bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cardiogenic shock and coronary endothelial dysfunction predict cardiac allograft vasculopathy after heart transplantation
Authors: Lopez‐Fernandez Silvia , Manito‐Lorite Nicolas , Gómez‐Hospital Joan Antoni , Roca Josep , Fontanillas Carles , Melgares‐Moreno Rafael , Azpitarte‐Almagro José , Cequier‐Fillat Angel 
Published: October 2014

AbstractCardiac allograft vasculopathy remains one of the major causes of death post‐heart transplantation. Its etiology is multifactorial and prevention is challenging. The aim of this study was to prospectively determine factors related to cardiac allograft vasculopathy after heart transplantation. This research was planned on 179 patients submitted to heart transplant. Performance of an early coronary angiography with endothelial function evaluation was scheduled at three‐month post‐transplant. Patients underwent a second coronary angiography after five‐yr follow‐up. At the 5‐ ± 2‐yr follow‐up, 43% of the patients had developed cardiac allograft vasculopathy (severe in 26% of them). Three independent predictors of cardiac allograft vasculopathy were identified: cardiogenic shock at the time of the transplant operation (OR: 6.49; 95% CI: 1.86–22.7, p = 0.003); early coronary endothelial dysfunction (OR: 3.9; 95% CI: 1.49–10.2, p = 0.006), and older donor age (OR: 1.05; 95% CI: 1.00–1.10, p = 0.044). Besides early endothelial coronary dysfunction and older donor age, a new predictor for development of cardiac allograft vasculopathy was identified: cardiogenic shock at the time of transplantation. In these high‐risk patient subgroups, preventive measures (treatment of cardiovascular risk factors, use of novel immunosuppressive agents such as mTOR inhibitors) should be earlier and much more aggressive.
Cardiophrenic lymph nodes in liver transplant candidates with hepatocellular carcinoma: imaging characteristics and post‐transplant outcomes
Authors: Lee Christopher , Kim Andrew , Santos Idoia , Cen Yong , Alexopoulos Sophoclis , Navarro Shannon , Wallman Melissa , Dhanireddy Kiran , Grant Edward 
Published: October 2014

AbstractBackgroundNo guidelines exist for the management of cardiophrenic lymph nodes in patients with hepatocellular carcinoma (HCC) being evaluated for liver transplantation.MethodsOne hundred and seventy‐eight patients with HCC listed for liver transplant received both pre‐transplant computed tomography (CT) and follow‐up CT scans. Enlarged cardiophrenic lymph nodes on CT were characterized and followed on subsequent scans; lymph node outcomes were assigned to “reduced” and “not reduced” categories. Tumor and patient characteristics were also recorded.ResultsSeventy‐one of one hundred and seventy‐eight patients (39.9%) had at least one cardiophrenic lymph node larger than 8 mm in diameter on pre‐transplant CT. One hundred and sixty‐six total lymph nodes were characterized. Six lymph nodes (3.6%) in two patients increased in size on follow‐up imaging; all six cardiophrenic lymph nodes were presumed to represent metastases. There was a statistically significant reduction in lymph node size in patients who were transplanted vs. those who were not transplanted. Furthermore, a statistically significant association was found between increasing Model for End‐Stage Liver Disease score and lymph node size reduction. There were no significant differences in post‐transplant survival between patients with different lymph node outcomes.ConclusionIn the absence of metastatic disease in other sites, these lymph nodes are probably reactive; further workup is likely not necessary.
The development of route learning in Down syndrome, Williams syndrome and typical development: investigations with virtual environments
Authors: Purser Harry R.M. , Farran Emily K. , Courbois Yannick , Lemahieu Axelle , Sockeel Pascal , Mellier Daniel , Blades Mark 
Published: October 2014

