bluuebunny/crossref_metadata_2025 huggingface dataset:
The phosphatase PTPRG controls FGFR1 activity and influences sensitivity to FGFR kinase inhibitors
Authors: Kostas Michal , Haugsten Ellen Margrethe , Zhen Yan , Sørensen Vigdis , Szybowska Patrycja , Fiorito Elisa , Lorenz Susanne , de Souza Gustavo Antonio , Wiedlocha Antoni , Wesche Jørgen
Published: March 2017

FGFR1 represents an important target for precision medicine and a detailed molecular understanding of the target is important in order to increase the efficacy of FGFR inhibitors. We have here applied proximity labelling of FGFR1 in an osteosarcoma cell line to identify determinants of FGFR1 activity. Many known FGFR interactors were identified (e.g. FRS2, PLCγ, RSK2, SHC4, SRC), but the data also suggested novel determinants. A strong hit in our screen was the tyrosine phosphatase PTPRG. We show that PTPRG and FGFR1 interact and colocalize at the plasma membrane where PTPRG directly dephosphorylates activated FGFR1. We further show that osteosarcoma cell lines depleted for PTPRG display increased FGFR activity and are hypersensitive to stimulation by FGF1. In addition, PTPRG depletion elevated cell growth and negatively affected the efficacy of FGFR kinase inhibitors. Thus, PTPRG may have future clinical relevance by being a predictor of outcome after FGFR inhibitor treatment.
Regulatory remodeling in the allo-tetraploid frog Xenopus laevis
Authors: Elurbe Dei M. , Paranjpe Sarita S. , Georgiou Georgios , van Kruijsbergen Ila , Bogdanovic Ozren , Gibeaux Romain , Heald Rebecca , Lister Ryan , Huynen Martijn A. , van Heeringen Simon J. , Veenstra Gert Jan C.
Published: March 2017

Background

Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. The most recent vertebrate genome duplication is that in Xenopus laevis, resulting from the hybridization of two closely related species about 17 million years ago [1]. However, little is known about the consequences of this duplication at the level of the genome, the epigenome and gene expression.

Results

Of the parental subgenomes, S chromosomes have degraded faster than L chromosomes ever since the genome duplication and until the present day. Deletions appear to have the largest effect on pseudogene formation and loss of regulatory regions. Deleted regions are enriched for long DNA repeats and the flanking regions have high alignment scores, suggesting that non-allelic homologous recombination (NAHR) has played a significant role in the loss of DNA. To assess innovations in the X. laevis subgenomes we examined p300 (Ep300)-bound enhancer peaks that are unique to one subgenome and absent from X. tropicalis. A large majority of new enhancers are comprised of transposable elements. Finally, to dissect early and late events following interspecific hybridization, we examined the epigenome and the enhancer landscape in X. tropicalis × X. laevis hybrid embryos. Strikingly, young X. tropicalis DNA transposons are derepressed and recruit p300 in hybrid embryos.

Conclusions

The results show that erosion of X. laevis genes and functional regulatory elements is associated with repeats and NAHR, and furthermore that young repeats have also contributed to the p300-bound regulatory landscape following hybridization and whole genome duplication.
Differentially regulated orthologs in sorghum and the subgenomes of maize
Authors: Zhang Yang , Ngu Daniel W. , Carvalho Daniel , Liang Zhikai , Qiu Yumou , Roston Rebecca L. , Schnable James C.
Published: March 2017

Cross-species comparisons of transcriptional regulation have the potential to identify functionally constrained transcriptional regulation and genes for which a change in transcriptional regulation correlates with a change in phenotype. Conventional differential gene expression analysis and a different approach based on identifying differentially regulated orthologs (DROs) are compared using paired time course gene expression data from two species which respond similarly to cold – maize (Zea mays) and sorghum (Sorghum bicolor). Both approaches suggest that, for genes conserved at syntenic positions for millions of years, the majority of cold responsive transcriptional regulation is species specific, although initial transcriptional responses to cold appear to be more conserved between the two species than later responses. In maize, the promoters of genes with both species specific and conserved transcriptional responses to cold tend to contain more micrococcal nuclease hypersensitive sites in their promoters, a proxy for open chromatin. However, genes with conserved patterns of transcriptional regulation between the two species show lower ratios of nonsynonymous to synonymous substitutions consistent with this population of genes experiencing stronger purifying selection. We hypothesize that cold responsive transcriptional regulation is a fast evolving and largely neutral molecular phenotype for the majority of genes in Andropogoneae, while a smaller core set of genes involved in perceiving and responding to cold stress are subject to functionally constrained cold responsive regulation.
Intramolecular dynamics of single molecules in free diffusion
Authors: Limouse Charles , Bell Jason C. , Fuller Colin J. , Straight Aaron F. , Mabuchi Hideo
Published: March 2017

