bluuebunny/crossref_metadata_2025 huggingface dataset:
First Report of Bean common mosaic virus Infecting Mungbean (Vigna radiata) in China
Authors: Cui X. Y. , Shen L. , Yuan X. X. , Gu H. P. , Chen X.
Published: June 2014

Bean common mosaic virus (BCMV) is a member of the genus Potyvirus and one of the numerous viruses that can infect Phaseolus vulgaris. In May of 2013, we planted more than 100 varieties of mungbean in fields and a greenhouse of Nanjing. Mungbean (Vigna radiata (Linn.) Wilczek.) with leaves displaying mosaic and shrinkage typical of viral infection was observed in a greenhouse and a field in Nanjing. About 60% of the varieties can be infected. The symptoms in some sources from Southeast Asian countries and wild germplasm are heavier, while the symptoms are lighter on the local varieties. It can be transmitted to mungbean via aphid or mechanical inoculation, or by seeds. The infected leaves were collected for electron micrograph analysis. Pinwheel inclusion and filamentous virus particles were observed, indicating a Potyvirus infection. To confirm the presence of Potyvirus infection, total RNA was extracted from plants from the greenhouse and field, and RT-PCR was performed using universal Potyvirus primers (Sprimer (+) 5′-GGXAAYAAYAGYGGXCAZCC-3′; X=A, G, C or T, Y=T or C, Z=A or G); M4T (5′-GTTTTCCCAGTCACGAC(T)-3′), which amplify a region of the 3′ fragment of the RNA-dependent RNA polymerase of potyviruses (1). The 596-bp sequence was found to be 95% identical to the BCMV isolate HB (GenBank Accession No. KC478389.1). To confirm the presence of BCMV, three leaf samples were randomly collected and all were determined to be positive when subjected to ELISA using BCMV-specific antibodies. The virus infecting mungbean was identified as BCMV and the strain was named BCMV-JAAS (KJ866945). Using gene-specific primers (BCMV-cp-F: 5′-CAAAAGGACAAGGATTGAGGA, BCMV-cp-R: 3′-ACAACAAACATTGCCGTAGC) for the reported coat protein gene in BCMV, a 1,080-bp gene fragment was amplified from the total RNA of the isolate, and subsequent sequence analysis indicated that an 862-bp region contained the complete cp gene that encodes a 228 amino acid protein. The nucleotide sequences of the cp gene from the isolate shared 96% homology with the reported BCMV-HB. The phylogenetic trees based on the CP gene show that BCMV-JAAS (KJ866945) was most closely related to other Chinese BCMV isolates (KF439722.1 and AJ132145.1) followed by Azuki mosaic virus (AB012663.1) and Peanut stripe virus (U34972.1). These results indicate that the virus associated with the mosaic disease in mungbean is an isolate of BCMV. To our knowledge, this is the first report of BCMV infecting mungbean in China. BCMV affects a wide range of legume crops and can spread rapidly, causing serious harm. The discovery could effectively control BCMV and characterize the prevalent BCMV strains. Research utilizing whole-genome sequencing of the mungbean isolate is continuing and is currently being expanded to characterize the genetic diversity of the virus, assisting in the study of the evolution of the virus.

Reference: (1) J. Chen and J. P. Chen. Chin. J. Virol. 18:372, 2002.
Plague epizootic cycles in Central Asia
Authors: Reijniers Jonas , Begon Mike , Ageyev Vladimir S. , Leirs Herwig
Published: June 2014

Infection thresholds, widely used in disease epidemiology, may operate on host abundance and, if present, on vector abundance. For wildlife populations, host and vector abundances often vary greatly across years and consequently the threshold may be crossed regularly, both up- and downward. Moreover, vector and host abundances may be interdependent, which may affect the infection dynamics. Theory predicts that if the relevant abundance, or combination of abundances, is above the threshold, then the infection is able to spread; if not, it is bound to fade out. In practice, though, the observed level of infection may depend more on past than on current abundances. Here, we study the temporal dynamics of plague (
Yersinia pestis
infection), its vector (flea) and its host (great gerbil) in the PreBalkhash region in Kazakhstan. We describe how host and vector abundances interact over time and how this interaction drives the dynamics of the system around the infection threshold, consequently affecting the proportion of plague-infected sectors. We also explore the importance of the interplay between biological and detectability delays in generating the observed dynamics.
Variation in palaeo-shorelines explains contemporary population genetic patterns of rocky shore species
Authors: Toms Jessica A. , Compton John S. , Smale Malcolm , von der Heyden Sophie
Published: June 2014

Processes driving and maintaining disjunct genetic populations in marine systems are poorly understood, owing to a lack of evidence of hard barriers that could have shaped patterns of extant population structure. Here, we map two genetically divergent lineages of an obligate rocky shore fish,Clinus cottoides, and model sea-level change during the last 110 000 years to provide the first evidence of a vicariant event along the southern coastline of Africa. Results reveal that lowered sea levels during glacial periods drastically reduced rocky intertidal habitat, which may have isolated populations in two refugia for at least 40 000 years. Contemporary coastal dynamics and oceanography explain secondary contact between lineages. This scenario provides an explanation for the origin of population genetic breaks despite a lack of obvious present-day geographical barriers and highlights the need for including palaeo-oceanography in unravelling extant population patterns.
John Lennox Monteith. 3 September 1929 — 20 July 2012
Authors: Unsworth Michael H.
Published: June 2014

