bluuebunny/crossref_metadata_2025 huggingface dataset:
Reproducibility of cardiorespiratory and cellular responses to steady state exercise in hypoxia and preloaded cycling time trial performance reliability in normoxia and acute hypoxia
Authors: Lee Ben J , Thake Charles D
Published: January 2018

Background. The purpose of this study was to assess the reproducibility of cardiorespiratory and cellular (monocyte heat shock protein 70; mHSP70) responses to a fixed load hypoxic stress test (HST) and the reliability of a pre-loaded 16.1km cycling time trial (pTT) conducted under both normoxic and hypoxic conditions. Methods. Eighteen participants (age, 22 ± 4 years; height, 1.77 ± 0.04 meters; body mass, 76.8 kg; estimated body fat and VO2peak = 3.50 ± 0.60 L.min-1) were divided into three groups. Reliability of responses (HR, SPO2, VO2, VCO2, VE and RER) to the HST (FIO2 0.14; 15 minutes rest, 60 minutes cycling at 50% normoxic VO2peak) was assessed across 3 repeat trials (HST 1, 2 and 3, n = 6); mHSP70 was measured via flow cytometry before and after each HST (n = 5); resting HSP was also quantified on 4 separate occasions (n=5). Reliability of the pTT (15 min rest, 40 minutes cycling at 50% normoxic VO2peak) was assessed across 3 repeat normoxic (N; FIO2 ≈ 0.21; n=6) and 3 repeat hypoxic (FIO2 ≈ 0.14; n = 6) trials. All exercise trials were undertaken at the same time of day, following exercise and dietary controls, 7 days apart. Results. Intra-class correlation coefficients (ICC’s) for mean and peak HR, SpO2, VE , VO2 , VCO2 and BLa within each trial were improved from HST1 to HST2 (mean data: 0.99, 0.95, 0.75, 0.62, 0.70, 0.90; peak data: 0.98, 0.96, 0.64, 0.69, 0.74, 0.75) to HST2 and HST3 (ICC = 0.99, 0.97, 0.82, 0.85, 0.87 and 0.96 respectively). mHSP70 was a reproducible at rest without (ICC > 0.95) and with HSTs conducted in the previous 7 days (ICC > 0.95), with no difference in pre to post increases in mHSP70 observed between tests. The reliability for time to pTT completion was improved following one trial, and the CV (test 2 vs. 3) was similar under normoxic (CV = 0.62) and hypoxic conditions (CV = 0.63). Conclusion. Cardiorespiratory and cellular responses to the HST were reproducible and the pTT performance time reliable in both N and H. Since the reproducibility of the measurements in HST trials and reliability of pTT improved between the second and third trials one familiarization visit is recommended prior to employing these protocols in future studies.
How are functionally similar code clones syntactically different? An empirical study and a benchmark
Authors: Wagner Stefan , Abdulkhaleq Asim , Bogicevic Ivan , Ostberg Jan-Peter , Ramadani Jasmin
Published: January 2018

Background. Today, redundancy in source code, so-called “clones”, caused by copy&paste can be found reliably using clone detection tools. Redundancy can arise also independently, however, caused not by copy&paste. At present, it is not clear how only functionally similar clones (FSC) differ from clones created by copy&paste. Our aim is to understand and categorise the syntactic differences in FSCs that distinguish them from copy&paste clones in a way that helps clone detection research. Methods. We conducted an experiment using known functionally similar programs in Java and C from coding contests. We analysed syntactic similarity with traditional detection tools and explored whether concolic clone detection can go beyond syntax. We ran all tools on 2,800 programs and manually categorised the differences in a random sample of 70 program pairs. Results. We found no FSCs where complete files were syntactically similar. We could detect a syntactic similarity in a part of the files in < 16 % of the program pairs. Concolic detection found 1 of the FSCs. The differences between program pairs were in the categories algorithm, data structure, OO design, I/O and libraries. We selected 58 pairs for an openly accessible benchmark representing these categories. Discussion. The majority of differences between functionally similar clones are beyond the capabilities of current clone detection approaches. Yet, our benchmark can help to drive further clone detection research.
Checklist of botanical collections from San Damián district (Huarochirí province, Lima department, Peru)
Authors: Molinari-Novoa Eduardo Antonio , Sánchez Ocharan Carlos E , Anaya Araujo Tatiana Giannina , Mayta Anco Luis Fernando , Carpio Lau Jessica Natalia , Mendoza Tincopa Miguel Enrique
Published: January 2018

