bluuebunny/crossref_metadata_2025 huggingface dataset:
Adenosine receptor and its downstream targets, mod(mdg4) and Hsp70, work as a signaling pathway modulating cytotoxic damage inDrosophila
Authors: Lin Yu-Hsien , Maaroufi Houda Ouns , Kucerova Lucie , Rouhova Lenka , Filip Tomas , Zurovec Michal
Published: December 2019

Adenosine (Ado) is an important signaling molecule involved in stress responses. Studies in mammalian models have shown that Ado regulates signaling mechanisms involved in ‘danger-sensing’ and tissue-protection. Yet, little is known about the role of Ado signaling inDrosophila. In the present study, we observed lower extracellular Ado concentration and suppressed expression of Ado transporters in flies expressing mutant huntingtin protein (mHTT). We altered Ado signaling using genetic tools and found that the overexpression of Ado metabolic enzymes, as well as the suppression of Ado receptor (AdoR) and transporters (ENTs), were able to minimize mHTT-induced mortality. We also identified the downstream targets of the AdoR pathway, the modifier of mdg4 (Mod(mdg4)) and heat-shock protein 70 (Hsp70), which carry out its function. Finally, we showed that a decrease in Ado signaling affect otherDrosophilastress reactions, including paraquat and heat-shock treatments. Our study provides important insights into how Ado regulates stress responses inDrosophila.
Plasticity ofMedicago truncatulaseed dormancy relates to large-scale environment variation
Authors: Renzi Juan Pablo , Duchoslav Martin , Brus Jan , Hradilová Iveta , Pechanec Vilém , Václavek Tadeáš , Machalová Jitka , Hron Karel , Verdier Jerome , Smýkal Petr
Published: December 2019

Seed dormancy and timing of its release is important developmental transition determining the survival of individual as well as population and species. We usedMedicago truncatulaas model to study legume seed dormancy in ecological and genomics context. The effect of oscillating temperatures as one of the dormancy release factor was tested over the period of 88 days on the set of 178 accessions originating from variable environmental conditions of Mediterranean basin. Phenotypic plasticity of final dormancy was significantly correlated with increased aridity, suggesting that plastic responses to external stimuli provide seeds with strong bet-hedging capacity and the potential to cope with high levels of environmental heterogeneity. Genome-wide association analysis identified candidate genes associated with dormancy release related to secondary metabolites synthesis, hormone regulation and modification of the cell wall likely mediating seed coat permeability and ultimately imbibition and germination.

Highlight

Medicago seed dormancy was correlated with increased aridity of the environment, suggesting that plastic responses provide seeds with a bet-hedging capacity. Genome-wide association analysis identified candidate genes associated with release from dormancy.
Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plantSaniculiphyllum guangxiense(Saxifragaceae)
Authors: Folk Ryan A. , Sewnath Neeka , Xiang Chun-Lei , Sinn Brandon T. , Guralnick Robert P.
Published: December 2019

Background

Plastid gene loss and pseudogenization has been widely documented in parasitic and mycoheterotrophic plants, which have relaxed selective constraints on photosynthetic function. More enigmatic are sporadic reports of degradation and loss of important photosynthesis genes in lineages thought to be fully photosynthetic. Here we report the complete plastid genome ofSaniculiphyllum guangxiense, a critically endangered and phylogenetically isolated plant lineage, along with genomic evidence of reduced chloroplast function. We also report 22 additional plastid genomes representing the diversity of its containing clade Saxifragales, characterizing gene content and placing variation in a broader phylogenetic context.

Results

We find that the plastid genome ofSaniculiphyllumhas experienced pseudogenization of five genes of the NDH complex (ndhA,ndhB, ndhD,ndhF, andndhK), previously reported in flowering plants with an aquatic habit, as well as the more surprising pseudogenization of two genes more central to photosynthesis (ccsAandcemA), contrasting with strong phylogenetic conservatism of plastid gene content in all other sampled Saxifragales. These genes participate in photooxidative protection, cytochrome synthesis, and carbon uptake. Nuclear paralogs exist for all seven plastid pseudogenes, yet these are also unlikely to be functional.

Conclusions

Saniculiphyllumappears to represent the greatest degree of plastid gene loss observed to date in any fully photosynthetic lineage, yet plastid genome length, structure, and substitution rate are within the variation previously reported for photosynthetic plants. These results highlight the increasingly appreciated dynamism of plastid genomes, otherwise highly conserved across a billion years of green plant evolution, in plants with highly specialized life history traits.
Alteration of the premature tRNA landscape by gammaherpesvirus infection
Authors: Tucker Jessica , Schaller Aaron M. , Willis Ian , Glaunsinger Britt A.
Published: December 2019

Transfer RNAs (tRNAs) are transcribed by RNA polymerase III (RNAPIII) and play a central role in decoding our genome, yet their expression and non-canonical function remain understudied. Many DNA tumor viruses enhance the activity of RNAPIII, yet whether infection alters tRNA expression is largely unknown. Here, we present the first genome-wide analysis of how viral infection alters the tRNAome. Using a tRNA-specific sequencing method (DM-tRNA-seq), we find that the murine gammaherpesvirus MHV68 induces global changes in pre-tRNA expression with 14% of tRNA genes upregulated more than 3-fold, indicating that differential tRNA gene induction is a characteristic of DNA virus infection. Elevated pre-tRNA expression corresponds to increased RNAPIII occupancy for the subset of tRNA genes tested; additionally, post-transcriptional mechanisms contribute to the accumulation of pre-tRNA species. We find increased abundance of tRNA fragments derived from pre-tRNAs upregulated by viral infection, suggesting that non-canonical tRNA cleavage is also affected. Further, pre-tRNA accumulation, but not RNAPIII recruitment, requires gammaherpesvirus-induced degradation of host mRNAs by the virally encoded mRNA endonuclease muSOX. We hypothesize that depletion of pre-tRNA maturation or turnover machinery contributes to robust accumulation of full-length pre-tRNAs in infected cells. Collectively, these findings reveal pervasive changes to tRNA expression during DNA virus infection and highlight the potential of using viruses to explore tRNA biology.

