bluuebunny/crossref_metadata_2025_split 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

AbstractFGFR1 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

AbstractBackgroundGenome 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.ResultsOf 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.ConclusionsThe 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

AbstractCross-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

AbstractBiomolecular 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

AbstractLeukocytes 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

AbstractOne 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

AbstractLittle 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 authorshipJD, 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

ABSTRACTWe 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.
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

AbstractSkin 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

AbstractWe 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

Summary

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

SummaryUnderstanding 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.