bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paraoxonase 1 and oxidative stress in paediatric non‐alcoholic steatohepatitis
Authors: Desai Sonal , Baker Susan S. , Liu Wensheng , Moya Diana A. , Browne Richard W. , Mastrandrea Lucy , Baker Robert D. , Zhu Lixin 
Published: August 2013

AbstractBackground & AimsNon‐alcoholic steatohepatitis (NASH) in children is a significant public health concern. Oxidative stress is an important component in the pathophysiology of NASH. Several enzymatic antioxidant mechanisms protect the liver from oxidative injury. Examination of the expression of these enzymes in NASH livers may provide insight on the roles for these antioxidant mechanisms in the pathophysiology of NASH.MethodsThe mRNA expression of catalase, glutathione peroxidase 1 (GPX1), glutathione reductase (GSR), paraoxonase 1 (PON1) and other reactive oxygen species‐related genes was evaluated by microarray and quantitative real‐time PCR analyses. The PON1 protein levels were evaluated in liver and serum by Western blot analyses. Serum enzymatic activities of GPX, GSR and PON1 (paraoxonase and arylesterase activities) were examined.ResultsNASH livers exhibited elevated mRNA expression of catalase and PON1, but not GPX1 or GSR. No difference in serum GPX or GSR activity was detected between NASH patients and controls. Elevated expression of PON1 mRNA and protein was detected in NASH livers, but serum PON1 protein and activities were not elevated.ConclusionsElevated expression of catalase and PON1 suggests protective roles for these antioxidants in NASH livers. Given the importance of oxidative stress in the pathophysiology of NASH, future studies focusing on these enzymes could identify important targets for therapeutic or preventive interventions for NASH patients.
Large‐scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss)
Authors: Abadía‐Cardoso Alicia , Anderson Eric C. , Pearse Devon E. , Carlos Garza John 
Published: August 2013

AbstractUnderstanding life history traits is an important first step in formulating effective conservation and management strategies. The use of artificial propagation and supplementation as such a strategy can have numerous effects on the supplemented natural populations and minimizing life history divergence is crucial in minimizing these effects. Here, we use single nucleotide polymorphism (SNP) genotypes for large‐scale parentage analysis and pedigree reconstruction in a hatchery population of steelhead, the anadromous form of rainbow trout. Nearly complete sampling of the broodstock for several consecutive years in two hatchery programmes allowed inference about multiple aspects of life history. Reconstruction of cohort age distribution revealed a strong component of fish that spawn at 2 years of age, in contrast to programme goals and distinct from naturally spawning steelhead in the region, which raises a significant conservation concern. The first estimates of variance in family size for steelhead in this region can be used to calculate effective population size and probabilities of inbreeding, and estimation of iteroparity rate indicates that it is reduced by hatchery production. Finally, correlations between family members in the day of spawning revealed for the first time a strongly heritable component to this important life history trait in steelhead and demonstrated the potential for selection to alter life history traits rapidly in response to changes in environmental conditions. Taken together, these results demonstrate the extraordinary promise of SNP‐based pedigree reconstruction for providing biological inference in high‐fecundity organisms that is not easily achievable with traditional physical tags.
Evidence for past and present hybridization in threeAntarctic icefish species provides new perspectives on an evolutionary radiation
Authors: Marino I. A. M. , Benazzo A. , Agostini C. , Mezzavilla M. , Hoban S. M. , Patarnello T. , Zane L. , Bertorelle G. 
Published: August 2013