Biomolecular systems such as multiprotein complexes or biopolymers can span several tens to several hundreds of nanometers, but the dynamics of such “mesocale” molecules remain challenging to probe. We have developed a single-molecule technique that uses Tracking Fluorescence Correlation Spectroscopy (tFCS) to measure the conformation and dynamics of molecular assemblies specifically at the mesoscale level (~100-1000 nm). tFCS is non-perturbative, as molecules, which are tracked in real-time, are untethered and freely diffusing. To achieve sub-diffraction spatial resolution, we use a feedback scheme which allows us to maintain the molecule at an optimal position within the laser intensity gradient. We find that tFCS is sufficiently sensitive to measure the distance fluctuations between two sites within a DNA molecule separated by distances as short as 1000 bp. We demonstrate that tFCS detects changes in the compaction of reconstituted chromatin, and can assay transient protein mediated interactions between distant sites in an individual DNA molecule. Our measurements highlight the impact that tFCS can have in the study of a wide variety of biochemical processes involving mesoscale conformational dynamics.
Three-dimensional actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes
Authors: Fritz-Laylin Lillian K. , Riel-Mehan Megan , Chen Bi-Chang , Lord Samuel J. , Goddard Thomas D. , Ferrin Thomas E. , Johnson Graham , Betzig Eric , Mullins R. Dyche
Published: March 2017

Leukocytes and other amoeboid cells change shape as they move, forming highly dynamic, actin-filled pseudopods. Although we understand much about the architecture and dynamics of thin lamellipodia made by slow-moving cells on flat surfaces, conventional light microscopy lacks the spatial and temporal resolution required to track complex pseudopods of cells moving in three dimensions. We therefore employed lattice light sheet microscopy to perform three-dimensional, time-lapse imaging of neutrophil-like HL-60 cells crawling through collagen matrices. To analyze three-dimensional pseudopods we: (i) developed fluorescent probe combinations that distinguish cortical actin from dynamic, pseudopod-forming actin networks, and (ii) adapted molecular visualization tools from structural biology to render and analyze complex cell surfaces. Surprisingly, three-dimensional pseudopods turn out to be composed of thin (<0.75 μm), flat sheets that sometimes interleave to form rosettes. Their laminar nature is not templated by an external surface, but likely reflects a linear arrangement of regulatory molecules. Although we find that pseudopods are dispensable for three-dimensional locomotion, their elimination dramatically decreases the frequency of cell turning, and pseudopod dynamics increase when cells change direction, highlighting the important role pseudopods play in pathfinding.
Evolutionarily Conserved Alternative Splicing Across Monocots
Authors: Mei Wenbin , Boatwright Lucas , Feng Guanqiao , Schnable James C. , Barbazuk W. Brad
Published: March 2017

One difficulty when identifying and analyzing alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction based conserved AS events from RNA-Seq data across nine plant species including: five grass monocots (maize, sorghum, rice,Brachpodiumand foxtail millet), plus two non-grass monocots (bananan and African oil palm), the eudicotArabidopsisand the basal angiospermAmborella. In total, 9,804 conserved AS events within 19,235 genes were identified conserved between 2 or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z subfamilies are highly connected with R2R3-MYB in splicing networks. Furthermore, we discovered that the network based on genes harboring conserved AS events is enriched for phosphatases, kinases and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.
The mismatch in distributions of vertebrates and the plants that they disperse
Authors: Dittel Jacob W. , Moore Christopher M. , Vander Wall Stephen B.
Published: March 2017

Little is known about how mutualistic interactions affect the distribution of species richness on broad geographic scales. It has been predicted that the richness of species involved in obligate mutualisms should be positively associated across their range. Whereas, if mutualisms are facilitative, the distribution of mutualists should be correlated with other factors. This study is the first study to compare the co-distribution of mutualist species in general and seed dispersal mutualisms specifically. We used geographic distributions of plant and animal mutualists to investigate the co-distribution and patterns of seed dispersal mutualisms. We found the mutualism between dispersers and plants does not account for the distribution of either group. In fact, there is a mismatch of richness between plants and the animals that disperse their seeds. Environmental factors are better predictors of both animal distribution and seed dispersal mutualisms across North America.

Statement of authorship

JD, CM, and SV conceived the original project idea. Plant data were compiled and analyzed by CM and SV, and JD compiled animal and environmental data. JD standardized and formatted all geographical data, and JD and CM performed all statistical analyses. JD wrote the first draft of the manuscript, and all authors contributed significantly to the revisions.
Enterovirus-A76 of South-East Asian ancestry in a Captive Chimpanzee (Pan troglodytes) in Jos, Nigeria
Authors: Oragwa A.O. , George U.E. , Faleye T.O.C. , Adewumi M.O. , Adeniji J.A.
Published: March 2017

We recently detected EV-A119 and EV-B111 (previously shown to co-circulate between nonhuman primates (NHPs) and humans) in Nigerian children diagnosed with acute flaccid paralysis (AFP). This study was designed to investigate and catalogue EVs present in captive NHPs in Nigeria.

Twenty-seven fecal samples collected from captive NHPs in a Wild Life Park and Zoological garden at Jos, Nigeria in April 2016 were analyzed in this study. Samples were resuspended in a phosphate buffered saline (PBS)/chloroform mixture, and the clarified supernatant was subjected to RNA extraction, cDNA synthesis, a Panenterovirus 5I-UTR assay, and three different enterovirus VP1 snPCR assays. All amplicons from the snPCR assays were sequenced, and enteroviruses identified using the enterovirus genotyping tool and phylogenetic analysis.

