bluuebunny/crossref_metadata_2025 huggingface dataset:
Motion and morphometry in clinical populations
Authors: Pardoe Heath R , Kucharsky Hiess Rebecca , Kuzniecky Ruben
Published: January 2018

Introduction The relationship between participant motion, demographic variables and MRI-derived morphometric estimates was investigated in autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD) and schizophrenia. Participant motion was estimated using resting state fMRI and used as a proxy measure for motion during T1-weighted MRI acquired in the same session. Analyses were carried out in scans qualitatively assessed as free from motion-related artifact.

Methods Whole brain T1-weighted MRI and resting state fMRI acquisitions from the ABIDE, ADHD-200 and COBRE databases were included in our analyses. Motion was estimated using coregistration of sequential resting state volumes. Morphometric estimates were obtained using Freesurfer v5.3. We investigated if motion is related to diagnosis, age and gender, and scanning site. We further determined if there is a relationship between participant motion and cortical thickness, contrast, and volumetric estimates.

Results 2131 participants were included in our analyses. Participant motion was higher in all clinical groups compared with healthy controls. Younger (age < 20 years) and older (age > 40 years) people move more than individuals aged 20 – 40 years. Increased motion is associated with reduced average cortical thickness (-0.02 mm thickness per mm motion, p = 4.03×10-5) and cortical contrast (0.95% contrast reduction per mm motion, p = 5.25×10-11) in scans that have been qualitatively assessed as free from motion artifact.

Conclusions Participant motion is increased in clinical groups and is systematically associated with morphometric estimates. These findings indicate that accounting for participant motion may be important for improving the statistical validity of morphometric studies.
Ecological Distribution of Protosteloid Amoebae in New Zealand
Authors: Zahn Geoffrey , Stephenson Steven L. , Spiegel Frederick W.
Published: January 2018

During the period of March 2004 to December 2007, samples of aerial litter (dead but still attached plant parts) and ground litter were collected from study sites representing a wide range of latitudes (34° S to 50° S) and a variety of different types of habitats throughout New Zealand (including Stewart Island and the Auckland Islands). The objective was to survey the assemblages of protosteloid amoebae present in this region of the world. Twenty-nine described species of protosteloid amoebae were recorded, along with the heterolobesean acrasid, Acrasis rosea. Of the species recovered, Protostelium mycophaga was by far the most abundant and was found in more than half of all samples. Most species were found in fewer than 10% of the samples collected. Seven abundant or common species were found to display significant preferences for aerial litter or ground litter microhabitats. There was some evidence of a general pattern of a decrease in species richness and diversity with increasing latitude and precipitation and elevation.
Saline stress in Amaranthaceous plants and pH stress on lettuce
Authors: Molinari-Novoa Eduardo A
Published: January 2018

Two experiments were carried to test stress reactions on plants. First, salinity experiments were performed in hydroponical cultures of spinach and beets. While the results were statistically untenable, a negative correlation between salinity and nitrate reductases was found. Second, pH stress experiments were conducted on lettuce. The optimal range for lettuce growth is near neutrality. The present work is the presentation of the first (mostly negative) results of a series of ecophysiological experiments carried since 2011.
Is heart rate variability related to cognitive performance in visuospatial working memory?
Authors: Suriya-Prakash Muthukrishnan , John-Preetham Gurja , Sharma Ratna
Published: January 2018

In the current study, we investigated the relation between cognitive performance and heart rate variability in visuospatial working memory. We used a visuospatial working memory paradigm involving simultaneous encoding, maintenance, active manipulation and retrieval to simulate routine daily activities. Subjects performed the visuospatial working memory paradigm which had 3 memory loads and simultaneous ECG recording was acquired for measuring heart rate variability. Based on the performance in the visuospatial working memory task, subjects were segregated into two groups: Good performers and poor performers. Two major findings emerged in this study. First, the heart rate variability decreased with an increase in the working memory load. Second, good performers had relatively higher heart rate variability compared to poor performers while performing the visuospatial working memory task. Our results highlighted the influence of cognitive performance on heart rate variability. In summary, the current study indicates that the heart rate variability during the visuospatial working memory task could predict the qualitative differences in the cognitive performance between the individuals.
Seasonal availability of edible underground and aboveground carbohydrate resources to human foragers on the Cape south coast, South Africa
Authors: De Vynck Jan C , Cowling Richard M , Potts Alastair J , Marean Curtis W
Published: January 2018

