bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survival at 2 years among liver cirrhotic patients is influenced by left atrial volume and left ventricular mass
Authors: Merli Manuela , Torromeo Concetta , Giusto Michela , Iacovone Gianna , Riggio Oliviero , Puddu Paolo E. 
Published: November 2016

AbstractBackground & AimsCirrhotic cardiomyopathy (CC) may interact with the clinical course of cirrhosis and can be implicated in the development of several complications in advanced liver disease. The best and easiest parameters which should define a condition of reduced cardiac reserve in cirrhosis are still controversial. This study was aimed at selecting the cardiac parameters, derived by Doppler echocardiography, predictive of survival during follow‐up.MethodsThis study included cirrhotic patients without cardiovascular or pulmonary diseases. Patients were studied in stable conditions. Doppler echocardiography was used to select parameters associated with survival. Among the others, left atrial volume (LAVi) and left ventricular mass indexed to body surface area (LVMi) were evaluated. A comparison was performed with the parameters presently applied for the definition of CC according to the Montreal criteria.ResultsNinety cirrhotic patients have been included (males 66%, alcohol origin 31%, post‐viral 54%, Child‐Pugh A 53%, B 29% and C 18%). Patients were followed up for at least 24 months. Twenty‐six patients had a diagnosis of CC according to the Montreal criteria. During follow‐up, 24 patients died. Overall mortality was 26.7%. Patients presenting higher LAVi and lower LVMi were those at higher risk to die (P=.04 and P=.007 respectively). No difference in survival was seen in patients with a diagnosis of CC.ConclusionsAn increased LAVi and a decreased LVMi were able to differentiate among patients with a lower survival at 2 years. These parameters need to be considered for prognostic evaluation in cirrhotics.
Prevention of hepatitis C recurrence by bridging sofosbuvir/ribavirin from pre‐ to post‐liver transplant: a real‐life strategy
Authors: Donato Maria Francesca , Morelli Cristina , Romagnoli Renato , Invernizzi Federica , Mazzarelli Chiara , Iemmolo Rosa Maria , Montalbano Marzia , Lenci Ilaria , Bhoori Sherrie , Pieri Giulia , Berardi Sonia , Caraceni Paolo , Martini Silvia ,   ITACOPS‐SOF Bridging Study Group
Published: November 2016

AbstractBackground & AimsHepatitis C virus (HCV) re‐infection following liver transplant (LT) is associated with reduced graft and patient survival. Before transplant, Sofosbuvir/Ribavirin (SOF/R) treatment prevents recurrent HCV in 96% of those patients achieving viral suppression for at least 4 weeks before transplant. We evaluated whether a bridging SOF‐regimen from pre‐ to post‐transplant is safe and effective to prevent HCV recurrence in those patients with less than 4 weeks of HCV‐RNA undetectability at the time of transplant.MethodsFrom July 2014 SOF/R was given in 233 waitlisted HCV cirrhotics with/without hepatocellular carcinoma (HCC) within an Italian Compassionate Program. One hundred patients were transplanted and 31 patients (31%) treated with SOF/R bridging therapy were studied.ResultsLiver transplant indication in bridge subgroup was HCC in 22 and decompensated cirrhosis in 9. HCV‐genotype was 1/4 in 18 patients. SOF 400 mg/day and R (median dosage 800 mg/day) were given for a median of 35 days before LT. At transplant time, 19 patients were still HCV‐RNA positive (median HCV‐RNA 58 IU/mL). One recipient had a virological breakthrough at week 4 post‐transplant; one died, on treatment, 1‐month post‐transplant for sepsis and 29/31 achieved a 12‐week sustained virological response (94%). Acute cellular rejection occurred in three recipients. On September 2016, 30 recipients (97%) were alive with a median follow‐up of 18 months (range 13‐25).ConclusionsIn patients with suboptimal virological response at LT, a bridging SOF/R regimen helps avoiding post‐transplant graft reinfection.
Introgression of mtDNA in Urosaurus lizards: historical and ecological processes
Authors: Haenel Gregory J. 
Published: November 2016