Eight (29.63%) (two each from Chimpanzees, Patas Monkey, Mona Monkey and Baboon) of the 27 samples were positive for the 5I-UTR assay. One (3.70%) of the 27 samples was positive for the enterovirus VP1 snPCR assays in addition to its positivity by 5I-UTR assay. The same sample happens to be one of the two samples from Chimpanzees that tested positive for the 5I-UTR assay, and it was subsequently identified as EV-A76 of South-East Asia ancestry.

This study documents the first recorded attempt to detect and identify enteroviruses in NHPs in Nigeria. It also reports the first detection and identification of EV-A76 in Nigeria and particularly in a NHP. It is of utmost importance that the enterovirus VP1 assays be improved to enable detection of EVs that have been detected in NHPs but yet to be described in humans.
Small chromosomal regions position themselves autonomously according to their chromatin class
Authors: van de Werken Harmen J.G. , Haan Josien C. , Feodorova Yana , Bijos Dominika , Weuts An , Theunis Koen , Holwerda Sjoerd J.B. , Meuleman Wouter , Pagie Ludo , Thanisch Katharina , Kumar Parveen , Leonhardt Heinrich , Marynen Peter , van Steensel Bas , Voet Thierry , de Laat Wouter , Solovei Irina , Joffe Boris
Published: March 2017

The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatic and euchromatic domains. The mechanisms of this chromatin segregation are still poorly understood. In this work, we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background in comparison to an orthologous region of native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (1) gene-rich and SINE-rich euchromatin; (2) gene-poor and LINE/LTR-rich heterochromatin; and (3) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show, using fluorescence in situ hybridization (FISH) and 4C-seq technologies, that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespective of their chromosomal context, thereby strongly suggesting that this is their autonomous property. Interactions with the nuclear lamina, although largely retained in the HAC, reveal less autonomy. Taken together, our results suggest that building of a functional nucleus is largely a self-organizing process based on mutual recognition of chromosome segments belonging to the major chromatin classes.
Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock
Authors: Mange François , Praz Viviane , Migliavacca Eugenia , Willis Ian M. , Schütz Frédéric , Hernandez Nouria ,   the CycliX Consortium
Published: March 2017

RNA polymerase III (Pol III) synthesizes short noncoding RNAs, many of which are essential for translation. Accordingly, Pol III activity is tightly regulated with cell growth and proliferation by factors such as MYC, RB1, TRP53, and MAF1. MAF1 is a repressor of Pol III transcription whose activity is controlled by phosphorylation; in particular, it is inactivated through phosphorylation by the TORC1 kinase complex, a sensor of nutrient availability. Pol III regulation is thus sensitive to environmental cues, yet a diurnal profile of Pol III transcription activity is so far lacking. Here, we first use gene expression arrays to measure mRNA accumulation during the diurnal cycle in the livers of (1) wild-type mice, (2) arrhythmic Arntl knockout mice, (3) mice fed at regular intervals during both night and day, and (4) mice lacking the Maf1 gene, and so provide a comprehensive view of the changes in cyclic mRNA accumulation occurring in these different systems. We then show that Pol III occupancy of its target genes rises before the onset of the night, stays high during the night, when mice normally ingest food and when translation is known to be increased, and decreases in daytime. Whereas higher Pol III occupancy during the night reflects a MAF1-dependent response to feeding, the rise of Pol III occupancy before the onset of the night reflects a circadian clock-dependent response. Thus, Pol III transcription during the diurnal cycle is regulated both in response to nutrients and by the circadian clock, which allows anticipatory Pol III transcription.
Standardized ICU to OR handoff increases communication without delaying surgery
Authors: Caruso Thomas J. , Marquez Juan Luis Sandin , Gipp Melanie S. , Kelleher Stephen P. , Sharek Paul J.
Published: March 2017

Purpose

No studies have examined preoperative handoffs from the intensive care unit (ICU) to OR. Given the risk of patient harm, the authors developed a standardized ICU to OR handoff using a previously published handoff model. The purpose of this paper is to determine whether a standardized ICU to OR handoff process would increase the number of team handoffs and improve patient transport readiness.

Design/methodology/approach

The intervention consisted of designing a multidisciplinary, face-to-face handoff between sending ICU providers and receiving anesthesiologist and OR nurse, verbally presented in the I-PASS format. Anticipatory calls from the OR nurse to the ICU nurse were made to prepare the patient for transport. Data collected included frequency of handoff, patient transport readiness, turnover time between OR cases, and anesthesia provider satisfaction.

Findings

In total, 57 audits were completed. The frequency of handoffs increased from 25 to 86 percent (p<0.0001) and the frequency of patient readiness increased from 61 to 97 percent (p=0.001). There were no changes in timeliness of first start cases and no significant change in turnover times between cases. Anesthesia provider satisfaction scores increased significantly.

Practical implications

A standardized, team based ICU to OR handoff increased the frequency of face-to-face handoffs, patient readiness and anesthesia provider satisfaction within increasing turnover between cases.