The coastal environments of South Africa’s Cape Floristic Region (CFR) provide some of the earliest and most abundant evidence for the emergence of cognitively modern humans. In particular, the south coast of the CFR provided for hunter-gatherers a uniquely diverse resource base, namely marine shellfish, game, and carbohydrate-bearing plants, especially those with underground storage organs (USOs). It has been hypothesized that these resource underpinned the continuity of human occupation in the region since the Middle Pleistocene. Very little research has been conducted on the foraging potential of carbohydrate resources in the CFR. This study focuses on the seasonal availability of plants with edible carbohydrate by assessing their visibility to foragers at six-weekly intervals over a two-year period in four vegetation types on South Africa’s Cape south coast. A total of 52 edible plant species were recorded across all vegetation types. Of these, 33 species were geophytes with edible USOs and 21 species had aboveground edible carbohydrates. Limestone Fynbos had the richest flora, followed by Strandveld, Renosterveld and lastly, Sand Fynbos. The availability of USO species differed across vegetation types and between survey years. The number of available USO species was highest for a six-month period from winter to early summer (Jul-Dec) across all vegetation types. Months of lowest species’ availability were in mid-summer to early autumn (Jan-Apr); the early winter (May-Jun) values were variable, being highest in Limestone Fynbos. However, even during the late summer carbohydrate “crunch”, 25 carbohydrate bearing species were visible across the four vegetation types. Overall, the plant-based carbohydrate resources available to Stone Age foragers of the Cape south coast, especially USOs belonging to the Iridaceae family, are likely to have comprised a reliable and nutritious source of calories over most of the year. The winter and early spring months likely coincided with a scarcity of protein, especially marine invertebrates, but an abundance of carbohydrates. At these times, plant carbohydrates, especially USOs, may have comprised 100% of dietary intake. However, recognising which vegetation types are most productive, identifying hotspots of productivity and distinguishing between edible and toxic USOs must have required considerable cognitive skills.
Intrinsic disorder in biomarkers of insulin resistance, hypoadiponectinemia, and endothelial dysfunction among the type 2 diabetic patients
Authors: Jiffri Osama H. , Al-Sharif Fadwa M. , Jiffri Essam H. , Uversky Vladimir N.
Published: January 2018

Type 2 diabetes mellitus (T2DM) is a chronic and progressive disease that is strongly associated with the all-cause and cardiovascular mortality. The present study aimed to analyze the abundance and functionality of intrinsically disordered regions in several biomarkers of insulin resistance, adiponectin, and endothelial dysfunction found in the T2DM patients. In fact, in comparison to controls, obese T2DM patients are known to have significantly higher levels of inter-cellular adhesion molecule (iCAM-1), vascular cell adhesion molecule (vCAM-1), and E-selectin, whereas their adiponectin levels are relatively low. Bioinformatics analysis revealed that these selected biomarkers (iCAM-1, vCAM-1, E-selectin, and adiponectin) are characterized by the noticeable levels of intrinsic disorder propensity and high binding promiscuity, which are important features expected for proteins serving as biomarkers. Within the limit of studied groups, there is an association between insulin resistance and both hypoadiponectinemia and endothelial dysfunction.
Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon
Authors: Tartally András , Kelager Andreas , Fürst Matthias A , Nash David R
Published: January 2018

The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats, and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occurs syntopically. We examined the genetic differentiation between the two forms using eight microsatellite markers, using samples from a nearby hygric site as out group. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within-nest relatedness, not association with host ants use, indicating very limited dispersal of most ovipositing females. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, and is an example of a genetic barrier operating on a temporal scale rather than spatial
Not so sluggish: the success of the Felimare picta complex (Gastropoda, Nudibranchia) crossing Atlantic biogeographic barriers
Authors: Almada Frederico , Levy André , Robalo Joana I
Published: January 2018

The molecular phylogeny of the Atlanto-Mediterranean species of the genus Felimare, particularly those attributed to the species F. picta, was inferred using two mitochondrial markers (16S and COI). A recent revision of the Chromodorididae clarified the taxonomic relationships at the family level reclassifying all eastern Pacific, Atlantic and Mediterranean species of the genus Hypselodoris and two species of the genus Mexichromis, within the genus Felimare. However, conflicting taxonomic classifications have been proposed for a group with overlapping morphological characteristics and geographical distributions designated here as the Felimare picta complex. Three major groups were identified: one Mediterranean and amphi-Atlantic group; a western Atlantic group and a tropical eastern Atlantic group. F. picta forms a paraphyletic group since some subspecies are more closely related with taxa traditionaly classified as independent species (e.g. F. zebra) than with other subspecies with allopatric distributions (e.g. F. picta picta and F. picta tema). Usually, nudibranchs have adhesive demersal eggs, short planktonic larval phases and low mobility as adults unless rafting on floating materials occurs. However, the phylogeny of the F. picta complex suggests they had an unusual success crossing main Atlantic biogeographic barriers including the mid-Atlantic barrier. This ability to cross different biogeographic barriers may be related with F. picta distinct life history and ecological traits. Compared to other Chromodorididae F. picta presents large eggs and planktotrophic larvae which could be related with a longer planktonic phase.
Predictability of cockle (Austrovenus stutchburyi) population trends in New Zealand’s northern North Island
Authors: Neubauer Philipp , Abraham Edward R , Berkenbusch Katrin
Published: January 2018

