gebhart/patrepeval huggingface dataset:
Diatomics: Toward Diatom Functional Genomics (2005)

For diatom biologists one of the most interesting research areas over the next years will be in linking mathematical models for pattern formation with information derived from molecular genetic, biochemical, and physiological studies. A major goal of this research is to exploit diatom proficiency in biogenic silica formation to develop strategies for bio-inspired nanofabrication of silicon based materials. Development of high-throughput methods for the functional analysis of diatom genes is a key step toward this goal. In this article we review the different techniques available to investigate gene and protein function in diatoms. Furthermore, to make diatom research as effective as possible the research community must address the question of which diatom species should be developed as a model. Choice of a diatom model organism should be made on the basis of several criteria, such as the ease of genetic manipulation, ecological relevance, or biomineralization capability. Phaeodactylum tricornutum is one of the principal three species that are candidates for such a model. For this species we have accomplished the first large-scale analysis of 12000 expressed sequence tags (ESTs) and have organized it in a queryable database, Phaeodactylum tricornutum database (PtDB). A summary of the functional analysis of this EST collection is presented, and genes of particular interest are highlighted.
Phonon Focusing in Solids (1969)

In phonon-propagation studies using heat pulses it has been found that predominantly transverse phonons are observed for [100] propagation in LiF whereas mainly longitudinal phonons are observed for this direction in KCl. This result and similar effects previously reported on other crystals are explained in terms of a phonon-focusing effect that arises from elastic anisotropy.
Methylprednisolone neutralizes the beneficial effects of erythropoietin in experimental spinal cord injury (2005)

Inflammation plays a major pathological role in spinal cord injury (SCI). Although antiinflammatory treatment using the glucocorticoid methyprednisolone sodium succinate (MPSS) improved outcomes in several multicenter clinical trials, additional clinical experience suggests that MPSS is only modestly beneficial in SCI and poses a risk for serious complications. Recent work has shown that erythropoietin (EPO) moderates CNS tissue injury, in part by reducing inflammation, limiting neuronal apoptosis, and restoring vascular autoregulation. We determined whether EPO and MPSS act synergistically in SCI. Using a rat model of contusive SCI, we compared the effects of EPO [500-5,000 units/kg of body weight (kg-bw)] with MPSS (30 mg/kg-bw) for proinflammatory cytokine production, histological damage, and motor function at 1 month after a compression injury. Although high-dose EPO and MPSS suppressed proinflammatory cytokines within the injured spinal cord, only EPO was associated with reduced microglial infiltration, attenuated scar formation, and sustained neurological improvement. Unexpectedly, coadministration of MPSS antagonized the protective effects of EPO, even though the EPO receptor was up-regulated normally after injury. These data illustrate that the suppression of proinflammatory cytokines alone does not necessarily prevent secondary injury and suggest that glucocorticoids should not be coadministered in clinical trials evaluating the use of EPO for treatment of SCI.
The Coordination Chemistry of 3,3′-Diamino-2,2′-bipyridine and Its Dication: Exploring the Role of the Amino Groups by X-ray Crystallography (2002)

The synthesis and structural chemistry of a series of new divalent transition metal complexes of the bis-bidentate ligand 3,3′-diamino-2,2′-bipyridine (L1) and its dication L1H2 are described. Ligand L1 reacts with salts of divalent transition metals to afford the (1:1) metal-ligand complexes (2a−2d) as well as the tris complexes (3a−3f). All complexes were fully characterised by spectroscopic methods and the following compounds [Cu(L1)Cl2]2 (2a), [Cu(L1)(OAc)2] (2b), [Zn(L1)3][OTf]2 (3a), and [Zn(L1)3][ZnCl4] (3e and 3f) were structurally characterised. Results from single crystal X-ray diffraction measurements indicate that formation of an intramolecular hydrogen bond between the two amino groups allows the ligand to coordinate divalent metal ions through their diimine binding sites. Furthermore, the structure of compound 2a reveals that it crystallises as a dimer in which each copper ion is bound to two pyridine nitrogen atoms and two chloride ions in a distorted square planar arrangement, with a long axial contact from a neighbouring amino group completing the approximately square-pyramidal geometry at CuII. Complexation of this ligand in acidic conditions afforded the compound [Cu(L1H2)Cl4] (4), as well as the two salts [L1H2][CuCl4] (5a) and [L1H2][ZnCl4] (5b). All three compounds have been structurally characterised and results indicate that the dication (L1H2) displays a different coordination preference for the chelation of metal ions. In all three cases, both of the heterocyclic N atoms of the ligand are protonated, thus preventing chelation to the metal ion, although for compound 4 crystallographic studies reveal that the two amino functionalities coordinate the copper(II) ion. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)
Accumulation of a non-(1-84) molecular form of parathyroid hormone (PTH) detected by intact PTH assay in renal failure: importance in the interpretation of PTH values. (1996)