A list with the names of miscellaneous botanical collections made by the authors in San Damián district (Huarochirí province, Lima department), in Central Peru, is provided. Most reported species are rosids, and will be thoroughly treated later. We report more than fifty records for the general flora of the place, including asterids, rosids, grasses and lichens. The present work is a support document for the License thesis of the first author, where further explanations and insights are to be provided.
The orange spotted cockroach (Blaptica dubia, Serville 1839) is a permissive experimental host for Francisella tularensis
Authors: Eklund Bridget E , Gilson Tricia , Mahdi Osama , Huntley Jason F , Horzempa Joseph , Fisher Nathan A
Published: January 2018

Francisella tularensis is a zoonotic bacterial pathogen that causes severe disease in a wide range of host animals, including humans. Well-developed murine models of F. tularensis pathogenesis are available, but they do not meet the needs of all investigators. Instead, researchers are increasingly turning to insect host systems to: (1) allow high-throughput that is cost-prohibitive or ethically-questionable in mammals; (2) enable studies of host-pathogen interactions when mammalian facilities are unavailable; and (3) provide valuable information about environmental persistence and transmission. However, the utility of previously-described insect hosts is limited because of temperature restriction, short lifespans, and concerns about the immunological status of insects mass-produced for other purposes. Here, we present a novel host species, the orange spotted (OS) cockroach (Blaptica dubia), that overcomes these limitations and is readily infected by F. tularensis. Intrahemocoel inoculation was accomplished using standard laboratory equipment and lethality was directly proportional to the number of bacteria injected. Disease progression differed in insects housed at low and high temperatures, a pattern indicative of a switch between virulence and transmission phenotypes. As in mammalian hosts, F. tularensis mutants lacking key virulence components were attenuated in OS cockroaches. Finally, antibiotics were delivered to infected OS cockroaches by systemic injection and controlled feeding; in the latter case, protection correlated with oral bioavailability in mammals. Collectively, these results demonstrate that this new host system should facilitate discovery of factors that control F. tularensis virulence, immune evasion, and transmission while also providing a platform for early stage drug discovery and development.
Extinctions and threats to avifaunas on oceanic islands: Tests of influences of human populations and the filter effect
Authors: Zimbler-DeLorenzo Heather , Zinner Bertram , Scheibel Ronald J , Dobson F. Stephen
Published: January 2018

Extinctions and threats of extinctions in avifaunas on oceanic islands appear to be influenced by several island characteristics and introduced mammalian predators. These predators may have caused a “filter effect”; low numbers of threatened avian species on some islands might be due to high rates of past extinctions. Using path analysis, we examined these factors and the influence of human population size (as an indicator of human activity) on the number of species extinctions and threatened bird species on islands. Human population size had substantial influences on the number of extinctions (standardized partial regression coefficient ρ = 0.315, N = 172, P = 0.0005) but not on the number of threatened species on oceanic islands (ρ = -0.061, P = 0.43), independent of the number of introductions of predator species. The number of extinctions on islands produced a significant filter effect (viz., had a negative impact; ρ = -0.186, P = 0.003) on the number of currently threatened species. The activities of human populations, including mammalian predators they introduced, have likely resulted in a greater number of bird extinctions on these islands, and producing a significant filter effect, wherein islands with larger human populations now have fewer threatened species.
The potential of using sets of specimens to handle species concepts
Authors: Baker Edward
Published: January 2018

The use of notation and concepts from mathematical set theory is investigated as a method for describing species concepts, and potentially higher level taxa. These methods may facilitate the easy databasing of species concepts, allowing the concepts themselves to become citable through the provision of unique identifiers. The increase in unique identifiers (such as Life Science Identifiers or Digital Object Identifiers) for biological specimens in recent years may make this approach more feasible than it would have been previously.
Integrated microRNA, gene expression and transcription factors signature in papillary thyroid cancer with lymph node metastasis
Authors: Ab Mutalib Nurul-Syakima , Othman Sri Noraima , Mohamad Yusof Azliana , Abdullah Suhaimi Shahrun Niza , Muhammad Rohaizak , Jamal Rahman
Published: January 2018

