bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding the role of Oryza sativa OsPILS (PIN Like) genes in auxin signaling
Authors: Mohanta Tapan Kumar , Mohanta Nibedita
Published: January 2018

The phytohormone auxin is one of the most important signaling molecule that undergo accumulation or depletion in temporal or spatial manner due to wide arrays of changes in developmental or stress programme. Proper distribution, maintenance and homeostasis of auxin molecules across the plant system is one of the most important phenomena. The distribution and homeostasis of auxin is maintained by auxin transport system across the plant. Auxin transportation is carried out by auxin transporter family proteins, popularly known as auxin efflux carriers (PINs). Besides, auxin efflux carrier family proteins, a sub-family of auxin efflux carriers (OsPILS) being identified from Oryza sativa and reported here. Oryza sativa encodes for seven putative sub-cellularly localized transmembrane PILS proteins. Differential expression of OsPILS genes are found to be regulated by auxin and cytokinin dependent manner. In auxin treated plants, all OsPILS genes are up-regulated in leaf tissues and down regulated in root tissues during third week time point. In cytokinin treated plants, maximum of OsPILS genes were up-regulated both in leafs and roots tissues during third week time period. Regulation of gene expression of OsPILS genes by auxin and cytokinin during third week time period reflects its important roles during plant growth and development.
An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester,1857) Looss, 1899
Authors: Biswal Devendra Kumar , Ghatani Sudeep , Shylla Jollin A , Sahu Ranjana , Mullapudi Nandita , Bhattacharya Alok , Tandon Veena
Published: January 2018

Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear genome houses suitable genetic markers (e.g., in ribosomal (r) DNA) for species identification and molecular characterization, the mitochondrial (mt) genome consistently provides a rich source of novel markers for informative systematics and epidemiological studies. In the last decade, there have been some important advances in mtDNA genomics of helminths, especially lung flukes, liver flukes and intestinal flukes. Fasciolopsis buski, often called the giant intestinal fluke, is one of the largest digenean trematodes infecting humans and found primarily in Asia, in particular the Indian subcontinent. Next-generation sequencing (NGS) technologies now provide opportunities for high throughput sequencing, assembly and annotation within a short span of time. Herein, we describe a high-throughput sequencing and bioinformatics pipeline for mt genomics for F. buski that emphasizes the utility of short read NGS platforms such as Ion Torrent and Illumina in successfully sequencing and assembling the mt genome using innovative approaches for PCR primer design as well as assembly. We took advantage of our NGS whole genome sequence data (unpublished so far) for F. buski and its comparison with available data for the Fasciola hepatica mtDNA as the reference genome for design of precise and specific primers for amplification of mt genome sequences from F. buski. A long-range PCR was carried out to create a NGS library enriched in mt DNA sequences. Two different NGS platforms were employed for complete sequencing, assembly and annotation of the F. buski mt genome. The complete mt genome sequences of the intestinal fluke comprise 14,118 bp and is thus the shortest trematode mitochondrial genome sequenced to date. The noncoding control regions are separated into two parts by the tRNA-Gly gene and donot contain either tandem repeats or secondary structures, which are typical for trematode control regions. The gene content and arrangement are identical to that of F. hepatica. The F. buski mtDNA genome has a close resemblance with F. hepatica and has a similar gene order tallying with that of other trematodes. The mtDNA for the intestinal fluke is reported herein for the first time by our group that would help invesigate Fasciolidae taxonomy and systematics with the aid of mtDNA NGS data. More so, it would serve as a resource for comparative mitochondrial genomics and systematic studies of trematode parasites.
Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR
Authors: Estrada April D , Freese Nowlan H , Blakley Ivory C , Loraine Ann E
Published: January 2018

Alternative splicing enables a single gene to produce multiple mRNA isoforms by varying splice site selection. In animals, alternative splicing of mRNA isoforms between cell types is widespread and supports cellular differentiation. In plants, at least 20% of multi-exon genes are alternatively spliced, but the extent and significance of tissue-specific splicing is less well understood, partly because it is difficult to isolate cells of a single type. Pollen is a useful model system to study tissue-specific splicing in higher plants because pollen grains contain only two cell types and can be collected in large amounts without damaging cells. Previously, we identified pollen-specific splicing patterns by comparing RNA-Seq data from Arabidopsis pollen and leaves. Here, we used semi-quantitative PCR to validate pollen-specific splicing patterns among genes where RNA-Seq data analysis indicated splicing was most different between pollen and leaves. PCR testing confirmed eight of nine alternative splicing patterns, and results from the ninth were inconclusive. In four genes, alternative transcriptional start sites coincided with alternative splicing. This study highlights the value of the low-cost PCR assay as a method of validating RNA-Seq results.
Metal to phosphorus stoichiometries for freshwater phytoplankton in three Scottish lakes
Authors: Gormley-Gallagher Aine M , Douglas Richard , Rippey Brian
Published: January 2018

