bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved classification of indeterminate biliary strictures by probe‐based confocal laser endomicroscopy using the Paris Criteria following biliary stenting
Authors: Taunk Pushpak , Singh Satish , Lichtenstein David , Joshi Virendra , Gold Jason , Sharma Ashish 
Published: March 2017

AbstractBackground and AimsProbe‐based confocal laser endomicroscopy (pCLE) using the Miami Criteria has improved classification of indeterminate biliary strictures. However, previous biliary stenting may result in their misclassification as malignant strictures. Inflammatory criteria were added to form the Paris Classification to prevent this misclassification and reduce false positives. The aim of this study was to assess if the Paris Classification was more accurate than the Miami Classification in classifying indeterminate biliary strictures after biliary stenting.MethodsThis was a retrospective observational study involving 21 patients with indeterminate biliary strictures from whom 27 pCLE video sequences were obtained (20 benign and seven malignant). Patients with and without prior biliary stenting underwent pCLE. Two investigators classified the strictures as malignant or benign using the Miami and Paris Classifications. Diagnostic accuracy, sensitivity (Se), and specificity (Sp) of endoscopic retrograde‐guided pCLE were compared with final histopathology.ResultsIn those without biliary stenting, the Miami Criteria resulted in Se 88%, Sp 75%, positive predictive value (PPV) 64%, negative predictive value (NPV) 92%, and accuracy 79%, while the Paris Classification resulted in Se 63%, Sp 88%, PPV 71%, NPV 82%, and accuracy 79%. In those with prior biliary stenting, the Miami Criteria resulted in Se 88%, Sp 36%, PPV 23%, NPV 93%, and accuracy 45%, while the Paris Classification resulted in Se 63%, Sp 73%, PPV 31%, NPV 91%, and accuracy 71%. The kappa statistic was 0.56.ConclusionThe Paris Classification improved specificity and accuracy of biliary stricture classification in those who had been previously stented and decreased the rate of misclassification of benign strictures as malignant.
A Systematic Review of Gay, Lesbian, and Bisexual Research Samples in Couple and Family Therapy Journals
Authors: Hartwell Erica E. , Serovich Julianne M. , Reed Sandra J. , Boisvert Danielle , Falbo Teresa 
Published: March 2017

The purpose of this study is to review samples from research on gay, lesbian, and bisexual (GLB) issues and to evaluate the suitability of this body of research to support affirmative and evidence‐based practice with GLB clients. The authors systematically reviewed the sampling methodology and sample composition of GLB‐related research. All original, quantitative articles focusing on GLB issues published in couple and family therapy (CFT)‐related journals since 1975 were coded (n = 153). Results suggest that within the GLB literature base there is some evidence of heterocentrism as well as neglect of issues of class, race, and gender. Suggestions to improve the diversity and representativeness of samples—and, thus, clinical implications—of GLB‐related research in CFT literature are provided.
Molecular phylogeny and taxonomic revision of the genus Wittrockiella (Pithophoraceae, Cladophorales), including the descriptions of W. australis sp. nov. and W. zosterae sp. nov.
Authors: Boedeker Christian , O'Kelly Charles J. , West John A. , Hanyuda Takeaki , Neale Adele , Wakana Isamu , Wilcox Mike D. , Karsten Ulf , Zuccarello Giuseppe C. 
Published: March 2017

Wittrockiella is a small genus of filamentous green algae that occurs in habitats with reduced or fluctuating salinities. Many aspects of the basic biology of these algae are still unknown and the phylogenetic relationships within the genus have not been fully explored. We provide a phylogeny based on three ribosomal markers (ITS, LSU, and SSU rDNA) of the genus, including broad intraspecific sampling for W. lyallii and W. salina, recommendations for the use of existing names are made, and highlight aspects of their physiology and life cycle. Molecular data indicate that there are five species of Wittrockiella. Two new species, W. australis and W. zosterae, are described, both are endophytes. Although W. lyallii and W. salina can be identified morphologically, there are no diagnostic morphological characters to distinguish between W. amphibia, W. australis, and W. zosterae. A range of low molecular weight carbohydrates were analyzed but proved to not be taxonomically informative. The distribution range of W. salina is extended to the Northern Hemisphere as this species has been found in brackish lakes in Japan. Furthermore, it is shown that there are no grounds to recognize W. salina var. kraftii, which was described as an endemic variety from a freshwater habitat on Lord Howe Island, Australia. Culture experiments indicate that W. australis has a preference for growth in lower salinities over full seawater. For W. amphibia and W. zosterae, sexual reproduction is documented, and the split of these species is possibly attributable to polyploidization.
A rare case of plastid protein‐coding gene duplication in the chloroplast genome of Euglena archaeoplastidiata (Euglenophyta)
Authors: Bennett Matthew S. , Shiu Shin‐Han , Triemer Richard E. 
Published: March 2017