Background: Papillary thyroid carcinoma (PTC) is the commonest thyroid malignancy originating from the follicle cells in the thyroid. Despite a good overall prognosis, certain high-risk cases as in those with lymph node metastasis (LNM) have progressive disease and poorer prognosis. MicroRNAs are a class of non-protein-coding, 19-24 nucleotides single-stranded RNAs which regulate gene expression and these molecules have been shown to play a role in LNM. The integrated analysis of miRNAs and gene expression profiles together with transcription factors (TFs) has been shown to improve the identification of functional miRNA-target gene-TF relationships, providing a more complete view of molecular events underlying metastasis process. Objectives: We reanalyzed The Cancer Genome Atlas (TCGA) datasets on PTC to identify differentially expressed miRNAs/genes in PTC patients with LNM-positive (LNM-P) versus lymph node negative (LNN) PTC patients and to investigate the miRNA-gene-TF regulatory circuit that regulate LNM in PTC. Results: PTC patients with LNM (PTC LNM-P) has significantly shorter disease-free survival rate compared to PTC patients without LNM (PTC LNN) (Log-rank Mantel Cox test, p = 0.0049). We identified 181 significantly differentially expressed miRNAs in PTC LNM-P versus PTC LNN; 110 were upregulated and 71 were downregulated. The five topmost deregulated miRNAs were hsa-miR-146b, hsa-miR-375, hsa-miR-31, hsa-miR-7-2 and hsa-miR-204. In addition, 395 miRNAs were differentially expressed between PTC LNM-P and normal thyroid while 400 miRNAs were differentially expressed between PTC LNN and normal thyroid. We found 4 significant enrichment pathways potentially involved in metastasis to the lymph nodes namely oxidative phosphorylation (OxPhos), cell adhesion molecules (CAMs), leukocyte transendothelial migration and cytokine-cytokine receptor interaction. OxPhos was the most significantly perturbed pathway (p = 4.70E-06) involving downregulation of 90 OxPhos-related genes. Significant interaction of hsa-miR-301b with HLF, HIF and REL/NFkB transcription factors were identified exclusively in PTC LNM-P versus PTC LNN. Conclusion: We found evidence of five miRNAs differentially expressed in PTC LNM-P. Alteration in OxPhos pathway could be the central event in metastasis to the lymph node in PTC. We postulate that hsa-miR-301b might be involved in regulating LNM in PTC via interactions with HLF, HIF and REL/NFkB. To the best of our knowledge, the roles of these TFs have been studied in PTC but the precise role of this miRNA with these TFs in LNM in PTC has not been investigated.
Influence of hydroxybosentan on determination of bosentan in human plasma
Authors: Gilant Edyta , Buś - Kwaśnik Katarzyna , Domel Izabela , Kaza Michał , Rudzki Piotr J.
Published: January 2018

Bosentan is a drug used in the treatment of pulmonary arterial hypertension. Evaluation of bosentan pharmacokinetics is an important step of the drug development. The aim of our study was to evaluate bioanalytical method reliability by assessing the influence of metabolite on the determination of bosentan in human plasma. In human body, bosentan is converted to three metabolites. Hydroxybosentan is an only pharmacologically active metabolite and its maximum concentration in plasma reaches 5-8% of the bosentan’s maximum concentration. Hydroxybosentan’s elimination half-life was reported to be very similar to that of bosentan (5-6 h) or slightly greater (6-14 h). It was observed that times to reach the maximum concentrations are similar for both compounds. Combination of high-performance liquid chromatography with UV-Vis detection and liquid-liquid extraction enabled to was determine bosentan in human plasma in the range of 50-4000 ng∙mL-1. During the method validation, metabolite back-conversion was studied using human plasma samples spkied with hydroxybosentan to obtain concentration of 500 ng·mL-1. Additionally, the influence of metabolite on extraction of bosentan and the internal standard was assessed. We found that there was no influence of metabolite on determination of bosentan in developed bioanalytical method. The method was validated according to European Medicines Agency (EMA) and Food and Drug Administration (FDA) guidelines, in compliance with the principles of Good Laboratory Practice (GLP). All of the validation parameters met acceptance criteria what confirmed method’s reliability.
Direct numerical simulation of transitional pulsatile stenotic flow using Lattice Boltzmann Method
Authors: Jain Kartik
Published: January 2018

The present contribution reports direct numerical simulations of pulsatile flow through a 75% eccentric stenosis using the Lattice Boltzmann Method (LBM). The stenosis was previously studied by Varghese, Frankel, and Fischer in a benchmark computation, and the goal of this work is to evaluate the LBM and the solver Musubi for transitional flows in anatomically realistic geometries. A part of the study compares the LBM simulation results against the benchmark and evaluates the efficacy of most basic LBM scheme for simulation of such flows. The novelty lies in the computation of Kolmogorov micro-scales by performing simulations that consist of up to ∼ 700 million cells. Recommendations on the choice of spatial and temporal resolutions for simulation of transitional flows in complex geometries naturally arise from the results. The LBM results show an excellent agreement with the previously published results thereby validating the method and the solver Musubi for the simulation of transitional flows. The study suggests that with a prudent calibration of the parameters, the LB method, due to its simplicity and compute efficiency has advantages for the simulation of such flows.
Selecting the best growth model for elasmobranches
Authors: Liu Kwang-Ming , Wu Chiao-Bin , Joung Shoou-Jeng , Tsai Wen-Pei
Published: January 2018

