bluuebunny/crossref_metadata_2025 huggingface dataset:
The first occurrence of the enigmatic archosaur Crosbysaurus (Heckert 2004) from the Chinle Formation of Southern Utah
Authors: Gay Robert J , St. Aude Isabella
Published: January 2018

Originally identified as an ornithisichian dinosaur, Crosbysaurus has been found in New Mexico, Arizona, and the type locality in Texas, the genus has been reassessed by other workers in light of revelations about the postcrania of another putative Triassic ornithischian, Revueltosaurus. The understanding of Triassic dental faunas has become more complicated by the extreme convergence between pseudosuchian archosaurus and ornithichian dinosaur dental morphologies. This new specimen does not help resolve the affinities of Crosbysaurus but does extend the range of this taxon into southern Utah. This specimen may also represent the youngest-known member of this genus
Odourous volatile compounds as mediators in possible interkingdom communication between Bacillus subtilis and flies
Authors: Ng Wenfa
Published: January 2018

Signalling helps connects different organisms in the biosphere into one integrated community by facilitating flows of metabolites, nutrients, energy, and genetic information between organisms. In particular, interactions between microbes and higher organisms are of special interest given accumulating evidence of microbial consortia’s roles in mediating various host physiological and metabolic processes in health and disease. Specifically, various studies have highlighted important ecophysiological roles of interkingdom signalling between bacteria and insects; for example, bacteria secrete odourous compounds to attract and enlist the help of blow flies for dispersal to new ecological niches. This abstract-only preprint describes the odour mediated attraction of flies to stationary phase aerobic liquid cultures of Bacillus subtilis NRS-762 (ATCC 8473) maintained on an open orbital shaker at 25 oC and 250 rpm. Specifically, odour emanation from late stationary phase culture coincided with the attraction of flies to the shake-flasks’ cotton plugs in a concentration-dependent manner. Further, observation of the flies’ more intense attempts at entering the cotton plugs’ matrix with greater odour intensity suggested possible behaviour modifying effects of the secreted compounds. Additionally, decline in optical density with increase in odour pungency suggested volatile compound(s) secretion was a nutritional stress response mediated by a feedback loop linking population size and cell survival response. Similar odour also emanated from B. subtilis cultivated at 30 and 37 oC, but the closed incubators prevented fly entry. Flies were not attracted to odourous stationary phase cultures of Escherichia coli DH5α, Pseudomonas aeruginosa PRD-10, and Pseudomonas protegens Pf-5, cultivated under identical conditions; thereby, pointing to the signalling molecules’ species-specificity. Altogether, the secreted volatile compound(s) might serve as interkingdom messengers for enlisting flies to disperse B. subtilis to habitats with more favourable nutritional and environmental conditions, while the bacteria provided the flies with physiological and metabolic functions in return. Further, interkingdom signalling might be one arm of a two-prong strategy helping to ensure bacteria population survival. Specifically, species dispersal via interkingdom signalling is a useful hedge against possible irreversible decline in a microcosm’s habitability, while other mechanisms (such as cannibalism) operate in parallel to help B. subtilis ride out short-term environmental fluctuations. Collectively, the observations highlighted possible ecophysiological roles of bacteria secreted volatile compounds in mediating interkingdom communication with flies – and opens up interesting lines of research in ecology, cell-cell signalling, stress response, and gut microbiota-host interactions
Possible odour-mediated attraction of flies to Bacillus subtilis NRS-762 stationary phase culture
Authors: Ng Wenfa
Published: January 2018

Signalling helps connects different organisms in the biosphere. This research note describes the possible concentration-dependent odour mediated attraction of flies to stationary phase aerobic liquid cultures of Bacillus subtilis NRS-762 maintained on an open orbital shaker at 25 oC. Greater odour pungency was observed to correlate with more intense “foraging” attempts, which suggested the compounds’ possible behaviour modifying effects. Additionally, co-occurrence of optical density decline and increase in odour pungency suggested volatile compound(s) secretion might be a cell survival response mediated by a cell density-based signalling mechanism. Flies were not attracted to odourous stationary phase cultures of other common bacteria (Escherichia coli DH5α, Pseudomonas aeruginosa PRD-10, and Pseudomonas protegens Pf-5, which suggested species-specificity of the volatile compound(s). Altogether, volatile compound(s) might serve as interkingdom messengers to enlist flies for dispersing B. subtilis to habitats with more favourable conditions in coping with possible irreversible decline in habitability, and operate in parallel with other in situ mechanisms such as cannibalism and sporulation that help B. subtilis ride out short- and long-term environmental fluctuations, respectively. Interested researchers are invited to build upon the preliminary findings.
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Authors: Parks Donovan H , Imelfort Michael , Skennerton Connor T , Hugenholtz Philip , Tyson Gene W
Published: January 2018

