bluuebunny/crossref_metadata_2025 huggingface dataset:
What doesn’t kill them makes them stronger: An association between elongation factor 1-α overdominance in the sea star Pisaster ochraceus and "sea star wasting disease”
Authors: Wares John P. , Schiebelhut Lauren M
Published: January 2018

In recent years, a massive plague has killed millions of sea stars, of many different species, along the Pacific coast of North America. This disease, known as 'sea star wasting disease' (SSWD), is thought to be caused by viral infection. In the affected sea star Pisaster ochraceus, previous work had identified that the elongation factor 1-α (EF1A) locus harbored an intronic insertion allele that is lethal when homozygous yet appears to be maintained at moderate frequency in populations through increased fitness for heterozygotes. The environmental conditions supporting this increased fitness are unknown, but overdominance is often associated with disease. Here, we evaluate populations of P. ochraceus to identify the relationship between SSWD and EF1A genotype. Our data suggest that there may be significantly decreased infection or mortality rates in individuals that are heterozygous at this locus. These results suggest further studies to understand the functional relationship between diversity at EF1A and survival in P. ochraceus.
rotl, an R package to interact with the Open Tree of Life data
Authors: Michonneau François , Brown Joseph W. , Winter David
Published: January 2018

1. 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. 2. 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. 3. 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. Here, and in the vignettes accompanying the package, we demonstrate how rotl can be used with other R packages to analyze biodiversity data. 4. As phylogenies are being used in a growing number of applications, rotl facilitates access to phylogenetic data, and allows their integration with statistical methods and data sources available in R.
Public health semantics of the YY paradox
Authors: Mishra Mili , Srivastava Anup K , Srivastava Vinod K
Published: January 2018

Background: Body Mass Index (BMI) has lost its credibility as an indicator of fatness. 3D scan and body composition details of Yajnik and Yudnik, the authors with similar BMI but very different body fat percentage was labelled as ‘YY paradox’. 3D scanners are not widely available; as such dependence on less specific tools is still high. It was assumed that such paradoxes may frequently occur in anthropometrically derived body composition indices and paucity of such information prompted us to explore the nature and usage of YY paradox. Methods: Body composition of 89 medical students from North India was studied using bioelectric-impedance fat monitor and anthropometric techniques. YY phenomenon were identified and studied in 1) same BMI but different body fat (Classic YY), 2) same BVI but different BMI (yy BVI~BMI), 3) same Skeletal mass/body fat but different body volume (yy SKM/BF ~ BV) and 4) same Lean Body mass/body fat but different body volume (yy LBM/BF ~ BV). Results: The study population comprised young adults aged 18 -26 years. Males comprised 51.7 % of the study group. YY phenomenon was found in 44 individuals with respect to same BMI but different body fat; 47 individuals of same BVI but different BMI. Of all the indices studied, lowest number of YYs were found in yy LBM/BF ~ BV index. 14.6% study subjects had high visceral fat. Odds Ratio (OR) for high visceral fat in all the studied indices among subjects showing yy-phenomenon and those not showing yy-phenomenon revealed an OR of 1.09 (CI 0.3-3.7) for yy LBM/BF ~ BV index. This suggests that high visceral fat (VF) is the same in both groups and implies that there is no difference between the two arms i.e., YY and non-YY group contains approximately similar proportion of subjects with high VF. Conclusion: We found a high frequency of such paradoxes in this population and also demonstrated that these are not normally distributed. It is also suggested that a deeper look in this issue could be used for deriving predictive models for disease linked anthropometric markers.
Attending and inhibiting stimuli that match the contents of visual working memory: Evidence from eye movements and pupillometry
Authors: Mathôt Sebastiaan , Van Heusden Elle , Van der Stigchel Stefan
Published: January 2018

When you keep a red apple in working memory, your attention is usually—but not always—attracted by other red objects. The conditions under which the contents of visual working memory guide visual attention are still unclear. Here we tested whether attention is indeed biased toward memory-match stimuli, and, if so, whether this bias is transient or sustained. We used a new pupillometric technique, which exploits that the pupil is larger when you covertly attend to dark, compared to bright, stimuli. This allowed us to test whether and when attention was biased toward memory-match stimuli, by placing them either on a dark or a bright background, while measuring pupil size over time. We found that the eyes were captured by memory-match probes early on in the trial. However, the pupillary data suggested that there was no sustained attention bias toward memory-match probes later in time; rather, attention appeared to be biased away from them. Together, our results suggest that: (1) memory-match stimuli automatically capture attention; but (2) they do so only briefly; and (3) they may even become inhibited later in time.
Effects of shoreline oiling on salt marsh epifaunal macroinvertebrates
Authors: Deis Donald R , Fleeger John W , Bourgoin Stefan M , Mendelssohn Irving A , Lin Qianxin , Hou Aixin
Published: January 2018