Simultaneous measurements of changes in phytoplankton biomass and the metal and phosphorus (P) content of cells have been captured to attest metal to P stoichiometries for freshwater phytoplankton. Three remote Scottish lakes that have received high, medium or low metal contamination from the atmosphere were selected for study. Phytoplankton cells were collected, their biomass determined microscopically, and Inductively Coupled Plasma-Mass Spectrometry was used to measure their lead (Pb), cadmium (Cd), mercury (Hg), copper (Cu), zinc (Zn), nickel (Ni), chromium (Cr), manganese (Mn), cobalt (Co) and P content. A greater phytoplankton biomass in the lakes resulted in significant algae growth dilution of the mass-specific Pb, Cd, Hg, Cu, Ni and Cr in the phytoplankton. Changes in the phytoplankton cell count and their Hg, Pb, Cd, Cu, Mn, Co, Ni and Cr concentrations showed the process of algae bloom dilution to be subject to exponential decay, which accelerated in the order of Mn < Cu < Ni < Pb and Cd < Cr and Hg < Co. This indicated a metabolic and detoxification mechanism was involved in the active selection of metals. For the first time simultaneous measurements of metals and P stoichiometry in freshwater phytoplankton are reported. The mean metal to P stoichiometry generated was (C106P1N16)1000Pb0.019Hg0.00004Cu0.013Cd0.005Cr0.2Co0.0008 Mn0.2Ni0.012 based on the field measurements and the Redfield average C, N and P stoichiometry of (CH2O)106(NH3)16H3PO4.
Leaf litter decomposition rates increase with rising mean annual temperature in Hawaiian tropical montane wet forests
Authors: Bothwell Lori D , Selmants Paul C , Giardina Christian P , Litton Creighton M.
Published: January 2018

Decomposing litter in forest ecosystems supplies nutrients to plants, carbon to heterotrophic soil microorganisms and is a large source of CO2 to the atmosphere. Despite its essential role in carbon and nutrient cycling, the temperature sensitivity of leaf litter decay in tropical forest ecosystems remains poorly resolved, especially in tropical montane wet forests where the warming trend may be amplified compared to tropical wet forests at lower elevations. We quantified leaf litter decomposition rates along a highly constrained 5.2 °C mean annual temperature (MAT) gradient in tropical montane wet forests on the Island of Hawaii. Dominant vegetation, substrate type and age, soil moisture, and disturbance history are all nearly constant across this gradient, allowing us to isolate the effect of rising MAT on leaf litter decomposition and nutrient release. Leaf litter decomposition rates were a positive linear function of MAT, causing the residence time of leaf litter on the forest floor to decline by ~31 days for each 1 °C increase in MAT. Our estimate of the Q10 temperature coefficient for leaf litter decomposition was 2.17, within the commonly reported range for heterotrophic organic matter decomposition (1.5 – 2.5) across a broad range of ecosystems. The percentage of leaf litter nitrogen (N) remaining after six months declined linearly with increasing MAT from ~ 88% of initial N at the coolest site to ~74% at the warmest site. The lack of net N immobilization during all three litter collection periods at all MAT plots indicates that N was not limiting to leaf litter decomposition, regardless of temperature. These results suggest that leaf litter decay in tropical montane wet forests may be more sensitive to rising MAT than in tropical lowland wet forests, and that increased rates of N release from decomposing litter could delay or prevent progressive N limitation to net primary productivity with climate warming.
Body mass control and unresolved sociocultural stress: application of the generalized Data-Rate Theorem
Authors: Wallace Rodrick
Published: January 2018

New results from control theory allow construction of necessary conditions statistical models of body mass regulation in the context of interaction with a complex dynamic environment. Focusing on the stress-related induction of central obesity via HPA axis regulation, we explore implications for strategies of prevention and treatment. It rapidly becomes evident that individual-oriented biomedical reductionism is an inadequate paradigm. Absent mitigation of HPA axis or related dysfunctions arising from social pathologies of power imbalance, economic insecurity, and so on, it is unlikely that permanent changes in visceral obesity can be maintained without constant therapeutic effort, an expensive -- and likely unsustainable -- public policy.
Temporal changes in nasopharyngeal carriage of Streptococcus pneumoniae serotype 1 genotypes in healthy Gambians before and after the 7-valent pneumococcal conjugate vaccine
Authors: Ebruke Chinelo , Roca Anna , Egere Uzochukwu , Darboe Ousainou , Hill Philip C , Greenwood Brian , Wren Brendan W , Adegbola Richard A , Antonio Martin
Published: January 2018