Population monitoring programmes are used to gain knowledge about system functioning or about the response of a system's state to management measures. The current study provided an assessment of comprehensive monitoring data of intertidal bivalve populations in northern New Zealand. In this region, a number of bivalve species are targeted in recreational and customary fisheries, including cockles (Austrovenus stutchburyi) that are one of the main target species. To monitor the sustainability of cockle populations, regular population surveys have been conducted since the 1990s at different northern New Zealand sites, although the sampling frequency has varied greatly across sites. Furthermore, a general lack of fishing data for the target populations prevents a systematic assessment of management measures and population trends within a fishery assessment framework. In view of these shortcomings, the current study provided a systematic phenomenological assessment of the survey data to make general recommendations about the effectiveness of management and for guiding prioritisation and design for future surveys. The assessment was based on a Bayesian state-space model that simultaneously analysed monitoring data from 21 incomplete survey time-series between 1999-2000 and 2014-15. The model showed that the predictability of estimated large-size cockle densities was highly site-specific. Across all sites, the predictability of density trends could be used to guide the prioritisation of sites to be included in the survey, or to adjust the sampling frequency at individual sites. Based on the current analysis, existing management measures in the form of fishery closures at some of the sites appear to be effective in allowing recovery of depleted cockle populations. Only those sites that had management measures in place showed an increase in large cockle densities. In the absence of fishing data, adaptive management and targeted intervention could be used to further assess the efficacy of management measures.
Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa
Authors: Franks Steven J , Perez-Sweeney Beatriz , Strahl Maya , Nowogrodzki Anna , Weber Jennifer J , Lalchan Rebecca , Jordan Kevin P , Litt Amy
Published: January 2018

Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ~ 30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of natural variation in such a quantitative trait is challenging.
Detect ‘protein word’ based on unsupervised word segmentation
Authors: Wang Liang , Zhao Kaiyong
Published: January 2018

Unsupervised word segmentation methods were applied to analyze the protein sequence. Protein sequences, such as ‘MTMDKSELVQKA …..’, were used as input to these methods. Segmented ‘protein word’ sequences, such as ‘MTM DKSE LVQKA’, were then obtained. We compare the ‘protein words’ produced by unsupervised segmentation and the protein secondary structure segmentation. An interesting finding is that the unsupervised word segmentation is more efficient than secondary structure segmentation in expressing information. Our experiment also suggests there may be some ‘protein ruins’ in current noncoding regions.
PEPR: Pipelines for evaluating prokaryotic references
Authors: Olson Nathan D. , Zook Justin M. , Samarov Daniel V. , Jackson Scott A. , Salit Marc L.
Published: January 2018

The rapid adoption of microbial whole genome sequencing in public health, clinical testing, and forensic laboratories requires the use of validated measurement processes. Reference materials that are well characterized, homogeneous, and stable can be used to evaluate measurement processes and help to establish confidence in the results. Given the variety of microbial genome sequencing applications and platforms, as well as the vast microbial genomic diversity, there is a need for application-specific genomic materials for method validation. We have developed a reproducible and transparent bioinformatics tool for characterizing prokaryotic genomic materials; ”PEPR”, Pipelines for Evaluating Prokaryotic References. We demonstrate the tool and its output using sequencing data while developing a Staphylococcus aureus candidate genomic reference material.
Intron gain by tandem genomic duplication: a novel case and a new version of the model
Authors: Ma Ming-Yue , Lan Xin-Ran , Niu Deng-Ke
Published: January 2018

Origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. Recently gained introns would be especially useful for the study of the mechanisms of intron gain because randomly accumulated mutations might erase the evolutionary traces. The mechanisms of intron gain remain unclear due to the presence of very few solid cases. A widely cited model of intron gain is tandem genomic duplication, in which the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. We found that the second intron of the potato RNA-dependent RNA polymerase gene PGSC0003DMG402000361 originated mainly from a direct duplication of the 3′ side of the upstream intron. The 5' splicing site of this new intron was recruited from the upstream exonic sequence. In addition to the new intron, a downstream exonic segment of 178 bp also arose from duplication. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3′ splicing site, two putative exonic splicing enhancers and the GC contents differentiated between the intron and exon. We propose a new version of the tandem genomic duplication model, termed as the partial duplication of the preexisting intron/exon structure. This new version and the widely cited version are not mutually exclusive.
Realization of multiple neural activity resolutions via multidimensional ensemble empirical mode decomposition of calcium imaging data: a proof of concept
Authors: Akwei-Sekyere Samuel
Published: January 2018

One of the goals of systems and computational neuroscience is to understand how information is processed by a single neuron and integrated by a network of neurons. A plausible approach to identifying spatial neighborhoods of the brain that host potential neural networks of interest is by observing spatially-bounded aggregates of neural activity. To this end, the potential of the multidimensional ensemble empirical mode decomposition algorithm in extracting multiple resolutions of neural activity from calcium imaging data is evaluated.
Strategies for improved rhamnolipid production by Pseudomonas aeruginosa PA1
Authors: Soares dos Santos Alexandre , Pereira Jr Nei , Freire Denise M G
Published: January 2018

Rhamnolipids are biosurfactants with potential for diversified industrial and environmental uses. The present study evaluated three strategies to increase the production of rhamnolipid-type biosurfactants produced by Pseudomonas aeruginosa strain PA1. The influence of pH, the addition of endogenous autoinducers and the use of a fed batch process were examined. The culture medium adjusted to pH 7.0 was the most productive. Furthermore, the pH of the culture medium had a measurable effect on the ratio of mono- and dirhamnolipids synthesized. At pH values below 7.3, the proportion of monorhamnolipids decreased from 45 to 24%. Additionally, recycling 20% of the spent culture medium where P. aeruginosa was grown up to the later stationary phase was responsible for a 100% increase in rhamnolipid volumetric productivity in the new culture medium. Finally, the use of fed batch operation under conditions of limited nitrogen resulted in a 3.8-fold increase in the amount of rhamnolipids produced (1.29 g L-1 to 4.90 g L-1, as rhamnose). These results offer promising paths to optimize processes for the production of rhamnolipids.
Homeotic transformations and number changes in the vertebral column of Triturus newts
Authors: Slijepčević Maja , Galis Frietson F , Arntzen Jan W , Ivanović Ana
Published: January 2018

We explored intraspecific variation in vertebral formulae, more specifically the variation in the number of thoracic vertebrae and frequencies of transitional sacral vertebrae in Triturus newts (Caudata: Salamandridae). Within salamandrid salamanders this monophyletic group shows the highest disparity in the number of thoracic vertebrae and considerable intraspecific variation in the number of thoracic vertebrae. Triturus species also differ in their ecological preferences, from predominantly terrestrial to largely aquatic. Following Geoffroy St. Hilaire’s and Darwin’s rule which states that structures with a large number of serially homologous repetitive elements are more variable than structures with smaller numbers, we hypothesized that the variation in vertebral formulae increases in more elongated species with a larger number of thoracic vertebrae. We furthermore hypothesized that the frequency of transitional vertebrae will be correlated with the variation in the number of thoracic vertebrae within the species. We also investigated potential effects of species hybridization on the vertebral formula. The proportion of individuals with a number of thoracic vertebrae different from the modal number and the range of variation in number of vertebrae significantly increased in species with a larger number of thoracic vertebrae. Contrary to our expectation, the frequencies of transitional vertebrae were not correlated with frequencies of change in the complete vertebrae number. The frequency of transitional sacral vertebra in hybrids did not significantly differ from that of the parental species. Such a pattern could be a result of selection pressure against transitional vertebrae and/or a bias towards the development of full vertebrae numbers. Although our data indicate relaxed selection for vertebral count changes in more elongated, aquatic species, more data on different selective pressures in species with different numbers of vertebrae in the two contrasting, terrestrial and aquatic environments are needed to test for causality.
Mining PubMed for biomarker-disease associations to guide discovery
Authors: Jessen Walter J , Landschulz Katherine T , Turi Thomas G , Reams Rachel Y
Published: January 2018