Significance

Viral infection can dramatically change the gene expression landscape of the host cell, yet little is known regarding changes in non-coding gene transcription by RNA polymerase III (RNAPIII). Among these are transfer RNAs (tRNAs), which are fundamental in protein translation, yet whose gene regulatory features remain largely undefined in mammalian cells. Here, we perform the first genome-wide analysis of tRNA expression changes during viral infection. We show that premature tRNAs accumulate during infection with the model gammaherpesvirus MHV68 as a consequence of increased transcription, but that transcripts do not undergo canonical maturation into mature tRNAs. These findings underscore how tRNA expression is a highly-regulated process and that cells have strategies to balance tRNA pools during conditions of elevated RNAPIII activity.
Individual head models for estimating the TMS-induced electric field in rat brain
Authors: Koponen Lari M. , Stenroos Matti , Nieminen Jaakko O. , Jokivarsi Kimmo , Gröhn Olli , Ilmoniemi Risto J.
Published: December 2019

In transcranial magnetic stimulation (TMS), the initial cortical activation due to stimulation is determined by the state of the brain and the magnitude, waveform, and direction of the induced electric field (E-field) in the cortex. The E-field distribution depends on the conductivity geometry of the head. The effects of deviations from a spherically symmetric conductivity profile have been studied in detail in humans. In small mammals, such as rats, these effects are more pronounced due to their smaller and less spherical heads. In this study, we describe a simple method for building individual realistically shaped head models for rats from high-resolution X-ray tomography images. We computed the TMS-induced E-field with the boundary element method and assessed the effect of head-model simplifications on the estimated E-field. The deviations from spherical symmetry have large, non-trivial effects on the E-field distribution: in some cases, even the direction of the E-field in the cortex cannot be reliably predicted by the coil orientation unless these deviations are properly considered.
Functional redundancy and crosstalk between flavodiiron proteins and NDH-1 inSynechocystissp. PCC 6803
Authors: Nikkanen Lauri , Sánchez Anita Santana , Ermakova Maria , Rögner Matthias , Cournac Laurent , Allahverdiyeva Yagut
Published: December 2019

In oxygenic photosynthetic organisms excluding angiosperms, flavodiiron proteins (FDPs) catalyze light-dependent reduction of O2to H2O. This alleviates electron pressure on the photosynthetic apparatus and protects it from photodamage. InSynechocystissp. PCC 6803, four FDP isoforms function as hetero-oligomers of Flv1 and Flv3 and/or Flv2 and Flv4. An alternative electron transport pathway mediated by the NAD(P)H dehydrogenase-like complex (NDH-1) also contributes to redox hemostasis and the photoprotection of photosynthesis. Four NDH-1 types haven been characterized in cyanobacteria: NDH-11and NDH-12, which function in respiration; and NDH-13and NDH-14, which function in CO2uptake. All four types are involved in cyclic electron transport. Along with single FDP mutants (Δflv1and Δflv3) and the double NDH-1 mutants (Δd1d2, which is deficient in NDH-11,2and Δd3d4, which is deficient in NDH-13,4), we studied triple mutants lacking either one of Flv1 or Flv3, and NDH-11,2or NDH-13,4. We show that the presence of either Flv1/3 or NDH-11,2, but not NDH-13,4, is indispensable for survival during changes in growth conditions from high CO2/moderate light to low CO2/ high light. Our results suggest functional redundancy and crosstalk between FDPs and NDH-11,2under the studied conditions, and demonstrate that the functions of FDPs and NDH-11,2are dynamically coordinated for the efficient oxidation of PSI and for photoprotection under variable CO2and light availability.

One sentence summary

Flavodiiron proteins and NDH-1 complex ensure survival of cyanobacterial cells by cooperatively safeguarding the photosynthetic apparatus against excessive reduction
A Cell Penetrating Peptide from Type I Interferon Protects the Retina in a Mouse Model of Autoimmune Uveitis
Authors: Ahmed Chulbul M , Ildefonso Cristhian J , Johnson Howard M , Lewin Alfred S
Published: December 2019