AbstractThe ability to navigate new environments has a significant impact on the daily life and independence of people with learning difficulties. The aims of this study were to investigate the development of route learning in Down syndrome (N= 50), Williams syndrome (N= 19), and typically developing children between 5 and 11 years old (N= 108); to investigate use of landmarks; and to relate cognitive functions to route‐learning ability in these groups. Overall, measures of attention and long‐term memory were strongly associated with route learning, even once non‐verbal ability was controlled for. All of the groups, including 5‐ to 6‐year‐oldTDchildren, demonstrated the ability to make use of all landmark types to aid route learning; those near junctions, those further from junctions, and also distant landmarks (e.g. church spire, radio mast). Individuals withWSperformed better than a matched subset ofTDchildren on more difficult routes; we suggest that this is supported by relatively strong visual feature recognition in the disorder. Participants withDSwho had relatively high levels of non‐verbal ability performed at a similar level toTDparticipants.
Biochemical characterization of the water‐soluble squalene synthase from Methylococcus capsulatus and the functional analyses of its two DXXD(E)D motifs and the highly conserved aromatic amino acid residues
Authors: Ohtake Kana , Saito Naoki , Shibuya Satoshi , Kobayashi Wakako , Amano Ryosuke , Hirai Takumi , Sasaki Shinji , Nakano Chiaki , Hoshino Tsutomu 
Published: October 2014

Information regarding squalene synthases (SQSs) from prokaryotes is scarce. We aimed to characterize the SQS from Methylococcus capsulatus. We studied its reaction mechanism by kinetic analysis and evaluated the structure of the substrate/inhibitor‐binding sites via homology modeling. The cloned M. capsulatus SQS was expressed in Escherichia coli and purified by nickel‐nitrilotriacetic acid column chromatography. Interestingly, M. capsulatus SQS was water‐soluble and did not require any detergent for its higher activity, unlike other SQSs studied previously; supplementation of any type of detergent inhibited enzyme activity. The specific activity and the kinetic values (Km and kcat) for the substrate farnesyl diphosphate and NADPH are reported. The substrate analog farnesyl methylenediphosphonate showed potent inhibition toward the enzyme. We prepared the site‐specific mutants directed at potential active‐site residues 58DXX61E62D (S1 site) and 213DXX216D217D (S2 site), which were assumed to be involved in the binding of the substrate farnesyl diphosphate through the Mg2+ ion. We first demonstrated that the S1 site and the two basic residues (R55 and K212) were responsible for the binding of farnesyl diphosphate. Furthermore, we examined the catalytic roles of the highly conserved aromatic residues and demonstrated that the Y164 residue abstracts the proton of cation 5, which is produced during the first half‐reaction (Scheme 1), to afford presqualene diphosphate, and that the W224 residue stabilizes the intermediary cation 5 via the cation–π interaction. Furthermore, we confirm for the first time that the F32 and the Y51 residues also stabilize the carbocation intermediate(s) generated during the second half‐reaction.
Structural basis for the binding of the membrane‐proximal C‐terminal region of chemokine receptor CCR2 with the cytosolic regulator FROUNT
Authors: Esaki Kaori , Yoshinaga Sosuke , Tsuji Tatsuichiro , Toda Etsuko , Terashima Yuya , Saitoh Takashi , Kohda Daisuke , Kohno Toshiyuki , Osawa Masanori , Ueda Takumi , Shimada Ichio , Matsushima Kouji , Terasawa Hiroaki 
Published: October 2014

The membrane‐proximal C‐terminal region (Pro‐C) is important for the regulation of G‐protein‐coupled receptors (GPCRs), but the binding of the Pro‐C region to a cytosolic regulator has not been structurally analyzed. The chemokine receptor CCR2 is a member of the GPCR superfamily, and the Pro‐C region of CCR2 binds to the cytosolic regulator FROUNT. Studying the interaction between CCR2 Pro‐C and FROUNT at an atomic level provides a basis for understanding the signal transduction mechanism via GPCRs. NOE‐based NMR experiments showed that, when bound to FROUNT, CCR2 Pro‐C adopted a helical conformation, as well as when embedded in dodecylphosphocholine micelles. A comparison of two types of cross‐saturation‐based NMR experiments, applied to a three‐component mixture of Pro‐C, FROUNT and micelles or a two‐component mixture of Pro‐C and micelles, revealed that the hydrophobic binding surface on Pro‐C for FROUNT mostly overlapped with the binding site for micelles, suggesting competitive binding of Pro‐C between FROUNT and micelles. Leu316 was important for both FROUNT and micelle binding. Phe319 was newly identified to be crucial for FROUNT binding, by NMR and mutational analyses. The association and dissociation rates of CCR2 Pro‐C for lipid bilayer biomembranes were faster than those for FROUNT. We previously reported that FROUNT binding to CCR2 is detectable even in unstimulated cells and increases in response to chemokine stimulation. Taken together, these results support a model of CCR2 equilibrium: chemokine binding changes the conformational equilibrium of CCR2 toward the active state, and Pro‐C switches its binding partner from the membrane to FROUNT.DatabaseProtein Data Bank submission codes of FROUNT‐bound form and DPC micelle‐bound form are PDB ID 2MLQ and PDB ID 2MLO, respectively. Biological Magnetic Resonance Bank submission codes of the samples of 800 μm 13C/15N‐labeled CCR2 Pro‐C mixed with 8 μm unlabeled FROUNT and the samples of 200 μm 13C/15N‐labeled CCR2 Pro‐C mixed with 10 mm DPC‐d38 are BMRB ID 19829 and BMRB ID 19828, respectively.Structured digital abstract