Originality/value

Although studies have identified the transition of patients from the ICU to the OR as a period of increased harm, the development of a preoperative ICU to OR handoff had not been described. This intervention may be used in other institutions to design ICU to OR transitions of care.
Japanese version of the Family Dermatology Life Quality Index: Translation and validation
Authors: Higaki Yuko , Tanaka Masaru , Futei Yuko , Kamo Toshiko , Basra Mohammad Khurshid Azam , Finlay Andrew Yule
Published: March 2017

Skin conditions affect the quality of life (QoL) of patients and their family. To assess family members' QoL, a questionnaire uniquely designed for family members is necessary. We translated the Family Dermatology Life Quality Index (FDLQI), originally created and validated by Basra et al., into Japanese, and evaluated its reliability and validity. For psychometric evaluations, 150 dermatology patients and their family members were included. The Japanese version of the FDLQI showed high test–retest reliability (intraclass correlation coefficient = 0.95) and internal consistency reliability (Cronbach's alpha = 0.86). FDLQI scores significantly correlated with DLQI scores (r = 0.58, P < 0.01, Spearman's rho) and global question (GQ) which measured the patient's skin condition on a visual analog scale (r = 0.36, P < 0.01). Family members of patients with inflammatory skin diseases showed higher FDLQI scores than those with isolated lesions, but the difference was not statistically significant (P = 0.062, Mann–Whitney U‐test). Responsiveness to change was demonstrated in a group in which the patient's skin condition was assessed as improved (n = 37, r = 0.46, P < 0.01) but not in that in which it became worse. The difference of the change between the two groups was statistically significant (P < 0.01). Additionally, the change in FDLQI scores and GQ were significantly correlated (r = 0.40, P < 0.01). Exploratory factor analysis suggested essential unidimensionality of the instrument. We showed acceptable validity and responsiveness of this Japanese version of FDLQI. Further clinical epidemiological studies are required to confirm this.
Acral lentiginous melanoma versus other melanoma: A single‐center analysis in Japan
Authors: Wada Maiko , Ito Takamichi , Tsuji Gaku , Nakahara Takeshi , Hagihara Akihito , Furue Masutaka , Uchi Hiroshi
Published: March 2017

We summarize herein our 14‐year experience of conventional treatment outcomes before the era of molecular‐targeted therapy and immunotherapy. Specifically, we conducted a retrospective review of our 252 patients with primary cutaneous melanoma (acral lentiginous melanoma [ALM], n = 121; non‐acral lentiginous melanoma [non‐ALM], n = 131), and compared the prognostic factors between ALM and non‐ALM. Melanoma‐specific survival and disease‐free survival were estimated using the Kaplan–Meier method. Regarding the results, all patients were Japanese (106 male and 146 female), with a mean age of 60.1 years. Among ALM patients, age was elder and primary tumor size was larger than non‐ALM. As for tumor thickness, in situ lesions were more frequently observed in ALM. There was no significant difference in the distribution of tumor thickness between the two groups when excluding the in situ lesions. For treatment of the primary melanoma, 248 patients (98.4%) had undergone curative surgical excision and 120 patients with more than 1 mm or ulcerated melanoma had undergone sentinel lymph node biopsy. Patients with systemic metastasis primarily underwent dacarbazine‐based chemotherapy. The Kaplan–Meier survival curves revealed no significant difference in melanoma‐specific survival and disease‐free survival between those with ALM and non‐ALM. The results also showed that both ALM and non‐ALM, when they initially metastasize, first affect the regional lymph nodes. Incisional biopsy was not an adverse prognostic factor. These results suggest that ALM does not differ in its biological behavior from non‐ALM, so we can consider ALM as being equivalent to non‐ALM. The initial treatment for ALM and non‐ALM can involve the same strategy.
Plant defence negates pathogen manipulation of vector behaviour
Authors: Liu Baiming , Preisser Evan L. , Shi Xiaobin , Wu Huaitong , Li Chuanyou , Xie Wen , Wang Shaoli , Wu Qingjun , Zhang Youjun
Published: March 2017

Although many vector‐borne plant pathogens can alter vector behaviour to the pathogen's benefit, how plants might counter such manipulation is unknown.

In the Tomato yellow leaf curl virus (‘TYLCV’)–Bemisia tabaci–tomato interaction, TYLCV‐mediated changes in Bemisia feeding improves viral uptake and transmission. We tested how jasmonic acid (‘JA’), a central regulator of plant antiherbivore defences, affected the ability of TYLCV to (A) manipulate Bemisia behaviour; and (B) infect plants.

Viruliferous Bemisia fed much more than virus‐free whiteflies on JA‐deficient plants, more than virus‐free whiteflies on controls, and similarly on high‐JA plants.

When TYLCV was transmitted via whiteflies, infection levels were lower in high‐JA plants relative to JA‐deficient and control plants. When TYLCV was transmitted via direct injection, JA‐overexpressed and JA‐deficient plants had similar infection levels. The JA‐mediated cessation of vector manipulation thus reduced infection and lessened pathogen impact.

The presence of the JA pathway in many plant species suggests that similar interactions may be widespread in nature.

