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In this study, arsenic (As) speciation was investigated in the freshwater alga Chlamydomonas reinhardtii treated with 20 μg/L arsenate using fractionation as well as ICP-MS/ESI-MS analyses and was compared with the known As metabolite profile of wild-grown Saccharina latissima. While the total As accumulation in C. reinhardtii was about 85% lower than in S. latissima, the relative percentage of arsenolipids was significantly higher in C. reinhardtii (57.0% vs. 5.01%). As-containing hydrocarbons and phospholipids dominated the hydrophobic As profile in S. latissima, but no As-containing hydrocarbons were detectable in C. reinhardtii. Instead for the first time, an arsenoriboside-containing phytol (AsSugPhytol) was found to dominate the hydrophobic arsenicals of C. reinhardtii. Interestingly, this compound and its relatives had so far been only found in green marine microalgae, open sea plankton (mixed assemblage), and sediments but not in brown or red macroalgae. This compound family might therefore relate to differences in the arsenic metabolism between the algae phyla. [ABSTRACT FROM AUTHOR]

It is known that every hereditary property can be characterized by finitely many minimal obstructions when restricted to either the class of cographs or the class of P 4 -reducible graphs. In this work, we prove that the same is true when restricted to some other superclasses of cographs, including P 4 -sparse and P 4 -extendible graphs (both of which extend P 4 -reducible graphs). We also present complete lists of P 4 -sparse and P 4 -extendible minimal obstructions for polarity, monopolarity, unipolarity, and (s, 1)-polarity, where s is a positive integer. In parallel to the case of P 4 -reducible graphs, all the P 4 -sparse minimal obstructions for these hereditary properties are cographs. [ABSTRACT FROM AUTHOR]

Lichens host highly diverse microbial communities, with bacteria being one of the most explored groups in terms of their diversity and functioning. These bacteria could partly originate from symbiotic propagules developed by many lichens and, perhaps more commonly and depending on environmental conditions, from different sources of the surroundings. Using the narrowly distributed species Peltigera frigida as an object of study, we propose that bacterial communities in these lichens are different from those in their subjacent substrates, even if some taxa might be shared. Ten terricolous P. frigida lichens and their substrates were sampled from forested sites in the Coyhaique National Reserve, located in an understudied region in Chile. The mycobiont identity was confirmed using partial 28S and ITS sequences. Besides, 16S fragments revealed that mycobionts were associated with the same cyanobacterial haplotype. From both lichens and substrates, Illumina 16S amplicon sequencing was performed using primers that exclude cyanobacteria. In lichens, Proteobacteria was the most abundant phylum (37%), whereas soil substrates were dominated by Acidobacteriota (39%). At lower taxonomic levels, several bacterial groups differed in relative abundance among P. frigida lichens and their substrates, some of them being highly abundant in lichens but almost absent in substrates, like Sphingomonas (8% vs 0.2%), and others enriched in lichens, as an unassigned genus of Chitinophagaceae (10% vs 2%). These results reinforce the idea that lichens would carry some components of their microbiome when propagating, but they also could acquire part of their bacterial community from the substrates. [ABSTRACT FROM AUTHOR]

Lichens are present in most terrestrial ecosystems on Earth and colonize extreme habitats, where vascular plants are unable to thrive, due to unique properties of the fungal-algal symbiosis. Here, we explored the phylogeographic structure of green algae engaged in symbiosis with species in the genus Pseudephebe (Parmeliaceae). These often form deep brown to blackish fruticose thalli on acidic rocks, and have partially overlapping distributions: P. minuscula is bipolar and co-occurs with P. pubescens in Europe. Based on a broad sampling, including the Arctic and Antarctica, we focused on photobionts (1) to identify genetic lineages and their phylogenetic assignment, (2) to infer the haplotype distribution in relation with geography and the mycobiont's identity, and (3) to evaluate spatial genetic structure and polymorphism. Results revealed three Trebouxia clade S lineages (Trebouxia S02, T. suecica and T. angustilobata) associated to Pseudephebe species, with predominant haplotypes distributed throughout the entire geographic distribution, and some, less frequent, shared between widely distant localities. Photobiont switching was evident in the Mediterranean region, and algal co-occurrence was frequent in both mycobionts, which shared the same set of photobionts; this could explain, at least partially, their overlapping distribution. Furthermore, genetic structure was influenced by geography given the substantial percentages of genetic variation (ca. 25–50%) explained by the different delimited eco−/biogeographic regions. In Continental Antarctica, mycobionts showed a high specialization towards the photobionts, which are probably endemic of this climatically extreme region. Taken together, our findings provide further insight about the processes shaping lichen biogeography. [ABSTRACT FROM AUTHOR]