Experimental autoimmune uveitis (EAU) in rodents recapitulates many features of the disease in humans and has served as a useful tool for the development of therapeutics. A peptide from C-terminus of interferon α1, conjugated to palmitoyl-lysine for cell penetration, denoted as IFNα–C, was tested for its anti-inflammatory properties in ARPE-19 cells, followed by testing in a mouse model of EAU. Treatment with IFNα–C and evaluation by RT-qPCR showed the induction of anti-inflammatory cytokines and chemokine. Inflammatory markers induced by treatment with TNFα were suppressed when IFNα–C was simultaneously present. TNF-α mediated induction of NF-kB and signaling by IL-17A were attenuated by IFNα–C. Differentiated ARPE-19 cells were treated with TNFα in the presence or absence IFNα–C and analyzed by immmunhistochemistry. IFNα–C protected against the disruption integrity of tight junction proteins. Similarly, loss of transepithelial resistance caused by TNFα was prevented by IFNα–C. B10.RIII mice were immunized with a peptide from interphotoreceptor binding protein (IRBP) and treated by gavage with IFNα–C. Development of uveitis was monitored by histology, fundoscopy, SD-OCT, and ERG. Treatment with IFNα–C prevented uveitis in mice immunized with the IRBP peptide. Splenocytes isolated from mice with ongoing EAU exhibited antigenspecific T cell proliferation that was inhibited in the presence of IFNα–C. IFNα–C peptide exhibits anti-inflammatory properties and protects mice against damage to retinal structure and function suggesting that it has therapeutic potential for the treatment of autoimmune uveitis.
Genome sequencing and functional characterization of aDictyopanus pusillusfungal extract offers a promising alternative for lignocellulose pretreatment of oil palm residues
Authors: Rueda Andrés M. , de los Santos Yossef López , Vincent Antony T. , Létourneau Myriam , Hernández Inés , Sánchez Clara I. , Molina V. Daniel , Ospina Sonia A. , Veyrier Frédéric J. , Doucet Nicolas
Published: December 2019

The pretreatment of biomass is a critical requirement of bio-renewable fuel production from lignocellulose. Although current processes primarily involve chemical and physical approaches, the biological breakdown of lignin using enzymes and microorganisms is quickly becoming an interesting eco-friendly alternative to classical processes. As a result, bioprospection of wild fungi from naturally occurring lignin-rich sources remains a suitable method to uncover and isolate new species exhibiting ligninolytic activity. In this study, wild species of white rot fungi were collected from Colombian forests based on their natural wood decay ability and high capacity to secrete oxidoreductases with high affinity for phenolic polymers such as lignin. Based on high activity obtained from solid-state fermentation using a lignocellulose source from oil palm as matrix, we describe the isolation and whole-genome sequencing ofDictyopanus pusillus, a wild basidiomycete fungus exhibiting ABTS oxidation as an indication of laccase activity. Functional characterization of a crude enzymatic extract identified laccase activity as the main enzymatic contributor to fungal extracts, an observation supported by the identification of 13 putative genes encoding for homologous laccases in the genome. To the best of our knowledge, this represents the first report of an enzymatic extract exhibiting laccase activity in theDictyopanusgenera, offering means to exploit this species and its enzymes for the delignification process of lignocellulosic by-products from oil palm.
Cross-Species Integration of Transcriptomic Effects of Tobacco and Nicotine Exposure Helps to Prioritize Genetic Effects on Human Tobacco Consumption
Authors: Palmer Rohan H C , Benca-Bachman Chelsie E. , Bubier Jason A. , McGeary John E , Ramgiri Nikhil , Srijeyanthan Jenani , Huggett Spencer , Yang Jingjing , Visscher Peter , Yang Jian , Knopik Valerie , Chesler Elissa J.
Published: December 2019

Computational advances have fostered the development of new methods and tools to integrate gene expression and functional evidence into human-genetic association analyses. Integrative functional genomics analysis for altered response to alcohol in mice provided the first evidence that multi-species analysis tools, such as GeneWeaver, can identify or confirm novel alcohol-related loci. The present study describes an integrative framework to investigate how highly-connected genes linked by their association to tobacco-related behaviors, contribute to individual differences in tobacco consumption. Data from individuals of European ancestry in the UKBiobank (N=139,043) were used to examine the relative contribution of orthologs of a set of genes that are transcriptionally co-regulated by tobacco or nicotine exposure in model organism experiments to human tobacco consumption. Multi-component mixed linear models using genotyped and imputed single nucleotide variants indicated that: (1) variation within human orthologs of these genes accounted for 2-5% of the observed heritability (meta h2SNP-Total=0.08 [95% CI: 0.07, 0.09]) of tobacco/nicotine consumption across three independent folds of unrelated individuals (enrichment ranging from 0.85 - 2.98), and (2) variation around (5, 10, 15, 25, and 50 Kb regions) the set of co-transcriptionally regulated genes accounted for 5-36% of the observed SNP-heritability (enrichment ranging from 1.60 – 31.45). Notably, the effects of variants in co-transcriptionally regulated genes were enriched in tobacco GWAS. These findings highlight the advantages of using multiple species evidence to isolate genetic factors to better understand the etiological complexity of tobacco and other nicotine consumption.
A Metric Space of Ranked Tree Shapes and Ranked Genealogies
Authors: Kim Jaehee , Rosenberg Noah A. , Palacios Julia A.
Published: December 2019

