bluuebunny/crossref_metadata_2025_split huggingface dataset:
A photonic self-oscillator based on porous silicon
Authors: Sánchez Castro N. , Palomino-Ovando M. A. , Estrada-Wiese D. , del Río J. A. , de la Mora M. B. , Doti R. , Faubert J. , Lugo J. E. 
Published: August 2016

Abstract
We induced mechanical self-oscillations in
a microcavity structure made of porous silicon onedimensional
photonic crystals (PSi-1DPC) with an air gap.
The electromagnetic force generated within the whole
photonic structure, by light with a wavelength of 633 nm,
is enough to overcome energy losses and sustain selfoscillations.
From these mechano-optical measurements
we estimated the stiffness and Young’s modulus of porous
silicon and compared the results with values reported elsewhere
and with values estimated herein by a mechanical
method.We obtained good agreement between all values.
Crystal structure of dichlorido(1,3-bis(2,6-dimethyl-phenyl)-1H-3λ4-imidazol-2-yl)(isoquinolinyl)palladium(IV), C28H27Cl2N3Pd
Authors: Liu Feng , Li Guo-Xing 
Published: August 2016

Abstract
C28H27Cl2N3Pd, monoclinic (no. 15), C2/c, a = 24.7394(17) Å, b = 15.9451(11) Å, c = 27.4301(19) Å, β = 107.8650°, V = 10293.7(12) Å3, Z = 16, R
gt(F) = 0.0249, wR
ref(F
2) = 0.1168, T = 100(2) K.
Ernährungs-Apps für den Ernährungsversorgungsalltag – Hindernisse und Chancen
Authors: Schnellbächer Carina 
Published: August 2016

Zusammenfassung:
Anwendungsprogramme in Form von Apps erobern viele Lebensbereiche, so auch den Sektor Ernährung und Gesundheit. Studien gaben erste Hinweise darauf, dass durch den Gebrauch von Applications (Apps) die Umsetzung von Ernährungsempfehlungen und die Gewichtskontrolle gefördert werden. Damit ernährungskompetente Handlungen im Ernährungsversorgungsalltag unterstützt werden können, ist es nötig, zielgruppenspezifisch auf fachlich fundierte Apps aufmerksam zu machen und die Nutzungskompetenz der Anwender zu stärken.
Idiome und ihre kommunikative Leistung
Authors: Dalmas Martine , Dobrovol’skij Dmitrij 
Published: August 2016

Abstract
The aim of this paper is to analyze the communicative function of idioms and their constituents in the information structure of an utterance. Usually idioms tend to occupy the final position in a sentence, which correlates with their inherent rhematic properties. However, structural transformations such as fronting, passivization and conversion can lead to changes in their communicative status. Among such changes, we single out (a) topicalization or thematization of the fronted sentence constituent, (b) its focusing or emphatic rhematization, (c) focusing of the postponed constituent, or (d) rhematization of the sentence as a whole, etc. In spite of their lexical stability, idioms make use of the possibilities provided by German syntax. This allows them to contribute to the communicative structuring of utterances.
Synthesis and structural characterization of Ca12Ge17B8O58
Authors: Bräuchle Sebastian , Wurst Klaus , Huppertz Hubert 
Published: August 2016

Abstract
Ca12Ge17B8O58 was prepared by high-temperature solid state synthesis at 1100°C in a platinum crucible from calcium carbonate, boric acid, and germanium(IV) oxide. The compound crystallizes in the tetragonal crystal system in the space group P4̅ (No. 81) isotypically to Cd12Ge17B8O58. The structure was refined from single-crystal X-ray diffraction data: a = 15.053(8), c = 4.723(2) Å, V = 1070.2(2) Å3, R1 = 0.0151, and wR2 = 0.0339 for all data. The crystal structure of Ca12Ge17B8O58 consists of [Ge4O12]
n
chains composed of GeO4 tetrahedra and GeO6 octahedra. The chains are interconnected into a [Ge4O10.5]
n
network via corner sharing. By additional [Ge(B2O7)4]28– clusters, these units are connected to a three-dimensional [Ge17B8O58]24– framework. The open structure forms three types of tunnels with five-, six-, and seven-membered rings (MRs) along the c axis, where the Ca2+ are located.
Neurons That UnderlieDrosophila melanogasterReproductive Behaviors: Detection of a Large Male-Bias in Gene Expression infruitless-Expressing Neurons
Authors: Newell Nicole R , New Felicia N , Dalton Justin E , McIntyre Lauren M , Arbeitman Michelle N 
Published: August 2016