Streptococcus pneumoniae serotype 1 is one of the leading causes of invasive pneumococcal disease. However this invasive serotype is hardly found in nasopharyngeal asymptomatic carriage and therefore large epidemiological studies are needed to assess the dynamics of serotype 1 infection. Within the context of a large cluster randomized trial conducted in rural Gambia to assess the impact of PCV-7 vaccination on nasopharyngeal carriage, we present an ancillary study describing the prevalence of nasopharyngeal carriage of pneumococcal serotype 1 and temporal changes of its more frequent genotypes. Nasopharyngeal swabs (NPS) were collected before PCV-7 vaccination (December 2003-May 2004) and up to 30 months after PCV-7 vaccination (post-vaccination periods 1 to 3: July 2006 – March 2007; April 2007 – March 2008 and April 2008 – Feb 2009). S. pneumoniae serotype 1 were genotyped by MLST. Serotype 1 was recovered from 87 (0.71%) of 12,319 NPS samples collected. In the pre-vaccination period, prevalence of serotype 1 was 0.47% in both study arms. In the post-vaccination periods, prevalence in the fully vaccinated villages ranged between 0.08% in period 1 and 0.165% in period 2; while prevalence in partly vaccinated villages was between 0.17% in period 3 and 1.34% in period 2. Overall four different genotypes were obtained with ST3081 the most prevalent (60.71%) followed by ST618 929.76%). ST3081 was found only in post-vaccination period 2 and 3 while ST618 had disappeared in post-vaccination period 3. Distribution of these major genotypes was similar in both study arms.Emergence of ST3081 and concomitant disappearance of ST618 may suggest a change in the molecular epidemiology of pneumococcal serotype 1 in this region. This change is not likely to be associated with the introduction of PCV-7 which lacks serotype 1 as it was observed simultaneously in both study arms. Future population-based epidemiological studies will provide further evidence of substantive changes in the pneumococcal serotype 1 epidemiology and the likely mechanisms.
Objective pain sensitivity affects sleep quality in opioid dependent males on methadone maintenance therapy
Authors: Zahari Zalina , Lee Chee Siong , Tan Soo Choon , Mohamad Nasir , Lee Yeong Yeh , Ismail Rusli
Published: January 2018

Aim Pain associated poor sleep quality has been reported among opioid dependent patients on methadone maintenance therapy (MMT) but objective pain data are lacking. This study aimed to investigate the rate of objective pain sensitivity and the relationship between pain sensitivity and sleep quality in this susceptible male population. Methods A total of 168 male patients from MMT clinic in Kelantan, Malaysia were included into the study. Objective pain tolerance to cold pressor test (CPT) was evaluated at 0 hour and at 24 hours after the first CPT. Malay version of the Pittsburgh Sleep Quality Index – PSQI and the subjective opiate withdrawal scale (SOWS) questionnaires were administered to evaluate the quality of sleep and withdrawal symptoms, respectively. Results The mean age of the study participants was 37.22 (SD 6.20) years old. The mean daily methadone dose was 76.64 (SD 37.63) mg/day. The mean averaged SOWS score was 5.43 (SD 6.91). The averaged pain tolerance time ranged from 7 to 300 s with a mean time of 32.16 (SE 2.72) s, slightly below the cut-off score of 37.53 s. More specifically, 78.6% (n = 132) of patients were identified as ‘pain-sensitive’ (averaged pain tolerance time ≤ 37.53 s), and 36 (21.4%) were ‘pain-tolerant’ patients (averaged pain tolerance time > 37.53 s). The mean global PSQI score was 5.47 (SD 2.74). The pain-sensitive patients reported poorer sleep quality with mean (SD) of 5.78 (2.80) compared with pain-tolerant patients with mean (SD) of 4.31 (2.18) (p = 0.005). With analysis of covariance, pain-sensitive patients were found to have higher global PSQI scores (adjusted mean 5.76, 95% CI 5.29; 6.22) than pain-tolerant patients (adjusted mean 4.42, 95% CI 3.52; 5.32) (p = 0.010). Conclusions Many opioid dependent male patients on MMT are pain-sensitive. A poorer sleep quality is associated with objective pain sensitivity. Pain and sleep complaints in this susceptible population should not be overlooked.
Chronic negative mood affects internal representations of negative facial expressions – An internet study
Authors: Jolij Jacob , Wriedt Sophia C. , Luckmann Annika
Published: January 2018

Facial expressions are an important source of information in social interactions, as they effectively communicate someone’s emotional state. Not surprisingly, the human visual system is highly specialized in processing facial expressions. Interestingly, processing of facial expressions is influenced by the emotional state of the observer: in a negative mood, observers are more sensitive to negative emotional expression than when they are in a positive mood, and vice versa. Here, we investigated the effects of chronic negative mood on perception of facial expressions by means of an online reverse correlation paradigm. We administered a depression questionnaire assessing chronic negative mood over the last two weeks. We constructed a classification image for negative emotion for each participant by means of an online reverse correlation task, which were rated for intensity of expression by an independent group of observers. Here we found a strong correlation between chronic mood and intensity of expression of the internal representation: the more negative chronic mood, the less intense the negative expression of the internal representation. This experiment corroborates earlier findings that the perception of facial expression is affected by an observer’s mood, and that this effect may be the result of altered top-down internal representations of facial expression. Equally importantly, though, our results demonstrate the feasibility of applying a reverse correlation paradigm via the Internet, opening up the possibility for large-sample studies using this technique.
Uneven distribution of enamel in the tooth crown of the hypsodont Plains Zebra Equus quagga
Authors: Winkler Daniela E , Kaiser Thomas M
Published: January 2018