Genealogical tree modeling is essential for estimating evolutionary parameters in population genetics and phylogenetics. Recent mathematical results concerning ranked genealogies without leaf labels enable new opportunities in the analysis of evolutionary trees. In particular, comparisons between ranked genealogies facilitate the study of evolutionary processes for organisms sampled in multiple time periods. We propose a metric space on ranked genealogies for lineages sampled from both isochronous and time-stamped heterochronous sampling. Our new tree metrics make it possible to conduct statistical analyses of ranked tree shapes and timed ranked tree shapes, or ranked genealogies. Such analyses allow us to assess differences in tree distributions, quantify estimation uncertainty, and summarize tree distributions. We show the utility of our metrics via simulations and an application in infectious diseases.
The dynamics of oligodendrocyte generation: how distinct is the mouse from the human?
Authors: Gonsalvez David G , Craig Georgina A , Walsh Darragh M , Hughes Barry D , Wood Rhiannon J , Yoo Sang Won , Murray Simon S , Xiao Junhua
Published: December 2019

Murine oligodendrocyte generation dynamics are considered distinct from those in the human, with implications for cross-species differences in neural homeostasis, injury response and ability to functionally adapt circuits through myelin plasticity. We identify that murine oligodendrocyte precursors do not vary their cell division times in vivo and determine how daily production rates change over a lifespan. We show that murine oligodendrogenesis closely resembles what is reported for the human.
A single cell transcriptional atlas of early synovial joint development
Authors: Bian Qin , Cheng Yu-Hao , Wilson Jordan P , Kim Dong Won , Wang Hong , Blackshaw Seth , Cahan Patrick
Published: December 2019

Synovial joint development begins with the formation of the interzone, a region of condensed mesenchymal cells at the site of the prospective joint. Recently, lineage tracing strategies have revealed that Gdf5-lineage cells native to and from outside the interzone contribute to most, if not all, of the major joint components. However, there is limited knowledge of the specific transcriptional and signaling programs that regulate interzone formation and fate diversification of synovial joint constituents. To address this, we have performed single cell RNA-Seq analysis of 6,202 synovial joint progenitor cells from the developing murine knee joint from E12.5 to E15.5. By using a combination of computational analytics,in situhybridization, and functional analysis of prospectively isolated populations, we have inferred the underlying transcriptional networks of the major developmental paths for joint progenitors. Our freely available single cell transcriptional atlas will serve as a resource for the community to uncover transcriptional programs and cell interactions that regulate synovial joint development.
A cellular stress response induced by the CRISPR/dCas9 activation system is not heritable through cell divisions
Authors: Johnston Andrew D. , Abdulrazak Alali , Sato Hanae , Maqbool Shahina B. , Suzuki Masako , Greally John M. , Simões-Pires Claudia A.
Published: December 2019

The CRISPR/Cas9 system can be modified to perform ‘epigenetic editing’ by utilizing the catalytically-inactive (dead) Cas9 (dCas9) to recruit regulatory proteins to specific genomic locations. In prior studies, epigenetic editing with multimers of the transactivator VP16 and guide RNAs (gRNAs) was found to cause adverse cellular responses. These side effects may confound studies inducing new cellular properties, especially if the cellular responses are maintained through cell divisions - an epigenetic regulatory property. Here we show how distinct components of this CRISPR/dCas9 activation system, particularly untargeted gRNAs, upregulate genes associated with transcriptional stress, defense response, and regulation of cell death. Our results highlight a previously undetected acute stress response to CRISPR/dCas9 components in human cells, which is transient and not maintained through cell divisions.
A Genetic Screen Links the Disease-Associated Nab2 RNA-Binding Protein to the Planar Cell Polarity Pathway inDrosophila melanogaster
Authors: Lee Wei-Hsuan , Corgiat Edwin , Rounds J. Christopher , Shepherd Zenyth , Corbett Anita H. , Moberg Kenneth H.
Published: December 2019

Mutations in the gene encoding the ubiquitously expressed RNA-binding protein ZC3H14 result in a non-syndromic form of autosomal recessive intellectual disability. Studies inDrosophilahave defined roles for the ZC3H14 ortholog, Nab2 (akaDrosophilaNab2 or dNab2), in axon guidance and memory due in part to interaction with a second RNA-binding protein, the fly Fragile X homolog Fmr1, and coregulation of shared Nab2-Fmr1 target mRNAs. Despite these advances, neurodevelopmental pathways regulated by Nab2 remain poorly defined. Structural defects inNab2null brains resemble defects observed upon disruption of the planar cell polarity (PCP) pathway, which regulates planar orientation of static and motile cells. A kinked bristle phenotype in survivingNab2mutant adults additionally suggests a defect in F-actin polymerization and bundling, which is also a PCP-regulated processes. To test for Nab2-PCP genetic interactions, a collection of PCP loss-of-function alleles was screened for modification of a rough-eye phenotype produced by Nab2 overexpression in the eye (GMR-Nab2) and subsequently for modification ofNab2null phenotypes. Multiple PCP alleles dominantly modifyGMR-Nab2eye roughening and a subset of these alleles also rescue low survival and thoracic bristle kinking inNab2zygotic nulls. Moreover, alleles of two X-linked PCP factors,dishevelled(dsh) and βamyloid protein precursor-like(Appl), rescueGMR-Nab2eye roughening in male progeny derived from hemizygousdshorApplmutant fathers, suggesting an additional effect inherited through the male germline. These findings demonstrate a consistent pattern of Nab2-PCP genetic interactions that suggest molecular links between Nab2 and the PCP pathway in the developing eye, wing and germline.
Transfer from number to size reveals abstract coding of magnitude in honeybees
Authors: Bortot Maria , Stancher Gionata , Vallortigara Giorgio
Published: December 2019