AbstractMale and female reproductive behaviors in Drosophila melanogaster are vastly different, but neurons that express sex-specifically spliced fruitless transcripts (fru P1) underlie these behaviors in both sexes. How this set of neurons can generate such different behaviors between the two sexes is an unresolved question. A particular challenge is that fru P1-expressing neurons comprise only 2–5% of the adult nervous system, and so studies of adult head tissue or whole brain may not reveal crucial differences. Translating Ribosome Affinity Purification (TRAP) identifies the actively translated pool of mRNAs from fru P1-expressing neurons, allowing a sensitive, cell-type-specific assay. We find four times more male-biased than female-biased genes in TRAP mRNAs from fru P1-expressing neurons. This suggests a potential mechanism to generate dimorphism in behavior. The male-biased genes may direct male behaviors by establishing cell fate in a similar context of gene expression observed in females. These results suggest a possible global mechanism for how distinct behaviors can arise from a shared set of neurons.
A Genetic Mosaic Screen Reveals Ecdysone-Responsive Genes RegulatingDrosophilaOogenesis
Authors: Ables Elizabeth T , Hwang Grace H , Finger Danielle S , Hinnant Taylor D , Drummond-Barbosa Daniela 
Published: August 2016

AbstractMultiple aspects of Drosophila oogenesis, including germline stem cell activity, germ cell differentiation, and follicle survival, are regulated by the steroid hormone ecdysone. While the transcriptional targets of ecdysone signaling during development have been studied extensively, targets in the ovary remain largely unknown. Early studies of salivary gland polytene chromosomes led to a model in which ecdysone stimulates a hierarchical transcriptional cascade, wherein a core group of ecdysone-sensitive transcription factors induce tissue-specific responses by activating secondary branches of transcriptional targets. More recently, genome-wide approaches have identified hundreds of putative ecdysone-responsive targets. Determining whether these putative targets represent bona fide targets in vivo, however, requires that they be tested via traditional mutant analysis in a cell-type specific fashion. To investigate the molecular mechanisms whereby ecdysone signaling regulates oogenesis, we used genetic mosaic analysis to screen putative ecdysone-responsive genes for novel roles in the control of the earliest steps of oogenesis. We identified a cohort of genes required for stem cell maintenance, stem and progenitor cell proliferation, and follicle encapsulation, growth, and survival. These genes encode transcription factors, chromatin modulators, and factors required for RNA transport, stability, and ribosome biogenesis, suggesting that ecdysone might control a wide range of molecular processes during oogenesis. Our results suggest that, although ecdysone target genes are known to have cell type-specific roles, many ecdysone response genes that control larval or pupal cell types at developmental transitions are used reiteratively in the adult ovary. These results provide novel insights into the molecular mechanisms by which ecdysone signaling controls oogenesis, laying new ground for future studies.
Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data
Authors: Tetreault Hannah M , Ungerer Mark C 
Published: August 2016

Abstract
The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia. Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius. We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny.
Diversifying Selection Between Pure-Breed and Free-Breeding Dogs Inferred from Genome-Wide SNP Analysis
Authors: Pilot Małgorzata , Malewski Tadeusz , Moura Andre E , Grzybowski Tomasz , Oleński Kamil , Kamiński Stanisław , Fadel Fernanda Ruiz , Alagaili Abdulaziz N , Mohammed Osama B , Bogdanowicz Wiesław 
Published: August 2016

