bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between a common immunoglobulin heavy chain allele and rheumatic heart disease risk in Oceania
Authors: Parks Tom , Mirabel Mariana M. , Kado Joseph , Auckland Kathryn , Nowak Jaroslaw , Rautanen Anna , Mentzer Alexander J. , Marijon Eloi , Jouven Xavier , Perman Mai Ling , Cua Tuliana , Kauwe John K. , Allen John B. , Taylor Henry , Robson Kathryn J. , Deane Charlotte M. , Steer Andrew C. , Hill Adrian V. S. ,   Pacific Islands Rheumatic Heart Disease Genetics Network, Allen Lori , Allen Marvin , Braunstein Corinne , Colquhoun Samantha M. , Jewine Aurélia , Ah Kee Maureen , Kumar Rina , John Martin William , Mataika Reapi , Nadra Marie , Nadu Shahin , Naseri Take , Noël Baptiste , Simon Nathalie , Ward Brenton 
Published: May 2017

AbstractThe indigenous populations of the South Pacific experience a high burden of rheumatic heart disease (RHD). Here we report a genome-wide association study (GWAS) of RHD susceptibility in 2,852 individuals recruited in eight Oceanian countries. Stratifying by ancestry, we analysed genotyped and imputed variants in Melanesians (607 cases and 1,229 controls) before follow-up of suggestive loci in three further ancestral groups: Polynesians, South Asians and Mixed or other populations (totalling 399 cases and 617 controls). We identify a novel susceptibility signal in the immunoglobulin heavy chain (IGH) locus centring on a haplotype of nonsynonymous variants in theIGHV4-61gene segment corresponding to theIGHV4-61*02 allele. We show each copy ofIGHV4-61*02 is associated with a 1.4-fold increase in the risk of RHD (odds ratio 1.43, 95% confidence intervals 1.27–1.61,P=4.1 × 10−9). These findings provide new insight into the role of germline variation in the IGH locus in disease susceptibility.
Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates
Authors: Kis Olena , Kaedbey Rayan , Chow Signy , Danesh Arnavaz , Dowar Mark , Li Tiantian , Li Zhihua , Liu Jessica , Mansour Mark , Masih-Khan Esther , Zhang Tong , Bratman Scott V. , Oza Amit M. , Kamel-Reid Suzanne , Trudel Suzanne , Pugh Trevor J. 
Published: May 2017

AbstractThe requirement for bone-marrow aspirates for genomic profiling of multiple myeloma poses an obstacle to enrolment and retention of patients in clinical trials. We evaluated whether circulating cell-free DNA (cfDNA) analysis is comparable to molecular profiling of myeloma using bone-marrow tumour cells. We report here a hybrid-capture-based Liquid Biopsy Sequencing (LB-Seq) method used to sequence all protein-coding exons of KRAS, NRAS, BRAF, EGFR and PIK3CA in 64 cfDNA specimens from 53 myeloma patients to >20,000 × median coverage. This method includes a variant filtering algorithm that enables detection of tumour-derived fragments present in cfDNA at allele frequencies as low as 0.25% (median 3.2%, range 0.25–46%). Using LB-Seq analysis of 48 cfDNA specimens with matched bone-marrow data, we detect 49/51 likely somatic mutations, with subclonal hierarchies reflecting tumour profiling (96% concordance), and four additional mutations likely missed by bone-marrow testing (>98% specificity). Overall, LB-Seq is a high fidelity adjunct to genetic profiling of bone-marrow in multiple myeloma.
ISCA1 is essential for mitochondrial Fe4S4 biogenesis in vivo
Authors: Beilschmidt Lena Kristina , Ollagnier de Choudens Sandrine , Fournier Marjorie , Sanakis Ioannis , Hograindleur Marc-André , Clémancey Martin , Blondin Geneviève , Schmucker Stéphane , Eisenmann Aurélie , Weiss Amélie , Koebel Pascale , Messaddeq Nadia , Puccio Hélène , Martelli Alain 
Published: May 2017