The Deepwater Horizon oil spill resulted in varying degrees of oiling in the salt marshes of northern Barataria Bay, Louisiana, USA. This study examines the effects of oiling intensity and recovery on two conspicuous marsh-platform macroinvertebrates, Uca spp., fiddler crabs, and Littoraria irrorata, the salt marsh periwinkle, from 2.5 to 4.5 years after the spill. The dominant fiddler crab within these marshes, Uca longisignalis, was the only species observed in field collections, and no significant difference in burrow density or burrow size was found among oiling levels over the study period indicating recovery from any negative effects of oiling already occurred for this species. The highest density of L. irrorata was found at moderately oiled sites compared to both reference (without visible oiling) and heavily oiled stations. Spartina alterniflora density recovered within two years after the spill at the moderately oiled stations facilitating recovery of L. irrorata approximately one year later. L. irrorata average shell length and length-frequency distributions were equivalent at moderately oiled and reference stations but snails were shorter at heavily oiled stations because of a greater proportion of subadults. Shell length data from the heavily oiled sites indicate that direct mortality due to oiling or oil-induced reductions in recruitment occurred in 2010 and that recovery was starting to occur at 48 months after the spill. The extent and duration of oil in the water during the spill and the biological responses we measured indicates that L. irrorata and Uca longisignalis were both affected in their ability to carry out their life cycle on the marsh and/or in the water column at all stations including the reference stations for some period following the entry of oil into the region.
Open Access dynamics and prospects
Authors: Grynkiewicz Grzegorz , Filip Katarzyna
Published: January 2018

The www has started a new era in dissemination of scientific information, which is already to such extent propagated by electronic media that it has become practically independent from the system of subscription driven printed journals. These developments of marked increase in availability of scientific information, commonly described as Open Access, have profound consequences for functioning of all segments of scientific community and also strategically influence education systems. Generally, there are growing expectations for freely available results of publicly funded research. Open Access (OA), which is developing for ca 25 years, has generated a number of large publishers (i.e. BioMedCentral) and over 5 000 of scholarly peer reviewed journals, which can be checked in the Directory of Open Access Journals (DOAJ; https://doaj.org/). Leaving aside new types of business models which evolved in connection with widespread of electronic publishing, we will analyze the OA phenomenon from the point of view of an active life science researcher, as a reader and an author. Thus, the OA “for profit” publishing modalities, distinguished as “green route” and “gold route” will be presented as well as some extracts from ongoing debate on the economics of particular variants. Finally, the question of choice between publishing options for prospective results in getting cited, will be touched upon.
Evaluation of candidate reference genes for expression study in Saccharum spp. hybrids under heavy metal stress
Authors: Ling Hui , Huang Ning , Xu Liping , Huang Long , Wu Qibin , Guo Jinlong , Su Yachun , Que Youxiong
Published: January 2018

Heavy metal contamination has been a significant problem limiting agricultural development, but sugarcane has recently emerged as a valuable phytoremediator. To better understand the molecular mechanism behind sugarcane's metal tolerance, it is necessary to analyze the expression of a novel gene(s) by qRT-PCR. Importantly, introducing internal reference gene(s) should be selected based upon gene stable expression, the inclusion of which could enhance both the accuracy and reliability of this method. In this study, 13 candidate genes were selected and evaluated stability of each genes. The results derived by statistical algorithms were then validated by normalizing the expression of metal related gene ScMTP (GenBank Accession No. KP864146), ScMT2-1-3 (GenBank Accession No. JQ627644), ScMPP (GenBank Accession No. CA267392.1) and ScHMA1 (GenBank Accession No. CA156665.1). Collectively, our qRT-PCR results indicated that in heavy metal-exposed sugarcane, APRT was the better single internal control in expression quantification. Moreover, the combination of CAC + CUL provide for a more accurate normalization for gene transcript profiles under these same conditions. The gene expression quantification that included APRT and CAC + CUL suggested that ScMTP had a differential expression pattern, ScMT2-1-3 and ScMPP were slightly inhibited, and ScHMA1 had minimal induction of expression in response to Cd2+ and Cu2+ stresses in sugarcane. Taken together, the suitable reference genes identified in this study will benefit future work aimed at the sugarcane gene functional characterization.
Relative contribution of ecological and biological attributes in the fine-grain structure of ant-plant networks
Authors: Díaz-Castelazo Cecilia , Rico-Gray Victor
Published: January 2018