Unworn teeth of herbivorous mammals are not immediately functional. They have to get in wear to expose enamel ridges which can then act as shear-cutting blades to disintegrate the food. We use the Plains Zebra (Equus quagga) as a hypsodont, herbivorous model organism to investigate how initial wear of the tooth crown is controlled by underlying structures. We find that the enamel proportion is smaller at the apical part of the tooth crown in all upper tooth positions. Measurements of enamel thickness on the first molar show that the outer enamel band is widest in the lower half of the tooth crown, where enamel content is also highest. We therefore find evidence that the distribution of enamel within the tooth crown is uneven and lower enamel content at the apex promotes early wear. This gradient in enamel distribution is less pronounced in the last molar (txM3), which has also a higher overall enamel content. The M3 is thus hypothesised to have a slightly different functional trait in mastication, resisting highest bite forces along the tooth row and maintaining functionality while anterior teeth are already worn down.
Metagenomic analysis of bacterial community composition among the cave sediments of Indo-Burman biodiversity hotspot region
Authors: De Mandal Surajit , Sanga Zothan , Nachimuthu Senthil Kumar
Published: January 2018

Caves in Mizoram, Northeast India are potential hotspot diversity regions due to the historical significance of the formation of Indo-Burman plateau and also because of their unexplored and unknown diversity. High throughput paired end illumina sequencing of V4 region of 16S rRNA was performed to systematically evaluate the bacterial community of three caves situated in Champhai district of Mizoram, Northeast India. A total of 10,643 operational taxonomic units (based on 97% cutoff) comprising 21 bacterial phyla and 21 candidate phyla with a sequencing depth of 11, 40013 were found in this study. The overall taxonomic profile obtained by BLAST against RDP classifier and Greengene OTU database revealed high diversity within the bacterial communities, dominated by Planctomycetes, Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes, while members of archea were less diverse and mainly comprising of eukaryoarchea. Analysis revealed that Farpuk (CFP) cave has low diversity and is mainly dominated by actinobacteria (80% reads), whereas diverse communities were found in the caves of Murapuk (CMP) and Lamsialpuk (CLP). Analysis of rare and abundant species also revealed that a major portion of the identified OTUs were falling under rare biosphere. Significantly, all these caves recorded a high number of unclassified OUTs which might represent novel species. Further, analysis with whole genome sequencing is needed to validate the novel species as well as to determine their functional significance.
Gynocentric communication among nuclear kin in the USA and Spain
Authors: Brewer Devon D
Published: January 2018

Paternity uncertainty seems to have shaped humans' differential investment in kin. I examined sex differences in communication among nuclear kin to expand inquiry on this matter and address some methodological limitations in prior work. I analyzed data from national surveys in the USA and Spain and a study of mobile phone communication in the immediate aftermath of the 2013 Boston Marathon bombings. Respondents communicated mildly to moderately more with mother than father and more with sister than brother. The differences in communication with mother and father appeared in both subjective survey data and objective mobile telephone records. Across communication modes and studies, women and men did not differ consistently in overall frequency of communication. Matricentric and sororicentric tendencies were larger for the modes likely to involve dyadic communication (such as telelphone calling and texting) than modes which often involve communication in group settings (face-to-face). The tendency to communicate more with female than male kin also appeared to be stronger in women respondents than in men. These results are consistent with paternity uncertainty as an ultimate evolutionary cause of differential investment in kin.
Haplotypes of “Candidatus Liberibacter europaeus” also separate by geography and host species
Authors: Nelson Warrick R
Published: January 2018

“Candidatus Liberibacter europaeus” (Leu) is one of six currently known Liberibacter species. It is known primarily from pear and related species across Europe, and from Scotch broom and its associated psyllids in New Zealand (introduced from Britain). The psyllids were introduced to New Zealand as a biocontrol agent for broom and it is thought the bacterium may have been introduced as an endosymbiont of the psyllids. No symptoms in apple or pear trees have been reported, but mild symptoms can occur in broom. 16S and 16S–23S intergenic spacer region DNA sequences of this species have been deposited in GenBank. Analysis of these sequences and associated ecological descriptions indicates the occurrence of two haplotypes, LeuA and LeuB, defined not only genetically but also by geographic range as well as by plant/psyllid host species composition. Liberibacter species are new to science and haplotype identifications enable historical accounts of relationships and spread to be generated.
Polyandry pays off: The effects of multiple mating and number of fathers on morphological traits and survival in clutches of nesting green turtles at Tortuguero
Authors: Alfaro-Núñez Alonzo , Jensen Michael P. , Abreu-Grobois F. Alberto
Published: January 2018