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. While this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of ‘marker’ genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate, single cell and metagenome derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination, and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.
Free Flow of Sweat due to Loss of Surface Tension at Sweat Droplet Causes Water-Induced Skin Wrinkling
Authors: Marasakatla Soumya , Marasakatla Karunakar
Published: January 2018

Sweat from the body is regulated by the surface tension of a sweat droplet at the pores and the pressure within the sweat duct. A sweat droplet grows in size until its surface tension and the pressure within the sweat duct are in equilibrium. When a hand is immersed in water, sweat droplets easily merge within the water, causing the pressure to drop at the pores. This in turn makes the sweat to flow freely into the water in the absence of counteracting pressure. Sweat glands produce more sweat because of the low pressure within the duct. To prevent loss of water from the body and to maintain the homeostasis, the body reacts by restricting the blood flow to the hand causing vasoconstriction and eventual wrinkling of the skin.
Free Flow of Sweat due to Loss of Surface Tension at Sweat Droplet Causes Water-Induced Skin Wrinkling
Authors: Marasakatla Soumya , Marasakatla Karunakar
Published: January 2018

Water immersion skin wrinkling appears to be a result of breaking the balance between the pressure within sweat duct and the pressure exerted by the surface tension of sweat droplet at the pore. When a hand is immersed in water, sweat droplets easily merge within the water causing pressure to drop at the pores. The resulted imbalance in pressure makes the sweat within the duct to flow freely into the water. To prevent loss of water from the body and to maintain homeostasis, the body reacts by restricting blood flow to hand causing vasoconstriction and eventual wrinkling of skin.
Free Flow of Sweat due to Loss of Surface Tension at Sweat Droplet Causes Water-Induced Skin Wrinkling
Authors: Marasakatla Soumya , Marasakatla Karunakar
Published: January 2018

Water immersion skin wrinkling appears to be the result of breaking the balance between secretory pressure of sweat glands and the pressure exerted by the surface tension of sweat droplet at the pore. When a hand is immersed in water, sweat droplet easily merge within the water causing pressure to drop at the pore. The resulted imbalance in pressure enables the sweat to flow freely into the water. Flow of sweat continues as long as there is a blood flow to hand. To prevent the loss of sweat from the body and to maintain homeostasis, sympathetic nerves trigger the reduction of blood flow to hand causing vasoconstriction. The overlying skin wrinkles due to loss of volume under the skin.
Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs
Authors: Taylor Michael P
Published: January 2018

Attempts to reconstruct the neutral neck posture of sauropod dinosaurs, or indeed any tetrapod, are doomed to failure when based only on the geometry of the bony cervical vertebrae. The thickness of the articular cartilage between the centra of adjacent vertebrae affects posture. It extends (raises) the neck by an amount roughly proportional to the thickness of the cartilage. It is possible to quantify the angle of extension at an intervertebral joint: it is roughly equal, in radians, to the cartilage thickness divided by the height of the zygapophyseal facets over the centre of rotation. Applying this formula to published measurements of well-known sauropod specimens suggests that if the thickness of cartilage were equal to 4.5%, 10% or 18% of centrum length, the neutral pose of the Apatosaurus louisae holotype CM 3018, would be extended by an average of 5.5, 11.8 or 21.2 degrees, respectively, at each intervertebral joint. For the Diplodocus carnegii holotype CM 84, the corresponding angles of additional extension are even greater: 8.4, 18.6 or 33.3 degrees. The neutral postures calculated for 10% cartilage – the most reasonable estimate – appear outlandish, but it must be remembered that these would not have been the habitual life postures, because animals habitually extend the base of their neck and flex the anterior part, yielding the distinctive S-curve most easily seen in birds.
A research data sharing game
Authors: Pronk Tessa E , Wiersma Paulien H , van Weerden Anne
Published: January 2018

While reusing research data has evident benefits for the scientific community as a whole, decisions to archive and share these data are primarily made by individual researchers. For individuals, it is less obvious that the benefits of sharing data outweigh the associated costs, for example time and money. In this sense the problem of data sharing resembles a typical game in interactive decision theory, more commonly known as game theory. Within this framework we analyse how measures to promote sharing and reuse of research data affect individuals who do and do not share data. We find that the scientific community can benefit from top-down policies to enhance sharing data even when the act of sharing itself implies a cost. Namely, if (almost) everyone shares, many individuals receive benefits, as datasets in our model can be reused to achieve a higher efficiency (i.e. more publications, higher quality papers). Surprisingly, as sharing implies a cost, even sharing individuals themselves, in a community in which sharing is common, can gain a higher efficiency than individuals who do not share, in a community in which sharing is not common. In addition to these findings, we find that measures to ensure better data retrieval and quality can compensate for sharing costs by further enabling reuse. Nevertheless, an individual researcher who decides not to share omits the costs of sharing. Assuming that the natural tendency will be to use a strategy that will lead to maximisation of individual efficiency, we see the average scientific community efficiency in our model steadily drop as more individuals decide not to share. With this in mind, we conclude that the key to motivate the researcher to share data lies in reducing the costs associated with sharing, or even better, turning it into a benefit.
The manufacture and preliminary testing of a novel Bio-MEMS filtration chip
Authors: Docker Peter T , Prince Mark , Ma Xianghong , Ward Mike , Kinnell Peter
Published: January 2018