Background. Ecological communities of interacting species analyzed as complex networks, revealed that species dependence on their counterpart is more complex than expected at random. For ant-plant networks (mediated by extrafloral nectar), links among species are asymmetric (nested), forming a core of generalist species. Proposed factors affecting network organization include encounter probability (species abundances, habitat heterogeneity), behavior, phylogeny and body size. While the importance of underlying factors that influence structure of ant-plant networks have been separately explored, simultaneous contribution of several biological and ecological attributes inherent to the species, guild or habitat level have not been addressed. Methods. For a tropical seasonal site we recorded frequency of pairwise ant-plant interactions mediated by extrafloral nectaries, attributes of interacting species, habitat attributes, cover of plants with EFNs, and studied the resultant network structure. We addressed for the first time the role of mechanistic versus neutral determinants at the “fine-grain” structure (pairwise interactions) of ant-plant networks, studying the simultaneous contribution of several plant, ant, and habitat attributes in prevailing interactions as well as in overall network topology (community). Results. Our studied network was highly-nested, non-modular, with core species in general having high species strengths (higher strength values for ants than plants) and low specialization; plants had higher dependences on their counterparts. The significant factor explaining network and fine-grain structure was habitat heterogeneity in vegetation structure (open vs. shaded habitats), with no evidence of neutral (abundance) effects. Discussion. Core ant species are relevant to most plants species at the network, the latter depending more on the former, core ants showing adaptations to nectar consumption and deterrent behavior, suggestive of potential biotic defense at a community scale. At our study site spatiotemporal heterogeneity is so strong, that emerges at community-level structural properties, depicting influence of abiotic factors in facultative mutualism. Frequent occurrence of morphologically-diverse EFNs at all habitats suggests plasticity in plant strategies for biotic defense provided by ants.
Characterization of two microsatellite PCR multiplexes for high throughput genotyping of the Caribbean spiny lobster, Panulirus argus
Authors: Truelove Nathan , Behringer Donald , Butler IV Mark , Preziosi Richard F
Published: January 2018

The spiny lobster Panulirus argus supports one of the most economically important commercial fisheries in the Caribbean, yet its sustainable management is problematic due to uncertainty regarding levels of population connectivity among Caribbean nations. We developed two microsatellite multiplex panels for P. argus to assist in future conservation genetics research studies of this important Caribbean species. Significant deviations from Hardy–Weinberg equilibrium were observed at locus Par7 in multiplex 1 and loci Fwc08 and Fwc17 in multiplex 2. No evidence of linkage disequilibrium was observed. All 12 loci were used in both microsatellite multiplexes were polymorphic, with an average of 12 alleles per locus (ranging from 3 to 29 alleles per locus) and HO ranging from 0.368 to 0.921. These two microsatellite multiplexes will be a valuable resource for ongoing and future studies of conservation genetics in the Caribbean spiny lobster, Panulirus argus.
XML schema validation using parsing expression grammars
Authors: Kuramitsu Kimio , Yamaguchi Shin'ya
Published: January 2018

Schema validation is an integral part of reliable information exchange on the Web. However, implementing an efficient schema validation tool is not easy. We highlight the use of parsing expression grammars (PEGs), a recognition-based foundation for describing syntax, and apply it to the XML/DTD validation. This paper shows that structural schema constraints in document type definitions (DTDs) can be validated by the converted PEGs with the linear time and constant space consumption. We study the performance of several existing PEG-based tools, and then confirm that the converted PEGs achieve a practical and even competitive level of performance under existing standard XML/DTD validators.
Reproducibility of cardiorespiratory and performance responses to exercise in hypoxia
Authors: Lee Ben J , Thake Charles D
Published: January 2018

Background. Knowledge of the variance in physiological performance measures between repeated trials can inform whether familiarization sessions are necessary prior to intervention studies. The purpose of this study was to assess the reliability of cardiorespiratory and exercise performance measures during both steady state hypoxic exercise and a preloaded 16.1 km hypoxic time trial. Methods. Eighteen male 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 respiratory exchange ratio; 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). Reliability of the preloaded time trial (pTT; 15 min rest, 40 minutes cycling at 50% normoxic VO2peak, 16.1km time trial) 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 blood lactate 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). 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 responses to the HST were reproducible and the pTT performance time reliable in both normoxia and hypoxia. Since the reproducibility of the measurements in HST trials and reliability of pTT improved between the second and third trials, two familiarization visit are recommended prior to employing these protocols in future studies.
Low-frequency, low-magnitude vibrations (LFLM) enhances chondrogenic differentiation potential of human adipose derived mesenchymal stromal stem cells (hASCs)
Authors: Marycz Krzysztof , Lewandowski Daniel , Tomaszewski Krzysztof A , Henry Brandon Michael , Golec Edward B , Marędziak Monika
Published: January 2018

