bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Infectious cDNA Clones of Hepatitis C Virus Genotype 3a (Strain S52) and 4a (Strain ED43): Genetic Analyses and
In Vivo
Pathogenesis Studies
Authors: Gottwein Judith M. , Scheel Troels K. H. , Callendret Benoit , Li Yi-Ping , Eccleston Heather B. , Engle Ronald E. , Govindarajan Sugantha , Satterfield William , Purcell Robert H. , Walker Christopher M. , Bukh Jens 
Published: March 2010

ABSTRACT

Previously, RNA transcripts of cDNA clones of hepatitis C virus (HCV) genotypes 1a (strains H77, HCV-1, and HC-TN), 1b (HC-J4, Con1, and HCV-N), and 2a (HC-J6 and JFH1) were found to be infectious in chimpanzees. However, only JFH1 was infectious in human hepatoma Huh7 cells. We performed genetic analysis of HCV genotype 3a (strain S52) and 4a (strain ED43) prototype strains and generated full-length consensus cDNA clones (pS52 and pED43). Transfection of Huh7.5 cells with RNA transcripts of these clones did not yield cells expressing HCV Core. However, intrahepatic transfection of chimpanzees resulted in robust infection with peak HCV RNA titers of ∼5.5 log
10
international units (IU)/ml. Genomic consensus sequences recovered from serum at the times of peak viral titers were identical to the sequences of the parental plasmids. Both chimpanzees developed acute hepatitis with elevated liver enzymes and significant necroinflammatory liver changes coinciding with detection of gamma interferon-secreting, intrahepatic T cells. However, the onset and broadness of intrahepatic T-cell responses varied greatly in the two animals, with an early (week 4) multispecific response in the ED43-infected animal (3 weeks before the first evidence of viral control) and a late (week 11) response with limited breadth in the S52-infected animal (without evidence of viral control). Autologous serum neutralizing antibodies were not detected during the acute infection in either animal. Both animals became persistently infected. In conclusion, we generated fully functional infectious cDNA clones of HCV genotypes 3a and 4a. Proof of functionality of all genes might further the development of recombinant cell culture systems for these important genotypes.
Lymphatics and D2-40/podoplanin expression in gastrointestinal stromal tumours of the stomach with and without lymph node metastasis: an immunohistochemical study with special reference to the Carney triad
Authors: Agaimy Abbas , Carney J Aidan 
Published: March 2010

BackgroundLymph node metastasis of gastric gastrointestinal stromal tumours (GISTs) in children and young adults, especially those with the Carney triad, is common (∼29%) and contrasts with that of sporadic gastric GISTs (≤2%). The mechanism responsible for this difference in tumour behaviour is not understood. In previous studies, expression of the lymphatic endothelial marker D2-40/podoplanin in carcinoma cells and the presence of intratumoural/peritumoural lymphatics have been correlated with tumour invasiveness and nodal metastasis.MethodsThis study investigated the presence of intratumoural and peritumoural lymphatics, and expression of D2-40/podoplanin, in 16 patients with syndromic/paediatric gastric GISTs (11 patients had Carney triad, two had Carney–Stratakis syndrome and three had paediatric GISTs suspicious for the Carney triad) with histologically verified metastasis to regional lymph nodes. The results were compared with those found in 35 sporadic gastric GISTs lacking nodal spread using the antibody D2-40/podoplanin.ResultsThe mean ages at GIST diagnosis in the patients with syndromic/paediatric GISTs and those with sporadic GISTs were 18 years and 67 years, respectively. Intratumoural lymphatics were detected with comparable frequency in the two tumour sets (25% and 17%, respectively; p=0.705). Peritumoural lymphatics were equally present in the tumours from both of the groups. Moderate/strong cytoplasmic/membranous staining for D2-40/podoplanin was frequent in the neoplastic cells of syndromic/paediatric GISTs (87%), and infrequent in sporadic GISTs (3%) (p<0.001).ConclusionThe results indicate that intratumoural lymphangiogenesis is probably not involved in lymphatic spread in syndromic/paediatric GISTs. The biological significance of D2-40/podoplanin expression in tumour cells of syndromic/paediatric GISTs and its possible role in lymphatic tumour spread remain to be further investigated.
A comparison of two DNA barcode markers for species discrimination in the red algal family Kallymeniaceae (Gigartinales, Florideophyceae), with a description of Euthora timburtonii sp. nov.
Authors: Clarkston Bridgette E. , Saunders Gary W. 
Published: March 2010