Although there is an abundance of species delimitation methods on the market, most approaches depend on predefined assignment of specimens to species or populations. Assignment-free methods, which can simultaneously infer boundaries and relationships among species, are of high importance in cases, when correct pre-assignment is difficult or not at all possible. In this study, we use assignment-free multispecies coalescent-based species delimitation (STACEY, tr2-delimitation, and BP&P), phylogenetic methods, and clustering algorithms to investigate the inter- and infraspecific relationships within a common and widespread group of lichens with contentious species boundaries. The Cetraria aculeata group presents a good example of extreme morphological variability and unclear species delimitation in lichens. Based on DNA-sequence data from 26 fungal loci and 10 microsatellite loci, as well as morphological and chemical data, our results provide evidence for the occurrence of five different taxa within the group and highlight the difficulties of morphologically distinguishing these species. We discovered a separate lineage (clade C) within C. aculeata s. str., which does not fully coincide with any of the a priori identified species C. aculeata, C. crespoae, or C. steppae and conclude that this clade constitutes a semi-cryptic, genetically isolated lineage within C. aculeata. We recognize this lineage at subspecific rank as C. aculeata subsp. steppae and synonymize Cetraria crespoae with C. aculeata subsp. aculeata. Epitypes are designated for all involved names to stabilize their usage. The PKS8 gene locus is recommended as a barcode for the separation of C. aculeata subsp. aculeata and subsp. steppae. We demonstrate the potential use of microsatellite data for species delimitation in lichens that might offer an alternative insight or be used to test species delimitation hypotheses, when dealing with closely related or potentially cryptic species. Our results also confirm the presence of an undescribed sister lineage to C. odontella previously misidentified as C. muricata and extend the known range of this lineage to Central Asia (Altay Mts.) and the Central European Alps (France, Switzerland), which calls for a critical reappraisal of records of C. aculeata and C. muricata from these mountain ranges. [ABSTRACT FROM AUTHOR]

Lichen thalli harbor complex fungal communities (mycobiomes) of species with divergent trophic and ecological strategies. The complexity and diversity of lichen mycobiomes are still largely unknown, despite surveys combining culture-based methods and high-throughput sequencing (HTS). The results of such surveys are strongly influenced by the barcode locus chosen, its sensitivity in discriminating taxa, and the depth to which public sequence repositories cover the phylogenetic spectrum of fungi. Here, we use HTS of the internal transcribed spacer 2 (ITS2) to assess the taxonomic composition and diversity of a well-characterized, alpine rock lichen community that includes thalli symptomatically infected by lichenicolous fungi as well as asymptomatic thalli. Taxa belonging to the order Chaetothyriales are the major components of the observed lichen mycobiomes. We predict sequences representative of lichenicolous fungi characterized morphologically and assess their asymptomatic presence in lichen thalli. We demonstrated the limitations of metabarcoding in fungi and show how the estimation of species diversity widely differs when ITS1 or ITS2 are used as barcode, and particularly biases the detection of Basidiomycota. The complementary analysis of both ITS1 and ITS2 loci is therefore required to reliably estimate the diversity of lichen mycobiomes. [ABSTRACT FROM AUTHOR]

Lichens represent an extremely successful symbiosis between fungi and photosynthetic partners. It has been suggested that lichens can enhance their adaptive potential and widen their ecological niches by associating with locally adapted photobionts. Based on a worldwide population sample of the lichen Cetraria aculeata we investigate the genetic diversity and composition of photobiont and mycobiont populations of this species with a special focus on tropical alpine regions that have never been studied before. Probably due to their geographic isolation and founder effects during colonization, tropical mycobiont populations display low genetical diversity. In sharp contrast, tropical photobiont populations are among the most diverse within the species and similar in composition to polar populations. These results support the hypothesis of photobiont switching as an adaptive strategy in lichens. [ABSTRACT FROM AUTHOR]

Key message: Fivefold diversity for cooking time found in a panel of 206 Phaseolus vulgaris accessions. Fastest accession cooks nearly 20 min faster than average. SNPs associated with cooking time on Pv02, 03, and 06. Abstract: Dry beans ( Phaseolus vulgaris L.) are a nutrient dense food and a dietary staple in parts of Africa and Latin America. One of the major factors that limits greater utilization of beans is their long cooking times compared to other foods. Cooking time is an important trait with implications for gender equity, nutritional value of diets, and energy utilization. Very little is known about the genetic diversity and genomic regions involved in determining cooking time. The objective of this research was to assess cooking time on a panel of 206 P. vulgaris accessions, use genome- wide association analysis (GWAS) to identify genomic regions influencing this trait, and to test the ability to predict cooking time by raw seed characteristics. In this study 5.5-fold variation for cooking time was found and five bean accessions were identified which cook in less than 27 min across 2 years, where the average cooking time was 37 min. One accession, ADP0367 cooked nearly 20 min faster than average. Four of these five accessions showed close phylogenetic relationship based on a NJ tree developed with ~5000 SNP markers, suggesting a potentially similar underlying genetic mechanism. GWAS revealed regions on chromosomes Pv02, Pv03, and Pv06 associated with cooking time. Vis/NIR scanning of raw seed explained 68 % of the phenotypic variation for cooking time, suggesting with additional experimentation, it may be possible to use this spectroscopy method to non-destructively identify fast cooking lines as part of a breeding program. [ABSTRACT FROM AUTHOR]