The aim of this study was to evaluate if low-frequency, low-magnitude vibrations (LFLM) could enhance chondrogenic differentiation potential of human adipose derived mesenchymal stem cells (hASCs) with simultaneous inhibition of their adipogenic properties for biomedical purposes. We developed a prototype device that induces low-magnitude (0.3 g) low-frequency vibrations with the following frequencies: 25, 35 and 45 Hz. Afterwards, we used human adipose derived mesenchymal stem cell (hASCS), to investigate their cellular response to the mechanical signals. We have also evaluated hASCs morphological and proliferative activity changes in response to each frequency. Induction of chondrogenesis in hASCs, under the influence of a 35 Hz signal leads to most effective and stable cartilaginous tissue formation through highest secretion of Bone Morphogenetic Protein 2 (BMP-2), and Collagen type II, with low concentration of Collagen type I. These results correlated well with appropriate gene expression level. Simultaneously, we observed significant up-regulation of α3, α4, β1 and β3 integrins in chondroblast progenitor cells treated with 35Hz vibrations, as well as Sox-9. Interestingly, we noticed that application of 35 Hz frequencies significantly inhibited adipogenesis of hASCs. The obtained results suggest that application of LFLM vibrations together with stem cell therapy might be a promising tool in cartilage regeneration.
Structural and evolutionary relationships among RuBisCOs inferred from their large and small subunits
Authors: Xiang Fu , Fang Yuanping , Xiang Jun
Published: January 2018

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme to assimilate CO2 into the biosphere. The structural and evolutionary relationships among RuBisCOs were discussed at the domain level. The nonredundant sets for three superfamilies of RuBisCO, i.e. large subunit C-terminal domain (LSC), large subunit N-terminal domain (LSN) and small subunit domain (SS) were defined using QR factorization based on the structural alignment of the RuBisCO domains with QH as the similarity measure, respectively. The results suggest: (1) the core structures of LSC, LSN and SS are well conserved and homologies; (2) the LSC could have occurred naturally in both bacteria and Achaean kingdoms, and the carboxyl-terminal structure evolves increasingly complicated in both bacteria and Eukaryotae kingdoms; (3) the structural variations, such as coil structures at 67-82 positions of LSN and the βA-βB-loop of SS, could make attribution to the CO2/O2 specificity of RuBisCO from different species. Such findings provide insights on RuBisCO improvement.
Can macroalgae provide promising anti-tumoral compounds? A closer look at Cystoseira tamariscifolia as a source for antioxidant and anti-hepatocarcinoma compounds
Authors: Vizetto-Duarte Catarina , Custódio Luísa , Acosta Gerardo , Lago João H G , Morais Thiago R , Bruno de Sousa Carolina , Gangadhar Katkam N , Rodrigues Maria João , Pereira Hugo , Lima Raquel T , Vasconcelos M. Helena , Barreira Luísa , Rauter Amélia P , Albericio Fernando , Varela João
Published: January 2018

Marine organisms are a prolific source of drug leads in a variety of therapeutic areas. In the last few years, biomedical, pharmaceutical and nutraceutical industries have shown growing interest in novel compounds from marine organisms, including macroalgae. Cystoseira is a genus of Phaeophyceae (Fucales) macroalgae known to contain bioactive compounds. Organic extracts (hexane, diethyl ether, ethyl acetate and methanol extracts) from three Cystoseira species (C. humilis, C. tamariscifolia and C. usneoides) were evaluated for their total phenolic content, radical scavenging activity against DPPH and ABTS radicals, and antiproliferative activity against a human hepatocarcinoma cell line (HepG2 cells). C. tamariscifolia had the highest TPC and RSA. The hexane extract of C. tamariscifolia (CTH) had the highest cytotoxic activity (IC50=2.31 µg/mL), and was further tested in four human tumor (cervical adenocarcinoma HeLa; gastric adenocarcinoma AGS; colorectal adenocarcinoma HCT-15; neuroblastoma SH-SY5Y), and two non-tumor (murine bone marrow stroma S17 and human umbilical vein endothelial HUVEC) cell lines in order to determine its selectivity. CTH strongly reduced viability of all tumor cell lines, especially of HepG2 cells. Cytotoxicity was particularly selective for the latter cells with a selectivity index = 12.6 as compared to non-tumor cells. Incubation with CTH led to a 2-fold decrease of HepG2 cell proliferation as shown by the BrdU incorporation assay. CTH-treated HepG2 cells presented also pro-apoptotic features, such as increased Annexin V/PI binding and dose-dependent morphological alterations in DAPI-stained cells. Moreover, it had a noticeable disaggregating effect on 3D multicellular tumor spheroids. Demethoxy cystoketal chromane, a derivative of the meroditerpenoid cystoketal, was identified as the active compound in CTH and was shown to display selective in vitro cytotoxicity towards HepG2 cells.
Fuzzy based binary feature profiling for modus operandi analysis
Authors: Chamikara Mahawaga Arachchige Pathum , Galappaththi Akalanka , Yapa Roshan D , Nawarathna Ruwan D , Kodituwakku Saluka Ranasinghe , Gunatilake Jagath , Jayathilake Aththanapola Arachchilage Chathranee Anumitha , Liyanage Liwan H
Published: January 2018