In the clinical/microbiological laboratory there are currently several ways of separating specific cells from a fluid suspension. Conventionally cells can be separated based on size, density, electrical charge, light-scattering properties, and antigenic surface properties. Separating cells using these parameters can require complex technologies and specialist equipment which may damage sensitive cells. The pumping mechanism described here leaves samples undamaged either mechanically or chemically unlike many other current filtration techniques. This paper proposes new Bio-MEMS filtration chips manufactured using micro systems technology (MST) that, when used in conjunction with an optical microscope and a syringe, can filter and grade cells for size without the requirement for additional expensive equipment. These chips also offer great versatility in terms of design and their low cost allows them to be disposable, eliminating sample contamination.
Species divergence, selection and polymorphism in the MHC of crows
Authors: Eimes John A , Townsend Andrea K , Sepil Irem , Nishiumi Isao , Satta Yoko
Published: January 2018

The relatively high level of polymorphism usually found in the major histocompatibility complex (MHC) is usually attributed to pathogen mediated selection; however, the timescale of selection is often unclear. Here we describe the MHC class II (IIB) in three passerine bird species in the genus Corvus: American, carrion and jungle crows. Carrion and American crows are recently diverged, but allopatric, sister species, whereas carrion and jungle crows are more distantly related but sympatric, likely sharing pathogens linked to MHC IIB polymorphisms. These patterns of evolutionary divergence and current geographic ranges enabled us to examine evidence for ancient versus recent selection, trans-species polymorphism, and convergent evolution of the MHC in closely related species. Among the three species, the MHC IIB genes were highly duplicated (7-20 variants per individual) and polymorphic (an average of 79 variants per species; N = 18/species). Phylogenetic reconstructions of MHC IIB revealed patterns that were inconsistent with the evolutionary histories of the species. Several well supported interspecific clusters were observed, indicating trans-species polymorphism within this genus. Clustering of positively selected amino acids by supertyping revealed a single supertype shared by only jungle and carrion crows, whereas all other supertypes were shared among the three species, a pattern consistent with convergent evolution.
Comparing size of morphospace occupation among extant and cretaceous fossil freshwater mussels using Elliptical Fourier Analysis
Authors: Burton-Kelly Matt , Hartman Joseph H
Published: January 2018

Background. Freshwater mussels of superfamily Unionoidea are a diverse group with an evolutionary history of at least 360 million years. Many fossil and modern species exhibit a generally unsculptured, roughly elliptical shell outline. Such morphology causes difficulties when attempting to identify or classify fossil material, as only hard parts are preserved. Several latest-Cretaceous fossil localities over a small area in southwestern North Dakota contain poorly preserved edentulous freshwater mussels that effectively lack all but shell outlines. This paper discusses methods that were used to attempt to determine how many fossil taxa were present at one of these assemblages. Methods. Elliptical Fourier Analysis was performed on two-dimensional shell outlines of both the fossils and edentulous modern taxa to create Fourier scores representing outline shape. Morphospace occupation, or the amount of variation within a sample of shell outlines, was calculated using two methods: within-group dispersion and sum of variance. Morphospace occupation was compared among each of the modern taxa (at both genus and species levels) and the fossil assemblage using confidence intervals, ANOVA, and Tukey’s HSD tests. Results. The amount of outline variation within the fossil assemblage tested is more than some modern genera and species and less than others. Morphospace occupation and confidence intervals are defined for the modern taxa that were examined. Discussion. Although results were inconclusive, discussion points are presented to drive future research. Methodological improvements are suggested including choice of extant (comparative) genera, ontogeny and size, morphological plasticity, phenotypic convergence, taphonomic deformation, and geometric morphometrics in general.
Two perils of binary categorization: Why the study of concepts can’t afford true/false testing
Authors: Jensen Greg , Altschul Drew
Published: January 2018

In this opinion piece, we outline two shortcomings in experimental design that limit the claims that can be made about concept learning in animals. On the one hand, most studies of concept learning train too few concepts in parallel to support general claims about their capacity of subsequent abstraction. On the other hand, even studies that train many categories of stimulus in parallel only test one or two stimuli at a time, allowing even a simplistic learning rule to succeed by making informed guesses. To demonstrate these shortcomings, we include simulations performed using an off-the-shelf image classifier. These simulations demonstrate that, when either training or testing are overly simplistic, a classification algorithm that is incapable of abstraction nevertheless yields levels of performance that have been described in the literature as proof of concept learning in animals.
Trail Making contributes to subjective judgment of visual efficiency in older adults
Authors: Setti Annalisa , Loughman James , Savva George M , Kenny RoseAnne
Published: January 2018