AbstractIntrogression of mtDNA appears common in animals, but the implications of acquiring a novel mitochondrial genome are not well known. This study investigates mito‐genome introgression between the lizard species Urosaurus graciosus, a thermal specialist, and U. ornatus, a species that occupies a wider range of thermal environments. As ectotherms, their metabolic rate is strongly influenced by the thermal environment; with mitochondria being linked to metabolic rates, overall energy budgets could be impacted by introgression. I use mitochondrial gene trees, inferred from Bayesian analyses of Cyt‐B and ND1 gene sequences, along with morphology and microsatellites from nineteen populations of these two species to address if the direction and location of mito‐nuclear discordance match predictions of introgression resulting from past population expansions. MtDNA is expected to move from resident species into expanding or invading species. Second, does having a heterospecific form of mitochondria impact body size, a trait strongly associated with fitness? Multiple independent introgression events of historic origin were detected. All introgression was unidirectional with U. ornatus‐type mtDNA found in U. graciosus parental type individuals. This result was consistent with population expansions detected in U. graciosus but not U. ornatus. Females with heterospecific mtDNA were significantly smaller than homospecific forms, and heterospecific males had a different relationship of body mass to body length than those with homospecific mtDNA. These changes indicate a potential selective disadvantage for individuals with heterospecific mitochondria and are consistent with the theoretical expectation that deleterious alleles are more likely to persist in expanding populations.
Recombination rate variation in mice from an isolated island
Authors: Wang Richard J. , Gray Melissa M. , Parmenter Michelle D. , Broman Karl W. , Payseur Bret A. 
Published: November 2016

AbstractRecombination rate is a heritable trait that varies among individuals. Despite the major impact of recombination rate on patterns of genetic diversity and the efficacy of selection, natural variation in this phenotype remains poorly characterized. We present a comparison of genetic maps, sampling 1212 meioses, from a unique population of wild house mice (Mus musculus domesticus) that recently colonized remote Gough Island. Crosses to a mainland reference strain (WSB/EiJ) reveal pervasive variation in recombination rate among Gough Island mice, including subchromosomal intervals spanning up to 28% of the genome. In spite of this high level of polymorphism, the genomewide recombination rate does not significantly vary. In general, we find that recombination rate varies more when measured in smaller genomic intervals. Using the current standard genetic map of the laboratory mouse to polarize intervals with divergent recombination rates, we infer that the majority of evolutionary change occurred in one of the two tested lines of Gough Island mice. Our results confirm that natural populations harbour a high level of recombination rate polymorphism and highlight the disparities in recombination rate evolution across genomic scales.
Genomic islands of divergence linked to ecotypic variation in sockeye salmon
Authors: Larson Wesley A. , Limborg Morten T. , McKinney Garrett J. , Schindler Daniel E. , Seeb James E. , Seeb Lisa W. 
Published: November 2016

AbstractRegions of the genome displaying elevated differentiation (genomic islands of divergence) are thought to play an important role in local adaptation, especially in populations experiencing high gene flow. However, the characteristics of these islands as well as the functional significance of genes located within them remain largely unknown. Here, we used data from thousands of SNPs aligned to a linkage map to investigate genomic islands of divergence in three ecotypes of sockeye salmon (Oncorhynchus nerka) from a single drainage in southwestern Alaska. We found ten islands displaying high differentiation among ecotypes. Conversely, neutral structure observed throughout the rest of the genome was low and not partitioned by ecotype. One island on linkage group So13 was particularly large and contained six SNPs with FST > 0.14 (average FST of neutral SNPs = 0.01). Functional annotation revealed that the peak of this island contained a nonsynonymous mutation in a gene involved in growth in other species (TULP4). The islands that we discovered were relatively small (80–402 Kb), loci found in islands did not show reduced levels of diversity, and loci in islands displayed slightly elevated linkage disequilibrium. These attributes suggest that the islands discovered here were likely generated by divergence hitchhiking; however, we cannot rule out the possibility that other mechanisms may have produced them. Our results suggest that islands of divergence serve an important role in local adaptation with gene flow and represent a significant advance towards understanding the genetic basis of ecotypic differentiation.
Stimulation effects of ciprofloxacin and sulphamethoxazole in Microcystis aeruginosa and isobaric tag for relative and absolute quantitation‐based screening of antibiotic targets
Authors: Liu Ying , Chen Shi , Zhang Jian , Li Xuewen , Gao Baoyu 
Published: November 2016