John Monteith fundamentally changed the way in which physical and biological scientists explore the interactions between living organisms and their environments. Trained in physics and meteorology, he pioneered innovative ways of measuring and analysing exchanges of heat, water vapour and carbon dioxide between leaves, crops, animals and the atmosphere. Building on the work of Howard Penman, with whom he worked for almost two decades, he developed the Penman–Monteith equation that is widely used in planning irrigation and water resource development. Subsequently, as the first Professor of Environmental Physics at the University of Nottingham, he brought together multidisciplinary groups to study the growth of temperate and tropical crops and the heat balance of animals. His Environmental Physics group trained graduates and postdoctoral scientists who have joined research establishments and universities worldwide. The final phase of his long career was spent at the International Crops Research Institute for the Semi-Arid Tropics, where he directed teams applying his experimental methods and analyses to benefit crop production in developing countries—a topic that epitomized his desire to have his science make an impact for the good of mankind. In addition to his exceptional ability in research and teaching, John Monteith was an outstanding communicator and leader who made substantial contributions to many national and international organizations.
Logic programming to predict cell fate patterns and retrodict genotypes in organogenesis
Authors: Hall Benjamin A. , Jackson Ethan , Hajnal Alex , Fisher Jasmin
Published: June 2014

Caenorhabditis elegans
vulval development is a paradigm system for understanding cell differentiation in the process of organogenesis. Through temporal and spatial controls, the fate pattern of six cells is determined by the competition of the LET-23 and the Notch signalling pathways. Modelling cell fate determination in vulval development using state-based models, coupled with formal analysis techniques, has been established as a powerful approach in predicting the outcome of combinations of mutations. However, computing the outcomes of complex and highly concurrent models can become prohibitive. Here, we show how logic programs derived from state machines describing the differentiation of
C. elegans
vulval precursor cells can increase the speed of prediction by four orders of magnitude relative to previous approaches. Moreover, this increase in speed allows us to infer, or ‘retrodict’, compatible genomes from cell fate patterns. We exploit this technique to predict highly variable cell fate patterns resulting from
dig-1
reduced-function mutations and
let-23
mosaics. In addition to the new insights offered, we propose our technique as a platform for aiding the design and analysis of experimental data.
Shear-induced force transmission in a multicomponent, multicell model of the endothelium
Authors: Dabagh Mahsa , Jalali Payman , Butler Peter J. , Tarbell John M.
Published: June 2014

Haemodynamic forces applied at the apical surface of vascular endothelial cells (ECs) provide the mechanical signals at intracellular organelles and through the inter-connected cellular network. The objective of this study is to quantify the intracellular and intercellular stresses in a confluent vascular EC monolayer. A novel three-dimensional, multiscale and multicomponent model of focally adhered ECs is developed to account for the role of potential mechanosensors (glycocalyx layer, actin cortical layer, nucleus, cytoskeleton, focal adhesions (FAs) and adherens junctions (ADJs)) in mechanotransmission and EC deformation. The overriding issue addressed is the stress amplification in these regions, which may play a role in subcellular localization of mechanotransmission. The model predicts that the stresses are amplified 250–600-fold over apical values at ADJs and 175–200-fold at FAs for ECs exposed to a mean shear stress of 10 dyne cm
−2
. Estimates of forces per molecule in the cell attachment points to the external cellular matrix and cell–cell adhesion points are of the order of 8 pN at FAs and as high as 3 pN at ADJs, suggesting that direct force-induced mechanotransmission by single molecules is possible in both. The maximum deformation of an EC in the monolayer is calculated as 400 nm in response to a mean shear stress of 1 Pa applied over the EC surface which is in accord with measurements. The model also predicts that the magnitude of the cell–cell junction inclination angle is independent of the cytoskeleton and glycocalyx. The inclination angle of the cell–cell junction is calculated to be 6.6° in an EC monolayer, which is somewhat below the measured value (9.9°) reported previously for ECs subjected to 1.6 Pa shear stress for 30 min. The present model is able, for the first time, to cross the boundaries between different length scales in order to provide a global view of potential locations of mechanotransmission.
Double flow reversal in thin liquid films driven by megahertz-order surface vibration
Authors: Rezk Amgad R. , Manor Ofer , Yeo Leslie Y. , Friend James R.
Published: June 2014

Arising from an interplay between capillary, acoustic and intermolecular forces, surface acoustic waves (SAWs) are observed to drive a unique and curious
double
flow reversal in the spreading of thin films. With a thickness at or less than the submicrometre viscous penetration depth, the film is seen to advance
along
the SAW propagation direction, and self-similarly over time
t
1/4
in the inertial limit. At intermediate film thicknesses, beyond one-fourth the sound wavelength λ
ℓ
in the liquid, the spreading direction
reverses,
and the film propagates
against
the direction of the SAW propagation. The film
reverses
yet again, once its depth is further increased beyond one SAW wavelength. An unstable thickness region, between λ
ℓ
/8 and λ
ℓ
/4, exists from which regions of the film either rapidly grow in thickness to exceed λ
ℓ
/4 and move
against
the SAW propagation, consistent with the intermediate thickness films, whereas other regions decrease in thickness below λ
ℓ
/8 to conserve mass and move
along
the SAW propagation direction, consistent with the thin submicrometre films.
Constitutive modelling of magnetic shape memory alloys with discrete and continuous symmetries
Authors: Haldar K. , Lagoudas D. C.
Published: June 2014

A free energy-based constitutive formulation is considered for magnetic shape memory alloys. Internal state variables are introduced whose evolution describes the transition from reference state to the deformed and transformed one. We impose material symmetry restrictions on the Gibbs free energy and on the evolution equations of the internal state variables. Discrete symmetry is considered for single crystals, whereas continuous symmetry is considered for polycrystalline materials.
Order reconstruction patterns in nematic liquid crystal wells
Authors: Kralj Samo , Majumdar Apala
Published: June 2014