A molecular form of PTH different from PTH-(1-84) and present in normal serum is recognized by two-site intact (I-) PTH assays; it responds to Ca2+ changes in the same way that PTH carboxyl-terminal fragments do. To evaluate the impact of this finding, we have compared basal, stimulated, and nonsuppressible I-PTH values in 14 normal subjects and 15 renal failure patients, subdivided into 8 patients with low (< 12 pmol/L; LBI) and 7 with high (> 12 pmol/L; HBI) basal I-PTH. Samples obtained under various calcemic conditions in these 3 groups were further fractionated by high performance liquid chromatography (HPLC) and assayed for I-PTH, and the various peaks observed were quantitated by planimetry. Differences among the 3 groups were reinterpreted knowing the exact composition of I-PTH. Basal I-PTH was greatly increased in HBI (mean +/- SD, 44.1 +/- 38.6 pmol/L) compared to that in normal subjects (2.5 +/- 0.8 pmol/L; P < 0.001) or LBI (6.1 +/- 2.4 pmol/L; P < 0.001); the difference was less in these last 2 groups (P < 0.01). Similar differences were observed for stimulated and nonsuppressible I-PTH, except for stimulated I-PTH, which was similar in normal and LBI subjects. Two I-PTH HPLC molecular forms accounted for I-PTH immunoreactivity in the 3 groups. In normal subjects, PTH-(1-84) accounted for 74.9 +/- 4.3%, 79.0 +/- 3.0%, and 87.2 +/- 1.0% of I-PTH in hyper-, normo-, and hypocalcemia, respectively, but only for 44.6 +/- 2.5%, 50.5 +/- 0.7%, and 63.6 +/- 0.1% in renal failure patients, with similar results in HBI and LBI. The accumulation of a non-(1-84) PTH peak accounted for the difference between normal subjects and renal failure patients. When basal, stimulated, and nonsuppressible I-PTH values were separated into their 2 components, prior differences between HBI and LBI or normal subjects remained unchanged because of very high I-PTH values in HBI, but differences between normal and LBI subjects were entirely explained by the accumulation of the non-(1-84) PTH peak [basal, 3.0 +/- 1.2 vs. 0.5 +/- 0.2 pmol/L (P < 0.001); stimulated, 6.8 +/- 2.3 vs. 2.3 +/- 1.0 pmol/L (P < 0.001); nonsuppressible, 1.3 +/- 0.7 vs. 0.2 +/- 0.08 pmol/L (P < 0.001)]; PTH-(1-84) values were similar (basal, 3.1 +/- 1.2 vs. 2.0 +/- 0.6 pmol/L; stimulated, 12.0 +/- 3.9 vs. 15.5 +/- 6.6 pmol/L; nonsuppressible, 1.1 +/- 0.6 vs. 0.52 +/- 0.22 pmol/L). Thus, a non-(1-84) PTH molecular form detected by two-site I-PTH assays accumulates in renal failure and accounts for a larger proportion of I-PTH than that in normal subjects. Levels of I-PTH 1.57 times higher than those in normocalcemic subjects are thus required in renal failure to achieve similar PTH-(1-84) concentrations. The composition of I-PTH is also identical in all hemodialyzed patients.
Renieramycins E and F from the sponge Reniera sp.: reassignment of the stereochemistry of the renieramycins (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRenieramycins E and F from the sponge Reniera sp.: reassignment of the stereochemistry of the renieramycinsHai Yin He and D. John FaulknerCite this: J. Org. Chem. 1989, 54, 24, 5822–5824Publication Date (Print):November 1, 1989Publication History Published online1 May 2002Published inissue 1 November 1989https://pubs.acs.org/doi/10.1021/jo00285a034https://doi.org/10.1021/jo00285a034research-articleACS PublicationsRequest reuse permissionsArticle Views242Altmetric-Citations66LEARN 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
T-DNA border sequences required for crown gall tumorigenesis. (1985)