Introduction: The determinant factors that influence self-reported quality of vision have yet to be fully elucidated. This study evaluated a range of contextual information, established psychophysical tests, and in particular, a series of cognitive tests as potentially novel determinant factors. Materials & Methods: Community dwelling adults (aged 50+) recruited to Wave 1 of The Irish Longitudinal Study on Ageing, excluding those registered blind, participated in this study (N=5021). Self-reports of vision were analysed in relation to visual acuity and contrast sensitivity, ocular pathology, visual (Choice Response Time task; Trail Making Test) and global cognition. Contextual factors such as having visited an optometrist and wearing glasses were also considered. Ordinal logistic regression was used to determine univariate and multivariate associations. Results and Discussion: Poor Trail Making Test performance (Odds ratio, OR= 1.36), visual acuity (OR =1.72) and ocular pathology (OR=2.25) were determinant factors for poor versus excellent vision in self-reports. Education, wealth, age, depressive symptoms and general cognitive fitness also contributed to determining self-reported vision. Conclusions: Trail Making Test contribution to self-reports may capture higher level visual processing and should be considered when using self-reports to assess vision and its role in cognitive and functional health.
Spatiotemporal diversity, structure and trophic guilds of insect assemblages in a semi-arid Sabkha ecosystem
Authors: Chenchouni Haroun , Menasria Taha , Neffar Souad , Chafaa Smail , Bradai Liès , Mekahlia Mohamed Nacer , Chaibi Rachid , Bendjoudi Djamel , Si Bachir Abdelkrim
Published: January 2018

The current study highlights some knowledge on the diversity and structure of insect communities and trophic groups living in Sabkha Djendli (semi-arid area of Northeastern Algeria). The entomofauna was monthly sampled from March to November 2006 using pitfall traps at eight sites located at the vicinity of the Sabkha. Structural and diversity parameters (species richness, Shannon index, evenness) were measured for both insect orders and trophic guilds. The canonical correspondence analysis (CCA) was applied to determine how vegetation parameters (species richness and cover) influence spatial and seasonal fluctuations of insect assemblages. The catches totalled 434 insect individuals classified into 75 species, 62 genera, 31 families and 7 orders, where Coleoptera and Hymenoptera were the most abundant and constant over seasons and study stations. Spring and autumn presented the highest values of diversity parameters. Based on catch abundance, the structure of functional trophic groups was predator (37.3%), saprophagous (26.7%), phytophagous (20.5%), polyphagous (10.8%), coprophagous (4.6%); whereas in terms of numbers of species, they can be classified as phytophagous (40%), predators (25.3%), polyphagous (13.3%), saprophagous (12%), coprophagous (9.3%). The CCA demonstrated that phytophagous and saprophagous as well as Coleoptera and Orthoptera were positively correlated with the two parameters of vegetation, especially in spring and summer. While the abundance of coprophagous was positively correlated with species richness of plants, polyphagous density was positively associated with vegetation cover. The insect community showed high taxonomic and functional diversity that is closely related to diversity and vegetation cover in different site stations and seasons.
Impact of wolf hunting policy on moose populations in northern Minnesota
Authors: Kelly Thomas B
Published: January 2018

An ongoing and politically sensitive aspect of proper ecological stewardship revolves around improving the conditions and health of all of the species in the area of concern including both predator and prey species. Human industrial activities have dramatically reduced the land area available to the native species which has placed stresses and fragility into the ecological web. Maintaining proper ecological dynamics has become a critical aspect of policy initiatives designed to safeguard our natural reserves including the establishment of ecological forests and sanctuaries. Herein we outline our proposal to tackle a central issue in wildlife management: improving our knowledge of predator-prey dynamics that vary both temporally and specially in non-linear ways. By leveraging techniques pioneered in other disciplines in addition to the traditional methods, we aim to drastically improve our understanding of the Moose-Grey Wolf interaction and to develop a system with applicability in other regions and other species.
Noise and metabolic free energy in high-order biocognition
Authors: Wallace Rodrick
Published: January 2018

We examine the possible role of 'noise' as a control signal for large-scale cognitive biological phenomena that recruit simpler cognitive modules into temporary, dynamic working coalitions. Noise color, as well as magnitude, may convey essential control information, a possibly important extension of the Data Rate Theorem. An adaptation of the Black-Scholes model suggests the availability of metabolic free energy can determine rates of coalition biocognition in the presence of noise. Evolutionary process may have exapted colored noise as a subtle tool for the regulation of biological phenomena, supplementing direct molecular signals. Experimental verification of this conjecture may be similarly subtle.
Efficient algorithms for sampling feasible sets of macroecological patterns
Authors: Locey Kenneth J. , McGlinn Daniel J.
Published: January 2018