Despite the long debate of whether or not multiple mating benefits the offspring, studies still show contradicting results. Multiple mating takes time and energy. Thus, if females fertilize their eggs with a single mating, why to mate more than once? We investigated and inferred paternal identity and number of sires in 12 clutches (240 hatchlings) of green turtles (Chelonia mydas) nests at Tortuguero, Costa Rica. Paternal alleles were inferred through comparison of maternal and hatchling genotypes, and indicated multiple paternity in at least 11 of the clutches (92%). The inferred average number of fathers was three (ranging from 1 to 5). This in returns suggests that most females successfully got fecundated by at least three males. Moreover, regression analyses were used to investigate for correlation of inferred clutch paternity with morphological traits of hatchlings fitness (emergence success, length, weight and crawling speed); and size of the mother; and an environmental variable (incubation temperature). We suggest and propose two different comparative approaches for evaluating morphological traits and clutch paternity, in order to infer greater offspring survival. First, clutches coded by the exact number of fathers and second by the exact paternal contribution (fathers who gives greater proportion of the offspring per nest). We found significant differences (P < 0.05) in clutches coded by the exact number of fathers for all morphological traits, where a tendency of higher values in offspring sired by two to three fathers was found. The second approach analysing the paternal contribution showed no significant difference (P > 0.05) for any of the traits. The main conclusion is that multiple mating analysed by the exact number of inferred fathers significantly affects the survival of the offspring regardless of morphological trait measured.
Multi-scale environmental filters and niche partitioning govern the distributions of riparian vegetation guilds
Authors: Hough-Snee Nate , Laub Brian , Merritt David M. , Long A. Lexine , Nackley Lloyd L. , Roper Brett B. , Wheaton Joseph M
Published: January 2018

Across landscapes, riparian plant communities assemble under varying levels of disturbance, environmental stress, and resource availability, leading to the development of distinct riparian life-history guilds. Identifying the environmental filters that exert selective pressures and favor specific vegetation guilds within riverscapes is a critical step in setting baseline expectations for how riparia may respond to the environmental conditions anticipated under future global change scenarios. In this study, we ask (1) what functional riparian plant guilds exist across two major North American river basins? (2) What environmental filters shape riparian guild distributions? (3) Does resource partitioning between guilds influence guild distributions and co-occurrence? We identified riparian plant guilds, examining relationships between regional climate and watershed hydrogeomorphic characteristics, stream channel form, and co-occurring riparian guilds. Woody species composition was measured at 703 streams and each species’ traits were extracted from a database in five functional areas: life form, persistence and growth, reproduction, and resource use. We clustered species into guilds by morphological characteristics and attributes related to environmental tolerances, modeling guild distributions as a product of environmental filters (stressors and resources) and guild co-existence. We identified five guilds, i) a tall, deeply rooted, long-lived, evergreen tree guild, ii) a xeric disturbance tolerant shrub guild, iii) a hydrophytic, thicket-forming shrub guild, iv) a low-statured, shade-tolerant, understory shrub guild and v) a flood tolerant, mesoriparian shrub guild. Guilds were most strongly discriminated by one another species’ rooting depth, canopy height and potential to resprout and grow following biomass-removing disturbance. Hydro-climatic variables including precipitation, watershed area, water table depth, and channel form attributes reflective of hydrologic regime were predictors of guilds whose life history strategies had affinity or aversion to flooding, drought, and fluvial disturbance. Biotic interactions excluded guilds with divergent life history strategies and/or allowed for the co-occurrence of guilds that partition resources differently in the same environment. We conclude that riparian guilding provides a useful framework for assessing how disturbance and bioclimatic gradients shape riparian functional plant diversity. Multiple processes should be considered when the riparian response guilds framework is to be used as a land-use decision-support tool framework
Blood, sweat and tears: non-invasive vs. non-disruptive DNA sampling for experimental biology
Authors: Lefort Marie-Caroline , Boyer Stephane , Barun Arijana , Emami Khoyi Arsalan , Ridden Johnathon , Smith Victoria R , Sprague Rowan , Waterhouse Benjamin R , Cruickshank Robert H.
Published: January 2018

DNA data are becoming increasingly important in experimental biology. For example, it may be necessary to obtain DNA from an organism before using it in a bioassay or an experiment, to identify and distinguish between cryptic species, or when comparing different morphocryptic genotypes. Another example could be the assessment of relatedness between organisms prior to a behavioural study. In such cases, DNA must be obtained without affecting the fitness or behaviour of the subject being tested, as this could bias the results of the experiment. This points out the existence of a gap in the current molecular and experimental biology terminology, for which we propose the use of the term non-disruptive DNA sampling, specifically addressing behaviour and/or fitness, rather than simply physical integrity (invasiveness). We refer to these methods as “non-disruptive”, and discuss when they are appropriate to use.
Order Hemiptera: The true host involved in Mycobacterium ulcerans transmission, or is it an innocent by-stander?
Authors: Avumegah Michael Selorm , Wejse Christian
Published: January 2018

Burul ulcer disease is an infection of the subcutaneous layer. The causative organism, Mycobacterium ulcerans is a slow-growing environmental pathogen often associated with wetland and slow moving streams. One insect order believed to be associated with M.ulcerans is the order hemiptera, in which the aquatic bugs (Naucoris sp and Belostoma sp) belong. Some Mycobacteria species are endosymbiont of Acanthamoeba and laboratory experiments has confirmed this in M. ulcerans in an endemic area in Benin persisting in an amoeba for 14 days. Aquatic insect are believed to feed on amoeba, planktons, snail and fish from which they get infected. Protozoan and planktons may be the true resorvior or host of M. ulcerans but little research has been done in this area. Though many studies have found M. ulcerans in these insects, the exact mechanism of transmission to humans is still elusive. This study aims to review the available data on aquatic bugs, protozoans and other invertebrates (snail and fish) to ascertain if aquatic insects are themselves victims of the M. ulcerans through feeding.
Calprotectin as a marker of bowel inflammation
Authors: Terrin Gianluca , Pietravalle Andrea
Published: January 2018

