bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conventional and hyperspectral time-series imaging of maize lines widely used in field trials
Authors: Liang Zhikai , Pandey Piyush , Stoerger Vincent , Xu Yuhang , Qiu Yumou , Ge Yufeng , Schnable James C 
Published: November 2017

Abstract

Background
Maize (Zea mays ssp. mays) is 1 of 3 crops, along with rice and wheat, responsible for more than one-half of all calories consumed around the world. Increasing the yield and stress tolerance of these crops is essential to meet the growing need for food. The cost and speed of plant phenotyping are currently the largest constraints on plant breeding efforts. Datasets linking new types of high-throughput phenotyping data collected from plants to the performance of the same genotypes under agronomic conditions across a wide range of environments are essential for developing new statistical approaches and computer vision–based tools.

Findings
A set of maize inbreds—primarily recently off patent lines—were phenotyped using a high-throughput platform at University of Nebraska-Lincoln. These lines have been previously subjected to high-density genotyping and scored for a core set of 13 phenotypes in field trials across 13 North American states in 2 years by the Genomes 2 Fields Consortium. A total of 485 GB of image data including RGB, hyperspectral, fluorescence, and thermal infrared photos has been released.

Conclusions
Correlations between image-based measurements and manual measurements demonstrated the feasibility of quantifying variation in plant architecture using image data. However, naive approaches to measuring traits such as biomass can introduce nonrandom measurement errors confounded with genotype variation. Analysis of hyperspectral image data demonstrated unique signatures from stem tissue. Integrating heritable phenotypes from high-throughput phenotyping data with field data from different environments can reveal previously unknown factors that influence yield plasticity.
Factorizable Module Algebras
Authors: Berenstein Arkady , Schmidt Karl 
Published: November 2017

AbstractThe aim of this paper is to introduce and study a large class of $\mathfrak{g}$-module algebras that we call factorizable by generalizing the Gauss factorization of square or rectangular matrices. This class includes coordinate algebras of corresponding reductive groups G, their parabolic subgroups, basic affine spaces, and many others. It turns out that products of factorizable algebras are also factorizable and it is easy to create a factorizable algebra out of virtually any $\mathfrak{g}$-module algebra. We also have quantum versions of all these constructions in the category of $U_{q}(\mathfrak{g})$-module algebras. Quite surprisingly, our quantum factorizable algebras are naturally acted on by the quantized enveloping algebra $U_{q}(\mathfrak{g}^{\ast })$ of the dual Lie bialgebra $\mathfrak{g}^{\ast }$ of $\mathfrak{g}$.
Neurocognitive functioning is associated with functional independence in newly diagnosed patients with temporal lobe glioma
Authors: Noll Kyle R , Bradshaw Mariana E , Weinberg Jeffrey S , Wefel Jeffrey S 
Published: November 2017

Abstract

Background
Cancer and treatment-related neurocognitive dysfunction has the potential to significantly disrupt the lives of survivors. While neurocognitive functioning is known to predict aspects of patient-reported quality of life in individuals with glioma, little is known regarding the association between neurocognitive functioning and clinician-rated functional independence.

Methods
Newly diagnosed patients with glioma in the left (n = 73; 49% glioblastoma) or right (n = 30; 57% glioblastoma) temporal lobe completed comprehensive neuropsychological testing. Clinicians rated patient functional independence using the Functional Independence Measure (FIM) and Karnofsky Performance Status (KPS) scale. Correlational and regression analyses were conducted to determine relationships between neurocognitive functioning and functional independence.

Results
Tests of verbal learning, executive function, and language comprehension were moderately to strongly associated with clinician-rated functional independence, particularly for items pertaining to need for assistance with memory, problem-solving, and language functions. Stepwise linear regression showed that tests of verbal learning, executive functioning, and language comprehension predicted FIM ratings, together accounting for 40% of variance (P < .001). A test of executive functioning also predicted KPS scores and accounted for 19% of variance (P < .001).