Ecological variables such as species richness (S) and total abundance (N) can strongly influence the forms of macroecological patterns. For example, the majority of variation in the species abundance distribution (SAD) can often be explained by the majority of possible forms having the same N and S, i.e. the feasible set. The feasible set reveals how variables such as N and S determine observable variation and whether empirical patterns are exceptional to the majority of possible forms. However, this approach has currently only been applied to the SAD using relatively inefficient random sampling algorithms. We extend the use of the feasible set approach by developing new algorithms to efficiently generate random samples of the feasible set for the SAD and the intraspecific spatial abundance distribution (SSAD). These algorithms are often several orders of magnitude faster than a previous method, which greatly increases the size and diversity of communities that can be examined.
Of mice, macaques and men: scaling of virus dynamics and immune responses
Authors: Althaus Christian L
Published: January 2018

In this Opinion piece, I argue that the dynamics of viruses and the cellular immune response depend on the body size of the host. I use allometric scaling theory to interpret observed quantitative differences in the infection dynamics of lymphocytic choriomeningitis virus (LCMV) in mice (Mus musculus), simian immunodeficiency virus (SIV) in rhesus macaques (Macaca mulatta) and human immunodeficiency virus (HIV) in humans. However, additional data on the kinetics of virus replication and the dynamics of T cell responses in different host species will be required to shed more light on the question whether the nature of viral infections is affected by the body size of their hosts.
Morphological diversity in tenrecs (Afrosoricida, Tenrecidae): comparing tenrec skull diversity to their closest relatives
Authors: Finlay Sive , Cooper Natalie
Published: January 2018

Morphological diversity is often studied qualitatively. However, to truly understand the evolution of exceptional diversity, it is important to take a quantitative approach instead of relying on subjective, qualitative assessments. Here, we present a quantitative analysis of morphological diversity in a Family of small mammals, the tenrecs (Afrosoricida, Tenrecidae). Tenrecs are often cited as an example of an exceptionally morphologically diverse group. However, this assumption has not been tested quantitatively. We use geometric morphometric analyses of skull shape to test whether tenrecs are more morphologically diverse than their closest relatives, the golden moles (Afrosoricida, Chrysochloridae). Tenrecs occupy a wider range of ecological niches than golden moles so we predict that they will be more morphologically diverse. Contrary to our expectations, We find that tenrec skulls are only more morphologically diverse than golden moles when measured in lateral view. Furthermore, similarities among the species-rich Microgale tenrec Genus appear to mask higher morphological diversity in the rest of the Family. These results reveal new insights into the morphological diversity of tenrecs and highlight the importance of using quantitative methods to test qualitative assumptions about patterns of morphological diversity.
Demographics and feeding ecology of whale sharks at Mafia Island, Tanzania
Authors: Cagua Edgar F , Cochran Jesse , Rohner Chris , Igulu Mathias M , Rubens Jason , Pierce Simon , Berumen Michael L
Published: January 2018

Background. The Western Indian Ocean is a globally important region for the whale shark Rhincodon typus, with well-studied coastal aggregation sites in southern Mozambique, Seychelles and Djibouti. Here we present an overview of a new study at Mafia Island, Tanzania.

Methods. We monitored whale shark abundances on 103 boat trips from October 2012–March 2013. We also used passive acoustic telemetry (VEMCO® V16 tags) and photographic identification to monitor the residency times and local movements of 29 tagged individuals. Shark sizes were estimated using laser photogrammetry.

Results. In total we observed 87 individual sharks with a mean of 5.1 ± 5.2 (± SD) per trip and a peak in December of 8.2 ± 6.3. Total length ranged from 4.1 to 9.7 m and almost all sharks were immature. After boat-based visual observations dropped to zero in March 2013 (with the same ongoing sampling effort), the acoustic array still detected 75% of tagged sharks. Tagged individuals were detected by the acoustic array for 73 ± 40 days on average. They showed a strong site fidelity to a 15 km2 area in the inner part of the bay and then progressively moved offshore at the end of the season, matching a decrease in plankton abundance. Sharks were mostly observed feeding on dense patches of the pelagic shrimp Lucifer hansoni, often in association with planktivorous fishes. Photo IDs from 2007-09 and 2012-13 indicate that a large proportion of the juvenile individuals return to Mafia Island each spring-summer.