A lay summary is available for this article.
Incorporatingin situhabitat patchiness in site selection models reveals that site fidelity is not always a consequence of animal choice
Authors: Martinez Aline S. , Queiroz Eduardo V. , Bryson Mitch , Byrne Maria , Coleman Ross A.
Published: March 2017

Understanding site fidelity is important in animal ecology, but evidence is lacking that this behaviour is due to an animal choosing a specific location. To discern site selection behaviour, it is necessary to consider the spatial distribution of habitats that animals can occupy within a landscape. Tracking animals and defining clear habitat boundaries, however, is often difficult.

We usein situhabitat distribution data and animal movement simulations to investigate behavioural choice in site fidelity patterns. We resolved the difficulty of gathering data by working with intertidal rock pool systems, which are of manageable size and where boundaries are easy to define. Movements of the intertidal starfishParvulastra exiguawere quantified to test the hypotheses that (1) this species displays fidelity to a particular rock pool and that (2) rock pool fidelity is due to site selection behaviour. Observed patterns of individuals (n = 10 starfish) returning to a previously occupied rock pool (n = 5 pools per location) were tested against an expected null distribution generated through simulations of random movements within their natural patchy environment.

Starfish exhibited site selection behaviour at only one location even though site fidelity was high (av. 7·4 starfish out of 10 found in test pools) in two of the three locations. The random chance of a starfish returning to a pool increased 67% for each metre further a rock pool was from the original pool, and 120% for each square metre increase in surface area of an original pool. The decision of returning to an original rock pool was influenced by food availability. When microalgal cover was >60%, there was a c. 50% chance of animals staying faithful to that pool.

Our results show the importance to consider spatial distribution of habitats in understanding patterns of animal movement associated with animal choices and site fidelity. Returning to a particular place does not necessarily mean that an animal is homing; it may be the only place to go.
Climatic variation modulates the indirect effects of large herbivores on small‐mammal habitat use
Authors: Long Ryan A. , Wambua Alois , Goheen Jacob R. , Palmer Todd M. , Pringle Robert M.
Published: March 2017

Large mammalian herbivores (LMH) strongly shape the composition and architecture of plant communities. A growing literature shows that negative direct effects of LMH on vegetation frequently propagate to suppress the abundance of smaller consumers. Indirect effects of LMH on the behaviour of these consumers, however, have received comparatively little attention despite their potential ecological significance.

We sought to understand (i) how LMH indirectly shape small‐mammal habitat use by altering the density and distribution of understorey plants; (ii) how these effects vary with climatic context (here, seasonality in rainfall); and (iii) the extent to which behavioural responses of small mammals are contingent upon small‐mammal density.

We tested the effects of a diverse LMH community on small‐mammal habitat use using 4 years of spatially explicit small‐mammal trapping and vegetation data from the UHURU Experiment, a replicated set of LMH exclosures in semi‐arid Kenyan savanna.

Small‐mammal habitat use was positively associated with tree density and negatively associated with bare (unvegetated) patches in all plots and seasons. In the presence of LMH, and especially during the dry season, small mammals consistently selected tree cover and avoided bare patches. In contrast, when LMH were excluded, small mammals were weakly associated with tree cover and did not avoid bare patches as strongly. These behavioural responses of small mammals were largely unaffected by changes in small‐mammal density associated with LMH exclusion.

Our results show that LMH indirectly affect small‐mammal behaviour, and that these effects are influenced by climate and can arise via density‐independent mechanisms. This raises the possibility that anthropogenic LMH declines might interact with changing patterns of rainfall to alter small‐mammal distribution and behaviour, independent of numerical responses by small mammals to these perturbations. For example, increased rainfall in East Africa (as predicted in many recent climate‐model simulations) may relax constraints on small‐mammal distribution where LMH are rare or absent, whereas increased aridity and/or drought frequency may tighten them.
Effects of predatory ants within and across ecosystems in bromeliad food webs
Authors: Gonçalves Ana Z. , Srivastava Diane S. , Oliveira Paulo S. , Romero Gustavo Q.
Published: March 2017

Predation is one of the most fundamental ecological processes affecting biotic communities. Terrestrial predators that live at ecosystem boundaries may alter the diversity of terrestrial organisms, but they may also have cross‐ecosystem cascading effects when they feed on organisms with complex life cycles (i.e. organisms that shift from aquatic juvenile stages to terrestrial adult stages) or inhibit female oviposition in the aquatic environment.

The predatory ant Odontomachus hastatus establishes its colonies among roots of Vriesea procera, an epiphytic bromeliad species with water‐filled tanks that shelters many terrestrial and aquatic organisms. Ants may impact terrestrial communities and deter adult insects from ovipositing in the water of bromeliads via consumptive and non‐consumptive effects. Ants do not forage within the aquatic environment; thus, they may be more efficient predators on terrestrial organisms. Therefore, we predict that ants will have stronger effects on terrestrial than aquatic food webs. However, such effects may also be site contingent and depend on the local composition of food webs.

To test our hypothesis, we surveyed bromeliads with and without O. hastatus colonies from three different coastal field sites in the Atlantic Forest of southeast Brazil, and quantified the effect of this predatory ant on the composition, density and richness of aquatic and terrestrial metazoans found in these bromeliads.