Biomedical knowledge is growing exponentially; however, meta-knowledge around the data is often lacking. PubMed is a database comprising more than 21 million citations for biomedical literature from MEDLINE and additional life science journals dating back to the 1950s. To explore the use and frequency of biomarkers across human disease, we mined PubMed for biomarker-disease associations. We then ranked the top 100 linked diseases by relevance and mapped them to medical subject headings (MeSH) and, subsequently, to the Disease Ontology. To identify biomarkers for each disease, we queried Covance BioPathways, an online data resource that maps commercial biomarker assays to biological and disease pathways. We then integrated pathways-based information to describe both known and potential biomarkers as well as disease-associated genes/proteins for select diseases. This approach identifies therapeutic areas with candidate or validated biomarkers, and highlights those areas where a paucity of biomarkers exists.
Ten simple rules for digital data storage
Authors: Hart Edmund , Barmby Pauline , LeBauer David , Michonneau François , Mount Sarah , Poisot Timothée , Woo Kara H , Zimmerman Naupaka , Hollister Jeffrey W
Published: January 2018

Data is the central currency of science, but the nature of scientific data has changed dramatically with the rapid pace of technology. This change has led to the development of a wide variety of data formats, dataset sizes, data complexity, data use cases, and data sharing practices. Improvements in high throughput DNA sequencing, sustained institutional support for large sensor networks, and sky surveys with large-format digital cameras have created massive quantities of data. At the same time, the combination of increasingly diverse research teams and data aggregation in portals (e.g. for biodiversity data, GBIF or iDigBio) necessitates increased coordination among data collectors and institutions. As a consequence, “data” can now mean anything from petabytes of information stored in professionally-maintained databases, through spreadsheets on a single computer, to hand-written tables in lab notebooks on shelves. All remain important, but data curation practices must continue to keep pace with the changes brought about by new forms and practices of data collection and storage.
Seasonal dosage-dependent hypersensitivity to the angiotensin II receptor blocker, losartan. A case report and review
Authors: Forsdyke Donald R
Published: January 2018

Since it has been in clinical use for two decades, individual data permitting evaluation of the long-term treatment of hypertension with losartan, which blocks the dominant angiotensin-II receptor (AT 1 R), should now be available. In the present case, by dosage adjustment according to daily home blood pressure (BP) readings, a mild degree of hypertension discovered during routine examination was kept in the 130/80 (mm Hg) range over an 11 year period (2003-2013). In the early years, control was achieved with 12.5 – 25.0 mg/day and dosage adjustment was seldom needed on a seasonal basis. However, on increasing to 50 mg/day, a profound downward adjustment to 0 – 12.5 mg/day was required in hot weather. The adjustment may have prevented recurrence of drug-induced postural hypotension and renal colic. Whether the adjustment facilitated an increased nocturnal BP, as suggested by some ambulatory BP studies, was not examined. A working hypothesis, consistent with animal experiments, is that under conditions of heat-stress (e.g. vascular dilation, salt loss), there is increased expression of a countervailing, losartan-insensitive, receptor subtype (AT 2 R). By lowering BP in response to angiotensin-II, AT 2 R would facilitate fine-tuningof the AT 1 R-mediated vasoconstriction that supports BP when superficial veins dilate to enhance body cooling. This AT 2 R activity might be sufficient to explain a small summertime BP dip found in normal human subjects whose Ang II levels are not increased. The dip would be greatly enhanced when Ang II levels were increased at higher losartan dosages. Close monitoring of losartan dosage may be necessary for those living in, or travelling to, geographical regions where temperatures are seasonally or continually high, and for those engaging in activities that involve such exposure (e.g. hot yoga, Turkish baths).
Influence of whole-wheat consumption on fecal microbial ecology of obese diabetic mice
Authors: Garcia-Mazcorro Jose F , Ivanov Ivan , Mills David A. , Noratto Giuliana
Published: January 2018