It is a well-known fact that some criminals follow perpetual methods of operations, known as modus operandi (MO) which is commonly used to describe the habits in committing something especially in the context of criminal investigations. These modus operandi are then used in relating criminals to other crimes where the suspect has not yet been recognized. This paper presents a method which is focused on identifying the perpetual modus operandi of criminals by analyzing their previous convictions. The method involves in generating a feature matrix for a particular suspect based on the flow of events. Then, based on the feature matrix, two representative modus operandi are generated: complete modus operandi and dynamic modus operandi. These two representative modus operandi will be compared with the flow of events of the crime in order to investigate and relate a particular criminal. This comparison uses several operations to generate two other outputs: completeness probability and deviation probability. These two outcomes are used as inputs to a fuzzy inference system to generate a score value which is used in providing a measurement for the similarity between the suspect and the crime at hand. The method was evaluated using actual crime data and four other open data sets. Then ROC analysis was performed to justify the validity and the generalizability of the proposed method. In addition, comparison with five other classification algorithms showed that the proposed method performs competitively with other related methods.
Does sadness impair color perception? Thorstenson et al.’s plan to find out is flawed
Authors: Holcombe Alex O , Brown Nicholas JL , Goodbourn Patrick T , Etz Alexander , Geukes Sebastian
Published: January 2018

In their article reporting the results of two experiments, Thorstenson, Pazda, & Elliot (2015a) found evidence that perception of colors on the blue-yellow axis was impaired if the participants had watched a sad movie clip, relative to participants who watched clips designed to induce a happy or neutral mood. Subsequently, these authors retracted their article (Thorstenson, Pazda, & Elliot, 2015b), citing a mistake in their statistical analyses and a problem with the data in one of their experiments. Here, we discuss a number of other methodological problems with Thorstenson et al.’s experimental design, and also demonstrate that the problems with the data go beyond what these authors reported. We conclude that repeating, with minor revision, one of the two experiments, as Thorstenson et al. (2015b) proposed, will not be sufficient to address the problems with this work.
Alien vs. Predator: Pathogens open niche space for opportunists, unless controlled by predators
Authors: Welsh Rory M , Rosales Stephanie M , Zaneveld Jesse R.R. , Payet Jérôme P , McMinds Ryan , Hubbs Steven L , Vega Thurber Rebecca L
Published: January 2018

Coral microbiomes are known to play important roles in organismal health, response to environmental stress, and resistance to disease. Pathogens invading the coral microbiome encounter diverse assemblages of resident bacteria, ranging from defensive and metabolic symbionts to opportunistic bacteria that may turn harmful in compromised hosts. However, little is known about how these bacterial interactions influence the overall structure, stability, and function of the microbiome during the course of pathogen challenge. We sought to test how coral microbiome dynamics were affected by interactions between two of its members: Vibrio coralliilyticus, a known temperature-dependent coral pathogen, and Halobacteriovorax, a unique bacterial predator of Vibrio and other gram-negative bacteria. We challenged specimens of the important reef-building coral Montastraea cavernosa with Vibrio coralliilyticus pathogens in the presence or absence of Halobacteriovorax predators, and monitored microbial community dynamics with 16S rRNA gene time-series. In addition to its direct effects on corals, pathogen challenge reshaped coral microbiomes in ways that allowed for secondary blooms of opportunistic bacteria. As expected, Vibrio coralliilyticus addition increased the infiltration of Vibrio into coral tissues. This increase of Vibrios in coral tissue was accompanied by increased richness, and reduced stability (increased beta-diversity) of the rest of the microbiome, suggesting strong secondary effects of pathogen invasion on commensal and mutualistic coral bacteria. Moreover, after an initial increase in Vibrios, two opportunistic lineages (Rhodobacterales and Cytophagales) increased in coral tissues, suggesting that this pathogen opens niche space for opportunists. Based on the keystone role of predators in many ecosystems, we hypothesized that Halobacteriovorax predators might help protect corals by consuming gram-negative pathogens. In keeping with a protective role, Halobacteriovorax addition alone had only minor effects on the microbiome, and no infiltration of Halobacteriovorax into coral tissues was detected in amplicon libraries. Simultaneous challenge with both pathogen and predator eliminated detectable V. corallyticus infiltration into coral tissue samples, ameliorated changes to the rest of the coral microbiome, and prevented secondary blooms of opportunistic Rhodobacterales and Cytophagales. Thus, we show that primary infection by a coral pathogen is sufficient to cause increases in opportunists, as seen in correlational studies. These data further provide a proof-of-principle demonstration that, under certain circumstances, host-associated bacterial predators can mitigate the ability of pathogens to infiltrate host tissue, and stabilize the microbiome against complex secondary changes that favor growth of opportunistic lineages.
LC-MS method for determination of olmesartan in human plasma
Authors: Musijowski Jacek , Piórkowska Edyta , Buś - Kwaśnik Katarzyna , Tycz Agnieszka , Rudzki Piotr J.
Published: January 2018