Black bean ( Phaseolus vulgaris L.) processing presents unique challenges because of discoloration, breakage, development of undesirable textures, and off-flavors during canning and storage. These quality issues strongly affect processing standards and consumer acceptance for beans. In this research, visible and near-infrared (Vis/NIR) reflectance data for the spectral region of 400-2,500 nm were acquired from intact dry beans for predicting five canning quality traits, i.e., hydration coefficient (HC), visual appearance (APP) and color (COL), washed drained coefficient (WDC), and texture (TXT), using partial least squares regression (PLSR). A total of 471 bean samples harvested and canned in 2010, 2011, and 2012 were used for analysis. PLSR models based on the Vis/NIR data showed low predictive performance, as measured by correlation coefficient for prediction ( R) for APP ( R = 0.275-0.566) and TXT ( R = 0.270-0.681), but better results for predicting HC ( R = 0.517-0.810), WDC ( R = 0.420-0.796), and COL ( R < 0.533-0.758). In comparison, color measurements from a colorimeter on drained canned beans showed consistently good predictions for COL ( R = 0.796-0.907). In spite of the low or relatively poor agreement among the sensory panelists as determined by multirater Kappa analysis ( K of 0.20 for APP and 0.18 for COL), a linear discriminant model using the Vis/NIR data was able to classify the canned bean samples into two sensory quality categories of 'acceptable' and 'unacceptable', based on panelists' ratings for APP and COL traits of canning beans, with classification accuracies of 72.6 % or higher. While Vis/NIR technique has the potential for assessing bean canning quality from intact dry beans, improvements in sensing and instrumentation are needed in order to meet the application requirements. [ABSTRACT FROM AUTHOR]

Hyperspectral imaging is useful for detecting internal defects of pickling cucumbers. The technique, however, is not yet suitable for high-speed online implementation due to the challenges in analyzing large-scale hyperspectral images. This research aimed to select the optimal wavebands from the hyperspectral image data, so that they can be deployed in either a hyperspectral or multispectral imaging-based inspection system for the automatic detection of internal defects of pickling cucumbers. Hyperspectral reflectance (400-700 nm) and transmittance (700-1,000 nm) images were acquired, using an in-house developed hyperspectral imaging system running at two conveyor speeds of 85 and 165 mm/s, for 300 'Journey' pickling cucumbers before and after internal damage was induced by mechanical load. Minimum redundancy-maximum relevance (MRMR) was used for optimal wavebands selection, and the loadings of principal component analysis (PCA) were also applied for qualitatively identifying the important wavebands that are related to the specific features. Discriminant analysis with Mahalanobis distance classifier was performed for the two-class (i.e., normal and defective) and three-class (i.e., normal, slightly defective, and severely defective) classifications using the mean spectra and textural features (energy and variance) from the regions of interest in the spectral images at selected waveband ratios. The classification results based on MRMR wavebands selection were generally better than those from PCA-based classifications. The two-band ratio of 887/837 nm from MRMR gave the best overall classification results, with the accuracy of 95.1 and 94.2 % at the conveyor speeds of 85 and 165 mm/s, respectively, for the two-class classification. The highest classification accuracies for the three-class classification based on the optimal two-band ratio of 887/837 nm were 82.8 and 81.3 % at the conveyor speeds of 85 and 165 mm/s, respectively. The mean spectra-based classification achieved better results than the textural feature-based classification, except in the three-class classification for the higher conveyor speed. The overall classification accuracies for all selected waveband ratios at the low conveyor speed were slightly higher than those at the higher conveyor speed, since the low speed resulted in more scan lines, thus higher spatial resolution hyperspectral images. The identified two-band ratio of 887/837 nm in transmittance mode could be applied for fast real-time internal defect detection of pickling cucumbers. [ABSTRACT FROM AUTHOR]