Gene duplication is an important evolutionary process that allows duplicate functions to diverge, or, in some cases, allows for new functional gains. However, in contrast to the nuclear genome, gene duplications within the chloroplast are extremely rare. Here, we present the chloroplast genome of the photosynthetic protist Euglena archaeoplastidiata. Upon annotation, it was found that the chloroplast genome contained a novel tandem direct duplication that encoded a portion of RuBisCO large subunit (rbcL) followed by a complete copy of ribosomal protein L32 (rpl32), as well as the associated intergenic sequences. Analyses of the duplicated rpl32 were inconclusive regarding selective pressures, although it was found that substitutions in the duplicated region, all non‐synonymous, likely had a neutral functional effect. The duplicated region did not exhibit patterns consistent with previously described mechanisms for tandem direct duplications, and demonstrated an unknown mechanism of duplication. In addition, a comparison of this chloroplast genome to other previously characterized chloroplast genomes from the same family revealed characteristics that indicated E. archaeoplastidiata was probably more closely related to taxa in the genera Monomorphina, Cryptoglena, and Euglenaria than it was to other Euglena taxa. Taken together, the chloroplast genome of E. archaeoplastidiata demonstrated multiple characteristics unique to the euglenoid world, and has justified the longstanding curiosity regarding this enigmatic taxon.
Early Devonian (~410 mya) microfossils resembling Characiopsis (Tribophyceae) and Characium (Chlorophyceae)
Authors: Krings Michael , Harper Carla J. , Taylor Edith L. , Kerp Hans 
Published: March 2017

Unusual microfossils that occurred associated with fungal spores in the Lower Devonian (~410 mya) Windyfield chert from Scotland were composed of a narrow stipe (2.5–9 μm long) to which was attached an obovoid or elongate drop‐shaped cell up to 14 μm long; a basal attachment pad was present in several specimens. The fossils were strikingly similar morphologically to certain present‐day unicellular freshwater Tribophyceae and Chlorophyceae, but affinities to the fungal phylum Chytridiomycota also cannot be ruled out. This discovery adds to the inventory of distinctive microbial morphologies in the early non‐marine paleoecosystems.
Interspecific hybridization causes long‐term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes
Authors: Wallis Graham P. , Cameron‐Christie Sophia R. , Kennedy Hannah L. , Palmer Gemma , Sanders Tessa R. , Winter David J. 
Published: March 2017

AbstractClassification, phylogeography and the testing of evolutionary hypotheses rely on correct estimation of species phylogeny. Early molecular phylogenies often relied on mtDNAalone, which acts as a single linkage group with one history. Over the last decade, the use of multiple nuclear sequences has often revealed conflict among gene trees. This observation can be attributed to hybridization, lineage sorting, paralogy or selection. Here, we use 54 groups of fishes from 48 studies to estimate the degree of concordance between mitochondrial and nuclear gene trees in two ecological grades of fishes: marine and freshwater. We test the hypothesis that freshwater fish phylogenies should, on average, show more discordance because of their higher propensity for hybridization in the past. In keeping with this idea, concordance between mitochondrial and nuclear gene trees (as measured by proportion of components shared) is on average 50% higher in marine fishes. We discuss why this difference almost certainly results from introgression caused by greater historical hybridization among lineages in freshwater groups, and further emphasize the need to use multiple nuclear genes, and identify conflict among them, in estimation of species phylogeny.
Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor
Authors: Luo Xin , Hu Quanjun , Zhou Pingping , Zhang Dan , Wang Qian , Abbott Richard J. , Liu Jianquan 
Published: March 2017