FROUNT binds to CCR2 Pro-C by surface plasmon resonance (1, 2)

FROUNT and CCR2 Pro-C bind by nuclear magnetic resonance (View interaction)
CBCT‐based volume of simulated root resorption – influence of FOV and voxel size
Authors: Da Silveira P. F. , Fontana M. P. , Oliveira H. W. , Vizzotto M. B. , Montagner F. , Silveira H. L. , Silveira H. E. 
Published: October 2014

AbstractAimTo examine the influence of the field of view (FOV) and voxel size on the measurement of the volume of simulated internal root resorption (IRR) lesions through cone‐beam computed tomography (CBCT).MethodologyEleven single‐rooted teeth with IRR simulated by acid demineralization were studied. CBCT images were acquired using large FOV (voxel sizes of 0.200, 0.250 and 0.300 mm) and limited FOV (voxel sizes of 0.076, 0.100 and 0.200 mm). The IRR volumes were calculated using the Dolphin® software. Volumetric measurements were validated using IRR silicone putty casts. The analysis of variance (anova) for randomized block design complemented with the Tukey's test was employed.ResultsIRR volumes obtained using voxel sizes of 0.200 and 0.250 mm were similar (P > 0.05). However, both these values were significantly different from that obtained using the 0.300‐mm voxel (P < 0.05). There was no significant difference between IRR volumes measured through voxel sizes of 0.076 and 0.100 mm (P > 0.05), but both differed significantly from that obtained through the 0.200‐mm voxel (P < 0.05). There was no significant difference between the volumetric measurements of the 0.200‐mm voxel images of the restricted and large FOV protocols. The mean volumes of the silicone casts were smaller than those calculated using a 0.200‐mm voxel, but were similar to those obtained using voxel sizes of 0.076 and 0.300 mm.ConclusionsDespite the FOV protocol, voxel size can influence measurement of simulated IRR volumes. The importance of standardization of CBCT image acquisition protocols is emphasized, especially during follow‐up of an IRR lesion, to prevent misinterpretation of its extent, which can create a bias in clinical decisions.
Human T helper type 1 dichotomy: origin, phenotype and biological activities
Authors: Annunziato Francesco , Cosmi Lorenzo , Liotta Francesco , Maggi Enrico , Romagnani Sergio 
Published: October 2014

SummaryThe great variety of pathogens present in the environment has obliged the immune system to evolve different mechanisms for tailored and maximally protective responses. Initially, two major types of CD4+ T helper (Th) effector cells were identified, and named as type 1 (Th1) and type 2 (Th2) cells because of the different cytokines they produce. More recently, a third type of CD4+ Th effectors has been identified and named as Th17 cells. Th17 cells, however, have been found to exhibit high plasticity because they rapidly shift into the Th1 phenotype in the inflammatory sites. Therefore, in these sites there is usually a dichotomous mixture of classic and non‐classic (Th17‐derived) Th1 cells. In humans, non‐classic Th1 cells express CD161, as well as the retinoic acid orphan receptor C, interleukin‐17 receptor E (IL‐17RE), IL‐1RI, CCR6, and IL‐4‐induced gene 1 and Tob‐1, which are all virtually absent from classic Th1 cells. The possibility to distinguish between these two cell subsets may allow the opportunity to better establish their respective pathogenic role in different chronic inflammatory disorders. In this review, we discuss the different origin, the distinctive phenotypic features and the major biological activities of classic and non‐classic Th1 cells.
Morphological Study of the Encystment and Excystment of Vermamoeba vermiformis Revealed Original Traits
Authors: Fouque Emilie , Yefimova Marina , Trouilhé Marie‐Cécile , Quellard Nathalie , Fernandez Béatrice , Rodier Marie‐Hélène , Thomas Vincent , Humeau Philippe , Héchard Yann 
Published: October 2014