Number discrimination has been documented in honeybees. It is not known, however, whether it reflects, as in vertebrates, the operating of an underlying general magnitude system that estimates quantities irrespective of dimensions (e.g., number, space, time) and format (discrete, continuous). We investigated whether bees spontaneously transfer discrete discrimination of number to continuous discrimination of size. Bees were trained to discriminate between different numerical comparisons having either a 0.5 (2vs.4 and 4vs.8) or 0.67 ratio (2vs.3 and 4vs.6). Half of the subjects learnt to choose the smaller quantity and the other half the larger quantity. Bees were then tested for spontaneous choice (in the absence of reward) using comparisons with identical numbers but different sizes. Irrespective of the ratio of the stimuli, bees trained to select the smaller numerical quantity chose the congruent smaller size; bees trained to choose the larger numerical quantity chose the congruent larger size. This finding provides the first evidence for a cross-dimensional transfer between discrete (numerical) and continuous (spatial) dimensions in an invertebrate species and supports the hypothesis of a cognitive universality of a coding for general magnitude.
Statistical physics of interacting proteins: impact of dataset size and quality assessed in synthetic sequences
Authors: Gandarilla-Pérez Carlos A. , Mergny Pierre , Weigt Martin , Bitbol Anne-Florence
Published: December 2019

Identifying protein-protein interactions is crucial for a systems-level understanding of the cell. Recently, algorithms based on inverse statistical physics, e.g. Direct Coupling Analysis (DCA), have allowed to use evolutionarily related sequences to address two conceptually related inference tasks: finding pairs of interacting proteins, and identifying pairs of residues which form contacts between interacting proteins. Here we address two underlying questions: How are the performances of both inference tasks related? How does performance depend on dataset size and the quality? To this end, we formalize both tasks using Ising models defined over stochastic block models, with individual blocks representing single proteins, and inter-block couplings protein-protein interactions; controlled synthetic sequence data are generated by Monte-Carlo simulations. We show that DCA is able to address both inference tasks accurately when sufficiently large training sets of known interaction partners are available, and that an iterative pairing algorithm (IPA) allows to make predictions even without a training set. Noise in the training data deteriorates performance. In both tasks we find a quadratic scaling relating dataset quality and size that is consistent with noise adding in square-root fashion and signal adding linearly when increasing the dataset. This implies that it is generally good to incorporate more data even if its quality is imperfect, thereby shedding light on the empirically observed performance of DCA applied to natural protein sequences.
Endogenous and exogenous control of visuospatial selective attention in freely behaving mice
Authors: You Wen-Kai , Mysore Shreesh P.
Published: December 2019

Selective spatial attention, the ability to dynamically prioritize the most important spatial location, is essential for adaptive behavior. It has been studied primarily in head-fixed animals, and almost exclusively in primates. Here, we report the development of two human-inspired, discrimination-based behavioral paradigms for studying selective visuospatial attention in the freely behaving mouse: the spatial probability task, and the flanker task. In the spatial probability task, we found enhanced response accuracy, perceptual discriminability, and rates of sensory evidence accumulation at the location with higher probability of target occurrence, and opposite effects at the lower probability location. In the absence of systematic differences in sensory input, motor biases, and trial structure, these results demonstrated endogenous expectation-driven shifts of spatial attention. In the flanker task, we found that a second, ‘flanker’ stimulus presented with the target, but with incongruent information, caused switch-like decrements in response accuracy and perceptual discriminability as a function of flanker contrast, as well as a reduced rate of evidence accumulation. These results demonstrated exogenous capture of spatial attention. The innovation of behavioral tasks for selective visuospatial attention in unrestrained mice opens up a rich avenue for future research dissecting the neural circuit mechanisms underlying this critical executive function.
Magnetic Guinier law
Authors: Michels Andreas , Malyeyev Artem , Titov Ivan , Honecker Dirk , Cubitt Robert , Blackburn Elizabeth , Suzuki Kiyonori
Published: December 2019

Small-angle scattering of X-rays and neutrons is a routine method for the determination of nanoparticle sizes. The so-called Guinier law represents the low-q approximation for the small-angle scattering curve from an assembly of particles. The Guinier law has originally been derived for nonmagnetic particle-matrix-type systems and it is successfully employed for the estimation of particle sizes in various scientific domains (e.g. soft-matter physics, biology, colloidal chemistry, materials science). An important prerequisite for it to apply is the presence of a discontinuous interface separating particles and matrix. Here, the Guinier law is introduced for the case of magnetic small-angle neutron scattering and its applicability is experimentally demonstrated for the example of nanocrystalline cobalt. It is well known that the magnetic microstructure of nanocrystalline ferromagnets is highly nonuniform on the nanometre length scale and characterized by a spectrum of continuously varying long-wavelength magnetization fluctuations, i.e. these systems do not manifest sharp interfaces in their magnetization profile. The magnetic Guinier radius depends on the applied magnetic field, on the magnetic interactions (exchange, magnetostatics) and on the magnetic anisotropy-field radius, which characterizes the size over which the magnetic anisotropy field is coherently aligned into the same direction. In contrast to the nonmagnetic conventional Guinier law, the magnetic version can be applied to fully dense random-anisotropy-type ferromagnets.
The 1:2 co-crystal formed betweenN,N′-bis(pyridin-4-ylmethyl)ethanediamide and benzoic acid: crystal structure, Hirshfeld surface analysis and computational study
Authors: Tan Sang Loon , Tiekink Edward R. T.
Published: December 2019

