bluuebunny/crossref_metadata_2025 huggingface dataset:
The natural selection of metabolism and mass selects allometric transitions from prokaryotes to mammals
Authors: Witting Lars
Published: November 2016

Inter-specific body mass allometries can evolve from the natural selection of mass, with ±1/4 and ±3/4 exponents following from the geometry of intra-specific interactions when density dependent foraging occurs in two spatial dimensions (2D, Witting, 1995). The corresponding values for three dimensional interactions (3D) are ±1/6 and ±5/6.

But the allometric exponents in mobile organisms are more diverse than the prediction. The exponent for mass specific metabolism tends to cluster around −1/4 and −1/6 in terrestrial and pelagic vertebrates, but it is strongly positive in prokaryotes with an apparent value around 5/6 (DeLong et al., 2010). And a value around zero has been reported in protozoa, and on the macro evolutionary scale from prokaryotes over larger unicells to multicellular vertebrates (Makarieva et al., 2005, 2008).

I show that mass specific metabolism can be selected as the pace of the resource handling that generates net energy for self-replication and the selection of mass, and that this selection of metabolism and mass is sufficient to explain metabolic exponents that decline from 5/6 over zero to −1/6 in 3D, and from 3/4 over zero to −1/4 in 2D. The decline follows from a decline in the importance of mass specific metabolism for the selection of mass, and it suggestsi) that the body mass variation in prokaryotes is selected from primary variation in mass specific metabolism,ii) that the variation in multicellular animals are selected from primary variation in the handling and/or densities of the underlying resources,iii) that protozoa are selected as an intermediate lifeform between prokaryotes and multicellular animals, andiv) that macro evolution proceeds along an upper bound on mass specific metabolism.
16S rRNA Gene Sequencing as a Clinical Diagnostic Aid for Gastrointestinal-related Conditions
Authors: Almonacid Daniel E. , Kraal Laurens , Ossandon Francisco J. , Budovskaya Yelena V. , Cardenas Juan Pablo , Richman Jessica , Apte Zachary S.
Published: November 2016

Accurate detection of the microorganisms underlying gut dysbiosis in the patient is critical to initiate the appropriate treatment. However, most clinical microbiology techniques used to detect gut bacteria were developed over a century ago and rely on culture-based approaches that are often laborious, unreliable, and subjective. Further, culturing does not scale well for multiple targets and detects only a minority of the microorganisms in the human gastrointestinal tract. Here we present a clinical test for gut microorganisms based on targeted sequencing of the prokaryotic 16S rRNA gene. We tested 46 clinical prokaryotic targets in the human gut, 28 of which can be identified by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. Using microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay accurately quantified all 28 targets and correctly reflected 38/38 verification samples of real and synthetic stool material containing known pathogens. Thus, we have established a new test to interrogate microbiome composition and diversity, which will improve patient diagnosis, treatment and monitoring. More broadly, our test will facilitate epidemiological studies of the microbiome as it relates to overall human health and disease.
Do latitudinal gradients exist in New Zealand stream invertebrate metacommunities?
Authors: Tonkin Jonathan D. , Death Russell G. , Muotka Timo , Astorga Anna , Lytle David A.
Published: November 2016

That biodiversity declines with latitude is well known, but whether a metacommunity process is behind this gradient has received limited attention. We tested the hypothesis that dispersal limitation is progressively replaced by mass effects with increasing latitude, along with a series of related hypotheses. We explored these hypotheses by examining metacommunity structure in stream invertebrate metacommunities spanning the length of New Zealand’s two largest islands (~1300 km), further disentangling the role of dispersal by deconstructing assemblages into strong and weak dispersers. Given the highly dynamic nature of New Zealand streams, our alternative hypothesis was that these systems are so unpredictable (at different stages of post-flood succession) that metacommunity structure is highly context dependent from region to region. We rejected our primary hypotheses, pinning this lack of fit on the strong unpredictability of New Zealand’s dynamic stream ecosystems and fauna that has evolved to cope with these conditions. While local community structure turned over along this latitudinal gradient, metacommunity structure was highly context dependent and dispersal traits did not elucidate patterns. Moreover, the emergent metacommunity types exhibited no trends, nor did the important environmental variables. These results provide a cautionary tale for examining singular metacommunities. The considerable level of unexplained contingency suggests that any inferences drawn from one-off snapshot sampling may be misleading and further points to the need for more studies on temporal dynamics of metacommunity processes.
Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification
Authors: Breitwieser Florian P. , Salzberg Steven L.
Published: November 2016

Pavian is a web application for exploring metagenomics classification results, with a special focus on infectious disease diagnosis. Pinpointing pathogens in metagenomics classification results is often complicated by host and laboratory contaminants as well as many non-pathogenic microbiota. With Pavian, researchers can analyze, display and transform results from the Kraken and Centrifuge classifiers using interactive tables, heatmaps and flow diagrams. Pavian also provides an alignment viewer for validation of matches to a particular genome.

Availability and implementation

Pavian is implemented in the R language and based on the Shiny framework. It can be hosted on Windows, Mac OS X and Linux systems, and used with any contemporary web browser. It is freely available under a GPL-3 license fromhttp://github.com/fbreitwieser/pavian. Furthermore a Docker image is provided athttps://hub.docker.com/r/florianbw/pavian.

