%). The Hidrostal pump transported a variety of sizes and numbers of native fishes with low mortality and injury rates over a range of pump velocities and environmental conditions. Hidrostal pumps that can safely transport fish screened from a water diversion canal through a bypass return to a river may have important fisheries management applications.
35 GHz FM-CW radar modules (2002)

At IRCTR, a collision avoidance radar demonstrator (Colarado) for autonomous vehicles is under development. The radar task is to avoid collisions by detecting the presence of obstacles and by determining the obstacle positions and velocities in the near range of the radar. In the years 1996-1999, an X-band (centre frequency 9.75 GHz, bandwidth 1.5 GHz) demonstrator was built to prove the concept. Since 1998, an IRCTR programme has started to upgrade the X-band system to the Ka-band (in the frequency band 33.4-35.2 GHz) and to the W-band (in the frequency band of 76-77 GHz). In these mm-wave bands, automotive applications can be realised. This paper focusses on Ka-band system design aspects and on the required transmit/receive (T/R) components to be used for integration into T/R modules.
Performance study of a compiler/hardware approach to embedded systems security (2005)

Abstract. Trusted software execution, prevention of code and data tampering, authentication, and providing a secure environment for software are some of the most important security challenges in the design of embedded systems. This short paper evaluates the performance of a hardware/software co-design methodology for embedded software protection. Secure software is created using a secure compiler that inserts hidden codes into the executable code which are then validated dynamically during execution by a reconfigurable hardware component constructed from Field Programmable Gate Array (FPGA) technology. While the overall approach has been described in other papers, this paper focuses on security-performance tradeoffs and the effect of using compiler optimizations in such an approach. Our results show that the approach provides software protection with modest performance penalty and hardware overhead. 1
ND10 Protein PML Is Recruited to Herpes Simplex Virus Type 1 Prereplicative Sites and Replication Compartments in the Presence of Viral DNA Polymerase (1998)

Herpes simplex virus type 1 (HSV-1) infection results in the disruption of ND10 (also called nuclear bodies, PODs, or PML-associated bodies), which are nuclear matrix domains of unknown function present in mammalian cells. After ND10 disruption, viral transcription and DNA replication occur in globular nuclear domains called replication compartments. In this report we define four stages of infection by using antibodies to ICP8 (also called SSB and UL29) and the ND10 antigen PML. Immediately after infection, cells contain intact ND10 as detected by staining for PMLs (stage I); within 1 hour, however, ND10 are disrupted and cells begin to exhibit diffuse staining for the major viral DNA binding protein, ICP8 (stage II). After all ND10 have been disrupted, foci which resemble but are not equivalent to ND10 appear, containing both PML and ICP8 (stage III). Cells infected with mutants defective in the helicase-primase or origin binding protein are unable to form stage III foci. Cells infected with a mutant that is null for the polymerase catalytic subunit, however, form stage III-like ICP8 foci which do not contain PML. Thus, stage III foci recruit the cellular PML protein in the presence but not the absence of HSV polymerase. PML was recruited to stage III foci in some but not all cells infected with a mutant defective in the polymerase accessory protein, UL42. Thus, UL42 is not required for the recruitment of PML to viral foci. In wild-type infection, stage III cells are quickly replaced by cells containing replication compartments (stage IV). PML and ICP8 staining are both observed within replication compartments, indicating a potential role for PML in HSV-1 replication. Models for the role of ND10 proteins in the formation of replication compartments are discussed.
STM-excited electroluminescence and spectroscopy on organic materials for display applications (2001)

We present an overview of the current status of our work on scanning-tunneling-microscope-based (STM) spectroscopy and electroluminescence (EL) excitation to study the physical and electronic structure of organic materials used in organic light-emitting devices (OLEDs). By these means we probe the critical device parameters in charge-carrier injection and transport, i.e., the height of the barrier for charge-carrier injection at interfaces between different materials and the energy gap between positive and negative polaronic states. In combination with optical absorption measurements, we gauge the exciton binding energy, a parameter that determines energy transport and EL efficiency. In STM experiments involving organic EL excitation, the tip functions as an OLED electrode in a highly localized fashion, allowing one to map the spatial distribution of the EL intensity across thin-film samples with nanometer lateral resolution as well as to measure the local EL emission spectra and the influence of thin-film morphology.
Impact of Terrain Changes on the Central Auckland Wind Environment (1999)