AbstractReconstructing the origin of a polyploid species is particularly challenging when an ancestor has become extinct. Under such circumstances, the extinct donor of a genome found in the polyploid may be treated as a ‘ghost’ species in that its prior existence is recognized through the presence of its genome in the polyploid. In this study, we aimed to determine the polyploid origin of Oxyria sinensis (2n = 40) for which only one congeneric species is known, that is diploid O. digyna (2n = 14). Genomic in situ hybridization (GISH), transcriptome, phylogenetic and demographic analyses, and ecological niche modelling were conducted for this purpose. GISH revealed that O. sinensis comprised 14 chromosomes from O. digyna and 26 chromosomes from an unknown ancestor. Transcriptome analysis indicated that following divergence from O. digyna, involving genome duplication around 12 million years ago (Ma), a second genome duplication occurred approximately 6 Ma to give rise to O. sinensis. Oxyria sinensis was shown to contain homologous gene sequences divergent from those present in O. digyna in addition to a set that clustered with those in O. digyna. Coalescent simulations indicated that O. sinensis expanded its distribution approximately 6–7 Ma, possibly following the second polyploidization event, whereas O. digyna expanded its range much later. It was also indicated that the distributions of both species contracted and re‐expanded during the Pleistocene climatic oscillations. Ecological niche modelling similarly suggested that both species experienced changes in their distributional ranges in response to Quaternary climatic changes. The extinction of the unknown ‘ghost’ tetraploid species implicated in the origin of O. sinensis could have resulted from superior adaptation of O. sinensis to repeated climatic changes in the region where it now occurs.
Hybridization between two cryptic filamentous brown seaweeds along the shore: analysing pre‐ and postzygotic barriers in populations of individuals with varying ploidy levels
Authors: Montecinos Alejandro E. , Guillemin Marie‐Laure , Couceiro Lucia , Peters Akira F. , Stoeckel Solenn , Valero Myriam 
Published: March 2017

AbstractWe aimed to study the importance of hybridization between two cryptic species of the genus Ectocarpus, a group of filamentous algae with haploid–diploid life cycles that include the principal genetic model organism for the brown algae. In haploid–diploid species, the genetic structure of the two phases of the life cycle can be analysed separately in natural populations. Such life cycles provide a unique opportunity to estimate the frequency of hybrid genotypes in diploid sporophytes and meiotic recombinant genotypes in haploid gametophytes allowing the effects of reproductive barriers preventing fertilization or preventing meiosis to be untangle. The level of hybridization between E. siliculosus and E. crouaniorum was quantified along the European coast. Clonal cultures (568 diploid, 336 haploid) isolated from field samples were genotyped using cytoplasmic and nuclear markers to estimate the frequency of hybrid genotypes in diploids and recombinant haploids. We identified admixed individuals using microsatellite loci, classical assignment methods and a newly developed Bayesian method (XPloidAssignment), which allows the analysis of populations that exhibit variations in ploidy level. Over all populations, the level of hybridization was estimated at 8.7%. Hybrids were exclusively observed in sympatric populations. More than 98% of hybrids were diploids (40% of which showed signs of aneuploidy) with a high frequency of rare alleles. The near absence of haploid recombinant hybrids demonstrates that the reproductive barriers are mostly postzygotic and suggests that abnormal chromosome segregation during meiosis following hybridization of species with different genome sizes could be a major cause of interspecific incompatibility in this system.
Development of a gastric carcinoid tumor following allogeneic hematopoietic stem cell transplantation for early T‐cell precursor acute lymphoblastic leukemia
Authors: Chang Tsung‐Yen , Lai Jin‐Yao , Wang Chao‐Jan , Chen Shih‐Yen , Jaing Tang‐Her , Hsueh Chuen , Shih Lee‐Yung , Chen Shih‐Hsiang 
Published: March 2017

AbstractGastric carcinoid tumor is rarely diagnosed in children. We report a case of gastric carcinoid tumor that occurred after allogeneic HSCT. A 13‐year‐old girl with ETP acute lymphoblastic leukemia underwent allogeneic HSCT from a 7/8 HLA‐matched unrelated donor. She presented with rashes, abdominal pain, and diarrhea, which were suggestive of GVHD, 7 months after HSCT. Immunosuppressive agents failed to resolve these symptoms well. After a series of evaluations, carcinoid syndrome caused by a gastric carcinoid tumor was diagnosed. The tumor was located in the antral region and resulted in partial gastric outlet obstruction. She received subtotal gastrectomy with regional lymph node dissection. However, she had a flare‐up of GVHD 1 month after surgery, and immunosuppressive therapy was intensified accordingly. Although her GVHD was getting better, she developed respiratory syncytial viral pneumonia with rapid progression to respiratory failure. She died of multiple organ failure 2 months postoperatively. This is the first pediatric case of a gastric carcinoid tumor following allogeneic HSCT. Our case also highlights the necessity for pediatric transplant physicians to be aware of carcinoid syndrome caused by this rare tumor in the setting of GVHD with poor response to immunosuppressive agents.
In vitro characterization of cell‐level neurophysiological diversity in the rostral nucleus reuniens of adult mice
Authors: Walsh Darren A. , Brown Jonathan T. , Randall Andrew D. 
Published: March 2017