Conclusion. The size range and gender distribution of whale sharks at Mafia Island is similar to other coastal aggregations in the Indian Ocean, but the relatively high site fidelity and residency time stands in contrast.
Dynamics of chlorophyll and N concentration on e0 and e3 leaves of maize hybrids in winter in subtropical region
Authors: Adhikari Nav Raj , Ghimire Surya Kant , Sah Shrawan Kumar , Koirala Keshab Babu
Published: January 2018

National maize productivity is very low in Nepal. Increase of the productivity is only possible through growing high grain yielding single cross hybrid maize cultivar. So, development and evaluation of maize hybrids are principal steps to select high grain yielding and superior hybrid for cultivar. For it, fifteen newly bred single cross hybrids of yellow maize were examined from the standpoint of chlorophyll (chl) dynamics and their effects on grain yield. For it, a trial of RCBD experiment was conducted in open field in winter in subtropical region in Nepal. Seeds were sown on October 3, 2012 plot in two row plot area of 1.4 x 3.0 m2. After anthesis, chl and N concentration (conc) implying RAT (red light absorbance-transmittance) SPAD measure were taken from the topmost ear (e0) and third (e3) leaf above the e0 in ten days interval during grain filling. SPAD measures were transformed to total chl and N conc. E0 leaf has been found more grain yield determining than e3 leaf and terminal grain filling duration has been found more determining than early grain filling from the standpoint of correlation of grain yield with chl, N conc and SPAD measure. From pooled variance analysis; SPAD and chl conc were not significant different in different leaves and among the hybrids (Hybrids x Leaves x Ages). But, the SPAD and chl conc were significant different among the two leaves and ages (Leaves x Ages) irrespective of the hybrids. Different to the SPAD and chl conc, N conc was significant different in the leaves among the hybrids with respect to ages of the plants among the hybrids (Hybrids x Leaves x Ages). Thirteen top high grain yielding hybrids (HGYHs) 8, 12, 11, 13, 5, 6, 10, 1, 7, 14, 2, 9 and 15 were non-significant different from the standpoint of grain yield. The SPADs were in the non-significant range of 51-55 in e0 leaf in the duration from 95 to 125 d among the fifteen hybrids. Among the top four HGYHs 8, 12, 11 and 13; hybrid 11 lost chl and N from e0 leaf significantly on 135th d relative to the most of the hybrids. It means that the hybrid 11 could efficiently degrade N containing soluble protein and chl even from e0 leaf relatively. Top five HGYHS 8, 12, 11, 5 and 6 except 13 among the top listed ten hybrids constantly maintained chl and N conc implying SPAD in the e0 leaf up to the 135th d. In addition, it implies that these five hybrids sent newly up-taken N to kernels without degradation of the proteins and chl from the e0 leaf till the age of 135 d. HGYH 8 had degraded soluble proteins and enzymes and chl in e3 leaf and mobilized the degraded N to the kernels more efficiently from the e3 leaf. It is not necessary that maize hybrids must constantly maintain soluble proteins and chl conc during most of early to mid-grain filling duration for high grain yield. Instead, efficient reasonable decline of the soluble protein and chl conc during early to mid-grain filling also accelerate grain filling phenomena.
Dynamics of chlorophyll and N concentration on e0 and e3 leaves of maize hybrids in winter in subtropical region
Authors: Adhikari Nav Raj , Ghimire Surya Kant , Sah Shrawan Kumar , Koirala Keshab Babu
Published: January 2018

National maize productivity is very low in Nepal. Increase of the productivity is only possible through growing high grain yielding single cross hybrid maize cultivar. So, development and evaluation of maize hybrids are principal steps to select high grain yielding and superior hybrid for cultivar. For it, fifteen newly bred single cross hybrids of yellow maize were examined from the standpoint of chlorophyll (chl) dynamics and their effects on grain yield. For it, a trial of RCBD experiment was conducted in open field in winter in subtropical region in Nepal. Seeds were sown on October 3, 2012 plot in two row plot area of 1.4 x 3.0 m2. After anthesis, chl and N concentration (conc) implying RAT (red light absorbance-transmittance) SPAD measure were taken from the topmost ear (e0 or E0) and third (e3 or E3) leaf above the e0 in ten days interval during grain filling. SPAD measures were transformed to total chl and N conc. E0 leaf has been found more grain yield determining than e3 leaf and terminal grain filling duration has been found more determining than early grain filling from the standpoint of correlation of grain yield with chl, N conc and SPAD measure. From pooled variance analysis; SPAD and chl conc were not significant different in different leaves and among the hybrids (Hybrids x Leaves x Ages). But, the SPAD and chl conc were significant different among the two leaves and ages (Leaves x Ages) irrespective of the hybrids. Different to the SPAD and chl conc, N conc was significant different in the leaves among the hybrids with respect to ages of the plants among the hybrids (Hybrids x Leaves x Ages). Thirteen top high grain yielding hybrids (HGYHs) 8, 12, 11, 13, 5, 6, 10, 1, 7, 14, 2, 9 and 15 were non-significant different from the standpoint of grain yield. The SPADs were in the non-significant range of 51-55 in e0 leaf in the duration from 95 to 125 d among the fifteen hybrids. Among the top four HGYHs 8, 12, 11 and 13; hybrid 11 lost chl and N from e0 leaf significantly on 135th d relative to the most of the hybrids. It means that the hybrid 11 could efficiently degrade N containing soluble protein and chl even on e0 leaf relatively. Top five HGYHs 8, 12, 11, 5 and 6 except 13 among the top listed ten hybrids constantly maintained chl and N conc implying SPAD on the e0 leaf up to the 135th d. In addition, it implies that these five hybrids sent newly up-taken N to kernels without degradation of the proteins and chl from the e0 leaf till the age of 135 d. HGYH 8 had degraded soluble proteins and enzymes and chl on e3 leaf and mobilized the degraded N to the kernels more efficiently from the e3 leaf. It is not necessary that maize hybrids must constantly maintain soluble proteins and chl conc during most of early to mid-grain filling duration for high grain yield. Instead, diagnostic decline of the soluble protein and chl conc during early to mid-grain filling also accelerate grain filling phenomena.
Exome sequencing, histoincompatibility and long-term kidney allograft function
Authors: Mesnard Laurent , Muthukumar Thangamani , Burbach Maren , Li Carol , Shang Huimin , Dadhania Darshana , Lee John R , Sharma Vijay K , Xiang Jenny , Friedewald John J , Abecassis Michael M , Suthanthiran Manikkam , Campagne Fabien
Published: January 2018