Each year Auckland city gains about ten new high rise buildings, each taller than the buildings they replace. While each has its own impact on its local wind environment, together they have a variety of effects on the general wind environment. Although the local effects are controlled to some degree by the requirements of the Resource Management Act and the Auckland City District Plan, the general effects occurring as the result of the combined growth of the city is less controlled. One example of this was discovered during a wind-tunnel study of the winds affecting Sky Tower, where it was shown that the combined effects of the tall buildings in the Central Business District create increased wind velocities and turbulence levels at heights between 70m and 200m. This paper will discuss both the local and general effects that tall buildings have on the wind environment of Auckland City.
Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing (2017)

The large number of SNPs and InDels identified in this study demonstrated that the quinoa genome is enriched with genomic variations. Genetic population structure, genetic core germplasms and dimorphic InDel markers are useful resources for genetic analysis and quinoa breeding.
In Vivo Protein Interaction Network Identified with a Novel Real-Time Cross-Linked Peptide Identification Strategy (2013)

Protein interaction topologies are critical determinants of biological function. Large-scale or proteome-wide measurements of protein interaction topologies in cells currently pose an unmet challenge that could dramatically improve understanding of complex biological systems. A primary impediment includes direct protein topology and interaction measurements from living systems since interactions that lack biological significance may be introduced during cell lysis. Furthermore, many biologically relevant protein interactions will likely not survive the lysis/sample preparation and may only be measured with in vivo methods. As a step toward meeting this challenge, a new mass spectrometry method called Real-time Analysis for Cross-linked peptide Technology (ReACT) has been developed that enables assignment of cross-linked peptides "on-the-fly". Using ReACT, 708 unique cross-linked (<5% FDR) peptide pairs were identified from cross-linked E. coli cells. These data allow assembly of the first protein interaction network that also contains topological features of every interaction, as it existed in cells during cross-linker application. Of the identified interprotein cross-linked peptide pairs, 40% are derived from known interactions and provide new topological data that can help visualize how these interactions exist in cells. Other identified cross-linked peptide pairs are from proteins known to be involved within the same complex, but yield newly discovered direct physical interactors. ReACT enables the first view of these interactions inside cells, and the results acquired with this method suggest cross-linking can play a major role in future efforts to map the interactome in cells.
Blind turbo multipath channel estimation of PAM signals exploiting multilevel codes (2008)

We present a blind turbo equalizer for pulse amplitude modulation (PAM) signals that exploits the statistics that a multilevel code imposes on the transmitted signal. The receiver here is an adaptation of previous work presented in A.F. Santos, et al, (2008), where a BPSK signal is encoded by a binary code and blindly recovered in a turbo way. The main concept is to exploit the constraints imposed by the parity check equations of the code at the transmitted sequence for estimating the channel. Here multilevel codes are used for imposing the necessary constraints on a PAM signal for blind channel estimation. The performance of the proposed system is encouraging. It shows that our blind channel estimator gets close to the same BER of the turbo equalizer with perfect channel knowledge.
The Disappearing Third Dimension (2011)

Three-dimensional computing is driving what many would call a revolution in scientific visualization. However, its power and advancement are held back by the absence of sustainable archives for raw data and derivative visualizations. Funding agencies, professional societies, and publishers each have unfulfilled roles in archive design and data management policy.
Wnt Ligands Secreted by Subepithelial Mesenchymal Cells Are Essential for the Survival of Intestinal Stem Cells and Gut Homeostasis (2016)

Targeting of Wnt signaling represents a promising anti-cancer therapy. However, the consequences of systemically attenuating the Wnt pathway in an adult organism are unknown. Here, we globally prevent Wnt secretion by genetically ablating Wntless. We find that preventing Wnt signaling in the entire body causes mortality due to impaired intestinal homeostasis. This is caused by the loss of intestinal stem cells. Reconstitution of Wnt/β-catenin signaling via delivery of external Wnt ligands prolongs the survival of intestinal stem cells and reveals the essential role of extra-epithelial Wnt ligands for the renewal of the intestinal epithelium. Wnt2b is a key extra-epithelial Wnt ligand capable of promoting Wnt/β-catenin signaling and intestinal homeostasis. Wnt2b is secreted by subepithelial mesenchymal cells that co-express either Gli1 or Acta2. Subepithelial mesenchymal cells expressing high levels of Wnt2b are predominantly Gli1 positive.
Evaluating approaches to find exon chains based on long reads (2016)

The simulated data and in-house scripts used for this article are available at http://www.cs.helsinki.fi/group/gsa/exon-chains/exon-chains-bib.tar.bz2.
Molecular Evidence for a Viral Etiology of Human Leukemias, Lymphomas, and Sarcomas (1973)