We numerically study structural transitions inside shallow sub-micrometre scale wells with square cross section, filled with nematic liquid crystal material. We model the wells within the Landau–de Gennes theory. We obtain two qualitatively different states: (i) the diagonal state with defects for relatively large wells with lateral dimension greater than a critical threshold and (ii) a new, two-dimensional star-like biaxial order reconstruction pattern called the well order-reconstruction structure (WORS), for wells smaller than the critical threshold. The WORS is defined by an uniaxial cross connecting the four vertices of the square cross section. We numerically compute the critical threshold in terms of the bare biaxial correlation length and study its dependence on the temperature and on the anchoring strength on the lateral well surfaces.
Sex-biased survival predicts adult sex ratio variation in wild birds
Authors: Székely Tamás , Liker András , Freckleton Robert P. , Fichtel Claudia , Kappeler Peter M.
Published: June 2014

Adult sex ratio (ASR) is a central concept in population demography and breeding system evolution, and has implications for population viability and biodiversity conservation. ASR exhibits immense interspecific variation in wild populations, although the causes of this variation have remained elusive. Using phylogenetic analyses of 187 avian species from 59 families, we show that neither hatching sex ratios nor fledging sex ratios correlate with ASR. However, sex-biased adult mortality is a significant predictor of ASR, and this relationship is robust to 100 alternative phylogenetic hypotheses, and potential ecological and life-history confounds. A significant component of adult mortality bias is sexual selection acting on males, whereas increased reproductive output predicts higher mortality in females. These results provide the most comprehensive insights into ASR variation to date, and suggest that ASR is an outcome of selective processes operating differentially on adult males and females. Therefore, revealing the causes of ASR variation in wild populations is essential for understanding breeding systems and population dynamics.
Induced tolerance expressed as relaxed behavioural threat response in millimetre-sized aquatic organisms
Authors: Hylander Samuel , Ekvall Mikael T. , Bianco Giuseppe , Yang Xi , Hansson Lars-Anders
Published: June 2014

Natural selection shapes behaviour in all organisms, but this is difficult to study in small, millimetre-sized, organisms. With novel labelling and tracking techniques, based on nanotechnology, we here show how behaviour in zooplankton (
Daphnia magna
) is affected by size, morphology and previous exposure to detrimental ultraviolet radiation (UVR). All individuals responded with immediate downward swimming to UVR exposure, but when released from the threat they rapidly returned to the surface. Large individuals swam faster and generally travelled longer distances than small individuals. Interestingly, individuals previously exposed to UVR (during several generations) showed a more relaxed response to UVR and travelled shorter total distances than those that were naive to UVR, suggesting induced tolerance to the threat. In addition, animals previously exposed to UVR also had smaller eyes than the naive ones, whereas UVR-protective melanin pigmentation of the animals was similar between populations. Finally, we show that smaller individuals have lower capacity to avoid UVR which could explain patterns in natural systems of lower migration amplitudes in small individuals. The ability to change behavioural patterns in response to a threat, in this case UVR, adds to our understanding of how organisms navigate in the ‘landscape of fear’, and this has important implications for individual fitness and for interaction strengths in biotic interactions.
Synchronous dynamics of zooplankton competitors prevail in temperate lake ecosystems
Authors: Vasseur David A. , Fox Jeremy W. , Gonzalez Andrew , Adrian Rita , Beisner Beatrix E. , Helmus Matthew R. , Johnson Catherine , Kratina Pavel , Kremer Colin , de Mazancourt Claire , Miller Elizabeth , Nelson William A. , Paterson Michael , Rusak James A. , Shurin Jonathan B. , Steiner Christopher F.
Published: June 2014

Although competing species are expected to exhibit compensatory dynamics (negative temporal covariation), empirical work has demonstrated that competitive communities often exhibit synchronous dynamics (positive temporal covariation). This has led to the suggestion that environmental forcing dominates species dynamics; however, synchronous and compensatory dynamics may appear at different length scales and/or at different times, making it challenging to identify their relative importance. We compiled 58 long-term datasets of zooplankton abundance in north-temperate and sub-tropical lakes and used wavelet analysis to quantify general patterns in the times and scales at which synchronous/compensatory dynamics dominated zooplankton communities in different regions and across the entire dataset. Synchronous dynamics were far more prevalent at all scales and times and were ubiquitous at the annual scale. Although we found compensatory dynamics in approximately 14% of all combinations of time period/scale/lake, there were no consistent scales or time periods during which compensatory dynamics were apparent across different regions. Our results suggest that the processes driving compensatory dynamics may be local in their extent, while those generating synchronous dynamics operate at much larger scales. This highlights an important gap in our understanding of the interaction between environmental and biotic forces that structure communities.
Hartmannibacter diazotrophicus gen. nov., sp. nov., a phosphate-solubilizing and nitrogen-fixing alphaproteobacterium isolated from the rhizosphere of a natural salt-meadow plant
Authors: Suarez Christian , Ratering Stefan , Geissler-Plaum Rita , Schnell Sylvia
Published: June 2014

A phosphate-mobilizing, Gram-negative bacterium was isolated from rhizospheric soil of Plantago winteri from a natural salt meadow as part of an investigation of rhizospheric bacteria from salt-resistant plant species and evaluation of their plant-growth-promoting abilities. Cells were rods, motile, strictly aerobic, oxidase-positive and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E19T was distinct from other taxa within the class