Abstract
Domesticated species are often composed of distinct populations differing in the character and strength of artificial and natural selection pressures, providing a valuable model to study adaptation. In contrast to pure-breed dogs that constitute artificially maintained inbred lines, free-ranging dogs are typically free-breeding, i.e., unrestrained in mate choice. Many traits in free-breeding dogs (FBDs) may be under similar natural and sexual selection conditions to wild canids, while relaxation of sexual selection is expected in pure-breed dogs. We used a Bayesian approach with strict false-positive control criteria to identify FST-outlier SNPs between FBDs and either European or East Asian breeds, based on 167,989 autosomal SNPs. By identifying outlier SNPs located within coding genes, we found four candidate genes under diversifying selection shared by these two comparisons. Three of them are associated with the Hedgehog (HH) signaling pathway regulating vertebrate morphogenesis. A comparison between FBDs and East Asian breeds also revealed diversifying selection on the BBS6 gene, which was earlier shown to cause snout shortening and dental crowding via disrupted HH signaling. Our results suggest that relaxation of natural and sexual selection in pure-breed dogs as opposed to FBDs could have led to mild changes in regulation of the HH signaling pathway. HH inhibits adhesion and the migration of neural crest cells from the neural tube, and minor deficits of these cells during embryonic development have been proposed as the underlying cause of “domestication syndrome.” This suggests that the process of breed formation involved the same genetic and developmental pathways as the process of domestication.
A Genetic Screen for Mutants with Supersized Lipid Droplets in Caenorhabditis elegans
Authors: Li Shiwei , Xu Shibin , Ma Yanli , Wu Shuang , Feng Yu , Cui Qingpo , Chen Lifeng , Zhou Shuang , Kong Yuanyuan , Zhang Xiaoyu , Yu Jialei , Wu Mengdi , Zhang Shaobing O 
Published: August 2016

Abstract
To identify genes that regulate the dynamics of lipid droplet (LD) size, we have used the genetically tractable model organism Caenorhabditis elegans, whose wild-type LD population displays a steady state of size with an upper limit of 3 μm in diameter. From a saturated forward genetic screen of 6.7 × 105 mutagenized haploid genomes, we isolated 118 mutants with supersized intestinal LDs often reaching 10 μm. These mutants define nine novel complementation groups, in addition to four known genes (maoc-1, dhs-28, daf-22, and prx-10). The nine groups are named drop (lipid droplet abnormal) and categorized into four classes. Class I mutants drop-5 and drop-9, similar to prx-10, are up-regulated in ACS-22-DGAT-2-dependent LD growth, resistant to LD hydrolysis, and defective in peroxisome import. Class II mutants drop-2, drop-3, drop-6, and drop-7 are up-regulated in LD growth, are resistant to LD hydrolysis, but are not defective in peroxisome import. Class III mutants drop-1 and drop-8 are neither up-regulated in LD growth nor resistant to LD hydrolysis, but seemingly up-regulated in LD fusion. Class IV mutant drop-4 is cloned as sams-1 and, different to the other three classes, is ACS-22-independent and hydrolysis-resistant. These four classes of supersized LD mutants should be valuable for mechanistic studies of LD cellular processes including growth, hydrolysis, and fusion.
Genetic Regulation of Transcriptional Variation in NaturalArabidopsis thalianaAccessions
Authors: Zan Yanjun , Shen Xia , Forsberg Simon K G , Carlborg Örjan 
Published: August 2016

AbstractAn increased knowledge of the genetic regulation of expression in Arabidopsis thaliana is likely to provide important insights about the basis of the plant’s extensive phenotypic variation. Here, we reanalyzed two publicly available datasets with genome-wide data on genetic and transcript variation in large collections of natural A. thaliana accessions. Transcripts from more than half of all genes were detected in the leaves of all accessions, and from nearly all annotated genes in at least one accession. Thousands of genes had high transcript levels in some accessions, but no transcripts at all in others, and this pattern was correlated with the genome-wide genotype. In total, 2669 eQTL were mapped in the largest population, and 717 of them were replicated in the other population. A total of 646 cis-eQTL-regulated genes that lacked detectable transcripts in some accessions was found, and for 159 of these we identified one, or several, common structural variants in the populations that were shown to be likely contributors to the lack of detectable RNA transcripts for these genes. This study thus provides new insights into the overall genetic regulation of global gene expression diversity in the leaf of natural A. thaliana accessions. Further, it also shows that strong cis-acting polymorphisms, many of which are likely to be structural variations, make important contributions to the transcriptional variation in the worldwide A. thaliana population.
MeSH-Informed Enrichment Analysis and MeSH-Guided Semantic Similarity Among Functional Terms and Gene Products in Chicken
Authors: Morota Gota , Beissinger Timothy M , Peñagaricano Francisco 
Published: August 2016