AbstractMammalian A-type proteins, ISCA1 and ISCA2, are evolutionarily conserved proteins involved in iron–sulfur cluster (Fe–S) biogenesis. Recently, it was shown that ISCA1 and ISCA2 form a heterocomplex that is implicated in the maturation of mitochondrial Fe4S4 proteins. Here we report that mouse ISCA1 and ISCA2 are Fe2S2-containing proteins that combine all features of Fe–S carrier proteins. We use biochemical, spectroscopic and in vivo approaches to demonstrate that despite forming a complex, ISCA1 and ISCA2 establish discrete interactions with components of the late Fe–S machinery. Surprisingly, knockdown experiments in mouse skeletal muscle and in primary cultures of neurons suggest that ISCA1, but not ISCA2, is required for mitochondrial Fe4S4 proteins biogenesis. Collectively, our data suggest that cellular processes with different requirements for ISCA1, ISCA2 and ISCA1–ISCA2 complex seem to exist.
The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis
Authors: Ritter Andrés , Iñigo Sabrina , Fernández-Calvo Patricia , Heyndrickx Ken S. , Dhondt Stijn , Shi Hua , De Milde Liesbeth , Vanden Bossche Robin , De Clercq Rebecca , Eeckhout Dominique , Ron Mily , Somers David E. , Inzé Dirk , Gevaert Kris , De Jaeger Geert , Vandepoele Klaas , Pauwels Laurens , Goossens Alain 
Published: May 2017

AbstractMost living organisms developed systems to efficiently time environmental changes. The plant-clock acts in coordination with external signals to generate output responses determining seasonal growth and flowering time. Here, we show that two Arabidopsis thaliana transcription factors, FAR1 RELATED SEQUENCE 7 (FRS7) and FRS12, act as negative regulators of these processes. These proteins accumulate particularly in short-day conditions and interact to form a complex. Loss-of-function of FRS7 and FRS12 results in early flowering plants with overly elongated hypocotyls mainly in short days. We demonstrate by molecular analysis that FRS7 and FRS12 affect these developmental processes in part by binding to the promoters and repressing the expression of GIGANTEA and PHYTOCHROME INTERACTING FACTOR 4 as well as several of their downstream signalling targets. Our data reveal a molecular machinery that controls the photoperiodic regulation of flowering and growth and offer insight into how plants adapt to seasonal changes.
C. elegans chromosomes connect to centrosomes by anchoring into the spindle network
Authors: Redemann Stefanie , Baumgart Johannes , Lindow Norbert , Shelley Michael , Nazockdast Ehssan , Kratz Andrea , Prohaska Steffen , Brugués Jan , Fürthauer Sebastian , Müller-Reichert Thomas 
Published: May 2017

AbstractThe mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient.
Dust-wind interactions can intensify aerosol pollution over eastern China
Authors: Yang Yang , Russell Lynn M. , Lou Sijia , Liao Hong , Guo Jianping , Liu Ying , Singh Balwinder , Ghan Steven J. 
Published: May 2017

AbstractEastern China has experienced severe and persistent winter haze episodes in recent years due to intensification of aerosol pollution. In addition to anthropogenic emissions, the winter aerosol pollution over eastern China is associated with unusual meteorological conditions, including weaker wind speeds. Here we show, based on model simulations, that during years with decreased wind speed, large decreases in dust emissions (29%) moderate the wintertime land–sea surface air temperature difference and further decrease winds by −0.06 (±0.05) m s−1 averaged over eastern China. The dust-induced lower winds enhance stagnation of air and account for about 13% of increasing aerosol concentrations over eastern China. Although recent increases in anthropogenic emissions are the main factor causing haze over eastern China, we conclude that natural emissions also exert a significant influence on the increases in wintertime aerosol concentrations, with important implications that need to be taken into account by air quality studies.
Distinguishing physical mechanisms using GISAXS experiments and linear theory: the importance of high wavenumbers
Authors: Norris Scott A. , Perkinson Joy C. , Mokhtarzadeh Mahsa , Anzenberg Eitan , Aziz Michael J. , Ludwig Karl F. 
Published: May 2017

AbstractIn this work we analyze GISAXS measurements of the structure factor of Si surfaces evolving during 1 keV Ar+ ion bombardment. Using newly-developed methods sensitive to the full range of experimentally-available wavenumbers q, we extract the linear amplification rate R(q) governing surface stability over a range of wavenumbers 4–5 times larger than has previously been obtained. Comparing with theoretical models also retaining full wavenumber-dependence, we find an excellent fit of the experimental data over the full range of irradiation angles and wavenumbers. Moreover, the fitted parameter values represent experimental evaluation of the magnitudes of most physical mechanisms currently believed to be important to the pattern-formation process. In all cases, the extracted values agree well with direct observations or atomistic simulations of the same quantities, suggesting that GISAXS analysis may allow more powerful comparison between experiment and theory than had previously been thought.
Disentangling the intricate atomic short-range order and electronic properties in amorphous transition metal oxides
Authors: Triana C. A. , Araujo C. Moyses , Ahuja R. , Niklasson G. A. , Edvinsson T. 
Published: May 2017