Alphaproteobacteria

. Strain E19T showed less than 93.5 % 16S rRNA gene sequence similarity with members of the genera

Rhizobium

(≤93.5 %),

Labrenzia

(≤93.1 %),

Stappia

(≤93.1 %),

Aureimonas

(≤93.1 %) and

Mesorhizobium

(≤93.0 %) and was most closely related to

Rhizobium rhizoryzae

(93.5 % 16S rRNA gene sequence similarity to the type strain). The sole respiratory quinone was Q-10, and the polar lipids comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an aminolipid and an unidentified phospholipid. Major fatty acids were C18 : 1ω7c (71.4 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1; 8.3 %), C20 : 0 (7.9 %) and C16 : 0 (6.1 %). The DNA G+C content of strain E19T was 59.9±0.7 mol%. The capacity for nitrogen fixation was confirmed by the presence of the nifH gene and the acetylene reduction assay. On the basis of the results of our polyphasic taxonomic study, the new isolate represents a novel genus and species, for which the name Hartmannibacter diazotrophicus gen. nov., sp. nov. is proposed. The type strain of Hartmannibacter diazotrophicus is E19T ( = LMG 27460T = KACC 17263T).
Are phylogenetic patterns the same in anthropology and biology?
Authors: Morrison David A.
Published: June 2014

The use of phylogenetic methods in anthropological fields such as archaeology, linguistics and stemmatology (involving what are often called “culture data”) is based on an analogy between human cultural evolution and biological evolution. We need to understand this analogy thoroughly, including how well anthropology data fit the model of a phylogenetic tree, as used in biology. I provide a direct comparison of anthropology datasets with both phenotype and genotype datasets from biology. The anthropology datasets fit the tree model approximately as well as do the genotype data, which is detectably worse than the fit of the phenotype data. This is true for datasets with <500 parsimony-informative characters, as well as for larger datasets. This implies that cross-cultural (horizontal) processes have been important in the evolution of cultural artifacts, as well as branching historical (vertical) processes, and thus a phylogenetic network will be a more appropriate model than a phylogenetic tree.
Compression of short-read sequences using path encoding
Authors: Kingsford Carl , Patro Rob
Published: June 2014

Storing, transmitting, and archiving the amount of data produced by next generation sequencing is becoming a significant computational burden. For example, large-scale RNA-seq meta-analyses may now routinely process tens of terabytes of sequence. We present here an approach to biological sequence compression that reduces the difficulty associated with managing the data produced by large-scale transcriptome sequencing. Our approach offers a new direction by sitting between pure reference-based compression and reference-free compression and combines much of the benefit of reference-based approaches with the flexibility ofde novoencoding. Our method, called path encoding, draws a connection between storing paths in de Bruijn graphs — a common task in genome assembly — and context-dependent arithmetic coding. Supporting this method is a system, called a bit tree, to compactly store sets of kmers that is of independent interest. Using these techniques, we are able to encode RNA-seq reads using 3% – 11% of the space of the sequence in raw FASTA files, which is on average more than 34% smaller than recent competing approaches. We also show that even if the reference is very poorly matched to the reads that are being encoded, good compression can still be achieved.
Environmental History Modulates Arabidopsis Pattern-Triggered Immunity in a HISTONE ACETYLTRANSFERASE1–Dependent Manner
Authors: Singh Prashant , Yekondi Shweta , Chen Po-Wen , Tsai Chia-Hong , Yu Chun-Wei , Wu Keqiang , Zimmerli Laurent
Published: June 2014

In nature, plants are exposed to a fluctuating environment, and individuals exposed to contrasting environmental factors develop different environmental histories. Whether different environmental histories alter plant responses to a current stress remains elusive. Here, we show that environmental history modulates the plant response to microbial pathogens. Arabidopsis thaliana plants exposed to repetitive heat, cold, or salt stress were more resistant to virulent bacteria than Arabidopsis grown in a more stable environment. By contrast, long-term exposure to heat, cold, or exposure to high concentrations of NaCl did not provide enhanced protection against bacteria. Enhanced resistance occurred with priming of Arabidopsis pattern-triggered immunity (PTI)–responsive genes and the potentiation of PTI-mediated callose deposition. In repetitively stress-challenged Arabidopsis, PTI-responsive genes showed enrichment for epigenetic marks associated with transcriptional activation. Upon bacterial infection, enrichment of RNA polymerase II at primed PTI marker genes was observed in environmentally challenged Arabidopsis. Finally, repetitively stress-challenged histone acetyltransferase1-1 (hac1-1) mutants failed to demonstrate enhanced resistance to bacteria, priming of PTI, and increased open chromatin states. These findings reveal that environmental history shapes the plant response to bacteria through the development of a HAC1-dependent epigenetic mark characteristic of a primed PTI response, demonstrating a mechanistic link between the primed state in plants and epigenetics.
The Cyclin-Dependent Kinase Inhibitor KRP6 Induces Mitosis and Impairs Cytokinesis in Giant Cells Induced by Plant-Parasitic Nematodes in Arabidopsis
Authors: Vieira Paulo , De Clercq Annelies , Stals Hilde , Van Leene Jelle , Van De Slijke Eveline , Van Isterdael Gert , Eeckhout Dominique , Persiau Geert , Van Damme Daniël , Verkest Aurine , Antonino de Souza José Dijair , Júnior  , Glab Nathalie , Abad Pierre , Engler Gilbert , Inzé Dirk , De Veylder Lieven , De Jaeger Geert , Engler Janice de Almeida
Published: June 2014