Age and growth information is essential for accurate stock assessment of fish, and growth model selection may influence the result of stock assessment. Previous descriptions of the age and growth of elasmobranches relied mainly on the von Bertalanffy growth model (VBGM). However, it has been noted that sharks, skates and rays exhibit significant variety in size, shape, and life-history traits. Given this variation, the VBGM may not necessarily provide the best fit for all elasmobranches. This study attempts to improve the accuracy of age estimates by testing four growth models—the VBGM, two-parameter VBGM, Robertson (Logistic) and Gompertz models—to fit observed and simulated length-at-age data for 37 species of elasmobranches. The best growth model was selected based on corrected Akaike’s Information Criterion (AICc), the AICc difference, and the AICc weight. The VBGM and two-parameter VBGM provide the best fit for species with slow growth and extended longevity (L∞ > 100 cm TL, 0.05 < k < 0.15 yr-1), such as pelagic sharks. For fast-growing small sharks (L∞ < 100 cm TL, kr or kg > 0.2 yr-1) in deep waters and for small-sized demersal skates/rays, the Robertson and the Gompertz models provide the best fit. The best growth models for small sharks in shallow waters are the two-parameter VBGM and the Robertson model, while all the species best fit by the Gompertz model are skates and rays.
Genome-wide analyses reveal clustering in Cannabis cultivars: the ancient domestication trilogy of a panacea
Authors: Henry Philippe
Published: January 2018

In the present research, I used an open access data set (Medicinal Genomics) consisting of nearly 200'000 genome-wide single nucleotide polymorphisms (SNPs) typed in 28 cannabis accessions to shed light on the plant's underlying genetic structure. Genome-wide loadings were used to sequentially cull less informative markers. The process involved reducing the number of SNPs to 100K, 10K, 1K, 100 until I identified a set of 42 highly informative SNPs that I present here. The two first principal components, encompass over 3/4 of the genetic variation present in the dataset (PCA1 = 48.6%, PCA2= 26.3%). This set of diagnostic SNPs is then used to identify clusters into which cannabis accession segregate. I identified three clear and consistent clusters; reflective of the ancient domestication trilogy of the genus Cannabis.
Origin of aromatase inhibitory activity via proteochemometric modeling
Authors: Simeon Saw , Spjuth Ola , Lapins Maris , Nabu Sunanta , Prachayasittikul Virapong , Wikberg Jarl ES , Nantasenamat Chanin
Published: January 2018

Aromatase, which is a rate-limiting enzyme that catalyzes the conversion of androgen to estrogen, plays an essential role in the development of estrogen-dependent breast cancer. Side effects due to aromatase inhibitors (AIs) necessitate the pursuit of novel inhibitor candidates with high selectivity, lower toxicity and increased potency. Designing a novel therapeutic agent against aromatase could be achieved computationally by means of ligand-based and structure-based methods. For over a decade, we have utilized both approaches to design potential AIs for which quantitative structure-activity relationship and molecular docking were used to explore inhibitory mechanisms of AIs towards aromatase. However, such approaches do not consider the effects that aromatase variants have on different AIs. In this study, proteochemometrics modeling was applied to analyze the interaction space between AIs and aromatase variants as a function of their substructural and amino acid features. Good predictive performance was achieved, as rigorously verified by 10-fold cross-validation, external validation, leave-one-compound-out cross-validation, leave-one-protein-out cross-validation and Y-scrambling tests. The investigations presented herein provide important insights into the mechanisms of aromatase inhibitory activity that could aid in the design of novel potent AIs as breast cancer therapeutic agents.
Environmental challenges may impact on somatic repair
Authors: Kyriazis Marios
Published: January 2018

During the process of ageing there is canalisation of repair resources which tend to flow from the soma towards the germ line. In the early periods of phylogenetic development there was a time when repair of germ line cells became more efficient compared to the repair of somatic cells. The level of somatic repair became just enough to ensure that the organism reached sexual maturity. It was the biological equivalent of the mathematical bifurcation, when the pathway developed preferentially towards the germ line attractor. We are now looking for evidence that this could be changing, that we may be witnessing a phase transition from effective germ line repair to an effective somatic repair. Here I consider mechanisms of fidelity-preservation which may be present in the germ line, and examine the possibility that these may be made to operate upon somatic cells instead. Mechanisms which safeguard the reliability of germ line repair and ensuring robustness/resilience in the germ line may also (or instead) be applicable upon somatic material (cells and molecules, factors) and ensure a continually effective repair of this somatic material. Thus the ability to continually repair and maintain somatic organic material within biological systems is not lost. Continual challenges from the environment ensure that the flow of information remains active and it persistently stimulates the ability to repair the soma. Apart from germ line cells, some unicellular organisms such as bacteria maintain their ability for ongoing repairs, a fact that indicates that, in principle, senescence is not unavoidable.
Molecular barcoding of red algae in the Cantabrian Sea reveals the presence of exotic asian seaweeds (Pachymeniopsis gargiuli, Grateloupia imbricata Holmes and Grateloupia turuturu Yamada)
Authors: Montes Marcos , Rico Jose Manuel , García-Vazquez Eva , Borrell Pichs Yaisel J.
Published: January 2018