Limited proven treatment options exist for patients with metastatic breast cancer (MBC) resistant to anthracycline and taxane treatment. Ixabepilone, a novel semisynthetic analog of epothilone B, has demonstrated single-agent activity in MBC resistant to anthracyclines and taxanes. In combination with capecitabine in a phase III trial (CA163-046) in this setting, ixabepilone prolonged progression-free survival and increased objective response rate relative to capecitabine (Thomas et al. J Clin Oncol 25:5210–5217, 2007). Here, we report the results of overall survival (OS), a secondary efficacy endpoint from the CA163-046 trial. Seven hundred fifty-two patients with MBC resistant to anthracyclines and taxanes were randomized to ixabepilone (40 mg/m2 intravenously on day 1 of a 21-day cycle) plus capecitabine (2,000 mg/m2 orally on days 1 through 14 of a 21-day cycle) or capecitabine alone (2,500 mg/m2 on the same schedule). Patients receiving ixabepilone plus capecitabine treatment had a median survival of 12.9 months compared to 11.1 months for patients receiving capecitabine alone (HR = 0.9; 95%CI: 077–1.05; P = 0.19). This observed increase in median OS favored the combination; however, the difference was not statistically significant. Predefined subset analyses showed a clinically meaningful increase in OS in KPS 70–80 patients receiving ixabepilone plus capecitabine (HR = 0.75; 95% CI: 0.58–0.98). Ixabepilone plus capecitabine did not show a significant improvement in survival compared to capecitabine alone in patients with MBC resistant to anthracyclines and taxanes. The observed differences in survival favored the combination arm. A clinical benefit was also seen in patients in the KPS 70–80 subgroup (ClinicalTrials.gov number, NCT000080301). [ABSTRACT FROM AUTHOR]

To compare health care access, utilization, and perceived health status for children with SHCN in immigrant and nonimmigrant families. This cross-sectional study used data from the 2003 California Health Interview Survey to identify 1404 children (ages 0–11) with a special health care need. Chi-square and logistic regression analyses were used to examine relations between immigrant status and health access, utilization, and health status variables. Compared to children with special health care needs (CSHCN) in nonimmigrant families, CSHCN in immigrant families are more likely to be uninsured (10.4 vs. 4.8%), lack a usual source of care (5.9 vs. 1.9%), report a delay in medical care (13.0 vs. 8.1%), and report no visit to the doctor in the past year (6.8 vs. 2.6%). They are less likely to report an emergency room visit in the past year (30.0 vs. 44.0%), yet more likely to report fair or poor perceived health status (33.0 vs. 16.0%). Multivariate analyses suggested that the bivariate findings for children with SHCN in immigrant families largely reflected differences in family socioeconomic status, parent’s language, parental education, ethnicity, and children’s insurance status. Limited resources, non-English language, and limited health-care use are some of the barriers to staying healthy for CSHCN in immigrant families. Public policies that improve access to existing insurance programs and provide culturally and linguistically appropriate care will likely decrease health and health care disparities for this population. [ABSTRACT FROM AUTHOR]

The microstructure and the connectivity of the pore space are important variables for better understanding of the complex gas transport phenomena that occur in plant tissues. In this study, we present an experimental procedure for image acquisition and image processing to quantitatively characterize in 3D the pore space of apple tissues ( Malus domestica Borkh.) for two cultivars (Jonagold and Braeburn) taken from the fleshy part of the cortex using X-ray computer microtomography. Preliminary sensitivity analyses were performed to determine the effect of the resolution and the volume size (REV, representative elementary volume analysis) on the computed porosity of apple samples. For comparison among cultivars, geometrical properties such as porosity, specific surface area, number of disconnected pore volumes and their distribution parameters were extracted and analyzed in triplicate based on the 3D skeletonization of the pore space (medial axis analysis). The results showed that microtomography provides a resolution at the micrometer level to quantitatively analyze and characterize the 3D topology of the pore space in apple tissue. The computed porosity was confirmed to be highly dependent of the resolution used, and the minimum REV of the cortical flesh of apple fruit was estimated to be 1.3 mm3. Comparisons among the two cultivars using a resolution of 8.5 μm with a minimum REV cube showed that in spite of the complexity and variability of the pore space network observed in Jonagold and Braeburn apples, the extracted parameters from the medial axis were significantly different ( P-value < 0.05). Medial axis parameters showed potential to differentiate the microstructure between the two evaluated apple cultivars. [ABSTRACT FROM AUTHOR]

The publisher regrets that the Table 3 of the original published version of this article is incorrect thus the table is now presented correctly. The original article has been corrected. [ABSTRACT FROM AUTHOR]

Background: Test bites have been recommended for collecting evidence of suspected dentition in bite mark analysis. However, these recommendations only suggest recording the interocclusal relationship without establishing number of records or characteristics to obtain proper records. This fails to consider not only the possibility that the recording material did not respond properly, but also that the evaluator has not detected simulations, habits or parafunctions that may affect the tests.Methods: This research establishes differences between three wax test bites taken from the same subjects to determine if the first bite offered the best quality.Results: No significant statistical association was found between the number of test bites recorded and respective quality. The interrater agreement produced almost perfect and substantial agreements.Conclusion: There is no significant evidence that a first and only test bite is the highest quality test bite. Therefore, it is recommended to take more than a single bite test in controlled situations. [ABSTRACT FROM AUTHOR]