BACKGROUND: Kidney transplantation is the treatment of choice for most patients with end-stage renal disease and existing data suggest that post transplant graft function is a predictor of kidney graft failure. METHODS: Exome sequencing of DNA from kidney graft recipients and their donors was used to determine recipient and donor mismatches at the amino acid level. The number of mismatches that are more likely to induce an immune response in the recipient was computationally estimated and designated the allogenomics mismatch score. The relationship between the allogenomics score and post transplant kidney allograft function was examined using linear regression. RESULTS: A significant inverse correlation between the allogenomics mismatch score and kidney graft function at 36 months post transplantation was observed in a discovery cohort of kidney recipient-donor pairs (r2>=0.57, P<0.05, the score vs. level of serum creatinine or estimated glomerular filtration rate). This relationship was confirmed in an independent validation cohort of kidney recipient-donor pairs. We observed that the strength of the correlation increased with time post-transplantation. This inverse correlation remained after excluding HLA loci from the calculation of the score. Exome sequencing yielded allogenomics scores with stronger correlations with graft function than simulations of genotyping assays which measure common polymorphisms only. CONCLUSIONS: The allogenomics mismatch score, derived by exome sequencing of recipient-donor pairs, facilitates quantification of histoincompatibility between the organ donor and recipient impacting long-term post transplant graft function. The allogenomics mismatch score, by serving as a prognostic biomarker, may help identify patients at risk for graft failure.
Phylogenetic relationships and biogeographical history of the large extinct European testudinids
Authors: Vlachos Evangelos , Pérez-García Adán , Rabi Márton
Published: January 2018

Background. Large-sized testudinids had a long evolutionary history in Europe during the last 50 million years before becoming extinct in the beginning of the Pleistocene. Despite a 150-year long history in research and a decent fossil record, the European large testudinids have received limited attention so far. Methods. New excavations, descriptions of new specimens from Greece, Spain and Germany, revisions of previously published European taxa and comparative studies with extant testudinids now provide a major advancement in understanding the anatomy and evolutionary history of these turtles. This contribution aims to provide an updated summary of the accumulated knowledge on European large tortoises and to explore in detail their phylogenetic relationships in a global context (including small-sized extinct and extant taxa). The phylogenetic analysis is based on a new character/taxon matrix of morphological characters. Parsimony analysis was performed both with and without molecular backbone constraints. Results. We describe new material of large testudinids from Greece, Spain and Germany and revise most of the available material that has been previously published. Our morphology-based results are promising since they are consistent with recent molecular studies in identifying large testudinids traditionally referred to the Geochelone complex as polyphyletic. Furthermore, we were able to reproduce the molecular phylogeny of Mediterranean tortoises (Testudona). Discussion. The phylogenetic framework presented here allows addressing several open questions of the history of testudinids. First of all, it hints to a more complex biogeographic history of European testudinids than previously recognized. Although the early Paleogene history of testudinids cannot be accurately traced at the moment it seems probable that, besides Asia and North America, Europe also played a major role in the early diversification of Testudinidae. We demonstrate that large European testudinids do not form a monophyletic lineage. The widely recognized genus Cheirogaster should only include the Eocene type species, and exclude other large Paleogene or giant Neogene taxa so far known. Our analysis reveals that large size evolved independently in several clades and in several continents during warmer parts of the Cenozoic. Besides this general scheme other factors might have played a role regionally (e.g. changes in vegetation, island isolation).
Using Bayesian hierarchical models and random forest algorithm for habitat use studies: a case of nest site selection of the crested ibis at regional scales
Authors: Li Xinhai , Zhai Tianqing , Jiao Yan , Wang Guiming
Published: January 2018