In Arabidopsis thaliana, seven cyclin-dependent kinase (CDK) inhibitors have been identified, designated interactors of CDKs or Kip-related proteins (KRPs). Here, the function of KRP6 was investigated during cell cycle progression in roots infected by plant-parasitic root-knot nematodes. Contrary to expectations, analysis of Meloidogyne incognita–induced galls of KRP6-overexpressing lines revealed a role for this particular KRP as an activator of the mitotic cell cycle. In accordance, KRP6-overexpressing suspension cultures displayed accelerated entry into mitosis, but delayed mitotic progression. Likewise, phenotypic analysis of cultured cells and nematode-induced giant cells revealed a failure in mitotic exit, with the appearance of multinucleated cells as a consequence. Strong KRP6 expression upon nematode infection and the phenotypic resemblance between KRP6 overexpression cell cultures and root-knot morphology point toward the involvement of KRP6 in the multinucleate and acytokinetic state of giant cells. Along these lines, the parasite might have evolved to manipulate plant KRP6 transcription to the benefit of gall establishment.
3-Oxo-N′,2-diphenyl-2,3-dihydro-1H-pyrazole-4-carbohydrazide
Authors: Mague Joel T. , Mohamed Shaaban K. , Akkurt Mehmet , Ahmed Eman A. , Albayati Mustafa R.
Published: June 2014

In the title compound, C16H14N4O2, the pyrazole ring makes a dihedral angle of 10.49 (8)° with its N-bound phenyl group, while it is nearly perpendicular to the other phenyl ring [dihedral angle = 88.47 (5)°]. The molecular conformation is stabilized by intramolecular C—H...O and N—H...O hydrogen bonds. In the crystal, the packing involves sheets of molecules parallel to (100) linked by N—H...O hydrogen bonds. A C—H...O interaction is also observed.
3,4,6-Triamino-N-phenylthieno[2,3-b]pyridine-2-carboxamide
Authors: Mohamed Shaaban K. , Mague Joel T. , Akkurt Mehmet , Hussein Bahgat R. M. , Albayati Mustafa R.
Published: June 2014

In the title compound, C14H13N5OS, the dihedral angle between the fused ring system (r.m.s. deviation = 0.028 Å) and the phenyl ring is 48.24 (4)°. The molecule features both an intramolecular N—H...O and an N—H...N hydrogen bond. In the crystal, molecules are linked by N—H...O and N—H...N hydrogen bonds, generating a three-dimensional network. A weak N—H...π interaction is also observed.
(E)-1-([1,1′-Biphenyl]-4-yl)-3-(2-methylphenyl)prop-2-en-1-one
Authors: Shanthi D. , Vidhya Sagar T. , Kayalvizhi M. , Vasuki G. , Thiruvalluvar A.
Published: June 2014

In the title molecule, C22H18O, theo-tolyl ring is connected through a conjugated double bond. The molecule adopts anEconformation and the C—C=C—C torsion angle is 178.77 (13)°. The overall conformation may be described by the values of dihedral angles between the different planes. The terminal rings are twisted by an angle of 54.75 (8)°, while the biphenyl part is not planar, the dihedral angle between the planes of the rings being 40.65 (8)°. The dihedral angle between the benzene rings is 14.10 (7)°. There are three weak C—H...π interactions found in the crystal structure. No classic hydrogen bonds are observed.
(4R)-3-Hydroxy-7-isopropyl-4-methyl-5,6-dihydrobenzofuran-2(4H)-one
Authors: Heinemann Frank W. , Herrera Alberto , Agrifoglio Giuseppe , Dorta Romano , Pastrán Jesús
Published: June 2014

In the title compound, alternatively called α-hydroxy-γ-alkylidenebutenolide, C12H16O3, two independent molecules (AandB) crystallize in the asymmetric unit in each of which the 5,6-dihydrobenzo ring has an envelope conformation. The torsion angle along the butadiene chain in the γ-alkylidenebutenolide core is −177.9 (2)° for moleculeAand 179.9 (2)° for moleculeB. In the crystal, O—H...O hydrogen bonds between hydroxyl and carbonyl groups of adjacent independent molecules form dimers withR22(10) loops.
2′,7′-Dibromospiro[cyclopropane-1,9′-fluorene]
Authors: Xue Yue-yuan , Qin Yong-qi
Published: June 2014

In the title compound, C15H10Br2, each molecule is situated on special postionmm, so the asymmetric unit contains one-quater of a molecule. The 2,7-dibromo-9H-fluorene fragment and three spirocyclopropane C atoms lie on different planes, which are perpendicular to each other. In the crystal, π–π interactions between aromatic rings [intercentroid distance = 3.699 (3) Å] pack the molecules into stacks extending in [001].
{4-Amino-N′-[(2-oxidonaphthalen-1-yl)methylidene]benzohydrazidato}dimethyltin(IV)
Authors: Cheng Miao , Zhao Yuhong , Dong Tiantian , Cui Jichun
Published: June 2014

In the title compound, [Sn(CH3)2(C18H13N3O2)], the SnIVion is coordinated by one N and two O atoms from the tridentate 4-amino-N′-[(2-oxidonaphthalen-1-yl)methylidene]benzohydrazidate(2−) ligand and two C atoms from methyl ligands in a distorted trigonal–bipyramidal geometry. The dihedral angle between the naphthalene ring system and the benzene ring is 19.2 (2)°. In the crystal, weak N—H...O hydrogen bonds link the molecules into zigzag chains along [010].
2,2,6,6-Tetrabromo-3,4,4,5-tetramethoxycyclohexanone
Authors: Faizi Md. Serajul Haque , Mashrai Ashraf , Shahid M.
Published: June 2014