In the last years the need for a non-invasive diagnostic tool that would help to discriminate between organic and functional gastrointestinal disorders directed research towards potential immunological markers. A great number of non-invasive bio-markers has been proposed, including eosinophilic cationic protein, elastase, esterase, myeloperoxidase, lysozyme, lactoferrin, and calprotectin. Compared to other biomarkers, calprotectin (also called MRP8/14, calgranulin A/B , S100 A8/A9) may offer advantages based on its biological characteristics. Calprotectin is a 36.5-kDa, calcium and zinc binding polypeptide which constitutes about 60% of soluble cytosol proteins in human neutrophils. It is also found in monocytes, keratinocytes, muscle tissue and infiltrating tissue macrophages. When bound to calcium it becomes resistant to proteolysis and colonic bacterial degradation. This make is stable for up to 1 week at room temperature and facilitate its determination in feces. Calprotectin is involved in the regulation of the inflammatory process, participate to the early innate immune response and exert antimicrobial, anti-proliferative and apoptotic properties. Fecal calprotectin is a direct measure of mucosal inflammation activity and becomes detectable when intestinal inflammation is still at an insufficient level to cause an increase in serum inflammation markers. In the last decade fecal calprotectin has been proposed as a marker to rule out acute and chronic intestinal inflammatory diseases in children with typical gastrointestinal symptoms. Many studies demonstrated its diagnostic utility in identifying children and adults with inflammatory bowel disease and correlate with the degree of disease activity. The detection of elevated levels of fecal calprotectin in healthy infants during the first few weeks of age, limits their use as screening test for intestinal inflammatory diseases in early life. Despite this evidence, the measurement of calprotectin in the serum has been proposed to identify neonates with necrotizing enterocolitis. Recent studies have shown higher fecal calprotectin levels in infants with irritable bowel syndrome and colics, compared with healthy controls. Additionally, a correlation was found between fecal calprotectin concentration and IBS clinical presentation severity. However, these studies do not provide data on diagnostic accuracy in distinguish between organic and functional gastrointestinal disorders. Despite significant limitations, these evidences suggest the presence of a subtle inflammatory process underlying functional gastrointestinal disorders and open new perspectives on their pathogenesis. Fecal calprotectin may play a role that could be revealed in further, specifically designed, studies. Changes in microflora, permeability, calprotectin excretion and other inflammatory biomarkers, should be investigated to clarify if a continuum exists between inflammatory conditions and intestinal functional diseases.
A workflow for characterizing nanoparticle monolayers for biosensors: Machine learning on real and artificial SEM images
Authors: Hughes Adam , Liu Zhaowen , Raftari Maryam , Reeves Mark E
Published: January 2018

A persistent challenge in materials science is the characterization of a large ensemble of heterogeneous nanostructures in a set of images. This often leads to practices such as manual particle counting, and sampling bias of a favorable region of the “best” image. Herein, we present the open-source software, imaging criteria and workflow necessary to fully characterize an ensemble of SEM nanoparticle images. Such characterization is critical to nanoparticle biosensors, whose performance and characteristics are determined by the distribution of the underlying nanoparticle film. We utilize novel artificial SEM images to objectively compare commonly-found image processing methods through each stage of the workflow: acquistion, preprocessing, segmentation, labeling and object classification. Using the semi- supervised machine learning application, Ilastik, we demonstrate the decomposition of a nanoparticle image into particle subtypes relevant to our application: singles, dimers, flat aggregates and piles. We outline a workflow for characterizing and classifying nanoscale features on low-magnification images with thousands of nanoparticles. This work is accompanied by a repository of supplementary materials, including videos, a bank of real and artificial SEM images, and ten IPython Notebook tutorials to reproduce and extend the presented results.
Seven years of experimental warming and nutrient addition causes decline of bryophytes and lichens in alpine meadow and heath communities
Authors: Alatalo Juha M , Jägerbrand Annika K , Molau Ulf
Published: January 2018

Global change is predicted to have large and rapid impact on polar and alpine regions. Bryophytes and lichens increase their importance in terms of biomass, carbon/nutrient cycling, cover and ecosystem functioning at higher latitudes/altitudes. Here we report from a seven year factorial experiment with nutrient addition and warming on the abundance of bryophytes and lichens in an alpine meadow and heath community. Treatments had significant negative effect on relative change of total abundance bryophytes and lichens, the largest decline to the nutrient addition and the combined nutrient addition and warming treatments, bryophytes decreasing most in the meadow, lichens most in the heath. Nutrient addition, and the combined nutrient addition and warming brought rapid decrease in both bryophytes and lichens, while warming had a delayed negative impact. Of sixteen species that were included the statistical analyses, we found significant negative effects on seven species. We show that impact of simulated global change on bryophytes and lichens differ in in time and magnitude among treatments and plant communities. Our results underscore the importance of longer-term studies to improve the quality of climate change models, as short-term studies are poor predictors of longer-term responses of bryophytes and lichens, similar to what have been shown for vascular plants. Species-specific responses may differ in time, and this will likely cause changes in the dominance structures of bryophytes and lichens over time.
A protocol for a systematic review into consumers’ attitudes, beliefs and perceived ethical obligations towards farm animal welfare
Authors: Clark Beth , Stewart Gavin B , Panzone Luca A , Frewer Lynn J
Published: January 2018