AbstractFree‐living amoebae are ubiquitous protozoa commonly found in water. Among them, Acanthamoeba and Vermamoeba (formerly Hartmannella) are the most represented genera. In case of stress, such as nutrient deprivation or osmotic stress, these amoebae initiate a differentiation process, named encystment. It leads to the cyst form, which is a resistant form enabling amoebae to survive in harsh conditions and resist disinfection treatments. Encystment has been thoroughly described in Acanthamoeba but poorly in Vermamoeba. Our study was aimed to follow the encystment/excystment processes by microscopic observations. We show that encystment is quite rapid, as mature cysts were obtained in 9 h, and that cyst wall is composed of two layers. A video shows that a locomotive form is likely involved in clustering cysts together during encystment. As for Acanthamoeba, autophagy is likely active during this process. Specific vesicles, possibly involved in ribophagy, were observed within the cytoplasm. Remarkably, mitochondria rearranged around the nucleus within the cyst, suggesting high needs in energy. Unlike Acanthamoeba and Naegleria, no ostioles were observed in the cyst wall suggesting that excystment is original. During excystment, large vesicles, likely filled with hydrolases, were found in close proximity to cyst wall and digest it. Trophozoite moves inside its cyst wall before exiting during excystment. In conclusion, Vermamoeba encystment/excystment displays original trends as compare to Acanthamoeba.
Phylogenetic Analysis and the Evolution of the 18S rRNA Gene Typing System of Acanthamoeba
Authors: Fuerst Paul A. , Booton Gregory C. , Crary Monica 
Published: October 2014

AbstractSpecies of Acanthamoeba were first described using morphological characters including cyst structure and cytology of nuclear division. More than 20 nominal species were proposed using these methods. Morphology, especially cyst shape and size, has proven to be plastic and dependent upon culture conditions. The DNA sequence of the nuclear small‐subunit (18S) rRNA, the Rns gene, has become the most widely accepted method for rapid diagnosis and classification of Acanthamoeba. The Byers–Fuerst lab first proposed an Rns typing system in 1996. Subsequent refinements, with an increasing DNA database and analysis of diagnostic fragments within the gene, have become widely accepted by the Acanthamoeba research community. The development of the typing system, including its current state of implementation is illustrated by three cases: (i) the division between sequence types T13 and T16; (ii) the diversity within sequence supertype T2/T6, and (iii) verification of a new sequence type, designated T20. Molecular studies make clear the disconnection between phylogenetic relatedness and species names, as applied for the genus Acanthamoeba. Future reconciliation of genetic types with species names must become a priority, but the possible shortcomings of the use of a single gene when reconstructing the evolutionary history of the acanthamoebidae must also be resolved.
Synechococcus: 3 billion years of global dominance
Authors: Dvořák Petr , Casamatta Dale A. , Poulíčková Aloisie , Hašler Petr , Ondřej Vladan , Sanges Remo 
Published: October 2014

AbstractCyanobacteria are among the most important primary producers on the Earth. However, the evolutionary forces driving cyanobacterial species diversity remain largely enigmatic due to both their distinction from macro‐organisms and an undersampling of sequenced genomes. Thus, we present a new genome of a Synechococcus‐like cyanobacterium from a novel evolutionary lineage. Further, we analyse all existing 16S rRNA sequences and genomes of Synechococcus‐like cyanobacteria. Chronograms showed extremely polyphyletic relationships in Synechococcus, which has not been observed in any other cyanobacteria. Moreover, most Synechococcus lineages bifurcated after the Great Oxidation Event, including the most abundant marine picoplankton lineage. Quantification of horizontal gene transfer among 70 cyanobacterial genomes revealed significant differences among studied genomes. Horizontal gene transfer levels were not correlated with ecology, genome size or phenotype, but were correlated with the age of divergence. All findings were synthetized into a novel model of cyanobacterial evolution, characterized by serial convergence of the features, that is multicellularity and ecology.
Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod
Authors: Andrews Kimberly R. , Norton Emily L. , Fernandez‐Silva Iria , Portner Elan , Goetze Erica 
Published: October 2014

AbstractZooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open‐ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite FST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.
Inspection of Feasible Calibration Conditions for UV Radiometer Detectors with the KI/KIO3 Actinometer
Authors: Qiang Zhimin , Li Wentao , Li Mengkai , Bolton James R. , Qu Jiuhui 
Published: October 2014

AbstractUV radiometers are widely employed for irradiance measurements, but their periodical calibrations not only induce an extra cost but also are time‐consuming. In this study, the KI/KIO3 actinometer was applied to calibrate UV radiometer detectors at 254 nm with a quasi‐collimated beam apparatus equipped with a low‐pressure UV lamp, and feasible calibration conditions were identified. Results indicate that a washer constraining the UV light was indispensable, while the size (10 or 50 mL) of a beaker containing the actinometer solution had little influence when a proper washer was used. The absorption or reflection of UV light by the internal beaker wall led to an underestimation or overestimation of the irradiance determined by the KI/KIO3 actinometer, respectively. The proper range of the washer internal diameter could be obtained via mathematical analysis. A radiometer with a longer service time showed a greater calibration factor. To minimize the interference from the inner wall reflection of the collimating tube, calibrations should be conducted at positions far enough away from the tube bottom. This study demonstrates that after the feasible calibration conditions are identified, the KI/KIO3 actinometer can be applied readily to calibrate UV radiometer detectors at 254 nm.
Photostability of Cosmetic UV Filters on Mammalian Skin Under UV Exposure
Authors: Stiefel Constanze , Schwack Wolfgang , Nguyen Yen‐Thi Hai 
Published: October 2014

AbstractPrevious studies showed that the common UV filter substances benzophenone‐3 (BP–3), butyl methoxydibenzoylmethane (BM–DBM), octocrylene (OCR), ethylhexyl methoxycinnamate (EHMC), ethylhexyl salicylate (EHS) and ethylhexyl triazone (EHT) were able to react with amino side chains of different proteins in vitro. To transfer the results to mammalian skin conditions, sunscreen products were applied on both prepared fresh porcine skin and glass plates, followed by UV irradiation and the determination of depletion of the respective UV filters. Significantly lower recoveries of the UV filters extracted from skin samples than from glass plates indicated the additional reaction of the UV filters with skin constituents, when proteins will be the most important reactants. Among the products tested, BP‐3 showed the greatest differences in recoveries between glass and skin samples of about 13% and 24% after 2 and 4 h of irradiation, respectively, followed by EHS > BM‐DBM > OCR > EHMC > EHT. The obtained results raise the question, whether the common in vitro evaluations of sunscreens, using inert substrate materials like roughened quartz or polymethyl methacrylate (PMMA) plates are really suitable to fully replace in vivo methods, as they cannot include skin‐typical reactions.
Interfacing Synthetic DNA Logic Operations with Protein Outputs
Authors: Prokup Alexander , Deiters Alexander 
Published: October 2014

AbstractDNA logic gates are devices composed entirely of DNA that perform Boolean logic operations on one or more oligonucleotide inputs. Typical outputs of DNA logic gates are oligonucleotides or fluorescent signals. Direct activation of protein function has not been engineered as an output of a DNA‐based computational circuit. Explicit control of protein activation enables the immediate triggering of enzyme function and could yield DNA computation outputs that are otherwise difficult to generate. By using zinc‐finger proteins, AND, OR, and NOR logic gates were created that respond to short oligonucleotide inputs and lead to the activation or deactivation of a split‐luciferase enzyme. The gate designs are simple and modular, thus enabling integration with larger multigate circuits, and the modular structure gives flexibility in the choice of protein output. The gates were also modified with translator circuits to provide protein activation in response to microRNA inputs as potential cellular cancer markers.