Abstract
Biomedical vocabularies and ontologies aid in recapitulating biological knowledge. The annotation of gene products is mainly accelerated by Gene Ontology (GO), and more recently by Medical Subject Headings (MeSH). Here, we report a suite of MeSH packages for chicken in Bioconductor, and illustrate some features of different MeSH-based analyses, including MeSH-informed enrichment analysis and MeSH-guided semantic similarity among terms and gene products, using two lists of chicken genes available in public repositories. The two published datasets that were employed represent (i) differentially expressed genes, and (ii) candidate genes under selective sweep or epistatic selection. The comparison of MeSH with GO overrepresentation analyses suggested not only that MeSH supports the findings obtained from GO analysis, but also that MeSH is able to further enrich the representation of biological knowledge and often provide more interpretable results. Based on the hierarchical structures of MeSH and GO, we computed semantic similarities among vocabularies, as well as semantic similarities among selected genes. These yielded the similarity levels between significant functional terms, and the annotation of each gene yielded the measures of gene similarity. Our findings show the benefits of using MeSH as an alternative choice of annotation in order to draw biological inferences from a list of genes of interest. We argue that the use of MeSH in conjunction with GO will be instrumental in facilitating the understanding of the genetic basis of complex traits.
Septate Junction Proteins Play Essential Roles in Morphogenesis Throughout Embryonic Development inDrosophila
Authors: Hall Sonia , Ward Robert E 
Published: August 2016

AbstractThe septate junction (SJ) is the occluding junction found in the ectodermal epithelia of invertebrate organisms, and is essential to maintain chemically distinct compartments in epithelial organs, to provide the blood–brain barrier in the nervous system, and to provide an important line of defense against invading pathogens. More than 20 genes have been identified to function in the establishment or maintenance of SJs in Drosophila melanogaster. Numerous studies have demonstrated the cell biological function of these proteins in establishing the occluding junction, whereas very few studies have examined further developmental roles for them. Here we examined embryos with mutations in nine different core SJ genes and found that all nine result in defects in embryonic development as early as germ band retraction, with the most penetrant defect observed in head involution. SJ genes are also required for cell shape changes and cell rearrangements that drive the elongation of the salivary gland during midembryogenesis. Interestingly, these developmental events occur at a time prior to the formation of the occluding junction, when SJ proteins localize along the lateral membrane and have not yet coalesced into the region of the SJ. Together, these observations reveal an underappreciated role for a large group of SJ genes in essential developmental events during embryogenesis, and suggest that the function of these proteins in facilitating cell shape changes and rearrangements is independent of their role in the occluding junction.
Glucose or Altered Ceramide Biosynthesis Mediate Oxygen Deprivation Sensitivity Through Novel Pathways Revealed by Transcriptome Analysis inCaenorhabditis elegans
Authors: Ladage Mary L , King Skylar D , Burks David J , Quan Daniel L , Garcia Anastacia M , Azad Rajeev K , Padilla Pamela A 
Published: August 2016