This article outlines a protocol for a systematic review into consumer attitudes, beliefs and perceived ethical obligations towards farm animal welfare, utilizing both the Theory of Reasoned Action and the Theory of Planned Behavior. A number of secondary objectives will also be explored in relation to the heterogeneity within the data relating to a number of variables known to vary within existing data including; animal species, welfare measures, socio-demographic and socio-economic characteristics. The protocol outlines the rationale, objectives, inclusion criteria, search strategy and screening processes for the meta-analysis, and the plans for data extraction, risk of bias and data synthesis.
How much biomass can plant communities pack per unit volume?
Authors: Proulx Raphael , Rheault Guillaume , Bonin Laurianne , Roca Irene T , Martin Charles A , Desrochers Louis , Seiferling Ian S
Published: January 2018

Aboveground production in terrestrial plant communities is commonly expressed in amount of carbon, or biomass, per unit surface. Alternatively, expressing production per unit volume allows the comparison of communities by their fundamental limits in packing carbon. In this work we reanalyzed published data from more than 900 plant communities across nine ecosystems to show that standing dry biomass per unit volume (biomass packing) consistently averages around 1 kg/m3 and rarely exceeds 5 kg/m3 across ecosystem types. Furthermore, we examined how empirical relationships between aboveground production and plant species richness are modified when standing biomass is expressed per unit volume rather than surface. We propose that biomass packing emphasizes species coexistence mechanisms and is an indicator of resource use efficiency in plant communities.
Evaluation of autotrophic and mixotrophic regimen Chlorella pyrenoidosa cells in various wastes water for its biochemical composition and biomass production
Authors: Dhull Nisha Phour , Soni Raman , Rahi Deepak Kumar , Soni Sanjeev Kumar
Published: January 2018

The present study investigates the possibility of integrating an existing industrial large scale biomass production with the treatment of waste water in which a mixture of organic and inorganic rich pollutants was used as a medium. This study suggests that the replacement of a defined medium with a complete mixotrophic medium gives a significant statistical difference in terms of growth parameters i.e. biomass production and specific growth rate. The green microalga C. pyrenoidosa was cultivated under different mixotrophic conditions for evaluation of biomass production. Inorganic defined fog’s medium supplemented, with raw dairy wastewater led to 1.37g/L biomass production in comparison to 1.2g/L obtained with pure glucose revealing 14.16% increase. The study also involves the supplementation of raw dairy wastewater as an organic carbon source in an inorganic medium comprising municipal treated water and reverse osmosis (RO) treated wastewater and attained 2.4g/L and 1.6g/L of biomass respectively, as compared to 0.3g/L and 0.16g/L obtained in the wastewaters alone revealing 700% and 900% increase respectively. Mixotrophic regimen cells as analyzed by a 2D Fourier transform infrared (FTIR) spectroscopy for its biochemical content revealed that fog’s blended raw dairy waste (RDW) regimen cells had maximum Carbohydrate/Amide ratio. The study suggests that the mixotrophic regimen C. pyrenoidosa cells can show appropriate growth in a mixture of waste waters and the same comes out to be a cost effective and feasible alternative commercial medium for biomass production without requiring any expensive organic carbon sources in the culture medium.
Pronounced and prevalent intersexuality does not impede the ‘Demon Shrimp’ invasion
Authors: Green Etxabe Amaia , Short Stephen , Flood Tim , Johns Tim , Ford Alex T
Published: January 2018

Crustacean intersexuality is widespread and often linked to infection by sex-distorting parasites. However, unlike vertebrate intersexuality, its association with sexual dysfunction is unclear and remains a matter of debate. The ‘Demon Shrimp’, Dikerogammarus haemobaphes, an amphipod that has invaded continental waterways, has recently become widespread in Britain. Intersexuality has been noted in D. haemobaphes but not investigated further. We hypothesise that a successful invasive population should not display a high prevalence of intersexuality if this condition represents a truly dysfunctional phenotype. Experiments have indicated that particular parasite burdens in amphipods may facilitate invasions. The rapid and ongoing invasion of British waterways represents an opportunity to determine whether these hypotheses are consistent with field observations. This study investigates the parasites and sexual phenotypes of D. haemobaphes in British waterways, characterising parasite burdens using molecular screening, and make comparisons with the threatened Gammarus pulex natives. We reveal that invasive and native populations have distinct parasitic profiles, suggesting the loss of G. pulex may have parasite-mediated eco-system impacts. Furthermore, the parasite burdens are consistent with those previously proposed to facilitate biological invasions. Our study also indicates that while no intersexuality occurs in the native G. pulex, approximately 50% of D. haemobaphes males present pronounced intersexuality associated with infection by the microsporidian Dictyocoela berillonum. This unambiguously successful invasive population presents, to our knowledge, the highest reported prevalence of male intersexuality. This is the clearest evidence to date that such intersexuality does not represent a form of debilitating sexual dysfunction that negatively impacts amphipod populations.
An effective rectal administration method in the left semiprone position
Authors: Awazu Satoshi , Araki Risa , Awazu Toshihiko
Published: January 2018