Contact

fbreitw1@jhu.edu

Supplementary information

Supplementary data is available at Bioinformatics online.
Adeno-Associated Virus–Mediated Delivery of CRISPR–Cas Systems for Genome Engineering in Mammalian Cells
Authors: Gaj Thomas , Schaffer David V.
Published: November 2016

The CRISPR–Cas9 system has emerged as a highly versatile platform for introducing targeted genome modifications into mammalian cells and model organisms. However, fully capitalizing on the therapeutic potential for this system requires its safe and efficient delivery into relevant cell types. Adeno-associated virus (AAV) vectors are a clinically promising class of engineered gene-delivery vehicles capable of safely infecting a broad range of dividing and nondividing cell types, while also serving as a highly effective donor template for homology-directed repair. Together, CRISPR–Cas9 and AAV technologies have the potential to accelerate both basic research and clinical applications of genome engineering. Here, we present a step-by-step protocol for AAV-mediated delivery of CRISPR–Cas systems into mammalian cells. Procedures are given for the preparation of high-titer virus capable of achieving a diverse range of genetic modifications, including gene knockout and integration.
Quantitation of Apoptosis and Necrosis by Annexin V Binding, Propidium Iodide Uptake, and Flow Cytometry
Authors: Crowley Lisa C. , Marfell Brooke J. , Scott Adrian P. , Waterhouse Nigel J.
Published: November 2016

The surface of healthy cells is composed of lipids that are asymmetrically distributed on the inner and outer leaflet of the plasma membrane. One of these lipids, phosphatidylserine (PS), is normally restricted to the inner leaflet of the plasma membrane and is, therefore, only exposed to the cell cytoplasm. However, during apoptosis lipid asymmetry is lost and PS becomes exposed on the outer leaflet of the plasma membrane. Annexin V, a 36-kDa calcium-binding protein, binds to PS; therefore, fluorescently labeled Annexin V can be used to detect PS that is exposed on the outside of apoptotic cells. Annexin V can also stain necrotic cells because these cells have ruptured membranes that permit Annexin V to access the entire plasma membrane. However, apoptotic cells can be distinguished from necrotic cells by co-staining with propidium iodide (PI) because PI enters necrotic cells but is excluded from apoptotic cells. This protocol describes Annexin V binding and PI uptake followed by flow cytometry to detect and quantify apoptotic and necrotic cells.
Detecting Cleaved Caspase-3 in Apoptotic Cells by Flow Cytometry
Authors: Crowley Lisa C. , Waterhouse Nigel J.
Published: November 2016

Apoptosis is orchestrated by caspases, a family of cysteine proteases that cleave their substrates on the carboxy-terminal side of specific aspartic acid residues. These proteases are generally present in healthy cells as inactive zymogens, but when stimulated they undergo autolytic cleavage to become fully active. They subsequently cleave their substrates at one or two specific sites, which can result in activation, inactivation, relocalization, or remodeling of the substrate. Consequently, many of the cleaved fragments remain intact during apoptosis and can be detected using substrate-specific antibodies. These fragments are most commonly detected by western blotting, which resolves proteins and their fragments based on molecular mass. However, antibodies that only recognize cleaved fragments can be used to specifically label cells in which caspase cleavage has occurred. It is then possible to quantify these cells by flow cytometry. A number of antibodies that specifically recognize caspase-cleaved fragments have been generated, including antibodies that recognize the cleaved form of caspase-3. This caspase is responsible for the majority of proteolysis during apoptosis, and detection of cleaved caspase-3 is therefore considered a reliable marker for cells that are dying, or have died by apoptosis. This protocol outlines the quantification of apoptosis by flow cytometric detection of cleaved caspase-3.
Sequence Alignment and Homology Search
Authors: Hung Jui-Hung , Weng Zhiping
Published: November 2016

Bioinformatics was brought into the spotlight in the late 1990s through the Human Genome Project. With the rapid accumulation of completed genomes, it was soon realized that for the vast majority of the newly identified genes and other functional regions of the genomes there were no other biological data. One way of inferring biological function is through homology: Because homologous genes have a common evolutionary descent, they are likely to have the same biological function. A large number of bioinformatics tools have been designed for rapidly and accurately comparing sequences of genes or proteins, comparing gene sequences with genomes, and comparing genomes. Two widely used tools for sequence alignment and homology searches, BLAST and ClustalW, are introduced here.
Thermal evolution of Mg–Al and Ni–Al layered double hydroxides: the structure of the dehydrated phase
Authors: Cherepanova Svetlana , Leont'eva Natalya , Drozdov Vladimir , Doronin Vladimir
Published: November 2016

Simulation of X-ray diffraction patterns on the basis of the models of one-dimensional disordered crystals was used to investigate the structure of the dehydrated phase produced by dehydration of Mg–Al and Ni–Al layered double hydroxides at a temperature of ∼473–498 K. It was found that the removal of water molecules transforms the initial structure, which is a mixture of 3R1and 2H1polytypes, into a structure that comprises preferentially fragments of 3R2and 1Hpolytypes and has some turbostratic disorder.
100 years of Debye's scattering equation
Authors: Gelisio Luca , Scardi Paolo
Published: November 2016