Accurate identification of many red algae to the species level using only morphological characters can be difficult. The emerging field of “molecular-assisted alpha taxonomy” can greatly alleviate this issue. In this approach, a large number of specimens are sequenced for a standard DNA marker as a first step to genetic species assignment, followed by detailed morphological observations. Regions of both the mitochondrial cytochrome c oxidase I gene (COI-5P) and the plastid 23S rRNA gene (UPA) have been proposed as DNA barcode markers to accomplish this task. We compared the utility of each marker as a species identification tool using members of the marine red algal family Kallymeniaceae from British Columbia, Canada. Our results indicate that COI-5P is a more sensitive marker for delimiting species, but that it can be difficult to acquire clean amplification products for many isolates of Kallymeniaceae, owing to biological contamination. This problem can be overcome by using specific primers. UPA, on the other hand, has universal primers that work in diverse lineages (e.g., red, brown, and green algae), but lower interspecific sequence variation, which has the potential to underestimate species diversity, although this was not observed in our study. During our survey, we uncovered a new species of the Kallymeniaceae, Euthora timburtonii Clarkston et G.W. Saunders sp. nov., which we describe here.
Nitrogen use efficiency: re-consideration of the bioengineering approach
Authors: Brauer Elizabeth K. , Shelp Barry J. 
Published: March 2010

There is considerable confusion about N use efficiency (NUE) in the plant literature. We would like to propose the simple and ubiquitous definitions described by Good et al. (2004) as a starting point for studies of NUE. Based on this terminology, there is evidence from breeding programs for variation in both uptake efficiency (UpE) and utilization efficiency (UtE). Molecular physiology studies typically address mechanisms for improving NUE, but often do not calculate NUE or even acquire appropriate data for calculating NUE. Herein, we report in detail on recent studies involving molecular approaches for improving NUE, and calculate changes in NUE where possible. The evidence suggests that there is potential for improving usage index and UpE in dicots and UpE and UtE in monocots by overexpressing enzymes for N assimilation, specifically glutamine synthetase 1, glutamate synthase, and alanine aminotransferase. If decreased fertilizer-N input and improved NUE are truly goals of the plant biology community, researchers are encouraged to (i) consider the use of both wild type and azygous controls, (ii) compare general NUE (on the basis of grain or biomass yield per unit of applied N) of overexpression mutants and controls at both limiting and non-limiting N levels, (iii) select an appropriate type of specific NUE for assessing the physiological mechanisms involved (uptake versus internal utilization), and (iv) confirm promising results under field conditions.
Diagenesis to metamorphism transition in an episutural basin: the late Paleozoic St. Mary’s Basin, Nova Scotia, Canada
Authors: Abad Isabel , Murphy J. Brendan , Nieto Fernando , Gutiérrez-Alonso Gabriel 
Published: March 2010

The Late Devonian – Early Carboniferous St. Mary’s Basin in the Canadian Appalachians consists of Horton Group fluviatile and lacustrine clastic rocks. The basin occurs along the boundary between the Avalon and Meguma terranes and developed during coeval dextral shear along that boundary. X-ray diffraction reveals that the rocks contain ubiquitous quartz, K-white mica, and albite; illite–smectite mixed layers and chlorite are very common and Na–K mica, kaolinite, chlorite–smectite mixed layers, K-feldspar, berthierine, and rutile occur in some samples. Crystal-chemical parameters of white mica indicate the pressure and temperature of mineral growth and discriminate between diagenetic, anchizone, and low-grade metamorphic processes. Kübler index values measured in the 5 Å peak and the presence of chlorite–mica stacks are indicative of high-anchizone–epizone grades, with a crystallinity (crystal size and number of defects) that increases towards the Chedabucto Fault, which defines the northern margin of the basin. Kübler index values measured in the 10 Å peak indicate that a late fluid-rich event could have produced the observed illite–smectite mixed layers. The overall clay-mineral content and the b-cell dimension of the K-white micas are typical of postdepositional evolution in extensional sedimentary basins with high heat flow (>35 °C/km). Taken together, our data record two superposed events related to deformation along the basin margins and coeval regional fluid flow, in which retrograde reactions at temperature T < 200 °C were superimposed on a pre-existing prograde assemblage typical of high-anchizone – lower greenschist-facies conditions (T > 300 °C). Regional syntheses indicate that this fluid flow may have occurred during episodes of Late Carboniferous dextral shear along the Avalon–Meguma terrane boundary.
Tidal movements and residency of subyearling Chinook salmon (Oncorhynchus tshawytscha) in an Oregon salt marsh channel
Authors: Hering David K. , Bottom Daniel L. , Prentice Earl F. , Jones Kim K. , Fleming Ian A. 
Published: March 2010