A previous study has shown barium is instilled in the left lateral position or the prone position. However, we previously reported that the colonoscope can be readily inserted into the descending colon in the left semiprone position. Indeed, when the colonoscope was inserted in the left semiprone position, the lumen of the sigmoid colon was observed linearly and the colon position lowered toward the oral side. In addition, it was often observed that the rectosigmoid colon nearly overlapped with the sigmoid-descending colon junction when the patient was placed in the left semiprone position in the single-contrast enema examination. Therefore, we considered that the rectosigmoid colon is located in the highest position while the sigmoid-descending colon junction is located in the lowest position and various kinds of drugs can be readily administered into the proximal colon in the left semiprone position. Our new barium instillation method was devised and this method was performed to determine whether barium can be readily instilled into the proximal colon. Barium (300 ml) passed the hepatic flexure before air insufflation in 32 (67%) of the 48 patients by using our new barium instillation method. By contrast, barium (300 ml) passed the hepatic flexure before air insufflation in 3 (6%) of the 48 patients by using our conventional barium instillation method. These results suggest that effective rectal administration is possible by using our new barium instillation method compared with our conventional barium instillation method.
Achieving human and machine accessibility of cited data in scholarly publications
Authors: Starr Joan , Castro Eleni , Crosas Mercè , Dumontier Michel , Downs Robert R. , Duerr Ruth , Haak Laurel , Haendel Melissa , Herman Ivan , Hodson Simon , Hourclé Joe , Kratz John Ernest , Lin Jennifer , Nielsen Lars Holm , Nurnberger Amy , Pröll Stefan , Rauber Andreas , Sacchi Simone , Smith Arthur P. , Taylor Michael , Clark Tim
Published: January 2018

Reproducibility and reusability of research results is an important concern in scientific communication and science policy. A foundational element of reproducibility and reusability is the open and persistently available presentation of research data. However, many common approaches for primary data publication in use today do not achieve sufficient long-term robustness, openness, accessibility or uniformity. Nor do they permit comprehensive exploitation by modern Web technologies. This has led to several authoritative studies recommending uniform direct citation of data archived in persistent repositories. Data are to be considered as first-class scholarly objects, and treated similarly in many ways to cited and archived scientific and scholarly literature. Here we briefly review the most current and widely agreed set of principle-based recommendations for scholarly data citation, the Joint Declaration of Data Citation Principles (JDDCP). We then present a framework for operationalizing the JDDCP; and a set of initial recommendations on identifier schemes, identifier resolution behavior, required metadata elements, and best practices for realizing programmatic machine actionability of cited data. The main target audience for the common implementation guidelines in this article consists of publishers, scholarly organizations, and persistent data repositories, including technical staff members in these organizations. But ordinary researchers can also benefit from these recommendations. The guidance provided here is intended to help achieve widespread, uniform human and machine accessibility of deposited data, in support of significantly improved verification, validation, reproducibility and re-use of scholarly/scientific data.
Fast Track DNA Analysis Suite for human identification
Authors: Docker Peter T , Baker Joanna , Haswell Steve
Published: January 2018

This paper details the development of a portable ‘Lab on chip’ DNA analyser that was developed to facilitate rapid analysis of DNA samples for ‘at scene of crime’ and in custody suite situations where human identification is required rapidly. This system was proven to work with human DNA for 3 loci, namely VWA, D21 and D18 taken from raw sample through PCR separation to detection within 90miniutes. Once the sample was loaded onto the microfluidic chip which in turn was loaded into the instrument no further human interaction took place. This paper details the approach to the biochemistry, hardware before going on to give results proving the proof of principle and then the authors’ conclusions.
Differential contribution of soil biota groups to plant litter decomposition as mediated by soil use
Authors: Casttro-Huerta Ricardo A , Falco Liliana B , Sandler Rosana V , Coviella Carlos
Published: January 2018

Plant decomposition is dependant on the activity of the soil biota and its interactions with climate, soil properties, and plant residue inputs. This work assessed the roles of different groups of the soil biota on litter decomposition, and the way they are modulated by soil use. Litterbags of different mesh sizes were filled with standardized dried leaves and placed on the same soil different use intensities: Naturalized grasslands, recent agriculture, and intensive agriculture fields. During sixth months, litterbags of each mesh size were collected once a month per system with five replicates. The remaining mass was measured and decomposition rates calculated. Differences were found for the different biota groups, and they were dependant on soil use. Within systems, the results show that in the naturalized grasslands, the macrofauna had the highest contribution to decomposition. In the recent agricultural system it was the combined activity of the macro and mesofauna, and in the intensive agricultural use it was the mesofauna activity. These results underscore the relative importance and activity of the different groups of the edaphic biota and the effects of different soil uses on soil biota activity.