AbstractAntibiotics are normally regarded as safe to aquatic ecosystems when their contamination concentrations are lower than the toxic threshold. This study observed the hazard of ciprofloxacin, sulphamethoxazole and their binary mixture to the aquatic environment at environmentally relevant concentrations lower than the toxic threshold, due to the stimulation on the bloom of Microcystis aeruginosa. The enhanced growth of M. aeruginosa, coupled with elevated photosynthesis activity, was exerted by 50–200 ng/L of ciprofloxacin, 100–200 ng/L of sulphamethoxazole and 20–100 ng/L of the binary antibiotic mixture. Stimulated production and release of microcystins were observed at even lower concentrations. The upregulation of transcription‐related proteins, cell division‐related proteins, a gas vesicle protein, a global nitrogen regulator (ntcA), two microcystin synthetases (mcyC and mcyH) and ATP‐binding cassette transporters provided direct proteomic evidence for the regulation of target antibiotics on M. aeruginosa bloom. Cytochrome P450 was an essential component involved in stress responses and antibiotic biodegradation. Proteomic responses to antibiotic exposure presented a shift in the energy metabolism of M. aeruginosa towards the excitation of photosynthesis, an increase of carbohydrate biosynthesis and the inhibition of carbohydrate catabolism. Superoxide dismutase, enolase and D1 protein were candidate target proteins of different antibiotics in M. aeruginosa. The antibiotic mixture showed a greater hazard than single antibiotics, and a safe threshold of 5 ng/L was suggested for each target antibiotic under the coexistence condition.
Spatio‐temporal variation in parasite communities maintains diversity at the major histocompatibility complex class IIβ in the endangered Rio Grande silvery minnow
Authors: Osborne Megan J. , Pilger Tyler J. , Lusk Joel D. , Turner Thomas F. 
Published: November 2016

AbstractClimate change will strongly impact aquatic ecosystems particularly in arid and semi‐arid regions. Fish–parasite interactions will also be affected by predicted altered flow and temperature regimes, and other environmental stressors. Hence, identifying environmental and genetic factors associated with maintaining diversity at immune genes is critical for understanding species’ adaptive capacity. Here, we combine genetic (MHC class IIβ and microsatellites), parasitological and ecological data to explore the relationship between these factors in the remnant wild Rio Grande silvery minnow (Hybognathus amarus) population, an endangered species found in the southwestern United States. Infections with multiple parasites on the gills were observed and there was spatio‐temporal variation in parasite communities and patterns of infection among individuals. Despite its highly endangered status and chronically low genetic effective size, Rio Grande silvery minnow had high allelic diversity at MHC class IIβ with more alleles recognized at the presumptive DAB1 locus compared to the DAB3 locus. We identified significant associations between specific parasites and MHC alleles against a backdrop of generalist parasite prevalence. We also found that individuals with higher individual neutral heterozygosity and higher amino acid divergence between MHC alleles had lower parasite abundance and diversity. Taken together, these results suggest a role for fluctuating selection imposed by spatio‐temporal variation in pathogen communities and divergent allele advantage in maintenance of high MHC polymorphism. Understanding the complex interaction of habitat, pathogens and immunity in protected species will require integrated experimental, genetic and field studies.
Molecular and microstructural inventory of an isolated fossil bird feather from the Eocene Fur Formation of Denmark
Authors: Gren Johan A. , Sjövall Peter , Eriksson Mats E. , Sylvestersen Rene L. , Marone Federica , Sigfridsson Clauss Kajsa G. V. , Taylor Gavin J. , Carlson Stefan , Uvdal Per , Lindgren Johan 
Published: November 2016