A novel application of full-duplex passive integrated transponder (PIT) tag technology was used to investigate movements of individual subyearling Chinook salmon ( Oncorhynchus tshawytscha ; fork length ≥ 60 mm) into and out of tidally flooded salt marsh habitat in the Salmon River estuary, Oregon, USA. PIT interrogation was effective, with mean tag detection ≥ 92%. Salmon movement peaked late during both flood and ebb tide periods, indicating that salmon did not drift passively. Most movements were in the direction of tidal currents, but 20% of individuals entered the channel against the ebbing tide. Individuals occupied the intertidal channel for a median 4.9 h and as long as 8.9 h per tidal cycle, and few were detected moving when water depth was <0.4 m. Some individuals used the channel on multiple successive tidal cycles, and others entered intermittently over periods of up to 109 days. Using an individual-based approach, we characterized diversity of juvenile Chinook salmon behavior within a marsh channel, providing insight into the value of such habitats for conservation and restoration of salmon populations.
Experimental assessment of the bioenergetic and behavioural differences between two morphologically distinct populations of Arctic char (Salvelinus alpinus)
Authors: Guénard Guillaume , Boisclair Daniel , Ugedal Ola , Forseth Torbjørn , Jonsson Bror , Fleming Ian A. 
Published: March 2010

A common environment experiment was conducted to assess the magnitude of the difference in growth, consumption, activity rate, and spatial and temporal patterns of habitat use between morphologically different populations of Arctic char ( Salvelinus alpinus ) originating from two Norwegian lakes. These two lakes contrasted sharply in terms of surface area, depth, elevation, length of the winter period, and fish community structure (presence–absence of brown trout, Salmo trutta ). The experimental framework encompassed four littoral enclosures (average volume, 146 m3) stocked with char from either of the two populations with duplicated treatments. Char morphology was quantified with numerical image analysis, food consumption was estimated using caesium analysis (133Cs), and activity cost and patterns were determined using video cameras. Char populations were morphologically distinct and reacted differently in growth (1.9-fold difference between populations), food consumption (3-fold difference), and spatial activity patterns (20-fold difference) to the conditions prevailing in the enclosures. The results highlight that functional differences between morphologically distinct char may drive important differences in their bioenergetic and behavioural responses when exposed to similar environmental conditions. Such functional differences should be incorporated when developing habitat or trophic cascade models.
Design, synthesis, and properties of benzobisthiadiazole-based donor–π–acceptor–π–donor type of low-band-gap chromophores and polymers
Authors: Qian Gang , Wang Zhi Yuan 
Published: March 2010