The digestive tract of mammals and other animals is colonized by trillions of metabolically active microorganisms. Changes in the gut microbiota have been associated with obesity in both humans and laboratory animals. Dietary modifications can often modulate the obese gut microbial ecosystem towards a more healthy state. This phenomenon should preferably be studied using dietary ingredients that are relevant to human nutrition. This study was designed to evaluate the influence of whole-wheat, a food ingredient with several beneficial properties, on gut microorganisms of obese diabetic mice. Diabetic (db/db) mice were fed standard (obese-control) or WW isocaloric diets (WW group) for eight weeks; non-obese mice were used as control (lean-control). High-throughput sequencing using the MiSeq platform coupled with freely-available computational tools and quantitative real-time PCR were used to analyze fecal bacterial 16S rRNA gene sequences. SCFAs were measured in feces using HPLC-PDA. Results showed no statistical difference in final body weights between the obese-control and the WW group. Almost 9,000 different bacterial species (Operational Taxonomic Units at 97% similarity) were detected in all mice but the bacterial diversity (number of OTUs) did not differ among the treatment groups. The abundance of Ruminococcaceae, a family containing several butyrate-producing bacteria, was found to be higher in obese (median: 6.9%) and WW-supplemented mice (5.6%) compared to lean (2.7%, p = 0.02, Kruskal-Wallis test). Fecal concentrations of butyrate were higher in obese (average: 2.91 mmol/mg of feces) but especially in WW-supplemented mice (4.27 mmol/mg) compared to lean controls (0.97 mmol/mg), while fecal succinic acid was lower in the WW group compared to obese but especially to the lean group. WW consumption was associated with ~3 times more relative abundance of Lactobacillus spp. compared to both obese and lean control mice. PCoA plots of weighted UniFrac distances revealed a distinctive clustering of lean microbial communities separately from both obese and WW-supplemented mice (p = 0.001, ANOSIM test). Predictive metagenome analysis using PICRUSt revealed significant differences in several metabolic features of the microbiota among the treatment groups, including fatty acid biosynthesis, carbohydrate and energy metabolism as well as synthesis and degradation of ketone bodies (p < 0.01). However, obese and WW groups tended to share more similar abundances of gene families compared to lean mice. Using an in vivo model of obesity and diabetes, this study suggests that daily WW supplementation for eight weeks may not be enough to influence body weight or to output a lean-like microbiome, both taxonomically and metabolically. However, WW-supplementation was associated with several statistically significant differences in the gut microbiome compared to obese controls that deserve further investigation.
Using machine translation for converting Python 2 to Python 3 code
Authors: Aggarwal Karan , Salameh Mohammad , Hindle Abram
Published: January 2018

In this paper, we have tried to use statistical machine translation in order to convert Python 2 code to Python 3 code. We use data from two projects and achieve a high BLEU score. We also investigate the cross-project training and testing to analyze the errors so as to ascertain differences with previous case. We have described a pilot study on modeling programming languages as natural language to build translation models on the lines of natural languages. This can be further worked on to translate between versions of a programming language or cross-programming-languages code translation.
rotl, an R package to interact with the Open Tree of Life data
Authors: Michonneau François , Brown Joseph W. , Winter David
Published: January 2018

While phylogenies have been getting easier to build, it has been difficult to re-use, combine, and synthesize the information they provide because published trees are often only available as image files, and taxonomic information is not standardized across studies. The Open Tree of Life (OTL) project addresses these issues by providing a digital tree that encompasses all organisms, built by combining taxonomic information and published phylogenies. The project also provides tools and services to query and download parts of this synthetic tree, as well as the source data used to build it. Here, we present rotl, an R package to search and download data from the Open Tree of Life directly in R. rotl uses common data structures allowing researchers to take advantage of the rich set of tools and methods that are available in R to manipulate, analyze, and visualize phylogenies.
A tide prediction and tide height control system for laboratory mesocosms
Authors: Miller Luke P , Long Jeremy D
Published: January 2018

Experimental mesocosm studies of rocky shore and estuarine intertidal systems may benefit from the application of natural tide cycles to better replicate variation in immersion time, water depth, and attendant fluctuations in abiotic and edaphic conditions. Here we describe a stand-alone microcontroller tide prediction open-source software program, coupled with a mechanical tidal elevation control system, which allows continuous adjustment of aquarium water depths in synchrony with local tide cycles. We used this system to monitor the growth of Spartina foliosa marsh cordgrass and scale insect herbivores at three simulated shore elevations in laboratory mesocosms. Plant growth decreased with increasing shore elevation, while scale insect population growth on the plants was not strongly affected by immersion time. This system shows promise for a range of laboratory mesocosm studies where natural tide cycling could impact organism performance or behavior, while the tide prediction system could additionally be utilized in field experiments where treatments need to be applied at certain stages of the tide cycle.
Can we set a global threshold age to define mature forests?
Authors: Martin Philip , Jung Martin , Brearley Francis Q , Ribbons Relena , Lines Emily R , Jacob Aerin L.
Published: January 2018