Olmesartan belongs to a class of drugs called angiotensin II receptor blockers (ARBs). It works by relaxing blood vessels so that blood can flow more easily and is used to treat high blood pressure (hypertension). Lowering high blood pressure helps prevent strokes, heart attacks, and kidney problems. Olmesartan medoxomil is an ester prodrug that is hydrolysed during absorption from gastrointestinal tract to the active form olmesartan. Due to rapid metabolism determination of the concentration of the prodrug in plasma is impossible. Previous human pharmacokinetic studies indicated that olmesartan is the only metabolite of olmesartan medoxomil. The aim of the study was to develop a method for the determination of olmesartan in human plasma. The developed LC-MS method is linear within the range of 5.00-2500.00 ng/mL which is suitable for pharmacokinetic studies after administration of 40 mg olmesartan medoxomil single oral dose. The sample preparation procedure is fast and allows examination of large numbers of samples in a short time. 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 and the method was successfully applied in the pharmacokinetic study in humans.
Mitochondrial phylogenomics and genetic population structure of anchovies (Engraulis encrasicolus) along the Moroccan coast using sequence analysis of the mitochondrial DNA cytochrome b
Authors: Chahdi Ouazzani Khalil , Benazzou Touria , Tojo Naoki , Chlaida Malika
Published: January 2018

A fragment of 680 bp of mitochondrial cytochrome b locus of European anchovies, Engraulis encrasicolus, was sequenced for 138 individuals collected from three Moroccan Atlantic areas and from Moroccan Alboran Sea. These samples were surveyed for diversity and differentiation with a range of summary statistics. The results showed that the most dominant clade in Moroccan anchovy is Clade A with a percentage ranging from 89% in Alboran Sea to 91% - 95 % in the Moroccan Atlantic coast. Overall, there was a significant genetic differentiation among the 4 Moroccan anchovy zones (Φst = 0.01283; p=0.03910). Pairwise Φst among populations and multidimensional scaling revealed a high homogeneity among Atlantic populations but some heterogeneity between Alboran population and Atlantic populations, mainly between the populations from Central Atlantic of Morocco with a significant difference.
hormLong: An R package for longitudinal data analysis in wildlife endocrinology studies
Authors: Fanson Benjamin , Fanson Kerry V
Published: January 2018

The growing number of wildlife endocrinology studies have greatly enhanced our understanding of comparative endocrinology, and have also generated extensive longitudinal data for a vast number of species. However, the extensive graphical analysis required for these longitudinal datasets can be time consuming because there is often a need to create tens, if not hundreds, of graphs. Furthermore, routine methods for summarising hormone profiles, such as the iterative baseline approach and area under the curve (AUC), can be tedious and non-reproducible, especially for large number of individuals. We developed an R package, hormLong, which provides the basic functions to perform graphical and numerical analyses routinely used by wildlife endocrinologists. To encourage its use, hormLong has been developed such that no familiarity with R is necessary. Here, we provide a brief overview of the functions currently available and demonstrate their utility with previously published Asian elephant data. We hope that this package will promote reproducibility and encourage standardization of wildlife hormone data analysis.
Investigation of the suitability of Remane’s “species minimum” concept in a Mediterranean transitional waters ecosystem
Authors: Pavloudi Christina , Oulas Anastasis , Kristoffersen Jon B , Friedrich Michael W , Arvanitidis Christos
Published: January 2018

Remane’s Artenminimum (“species minimum”) concept was developed for the Baltic Sea, the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient. It argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum, which occurs at salinity 5 to 8, because the number of brackish specialists does not compensate for the decline in marine and freshwater diversity. The aim of the present study was to investigate the sediment bacterial diversity of a transect river-lagoon-open sea, i.e. from freshwater to marine, occurring at Amvrakikos Gulf (Ionian Sea, Western Greece) and to test whether it follows the Remane's concept, both in terms of species composition but also of functionality. DNA was extracted from sediment samples collected in situ from four stations along the aforementioned transect and sequenced for the 16S rRNA gene. In addition, sediment samples were collected for the assessment of benthic macroorganismic diversity. Moreover, several environmental parameters were measured and their correlation with the diversity patterns was explored. The results of the study shed light on the microbial biodiversity of transitional water ecosystems and reveal the effect of salinity on species diversity, both on microorganisms and on macrobenthic organisms.
Bioinformatiс properties of sign language motion indicated by fractal complexity
Authors: Malaia Evie , Borneman Joshua , Wilbur Ronnie B.
Published: January 2018

We make a first attempt at distinguishing information-carrying visual signal by comparing visual characteristics of American Sign Language and everyday human motion, to identify what clues might be available in one but not in the other. The comparison indicated significantly higher fractal complexity in sign language across tested frequency bands (0.01-15 Hz), as compared to everyday motion. A comparison of our results with the work also showing high fractal complexity in the speech signal allows us to suggest the underlying properties of linguistic signals which allow babies to 'tune to' a specific channel, or modality, during language acquisition.
Density and distribution patterns of the endangered species Pinna nobilis within the harbour bay of Favignana (Egadi Islands MPA)
Authors: D'agostaro Riccardo , Donati Stefano , Chemello Renato
Published: January 2018