Introduction of exotic species may cause serious consequences for marine ecosystems. On the shores of the Cantabrian Sea (North of Spain) there is no routine examinations of seaweeds combining molecular and morphological methods for early detection of exotic species and thereby to assess in early stages their establishment and expansion processes as a result of anthropogenic activities (e.g.: shipping, aquaculture, etc). In this work we conducted molecular barcoding (COI and RbcL genes) of red algae collected in Asturias, Bay of Biscay (Gijón and Candás harbours). The results reveal the presence of the exotic Asian seaweeds (Pachymeniopsis gargiuli, Grateloupia imbricata Holmes and Grateloupia turuturu Yamada). This study constitutes the first report where the presence of these asian algae in this area of the Bay of Biscay is confirmed. The work demonstrates the success in combining morphological and genetic methods in the early detection of exotic algae and proposes that the "molecular barcoding" must be made primarily using the Rbcl gene. The COI Databases are still incomplete and imprecise to obtain successful results in red algae species-level identifications.
Dopamine modulates synaptic transmission in the premotor nuclei of songbirds
Authors: Wang Songhua , Liu Shaoyi , Liao Congshu , Meng Wei , LI Dongfeng
Published: January 2018

Songbirds, such as zebra finches, contribute to explore behaviors underlying neural activities. Birdsong is controlled by the song system. The robust nucleus of the arcopallium (RA) is a key nucleus for producing birdsong in the song system. The RA receives dopaminergic （DArgic） inputs from the midbrain, however, the function of these inputs involved excitatory synaptic transmission is still unclear. Excitatory synaptic transmission is critical in the signal integration activities of the brain. We examined the effects of dopamine (DA) on excitatory synaptic transmission of the projection neurons in the RA of adult male zebra finches, using whole-cell recording technique. We found that DA (100 μM) decreases the frequency of spontaneous and miniature excitatory postsynaptic currents (sEPSCs/mEPSCs). In our further study, these effects of DA were reversed by the D1-like dopamine receptor (D1R) antagonist and stimulated by a D1R agonist. However, a D2-like dopamine receptor (D2R) has no influence on the effects of DA. These results demonstrate that DA can inhibit excitatory synaptic transmission mainly via activation of D1R in adult male zebra finches.
Evolution of b-type cytochromes in prokaryotes
Authors: Koumandou Vassiliki Lila , Kossida Sophia
Published: January 2018

Prokaryotes use a wide variety of bioenergetic pathways but the order of emergence of these pathways and their evolutionary relationships are still unresolved issues. In this study we focus on the evolutionary relationships of different families of b-type cytochromes, which form part of a variety of bioenergetic enzymes (the cytochrome b6f complex, ubiquinol and menaquinol reductases, formate dehydrogenase, Ni/Fe-hydrogenase, and succinate dehydrogenase). We use data from 272 species of fully sequenced bacteria and archaea, which represent the full diversity of prokaryotic lineages and multiple bioenergetic modes, to examine the distribution of these cytochromes across lineages, and ask the question of whether sequences from different species cluster by cytochrome-b family, by bioenergetic mode or by taxonomic group. Different cytochrome-b types are found in many lineages of the bacteria and archaea, and form distinct groups in phylogenetic analysis, which indicates an ancient origin for this complex, and diversification of different cytochrome-b types before the diversification of lineages. We find that species do not cluster based on bioenergetic mode. We also re-examine data from previous studies using this expanded sample of organisms spanning the full diversity of prokaryotic lineages. Concerning the b6f complex of photosynthetic organisms, our expanded phylogenies do not show significant bootstrap support for a "green clade" of cytochrome b6; also, the split form of b6 is not monophyletic, indicating that the split form arose independently multiple times. We also present data on the similarities between prokaryotic and eukaryotic cytochrome b561 sequences, in light of the recently reported structure of eukaryotic cytochrome b561.
Rethinking childhood adversity in chronic fatigue syndrome
Authors: Clark James E , Davidson Sean , Maclachlan Laura , Lynn Megan , Newton Julia L , Watson Stuart
Published: January 2018

