bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enantioselectivity in the cytochrome P450‐dependent conversion of tegafur to 5‐fluorouracil in human liver microsomes
Authors: Yamamiya Ikuo , Yoshisue Kunihiro , Ishii Yuji , Yamada Hideyuki , Yoshida Ken‐ichiro 
Published: December 2013

AbstractTegafur (FT) is a prodrug of 5‐fluorouracil (5‐FU) used in cancer chemotherapy, and the bioactivation of FT to 5‐FU is mainly catalyzed by cytochrome P450 (CYP) in hepatic microsomes. FT has a chiral center and is a racemate consisting of the enantiomers, R‐ and S‐FT. In the present study, we clarified the enantioselectivity in the conversion of FT to 5‐FU and identified human CYP isoforms involved in the metabolism of its enantiomers using human hepatic preparations and recombinant CYP isoforms. Although 5‐FU was generated from both FT enantiomers, R‐FT was a preferred substrate than S‐FT, because of the considerably higher intrinsic clearance for 5‐FU formation from R‐FT in liver. Eadie–Hofstee plots in microsomes showed that the conversions of R‐ and S‐FT to 5‐FU followed biphasic and monophasic kinetics, respectively. Based on the evaluation using cDNA‐expressed enzymes, CYP2A6 showed the highest activity for 5‐FU formation from R‐FT with the Km value similar to that of the high‐affinity component in microsomes. Also, CYP2A6 was the most effective catalyst for S‐FT. Inhibition studies using CYP‐selective inhibitors and anti‐CYP antibodies demonstrated that CYP2A6 mainly contributed to the enantioselective metabolism of FT, and were almost in accordance with the relative percentage contribution of each CYP isoform to the metabolism of FT estimated using relative activity factor methods. These results suggest that the enantioselectivity in the bioactivation of FT to 5‐FU in humans is mainly due to the large difference of the catalytic activity of CYP2A6 between R‐ and S‐FT.
Conductivity of anodic TiO2 nanotubes: Influence of annealing conditions
Authors: Tighineanu Alexei , Albu Sergiu P. , Schmuki Patrik 
Published: December 2013

AbstractThe present work reports on the resistivity of anodic TiO2 nanotubes as function of annealing temperature and atmosphere. Significant effects of several orders of magnitude are observed and explained by different crystallinity and self‐doping level. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing
Authors: Burroughs Alexander Maxwell , Ando Yoshinari , Aravind L 
Published: December 2013

Our understanding of the pervasive involvement of small RNAs in regulating diverse biological processes has been greatly augmented by recent application of deep‐sequencing technologies to small RNA across diverse eukaryotes. We review the currently known small RNA classes and place them in context of the reconstructed evolutionary history of the RNA interference (RNAi) protein machinery. This synthesis indicates that the earliest versions of eukaryotic RNAi systems likely utilized small RNA processed from three types of precursors: (1) sense–antisense transcriptional products, (2) genome‐encoded, imperfectly complementary hairpin sequences, and (3) larger noncoding RNA precursor sequences. Structural dissection of PIWI proteins along with recent discovery of novel families (including Med13 of the Mediator complex) suggest that emergence of a distinct architecture with the N‐terminal domains (also occurring separately fused to endoDNases in prokaryotes) formed via duplication of an ancestral unit was key to their recruitment as primary RNAi effectors and use of small RNAs of certain preferred lengths. Prokaryotic PIWI proteins are typically components of several RNA‐directed DNA restriction or CRISPR/Cas systems. However, eukaryotic versions appear to have emerged from a subset that evolved RNA‐directed RNAi. They were recruited alongside RNaseIII domains and RNA‐dependent RNA polymerase (RdRP) domains, also from prokaryotic systems, to form the core eukaryotic RNAi system. Like certain regulatory systems, RNAi diversified into two distinct but linked arms concomitant with eukaryotic nucleocytoplasmic compartmentalization. Subsequent elaboration of RNAi proceeded via diversification of the core protein machinery through lineage‐specific expansions and recruitment of new components from prokaryotes (nucleases and small RNA‐modifying enzymes), allowing for diversification of associating small RNAs. WIREs RNA 2014, 5:141–182. doi: 10.1002/wrna.1210This article is categorized under:

RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution
RNA Evolution and Genomics > Computational Analyses of RNA
Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Effective ablation therapy of adenomyosis with ultrasound‐guided high‐intensity focused ultrasound
Authors: Zhang Xin , Li Kequan , Xie Bin , He Min , He Jia , Zhang Lian 
Published: December 2013

AbstractObjectiveTo evaluate the effects of ultrasound‐guided high‐intensity focused ultrasound (HIFU) on adenomyosis.MethodsIn a retrospective analysis, data were reviewed from 202 patients with adenomyosis who underwent ultrasound‐guided HIFU between November 2010 and June 2012 at Suining Central Hospital, Sichuan, China. Among these patients, 120 and 82 were classified as having focal adenomyosis and diffuse adenomyosis, respectively. All patients underwent pre‐treatment and post‐treatment magnetic resonance imaging by a standardized protocol to evaluate the treatment. All adverse effects were recorded.ResultsAll patients completed the ultrasound‐guided HIFU treatment in 1 session. A non‐perfused volume ratio of 71.6% ± 19.1% was achieved. Compared with baseline data, the average menorrhagia severity score and the average dysmenorrhea severity pain score decreased significantly after ultrasound‐guided HIFU (both P < 0.001). The proportion of women with complete relief of dysmenorrhea at the 3‐month follow‐up was significantly higher among women with focal adenomyosis than among those with diffuse adenomyosis (P = 0.02). No other significant differences were observed between the 2 patient groups.ConclusionUltrasound‐guided HIFU was found to be an effective technique for treating both focal and diffuse adenomyotic lesions to alleviate the symptoms of menorrhagia or dysmenorrhea.
A case of mucositis due to the allergy to self‐curing resin
Authors: Hashimoto Ken‐ichiro , Naganuma Kaori , Yamashita Yoshihiro , Ikebe Tetsuro , Ozeki Satoru 
Published: December 2013

AbstractA 59‐year‐old woman noticed a swelling and redness in the buccal and palatal mucosa 12 h after setting of a temporary crown (TEK) made of self‐curing resin at a dental clinic. When she came to our hospital, the edema and redness in the buccal and palatal mucosa around the right upper molar were seen. The TEK had already been removed at the clinic. We suspected an allergy to TEK, and performed a patch test to the chemicals of the resin. The only liquid component of resin showed a positive reaction. Topical glucocorticoid ointment was applied, and the symptoms almost subsided 3 days later.
Host immune responses accelerate pathogen evolution
Authors: Trivedi Pankaj , Wang Nian 
Published: December 2013

Abstract
Pathogens face a hostile and often novel environment when infecting a new host, and adaptation is likely to be an important determinant of the success in colonization and establishment. We hypothesized that resistant hosts will impose stronger selection on pathogens than susceptible hosts, which should accelerate pathogen evolution through selection biased toward effector genes. To test this hypothesis, we conducted an experimental evolution study on Xanthomonas citri subsp. citri (Xcc) in a susceptible plant species and a resistant plant species. We performed 55 rounds of repeated reinoculation of Xcc through susceptible host grapefruit (isolates G1, G2, G3) and resistant host kumquat (isolates K1, K2, K3). Consequently, only K1 and K3 isolates lost their ability to elicit a hypersensitive response (HR) in kumquat. Illumina sequencing of the parental and descendant strains P, G1, G2, G3, K1, K2 and K3 revealed that fixed mutations were biased toward type three secretion system effectors in isolates K1 and K3. Parallel evolution was observed in the K1 and K3 strains, suggesting that the mutations result from selection rather than by random drift. Our results support our hypothesis and suggest that repeated infection of resistant hosts by pathogens should be prevented to avoid selecting for adaptive pathogens.
Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition
Authors: Ankrah Nana Yaw D , May Amanda L , Middleton Jesse L , Jones Daniel R , Hadden Mary K , Gooding Jessica R , LeCleir Gary R , Wilhelm Steven W , Campagna Shawn R , Buchan Alison 
Published: December 2013