AbstractDetermining the timing, extent and underlying causes of interspecific gene exchange during or following speciation is central to understanding species' evolution. Antarctic notothenioid fish, thanks to the acquisition of antifreeze glycoproteins during Oligocene transition to polar conditions, experienced a spectacular radiation to >100 species during Late Miocene cooling events. The impact of recent glacial cycles on this group is poorly known, but alternating warming and cooling periods may have affected species' distributions, promoted ecological divergence into recurrently opening niches and/or possibly brought allopatric species into contact. Using microsatellite markers and statistical methods including Approximate Bayesian Computation, we investigated genetic differentiation, hybridization and the possible influence of the last glaciation/deglaciation events in three icefish species of the genusChionodraco. Our results provide strong evidence of contemporary and past introgression by showing that: (i) a substantial fraction of contemporary individuals in each species has mixed ancestry, (ii) evolutionary scenarios excluding hybridization or including it only in ancient times have small or zero posterior probabilities, (iii) the data support a scenario of interspecific gene flow associated with the two most recent interglacial periods. Glacial cycles might therefore have had a profound impact on the genetic composition of Antarctic fauna, as newly available shelf areas during the warmer intervals might have favoured secondary contacts and hybridization between diversified groups. If our findings are confirmed in other notothenioids, they offer new perspectives for understanding evolutionary dynamics of Antarctic fish and suggest a need for new predictions on the effects of global warming in this group.
GarA is an essential regulator of metabolism in Mycobacterium tuberculosis
Authors: Ventura Marcello , Rieck Barbara , Boldrin Francesca , Degiacomi Giulia , Bellinzoni Marco , Barilone Nathalie , Alzaidi Faisal , Alzari Pedro M. , Manganelli Riccardo , O'Hare Helen M. 
Published: August 2013

SummaryAlpha‐ketoglutarate is a key metabolic intermediate at the crossroads of carbon and nitrogen metabolism, whose fate is tightly regulated. In mycobacteria the protein GarA regulates the tricarboxylic acid cycle and glutamate synthesis by direct binding and regulation of three enzymes that use α‐ketoglutarate. GarA, in turn, is thought to be regulated via phosphorylation by protein kinase G and other kinases. We have investigated the requirement for GarA for metabolic regulation during growth in vitro and in macrophages. GarA was found to be essential to Mycobacterium tuberculosis, but dispensable in non‐pathogenic Mycobacterium smegmatis. Disruption of garA caused a distinctive, nutrient‐dependent phenotype, fitting with its proposed role in regulating glutamate metabolism. The data underline the importance of the TCA cycle and the balance with glutamate synthesis in M. tuberculosis and reveal vulnerability to disruption of these pathways.
The chromosome cycle of prokaryotes
Authors: Kuzminov Andrei 
Published: August 2013

SummaryIn both eukaryotes and prokaryotes, chromosomal DNA undergoes replication, condensation–decondensation and segregation, sequentially, in some fixed order. Other conditions, like sister‐chromatid cohesion (SCC), may span several chromosomal events. One set of these chromosomal transactions within a single cell cycle constitutes the ‘chromosome cycle’. For many years it was generally assumed that the prokaryotic chromosome cycle follows major phases of the eukaryotic one: –replication–condensation–segregation–(cell division)–decondensation–, with SCC of unspecified length. Eventually it became evident that, in contrast to the strictly consecutive chromosome cycle of eukaryotes, all stages of the prokaryotic chromosome cycle run concurrently. Thus, prokaryotes practice ‘progressive’ chromosome segregation separated from replication by a brief SCC, and all three transactions move along the chromosome at the same fast rate. In other words, in addition to replication forks, there are ‘segregation forks’ in prokaryotic chromosomes. Moreover, the bulk of prokaryotic DNA outside the replication–segregation transition stays compacted. I consider possible origins of this concurrent replication–segregation and outline the ‘nucleoid administration’ system that organizes the dynamic part of the prokaryotic chromosome cycle.
Neurocognitive outcomes at kindergarten entry after liver transplantation at <3 yr of age
Authors: Robertson Charlene M. T. , Dinu Irina A. , Joffe Ari R. , Alton Gwen Y. , Yap Jason Y. K. , Asthana Sonel , Acton Bryan V. , Sauve Reg S. , Martin Steven R. , Kneteman Norman M. , Gilmour Susan M. ,   Western Canadian Therapies Follow‐up Group
Published: August 2013