Similar 23-base-pair (bp) direct repeats occur at the ends of two adjacent but noncontiguous T-DNAs, TL and TR (left and right T-DNA), in the tumor-inducing plasmid pTiA6NC. Thus, three border repeats lie right and one lies left of TL, which carries the genes needed for tumor maintenance. To determine whether T-DNA transfer and integration (subsequently called T-DNA transmission) require sequences in addition to the 23-bp border repeat, we constructed a deletion removing the three potential TL right borders (the TL right border and both TR borders). Since this deletion severely attenuated virulence, we reintroduced restriction fragments containing the TL right border repeat at a new location to the right of TL and tested their ability to restore virulence. Fragments that carried the border repeat flanked by at least 67 bp of wild-type Ti plasmid sequences on the left and 1035 bp on the right restored virulence completely. Smaller fragments restored virulence significantly but not fully, even though the border repeat remained intact. Therefore, T-region sequences flanking the border repeat in the fully active fragments stimulated T-DNA integration. Fragments that restored virulence fully when inserted in the wild-type orientation stimulated virulence only slightly in the opposite orientation. Thus, the right border sequence promotes T-DNA transfer and integration best in one direction.
Scalable Distributed Stream Processing (2003)

Stream processing fits a large class of new applications for which conventional DBMSs fall short. Because many stream-oriented systems are inherently geographically distributed and because distribution offers scalable load management and higher availability, future stream processing systems will operate in a distributed fashion. They will run across the Internet on computers typically owned by multiple cooperating administrative domains. This paper describes the architectural challenges facing the design of large-scale distributed stream processing systems, and discusses novel approaches for addressing load management, high availability, and federated operation issues. We describe two stream processing systems, Aurora * and Medusa, which are being designed to explore complementary solutions to these challenges. 1
Demonstration and analysis of a 40-gigasample/s interferometric analog-to-digital converter (2006)

A novel interferometric scheme for photonic analog-to-digital conversion is for the first time experimentally demonstrated at a real-time sample rate of 40 gigasamples/s. The scheme includes sampling as well as binary encoding, and the input signal in the experiment was a 1.25-GHz sinusoidal tone that was successfully digitized with a nominal resolution of 21 digital levels. Single-sample measurements yielded an effective number of bits (ENOB) of 2.6, which was limited by thermal detection noise while multisample averaged measurements resulted in an ENOB of 3.6 bits, mainly limited by phase drift. Apart from the experimental results, this paper covers an extensive theoretical analysis of the system, including calculations on the fundamental maximum bandwidth, the required optical power, the generated binary code, and its error robustness, as well as the impact of detection noise on the signal-to-noise ratio of the digitized signal. The major benefits of this interferometric scheme are that only one standard phase modulator is required and that the phase swing does not have to be larger than plusmnpi to reach the full digital value space
A 2–20-GHz Analog Lag Correlator for Radio Interferometry (2012)

We present the design and testing of a 2-20-GHz continuum-band analog lag correlator with 16 frequency channels for astronomical interferometry. The correlator has been designed for future use with a prototype single-baseline interferometer operating at 185-275 GHz. The design uses a broad-band Wilkinson divider tree with integral thin-film resistors implemented on an alumina substrate, and custom-made broad-band InGaP/GaAs Gilbert Cell multipliers. The prototype correlator has been fully bench-tested, together with the necessary readout electronics for acquisition of the output signals. The results of these measurements show that the response of the correlator is well behaved over the band. An investigation of the noise behavior also shows that the signal-to-noise ratio of the system is not limited by the correlator performance.
Purification and Assay of Mammalian Group I and Group Ila Secretory Phospholipase A<sub>2</sub> (2003)