Abstract
Viruses contribute to the mortality of marine microbes, consequentially altering biological species composition and system biogeochemistry. Although it is well established that host cells provide metabolic resources for virus replication, the extent to which infection reshapes host metabolism at a global level and the effect of this alteration on the cellular material released following viral lysis is less understood. To address this knowledge gap, the growth dynamics, metabolism and extracellular lysate of roseophage-infected Sulfitobacter sp. 2047 was studied using a variety of techniques, including liquid chromatography–tandem mass spectrometry (LC-MS/MS)-based metabolomics. Quantitative estimates of the total amount of carbon and nitrogen sequestered into particulate biomass indicate that phage infection redirects ∼75% of nutrients into virions. Intracellular concentrations for 82 metabolites were measured at seven time points over the infection cycle. By the end of this period, 71% of the detected metabolites were significantly elevated in infected populations, and stable isotope-based flux measurements showed that these cells had elevated metabolic activity. In contrast to simple hypothetical models that assume that extracellular compounds increase because of lysis, a profile of metabolites from infected cultures showed that &gt;70% of the 56 quantified compounds had decreased concentrations in the lysate relative to uninfected controls, suggesting that these small, labile nutrients were being utilized by surviving cells. These results indicate that virus-infected cells are physiologically distinct from their uninfected counterparts, which has implications for microbial community ecology and biogeochemistry.
Mechanisms of leading edge protrusion in interstitial migration
Authors: Wilson Kerry , Lewalle Alexandre , Fritzsche Marco , Thorogate Richard , Duke Tom , Charras Guillaume 
Published: December 2013

AbstractWhile the molecular and biophysical mechanisms underlying cell protrusion on two-dimensional substrates are well understood, our knowledge of the actin structures driving protrusion in three-dimensional environments is poor, despite relevance to inflammation, development and cancer. Here we report that, during chemotactic migration through microchannels with 5 μm × 5 μm cross-sections, HL60 neutrophil-like cells assemble an actin-rich slab filling the whole channel cross-section at their front. This leading edge comprises two distinct F-actin networks: an adherent network that polymerizes perpendicular to cell-wall interfaces and a ‘free’ network that grows from the free membrane at the cell front. Each network is polymerized by a distinct nucleator and, due to their geometrical arrangement, the networks interact mechanically. On the basis of our experimental data, we propose that, during interstitial migration, medial growth of the adherent network compresses the free network preventing its retrograde movement and enabling new polymerization to be converted into forward protrusion.
Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network
Authors: Jung Nicolas , Bertrand Frédéric , Bahram Seiamak , Vallat Laurent , Maumy-Bertrand Myriam 
Published: December 2013

Abstract
Summary: Temporal gene interactions, in response to environmental stress, form a complex system that can be efficiently described using gene regulatory networks. They allow highlighting the more influential genes and spotting some targets for biological intervention experiments. Despite that many reverse engineering tools have been designed, the Cascade package is an integrated solution adding several new and original key features such as the ability to predict changes in gene expressions after a biological perturbation in the network and graphical outputs that allow monitoring the spread of a signal through the network.
Availability and implementation: The R package Cascade is available online at http://www-math.u-strasbg.fr/genpred/spip.php?rubrique4.
Contact: fbertran@math.unistra.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
The dual role of HOP2 in mammalian meiotic homologous recombination
Authors: Pezza Roberto J. , Voloshin Oleg N. , Volodin Alexander A. , Boateng Kingsley A. , Bellani Marina A. , Mazin Alexander V. , Camerini-Otero R. Daniel 
Published: December 2013