We found that ants changed the composition and reduced the overall density of aquatic and terrestrial metazoans in bromeliad ecosystems. However, effects of ants on species diversity were contingent on site. In general terms, the effects of the ant on aquatic and terrestrial metazoan communities were similar in strength and magnitude. Ants reduced the density of virtually all aquatic functional groups, especially detritivore insects as well as metazoans that reach bromeliads through phoresy on the skin of terrestrial animals (i.e. Ostracoda and Helobdella sp.).

Our results suggest that the cross‐ecosystem effect of this terrestrial predator on the aquatic metazoans was at least as strong as its within‐ecosystem effect on the terrestrial ecosystem, and demonstrates that the same predator can simultaneously initiate cascades in multiple ecosystems.
The Situations of Urban Inquiry: Thinking Problematically about the City
Authors: Barnett Clive , Bridge Gary
Published: March 2017

In the context of debates about the epistemological and ontological coherence of concepts of critical urban studies, we argue that urban concepts should be conceptualized problematically. We do so by aligning Michel Foucault's genealogical work on problematization with John Dewey's pragmatist understanding of problem formation and responsiveness. This approach brings into view the degree to which debates about urban futures are shaped by a variety of critical perspectives that extend beyond the academy and activism. We elaborate this argument through examples of global urban policy formation and practices of neighbourhood change. Approaching urban concepts problematically suggests a move away from the idea of critique as a form of scholastic correction towards an appreciation of the contested fields of practice in and through which critical understandings of urban problems emerge.
Exploring the hypothesis of differential care for African immigrant and native women in France with hypertensive disorders during pregnancy: a qualitative study
Authors: Sauvegrain P , Azria E , Chiesa‐Dubruille C , Deneux‐Tharaux C
Published: March 2017

Objective

To analyse whether prenatal care trajectories among women with hypertensive disorders during pregnancy in France differ between immigrants from sub‐Saharan Africa (SSA) and native French women.

Design

Qualitative interview study.

Setting

Three public maternity units in the Paris region.

Population

Women born in SSA or in France of French parents and treated for hypertension or pre‐eclampsia during their pregnancy.

Methods

A sociologist conducted semi‐structured in‐depth interviews of 33 women during their postpartum hospitalisation and collected data from their medical files. n’vivo 10 (QSR International) was used for line‐by‐line coding of the transcriptions, to identify emerging themes. Strauss's concept of illness trajectories was then applied to these data.

Main outcome measures

Themes derived from interviews.

Results

Women reported during the interviews that the blood pressure measurement procedures used by hospital staff varied between the two groups, and their medical records supported this finding. Repeated urinary dipstick testing of proteinuria before laboratory testing was more frequent for African women, as was the failure to further test proteinuria levels requiring additional action. The two groups received similar standardised care after severe complications. Other findings showed that African women were less likely to rely on healthcare services.

Conclusions

These results suggest non‐medically justified differential prenatal care between African and native women that may have helped delay the diagnosis of hypertension or pre‐eclampsia. This study suggests hypotheses for further quantitative studies to explore the potential involvement of this differential care in the higher frequency of severe complications in this subgroup, concordantly reported in European countries hosting SSA migrants.

Tweetable abstract

Differential prenatal care may delay diagnosis of pre‐eclampsia among African compared with native French women.
Transferable Antibiotic Resistances in Marketed Edible Grasshoppers (Locusta migratoria migratorioides)
Authors: Osimani Andrea , Garofalo Cristiana , Aquilanti Lucia , Milanović Vesna , Cardinali Federica , Taccari Manuela , Pasquini Marina , Tavoletti Stefano , Clementi Francesca
Published: March 2017

Grasshoppers are the most commonly eaten insects by humans worldwide, as they are rich in proteins and micronutrients. This study aimed to assess the occurrence of transferable antibiotic resistance genes in commercialized edible grasshoppers. To this end, the prevalence of 12 selected genes [aac(6’)‐Ie aph(2″)‐Ia, blaZ, erm(A), erm(B), erm(C), mecA, tet(M), tet(O), tet(S), tet(K), vanA, vanB] coding for resistance to antibiotics conventionally used in clinical practice was determined. The majority of samples were positive for tet(M) (70.0%), tet(K) (83.3%) and blaZ (83.3%). A low percentage of samples were positive for erm(B) (16.7%), erm(C) (26.7%), and aac(6’)‐Ie aph(2″)‐Ia (13.3%), whereas no samples were positive for erm(A), vanA, vanB, tet(O), and mecA. Cluster analysis identified 4 main clusters, allowing a separation of samples on the basis of their country of origin.
Diagnostic performance of confocal laser endomicroscopy for atrophy and gastric intestinal metaplasia: A meta‐analysis
Authors: Bai Tao , Zhang Lei , Sharma Stuti , Jiang Yu Dong , Xia Jing , Wang Huan , Qian Wei , Song Jun , Hou Xiao Hua
Published: March 2017

OBJECTIVE

To systematically evaluate the diagnostic efficacy of confocal laser endomicroscopy (CLE) for gastric atrophy (GA) and gastric intestinal metaplasia (GIM).

METHODS

Literature search was performed in PubMed and the Cochrane Library for CLE, GA and GIM. The sensitivity, specificity and diagnostic odds ratio (DOR) in diagnosing GA and GIM were pooled for analysis. A summary receiver operating curve (SROC) was documented and the area under the curve was calculated.