Phospholipases A2 (PLA2) are a family of ubiquitous lipolytic enzymes that are found both as intracellular and secreted proteins. Secretory PLA2s are small (14 kDa), homologous proteins that require millimolar Ca2+ for catalytic activity. They can be classified into at least four groups based on minor structural differences (1,2). In particular, two major classes of highly homologous secretory enzymes (class I and IIa) have been found in mammalian tissues. Mammalian class I PLA2s are synthesized in the pancreas as pro-enzymes and activated by proteolytic cleavage in the intestine (for review see ref. 3 and references therein). All known mammalian pancreatic PLA2s show strong sequence homology. The main function of these pancreatic PLA2s is to digest dietary phospholipids emulsified with bile juice (3). Recently, several lines of evidence have indicated that mammalian pancreatic PLA2s are present in different tissues and might play other physiological roles, including cell surface receptor-mediated inflammation (4).
A Benchtop Method for the Fabrication and Patterning of Nanoscale Structures on Polymers (2003)

A benchtop method for the facile production of nanoscale metal structures on polymers is demonstrated. This approach allows for the design and patterning of a wide range of metallic structures on inexpensive polymer surfaces, affording the fabrication of nanoscaled platforms for use in the design of sensors, actuators, and disposable electronic and photonic devices. Numerous structures, from simple nanowires to multilayered metallic gratings, are demonstrated, with sizes ranging from microns to the nanoscale. The process involves molding a malleable metal film deposited on a rigid substrate such as mica, by the compression of a plastic polymer stamp with the desired pattern against the metal film. While under compression, an etchant is then used to modify the metal. Upon separation of the stamp from the support, micro- to nanoscaled metallic structures are found on the stamp and/or on the substrate. The sizes of the structures formed depend on the sizes of the features on the stamp but can be fine-tuned by about 4-fold through variations in both pressure and duration of etching. Also, depending on the processing, multiple dimension metallic structures can be obtained simultaneously in a single stamping procedure. The metallic structures formed on the stamp can also be subsequently transferred to another surface allowing for the construction of multilayered materials such as band gap gratings or the application of electrical contacts. Using this approach, fabrication of both simple and complex micro- to nanoscaled structures can be accomplished by most any researcher as even the grating structure of commercial compact disks may be used as stamps, eliminating the requirement of expensive lithographic processes to form simple structures.
Protection of Mice and Poultry from Lethal H5N1 Avian Influenza Virus through Adenovirus-Based Immunization (2006)

ABSTRACT The recent emergence of highly pathogenic avian influenza virus (HPAI) strains in poultry and their subsequent transmission to humans in Southeast Asia have raised concerns about the potential pandemic spread of lethal disease. In this paper we describe the development and testing of an adenovirus-based influenza A virus vaccine directed against the hemagglutinin (HA) protein of the A/Vietnam/1203/2004 (H5N1) (VN/1203/04) strain isolated during the lethal human outbreak in Vietnam from 2003 to 2005. We expressed different portions of HA from a recombinant replication-incompetent adenoviral vector, achieving vaccine production within 36 days of acquiring the virus sequence. BALB/c mice were immunized with a prime-boost vaccine and exposed to a lethal intranasal dose of VN/1203/04 H5N1 virus 70 days later. Vaccination induced both HA-specific antibodies and cellular immunity likely to provide heterotypic immunity. Mice vaccinated with full-length HA were fully protected from challenge with VN/1203/04. We next evaluated the efficacy of adenovirus-based vaccination in domestic chickens, given the critical role of fowl species in the spread of HPAI worldwide. A single subcutaneous immunization completely protected chickens from an intranasal challenge 21 days later with VN/1203/04, which proved lethal to all control-vaccinated chickens within 2 days. These data indicate that the rapid production and subsequent administration of recombinant adenovirus-based vaccines to both birds and high-risk individuals in the face of an outbreak may serve to control the pandemic spread of lethal avian influenza.
Calcaneocuboid joint and stability of the longitudinal arch of the foot at high and low gear push off. (1979)