The association of species distribution and environmental variables is often complex, with nonlinear and interacting effects. Bayesian hierarchical models can quantify linear and high order effects of the variables, as well as their interaction effects. Their strength is to take into account the uncertainties in observation, models, and parameters. However, the model selection process is usually time-consuming, especially when the number of environmental variables is large. Random forest, an efficient machine learning algorithm, can rank the environmental variables so as to facilitate the model selection process. We analyzed the nest site selection of the crested ibis (Nipponia nippon) at watersheds in its distribution range. The crested ibis has attracted much attention in the past 30 years due to its extremely low population level, and now it has recovered to over 1,000 individuals in the wild. We built Bayesian hierarchical models to quantify the association between the number of nests in 95 watersheds and nine environmental variables of these watersheds. We applied random forest to check the effect of every variable and removed the unimportant variables from the hierarchical models. Unlike our previous studies, we found that the interaction between the area of rice paddy and the area of water bodies (i.e. rivers, lakes and ponds) had most contribution to the nest site selection, whereas the linear terms of either rice paddy or water body had little effects. The detection probability of the nests during the surveys was inversely associated with elevation and the standard deviation of elevation (i.e. roughness of the landscape) in the watershed. Our models provide the insight that the crested ibis need both rice paddies and water bodies in their annual life cycle. Habitat protection practices should cover not only rice paddies, but also water bodies to ensure long term survival of this endangered bird.
Colourless agar for enhanced colour contrast between microbial colonies and solid medium
Authors: Ng Wenfa
Published: January 2018

Agar medium enables spatially-resolved simultaneous cultivation of different microbes in a simple and relatively low-cost format useful for preliminary screening of microbial diversity. Lack of colour contrast between colonies and agar, however, hampers colony identification by automated image analysis – thus, presenting a challenge for phenotype screening experiments and viable cell counting. Since microbes secrete pigments of myriad hues, this research sought to develop a colourless agar - which when placed on coloured paper of suitable hue – would enhance the colour contrast between agar and colonies of any colour. Nevertheless, the concept is confounded by formation of coloured compounds between medium components during autoclave sterilisation, which, in this study, was prevented by dissolving glucose and ammonium chloride in two separate solutions containing other medium components. Upon mixing the two solutions after heat sterilisation, a colourless agar was obtained – which remained colourless even after adding sterile yeast extract (max: 1 g/L) for providing essential vitamins to microbes unable to synthesise them. Culture experiments revealed good growth of Escherichia coli DH5α (ATCC 53868), Pseudomonas fluorescens Pf-5 (ATCC BAA-477), Pseudomonas aeruginosa (ATCC 15442), and Bacillus subtilis (ATCC 8473) with cell yield positively correlated with yeast extract concentration. Additionally, identical viable cell concentration and colonies of similar morphologies were observed on both the colourless and LB agar; thus, suggesting that no inhibitory compounds were formed during agar preparation. Collectively, using commonly used buffer components, salts and nutrients, a colourless agar was prepared by segregating chromogenic compounds during heat sterilisation; thereby, opening up its potential use in enhancing colour contrast between colonies and agar medium for revealing finer details of pure culture colonies, or more accurate automated colony identification and counting in screening and viable cell count assays.
Colourless agar for enhanced colour contrast between microbial colonies and solid medium
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Solid medium enables spatially resolved simultaneous cultivation of different microbes in a simple and relatively low cost format useful for preliminary screening of microbial diversity. Lack of colour contrast between colonies and agar, however, hampers colony identification by automated image analysis – thus, presenting a challenge for phenotype screening experiments and viable cell counting. Since microbes secrete pigments of myriad hues, this research sought to develop a colourless agar - which when placed on coloured paper of suitable hue – would enhance the colour contrast between agar and colonies of any colour. However, the concept is confounded by formation of coloured compounds between medium components during autoclave sterilization, which, in this study, was prevented by dissolving glucose and ammonium chloride in two separate solutions containing other medium components. Upon mixing the two solutions after heat sterilization, a colourless agar was obtained – which remained colourless even after adding sterile yeast extract (max: 1 g/L) for providing essential vitamins to microbes unable to synthesize them. Culture experiments revealed good growth of Escherichia coli DH5α (ATCC 53868), Pseudomonas protegens Pf-5 (ATCC BAA-477), Pseudomonas aeruginosa (ATCC 15442), and Bacillus subtilis (ATCC 8473) with cell yield positively correlated with yeast extract concentration. Additionally, identical viable cell concentration and colonies of similar morphologies were observed on both the colourless and LB agar; thus, suggesting that no inhibitory compounds were formed during agar preparation. Collectively, using commonly used buffer components, salts and nutrients, a colourless agar was prepared by segregating chromogenic compounds during heat sterilization; thereby, opening up its potential use in enhancing colour contrast between colonies and agar medium for revealing finer details of pure culture colonies, or more accurate automated colony identification and counting in screening and viable cell count assays.