Key points
The nucleus reuniens (Re), a nucleus of the midline thalamus, is part of a cognitive network including the hippocampus and the medial prefrontal cortex. To date, very few studies have examined the electrophysiological properties of Re neurons at a cellular level.
The majority of Re neurons exhibit spontaneous action potential firing at rest. This is independent of classical amino‐acid mediated synaptic transmission. When driven by various forms of depolarizing current stimulus, Re neurons display considerable diversity in their firing patterns. As a result of the presence of a low threshold Ca2+ channel, spike output functions are strongly modulated by the prestimulus membrane potential.
Finally, we describe a novel form of activity‐dependant intrinsic plasticity that eliminates the high‐frequency burst firing present in many Re neurons.
These results provide a comprehensive summary of the intrinsic electrophysiological properties of Re neurons allowing us to better consider the role of the Re in cognitive processes.
AbstractThe nucleus reuniens (Re) is the largest of the midline thalamic nuclei. We have performed a detailed neurophysiological characterization of neurons in the rostral Re of brain slices prepared from adult male mice. At resting potential (−63.7 ± 0.6 mV), ∼90% of Re neurons fired action potentials, typically continuously at ∼8 Hz. Although Re neurons experience a significant spontaneous barrage of fast, amino‐acid‐mediate synaptic transmission, this was not predominantly responsible for spontaneous spiking because firing persisted in the presence of glutamate and GABA receptor antagonists. With resting potential preset to −80 mV, −20 pA current injections revealed a mean input resistance of 615 MΩ and a mean time constant of 38 ms. Following cessation of this stimulus, a significant rebound potential was seen that was sometimes sufficiently large to trigger a short burst of very high frequency (100–300 Hz) firing. In most cells, short (2 ms), strong (2 nA) current injections elicited a single spike followed by a large afterdepolarizing potential which, when suprathreshold, generated high‐frequency spiking. Similarly, in the majority of cells preset at −80 mV, 500 ms depolarizing current injections to cells led to a brief initial burst of very high‐frequency firing, although this was lost when cells were preset at −72 mV. Biophysical and pharmacological experiments indicate a prominent role for T‐type Ca2+ channels in the high‐frequency bursting of Re neurons. Finally, we describe a novel form of activity‐dependent intrinsic plasticity that persistently eliminates the burst firing potential of Re neurons.
Mechanisms of Inactivation of Dry Escherichia coli by High-Pressure Carbon Dioxide
Authors: Chen Yuan Yao , Temelli Feral , Gänzle Michael G. 
Published: March 2017

ABSTRACT

High-pressure carbon dioxide processing is a promising technology for nonthermal food preservation. However, few studies have determined the lethality of high-pressure CO
2
on dry bacterial cells, and the mechanism of inactivation remains unknown. This study explored the mechanisms of inactivation by using
Escherichia coli
AW1.7 and mutant strains differing in heat and acid resistance, in membrane composition based on disruption of the locus of heat resistance, and in genes coding for glutamate decarboxylases and cyclopropane fatty acid synthase. The levels of lethality of treatments with liquid, gaseous, and supercritical CO
2
were compared. The cell counts of
E. coli
AW1.7 and mutants with a water activity (a
W
) of 1.0 were reduced by more than 3 log
10
(CFU/ml) after supercritical CO
2
treatment at 35°C for 15 min; increasing the pressure generally enhanced inactivation, except for
E. coli
AW1.7 Δ
gadAB
.
E. coli
AW1.7 Δ
cfa
was more susceptible than
E. coli
AW1.7 after treatment at 10 and 40 MPa; other mutations did not affect survival. Dry cells of
E. coli
were resistant to treatments with supercritical and liquid CO
2
at any temperature. Treatments with gaseous CO
2
at 65°C were more bactericidal than those with supercritical CO
2
or treatments at 65°C only. Remarkably,
E. coli
AW1.7 was more susceptible than
E. coli
AW1.7 Δ
cfa
when subjected to the gaseous CO
2
treatment. This study identified CO
2
-induced membrane fluidization and permeabilization as causes of supercritical mediated microbial inactivation, and diffusivity was a dominant factor for gaseous CO
2
.