AbstractIndividuals with type 2 diabetes display metabolic abnormalities, such as hyperglycemia, increased free fatty acids, insulin resistance, and altered ceramide levels, that contribute to vascular dysfunctions and compromised oxygen delivery. Caenorhabditis elegans fed a glucose-supplemented diet or with altered ceramide metabolism, due to a hyl-2 mutation, are sensitive to oxygen deprivation (anoxia). Our experiments showed that the combination of these factors further decreased the anoxia survival. RNA-sequencing analysis was performed to assess how a glucose-supplemented diet and/or a hyl-2 mutation altered the transcriptome. Comparison analysis of transcripts associated with anoxia-sensitive animals [hyl-2(tm2031) mutation or a glucose diet] revealed 199 common transcripts encoded by genes with known or predicted functions involving innate immunity, cuticle function (collagens), or xenobiotic and endobiotic phase I and II detoxification system. Use of RNA interference (RNAi) to target gene products of the xenobiotic and endobiotic phase I and II detoxification system (UDP-glycosyltransferase and Cytochrome p450 genes; ugt-15, ugt-18, ugt-19, ugt-41, ugt-63, cyp-13A12, cyp-25A1, and cyp-33C8) increased anoxia survival in wild-type animals fed a standard diet. Anoxia sensitivity of the hyl-2(tm2031) animals was suppressed by RNAi of cyp-25A1 or cyp-33C8 genes. A glucose diet fed to the P0 hermaphrodite decreased the anoxia survival of its F1 embryos; however, the RNAi of ugt-63 and cyp-33C8 suppressed anoxia sensitivity. These studies provide evidence that the detoxification system impacts oxygen deprivation responses and that C. elegans can be used to model the conserved detoxification system.
Synthetic Physical Interactions Map Kinetochore-Checkpoint Activation Regions
Authors: Ólafsson Guðjón , Thorpe Peter H 
Published: August 2016

Abstract
The spindle assembly checkpoint (SAC) is a key mechanism to regulate the timing of mitosis and ensure that chromosomes are correctly segregated to daughter cells. The recruitment of the Mad1 and Mad2 proteins to the kinetochore is normally necessary for SAC activation. This recruitment is coordinated by the SAC kinase Mps1, which phosphorylates residues at the kinetochore to facilitate binding of Bub1, Bub3, Mad1, and Mad2. There is evidence that the essential function of Mps1 is to direct recruitment of Mad1/2. To test this model, we have systematically recruited Mad1, Mad2, and Mps1 to most proteins in the yeast kinetochore, and find that, while Mps1 is sufficient for checkpoint activation, recruitment of either Mad1 or Mad2 is not. These data indicate an important role for Mps1 phosphorylation in SAC activation, beyond the direct recruitment of Mad1 and Mad2.
Prenatal Substance Exposure and Reporting of Child Maltreatment by Race and Ethnicity
Authors: Putnam-Hornstein Emily , Prindle John J. , Leventhal John M. 
Published: August 2016

BACKGROUND:
Substance exposure is thought to contribute to reports of suspected maltreatment made to child protective services (CPS) at or shortly after birth. There are limited data, however, on whether clinicians are more likely to report black and Hispanic substance-exposed infants compared with white infants.

METHODS:
We examined racial differences in diagnosed substance exposure and subsequent maltreatment reports by using linked birth, hospital discharge, and CPS records. Diagnostic codes were used to document substance exposure; CPS records provided information on maltreatment reports. Prevalence of infant exposure was calculated by race or ethnicity, substance type, and sociodemographic covariates. We estimated racial differences in maltreatment reporting among substance-exposed infants using multivariable models.

RESULTS:
In a 2006 population-based California birth cohort of 474 071 black, Hispanic, and white infants, substance exposure diagnoses were identified for 1.6% of infants (n = 7428). Exposure varied significantly across racial groups (P &lt; .001), with the highest prevalence observed among black infants (4.1%) and the lowest among Hispanic infants (1.0%). Among white and Hispanic infants, the most frequently observed substances were amphetamine and cannabis; for black infants, cannabis was the most common, followed by cocaine. After adjusting for sociodemographic and pregnancy factors, we found that substance-exposed black and Hispanic infants were reported at significantly lower or statistically comparable rates to substance-exposed white infants.

CONCLUSIONS:
Although we were unable to address potential racial and ethnic disparities in screening for substances at birth, we found no evidence that racial disparities in infant CPS reports arise from variable responses to prenatal substance exposure.