AbstractAn isolated, yet virtually intact contour feather (FUM‐1980) from the lower Eocene Fur Formation of Denmark was analysed using multiple imaging and molecular techniques, including field emission gun scanning electron microscopy (FEG‐SEM), X‐ray absorption spectroscopy and time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS). Additionally, synchrotron radiation X‐ray tomographic microscopy (SRXTM) was employed in order to produce a digital reconstruction of the fossil. Under FEG‐SEM, the proximal, plumulaceous part of the feather revealed masses of ovoid microstructures, about 1.7 μm long and 0.5 μm wide. Microbodies in the distal, pennaceous portion were substantially smaller (averaging 0.9 × 0.2 μm), highly elongate, and more densely packed. Generally, the microbodies in both the plumulaceous and pennaceous segments were aligned along the barbs and located within shallow depressions on the exposed surfaces. Biomarkers consistent with animal eumelanins were co‐localized with the microstructures, to suggest that they represent remnant eumelanosomes (i.e. eumelanin‐housing cellular organelles). Additionally, ToF‐SIMS analysis revealed the presence of sulfur‐containing organics – potentially indicative of pheomelanins – associated with eumelanin‐like compounds. However, since there was no correlation between melanosome morphology and sulfur content, we conclude these molecular structures derive from diagenetically incorporated sulfur rather than pheomelanin. Melanosomes corresponding roughly in both size and morphology with those in the proximal part of FUM‐1980 are known from contour feathers of extant parrots (Psittaciformes), an avian clade that has previously been reported from the Fur Formation.
Repigmentation in vitiligo: position paper of the Vitiligo Global Issues Consensus Conference
Authors: Gan Emily Y. , Eleftheriadou Viktoria , Esmat Samia , Hamzavi Iltefat , Passeron Thierry , Böhm Markus , Anbar Tag , Goh Boon Kee , Lan Cheng‐Che E. , Lui Harvey , Ramam M. , Raboobee Noufal , Katayama Ichiro , Suzuki Tamio , Parsad Davinder , Seth Vaneeta , Lim Henry W. , van Geel Nanja , Mulekar Sanjeev , Harris John , Wittal Richard , Benzekri Laila , Gauthier Yvon , Kumarasinghe Prasad , Thng Steven T. G. , Silva de Castro Caio Cesar , Abdallah Marwa , Vrijman Charlotte , Bekkenk Marcel , Seneschal Julien , Pandya Amit G. , Ezzedine Khaled , Picardo Mauro , Taïeb Alain ,   the VGICC
Published: November 2016

SummaryThe Vitiligo Global Issues Consensus Conference (VGICC), through an international e‐Delphi consensus, concluded that ‘repigmentation’ and ‘maintenance of gained repigmentation’ are essential core outcome measures in future vitiligo trials. This VGICC position paper addresses these core topics in two sections and includes an atlas depicting vitiligo repigmentation patterns and color match. The first section delineates mechanisms and characteristics of vitiligo repigmentation, and the second section summarizes the outcomes of international meeting discussions and two e‐surveys on vitiligo repigmentation, which had been carried out over 3 yr. Treatment is defined as successful if repigmentation exceeds 80% and at least 80% of the gained repigmentation is maintained for over 6 months. No agreement was found on the best outcome measure for assessing target or global repigmentation, therefore highlighting the limitations of e‐surveys in addressing clinical measurements. Until there is a clear consensus, existing tools should be selected according to the specific needs of each study. A workshop will be conducted to address the remaining issues so as to achieve a consensus.
Mfd Protein and Transcription–Repair Coupling in Escherichia coli
Authors: Selby Christopher P. 
Published: November 2016

AbstractIn 1989, transcription–repair coupling (TRC) was first described in Escherichia coli, as the transcription‐dependent, preferential nucleotide excision repair (NER) of UV photoproducts located in the template DNA strand. This finding led to pioneering biochemical studies of TRC in the laboratory of Professor Aziz Sancar, where, at the time, major contributions were being made toward understanding the roles of the UvrA, UvrB and UvrC proteins in NER. When the repair studies were extended to TRC, template but not coding strand lesions were found to block RNA polymerase (RNAP) in vitro, and unexpectedly, the blocked RNAP inhibited NER. A transcription–repair coupling factor, also called Mfd protein, was found to remove the blocked RNAP, deliver the repair enzyme to the lesion and thereby mediate more rapid repair of the transcription‐blocking lesion compared with lesions elsewhere. Structural and functional analyses of Mfd protein revealed helicase motifs responsible for ATP hydrolysis and DNA binding, and regions that interact with RNAP and UvrA. These and additional studies provided a basis upon which other investigators, in following decades, have characterized fascinating and unexpected structural and mechanistic features of Mfd, revealed the possible existence of additional pathways of TRC and discovered additional roles of Mfd in the cell.
Phylogenetic and Functional Classification of the Photolyase/Cryptochrome Family
Authors: Ozturk Nuri 
Published: November 2016