Debye's scattering equation (DSE) has spanned a century of scientific development, from the dawn of quantum mechanics and the investigation of the structure of atoms and molecules to the era of nanotechnology, paving the way tototal scatteringmethods. The formulation offers the most accurate representation of the intensity scattered by randomly oriented atomic aggregates, constructed by superimposing the signal from each atomic distance in the molecule. The present paper reviews some of the milestone applications, from the interpretation of the intensity curves from gases and vapours, to aggregates of increasing size and more extended order. Important developments, aimed at mitigating the prohibitive computational complexity of the DSE, and state-of-the-art methods for the characterization of static and dynamic displacements are also discussed.
Celebrating 100 years of the Debye scattering equation
Authors: Scardi Paolo , Billinge Simon J. L. , Neder Reinhard , Cervellino Antonio
Published: November 2016

One hundred years of the Debye scattering equation are celebrated with a series of articles arising from the DSE 2015 conference.
Crystal structure of [UO2(NH3)5]NO3·NH3
Authors: Woidy Patrick , Kraus Florian
Published: November 2016

Pentaammine dioxide uranium(V) nitrate ammonia (1/1), [UO2(NH3)5]NO3·NH3, was obtained in the form of yellow crystals from the reaction of caesium uranyl nitrate, Cs[UO2(NO3)3], and uranium tetrafluoride, UF4, in dry liquid ammonia. The [UO2]+cation is coordinated by five ammine ligands. The resulting [UO2(NH3)5] coordination polyhedron is best described as a pentagonal bipyramid with the O atoms forming the apices. In the crystal, numerous N—H...N and N—H...O hydrogen bonds are present between the cation, anion and solvent molecules, leading to a three-dimensional network.
Crystal structure of aquatris{μ-N-[bis(diethylamino)phosphoryl]-2,2,2-trichloroacetamidato-κ3O,O′:O}calciumsodium
Authors: Shatrava Iuliia , Gubina Kateryna , Ovchynnikov Vladimir , Dyakonenko Viktoriya , Amirkhanov Vladimir
Published: November 2016

In the molecular structure of the title compound, [CaNa(C10H20Cl3N3O2P)3(H2O)], the Ca2+ion has a slightly distorted octahedral coordination environment defined by six O atoms which belong to the carbonyl and phosphoryl groups of the three coordinating ligands. Two Cl atoms of CCl3groups and four O atoms form the coordination environment of the Na+ion: three from the carbonyl groups of ligands and one O atom from a coordinating water molecule. In the crystal, the bimetallic complexes are assembled into chains along thec-axis directionviaO—H...O hydrogen bonds that involve the coordinating water molecules and the phosphoryl groups.
Poly[butane-1,4-diammonium [tri-μ-oxalato-dimanganese(II)] hexahydrate]
Authors: Sadakiyo Masaaki , Yamada Teppei , Kitagawa Hiroshi
Published: November 2016

In the title coordination polymer, {(C4H14N2)[Mn2(C2O4)3]·6H2O}n, the MnIIions are octahedrally coordinated by the oxalate ligands to form a two-dimensional honeycomb-like network. This anionic framework incorporates the centrosymmetric butane-1,4-diammonium ions as counter-cations. The two-dimensional network is slightly distorted as a result of the vertically incorporated cations. Three kinds of water molecules are located in an interlayer space, forming hydrogen bonds with the ammonium cations and the oxalate ligands of the framework.
1-Benzyl-3′-[(1H-indol-3-yl)carbonyl]-1′-methyl-2-oxo-4′-(pyridin-3-yl)spiro[indoline-3,2′-pyrrolidine]-3′-carbonitrile
Authors: Seethalakshmi P. , Palanivel C.
Published: November 2016

In the title compound, C34H27N5O2, the central pyrrolidine ring adopts an envelope conformation, with the N atom as the flap. The mean planes of the two indoline ring systems are inclined to the mean plane of the central pyrrolidine ring by 86.26 (9) and 69.30 (9)°, respectively. The dihedral angle between the benzene and pyridine rings is 75.09 (11)°. In the crystal, molecules are linked by N—H...N and C—H...N hydrogen bonds, forming sheets parallel to theabplane.
(E)-4-[4-(Dimethylamino)styryl]-1-methylpyridin-1-ium tetrakis[(Z)-4,4,4-trifluoro-3-oxo-1-(thiophen-2-yl)but-1-en-1-olato]gadolinate(III) with an unknown amount of water as solvate
Authors: Wu Da-Jun , Fang Bin
Published: November 2016

In the complex anion of the title salt, (C16H19N2)[Gd(C8H4F3S)4], the GaIIIcation isO,O′-chelated by four anionic 4,4,4-trifluoro-3-oxo-1-(thiophen-2-yl)but-1-en-1-olate ligands in a distorted square-antiprismatic geometry; the 4-[4-(dimethylamino)styryl]-1-methylpyridin-1-ium cation is nearly planar, with a dihedral angle of 9.6 (5)° between the planes of the pyridine and benzene rings. In the crystal, the cations are linked with the complex anionsviaweak C—H...F and C—H...π interactions. Two of the four independent thiophene rings are disordered over two sites; occupancies were refined to 0.662 (10):0.338 (10). The solvent water molecules are highly disordered in a solvent-accessible void of 54 (3) Å3; the diffuse electron densities were removed from the data set using SQUEEZE [Spek (2015).Acta Cryst. C71, 9–16]. These solvent molecules are not considered in the given chemical formula and other crystal data.
Dyslexia: is it genetic and what does this mean for social inclusion?
Authors: Holttum Sue
Published: November 2016

Purpose

This paper starts by considering what it means if dyslexia has genetic or environmental causes. The author also explains phrases used by genetic researchers and the kind of things they look for in genetic material. The purpose of this paper is to discuss two recent studies on dyslexia that shed light on either genetic or environmental causes.