Conclusions
In patients with newly diagnosed temporal lobe glioma, neurocognitive functioning is associated with functional independence. Verbal learning, executive functioning, and language comprehension demonstrated the strongest associations across both measures of functional independence. These findings provide support for the ecological validity of neuropsychological assessment by demonstrating the real-world clinical significance of objectively assessed neurocognitive functioning in glioma patients.
Returning research results: caregivers’ reactions following computerized cognitive training among childhood cancer survivors
Authors: Scott Sarah M , Ashford Jason M , Clark Kellie N , Martin-Elbahesh Karen , Conklin Heather M 
Published: November 2017

AbstractBackgroundFew researchers routinely disseminate results to participants; however, there is increasing acknowledgment that benefits of returning results outweigh potential risks. Our objective was to determine whether use of specific guidelines developed by the Children’s Oncology Group (COG) when preparing a lay summary would aid in understanding results. Specifically, to determine if caregivers of childhood cancer survivors found a lay summary comprehensive, easy to understand, and helpful following participation in a computerized cognitive training program.MethodsIn a previous study, 68 childhood survivors of acute lymphoblastic leukemia or brain tumor with identified cognitive deficits were randomly assigned to participate in a computerized cognitive intervention or assigned to a wait list. Following conclusion of this study, participants’ caregivers were contacted and provided with a summary of results based on COG guidelines and survey. Forty-three participants returned the surveys, examining caregivers’ interpretation of the summary, reaction to the results, and information regarding preference for receiving results.ResultsCaregivers reported results as important (93%), helpful (93%), easy to understand (98%), and relevant to their child (91%). They interpreted the results as generally positive, with many caregivers endorsing satisfaction (84%); however, concern of long-term implications was expressed (25%). Most preferred receiving results through postal letter (88%) or email (47%).ConclusionsBenefits of returning research results to families appear to outweigh potential negative consequences. Returning results may help inform families when making future health care-related decisions. There is a great need to develop and assess the utility of guidelines for returning research results.
In-flight calibration of Hitomi Soft X-ray Spectrometer. (1) Background
Authors: Kilbourne Caroline A , Sawada Makoto , Tsujimoto Masahiro , Angellini Lorella , Boyce Kevin R , Eckart Megan E , Fujimoto Ryuichi , Ishisaki Yoshitaka , Kelley Richard L , Koyama Shu , Leutenegger Maurice A , Loewenstein Michael , McCammon Dan , Mitsuda Kazuhisa , Nakashima Shinya , Porter Frederick S , Seta Hiromi , Takei Yoh , Tashiro Makoto S , Terada Yukikatsu , Yamada Shinya , Yamasaki Noriko Y 
Published: November 2017

AbstractThe X-Ray Spectrometer (XRS) instrument of Suzaku provided the first measurement of the non-X-ray background (NXB) of an X-ray calorimeter spectrometer, but the data set was limited. The Soft X-ray Spectrometer (SXS) instrument of Hitomi was able to provide a more detailed picture of X-ray calorimeter background, with more than 360 ks of data while pointed at the Earth, and a comparable amount of blank-sky data. These data are important not only for analyzing SXS science data, but also for categorizing the contributions to the NXB in X-ray calorimeters as a class. In this paper, we present the contributions to the SXS NXB, the types and effectiveness of the screening, the interaction of the screening with the broad-band redistribution, and the residual background spectrum as a function of magnetic cut-off rigidity. The orbit-averaged SXS NXB in the range 0.3–12 keV was 4 × 10−2 counts s−1 cm−2. This very low background in combination with groundbreaking spectral resolution gave SXS unprecedented sensitivity to weak spectral lines.
Coarse-grained simulations of actomyosin rings point to a nodeless model involving both unipolar and bipolar myosins
Authors: Nguyen Lam T. , Swulius Matthew T. , Aich Samya , Mishra Mithilesh , Jensen Grant J. 
Published: November 2017