In the title compound, C10H14Br4O5, synthesized from the methoxy Schiff baseN-(pyridin-2-ylmethyl)methoxyaniline and molecular bromine, the cyclohexanone ring has a chair conformation with one of the four methoxy groups equatorially orientated with respect to the carbonyl group and the others axially orientated. The C—Br bond lengthsvary from 1.942 (4) to1.964 (4) Å. In the crystal, weak C—H...Ocarbonylhydrogen-bonding interactions generate chains extending along theb-axis direction. Also present in the structure are two short intermolecular Br...Omethoxyinteractions [3.020 (3) and 3.073 (4) Å].
How to assess Drosophila cold tolerance: chill coma temperature and lower lethal temperature are the best predictors of cold distribution limits
Authors: Andersen Jonas L. , Manenti Tommaso , Sørensen Jesper G. , MacMillan Heath A. , Loeschcke Volker , Overgaard Johannes
Published: June 2014

Thermal tolerance may limit and therefore predict ectotherm geographic distributions. However, which of the many metrics of thermal tolerance best predict distribution is often unclear, even for drosophilids, which constitute a popular and well‐described animal model.

Five metrics of cold tolerance were measured for 14 Drosophila species to determine which metrics most strongly correlate with geographic distribution. The species represent tropical to temperate regions but all were reared under similar (common garden) conditions (20 °C). The traits measured were: chill coma temperature (CTmin), lethal temperature (LTe50), lethal time at low temperature (LTi50), chill coma recovery time (CCRT) and supercooling point (SCP).

Measures of CTmin, LTe50 and LTi50 proved to be the best predictors to describe the variation in realized latitudinal distributions (R2 = 0·699, R2 = 0·741 and 0·550, respectively) and estimated environmental cold exposure (R2 = 0·633, R2 = 0·641 and 0·511, respectively). Measures of CCRT also correlated significantly with estimated minimum temperature (R2 = 0·373), while the SCP did not. These results remained consistent after phylogenetically independent analysis or when applying nonlinear regression. Moreover, our findings were supported by a similar analysis based on existing data compiled from the Drosophila cold tolerance literature.

Trait correlations were strong between LTe50, LTi50 and CTmin, respectively (0·83 > R2 > 0·55). However, surprisingly, there was only a weak correlation between the entrance into coma (CTmin) and the recovery from chill coma (CCRT) (R2 = 0·256).

Considering the findings of the present study, data from previous studies and the logistical constraints of each measure of cold tolerance, we conclude that CTmin and LTe50 are superior measures when estimating the ecologically relevant cold tolerance of drosophilids. Of these two traits, CTmin requires less equipment, time and animals and thereby presents a relatively fast, simple and dynamic measure of cold tolerance.
Influence of brown stink bug feeding, planting date and sampling time on common smut infection of maize
Authors: Ni Xinzhi , Toews Michael D. , Buntin G. David , Carpenter James E. , Huffaker Alisa , Schmelz Eric A. , Cottrell Ted E. , Abdo Zaid
Published: June 2014

Phytopathogen infections are frequently influenced by both biotic and abiotic factors in a crop field. The effect of brown stink bug, Euschistus servus (Hemiptera: Pentatomidae), feeding and planting date and sampling time on common smut (Ustilago maydis) infection percentage of maize plants was examined in 2005 and 2006, and 2010 and 2011, respectively. Brown stink bug adult feeding on maize hybrid “DKC6971” at flowering in 2005 and 2006 did not influence smut infection percentage when examined using 3 treatments (i.e., 0 adult, 5 adults, and 5 adults mixed with the smut spores). The smut infection percentages were <3% (n = 12) in the 3 treatments. The smut infection percentage among the 4 weekly samplings was the same, so was natural aflatoxin contamination at harvest among the treatments. The 2nd experiment showed that planting date did not affect the smut infection percentage in either 2010 or 2011. But, the smut infection percentage from the postflowering sampling was greater than preflowering sampling in both years. The smut infection percentage varied among the germplasm lines in 2010, but not in 2011. This study demonstrated that brown stink bug feeding at flowering had no effect on smut infection in maize, and the best time for smut evaluation would be after flowering. The temperature and precipitation might have also influenced the percentage of smut‐infected maize plants during the 4 years when the experiments were conducted. The similarity between kernel‐colonizing U. maydis and Aspergillus flavus infections and genotype × environment interaction were also discussed.
Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon‐date and calibration error into Bayesian phylogenetic analyses of ancient DNA
Authors: Molak Martyna , Suchard Marc A. , Ho Simon Y. W. , Beilman David W. , Shapiro Beth
Published: June 2014

Studies of DNA from ancient samples provide a valuable opportunity to gain insight into past evolutionary and demographic processes. Bayesian phylogenetic methods can estimate evolutionary rates and timescales from ancient DNA sequences, with the ages of the samples acting as calibrations for the molecular clock. Sample ages are often estimated using radiocarbon dating, but the associated measurement error is rarely taken into account. In addition, the total uncertainty quantified by converting radiocarbon dates to calendar dates is typically ignored. Here, we present a tool for incorporating both of these sources of uncertainty into Bayesian phylogenetic analyses of ancient DNA. This empirical calibrated radiocarbon sampler (ECRS) integrates the age uncertainty for each ancient sequence over the calibrated probability density function estimated for its radiocarbon date and associated error. We use the ECRS to analyse three ancient DNA data sets. Accounting for radiocarbon‐dating and calibration error appeared to have little impact on estimates of evolutionary rates and related parameters for these data sets. However, analyses of other data sets, particularly those with few or only very old radiocarbon dates, might be more sensitive to using artificially precise sample ages and should benefit from use of the ECRS.
Umbilical cord blood acid–base status in pregnancy with congenital heart disease
Authors: ZHAN Q. , WANG X. , YU J. , FAN Y.
Published: June 2014

Background

The risk of fetal and neonatal complications is higher in pregnant women with congenital heart disease (CHD). It remains unknown whether umbilical cord blood gas values are different between pregnant women with CHD and healthy women undergoing elective cesarean section during combined spinal‐epidural anesthesia. The purpose of the present study was to compare umbilical cord blood acid–base status and gas values in pregnant women with CHD vs. healthy pregnant women undergoing elective cesarean section during combined spinal–epidural (CSE) anesthesia.