Design/methodology/approach

One study was a thorough exploration of possible genetic differences that could be present in children experiencing reading and language difficulties. The other study examined a large sample of the Canadian public to see whether there was a link between dyslexia and having experienced physical abuse as a child or teenager.

Findings

The study on genetic differences found no evidence for some previously suggested genetic causes of dyslexia. Although previous studies have suggested dyslexia runs in families, the genetic contribution may have been overestimated. The study on the Canadian public found that people who reported experiencing physical abuse in their younger years were six to seven times more likely also to have a diagnosis of dyslexia. Childhood trauma is known to affect brain development.

Originality/value

Although this paper only discusses two papers in detail, they are two of the most recent explorations of genetic and environmental links to dyslexia. There could be a case for greater attention to possible traumatic experiences in children identified as dyslexic. Physical abuse is one possibility but should never be assumed. Families can be under strain and may need more support. However, dyslexia and the mental health difficulties that can result from childhood trauma can reduce a child’s current and future social inclusion. Early intervention may avert this outcome.
The Corporeal Empire: Physical Education and Politicising Children's Bodies in Late Colonial Bengal
Authors: Topdar Sudipa
Published: November 2016

This article deploys children's bodies as an analytical lens to examine the political significance of knowledge production and childhood in British colonial projects in late colonial India. Scholars have theorised the ‘body as method’ of history to argue that bodies are imbued with meanings, become stakes in power struggles and are sites of knowledge and power. I examine this theme by investigating a key locus of knowledge production for children – the colonial school and its curriculum, specifically physical education. To underline the multi‐stranded processes and loci of colonial knowledge production, I examine nationalist pedagogies of two Bengali children's magazines (Amaar Desh and Mouchak) as a form of informal schooling. I argue that the colonial state's engagement with physical education in schools stemmed from anxieties to both discipline native children's bodies, and to discourage students’ ‘seditious’ political activism. Second, I demonstrate that for Bengali educated elites, children embodied a political space for contestation and undertaking their projects of re‐masculinising the youth. These nation‐building projects placed a premium on masculinity, influenced boy cultures to imitate adult male cultures, and inscribed gender roles on the bodies of Bengali boys and girls. By doing so, these colonial encounters restructured and redefined childhood in crucial ways.
Characterization of a laccase from a wood‐feeding termite, Coptotermes formosanus
Authors: Geng Alei , Wu Jian , Xie Rong‐Rong , Li Xia , Chang Fu‐Xiang , Sun Jian‐Zhong
Published: November 2016

Coptotermes formosanus Shiraki is a wood‐feeding termite which secretes a series of lignolytic and cellulolytic enzymes for woody biomass degradation. However, the lignin modification mechanism in the termite is largely elusive, and the characteristics of most lignolytic enzymes in termites remain unknown. In this study, a laccase gene lac1 from C. formosanus was heterogeneously expressed in insect Sf9 cells. The purified Lac1 showed strong activities toward hydroquinone (305 mU/mg) and 2,6‐dimethoxyphenol (2.9 mU/mg) with low Km values, but not veratryl alcohol or 2,2’‐azino‐bis (3‐ethylbenzothiazoline‐6‐sulfonic acid). Lac1 could function well from pH 4.5 to 7.5, and its activity was significantly inhibited by H2O2 at above 4.85 mmol/L (P < 0.01). In addition, the lac1 gene was found to be mainly expressed in the salivary glands and foregut of C. formosanus, and seldom in the midgut or hindgut. These findings suggested that Lac1 is a phenol‐oxidizing laccase like RflacA and RflacB from termite Reticulitermes flavipes, except that Lac1 was found to be more efficient in phenol oxidation, and it did not require H2O2 for its function. It is suspected that this kind of termite laccase might only be able to directly oxidize low redox‐potential substrates, and the high redox‐potential groups in lignin might be oxidized by other enzymes in the termite or by using the Fenton reaction.
Hippocampal volume and the course of depressive symptoms over eight years of follow‐up
Authors: Buddeke J. , Kooistra M. , Zuithoff N. P. A. , Gerritsen L. , Biessels G. J. , van der Graaf Y. , Geerlings M. I. ,   the SMART Study Group
Published: November 2016

Objective

To estimate the association between hippocampal and total brain volume and the course of depressive symptoms over eight years of follow‐up in patients with a history of vascular disease.

Method

Within the SMART‐Medea study, 636 participants (62 ± 10 years) had a 1.5‐tesla brain MRI obtaining hippocampal and total brain volumes. Depressive symptoms were assessed with the Patient Health Questionnaire‐9 biannually during eight‐year follow‐up. Generalized estimating equation models with robust standard errors were used to assess the associations of hippocampal and total brain volumes with depressive symptoms during follow‐up adjusting for age, sex, education, and intracranial volume. An interaction term between volume and time (6‐month intervals) was included to examine whether the course of depressive symptoms differed according to hippocampal and total brain volume.

Results

The mean PHQ‐9 score was 2.8 ± 3.5. Smaller hippocampal volumes were associated with an increasing course of depressive symptom levels, while larger volumes were associated with decreasing levels (P‐value interaction = 0.07). Smaller total brain volume was associated with consistently higher levels of depressive symptoms, but not with change in course of depressive symptoms (P‐value interaction = 0.45).