Objectives: Previous studies have consistently shown increased rates of childhood adversity in chronic fatigue syndrome (CFS). However, such aetiopathogenic studies of CFS are potentially confounded by co-morbidity and misdiagnosis particularly with depression. We used a modelling approach with existing data and data generated in our examination of the rates of childhood adversity in a sample of CFS patients who had no lifetime history of depression. Methods: The childhood trauma questionnaire (CTQ) was completed by a sample of 52 participants and 19 controls with chronic fatigue syndrome who did not meet criteria for a psychiatric disorder (confirmed using the Structured Clinical Interview for DSM-IV). Subsequently, Mediation Analysis (Baye’s Rules) was used to establish the risk childhood adversity poses for CFS with and without depression. Results: In a cohort of CFS patients with depression robustly excluded, CTQ scores were markedly lower than in all previous studies and, in contrast to these previous studies, not increased compared with healthy controls. Post-hoc analysis showed that CTQ scores correlated with the number of depressive symptoms during the lifetime worst period of low mood. The probability of developing CFS given a history of childhood trauma was shown to be 4%, a two-fold increased risk compared to the general population. However, much of this risk is mediated by the concomitant development of major depression. Discussion: The data suggests that previous studies showing a relationship between childhood adversity and CFS may be mediated by depression
Mass spectrometry-based profiling of the carbon starved Escherichia coli proteome reveals upregulation of stress-inducible pathways implicated in biofilm formation and antibiotic resistance
Authors: Aimbetov Rakhan , Ogryzko Vasily
Published: January 2018

Starvation is a complex adaptive response to insufficiency of nutrients that has been known to implicate a number of stress networks, and modulate pathogenicity and antibiotic resistance in bacteria. However, naturally occurring abrupt elimination of nutrients and prolonged periods of their complete absence, e.g. when bacteria are placed in natural or artificial water reservoirs, are qualitatively different from in-culture late stationary phase energy source diminution. Despite the obvious importance of proteomic investigation of bacteria exposed to nutrient deficiency, no comprehensive study on the subject has been published. In order to address the said shortage of knowledge, we decided to quantitatively look into the proteome-level alterations elicited by the complete lack of nutrients that constitute a viable source of carbon, i.e. carbon starvation, in the Escherichia coli HT115-derived SLE1 strain cells using the combination of label-free and SILAC-based proteomics. As a result, we obtained protein ratios for 1,757 and 1,241 protein groups for each technique respectively, 2D-annotated the quantifiable proteins present in both datasets, identified over- and underrepresented Gene Ontology terms, and isolated protein groups ≥2-fold up- and downregulated in response to carbon starvation (44 and 36 protein groups respectively). We observed upregulation of proteins implicated in various stress-related networks, most notably those that constitute the Gene Ontology term 'Biological adhesion', as well as various terms related to stress. Additionally, we identified several uncharacterized proteins, and our report is the first to ascribe them to a stress-induced proteome. Our data are available via ProteomeXchange with identifier PXD003255 and DOI:10.6019/PXD003255.
Realities of rarity: climatically and ecologically restricted, critically endangered Kandian Torrent Toads (Adenomus kandianus) breed en masse
Authors: Meegaskumbura Madhava , Wijayathilaka Nayana , Abayalath Nirodha , Senevirathne Gayani
Published: January 2018

Endemic to Sri Lanka, genus Adenomus contains two torrent-associated toad species whose ecology and natural history in the wild is virtually unknown. Adenomus kelaartii is relatively common, with a wide geographic distribution. Its sister species, A. kandianus, however, is restricted to two isolated populations in fast-disappearing montane and sub-montane forests. Formally declared extinct after not being recorded for over a century, following several years of surveying, a few A. kandianus were found in 2012 and referred to as "the world's rarest toad." However, tadpoles of A. kandianus bearing unique ventral suckers were soon discovered, but the rarity of the adult and the profusion of tadpoles were never explained. Here, using ecological methods, niche modeling and DNA-barcoding, we aim to understand the ecology, natural history and distribution of this rare toad. Following a two-year study of occurrence, habits and habitat associations of adults and larvae, we show this to be a secretive species with a patchy distribution. During non-mating periods female toads (N = 23) were found in primary forests habitat up to 650 m away from the breeding streams, and predominantly males in the riparian zone (12 males, 2 females). Following heavy rain they form large (N = 388) but patchy mating congregations in torrential streams (six sites; range 0−95 mating pairs; mean = 25, SD = 38.16, CV = 152%). Amplexed pairs swim synchronously, enabling them to traverse fast currents. Egg-laying sites remain unknown, but ability to dive, vocalize underwater, and characteristics of the eggs, suggests that they lay eggs in dark recesses of the stream. Quadrat sampling of tadpoles show microhabitat partitioning (in depth, flow-rate and substrate conditions) within the stream: the greatest diversity of larval developmental stages (25-42) in slow-flowing (depth, 0.75−1.5 m) rocky areas; more robust stages (31−39) bearing sucker discs utilise rocky-rapids (depth, 0.25−0.75 m); metamorphic stages (43-45) use stream margins (depth, <0.25 m); slow flowing silt covered areas of the stream were unoccupied, irrespective of the depth. DNA barcoding of the 16S rRNA gene fragment from the two known localities confirms the identity of the Pedro population also as A. kandianus. The uncorrected pairwise genetic distance of 0.1−0.7% suggests historical gene flow between the two populations. Distribution modeling (using MaxEnt), with forest-cover layers added, predicts a very small remaining area of suitable habitats (an area of occupancy of 16 km2 and an extent of occurrence of 128 km2) isolated by habitats that are not conducive to these toads. While the healthy population recorded at one site gives hope for the survival of the species, long-term conservation of this climatically and ecologically restricted species hinges largely on the preservation of cloud and riparian forests and the unpolluted high-flow torrents.
A method for quantifying, visualising, and analysing gastropod shell form
Authors: Liew Thor-Seng , Schilthuizen Menno
Published: January 2018

Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genus Opisthostoma, which exhibit great variability in shell form. The outcome suggests that our method is more robust, reproducible, and versatile than the conventional traditional and geometric morphometric approaches for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.
A method for quantifying, visualising, and analysing gastropod shell form
Authors: Liew Thor-Seng , Schilthuizen Menno
Published: January 2018

Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genus Opisthostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approach for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.
Reproductive biology of the biofuel plant Jatropha curcas in its center of origin
Authors: Rincón-Rabanales Manuel , Vargas-López Laura I. , Adriano-Anaya Lourdes , Vázquez-Ovando Alfredo , Salvador-Figueroa Miguel , Ovando-Medina Isidro
Published: January 2018

In this work, we studied the main characteristics of flowering, reproductive system and diversity of pollinators for the biofuel plant Jatropha curcas (L.) in a site of tropical southeastern Mexico, within its center of origin. The plants were monoecious with inflorescences of unisexual flowers. The male flowers produced from 3062 to 5016 pollen grains (266-647 per anther). The plants produced fruits with both geitonogamy and xenogamy, although insect pollination significantly increased the number and quality of fruits. A high diversity of flower visiting insects (36 species) was found, of which nine were classified as efficient pollinators. The native stingless bees Scaptotrigona mexicana (Guérin-Meneville) and Trigona (Tetragonisca) angustula (Latreille) were the most frequent visitors and their presence coincided with the hours when the stigma was receptive. It is noteworthy that the female flowers open before the male flowers, favoring xenogamy, which may explain the high genetic variability reported in J. curcas for this region of the world.
Further spreading of the non-indigenous bryozoan Celleporaria brunnea in the Mediterranean Sea: port to port morphological variations
Authors: Ferrario Jasmine , Marchini Agnese , Marić Martina , Minchin Dan , Occhipinti-Ambrogi Anna
Published: January 2018

The Pacific cheilostome bryozoan Celleporaria brunnea (Hincks, 1884), a non-indigenous species already known for the Mediterranean Sea, was recorded in 2013-2014 from nine Italian port localities (Genoa, Santa Margherita Ligure, La Spezia, Leghorn, Viareggio, Olbia, Porto Rotondo, Porto Torres and Castelsardo) in the North-western Mediterranean Sea; in 2014 it was also found for the first time in the Adriatic Sea, in the marina “Kornati”, Biograd na Moru (Croatia). In Italy, specimens of C. brunnea were found in 44 out of 105 samples (48% from harbour sites ad 52% from marinas). These data confirm and update the distribution of C. brunnea in the Mediterranean Sea, and provide evidence that recreational boating is a vector responsible for the successful spread of this species. Previous literature data have shown the existence of differences in orifice and interzooidal avicularia length and width among different localities of the invaded range of C. brunnea. Therefore, measurements of orifice and avicularia were assessed for respectively 30 zooids and 8 to 30 interzooidal avicularia for both Italian and Croatian localities, and compared with literature data, in order to verify the existence of differences in the populations of C. brunnea that could reflect the geographic pattern of its invasion range. Our data show high variability of orifice measures among and within localities: zooids with broader than long orifice coexisted with others displaying longer than broad orifice, or similar values for both length and width. The morphological variation of C. brunnea in these localities, and above all the large variability of samples within single localities or even within colonies poses questions on the reliability of such morphometric characters for inter and intraspecific evaluations.
Enriching scientific publications with interactive 3D PDF: An integrated toolbox for creating ready-to-publish figures
Authors: Newe Axel
Published: January 2018

Three-dimensional (3D) data of many kinds is produced at an increasing rate throughout all scientific disciplines. The Portable Document Format (PDF) is the de-facto standard for the exchange of electronic documents and allows for embedding three-dimensional models. Therefore, it is a well suited medium for the visualization and the publication of this kind of data. The generation of the appropriate files has been cumbersome so far. This article presents the first release of a software toolbox which integrates the complete workflow for generating 3D model files and ready-to-publish 3D PDF documents for scholarly publications in a consolidated working environment. It can be used out-of-the-box as a simple working tool or as a basis for specifically tailored solutions. A comprehensive documentation, an example project and a project wizard facilitate the customization. It is available royalty-free and for Windows, MacOS and Linux.
MonoPhy: A simple R package to find and visualize monophyly issues
Authors: Schwery Orlando , O'Meara Brian C
Published: January 2018