The crystal and molecular structures of the title 1:2 co-crystal, C14H14N4O2·2C7H6O2, are described. The oxalamide molecule has a (+)-antiperiplanar conformation with the 4-pyridyl residues lying to either side of the central, almost planar C2N2O2chromophore (r.m.s. deviation = 0.0555 Å). The benzoic acid molecules have equivalent, close to planar conformations [C6/CO2dihedral angle = 6.33 (14) and 3.43 (10)°]. The formation of hydroxy-O—H...N(pyridyl) hydrogen bonds between the benzoic acid molecules and the pyridyl residues of the diamide leads to a three-molecule aggregate. Centrosymmetrically related aggregates assemble into a six-molecule aggregateviaamide-N—H...O(amide) hydrogen bonds through a 10-membered {...HNC2O}2synthon. These are linked into a supramolecular tapeviaamide-N—H...O(carbonyl) hydrogen bonds and 22-membered {...HOCO...NC4NH}2synthons. The contacts between tapes to consolidate the three-dimensional architecture are of the type methylene-C—H...O(amide) and pyridyl-C—H...O(carbonyl). These interactions are largely electrostatic in nature. Additional non-covalent contacts are identified from an analysis of the calculated Hirshfeld surfaces.
Synthesis, crystal structure and Hirshfeld analysis of a crystalline compound comprising a 1/1 mixture of 1-[(1R,4S)- and 1-[(1S,4R)-1,7,7-trimethyl-2-oxobicyclo[2.2.1]heptan-3-ylidene]hydrazinecarbothioamide
Authors: Pires Fabrício Carvalho , Bresolin Leandro , Gervini Vanessa Carratu , Tirloni Bárbara , Bof de Oliveira Adriano
Published: December 2019

The equimolar reaction between a racemic mixture of (R)- and (S)-camphorquinone with thiosemicarbazide yielded the title compound, C11H17N3OS [common name: (R)- and (S)-camphor thiosemicarbazone], which maintains the chirality of the methylated chiral carbon atoms and crystallizes in the centrosymmetric space group C2/c. There are two molecules in general positions in the asymmetric unit, one of them being the (1R)-camphor thiosemicarbazone isomer and the second the (1S)- isomer. In the crystal, the molecular units are linked by C—H...S, N—H...O and N—H...S interactions, building a tape-like structure parallel to the (\overline{1}01) plane, generating R
2
1(7) and R
2
2(8) graph-set motifs for the H...S interactions. The Hirshfeld surface analysis indicates that the major contributions for crystal cohesion are from H...H (55.00%), H...S (22.00%), H...N (8.90%) and H...O (8.40%) interactions.
Postpartum psychological distress associated with anal incontinence in the EDEN mother–child cohort
Authors: Fritel X , Gachon B , Saurel‐Cubizolles MJ ,   the EDEN Mother–Child Cohort Study Group
Published: December 2019

Objective

To estimate the prevalence of flatus‐only and faecal incontinence, to describe their risk factors and to analyse the association between anal incontinence and psychological distress over the first year postpartum.

Design

Cohort study from pregnancy to 12 months postpartum.

Setting

Two university hospital maternity wards in France.

Population

A total of 2002 pregnant women were recruited between 2003 and 2006. Data on anal incontinence were available for the 1632 women who comprise the sample for analysis.

Methods

Women were enrolled during pregnancy. A postal questionnaire was sent at 4 and 12 months postpartum.

Main outcome measures

Anal (flatus‐only and faecal) incontinence was assessed at 4 months postpartum. Mental health was assessed at 4 and 12 months postpartum by the Edinburgh Postpartum Depression Scale (EPDS) and use of antidepressant drugs as well as by self‐rated mental health.

Results

At 4 months postpartum, the prevalence for flatus‐only incontinence was 14.4% and for faecal incontinence 1.7%; multivariate analysis, restricted to women reporting no anal incontinence before the index pregnancy, showed that continuing breastfeeding at 4 months was related to a higher risk of de novo postpartum anal incontinence (OR = 2.23). Women who reported anal incontinence at 4 months were more frequently depressed (EPDS ≥10 or antidepressant use) at 12 months postpartum: 36.0% of those with faecal incontinence were depressed, 23.3% of those with flatus‐only incontinence and only 14.8% of the continent women.

Conclusion

Postnatal faecal incontinence was rare but associated with poorer maternal mental health. Postnatal screening should be encouraged, and psychological support offered.

Tweetable abstract

Postnatal faecal incontinence was associated with depression; postnatal screening should be encouraged and psychological support offered.
Development of a professional competency framework for UK food science graduates
Authors: Weston Emma , Foster Tim , Crilly Jim , Mossop Liz
Published: December 2019