Conclusion

Smaller hippocampal volume but not total brain volume is associated with poorer course of depressive symptoms over eight years of follow‐up.
Value of temporal artery biopsy length in diagnosing giant cell arteritis
Authors: Oh Lawrence J. , Wong Eugene , Gill Anthony J. , McCluskey Peter , Smith James E. H.
Published: November 2016

Background

Giant cell arteritis (GCA) is considered an ophthalmological emergency with severe sight and life‐threatening sequelae. Temporal artery biopsy (TAB) is the current gold standard for the diagnosis of GCA; however, the required length of biopsy remains an issue of contention in the literature.

Methods

Retrospective case–control study of a consecutive cohort of 545 patients who had undergone TABs across five hospitals between 1 January 1992 and 1 January 2016. In patients with either positive or negative TABs, we collected age, sex, biopsy length and erythrocyte sedimentation rate (ESR).

Results

A total of 538 patients were included in the final analysis. Of these, 23.4% of TABs were positive, with the average length being 17.6 mm. There was a significant difference in means for positive (19.9 mm) and negative (16.8 mm) biopsies (P = 0.0009). Each millimetre increase in TAB length increased the odds of a positive TAB by 3.4% (P = 0.024). A cut‐off point of ≥15 mm increased the odds of a positive TAB by 2.25 compared with a TAB <15 mm (P = 0.003). We also found that ESR ≥50 mm/h was a very strong predictor for a positive TAB result (P < 0.0001).

Conclusion

Biopsy length and ESR were significant predictors of a pathological diagnosis of GCA. We also found that the optimal length threshold predictive for GCA was 15 mm in order to avoid a false‐negative GCA diagnosis. Although TAB remains the gold standard for diagnosis, clinicians should refer to both clinical and pathological data to guide their management.
Computed tomography findings and surgical outcomes of dermoid sinuses: a case series
Authors: Appelgrein C , Hosgood G , Reese SL
Published: November 2016

Objective

This case series describes the computed tomography (CT) and surgical findings of nine dogs with dermoid sinuses.

Methods

Medical records were reviewed and summarised.

Results

CT with intravenous contrast showed a superficial, peripherally contrast‐enhancing, fluid‐filled structure with a contrast‐enhancing, soft tissue‐attenuating tract that extended from the skin through the dorsal midline soft tissues, often to the level of the nuchal ligament. The tract often extended in an oblique direction to the nuchal ligament, but the tract ventral to the nuchal ligament, found at surgery, was not always discernible on CT. The dermoid sinuses were excised from all dogs. At surgery, the tract often extended ventral to the nuchal ligament, terminating on the vertebra. The most ventral aspect of the tracts involved a fibrous strand extension of the sinus, which was not discernible on CT.

Conclusion

Preoperative CT facilitated the diagnosis of a dermoid sinus and directed surgical planning; however, careful dissection beyond the nuchal ligament is imperative for complete excision.
Children's Intrinsic Motivation to Provide Help Themselves After Accidentally Harming Others
Authors: Hepach Robert , Vaish Amrisha , Tomasello Michael
Published: November 2016

Little is known about the flexibility of children's prosocial motivation. Here, 2‐ and 3‐year‐old children's (n = 128) internal arousal, as measured via changes in pupil dilation, was increased after they accidentally harmed a victim but were unable to repair the harm. If they were able to repair (or if they themselves did not cause the harm and the help was provided by someone else) their arousal subsided. This suggests that children are especially motivated to help those whom they have harmed, perhaps out of a sense of guilt and a desire to reconcile with them. Young children care not only about the well‐being of others but also about the relationship they have with those who depend on their help.
Non‐coding variation in disorders of sex development
Authors: Baetens D. , Mendonça B.B. , Verdin H. , Cools M. , De Baere E.
Published: November 2016

Genetic studies in Disorders of Sex Development (DSD), representing a wide spectrum of developmental or functional conditions of the gonad, have mainly been oriented towards the coding genome. Application of genomic technologies, such as whole‐exome sequencing, result in a molecular genetic diagnosis in ∼50% of cases with DSD. Many of the genes mutated in DSD encode transcription factors such as SRY, SOX9, NR5A1, and FOXL2, characterized by a strictly regulated spatiotemporal expression. Hence, it can be hypothesized that at least part of the missing genetic variation in DSD can be explained by non‐coding mutations in regulatory elements that alter gene expression, either by reduced, mis‐ or overexpression of their target genes. In addition, structural variations such as translocations, deletions, duplications or inversions can affect the normal chromatin conformation by different mechanisms. Here, we review non‐coding defects in human DSD phenotypes and in animal models. The wide variety of non‐coding defects found in DSD emphasizes that the regulatory landscape of known and to be discovered DSD genes has to be taken into consideration when investigating the molecular pathogenesis of DSD.
Estimating the Extent of CITES Noncompliance among Traders and End‐Consumers; Lessons from the Global Orchid Trade
Authors: Hinsley Amy , Nuno Ana , Ridout Martin , John Freya A.V. St , Roberts David L.
Published: November 2016

The Convention on the International Trade in Endangered Species of Wild Flora and Fauna (CITES) regulates trade in over 35,000 species, over 70% of which are orchids. To investigate rule‐breaking behavior among traders and buyers in a specific international wildlife trading community, we used direct questions (DQs) and the unmatched count technique (UCT) to survey the orchid growing community about CITES compliance and their knowledge and opinions of the rules. In DQ, 9.9% had smuggled, 4.8% had laundered, and 10.8% had been sent orchids from online purchases without paperwork; UCT estimates did not differ significantly. Growers with greater knowledge of CITES rules were more likely to break them, and there were widespread negative views of CITES among respondents. We recommend targeted enforcement focusing on both online trade and at the point of import, coupled with efforts to encourage traders and end‐consumers to engage with discussions on CITES rule implementation
Relative contributions of environmental and maternal factors to trans‐generational immune priming in T. castaneum
Authors: KENNEDY MEGAN , GRAHAM ANDREA L. , TATE ANN T.
Published: November 2016

1. Trans‐generational immune priming is a phenomenon in insects in which the offspring of mothers previously challenged with a focal microbe exhibit a survival advantage when challenged with that microbe.