The fan shell P. nobilis (Linnaeus, 1758) is the largest marine bivalve in the Mediterranean Sea which acts as ecosystem engineer, offering an adequate substratum to several associated benthic species. P. nobilis is threatened by the reduction and loss of its natural habitat and by increased anthropogenic inputs into coastal waters. The knowledge on the population of this species are scarce, especially as concerns Sicily and its coasts. This study focused on the density of population, spatial distribution, level of burial and orientation of the population of P. nobilis in the harbour area of Favignana island (western coast of Sicily, Italy). The fan shell surveys were carried out by SCUBA diving using a 50m-transect line perpendicular to the coastline. For each P. nobilis censused, maximum (W) width, minimum width (w) and unburied length (UL) were measured; shell orientation (Or) was determined using an underwater compass and considering the magnitude of the angle formed by the vector and the magnetic north. The specimen status (dead or alive), the depth (by using the electronic depth meter of a diving computer) were recorded. In addition, the geographical coordinates were marked for each individual along the transect by means of a Global Positioning System (GPS). Total shell height (HT) was estimated using a formula considered suitable for the populations of this studied area. The density of P. nobilis was ±11 ind. 100m2, the total height (HT) and the maximum width (W) of the shells was 33 cm and 13,6 cm respectively. In the aim of the "MPA of Egadi Islands" to confirm the need of a new management to protect the biodiversity of the harbour area, more conservation measures are necessary in order to improve the preservation of this endangered species.
Effective protein inhibition in intact mouse oocytes through peptide nanoparticle-mediated antibody transfection
Authors: Li Ruichao , Jin Zhen , Gao Leilei , Liu Peng , Yang Zhixia , Zhang Dong
Published: January 2018

Female meiosis is a fundamental area of study in reproductive medicine, and the mouse oocyte model of in vitro maturation (IVM) to study female meiosis is the most widely used. To investigate the probable role(s) of an unknown protein in female meiosis, the method traditionally used involves microinjecting a specific antibody into mouse oocytes. Recently, in studies on somatic cells, peptide nanoparticle-mediated antibody transfection has become a popular tool because of its high efficiency, low toxicity, good stability, and strong serum compatibility. However, till now, no researchers have tried using this technique on mouse oocytes because the zona pellucida surrounding the oocyte membrane (vitelline membrane) is usually thought or proved to be a tough barrier to macromolecules, such as antibodies and proteins. Therefore, we attempted to introduce an antibody into mouse oocytes using a peptide nanoparticle. Here we show for the first time that with our optimized method, an antibody can be effectively delivered into mouse oocytes and inhibit its target protein with high specificity. We obtained significant results using small GTPase Arl2 as a test subject protein. We propose peptide nanoparticle-mediated antibody transfection to be a superior alternative to antibody microinjection for preliminary functional studies of unknown proteins in mouse oocytes.
Consideration of uncertainties in environmental science and management with examples from Pacific salmon
Authors: Peterman Randall
Published: January 2018

An informal review of the history of new quantitative methods in environmental science, including environmental risk assessment, shows about a 10- to 20-year lag in wide acceptance of such methods by management agencies. To reduce that lag time as innovative methods continue to emerge, environmental scientists will need to work much more intensively with communications specialists on better ways to explain risk analyses and decision-making strategies to non-technical decision makers and the public. Four key uncertainties make such communication difficult: (1) natural variability in both physical and biological processes, (2) imperfect data arising from observation error (i.e., measurement error), (3) incomplete understanding of an environmental system's structure and dynamics, and (4) outcome uncertainty (deviations between realized outcomes and management targets). These uncertainties create risks -- risks to natural populations as well as to people who use them. Examples of these four sources of uncertainty are presented here for Pacific salmon (Oncorhynchus spp.). One promising framework for explicitly taking such uncertainties into account was initially developed in the early 1990s by scientific advisors to the International Whaling Commission. They built stochastic models, which essentially were comprehensive formal decision analyses, to derive management procedures (i.e., sampling designs for collecting data, methods to analyze those data, and state-dependent harvest-control rules for use by managers) that were robust to all the uncertainties considered. This method of "Management Strategy Evaluation" or "Management Procedure Evaluation" is now considered the "gold standard" for conducting risk assessments and making risk-management decisions in marine fisheries.
The furculae of the dromaeosaurid dinosaur Dakotaraptor steini are trionychid turtle entoplastra
Authors: Arbour Victoria M. , Zanno Lindsay E. , Larson Derek W. , Evans David C. , Sues Hans-Dieter
Published: January 2018