Background. The monophyly of taxa is an important attribute of a phylogenetic tree, as a lack of it may hint at shortcomings of either the tree or the current taxonomy and can misguide subsequent analyses. While monophyly is conceptually simple, it is manually tedious and time consuming to assess on modern phylogenies of hundreds to thousands of species. Results. The R package MonoPhy allows assessment and exploration of monophyly of taxa in a phylogeny. It can assess the monophyly of genera using the phylogeny only, and with an additional input file, any other desired higher taxa or unranked groups can be checked as well. Conclusion. Summary tables, easily subsettable results and several visualization options allow quick and convenient exploration of monophyly issues, thus making MonoPhy a valuable tool for any researcher working with phylogenies.
A primer on regeneration
Authors: Rouhana Labib , Tasaki Junichi
Published: January 2018

Centuries of observation have uncovered a diverse range of organisms capable of overcoming loss of tissue. The act of restoring lost anatomy and function is known as regeneration, and it is broadly represented in both plant and animal kingdoms. Cumulative studies have identified a series of events that take place during regeneration of complex animal structures. First, the organism recognizes damage and undergoes wound healing. Then, programmed cell death in the vicinity of the damaged tissue precedes proliferation and migration of cells that foster the development of replacement tissue. Finally, rearrangement of pre-existing tissue and integration with newly differentiated cells take place to restore the function and proportionality displayed previous to damage . Although the ability to regenerate is believed to be ancestrally common and lost throughout evolution, there is significant heterogeneity of some basic mechanisms displayed during regeneration in different animal species. Perhaps one of the most noticeable differences is the cellular source contributing to formation of the new tissue during regeneration. Organisms such as planarians and Hydra rely on active reservoirs of somatic pluripotent stem cells abundantly distributed throughout their bodies and maintained throughout their life. On the other hand, vertebrates rely mostly on progenitor cell activation and dedifferentiation, to regenerate cells with limited potential to regenerate specific structures. However, not all regenerative events rely on cellular replacement. Leading edge research has begun to uncover mechanisms involved in autonomous repair and functional regeneration of single cells – be it neurons or ciliated protozoa. The fact that organisms can achieve regeneration through diverse cellular sources is remarkable, but just as remarkable is the possibility that conserved molecular pathways could be activated to achieve regeneration in different species. Analysis of these pathways will contribute to understanding human development and potential avenues for regenerative medicine.
The sex lives of ctenophores: the influence of light, body size, and self-fertilization on the reproductive output of the sea walnut, Mnemiopsis leidyi
Authors: Sasson Daniel A , Ryan Joseph F
Published: January 2018

Ctenophores (comb jellies) are emerging as important animals for investigating fundamental questions across numerous branches of biology (e.g., evodevo, neuroscience. and biogeography). Several ctenophore species including, most notably, Mnemiopsis leidyi, are known as invasive species, adding to the importance of studying the ecology of these animals. Despite the growing interest, relatively little is known about ctenophore reproduction. Like most ctenophores, M. leidyi is a simultaneous hermaphrodite capable of self-fertilization. In this study, we assess the influence of light on spawning, the effect of body size on spawning likelihood and reproductive output, and the cost of self-fertilization on egg viability in M. leidyi. Our results suggest that M. leidyi spawning is more strongly influenced by circadian rhythms than specific light clues, and that body size significantly impacts spawning and reproductive output. We also find a lower percentage of viable embryos from M. leidyi that were spawned alone versus those that were spawned in pairs, suggesting that self-fertilization may be costly in these animals. These results provide critical insight into the reproductive ecology of these ctenophores and provide a fundamental resource for researchers working with M. leidyi in the laboratory.
Certified Family Service Coordinator: A model for professional practice and recognition
Authors: Stouder Donald B.
Published: January 2018

The use of the Family Service Coordinator is still a relative newcomer to the organ procurement/transplantation field. Since no comprehensive training and recognition program exists, Lifesharing, A Donate Life Organization, decided to develop a Certified Family Service Coordinator program. We defined the goals of the program as 1) to improve the care we provide to our families and increase consent for organ donation; 2) to streamline and standardize our best practices; 3) to learn new skills and improve individual understanding and practice; 4) to share our own wealth of experience; and 5) to provide professional certification and recognition. In addition, given the limitations of time and resources that affect most organ procurement organizations, we wanted to see if a comprehensive training program could be developed using resources that were easily and inexpensively acquired on the Internet.