2. Maternal egg provisioning with immune factors such as antimicrobial peptides (AMPs) is widely believed to contribute to the primed phenotype. However, other ‘socially mediated’ environmental factors secreted or excreted by the mother and others in the community, such as the gut microbiota or pheromones, may also affect offspring immune phenotype.

3. The relative contributions of maternal egg provisioning and socially mediated environmental factors to the primed larval phenotype were assessed by performing a cross‐fostering survival experiment with Tribolium castaneum, in which the eggs of primed or naïve mothers were sterilised, treated with the frass of primed or naïve beetles, and challenged as larvae with the maternal pathogen, Bacillus thuringiensis.

4. Larvae from primed mothers showed greater survival than unprimed larvae, regardless of frass treatment; maternal treatment therefore showed a substantially greater contribution to larval priming than frass treatment.

5. Planned contrast tests to quantify the contributions of maternal and environmental matching revealed that maternal treatment mattered more for larvae exposed to primed, rather than unprimed, frass. This suggests that the effects of maternal egg provisioning may be exacerbated or mitigated by environmental factors.

6. Thus, although maternal egg provisioning plays a predominant role in producing the primed phenotype, environmental matching may matter for priming in some contexts.
Aphid‐tending ants on introduced fennel: can resources derived from non‐native plants alter the trophic position of higher‐order consumers?
Authors: HANNA CAUSE , NAUGHTON IDA , BOSER CHRISTINA , HOLWAY DAVID A.
Published: November 2016

1. Although plant invasions often reduce insect abundance and diversity, non‐native plants that support phytophagous insects can subsidise higher trophic levels via elevated herbivore abundance.

2. Here ant–aphid interactions on non‐native fennel on Santa Cruz Island, California are examined. Fennel hosts abundant, honeydew‐producing fennel aphids. The patchiness of fennel and the relative lack of honeydew‐producing insects on other plants at our study sites suggest that assimilation of fennel‐derived honeydew would increase the abundance and decrease the trophic position of the omnivorous, aphid‐tending Argentine ant.

3. To assess the strength of the ant–aphid interaction, a comparison of ant abundance on and adjacent to fennel prior to and 3 weeks after experimental aphid removal was performed. Compared with control plants with aphids, ants declined in abundance on and around fennel plants following aphid removal. At the habitat scale, pitfall traps in fennel‐dominated habitats captured more ants than in fennel‐free scrub habitats.

4. To determine if assimilation of aphid‐produced honeydew reduces the ant's trophic position, variation in δ15N values among ants, plants and other arthropods was analysed. Unexpectedly, δ15N values for ants in fennel‐dominated habitats were higher than those of arthropod predators from the same sites and also higher than those of ants from fennel‐free habitats.

5. Our results illustrate how introduced plants that support phytophagous insects appear to transfer energy to higher trophic levels via elevated herbivore abundance. Although assimilation of fennel‐derived honeydew did not appear to reduce consumer trophic position, spatial variation in alternative food resources might obscure contributions from honeydew.
Added value of multimodal computed tomography imaging: analysis of 1994 acute ischaemic strokes
Authors: Bill O. , Faouzi M. , Meuli R. , Maeder P. , Wintermark M. , Michel P.
Published: November 2016

Background and purpose

Multimodal computed tomography (CT) based imaging (MCTI) is widely used in acute ischaemic stroke. It was postulated that the use of MCTI is associated with improved patient outcome without causing harm.

Methods

All patients with an acute ischaemic stroke and CT‐based imaging within 24 h from the ASTRAL (Acute Stroke Registry and Analysis of Lausanne) registry were included. Preceding demographic, clinical, biological, radiological and follow‐up data were collected. Significant predictors of MCTI use were identified retrospectively to go on to fit a multivariable analysis. Then, patients undergoing additional CT angiography (CTA) or CTA and perfusion CT (CTP) were compared with non‐contrast CT only patients with regard to 3‐month favourable outcome (modified Rankin Scale score ≤2), 12‐month mortality, stroke mechanism, short‐term renal failure, use of ancillary diagnostic tests, duration of hospitalization and 12‐month stroke recurrence.

Results

Of the 1994 included patients, 273 had only non‐contrast CT, 411 had both non‐contrast CT and CTA and 1310 had all three examinations. Factors independently associated with MCTI were younger age, low pre‐stroke modified Rankin Scale score, low creatinine value, known stroke onset, anterior circulation stroke, anticoagulation or antihypertensive therapy (CTA only) and higher National Institutes of Health Stroke Scale scores (CTP only). After adjustment, MCTI was associated with a 50% reduction of 12‐month mortality and a lower likelihood of unknown stroke mechanism. No association was found between MCTI and 3‐month outcome, contrast‐induced nephropathy, hospitalization duration, number of ancillary diagnostic tests or with stroke recurrence.