Food science‐based graduates are a significant proportion of the United Kingdom (UK) food and drink industry's workforce. Aside from technical standards, there is no cohesive competency framework to support key stakeholders; employers, students, and degree providers. Clarity of desirable competencies for the range of graduate opportunities available would enable students to undertake effective career planning and personal development, and educators to refine programs to satisfy market needs. Using a previously developed language tool, a Likert style, industry‐wide online survey in UK and Republic of Ireland (ROI) was conducted involving 218 participants from a broad range of food science‐related employment areas, evaluated by a combination of descriptive and multivariate data analysis. The survey outcomes indicate types of desirable competencies in a food science graduate. The tailored competency framework, Competencies for Food Graduate Careers (CFGC), is a set of 48elementsacross eightthemes, outlining which are desirable for each of 14 typical initial graduate roles. To enhance the quality of “oven‐ready” graduates entering the food industry, it is recommended CFGC be used for careers education and competency development in higher education. The framework is aimed to have further applications for job specification development and also to improve awareness of careers in the food industry.
Dirichlet‐multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data
Authors: Harrison Joshua G. , Calder W. John , Shastry Vivaswat , Buerkle C. Alex
Published: December 2019

Molecular ecology regularly requires the analysis of count data that reflect the relative abundance of features of a composition (e.g., taxa in a community, gene transcripts in a tissue). The sampling process that generates these data can be modelled using the multinomial distribution. Replicate multinomial samples inform the relative abundances of features in an underlying Dirichlet distribution. These distributions together form a hierarchical model for relative abundances among replicates and sampling groups. This type of Dirichlet‐multinomial modelling (DMM) has been described previously, but its benefits and limitations are largely untested. With simulated data, we quantified the ability of DMM to detect differences in proportions between treatment and control groups, and compared the efficacy of three computational methods to implement DMM—Hamiltonian Monte Carlo (HMC), variational inference (VI), and Gibbs Markov chain Monte Carlo. We report that DMM was better able to detect shifts in relative abundances than analogous analytical tools, while identifying an acceptably low number of false positives. Among methods for implementing DMM, HMC provided the most accurate estimates of relative abundances, and VI was the most computationally efficient. The sensitivity of DMM was exemplified through analysis of previously published data describing lung microbiomes. We report that DMM identified several potentially pathogenic, bacterial taxa as more abundant in the lungs of children who aspirated foreign material during swallowing; these differences went undetected with different statistical approaches. Our results suggest that DMM has strong potential as a statistical method to guide inference in molecular ecology.
When the company does not matter: High‐quality ant seed‐disperser does not drive the spatial distribution of large‐seeded myrmecochorous plants
Authors: Leal Laura C. , Silva Daniel Paiva , Peixoto Paulo E.C.
Published: December 2019

Mutualisms are one of the main forces shaping species spatial patterns at all geographic scales. In generalised mutualisms, however, the dependence among partners is highly variable in time and space, and therefore, the effect of diffuse mutualisms on species geographic distributions is unclear. Myrmecochorous seeds in Brazilian semi‐arid vegetation are dispersed by several ant species. However, large‐seeded species are especially dependent on dispersal by the giant ant Dinoponera quadriceps, which is the main disperser of such diaspores and the species that provide the longest dispersal distance among ant species in this system. Hence, we hypothesise that the presence of D. quadriceps shapes the distribution of large‐seeded, but not the distribution of small‐seeded myrmecochorous plant species. To evaluate this hypothesis, we modelled the potential distribution of two large‐seeded (which are predominantly dispersed by D. quadriceps) and two small‐seeded (which are barely dispersed by D. quadriceps) Euphorbiaceae species and the potential distribution of D. quadriceps. We analysed the relationship between the occurrence suitability of D. quadriceps and the occurrence suitability of plant species. We found that the potential distribution of both large‐seeded and small‐seeded myrmecochorous plants was unrelated to D. quadriceps occurrence suitability. It means that the disproportional benefits provided by high‐quality disperser at local scales may not emerge at broader geographical scales. In Caatinga vegetation, diaspores are submitted to strong abiotic filters that constraint seed germination and establishment after the dispersal phase. Such abiotic filters may dilute the initial benefit provided by long‐distance dispersers. Therefore, we suggest that in dry environments like the Caatinga, the benefits of long‐distance removals should be outweighed by the risk of reach new habitats with unfavourable conditions for germination and establishment.
Potential distribution patterns of scorpions in north‐eastern Brazil under scenarios of future climate change
Authors: Lira André Felipe de Araujo , Badillo‐Montaño Raúl , Lira‐Noriega Andrés , de Albuquerque Cleide Maria Ribeiro
Published: December 2019

Current predictions about the responses of species to climate change strongly rely on projecting altered environmental conditions on their distributions. In this study, we investigated the effects of future climate change scenarios on the potential distribution of 10 species of scorpions in north‐eastern Brazil in the context of their degree of specialisation to closed (Atlantic and Amazon Forests) and open (Caatinga and Cerrado) habitats. Scorpion species were classified as habitat specialists or generalists according to the IndVal index, and present and future species distribution models were prepared using minimum volume ellipsoids. According to IndVal, four species were classified as closed‐forest specialists (Ananteris mauryi, Tityus brazilae, Tityus pusillus and Tityus neglectus), four as open‐forest specialists (Jaguajir agamemnon, Jaguajir rochae, Physoctonus debilis and Bothriurus rochai), and two as generalists (Tityus stigmurus and Bothriurus asper). All species presented a drastic reduction in potential distribution, ranging from 44% to 72%, when compared with their current distribution. In addition, we found a reduction in scorpion species richness under future climate change scenarios. This finding has implications for scorpion conservation. Further, the results show that climate change may impact the composition of scorpion assemblages in north‐eastern Brazil, revealing important implications for human–scorpion interactions.
Male partners of infertile couples with congenital unilateral absence of the vas deferens are mainly non‐azoospermic
Authors: Mieusset Roger , Bieth Eric , Daudin Myriam , Isus Francois , Delaunay Boris , Bujan Louis , Monteil Laetitia , Fauquet Isabelle , Huyghe Eric , Hamdi Safouane M.
Published: December 2019

Background

Men with congenital unilateral absence of vas deferens were reported to be mainly azoospermic, with both unilateral renal absence and mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) but some have neither.