AbstractDeletion of Hop2 in mice eliminates homologous chromosome synapsis and disrupts double-strand break (DSB) repair through homologous recombination. HOP2 in vitro shows two distinctive activities: when it is incorporated into a HOP2–MND1 complex it stimulates DMC1 and RAD51 recombination activities and the purified HOP2 alone is proficient in promoting strand invasion. We observed that a fraction of Mnd1−/− spermatocytes, which express HOP2 but apparently have inactive DMC1 and RAD51 due to lack of the HOP2–MND1 complex, exhibits a high level of chromosome synapsis and that most DSBs in these spermatocytes are repaired. This suggests that DSB repair catalyzed solely by HOP2 supports homologous chromosome pairing and synapsis. In addition, we show that in vitro HOP2 promotes the co-aggregation of ssDNA with duplex DNA, binds to ssDNA leading to unstacking of the bases, and promotes the formation of a three-strand synaptic intermediate. However, HOP2 shows distinctive mechanistic signatures as a recombinase. Namely, HOP2-mediated strand exchange does not require ATP and, in contrast to DMC1, joint molecules formed by HOP2 are more sensitive to mismatches and are efficiently dissociated by RAD54. We propose that HOP2 may act as a recombinase with specific functions in meiosis.
Influence of walking speed on locomotor time production
Authors: Megrot Fabrice , Megrot Carole 
Published: December 2013

SummaryThe aim of the present study was to determine whether or not walking speed affects temporal perception. It was hypothesized that fast walking would reduce the perceived length of time while slow walking increase production estimates. 16 healthy subjects were included. After a first « calibration » phase allowing the determination of different walking speeds, the subjects were instructed to demonstrate periods of time or « target times » of 3s and 7s, by a walking movement. Then, subjects were asked to simulate walking by raising one foot after the other without advancing. Finally, a third condition, Motionless, involved producing the target times while standing without movement. The results of this study suggest that movement does influence the perception of time, causing an overestimation of time. In agreement with the results of Denner et al. (1963) the subjects produced times which were longer than the target times.
Plantation Forestry under Global Warming: Hybrid Poplars with Improved Thermotolerance Provide New Insights on the in Vivo Function of Small Heat Shock Protein Chaperones
Authors: Merino Irene , Contreras Angela , Jing Zhong-Ping , Gallardo Fernando , Cánovas Francisco M. , Gómez Luis 
Published: December 2013

Abstract
Climate-driven heat stress is a key factor affecting forest plantation yields. While its effects are expected to worsen during this century, breeding more tolerant genotypes has proven elusive. We report here a substantial and durable increase in the thermotolerance of hybrid poplar (Populus tremula × Populus alba) through overexpression of a major small heat shock protein (sHSP) with convenient features. Experimental evidence was obtained linking protective effects in the transgenic events with the unique chaperone activity of sHSPs. In addition, significant positive correlations were observed between phenotype strength and heterologous sHSP accumulation. The remarkable baseline levels of transgene product (up to 1.8% of total leaf protein) have not been reported in analogous studies with herbaceous species. As judged by protein analyses, such an accumulation is not matched either by endogenous sHSPs in both heat-stressed poplar plants and field-grown adult trees. Quantitative real time-polymerase chain reaction analyses supported these observations and allowed us to identify the poplar members most responsive to heat stress. Interestingly, sHSP overaccumulation was not associated with pleiotropic effects that might decrease yields. The poplar lines developed here also outperformed controls under in vitro and ex vitro culture conditions (callus biomass, shoot production, and ex vitro survival), even in the absence of thermal stress. These results reinforce the feasibility of improving valuable genotypes for plantation forestry, a field where in vitro recalcitrance, long breeding cycles, and other practical factors constrain conventional genetic approaches. They also provide new insights into the biological functions of the least understood family of heat shock protein chaperones.
Market Failure and Japanese Farmland Rents
Authors: Dawson P. J. 
Published: December 2013

AbstractSince the early 1950s, Japanese farmland rents have been regulated and a consensus emerged that rent control led to market failure. Hypothesising a rent‐formation model where rents are determined by prices, this paper estimates a threshold autoregressive model which integrates three tests of market failure, namely, inefficiency, bias and asymmetry. There are four results. First, a long‐run relationship exists between rents and prices, and the Japanese farmland rental market is efficient. Second, the rent‐price elasticity is unity and the market is unbiased. Third, rents are Granger‐caused by prices which supports the rent‐formation model. Fourth, asymmetry exists where more rapid error‐correction occurs immediately after policy reform when rent growth exceeds price growth by 3.6% or more, and rent control has benefitted tenants.
Spatial distribution of Vespa velutina individuals hunting at domestic honeybee hives: heterogeneity at a local scale
Authors: Monceau Karine , Bonnard Olivier , Moreau Jérôme , Thiéry Denis 
Published: December 2013