The calcaneocuboid joint was studied in ligamentous specimens of ten human feet, and in skeletons of two gorillas (Gorilla gorilla beringei), six chimpanzees (Pan troglodytes), three orangutans (Pongo pygmaeus) and 25 human feet. The movement of the transverse tarsal joint was further studied in a living foot on a walk-way with a glass plate inserted, and with an underlying mirror. In man the joint is shaped as an asymmetrical sector of one end of an hour-glass shaped surface of revolution with its main axis oriented longitudinally in the foot. The calcaneocuboid joint becomes close packed by a pronation of the forefoot in relation to the hind foot because of a congruency between the joint surfaces obtained in this position and because the calcaneus overhangs the cuboid dorsally and stops the movement. At low gear push off the foot is inverted and the calcaneocuboid joint loose packed. The stresses are absorbed across the fibular, postaxial border of the foot. At high high gear push off there is a functional pronation of the forefoot with a stabilization of the transverse tarsal joint and a more effective tightening of the plantar aponeurosis. The foot becomes a rigid lever for propulsion. In contrast to the human condition, the anthropoid calcaneus has an anteromedial extension associated with symmetry of the calcaneocuboid joint. The calcaneus does not overhang the cuboid and there appears to be no close packed position. Correspondingly, the anthropoid foot has a mid-tarsal break at each push off in addition to the metatarsophalangeal break.
Accelerating vector graphics rendering using the graphics hardware pipeline (2015)

We describe our successful initiative to accelerate Adobe Illustrator with the graphics hardware pipeline of modern GPUs. Relying on OpenGL 4.4 plus recent OpenGL extensions for advanced blend modes and first-class GPU-accelerated path rendering, we accelerate the Adobe Graphics Model (AGM) layer responsible for rendering sophisticated Illustrator scenes. Illustrator documents render in either an RGB or CMYK color mode. While GPUs are designed and optimized for RGB rendering, we orchestrate OpenGL rendering of vector content in the proper CMYK color space and accommodate the 5+ color components required. We support both non-isolated and isolated transparency groups, knockout, patterns, and arbitrary path clipping. We harness GPU tessellation to shade paths smoothly with gradient meshes. We do all this and render complex Illustrator scenes 2 to 6x faster than CPU rendering at Full HD resolutions; and 5 to 16x faster at Ultra HD resolutions.
Transcriptional regulation of the mouse metallothionein-I gene by heavy metals. (1981)

Administration of Cd, Zn, Cu, or Hg increases the rate of transcription from the metallothionein-I gene in mouse liver and kidney. Maximal transcription rates occur 1 h after Cd administration in both tissues. Metallothionein-I mRNA levels, measured by cDNA hybridization, and metallothionein protein synthesis, measured by [35S]cysteine incorporation, increase simultaneously, reaching maximal levels about 4 h after Cd administration. Cd also induces metallothionein-I mRNA in all other tissues examined (spleen, heart, skeletal muscle, brain, and intestine) except testes. Comparison of the inductions by Cd and Hg shows that the kinetics of metallothionein-I mRNA accumulation as well as the stability of the resultant metallothioneins differ.
A multivalent lacto-N-fucopentaose III-lysyllysine conjugate decompacts preimplantation mouse embryos, while the free oligosaccharide is ineffective. (1984)

A multivalent lacto-N-fucopentaose (LNFP) III-lysyllysine conjugate was observed to decompact preimplantation mouse embryos. Decompaction was not obtained with free oligosaccharides (LNFP II and III), nor with multivalent LNFP II-lysyllysine or chitotriose-lysyllysine conjugates. These results suggest a role for X hapten recognition during compaction and suggest further that X hapten valency may play a key role in modulating this developmental process.