Conclusion

Our study shows an association of MCTI use with lower adjusted 12‐month mortality, better identification of the stroke mechanism and no signs of harm.
The welfare of wild animals in zoological institutions: are we meeting our duty of care?
Authors: Blackett T. A. , McKenna C. , Kavanagh L. , Morgan D. R.
Published: November 2016

Across the world there are many different species of wild animals maintained in zoological institutions of one sort or another for a variety of purposes. Their welfare is directly dependent upon the quality of life they experience, which in turn is driven by the understanding the owner/keeper has of the needs of the animals. This ‘understanding’ may or may not be informed by scientific knowledge. Sub‐optimal conditions and/or husbandry practices can result in injury, disease and poor mental health; hence, it is critical that environmental conditions, management and husbandry techniques are employed that promote positive physical and psychological health for all wild animals in human care. An individual needs good psychological health, as well as good physical health, to achieve good welfare. Further complicating the issue is the variation in existing animal‐welfare legislation and in the range of species afforded protection under the legislation between different countries. This paper emerges from an initiative to improve and promote good welfare in zoological institutions that have suboptimal conditions in countries where help is needed most. This initiative included fostering relationships with zoo and aquarium officials and regulatory bodies based on an assessment of what needs to be done for specific facilities to improve welfare for the animals under their care. An approach to advancing animal welfare was developed by establishing the fundamental requirements for the welfare of wild animals in human care and developing an accompanying assessment tool. This approach incorporated the Five Domains animal‐welfare model as the central evaluative device.
Timing of Physical Activity, Apolipoprotein E ε4 Genotype, and Risk of Incident Mild Cognitive Impairment
Authors: Krell‐Roesch Janina , Pink Anna , Roberts Rosebud O. , Stokin Gorazd B. , Mielke Michelle M. , Spangehl Kathleen A. , Bartley Mairead M. , Knopman David S. , Christianson Teresa J.H. , Petersen Ronald C. , Geda Yonas E.
Published: November 2016

Objectives

To investigate the timing (mid‐ vs late life) of physical activity, apolipoprotein (APO)E ε4, and risk of incident mild cognitive impairment (MCI).

Design

Prospective cohort study.

Setting

Mayo Clinic Study of Aging (Olmsted County, MN).

Participants

Cognitively normal elderly adults (N = 1,830, median age 78, 50.2% female).

Measurements

Light, moderate, and vigorous physical activities in mid‐ and late life were assessed using a validated questionnaire. An expert consensus panel measured MCI based on published criteria. Cox proportional hazards models were used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) with age as a time scale after adjusting for sex, education, medical comorbidity, and depression.

Results

Light (HR = 0.58, 95% CI = 0.43–0.79) and vigorous (HR = 0.78, 95% CI = 0.63–0.97) physical activity in midlife were associated with lower risk of incident MCI. The association between moderate activity and incident MCI was not significant (HR = 0.85, 95% CI = 0.67–1.09). In late life, light (HR = 0.75, 95% CI = 0.58–0.97) and moderate (HR = 0.81, 95% CI = 0.66–0.99) but not vigorous physical activity were associated with lower risk of incident MCI. A synergistic interaction was also observed between mid‐ and late‐life activity in reducing risk of incident MCI. Furthermore, APOE ε4 carriers who did not exercise had a higher risk of incident MCI than noncarriers who reported physical activity.

Conclusion

Physical activity reduced the risk of incident MCI. Exercising in mid‐ and late life had an additive synergistic interaction in reducing the risk of MCI.
A differentially regulated AP2/ERF transcription factor gene cluster acts downstream of a MAP kinase cascade to modulate terpenoid indole alkaloid biosynthesis in Catharanthus roseus
Authors: Paul Priyanka , Singh Sanjay K. , Patra Barunava , Sui Xueyi , Pattanaik Sitakanta , Yuan Ling
Published: November 2016

Catharanthus roseus produces bioactive terpenoid indole alkaloids (TIAs), including the chemotherapeutics, vincristine and vinblastine. Transcriptional regulation of TIA biosynthesis is not fully understood.

The jasmonic acid (JA)‐responsive AP2/ERF transcription factor (TF), ORCA3, and its regulator, CrMYC2, play key roles in TIA biosynthesis. ORCA3 forms a physical cluster with two uncharacterized AP2/ERFs, ORCA4 and 5. Here, we report that (1) the ORCA gene cluster is differentially regulated; (2) ORCA4, while overlapping functionally with ORCA3, modulates an additional set of TIA genes. Unlike ORCA3, ORCA4 overexpression resulted in dramatic increase of TIA accumulation in C. roseus hairy roots. In addition, CrMYC2 is capable of activating ORCA3 and co‐regulating TIA pathway genes concomitantly with ORCA3.

The ORCA gene cluster and CrMYC2 act downstream of a MAP kinase cascade that includes a previously uncharacterized MAP kinase kinase, CrMAPKK1. Overexpression of CrMAPKK1 in C. roseus hairy roots upregulated TIA pathways genes and increased TIA accumulation.