IMPORTANCE
The safety of dry foods is of increasing concern for public health. Desiccated microorganisms, including pathogens, remain viable over long periods of storage and generally tolerate environmental insults that are lethal to the same organisms at high water activity. This study explored the use of high-pressure carbon dioxide to determine its lethality for dried
Escherichia coli
and to provide insight into the mechanisms of inactivation. The lethality of high-pressure CO
2
and the mechanisms of CO
2
-mediated inactivation of dry
E. coli
depended on the physical state of CO
2
. Liquid and supercritical CO
2
were ineffective in reducing the cell counts of dry
E. coli
isolates, and the effectiveness of gaseous CO
2
was related to the diffusivity of CO
2
. Results provide a novel and alternative method for the food industry to enhance the safety of low a
W
products.
Degradation of Diphenyl Ether in Sphingobium phenoxybenzoativorans SC_3 Is Initiated by a Novel Ring Cleavage Dioxygenase
Authors: Cai Shu , Chen Li-Wei , Ai Yu-Chun , Qiu Ji-Guo , Wang Cheng-Hong , Shi Chao , He Jian , Cai Tian-Ming 
Published: March 2017

ABSTRACT

Sphingobium phenoxybenzoativorans
SC_3 degrades and utilizes diphenyl ether (DE) or 2-carboxy-DE as its sole carbon and energy source. In this study, we report the degradation of DE and 2-carboxy-DE initiated by a novel ring cleavage angular dioxygenase (diphenyl ether dioxygenase [Dpe]) in the strain. Dpe functions at the angular carbon and its adjacent carbon (C-1a, C-2) of a benzene ring in DE (or the 2-carboxybenzene ring in 2-carboxy-DE) and cleaves the C-1a—C-2 bond (decarboxylation occurs simultaneously for 2-carboxy-DE), yielding 2,4-hexadienal phenyl ester, which is subsequently hydrolyzed to muconic acid semialdehyde and phenol. Dpe is a type IV Rieske non-heme iron oxygenase (RHO) and consists of three components: a hetero-oligomer oxygenase, a [2Fe-2S]-type ferredoxin, and a glutathione reductase (GR)-type reductase. Genetic analyses revealed that
dpeA1A2
plays an essential role in the degradation and utilization of DE and 2-carboxy-DE in
S. phenoxybenzoativorans
SC_3. Enzymatic study showed that transformation of 1 molecule of DE needs two molecules of oxygen and two molecules of NADH, supporting the assumption that the cleavage of DE catalyzed by Dpe is a continuous two-step dioxygenation process: DE is dioxygenated at C-1a and C-2 to form a hemiacetal-like intermediate, which is further deoxygenated, resulting in the cleavage of the C-1a—C-2 bond to form one molecule of 2,4-hexadienal phenyl ester and two molecules of H
2
O. This study extends our knowledge of the mode and mechanism of ring cleavage of aromatic compounds.

IMPORTANCE
Benzene ring cleavage, catalyzed by dioxygenase, is the key and speed-limiting step in the aerobic degradation of aromatic compounds. As previously reported, in the ring cleavage of DEs, the benzene ring needs to be first dihydroxylated at a lateral position and subsequently dehydrogenated and opened through extradiol cleavage. This process requires three enzymes (two dioxygenases and one dehydrogenase). In this study, we identified a novel angular dioxygenase (Dpe) in
S. phenoxybenzoativorans
SC_3. Under Dpe-mediated catalysis, the benzene ring of DE is dioxygenated at the angular position (C-1a, C-2), resulting in the cleavage of the C-1a—C-2 bond to generate a novel product, 2,4-hexadienal phenyl ester. This process needs only one angular dioxygenase, Dpe. Thus, the ring cleavage catalyzed by Dpe represents a novel mechanism of benzene ring cleavage.