Methods

Patients with singleton pregnancy undergoing elective cesarean delivery under CSE anesthesia were enrolled. Patients were divided into two groups: healthy pregnant women (group H) and pregnant with congenital heart disease (group CHD). Immediately after delivery, umbilical cord arterial blood sample and venous blood sample were collected and measured. The comparison between two groups was performed using grouped t‐test.

Results

Forty‐four women in group H and 33 women in group CHD were analyzed finally. Umbilical arterial blood pH, base excess (BE) and HCO3− (pH 7.29 ± 0.05, BE −1.4 ± 1.9 mmol/L, HCO3− 21.5 ± 1.4 mmol/L) were significantly lower in pregnant women with CHD than in healthy pregnant women (pH 7.33 ± 0.03, BE −0.1 ± 2.1 mmol/L, HCO3− 22.5 ± 1.4 mmol/L).

Conclusions

The lower values of umbilical arterial blood pH, BE and HCO3− were observed in pregnant women with CHD than in healthy women undergoing elective cesarean section during CSE anesthesia.
Polygenic risk score and the psychosis continuum model
Authors: Tesli M. , Espeseth T. , Bettella F. , Mattingsdal M. , Aas M. , Melle I. , Djurovic S. , Andreassen O. A.
Published: June 2014

Objective

Schizophrenia (SZ) and bipolar disorder (BD) are heritable, polygenic disorders with shared clinical characteristics and genetic risk indicating a psychosis continuum. This is the first study using polygenic risk score (PGRS) to investigate the localization of diagnostic subcategories along the entire psychosis spectrum.

Method

Based on results from the Psychiatric Genomics Consortium (PGC), we assigned a SZ and BD PGRS to each individual in our independent sample [N = 570 BD spectrum cases, 452 SZ spectrum cases and 415 healthy controls (CTR)]. Potential differences in mean SZ and BD PGRS across diagnostic spectrums and subcategories were explored.

Results

SZ and BD PGRSs were significantly associated with both SZ and BD spectrums compared with CTR. For the subcategories, SZ PGRS was significantly associated with SZ, schizoaffective disorder, psychosis not otherwise specified, and BD1, while BD PGRS was significantly associated with BD1 and BD2. There were no significant differences between any of the diagnostic spectrums or subgroups for neither the SZ nor BD PGRS. Lifetime psychosis was significantly associated with SZ PGRS but not with BD PGRS.

Conclusion

These findings further support the psychosis continuum model and provide molecular polygenetic validation of the localization of diagnostic subcategories within this continuum.
Early corticosteroids requirement after the diagnosis of ulcerative colitis diagnosis can predict a more severe long‐term course of the disease – a nationwide study of 1035 patients
Authors: Khan N. H. , Almukhtar R. M. , Cole E. B. , Abbas A. M.
Published: June 2014

Background

There are limited data regarding clinical outcomes in ulcerative colitis (UC) patients who require early corticosteroids (CS) use.

Aim

To evaluate the rate of early CS utilisation (within 30 days of diagnosis) as a predictive marker for long‐term outcomes, colectomy and CS dependency, in a population‐based cohort of incident UC cases.

Methods

Nationwide data were obtained from the Veterans Affairs (VA) health care system for the period 2001–2011. Incident UC cases were identified. A retrospective cohort design and time‐to‐event survival analysis were used to track outcomes of interest. Cox regression multivariate analysis was employed.

Results

One thousand and thirty‐five newly diagnosed patients with UC were identified and included in the analysis; 236 (23%) of those patients required early CS therapy. Patients were followed‐up over a median time of 4.7 years (IQR 2.8–6.8) after UC diagnosis. The 5‐year cumulative probability of requiring colectomy varied significantly by early CS use status (13% among early CS users compared to 4% among those who did not require early CS treatment, P < 0.001). Similar variation in the 5‐year cumulative probability of CS dependency by early CS status was observed. Early CS users were more likely to require colectomy 2.9 (CI 1.7–5.0, P < 0.001) and to become CS dependent 4.5 (95% CI 3.6–5.7, P < 0.001) than non‐users.

Conclusions

Early CS use can help identify those patients who have a more active disease course of UC. Recognising this can be among the indicators that can help physicians identify patients who may require early initiation of more aggressive therapy.
The overlap of atopy and functional gastrointestinal disorders among 23 471 patients in primary care
Authors: Jones M. P. , Walker M. M. , Ford A. C. , Talley N. J.
Published: June 2014

Background

Activation of the immune system has been demonstrated in atopy and functional gastrointestinal disorders (FGIDs). Previous data from our group have suggested a connection between immune dysregulation, FGIDs and mood disorders.

Aim

To investigate if these data translate to clinical practice and examine connections from the perspective of FGIDs to determine whether atopy and FGIDs are connected via mood disorders.