A novel low-band-gap chromophore (5, 0.86 eV) having fluorene as a donor, benzobisthiadiazole (BBTD) as an acceptor, and pyrrole as a π-spacer was successfully designed and synthesized, to probe the effect of π-spacer on the band-gap level of the donor–π–acceptor–π–donor type of chromophores. Compared with the thiophene spacer analogue (in compound 3), the intramolecular hydrogen bonding between the pyrrole and the neighboring BBTD unit pushes the absorption maximum and fluorescence emission of chromophore 5 into the near-infrared spectral region with a red shift of 172 and 158 nm, respectively. The same red-shift phenomenon can also be realized by addition of Lewis acid (e.g., BF3) to the BBTD-containing chromophores with other spacers. Attempt of using low-band-gap chromophore 5 in bulk heterojunction (BHJ) solar cells was made, showing a non-optimized photovoltaic device with the power conversion efficiency of 0.01%. A precursor approach to introduction of the alkaline-labile BBTD acceptor into the polymer backbone has been demonstrated by successful synthesis of low-band-gap polymer P2. The same strategy can be in principle applied to the synthesis of a series of low-band-gap chromophores or polymers with strong acceptors.
Synthesis, photophysics, and electrochemistry of thiophene–pyridine and thiophene–pyrimidine dyad comonomers
Authors: Bolduc Andréanne , Dufresne Stéphane , Hanan Garry S. , Skene W. G. 
Published: March 2010

A series of new π-conjugated donor (D) and acceptor (A) dyad comonomers were prepared using Suzuki coupling protocols. The D–A comonomers consisting of thiophene/bithiophene as donors and pyridine/pyrimidine as acceptors were prepared to investigate their photophysical and electrochemical properties. The dyads were spectroscopically confirmed to be highly conjugated. This was further supported by the X-ray crystal structure of the bithophene–pyridine dyad that showed all the heterocycles to be coplanar. It was further found that the fluorescence yields (Φfl) of the dyads were highly dependent on the number of thiophenes. The bithiophene derivatives exhibited Φfl values ≥ 0.3 while the thiophene derivatives did not fluoresce. The suppressed fluorescence observed for the thiophene derivatives was due to their higher triplet energy resulting in efficient intersystem crossing (ISC) to the triplet state with ΦISC ≥ 0.8. This was confirmed both by time-resolved and steady-state measurements. The singlet excited state of both thiophene and bithiophene dyads was deactivated solely by either fluorescence and (or) ISC. Owing to their donor and acceptor character, the dyads could be oxidized and reduced both electrochemically and photochemically to afford the radical cation and anion, respectively.
Climatic factors affecting radial growth of Betula ermanii and Betula platypylla in Kamchatka
Authors: Doležal Jiri , Ishii Hiroaki , Kyncl Tomáš , Takahashi Koichi , Vetrova Valentina P. , Homma Kosuke , Sumida Akihiro , Hara Toshihiko 
Published: March 2010

Radial growth responses to climate were studied in two species of birch broadly distributed across Kamchatka Peninsula. Wood cores were obtained in different locations and environments, from upper to lower treelines, and from wet maritime sites at the Pacific to the subcontinental interior of the peninsula. Response functions were calculated using the four longest meteorological records (1920s–2000) in Kamchatka. In Betula ermanii Cham., the dominant species in mountains and maritime woodlands, ring width in high-elevation (500–600 m) trees increased with warm and less rainy June and July and decreased with rainy/snowy cool weather during the prior September and October. Radial growth in B. ermanii low-elevation trees increased with higher winter precipitation, suggesting that water from melting snow prevents water stress and possibly desiccation in low-elevation trees. In Betula platyphylla Sukaczev, a common taiga species in interior Kamchatka, low summer temperatures limited growth at its upper distributional limit (300–350 m) and in cool, wet sites dominated by Picea ajanensis Lindl. et Gord. On drier sites dominated by Larix cajanderii Mayr., growth was limited by warm April and dry June weather. Variable responses along elevation–continentality gradients reinforce the necessity of a site-dependent differentiation for the assessment of impacts of climate change on species performance and geographic range shifts.
Sugar maple seedling carbon assimilation at the northern limit of its range: the importance of seasonal light
Authors: Kwit Matthew C. , Rigg Lesley S. , Goldblum David 
Published: March 2010