AbstractThis prospective inception cohort study determines kindergarten‐entry neurocognitive abilities and explores their predictors following liver transplantation at age <3 yr. Of 52 children transplanted (1999–2008), 33 (89.2%) of 37 eligible survivors had psychological assessment at age 54.7 (8.4) months: 21 with biliary atresia, seven chronic cholestasis, and five acute liver failure. Neurocognitive scores (mean [s.d.], 100 [15]) as tested by a pediatric‐experienced psychologist did not differ in relation to age group at transplant (≤12 months and >12 months): FSIQ, 93.9 (17.1); verbal (VIQ), 95.3 (16.5); performance (PIQ), 94.3 (18.1); and VMI, 90.5 (15.9), with >70% having scores ≥85, average or above. Adverse predictors from the pretransplant, transplant, and post‐transplant (30 days) periods using univariate linear regressions for FSIQ were post‐transplant use of inotropes, p = 0.029; longer transplant warm ischemia time, p = 0.035; and post‐transplant highest serum creatinine, (p = 0.04). For PIQ, they were pretransplant encephalopathy, p = 0.027; post‐transplant highest serum creatinine, p = 0.034; and post‐transplant inotrope use, p = 0.037. For VMI, they were number of post‐transplant infections, p = 0.019; post‐transplant highest serum creatinine, p = 0.025; and lower family socioeconomic index, p = 0.039. Changes in care addressing modifiable predictors, including reducing acute post‐transplant illness, pretransplant encephalopathy, transplant warm ischemia times, and preserving renal function, may improve neurocognitive outcomes.
Successful living‐related kidney transplantation in a boy with inherited dysfibrinogenemia
Authors: Imamura Hideaki , Akioka Yuko , Asano Tatsuo , Sugawara Noriko , Ishizuka Kiyonobu , Chikamoto Hiroko , Taki Masashi , Terasawa Fumiko , Okumura Nobuo , Hattori Motoshi 
Published: August 2013

AbstractIn kidney transplantation, it is essential to avoid acute vascular complications, such as hemorrhage and renal vascular thrombosis, which may often lead to allograft loss. Inherited dysfibrinogenemia is a rare coagulation disorder with a wide spectrum of clinical manifestations, such as excessive bleeding and thrombosis. A 12‐yr‐old boy, previously diagnosed with renal hypodysplasia, was found to have reduced fibrinogen concentrations. Coagulation tests assessing surgical risk during kidney transplantation showed a discrepancy between functional and immunologic fibrinogen concentrations. Gene analysis confirmed inherited dysfibrinogenemia, with a heterozygous mutation in FGA (Aα Arg16His) in the patient and his mother. Based on the molecular and functional properties of the mutation, and a familial phenotype, in which his aunt had experienced a previous bleeding episode, the patient was considered at greater risk of bleeding than of thrombosis. The patient was administered fibrinogen concentrate before surgery, and kidney transplantation was performed with his father as the organ donor. The patient received additional prophylactic infusions of fibrinogen concentrate postoperatively, and his postoperative course was uneventful. Accurate diagnosis of dysfibrinogenemia, including gene analysis, is important for correctly managing patients with this coagulation disorder who are undergoing kidney transplantation.
A Versatile Near‐Infrared Asymmetric Tricarbocyanine for Zinc Ion Sensing in Water
Authors: Menéndez Guillermo O. , López Cecilia Samaniego , Jares‐Erijman Elizabeth A. , Spagnuolo Carla C. 
Published: August 2013

AbstractWe have synthesized a near‐infrared emissive asymmetric tricarbocyanine conveniently functionalized to improve bioconjugation. The leading structure contains a versatile derivatization point at the meso position for facile radical‐nucleophilic aromatic substitution. We have evaluated a DPEN (N,N‐di(2‐picolyl)ethylendiamine) derivative of this dye as a highly selective sensor for zinc (II) in aqueous medium, which performs in an appropriate sensitivity range for biological studies. The probe was successfully conjugated to a protein‐ligand model with high affinity and specificity (biotin–streptavidin technology) rendering an excellent performance of sensing. In a general strategy to obtain sensitive probes combining fluorescent nanoparticles and molecular fluorophores, a preliminary design of a supramolecular assembly derived from the conjugation of the molecular sensor to quantum dots (QDs) was also investigated. The advantages and problems of FRET‐based sensors are also discussed.
Stem rot of jewel orchids caused by a new forma specialis, Fusarium oxysporum f. sp. anoectochili in Taiwan
Authors: Huang L.‐W. , Wang C.‐J. , Lin Y.‐S. , Chung W.‐C. , Chung W.‐H. 
Published: August 2013