Globally mature forests appear to be increasing in biomass density. There is disagreement whether these increases are the result of increases in CO2 concentrations or a legacy effect of previous land-use. Recently, it was suggested that a threshold of 450 years should be used to define mature forests and that many forests increasing in biomass may be younger than this. However, the study making these suggestions failed to account for interactions between forest age and climate. Here we revisit the issue to identify: (1) how climate and forest age control global forest biomass density and (2) whether we can set a threshold age for mature forests. Using data from previously published studies we modelled the impacts of forest age and climate on biomass density using linear mixed effects models. We examined the potential biases in the dataset by comparing how representative it was of global mature forests in terms of its distribution, the climate space it occupied and the ages of the forests used. Biomass density increased with forest age, mean annual temperature and annual precipitation. Importantly the effect of forest age increased with increasing temperature, but the effect of precipitation decreased with increasing temperatures. The dataset was biased towards Northern hemisphere forests in relatively dry, cold climates. The dataset was also clearly biased towards forests <250 years of age. Our analysis suggests that there is not a single threshold age for forest maturity. Since climate interacts with forest age to determine biomass density a threshold age at which they reach equilibrium can only be determined locally. We caution against using biomass as the only determinant of forest maturity since this ignores forest biodiversity which often takes longer to recover. Future study of the influence of climate on forest biomass should aim to use the data currently being generated by long-term monitoring networks and satellite based observations.
Mesenchymal stem cells (MSC): Identification, Proliferation and Differentiation
Authors: Sandhaanam Sylvestar Darvin , Pathalam Ganesan , Dorairaj Sudarsanam , Savariar Vincent
Published: January 2018

Stem cells have the remarkable potential to develop into many different specialized cells in the body. Serving as a sort of repair system for the body, they can theoretically divide without limit to repletion other cells as long as the person or animal is still alive. When a stem cell divides, each new cell has the potential to either endure a stem cell or become another type of cell with a more specialized function, such as a muscle cell, or a red blood cell, or a brain cell. Mesenchymal stem cells (MSC) are a group of cells present in bone-marrow stroma and the stroma of various organs with the capacity for mesoderm-like cell differentiation into, many types like osteoblasts, adipocytes, and chondrocytes. MSC are being use in the clinic for the treatment of a variety of clinical conditions. Cell-based therapies (CBTs) are quickly taking hold as a revolutionary new approach to treat many human diseases. Among the cells used for therapeutic functions, multipotent mesenchymal stromal cells, also often and imprecisely termed (MSC), are widely used because they are considered clinically safe, unique in their immune-capabilities, easily obtained from adult tissues, and easily developed and restore.
Phylogenetic and morphologic evidence confirm the presence of a new montane cloud forest associated bird species in Mexico, the Mountain Elaenia (Elaenia frantzii; Aves: Passeriformes: Tyrannidae)
Authors: Hanna Zachary R , Ortiz-Ramírez Marco F , Ríos-Muñoz César A. , Cayetano-Rosas Héctor , Bowie Rauri C. K. , Navarro-Sigüenza Adolfo G
Published: January 2018

We here provide evidence to support an extension of the recognized distributional range of the Mountain Elaenia (Elaenia frantzii) to include southern Mexico. We collected two specimens in breeding condition in northwestern Sierra Norte de Chiapas, Mexico. Morphologic and genetic evidence support their identity as Elaenia frantzii. We compared environmental parameters of records across the entire geographic range of the species to those at the northern Chiapas survey site and found no climatic differences among localities.
The potential urinary aging markers of 20-month-old rats
Authors: Gao Youhe Xundou , Li Xundou Xundou
Published: January 2018

Urine is a very good source for biomarker discovery because it accumulates the changes of body. The urinary proteome is influenced by various factors, which is a major challenge in urinary biomarker discovery. To circumvent these problems, simpler systems, such as animal models, should be used to establish associations between physiological or pathological conditions and changes in the urinary proteome. In this study, the urinary proteome of young (2-month-old) and old rats (20-month-old; 9 in each group) were analyzed using LC-MS/MS and quantified using the Progenesis LC-MS software. A total of 371 proteins were identified, 194 of which were shared between young and old rats. Based on the criteria of a fold change ≥ 2, P < 0.05 and being identified in each rat in the high abundance group, 33 proteins were changed (15 up-regulated and 18 down-regulated in old rats). By adding a more stringent standard (protein spectral counts from every rat in the higher group greater than those in the lower group), 8 proteins were changed consistently in all rats of between the groups, 2 of which are also altered in the urinary proteome of aging humans. There are no shared proteins between our results and the previous aging plasma proteome. Twenty of the 33 (60 %) changed proteins have been reported to be disease biomarkers, which implies that aging may share similar urinary changes with some diseases. The 33 proteins corresponded to 28 human orthologs, which are strongly expressed in the kidney, intestine, cerebellum and lung, according to the human protein ATLAS. Therefore, the urinary proteome may reflect aging conditions in these organs.
Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region
Authors: Peñas Julio , Barrios Sara , Bobo-Pinilla Javier , Lorite Juan , Martínez-Ortega M. Montserrat
Published: January 2018