Journal Article Molecular Evidence for a Viral Etiology of Human Leukemias, Lymphomas, and Sarcomas Get access R. Hehlmann, M.D., Ph.D., R. Hehlmann, M.D., Ph.D. Institute of Cancer Research and Department of Human Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, New York 10032 Reprints of this entire Research Symposium are available from the ASCP Convention Department, 2100 West Harrison Street, Chicago, Illinois 60612, for $3.00 per copy. Search for other works by this author on: Oxford Academic Google Scholar W. Baxt, M.D., W. Baxt, M.D. Institute of Cancer Research and Department of Human Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, New York 10032 Search for other works by this author on: Oxford Academic Google Scholar D. Kufe, M.D., D. Kufe, M.D. Institute of Cancer Research and Department of Human Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, New York 10032 Search for other works by this author on: Oxford Academic Google Scholar S. Spiegelman, Ph.D. S. Spiegelman, Ph.D. Institute of Cancer Research and Department of Human Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, New York 10032 Search for other works by this author on: Oxford Academic Google Scholar American Journal of Clinical Pathology, Volume 60, Issue 1, 1 July 1973, Pages 65–79, https://doi.org/10.1093/ajcp/60.1.65 Published: 01 July 1973 Article history Received: 19 December 1972 Published: 01 July 1973
Efficient 3D large-scale forward modeling of gravity anomaly in space-wavenumber mixing domain (2019)

A novel 3D numerical modeling method with topography for gravity anomaly in space-wavenumber mixing domain is proposed to reduce the computation time and memory requirements. By performing a two-dimensional Fourier transform along horizontal directions, three-dimensional partial differential equations in the spatial domain are transformed into a group of independent one-dimensional differential equations engaged with different wave numbers. By the method, the independent differential equations are highly parallel among different wave numbers. The method preserves the vertical component in the space domain, so a mesh for modeling can be fine at shallow depths and coarse at deep depth. The finite element method is used to solve the transformed differential equations with different wave numbers, and the efficiency of solving fixed-bandwidth linear equations is further improved by a chasing method. In synthetic test, using 1 processor, more than 40,401 observation points and 4,040,100 source elements are computed in 18.9 s. A traditional method with 3D Gauss-FFT requires 81.4 s. Hence, our new proposed algorithm can substantially accelerate the solution of 3D gravity inversion problems.
Supplementary Table 2 from Molecular Classification of Malignant Pleural Mesothelioma: Identification of a Poor Prognosis Subgroup Linked to the Epithelial-to-Mesenchymal Transition (2023)

&lt;p&gt;XLS file - 11306KB, Pathway analysis.&lt;/p&gt;
Co-authoring with structured annotations (2006)

Most co-authoring tools support basic annotations, such as edits and comments that are anchored at specific locations in the document. However, they do not support meta-commentary about a document (such as an author's summary of modifications) which gets separated from the document, often in the body of email messages. This causes unnecessary overhead in the write-review-edit workflow inherent in co-authoring. We present document-embedded structured annotations called "bundles" that incorporate the meta-commentary into a unified annotation model that meets a set of annotation requirements we identified through a small field investigation. A usability study with 20 subjects evaluated the annotation reviewing stage of co-authoring and showed that annotation bundles in our high-fidelity prototype reduced reviewing time and increased accuracy, compared to a system that only supports edits and comments.
Session 2 Microbial Catalysis and Metabolic Engineering (2005)

The engineering of microbial cell factories for production of fine or bulk chemicals is a multidisciplinary effort that involves genetic engineering (overexpression, deletion or introduction of genes), physiological engineering (cultivation and adaptation of the catalyst to the appropriate process conditions) and biochemical engineering (process configuration, protocols for down-stream processing etc.). Any application oriented project in the field of industrial biotechnology must involve an “omics” analysis. This does not necessarily mean the application of transcriptomics, proteomics, metabolomics, etc. but especially, and invariably, an economics analysis. As pointed out by Cameron and Lievense (Proceedings 25th Symposium p 805) any application oriented project should: be business driven, leverage existing infrastructure, provide for integration along the value chain, The goals for metabolic engineering of microbial biocatalysts for industrial application are: faster (reduction of proces s time), more (higher final concentrations for a beneficial down-stream processing), cheaper (scale-up to appropriate size of equipment, reduce feedstock costs, reduce power input etc.). more efficient (higher yield of product on substrate and thus less byproducts), cleaner (less pollution by the overall process).
Modulation of Intracellular Formation of Reactive Oxygen Intermediates in Peritoneal Macrophages and Microglia/Brain Macrophages by Propentofylline (1994)