Dakotaraptor steini is a recently described dromaeosaurid dinosaur from the Upper Cretaceous (Maastrichtian) Hell Creek Formation of South Dakota. Included within the D. steini hypodigm are three elements originally identified as furculae: one which is part of the holotype specimen and two referred specimens. We show that the elements described as D. steini ‘furculae’ are not theropod dinosaur furculae, but rather trionychid turtle entoplastra. Given that the holotype 'furcula' is not referable to Dromaeosauridae and that the specimen is a disarticulated individual based on skeletal remains from a multitaxic bonebed, the holotype of Dakotaraptor steini is a chimera.
Diet of the critically endangered brown-headed spider monkey (Ateles fusciceps fusciceps) in the Ecuadorian Chocó: Conflict between primates and loggers over fruiting tree species
Authors: Morelos-Juárez Citlalli , Tapia Andrea , Conde Galo , Peck Mika
Published: January 2018

Identifying key food resources for critically endangered species is vital in the design of effective conservation strategies, particularly if these resources are also targeted by anthropogenic activities such as logging. The province of Esmeraldas in NW Ecuador is heavily dependent on commercial logging. It also maintains the only healthy population of the critically endangered brown-headed spider monkey (Ateles fusciceps fusciceps). The unprotected forest remnant of Tesoro Escondido, in the buffer zone of the Cotacachi Cayapas Ecological Reserve, is home to an estimated 130 individuals of a global population of approximately 250. There is an urgent need for information to develop effective conservation action plans for the species, in particular the impact of logging activity on key feeding resources. We characterised the floristic composition of the habitat of A. f. fusciceps and estimated the availability of fruit resources for the annual cycle of 2012-2013 in sixteen 0.1 hectare vegetation plots. We determined feeding preferences for A. f. fusciceps using behavioural observations applying the Chesson ε index to identify key feeding tree species. We reviewed regional logging permits to identify species targeted for extraction by the timber industry and calculated extraction volumes in primary forest for key feeding tree species to identify potential conflict between logging and primate diet. We identified 65 fruiting tree species from 34 families that formed the diet of A. f. fusciceps. The Chesson ε index identified twelve species as preferred species with further phenological observations identifying seven species as staple foods and two palms as potential fall back fruits. Additionally, high densities of the lipid rich fruits of Brosimum utile make this an important resource for this primate throughout the year. Of 65 feeding tree species identified for A. f. fusciceps, 35 species are also targeted as sources of timber. Five key feeding species would be depleted under current sustainable management extraction protocols while two other species would be significantly impacted in terms of local abundance.Given the critically endangered status of A. f. fusciceps, remaining primary forest in NW Ecuador requires urgent protection, including thorough revision of current logging protocols to ensure long term survival of the species.
The essential need for research misconduct allegation audits
Authors: Loikith Lisa , Bauchwitz Robert P
Published: January 2018

Nearly ninety percent of allegations of biomedical research misconduct in the United States are dismissed by responsible institutions without any faculty assessment or auditable record. Recently, members of the U.S. Congress have complained that the penalties for those against whom findings of research misconduct are made are too light and that too few grant funds associated with research misconduct have been recovered for use by other researchers and taxpayers. Here we describe the laws that empower federal agencies which can oversee investigations of biomedical research misconduct: the Office of Research Integrity (ORI) and Office of the Inspector General (OIG), both located within the Department of Health and Human Services (HHS). Research misconduct pertaining to U.S. physical sciences funded through the National Science Foundation (NSF) is overseen by the NSF's OIG. While OIGs may provide some improvement over ORI in the handling of research misconduct, we have found that a much more serious flaw exists which undermines an ability to conduct performance audits as to the effectiveness by which allegations of research misconduct are handled in the United States. Federal audit standards (GAGAS/Yellow Book), if applied to the handling of research misconduct, would allow a determination as to whether the handling of allegations of biomedical research misconduct actually functions adequately, and if not, how it might be improved. Specifically, we propose that independent, external peer review under GAGAS audit standards should be instituted without delay in assessing the performance of ORI, or any other similarly tasked federal agency, in handling allegations of research misconduct.
A risk assessment approach to ecological decision-making
Authors: Himes Boor Gina K , Wade Paul
Published: January 2018

The conservation and management of wild populations and ecosystems almost always involves making decisions in the face of uncertainty and risk. The application of science to the ecological decision-making process was something that the late Professor Daniel Goodman thought deeply about. In this paper we outline the three main principles that Dr. Goodman espoused for good practice when conducting analyses for ecological decision-making: 1) the results should be conditioned on all relevant data and information, 2) there must be a full characterization of all uncertainty, and it should be fully propagated into the result, and 3) doing so in the correct way will result in the calculation of an accurate probability distribution (conditioned on our understanding of the state of nature) that should be used directly for ecological decision-making. Dr. Goodman believed that in the context of threatened and endangered species management Population Viability Analysis (PVA), Bayesian statistics, and structured decision-making are the most logical tools to achieve the three principles. To illustrate the application of the principles and tools in a real management setting, we discuss a Bayesian PVA that Dr. Goodman produced for the endangered Steller sea lion. We conclude by discussing the practical and philosophical impediments that may limit the full realization of the three principles and we offer some suggested solutions.