AbstractCytokinesis in most eukaryotic cells is orchestrated by a contractile actomyosin ring. While many of the proteins involved are known, the mechanism of constriction remains unclear. Informed by existing literature and new 3D molecular details from electron cryotomography, here we develop 3D coarse-grained models of actin filaments, unipolar and bipolar myosins, actin crosslinkers, and membranes and simulate their nteractions. Exploring a matrix of possible actomyosin configurations suggested that node-based architectures ike those presently described for ring assembly result in membrane puckers not seen in EM images of real cells. Instead, the model that best matches data from fluorescence microscopy, electron cryotomography, and biochemical experiments is one in which actin filaments transmit force to the membrane through evenly-distributed, membrane-attached, unipolar myosins, with bipolar myosins in the ring driving contraction. While at this point this model is only favored (not proven), the work highlights the power of coarse-grained biophysical simulations to compare complex mechanistic hypotheses.Significance StatementIn most eukaryotes, a ring of actin and myosin drives cell division, but how the elements of the ring are arranged and constrict remain unclear. Here we use 3D coarse-grained simulations to explore various possibilities. Our simulations suggest that if actomyosin is arranged in nodes (as suggested by a popular model of ring assembly), the membrane distorts in ways not seen experimentally. Instead, actin and myosin are more ikely uniformly distributed around the ring. In the model that best fits experimental data, ring tension is generated by interactions between bipolar myosins and actin, and transmitted to the membrane via unipolar myosins. Technologically the study highlights how coarse-grained simulations can test specific mechanistic hypotheses by comparing their predicted outcomes to experimental results.
Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus
Authors: Quinodoz Sofia A. , Ollikainen Noah , Tabak Barbara , Palla Ali , Schmidt Jan Marten , Detmar Elizabeth , Lai Mason , Shishkin Alexander , Bhat Prashant , Trinh Vickie , Aznauryan Erik , Russell Pamela , Cheng Christine , Jovanovic Marko , Chow Amy , McDonel Patrick , Garber Manuel , Guttman Mitchell 
Published: November 2017

ABSTRACTEukaryotic genomes are packaged into a 3-dimensional structure in the nucleus of each cell. There are currently two distinct views of genome organization that are derived from different technologies. The first view, derived from genome-wide proximity ligation methods (e.g. Hi-C), suggests that genome organization is largely organized around chromosomes. The second view, derived fromin situimaging, suggests a central role for nuclear bodies. Yet, because microscopy and proximity-ligation methods measure different aspects of genome organization, these two views remain poorly reconciled and our overall understanding of how genomic DNA is organized within the nucleus remains incomplete. Here, we develop Split-Pool Recognition of Interactions by Tag Extension (SPRITE), which moves away from proximity-ligation and enables genome-wide detection of higher-order DNA interactions within the nucleus. Using SPRITE, we recapitulate known genome structures identified by Hi-C and show that the contact frequencies measured by SPRITE strongly correlate with the 3-dimensional distances measured by microscopy. In addition to known structures, SPRITE identifies two major hubs of inter-chromosomal interactions that are spatially arranged around the nucleolus and nuclear speckles, respectively. We find that the majority of genomic regions exhibit preferential spatial association relative to one of these nuclear bodies, with regions that are highly transcribed by RNA Polymerase II organizing around nuclear speckles and transcriptionally inactive and centromere-proximal regions organizing around the nucleolus. Together, our results reconcile the two distinct pictures of nuclear structure and demonstrate that nuclear bodies act as inter-chromosomal hubs that shape the overall 3-dimensional packaging of genomic DNA in the nucleus.
Targeted Genotyping of Variable Number Tandem Repeats with adVNTR
Authors: Bakhtiari Mehrdad , Shleizer-Burko Sharona , Gymrek Melissa , Bansal Vikas , Bafna Vineet 
Published: November 2017