Methods

Evidence of irritable bowel syndrome (IBS), functional dyspepsia (FD) and constipation was sought from the medical records of 30 000 primary care records over a minimum 5 year period. The same records yielded diagnoses of four atopic conditions (asthma, eczema, allergic rhinitis/hay fever and conjunctivitis).

Results

Atopic conditions were found in excess among all FGID groups considered when compared with controls. In the groups with IBS alone (OR = 1.43, 1.29–1.58), FD alone (OR = 1.41, 1.26–1.58) and those with multiple FGIDs (OR = 1.92, 1.75–2.12) there was elevated prevalence of asthma compared with controls without a FGID. Across disorders the excess was generally highest among patients diagnosed with multiple FGIDs (rhinitis/hay fever OR = 3.74, 3.32–4.20; conjunctivitis OR = 3.00, 2.49–3.62) and was only partly explained by a common association between both FGIDs and atopic conditions with mood disorders, although not for every atopic/FGID combination (rhinitis/hay fever OR = 2.60, 2.29–2.96, conjunctivitis OR = 2.34, 1.90–2.87).

Conclusions

Irritable bowel syndrome, functional dyspepsia and constipation share an association with atopy that is only partly explained via a common connection with mood disorders. These data have important implications for understanding both the pathophysiology of functional gastrointestinal disorders and development of new treatments.
Effect of nutritive level on carcass traits and meat quality of IHDH foals
Authors: De Palo Pasquale , Tateo Alessandra , Maggiolino Aristide , Centoducati Pasquale
Published: June 2014

The present work describes the effect of nutritive level on horse carcass traits and on meat quality. Eighteen male Italian Heavy Draught Horse (IHDH) breed foals were employed in the study. Soon after foaling they were randomly subdivided into three groups according to three nutritive level classes: 150%, 180% and 200% of maintenance requirements. Live weight, hot carcass weight and dressing percentage of each animal were recorded. After slaughtering, meat samples were collected from Longissimus dorsi muscle. The right half carcass of each animal was then divided into cuts. Each one was subdivided into lean, fat and bones. Live weight, carcass weight and dressing percentage were not affected by nutritive level (P > 0.05). Horses fed with the lower nutritive level showed a higher incidence of lean and a lower incidence of fat (P < 0.01). Moreover, fatty acid profile was not affected by nutritive level (P > 0.05). Probably the tendency of IHDH foals to concentrate adipogenesis in the subcutaneous district could explain the lack of influence of nutritive level on meat quality parameters and its influence on carcass and cut composition, which tend to be richer in fat.
Evaluation of vaginal discharge with the Metricheck device and the relationship to reproductive performance in postpartum dairy cows
Authors: Lambertz Christian , Völker Denise , Janowitz Ulrich , Gauly Matthias
Published: June 2014

Vaginal mucus during estrus was examined with the Metricheck device and the relationship to the reproduction of high‐yielding dairy cows was studied. The study was conducted in 99 dairy herds located in Western Germany and 1348 Holstein‐Friesian heifers and cows showing spontaneous estrus were examined. Independent of the Metricheck result, the animals were inspected by professional insemination technicians and those suitable for insemination (n = 989) were bred by artificial insemination (AI). Reproductive performance was characterized by non‐return rate at 90 days (NRR90). The discharge of the animals predominantly had a clear appearance (70%) and a stringy consistency (80%). Animals with clear vaginal discharge had higher NRR90 (56%; n = 697) than animals with abnormal (turbid, mucopurulent, purulent, sanguineous) vaginal secretion (48%, n = 292; P < 0.05). NRR90 was lower in animals with short calving to AI interval (< 70 days; 39%) than with medium (70–130 days; 54%) or long (> 130 days; 62%) intervals (P < 0.05). NRR90 decreased by 12% from the lowest (< 15 kg) to the highest (> 45 kg) milk yield class. In conclusion, the use of the Metricheck device integrated into the insemination procedure is recommended to identify dairy cows suffering severely from uterine disease.
Fatty acid profile of plasma, muscle and adipose tissues in Chilota lambs grazing on two different low quality pasture types in Chiloé Archipelago (Chile)
Authors: Gallardo Maria A. , Dannenberger Dirk , Rivero Jordana , Pulido Ruben , Nuernberg Karin
Published: June 2014

There is no information about the effect of different pasture types on tissue fatty acid profiles of a native rustic lamb breed of the Chiloe Archipelago, the Chilota. Eight Chilota lambs were grazed on a ‘Calafatal’ pasture (CP), a typical secondary succession of Chiloé Archipelago (Chile) and eight Chilota lambs were located to graze on naturalized pasture (NP) of Chiloé. Botanical, chemical and lipid composition of the two types of pastures and of different lamb tissues (muscle, subcutaneous – and tail adipose tissues) and plasma were performed. Both pasture types induced high n‐3 polyunsaturated fatty acids (PUFA) and CLAcis‐9,trans‐11 proportions in Chilota meat. Thus, in muscle, Chilota lambs grazing CP showed higher sum PUFA, sum n‐6 PUFA proportion and n‐6/n‐3 PUFA ratio compared with Chilota lambs grazing NP. In tail fats of Chilota lambs grazing CP significantly higher proportions of 18:3n‐3, sum saturated fatty acids, sum PUFA, n‐3 and n‐6 PUFA were detected compared with Chilota lambs grazing NP. Feeding of different pasture types (CP vs. NP) caused significant differences in fatty acid composition of muscle and the two fat depots in Chilota lambs, but also point to tissue‐specific responses of de novo synthesized fatty acid deposition in the tissues.