Stem rot of Anoectochilus formosanus (Af) caused by Fusarium oxysporum (Fo) is a major limiting factor to jewel orchid production in Taiwan. Fo causes discoloration in vascular tissues. However, some newly collected Fo isolates from Af stem rot do not cause vascular discoloration, suggesting changes may have occurred in the pathogen. Among recent Fo isolates from Af there are two colony types, the cottony alba (CA) and the sporodochial (S). In order to confirm that both colony types cause Af stem rot, 200 isolates were obtained from diseased stems in Nantou County and characterized by colony type and whether or not the infected plants had vascular discoloration. Isolates of both the CA and S types caused stem rot of Af; some isolates in each colony type caused vascular discoloration whilst others did not. Pathogenicity tests with 22 isolates resulted in stem rot disease severity ratings on Af of 3·1–4·0 and 2·1–4·0 with CA and S type colonies, respectively. The same isolates failed to cause disease on Cattleya, Dendrobium or Phalaenopsis plants. Phylogenetic analysis of partial intergenic spacer sequences showed that these isolates were distinguishable from other formae speciales of Fo and could be separated into two groups correlated with the CA or S type colonies with high bootstrap. Based on pathogenic, morphological and molecular characterizations, the Fo that causes stem rot of Af is proposed to be a new forma specialis, F. oxysporum f. sp. anoectochili, with different pathotypes.
Thromboelastometric detection of clotting Factor XIII deficiency in cardiac surgery patients
Authors: Grossmann E. , Akyol D. , Eder L. , Hofmann B. , Haneya A. , Graf B. M. , Bucher M. , Raspé C. 
Published: August 2013

SUMMARYAim(s)In this article, we aimed to investigate plasma Factor XIII levels after extracorporeal circulation in cardiac surgery by thromboelastometric detection, as extracorporeal circulation causes various coagulation disorders due to the exposure of blood to artificial surfaces, inflammatory induction and mechanical destruction of platelets and coagulation factors, which may particularly affect factors with long half‐lives, such as Factor XIII.BackgroundSince transfusion algorithms are often empirical and laboratory analysis of Factor XIII plasma levels may not be available 24 h a day, bed‐side testing using rotational thromboelastometry (ROTEM) could offer a splendid option to define the cause of excessive peri‐operative bleeding disorders in general and Factor XIII levels in particular in a timely manner and thus facilitating exact substitution therapy.MethodsIn this trial, we investigated 25 cardiac surgery patients with extracorporeal bypass times over 100 min. Standard laboratory and ROTEM analyses were performed post‐operatively at the time of intensive care unit admission and 6 h later. We implemented EXTEM with additional Factor XIII (teenTEM) as additional test by adding 0·625 IU Factor XIII to standard EXTEM reagents.ResultsIn this observational study, we could not demonstrate a correlation between Factor XIII and MCFEXTEM, CFTEXTEM or MLEXTEM. Neither Factor XIII plasma levels nor MCFEXTEM could predict blood loss. In accordance with previous findings, we were able to demonstrate increased maximum clot firmness (MCF), decreased clot formation time and decreased maximum lysis by adding Factor XIII in vitro (teenTEM vs EXTEM) indicating an improvement in the coagulation process. As shown before, we also found a strong correlation between MCF and platelet and fibrinogen plasma levels.ConclusionIn summary, ‘teenTEM’ test does not seem to detect Factor XIII deficient patients in cardiac surgery. Furthermore, post‐operative blood loss could not be predicted neither by ROTEM nor by laboratory analysis of Factor XIII. In vitro administration of Factor XIII appears to improve laboratory measures of haemostasis.
3D prostate histology reconstruction: An evaluation of image‐based and fiducial‐based algorithms
Authors: Gibson E. , Gaed M. , Gómez J. A. , Moussa M. , Romagnoli C. , Pautler S. , Chin J. L. , Crukley C. , Bauman G. S. , Fenster A. , Ward A. D. 
Published: August 2013