Using in situ light curves and understory seasonal light measurements the importance of canopy avoidance was evaluated for a population of sugar maple ( Acer saccharum Marsh.) seedlings living at the boreal ecotone in Lake Superior Provincial Park, Ontario, Canada. At higher latitudes, the time period associated with canopy avoidance is shorter and occurs at cooler temperatures, increasing the risk of frost damage. In 2008, leaf-out began 5 days prior to the last frost of the season. By modeling the potential carbon gain of seedlings, it is clear that the short time period prior to canopy leaf-out still contributes a disproportionate amount of carbon to the overall budget of seedlings. Of the total seasonal carbon gain, 80.6% was assimilated in the initial 15 days following sugar maple seedling leaf-out. Based on our model, by leafing out only 6 days earlier than the average seedling leaf-out date, ∼200% more carbon could be assimilated during the course of the growing season. Vegetation phenology is cued by climatic triggers — as climate changes so too will phenological responses. These mechanisms add to the overall carbon budget of seedlings; recognizing these mechanisms is essential to thoroughly understand the natural history of this species.
COMPLETE TRAFFIC PATTERNS AROUND A T-SHAPED INTERSECTION
Authors: HUANG DING-WEI 
Published: March 2010

We propose Asymmetric Simple Exclusion Processes to analyze the traffic states around a T-shaped intersection. The system consists of six roadways connected by the intersection. There are nine control-parameters separated into three categories: injection αi, removal βi, and turning Pi, (where i = 1, 2, 3). As these nine parameters change, traffic states on each roadway reveal a two-phase transition: free flow (F) and jam (J). Together, there can be 64 (=26) possible combinations for the traffic phases. We observe 63 distinct phases. We analyze three major causes of congestion: (1) increase of traffic demand simulated by injection αi; (2) decrease of roadway capacity simulated by removal βi; (3) redistribution of traffic pattern simulated by turning Pi. In case (1), congestion can be confined to the roadways heading toward the intersection. In case (2), spillovers can be observed and congestion will pervade the whole system. In case (3), congestion can be triggered by both increasing Pi and decreasing Pi. The phase diagram can be a convenient tool to summarize the results of numerical simulations. We also compare the unsignalized intersection to an intersection regulated by traffic signals. We find that the operation of traffic signals is very inefficient in resolving the congestion around a T-shaped intersection.
Existence and Approximation of Fixed Points for Set-Valued Mappings
Authors: Reich Simeon , Zaslavski AlexanderJ 
Published: March 2010

AbstractTaking into account possibly inexact data, we study both existence and approximation of fixed points for certain set-valued mappings of contractive type. More precisely, we study the existence of convergent iterations in the presence of computational errors for two classes of set-valued mappings. The first class comprises certain mappings of contractive type, while the second one contains mappings satisfying a Caristi-type condition.
GATA-4 Is an Angiogenic Survival Factor of the Infarcted Heart
Authors: Rysä Jaana , Tenhunen Olli , Serpi Raisa , Soini Ylermi , Nemer Mona , Leskinen Hanna , Ruskoaho Heikki 
Published: March 2010

Background—
Recent data suggest that GATA-4 is an antiapoptotic factor required for adaptive responses and a key regulator of hypertrophy and hypertrophy-associated genes in the heart. As a leading cause of chronic heart failure, reversal of postinfarction left ventricular remodeling represents an important target for therapeutic interventions. Here, we studied the role of GATA-4 as a mediator of postinfarction remodeling in rats.

Methods and Results—
Myocardial infarction, caused by ligating the left anterior descending coronary artery, significantly decreased the DNA binding activity of GATA-4 at day 1, whereas at 2 weeks the GATA-4 DNA binding was significantly upregulated. To determine the functional role of GATA-4, peri-infarct intramyocardial delivery of adenoviral vector expressing GATA-4 was done before left anterior descending coronary artery ligation. Hearts treated with GATA-4 gene transfer exhibited significantly increased ejection fraction and fractional shortening. Accordingly, infarct size was significantly reduced. To determine the cardioprotective mechanisms of GATA-4, myocardial angiogenesis, rate of apoptosis, c-kit+ cardiac stemlike cells, and genes regulated by GATA-4 were studied. The number of capillaries and stemlike cells was significantly increased, and decreased apoptosis was observed.

Conclusion—
These results indicate that the reversal of reduced GATA-4 activity prevents adverse postinfarction remodeling through myocardial angiogenesis, antiapoptosis, and stem cell recruitment. GATA-4–based gene transfer may represent a novel, efficient therapeutic approach for heart failure.