Astragalus edulis (Fabaceae) is an endangered annual species from western Mediterranean region that colonized SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura). Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs) as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of the loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species.
Is type-D personality trait(s) or state? An examination of type-D temporal stability in older Israeli adults in the community
Authors: Zohar Ada H
Published: January 2018

Background: Type-D personality was suggested as a marker of poorer prognosis for patients of cardiovascular disease. It is defined by having a score of 10 or more on both sub-scales of the DS14 questionnaire, Social Inhibition (SI) and Negative Affect (NA). As Type-D was designed to predict risk, its temporal stability is of prime importance. Methods: Participants in the current study were 285 community volunteers, who completed the DS14, and other personality scales, at a mean interval of six years. Results: The prevalence of Type-D did not change. The component traits of Type-D showed rank order stability. Type-D caseness temporal stability was improved by using the total DS14 score. Using the scale's product as a criterion further improved temporal stability. Logistic hierarchical regression predicting Type-D classification from Time1 demonstrated that the best predictors were Time1 scores on NA and SI, with the character trait of Cooperation, and the alexithymia score adding some predictive power. Conclusions: Temporal stability of Type-D caseness may be improved by using a sum or product threshold, rather than the current rule. In any case, as the temporal stability of Type-D is limited, research is required to formulate the optimal timing for Type-D measurement for predictive purposes.
Multilevel models for the distribution of hosts and symbionts
Authors: Joseph Maxwell B , Stutz William E , Johnson Pieter TJ
Published: January 2018

Symbiont occurrence is influenced by host occurrence and vice versa, which leads to correlations in host-symbiont distributions at multiple levels. Interactions between co-infecting symbionts within host individuals can cause correlations in the abundance of two symbiont species across individual hosts. Similarly, interactions between symbiont transmission and host population dynamics can drive correlations between symbiont and host abundance across habitat patches. If ignored, these interactions can confound estimated responses of hosts and symbionts to other factors. Here, we present a general hierarchical modeling framework for distributions of hosts and symbionts, estimating correlations in host-symbiont distributions at the among-site, within-site, among-species, and among-individual levels. We present an empirical example from a multi-host multi-parasite system involving amphibians and their micro- and macroparasites. Amphibian hosts and their parasites were correlated at multiple levels of organization. Macroparasites often co-infected individual hosts, but rarely co-infected with the amphibian chytrid fungus. Such correlations may result from interactions among parasites and hosts, joint responses to environmental factors, or sampling bias. Joint host-symbiont models account for environmental constraints and species interactions while partitioning variance and dependence in abundance at multiple levels. This framework can be adapted to a wide variety of study systems and sampling designs.
Impact of demographics on human gut microbial diversity in a US Midwest population
Authors: Chen Jun , Ryu Euijung , Hathcock Matthew , Ballman Karla , Chia Nicholas , Olson Janet E , Nelson Heidi
Published: January 2018

The clinical utility of microbiome biomarkers depends on the reliable and reproducible nature of comparative results. Underappreciation of the variation associated with common demographic, health, and behavioral factors may confound associations of interest and generate false positives. Here, we present the Midwestern Reference Panel (MWRP), a resource for comparative gut microbiome studies conducted in the Midwestern United States. We analyzed the relationships between demographic and health behavior–related factors and the microbiota in this cohort, and estimated their effect sizes. Most variables investigated were associated with the gut microbiota. Specifically, body mass index (BMI), race, sex, and alcohol use were significantly associated with microbial β-diversity (P < 0.05, unweighted UniFrac). BMI, race and alcohol use were also significantly associated with microbial α-diversity (P < 0.05, species richness). Tobacco use showed a trend toward association with the microbiota (P < 0.1, unweighted UniFrac). The effect sizes of the associations, as quantified by adjusted R2 values based on unweighted UniFrac distances, were small (< 1% for all variables), indicating that these factors explain only a small percentage of overall microbiota variability. Nevertheless, the significant associations between these variables and the gut microbiota suggest that they could still be potential confounders in comparative studies and that controlling for these variables in study design, which is the main objective of the MWRP, is important for increasing reproducibility in comparative microbiome studies.