This work provides detailed characterization of a TF gene cluster and advances our understanding of the transcriptional and post‐translational regulatory mechanisms that govern TIA biosynthesis in C. roseus.
Big Data access and infrastructure for modern biology: case studies in data repository utility
Authors: Boles Nathan C. , Stone Tyler , Bergeron Charles , Kiehl Thomas R.
Published: November 2016

Big Data is no longer solely the purview of big organizations with big resources. Today's routine tools and experimental methods can generate large slices of data. For example, high‐throughput sequencing can quickly interrogate biological systems for the expression levels of thousands of different RNAs, examine epigenetic marks throughout the genome, and detect differences in the genomes of individuals. Multichannel electrophysiology platforms produce gigabytes of data in just a few minutes of recording. Imaging systems generate videos capturing biological behaviors over the course of days. Thus, any researcher now has access to a veritable wealth of data. However, the ability of any given researcher to utilize that data is limited by her/his own resources and skills for downloading, storing, and analyzing the data. In this paper, we examine the necessary resources required to engage Big Data, survey the state of modern data analysis pipelines, present a few data repository case studies, and touch on current institutions and programs supporting the work that relies on Big Data.
Structure and function of adipokinetic hormones of the large white butterfly Pieris brassicae
Authors: Marco Heather G. , Gäde Gerd
Published: November 2016

The large white butterfly Pieris brassicae L. (also called cabbage white) is very common in Europe, Asia and the northern region of Africa, and has also been found in South Africa during approximately the last 20 years. The species is considered a pest insect, with larvae attacking brassicaceous crops. The adult is a strong migratory flyer and new territory can be infested this way. As a first step to investigate methods for combating this pest species, the present study aims to determine the complement of adipokinetic peptides, here generically referred to as adipokinetic hormones (AKHs), which are required to regulate the mobilization of fuels for insect flight. Biological assays, as well as mass spectrometry, reveal information about the presence, structure and function of AKHs in P. brassicae: a methanolic extract of the corpora cardiaca has hypertrehalosaemic activity in cockroaches, does not cause hyperlipaemia in locusts, and has adipokinetic activity in P. brassicae itself. Liquid‐chromatography electrospray ion trap mass spectrometry reveals three peptides that can be associated with the AKH family: the non‐amidated undecapeptide Vanca‐AKH (pELTFTSSWGGK‐OH), the nonapeptide Manse‐AKH (pELTFTSSWG amide) and the novel octapeptide Piebr‐AKH (pELTFSSGW amide). Sequence confirmation of all three assigned structures is obtained from matching mass spectrometry spectra from synthetic and native peptides. Moreover, the synthetic peptides Manse‐AKH and Piebr‐AKH have significant hyperlipaemic (=adipokinetic) activity when injected into newly‐emerged adult cabbage white butterflies. The non‐amidated Vanca‐AKH is, apparently, incompletely processed Manse‐AKH without hormonal activity. Simulated dispersal flight is able to release AKHs, as indicated by the higher concentration of lipids in the haemolymph of adult P. brassicae after activity and rest periods.
Do Disagreeable Political Discussion Networks Undermine Attitude Strength?
Authors: Robison Joshua , Leeper Thomas J. , Druckman James N.
Published: November 2016

How attitudes change and affect behavior depends, in large part, on their strength. Strong attitudes are more resistant to persuasion and are more likely to produce attitude‐consistent behavior. But what influences attitude strength? In this article, we explore a widely discussed, but rarely investigated, factor: an individual's political discussion network. What prior work exists offers a somewhat mixed picture, finding sometimes that disagreeable networks weaken attitudes and other times that they strengthen attitudes. We use a novel national representative dataset to explore the relationship between disagreeable networks and attitude strength. We find, perhaps surprisingly, no evidence that disagreements in networks affect political attitude strength. We conclude by discussing likely reasons for our findings, which, in turn, provide a research agenda for the study of networks and attitude strength.
“I Don't Agree with Giving Cash”: A Survey Experiment Examining Support for Public Assistance
Authors: Campbell Colin , Gaddis S. Michael
Published: November 2016

Objective

Existing research on support for anti‐poverty programs largely focuses on broad categories of welfare. In this article, we examine variations in support across different public assistance programs.

Methods

We use an experimental survey design to examine whether support for public assistance is dependent on the type of aid offered.

Results

We find that programs that offer benefits in‐kind are more popular than cash transfers. Moreover, food stamps and child‐care subsidies enjoy more support than housing assistance. Open‐ended survey responses show that when evaluating anti‐poverty programs, respondents adopt one of two perspectives: (1) cash assistance is problematic but other forms of assistance are acceptable or (2) any assistance is problematic.

Conclusion

By too narrowly focusing on welfare, social scientists run the risk of developing theories and explanations that may not apply to the much larger part of the safety net that is delivered in‐kind.
Identification of a Plasmid‐Mediated Quinolone Resistance Gene in Salmonella Isolates from Texas Dairy Farm Environmental Samples
Authors: Cummings K. J. , Rodriguez‐Rivera L. D. , Norman K. N. , Ohta N. , Scott H. M.
Published: November 2016

A recent increase in plasmid‐mediated quinolone resistance (PMQR) has been detected among Salmonella isolated from humans in the United States, and it is necessary to determine the sources of human infection. We had previously isolated Salmonella from dairy farm environmental samples collected in Texas, and isolates were tested for anti‐microbial susceptibility. Two isolates, serotyped as Salmonella Muenster, showed the discordant pattern of nalidixic acid susceptibility and intermediate susceptibility to ciprofloxacin. For this project, whole‐genome sequencing of both isolates was performed to detect genes associated with quinolone resistance. The plasmid‐mediated qnrB19 gene and IncR plasmid type were identified in both isolates. To our knowledge, this is the first report of PMQR in Salmonella isolated from food animals or agricultural environments in the United States.