AbstractWhole Genome Sequencing is increasingly used to identify Mendelian variants in clinical pipelines. These pipelines focus on single nucleotide variants (SNVs) and also structural variants, while ignoring more complex repeat sequence variants. We consider the problem of genotypingVariable Number Tandem Repeats(VNTRs), composed of inexact tandem duplications of short (6-100bp) repeating units. VNTRs span 3% of the human genome, are frequently present in coding regions, and have been implicated in multiple Mendelian disorders. While existing tools recognize VNTR carrying sequence, genotyping VNTRs (determining repeat unit count and sequence variation) from whole genome sequenced reads remains challenging. We describe a method, adVNTR, that uses Hidden Markov Models to model each VNTR, count repeat units, and detect sequence variation. adVNTR models can be developed for short-read (Illumina) and single molecule (PacBio) whole genome and exome sequencing, and show good results on multiple simulated and real data sets. adVNTR is available athttps://github.com/mehrdadbakhtiari/adVNTR
Transgenic mouse lines expressing the 3xFLAG-dCas9 protein for enChIP analysis
Authors: Fujita Toshitsugu , Kitaura Fusako , Oji Asami , Tanigawa Naoki , Yuno Miyuki , Ikawa Masahito , Taniuchi Ichiro , Fujii Hodaka 
Published: November 2017

AbstractWe developed the engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) technology to isolate specific genomic regions while retaining their molecular interactions. In enChIP, the locus of interest is tagged with an engineered DNA-binding molecule, such as a modified form of the clustered regularly interspaced short palindromic repeats (CRISPR) system containing a guide RNA (gRNA) and a catalytically inactive form of Cas9 (dCas9). The locus is then affinity-purified to enable identification of associated molecules. In this study, we generated transgenic mice expressing 3xFLAG-tagged Streptococcus pyogenes dCas9 (3xFLAG-dCas9) and retrovirally transduced gRNA into primary CD4+ T cells from these mice for enChIP. Using this approach, we achieved high yields of enChIP at the targeted genomic region. Our novel transgenic mouse lines provide a valuable tool for enChIP analysis in primary mouse cells.
Standardizing microsatellite panels for individual identification of seabirds’ Snow PetrelPagodroma niveaand Wilson’s Storm PetrelOceanites oceanicusin Antarctica
Authors: Pande Anant , Rawat Nidhi , Sivakumar Kuppusamy , Sathyakumar Sambandan , Mathur Vinod B. , Mondol Samrat 
Published: November 2017

ABSTRACTSeabirds are known to be important indicators of marine ecosystems health. Procellariiformes are one of the most abundant seabird species distributed from warm tropical to cold temperate regions including Antarctica. With few long-term studies on breeding seabirds at the Antarctic continent, crucial biological parameters such as genetic variation, population genetic structure and past population demography is lacking for most of the commonly occurring species. Under the ‘Biology and Environmental Sciences’ component of the Indian Antarctic programme, long-term monitoring of Antarctic biodiversity is being conducted. In this paper, we describe a panel of 12 and 10 cross-species microsatellite markers for two relatively less studied seabird species in Antarctica, snow petrelPagodroma niveaand Wilson’s storm petrelOceanites oceanicus, respectively. These loci showed high amplification success and moderate level of polymorphism in snow petrel (mean no. of alleles 7.08±3.01 and mean observed heterozygosity 0.35±0.23), but low polymorphism in Wilson’s storm petrel (mean no. of alleles 3.9±1.3 and mean observed heterozygosity 0.28±0.18). The results demonstrate that these panels can unambiguously identify individuals of both species from various types of biological materials. This work forms a baseline for undertaking long-term genetic research of Antarctic seabird species and provides critical insights into their population genetics.
Genome-wide identification of directed gene networks using large-scale population genomics data
Authors: Luijk René , Dekkers Koen F. , van Iterson Maarten , Arindrarto Wibowo , Claringbould Annique , Hop Paul ,   BIOS Consortium, Boomsma Dorret I. , van Duin Cornelia M. , van Greevenbroek Marleen M.J. , Veldink Jan H. , Wijmenga Cisca , Franke Lude , ’t Hoen Peter A.C. , Jansen Rick , van Meurs Joyce , Mei Hailiang , Slagboom P. Eline , Heijmans Bastiaan T. , van Zwet Erik W. 
Published: November 2017