AbstractSince its recent introduction into Europe, the yellow‐legged hornet, Vespa velutina, has become a major predator of the domestic honeybee, Apis mellifera, but little is known about its hunting behavior. We studied V. velutina hunting behavior by a capture‐mark‐recapture procedure in an experimental apiary. A total of 360 hornets were captured and tagged, and we determined: (i) the number of hornets visiting the apiary and the changes in time, (ii) the average number of individual visits per half‐day and the time elapsed between consecutive recaptures, and (iii) the individual and global distribution of the hornets in the apiary. More than 50% of the marked hornets were recaptured at least once, this increased to 74% in considering the first marked individuals. We estimated 350 hornets visiting the patch daily with at least 1 visit per half‐day. The number of marked hornets decreased over time while the number of unmarked ones increased, suggesting a turnover of individuals. The reduction of the delay between consecutive visits indicates that hornets became more efficient over time. Most of the hornets (88%) were recaptured in front of different hives but, overall, the global distribution was aggregative. Hornets were mainly recaptured in front of 1 hive which was neither the smallest nor the biggest colony, suggesting that the major cue used by hornets is not the amount of food. We hypothesize that the defensive behavior of the honeybee colony could explain our results which may be promising to further studies.
Identification of quantitative trait loci affecting gastrointestinal parasite resistance in an experimental Angus population
Authors: Kim Eui‐Soo , Sonstegard Tad S. , Silva Marcos Vinicius G. B. , Gasbarre Louis C. , Van Tassell Curtis P. 
Published: December 2013

SummaryDNA markers associated with quantitative trait loci (QTL) affecting host tolerance to gastrointestinal (GI) parasite infection are ideal targets for marker‐assisted selection. However, few studies in cattle have attempted to identify this type of QTL due to the difficulty of generating accurate phenotypic data from a resource population with adequate statistical power for detection. For this effort, we amassed fecal egg count (FEC) measures from annual natural field challenges with GI nematodes that spanned 12 different contemporary groups of Angus calves (1992–2000) derived from a closed breeding population. FEC and blood pepsinogen measures were taken weekly over a 26‐week period post‐weaning, and the FEC data were Box‐Cox transformed to normalize the distribution of phenotypes. These 305 test animals and more than 100 founding animals from the extended pedigree were genotyped across 190 microsatellites markers. The genome‐wide analyses identified a suggestive genome‐wide QTL on bovine chromosome (Chr) 8 (P < 0.002) and nominal QTL on Chr 4, 12 and 17 (P < 0.05). These findings were unique for cattle, and some corresponded to previously identified QTL locations for parasite‐related traits in sheep to provide genome locations for further fine mapping of parasite resistance/susceptibility in Angus cattle.
Genome‐wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds
Authors: Ciani E. , Crepaldi P. , Nicoloso L. , Lasagna E. , Sarti F. M. , Moioli B. , Napolitano F. , Carta A. , Usai G. , D'Andrea M. , Marletta D. , Ciampolini R. , Riggio V. , Occidente M. , Matassino D. , Kompan D. , Modesto P. , Macciotta N. , Ajmone‐Marsan P. , Pilla F. 
Published: December 2013

SummaryItaly counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north–south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sardinian breeds diverged more from other breeds, a probable consequence of the combined effect of ancient sporadic introgression of feral mouflon and long‐lasting genetic isolation from continental sheep populations. The study allowed the detection of previously undocumented episodes of recent introgression (Delle Langhe into the endangered Altamurana breed) as well as signatures of known, or claimed, historical introgression (Merino into Sopravissana and Gentile di Puglia; Bergamasca into Fabrianese, Appenninica and, to a lesser extent, Leccese). Arguments that would question, from a genomic point of view, the current breed classification of Bergamasca and Biellese into two separate breeds are presented. Finally, a role for traditional transhumance practices in shaping the genetic makeup of Alpine sheep breeds is proposed. The study represents the first exhaustive analysis of Italian sheep diversity in an European context, and it bridges the gap in the previous HapMap panel between Western Mediterranean and Swiss breeds.