Objectives

To assess whether in infertile couples the male partners with congenital unilateral absence of vas deferens are mainly azoospermic men.

Material and Methods

Retrospective study in a unique university hospital; reproductive, clinical, CFTR analysis and seminal data of male partners of infertile couples (from 1998 to 2018) were analysed. Diagnosis of congenital unilateral absence of vas deferens was based on transrectal ultrasounds (TRUS): complete or partial absence of one vas deferens with complete contralateral vas deferens confirmed in 63 men. Distribution of sperm count in three classes: azoospermia, oligozoospermia or normozoospermia. Ultrasound determination of renal status; seminal biomarkers assays; and search for CFTR mutations.

Results

Among the 63 men, 39.7% displayed azoospermia, 27% oligozoospermia and 33.3% normozoospermia; 42% of the non‐azoospermic men (16/38) had previously obtained a natural pregnancy. We found unilateral renal absence in 17/59 patients (29%). Among 50 men with CFTR testing, five carried an allele associated with cystic fibrosis belonging to the 29 men without renal anomalies, indicating a high allelic frequency (8.6%). The 63 patients displayed high rates of surgical histories for undescended testicles or inguinal hernia, low values of semen volume and of total seminal glycerophosphocholine.

Conclusions

Our results indicate that men with congenital unilateral absence of vas deferens mainly display oligozoospermia or normozoospermia and that they were previously fertile. They clearly confirm, first, that CFTR testing is recommended in congenital unilateral absence of vas deferens men and it should be mandatory for those with normal kidneys; and, second, that TRUS is needed for the diagnosis of congenital unilateral absence of vas deferens. As congenital unilateral absence of vas deferens may be present whatever the sperm count, biological warnings are represented by semen volume and seminal epididymal markers and clinical warnings by surgical histories of undescended testes or inguinal hernia.
Power analysis for cluster randomized trials with multiple binary co‐primary endpoints
Authors: Li Dateng , Cao Jing , Zhang Song
Published: December 2019

Cluster randomized trials (CRTs) are widely used in different areas of medicine and public health. Recently, with increasing complexity of medical therapies and technological advances in monitoring multiple outcomes, many clinical trials attempt to evaluate multiple co‐primary endpoints. In this study, we present a power analysis method for CRTs with binary co‐primary endpoints. It is developed based on the GEE (generalized estimating equation) approach, and three types of correlations are considered: inter‐subject correlation within each endpoint, intra‐subject correlation across endpoints, and inter‐subject correlation across endpoints. A closed‐form joint distribution of the K test statistics is derived, which facilitates the evaluation of power and type I error for arbitrarily constructed hypotheses. We further present a theorem that characterizes the relationship between various correlations and testing power. We assess the performance of the proposed power analysis method based on extensive simulation studies. An application example to a real clinical trial is presented.
Immediate impact of fantastical television content on children’s executive functions
Authors: Rhodes Sinéad M. , Stewart Tracy M. , Kanevski Margarita
Published: December 2019

Recent research has suggested that particular content of television programmes, such as watching fantastical scenes, can have negative consequences on cognitive functions in young children. We examined the effects of watching fantastical programmes on executive functions measured at both pre‐ and post‐television viewing. Eighty 5‐ to 6‐year‐old children participated and were randomized into either fantastical or non‐fantastical conditions. They completed inhibition, working memory, cognitive flexibility, and planning tasks both before and after watching either the brief fantastical or non‐fantastical television clip. Whilst there were no differences between the groups at pre‐test on any of the cognitive measures, children in the fantastical condition were poorer on inhibition, working memory, and cognitive flexibility tasks at the post‐test session. Watching fantastical television content, even briefly, seems to disrupt cognitive function performance in young children across a broad range of aspects of executive function.

Statement of contribution

What is already known on this subject?

Exposure to fantastical content within a television programme may impair executive functions in young children.

What does this study add?

Exposure to fantastical content within television programmes impairs executive functions in children of early primary school age.

Impairment extends to all three core aspects of executive functions.

Watching fantastical clips slows down planning performance without improving accuracy.
Shared social identification in mass gatherings lowers health risk perceptions via lowered disgust
Authors: Hult Khazaie Daniella , Khan Sammyh S.
Published: December 2019

Previous research concerning mass gathering‐associated health risks has focused on physical factors while largely neglecting the role of psychological factors. The present research examined the effect of experiencing shared social identification on perceptions of susceptibility to health risks in mass gatherings. Participants in Study 1 were asked to either recall a crowd in which they shared a social identity with other crowd members or a crowd in which they did not. Participants subsequently completed measures assessing shared social identity, disgust, and health risk perceptions. Study 2 involved administering the same measures as part of a survey to participants who had recently attended a music festival. The results from both studies indicated that sharing a social identity lowered health risk perceptions; this effect was indirect and mediated via disgust. This highlights the importance of considering social identity processes in the design of health communication aimed at reducing mass gathering‐associated health risks.