ABSTRACTIdentification of causal drivers behind regulatory gene networks is crucial in understanding gene function. We developed a method for the large-scale inference of gene-gene interactions in observational population genomics data that are both directed (using local genetic instruments as causal anchors, akin to Mendelian Randomization) and specific (by controlling for linkage disequilibrium and pleiotropy). The analysis of genotype and whole-blood RNA-sequencing data from 3,072 individuals identified 49 genes as drivers of downstream transcriptional changes (P< 7 × 10−10), among which transcription factors were overrepresented (P= 3.3 × 10−7). Our analysis suggests new gene functions and targets including forSENP7(zinc-finger genes involved in retroviral repression) andBCL2A1(novel target genes possibly involved in auditory dysfunction). Our work highlights the utility of population genomics data in deriving directed gene expression networks. A resource oftrans-effects for all 6,600 genes with a genetic instrument can be explored individually using a web-based browser.
Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants
Authors: Gazara Rajesh K. , Moharana Kanhu C. , Bellieny-Rabelo Daniel , Venancio Thiago M. 
Published: November 2017

ABSTRACTGibberellic acid (gibberellins, GA) controls key developmental processes in the life-cycle of land plants. By interacting with the GIBBERELLIN INSENSITIVE DWARF1 (GID1) receptor, GA regulates the expression of a wide range of genes through different pathways. Here we report the systematic identification and classification of GID1s in 52 plants genomes, encompassing from bryophytes and lycophytes, to several monocots and eudicots. We investigated the evolutionary relationship of GID1s using a comparative genomics framework and found strong support a previously proposed phylogenetic classification of this family in land plants. We identified lineage-specific expansions of particular subfamilies (i.e. GID1ac and GID1b) in different eudicot lineages (e.g. GID1b in legumes). Further, we found both, shared and divergent structural features between GID1ac and GID1b subgroups in eudicots, which provide mechanistic insights on their functions. Gene expression data from several species show that at least one GID1 gene is expressed in every sampled tissue, with a strong bias of GID1b expression towards underground tissues and dry legume seeds (typically with low GA levels). Taken together, our results support that GID1ac retained canonical GA signaling roles, whereas GID1b specialized in conditions of low GA concentrations. We propose that this functional specialization occurred initially at the gene expression level and was later fine-tuned by specific mutations that conferred greater GA affinity to GID1b, including a Phe residue in the GA-binding pocket. Finally, we discuss the importance of our findings to understand the diversification of GA perception mechanisms in land plants.
Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities
Authors: Rennie Sarah , Dalby Maria , Lloret-Llinares Marta , Bakoulis Stylianos , Dalager Vaagensø Christian , Jensen Torben Heick , Andersson Robin 
Published: November 2017

ABSTRACTMammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in D. melanogaster. Surprisingly, we find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed. We observe quantitative relationships between enhancer potential, expression level and core promoter strength, providing an explanation for indirectly related histone modifications that are reflecting expression levels. Lowly abundant unstable RNAs initiated from weak core promoters are key characteristics of gene-distal developmental enhancers, while the housekeeping enhancer strengths of gene promoters reflect their expression strengths. The different layers of regulation mediated by gene-distal enhancers and gene promoters are also reflected in chromatin interaction data. Our results suggest a unified promoter architecture of many D. melanogaster regulatory elements, that is universal across Metazoa, whose regulatory functions seem to be related to their core promoter elements.
3D textile reconstruction based on KinectFusion and synthesized texture
Authors: Hu PengPeng , Komura Taku , Li Duan , Wu Ge , Zhong Yueqi 
Published: November 2017

Purpose
The purpose of this paper is to present a novel framework of reconstructing the 3D textile model with synthesized texture.

Design/methodology/approach
First, a pipeline of 3D textile reconstruction based on KinectFusion is proposed to obtain a better 3D model. Second, “DeepTextures” method is applied to generate new textures for various three-dimensional textile models.

Findings
Experimental results show that the proposed method can conveniently reconstruct a three-dimensional textile model with synthesized texture.

Originality/value
A novel pipeline is designed to obtain 3D high-quality textile models based on KinectFusion. The accuracy and robustness of KinectFusion are improved via a turntable. To the best of the authors’ knowledge, this is the first paper to explore the synthesized textile texture for the 3D textile model. This is not only simply mapping the texture onto the 3D model, but also exploring the application of artificial intelligence in the field of textile.