RESULTS

Of the 10 studies included in this current analysis, the pooled sensitivity, specificity and DOR of CLE to diagnose GA and GIM were found to be 88%, 98% and 330.85, and 93%, 98% and 439.97, respectively. The area under the SROC were 0.9491 and 0.9812 for the diagnosis of GA and GIM, respectively. Higher sensitivity and specificity of this technique in diagnosing GA and GIM were found in patients without representative disease spectrum and those received pCLE by subgroup analysis.

CONCLUSION

CLE is of great value and may be considered an alternative modality for the early diagnosis of GA and GIM.
Combination of growth pattern and tumor regression identifies a high‐risk group in neoadjuvant treated rectal cancer patients
Authors: Jessberger Jonas , Erlenbach‐Wünsch Katharina , Posselt Rebecca , Haderlein Marlen , Agaimy Abbas , Fietkau Rainer , Hartmann Arndt , Distel Luitpold
Published: March 2017

OBJECTIVE

To analyze the prognostic effect of E‐cadherin expression, the growth pattern of the tumor and the regression grade in a rectal cancer cohort treated with neoadjuvant radiochemotherapy (RCT).

METHODS

A total of 223 patients with rectal cancer treated with neoadjuvant RCT followed by surgery were included. Altogether 88 biopsies prior to RCT and 213 tumor resections in an average of 55 days post‐RCT were investigated. Protein expression of E‐cadherin and tumor growth pattern (solid glandular vs single‐cell pattern) was assessed by staining tissue microarrays. The regression grade at the invasion front was determined according to the Dworak scale.

RESULTS

There was a significant decrease of E‐cadherin expression (P = 0.002) and a significant increased single‐cell growth (P < 0.001) at the invasion front in tumor samples after RCT compared with primary biopsies of the tumor. A low E‐cadherin expression in the biopsy was related to a longer metastasis‐free survival (P = 0.033) and tumor‐specific survival (P = 0.030). Post‐RCT single‐cell growth at the tumor invasion front was a prognostic factor for longer tumor‐specific survival (P = 0.021). A combination of growth pattern and the Dworak regression grade was an independent prognostic parameter for tumor‐specific survival (P = 0.015).

CONCLUSIONS

Loss of E‐cadherin protein expression in the pretreatment biopsy of rectal cancer is associated with fewer metastases and improved survival. Furthermore, the growth pattern in the post‐RCT resection specimen has a prognostic value for survival. A combination of growth pattern and tumor regression score (the RegPat score) showed the highest discriminatory power to identify high‐risk patients.
gesp: A computer program for modelling genetic effective population size, inbreeding and divergence in substructured populations
Authors: Olsson Fredrik , Laikre Linda , Hössjer Ola , Ryman Nils
Published: March 2017

The genetically effective population size (Ne) is of key importance for quantifying rates of inbreeding and genetic drift and is often used in conservation management to set targets for genetic viability. The concept was developed for single, isolated populations and the mathematical means for analysing the expected Ne in complex, subdivided populations have previously not been available. We recently developed such analytical theory and central parts of that work have now been incorporated into a freely available software tool presented here. gesp (Genetic Effective population size, inbreeding and divergence in Substructured Populations) is R‐based and designed to model short‐ and long‐term patterns of genetic differentiation and effective population size of subdivided populations. The algorithms performed by gesp allow exact computation of global and local inbreeding and eigenvalue effective population size, predictions of genetic divergence among populations (GST) as well as departures from random mating (FIS, FIT) while varying (i) subpopulation census and effective size, separately or including trend of the global population size, (ii) rate and direction of migration between all pairs of subpopulations, (iii) degree of relatedness and divergence among subpopulations, (iv) ploidy (haploid or diploid) and (v) degree of selfing. Here, we describe gesp and exemplify its use in conservation genetics modelling.
Career Development Awards in Emergency Medicine: Resources and Challenges
Authors: Mumma Bryn E. , Chang Anna Marie , Kea Bory , Ranney Megan L. ,   the Society for Academic Emergency Medicine Research Committee
Published: March 2017

Objectives

In the United States, emergency medicine (EM) researchers hold proportionately fewer federal career development awards than researchers in other specialties. Others hypothesize that this deficit may partly be attributed to lack of mentors, departmental resources, and qualified applicants. Our objectives were to examine the association between departmental and institutional resources and career development awards and to describe the barriers to conducting research and btaining grants in EM.

Methods

We conducted an online, cross‐sectional survey study of vice chairs for research and research directors at academic emergency departments in the United States in January and February 2016. Participants provided quantitative information regarding their department's demographics, available research resources, number of funded independent investigators, and number of career development awards. They were also asked about the perceived adequacy of departmental and institutional resources and perceived barriers to research and grant success. Data were analyzed using descriptive statistics and multivariable linear regression, as appropriate.