Ischemia-induced nerve cell death can partly be prevented by propentofylline, a pharmacon structurally related to xanthine derivates that interacts with the neuromodulatory function of endogenous adenosine. To evaluate a possible mechanism of neuroprotection by propentofylline, we studied its effect on the cellular production of reactive oxygen intermediates in microglial cells, which under pathological conditions can differentiate into brain macrophages, in comparison to peritoneal macrophages. Using a flow cytometric assay, we determined the intracellular formation of reactive oxygen intermediates by measuring the oxidation of the membrane-permeable and nonfluorescent dihydrorhodamine 123 to the cationic and intracellularly trapped, green fluorescent rhodamine 123 in single viable cells. Propentofylline at the therapeutic concentration of 50 microM completely inhibited the Ca(2+)-dependent Con A-induced increase in the production of reactive oxygen intermediates in peritoneal macrophages. In isolated and cultured microglial cells, which have a high spontaneous respiratory burst activity, the spontaneous production of reactive oxygen intermediates was reduced by approximately 30%. A phorbol 12-myristate 13-acetate-induced rise in the respiratory burst activity could not be inhibited by propentofylline in either cell type. An increased generation of reactive oxygen intermediates is thought to contribute to nerve cell death after brain ischemia, edema, and neurodegenerative diseases like Alzheimer's disease. These pathological conditions are all accompanied by an activation of microglial cells. We therefore suggest that the neuroprotective properties of propentofylline might in part be due to a modulation of the microglial production of potentially harmful reactive oxygen intermediates.
An analysis of dielectric models of solvatochromism (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn analysis of dielectric models of solvatochromismJames E. Brady and Peter W. CarrCite this: J. Phys. Chem. 1985, 89, 26, 5759–5766Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://pubs.acs.org/doi/10.1021/j100272a037https://doi.org/10.1021/j100272a037research-articleACS PublicationsRequest reuse permissionsArticle Views455Altmetric-Citations61LEARN 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 options Get e-Alerts
Profiling of Phenolic Natural Products in the Seagrass Zostera noltei by UPLC-MS (2017)

Seagrasses are marine plants that play important ecological functions in coastal ecosystems. The species Zostera noltei is widely distributed along the European coasts thriving in a variety of environmental conditions. In this study, the phenolic natural products of Z. noltei have been analyzed quantitatively by using UPLC-MS. Plants from the Natural Park of the Bay of Cadiz (Spain) were shown to contain rosmarinic acid (1) and the flavonoids apigenin-7-0- glucoside (2), luteolin-7-sulfate (7), apigenin-7-sulfate (8), diosmetin-7-sulfate (9), and acacetin-7-sulfate (10). The analysis by UPLC-MS of extracts allowed the quantification of all the compounds and evidenced the intraspecific variations in the profile of natural products among plants collected at different dates and locations within the Bay. The flavonoids 2, and 7-10 were present in all the analyzed samples with a total flavonoid content in the range 12.8-72.3 mg/g dry wt, while rosmarinic acid (1) was only present in some samples, reaching up to 19.6 mg/g dry wt. A distinctive feature of plants from the Bay of Cadiz is the common presence of apigenin-7-sulfate (8) as major flavonoid, differing from plants from other regions whose major flavonoid is diosmetin-7-sulfate (9).
Selective Synthesis of 2,2-Diamino-4,4,6,6-tetrakis(aryloxy)cyclotriphosphazenes N3P3-2,2-(NH2)2-4,4,6,6-(ArO)4 (2023)

To synthesize cyclotriphosphazene derivatives having multi-functional groups, aryloxylation of 2,2-diamimo-4,4,6,6-tetrachlorocyclotriphosphazene 2 was examined.A mixture of gem-disubstituted N3P3(NH2)2(ArO)2Cl2 9gem, trisubstituted N3P3(NH2)2(ArO)3Cl 10, and tetra-substituted N3P3(NH2)2(ArO)4 11 was obtained, especially 11 was obtained selectively when excess amount (6 equiv.) of ArONa was used.On the other hand, mono-substituted N3P3(NH2)2(ArO)Cl3 8 and non-gem-di-substituted N3P3(NH2)2(ArO)2Cl2 9non-gem-cis and 9non-gem-trans were not detected.Hexachlorocyclotriphosphazene (HCCP, N3P3Cl6) has a flat six-membered ring in which three N atoms and three P atoms connect alternately, and two Cl atoms on each P atom. 1 The Cl-P bond of HCCP easily reacts with several kinds of nucleophiles.To prepare multi-functionalized cyclotriphosphazene derivatives for developing multi-functionalized materials, 2 partial substitution of HCCP would be an important method to introduce more than one kind of substituent (Figure 1). Figure 1. Preparation of Cyclotriphosphazene Derivatives Having Multi-types of NucleophilesWe previously reported that gaseous NH3 was allowed to react with HCCP to afford 2,2-diamino-4,4,6,6tetrachlorocyclotriphosphazene (2) (in Et2O) and/or 2,2,4,4-tetraamino-6,6-dichlorocyclotriphospohazene