Purpose:Evaluation ofin vivo prostate imaging modalities for determining the spatial distribution and aggressiveness of prostate cancer ideally requires accurate registration of images to an accepted reference standard, such as histopathological examination of radical prostatectomy specimens. Three‐dimensional (3D) reconstruction of prostate histology facilitates these registration‐based evaluations by reintroducing 3D spatial information lost during histology processing. Because the reconstruction accuracy may constrain the clinical questions that can be answered with these data, it is important to assess the tradeoffs between minimally disruptive methods based on intrinsic image information and potentially more robust methods based on extrinsic fiducial markers.Methods:Ex vivo magnetic resonance (MR) images and digitized whole‐mount histology images from 12 radical prostatectomy specimens were used to evaluate four 3D histology reconstruction algorithms. 3D reconstructions were computed by registering each histology image to the corresponding ex vivo MR image using one of two similarity metrics (mutual information or fiducial registration error) and one of two search domains (affine transformations or a constrained subset thereof). The algorithms were evaluated for accuracy using the mean target registration error (TRE) computed from homologous intrinsic point landmarks (3–16 per histology section; 232 total) identified on histology and MR images, and for the sensitivity of TRE to rotational, translational, and scaling initialization errors.Results:The algorithms using fiducial registration error and mutual information had mean ± standard deviation TREs of 0.7 ± 0.4 and 1.2 ± 0.7 mm, respectively, and one algorithm using fiducial registration error and affine transforms had negligible sensitivities to initialization errors. The postoptimization values of the mutual information‐based metric showed evidence of errors due to both the optimizer and the similarity metric, and variation of parameters of the mutual information‐based metric did not improve its performance.Conclusions:The extrinsic fiducial‐based algorithm had lower mean TRE and lower sensitivity to initialization than the intrinsic intensity‐based algorithm using mutual information. A model relating statistical power to registration error for certain imaging validation study designs estimated that a reconstruction algorithm with a mean TRE of 0.7 mm would require 27% fewer subjects than the method used to initialize the algorithms (mean TRE 1.3 ± 0.7 mm), suggesting the choice of reconstruction technique can have a substantial impact on the design of imaging validation studies, and on their overall cost.
4D tumor centroid tracking using orthogonal 2D dynamic MRI: Implications for radiotherapy planning
Authors: Tryggestad Erik , Flammang Aaron , Hales Russell , Herman Joseph , Lee Junghoon , McNutt Todd , Roland Teboh , Shea Steven M. , Wong John 
Published: August 2013

Purpose:Current pretreatment, 4D imaging techniques are suboptimal in that they sample breathing motion over a very limited “snapshot” in time. Heretofore, long‐duration, 4D motion characterization for radiotherapy planning, margin optimization, and validation have been impractical for safety reasons, requiring invasive markers imaged under x‐ray fluoroscopy. To characterize 3D tumor motion and associated variability over durations more consistent with treatments, the authors have developed a practical dynamic MRI (dMRI) technique employing two orthogonal planes acquired in a continuous, interleaved fashion.Methods:2D balanced steady‐state free precession MRI was acquired continuously over 9–14 min at approximately 4 Hz in three healthy volunteers using a commercial 1.5 T system; alternating orthogonal imaging planes (sagittal, coronal, sagittal, etc.) were employed. The 2D in‐plane pixel resolution was 2 × 2 mm2 with a 5 mm slice profile. Simultaneous with image acquisition, the authors monitored a 1D surrogate respiratory signal using a device available with the MRI system. 2D template matching‐based anatomic feature registration, or tracking, was performed independently in each orientation. 4D feature tracking at the raw frame rate was derived using spline interpolation.Results:Tracking vascular features in the lung for two volunteers and pancreatic features in one volunteer, the authors have successfully demonstrated this method. Registration error, defined here as the difference between the sagittal and coronal tracking result in the SI direction, ranged from 0.7 to 1.6 mm (1σ) which was less than the acquired image resolution. Although the healthy volunteers were instructed to relax and breathe normally, significantly variable respiration was observed. To demonstrate potential applications of this technique, the authors subsequently explored the intrafraction stability of hypothetical tumoral internal target volumes and 3D spatial probability distribution functions. The surrogate respiratory information allowed the authors to show how this technique can be used to study correlations between internal and external (surrogate) information over these prolonged durations. However, compared against the gold standard of the time stamps in the dMRI frames, the temporal synchronization of the surrogate 1D respiratory information was shown to be likely unreliable.Conclusions:The authors have established viability of a novel and practical pretreatment, 4D tumor centroid tracking method employing a commercially available dynamic MRI sequence. Further developments from the vendor are likely needed to provide a reliably synchronized surrogate 1D respiratory signal, which will likely broaden the utility of this method in the pretreatment radiotherapy planning context.