AbstractThe photolyase/cryptochrome (PHR/CRY) family is a large group of proteins with similar structure but very diverge functions such as DNA repair, circadian clock resetting and regulation of transcription. As a result of advances in the biochemistry of the CRY/PHR family and identification of new members, several adjustments have been made to the classification of this protein family. For example, a new class of PHRs, Class III, has been proposed. Furthermore, CRYs have been suggested to function as photosensory proteins in the primordial eye of sponge larvae. Additionally, a magnetosensory function has been attributed to certain CRYs. Recent advances in the field enabled us to propose a comprehensive classification scheme and nomenclatural system for this family. This review focuses on the computational and biochemical classifications of the PHR/CRY family. Several examples show that computational analysis can give a hinge about the function of newly discovered members before performing any biochemical study.
Evaluation of the efficacy of photodynamic therapy for the treatment of actinic cheilitis
Authors: Chaves Yuri N. , Torezan Luis Antonio , Lourenço Silvia Vanessa , Neto Cyro Festa 
Published: November 2016

SummaryIntroductionActinic cheilitis (AC) is a lip intraepithelial neoplasia, whose cells present alterations similar to those presented by invasive squamous cell carcinomas (SCCs).ObjectiveTo conduct clinical and laboratory evaluation by histopathology and immunohistochemistry of the efficacy of actinic cheilitis treatment using photodynamic therapy (PDT) with methyl aminolevulinate (MAL) and noncoherent red light.Materials and methodsPatients with actinic cheilitis detected by histopathological examination were submitted to two sessions of photodynamic therapy with a two‐week interval between them. They were examined immediately after the sessions, four, six, and twelve weeks after beginning treatment when a new biopsy was carried out. Clinical histopathological and immunohistochemical parameters were evaluated before and after treatment.ResultsOf the 23 patients who underwent biopsy, 16 completed two photodynamic therapy sessions and the material of one patient was insufficient for immunohistochemistry. Complete clinical response was achieved in 62.5% (10 of 16 patients) and 37.5% still remained with clinical evidence of AC. In spite of this, no case of cure by histopathological analysis was found. There was no significant statistical change among the values of Ki‐67, survivin, and p53 observed before and after treatment.ConclusionPhotodynamic therapy, as carried out in this trial, was not an efficacious therapeutic option for treating patients with actinic cheilitis included in this sample.
Parameter Stability and Semiparametric Inference in Time Varying Auto-Regressive Conditional Heteroscedasticity Models
Authors: Truquet Lionel 
Published: November 2016

SummaryWe develop a complete methodology for detecting time varying or non-time-varying parameters in auto-regressive conditional heteroscedasticity (ARCH) processes. For this, we estimate and test various semiparametric versions of time varying ARCH models which include two well-known non-stationary ARCH-type models introduced in the econometrics literature. Using kernel estimation, we show that non-time-varying parameters can be estimated at the usual parametric rate of convergence and, for Gaussian noise, we construct estimates that are asymptotically efficient in a semiparametric sense. Then we introduce two statistical tests which can be used for detecting non-time-varying parameters or for testing the second-order dynamics. An information criterion for selecting the number of lags is also provided. We illustrate our methodology with several real data sets.
Flooding scenarios due to land subsidence and sea‐level rise: a case study for Lipari Island (Italy)
Authors: Anzidei Marco , Bosman Alessandro , Carluccio Roberto , Casalbore Daniele , D'Ajello Caracciolo Francesca , Esposito Alessandra , Nicolosi Iacopo , Pietrantonio Grazia , Vecchio Antonio , Carmisciano Cosmo , Chiappini Massimo , Chiocci Francesco Latino , Muccini Filippo , Sepe Vincenzo 
Published: November 2016

AbstractArchaeological and instrumental data indicate that the southern sector of the volcanic island of Lipari has been subsiding for the last 2100 years due to isostatic and tectonic factors, at variable rates of up to ~11 mm a−1. Based on this data, a detailed marine flooding scenario for 2100 AD is provided for the bay of Marina Lunga in the eastern part of the island from (1) an ultra‐high‐resolution Digital Terrain and Marine Model (DTMM) generated from multibeam bathymetry (MB) and Unmanned Aerial Vehicles (UAV), (2) the rate of land subsidence from Global Positioning System (GPS) data and (3) the regional sea‐level projections of the International Panel on Climate Change (IPCC). When land subsidence is considered, the upper bound of sea‐level rise is estimated at 1.36 m and 1.60 m for RCP4.5 and RCP8.5 climate change scenarios, respectively. Here, we show the expected impact of marine flooding at Lipari for the next 85 years and discuss the hazard implications for the population living along the shore.