Results

Of 178 eligible participants, 103 (58%) completed the survey. Most departments reported some infrastructure for research and grant submission, including research coordinator(s) (n = 75/99; 76%, 95% confidence interval [CI] = 66%–84%), research associates (69/99; 70%, 95% CI = 60%–79%), and administrative/secretarial research support (79/101; 78%, 95% CI = 69%–86%). The majority of departments (56/103; 49%, 95% CI = 44%–64%) had no R01‐funded researchers, and only 15 (15%, 95% CI = 8%–23%) had three or more R01‐funded researchers. The most frequently reported challenge to junior faculty applying for grants was low motivation for applying (62/103; 60%, 95% CI = 50%–70%), followed closely by insufficient mentorship (50/103; 49%, 95% CI = 39%–59%) and discouragement from low funding rates (50/103; 49%, 95% CI = 39%–59%). In the multivariable model, only the number of departmental R‐level–funded researchers was associated with the number of departmental career development awards (coefficient = 0.75, 95% CI = 0.39–1.11; R2 = 0.57).

Conclusions

While more multiple departmental and institutional resources correlated with a greater number of funded career development awards, the single greatest predictor was the number of R‐level–funded researchers in the department. Low motivation and insufficient mentorship were the most frequently reported barriers to junior faculty applying for career development awards. Further studies are needed to describe junior faculty perspectives on these issues and to explore strategies for overcoming these barriers.
Academic Difficulties in Children with Prenatal Alcohol Exposure: Presence, Profile, and Neural Correlates
Authors: Glass Leila , Moore Eileen M. , Akshoomoff Natacha , Jones Kenneth Lyons , Riley Edward P. , Mattson Sarah N.
Published: March 2017

Background

Academic achievement was evaluated in children with heavy prenatal alcohol exposure to determine potential strengths and weaknesses, evaluate the utility of different definitions for identifying low academic performance, and explore the neural correlates that may underlie academic performance.

Methods

Children (8 to 16 years) were assessed using the WIAT‐II. Patterns of performance were examined in 2 subject groups: children with heavy prenatal alcohol exposure (n = 67) and controls (n = 61). A repeated‐measures MANCOVA examining group differences on academic domain (reading, spelling, math) scores was conducted. Post hoc comparisons examined within‐group profiles. Numbers and percentage of children with low achievement were calculated using several criteria. In a subsample (n = 42), neural correlates were analyzed using FreeSurfer v5.3 to examine relations between cortical structure (thickness and surface area) and performance.

Results

The alcohol‐exposed group performed worse than controls on all domains and had a unique academic profile, supported by a significant group × academic domain interaction (p < 0.001). For the alcohol‐exposed group, math reasoning was significantly lower than numerical operations, which was significantly lower than spelling and word reading. Over half of the alcohol‐exposed group (58.2%) demonstrated low achievement on 1 or more academic domains. The number and percentage of children meeting criteria for low achievement varied based on the domain and definition used. The imaging analysis identified several surface area clusters that were differentially related to math (L superior parietal and R lateral/middle occipital) and spelling (bilateral inferior and medial temporal) performance by group, with no relations for the other academic domains. Generally, scores improved as surface area decreased in controls, whereas no relation or a positive relation was observed in the alcohol‐exposed group.

Conclusions

Alcohol‐exposed children demonstrated deficits in academic performance across domains and definitions, with a relative weakness in math functioning. Atypical brain development may contribute to these impairments in academic achievement. Understanding academic difficulties can assist in advocating effectively for alcohol‐exposed children.
Psychopathology and personality traits associated with driving while intoxicated in Beijing, China: Implications for interventions
Authors: Zhao Rong‐Jiang , Sun Wei , Zhang Li‐Li , Bao Yan‐Ping , Huang Liang , Dong Ping , Zhou Shuang‐Jiang , Wang Zhi‐Qing , Kosten Thomas R. , Sun Hong‐Qiang
Published: March 2017

Background and Objectives

Driving while intoxicated (DWI) represents an area of grave concern in China, yet little research has focused on it or on the personality traits and psychiatric disorders among these drivers.

Methods

We enrolled 325 of 382 residents charged with DWI in a compulsory detention center in Beijing, China. And 351 male drivers who had never had any alcohol arrests as control participants. All were screened for Axis I disorders using the Chinese version of the Structured Clinical Interview for the Diagnostic Statistical Manual of Mental Disorders IV‐TR (SCID), the Minnesota Multiphasic Personality Inventory (MMPI‐2), and the Sixteen Personality Factor Questionnaire (16PF).

Results

The subjects were all males with a mean (±SD) age of 34.41 ± 8.48 years, and almost 30% met DSM‐IV criteria for alcohol abuse or dependence (n = 92). Compared to normal controls they showed greater Social Boldness, Abstractedness, Apprehension, Liveliness and Tension, and poorer Reasoning, Vigilance, Openness to Change, and Self‐reliance. On the MMPI‐2, DWI subjects showed greater Hypochondriasis, Psychopathic Deviate, Paranoia, Psychasthenia, Schizophrenia and Hypomania; and lower Social introversion.

Conclusions and Scientific Significance

Severe alcohol problems are more common in Beijing's drunk drivers than in the Chinese general population. These DWI drivers also have a broad variety of traits that increase their tendency to be venturesome and socially bold while enjoying excitement and risk‐taking. (Am J Addict 2017;26:374–378)