AbstractSolid state materials with crystalline order have been well-known and characterized for almost a century while the description of disordered materials still bears significant challenges. Among these are the atomic short-range order and electronic properties of amorphous transition metal oxides [aTMOs], that have emerged as novel multifunctional materials due to their optical switching properties and high-capacity to intercalate alkali metal ions at low voltages. For decades, research on aTMOs has dealt with technological optimization. However, it remains challenging to unveil their intricate atomic short-range order. Currently, no systematic and broadly applicable methods exist to assess atomic-size structure, and since electronic localization is structure-dependent, still there are not well-established optical and electronic mechanisms for modelling the properties of aTMOs. We present state-of-the-art systematic procedures involving theory and experiment in a self-consistent computational framework to unveil the atomic short-range order and its role for the electronic properties. The scheme is applied to amorphous tungsten trioxide aWO3, which is the most studied electrochromic aTMO in spite of its unidentified atomic-size structure. Our approach provides a one-to-one matching of experimental data and corresponding model structure from which electronic properties can be directly calculated in agreement with the electronic transitions observed in the XANES spectra.
Thermal radiation of Er doped dielectric crystals: Probing the range of applicability of the Kirchhoff’s law
Authors: Tanyi Ekembu K. , Burton Brandi T. , Narimanov Evgenii E. , Noginov M. A. 
Published: May 2017

AbstractKirchhoff’s law of thermal radiation, relating emissivity and absorptance is commonly formulated for opaque bodies in thermodynamic equilibrium with the environment. However, in many systems of practical importance, both assumptions are often not satisfied. We revisit the century-old law and examine the limits of its applicability in an example of Er:YAG and Er:YLF dielectric crystals–potential radiation converters for thermophotovoltaic applications. The (80 at.%) Er:YAG crystal is opaque between 1.45 μm and 1.64 μm. In this spectral range, its absorptance α(λ) is spectrally flat and differentiates from unity only by a small amount of reflection. The shape of the emissivity spectrum ɛ(λ) closely matches that of absorptance α(λ), implying that the Kirchhoff’s law can adequately describe thermal radiation of opaque bodies, even if thermodynamic equilibrium is not satisfied. The (20 at.%) Er:YLF crystal had smaller size, lower concentration of Er ions, and it was not opaque. Nevertheless, its spectrum of emissivity had almost the same shape (between 1.45 μm and 1.62 μm) as the absorptance derived from the transmission measurements. Our results are consistent with the conclusion that the Kirchhoff’s law of thermal radiation can be extended (with caution) to not-opaque bodies away from the thermodynamic equilibrium.
Cell morphology governs directional control in swimming bacteria
Authors: Guadayol Òscar , Thornton Katie L. , Humphries Stuart 
Published: May 2017

AbstractThe ability to rapidly detect and track nutrient gradients is key to the ecological success of motile bacteria in aquatic systems. Consequently, bacteria have evolved a number of chemotactic strategies that consist of sequences of straight runs and reorientations. Theoretically, both phases are affected by fluid drag and Brownian motion, which are themselves governed by cell geometry. Here, we experimentally explore the effect of cell length on control of swimming direction. We subjected Escherichia coli to an antibiotic to obtain motile cells of different lengths, and characterized their swimming patterns in a homogeneous medium. As cells elongated, angles between runs became smaller, forcing a change from a run-and-tumble to a run-and-stop/reverse pattern. Our results show that changes in the motility pattern of microorganisms can be induced by simple morphological variation, and raise the possibility that changes in swimming pattern may be triggered by both morphological plasticity and selection on morphology.
Gender-specific differential expression of exosomal miRNA in synovial fluid of patients with osteoarthritis
Authors: Kolhe Ravindra , Hunter Monte , Liu Siyang , Jadeja Ravirajsinh N. , Pundkar Chetan , Mondal Ashis K. , Mendhe Bharati , Drewry Michelle , Rojiani Mumtaz V. , Liu Yutao , Isales Carlos M. , Guldberg Robert E. , Hamrick Mark W. , Fulzele Sadanand 
Published: May 2017

AbstractThe pathogenesis of osteoarthritis (OA) is poorly understood, and therapeutic approaches are limited to preventing progression of the disease. Recent studies have shown that exosomes play a vital role in cell-to-cell communication, and pathogenesis of many age-related diseases. Molecular profiling of synovial fluid derived exosomal miRNAs may increase our understanding of OA progression and may lead to the discovery of novel biomarkers and therapeutic targets. In this article we report the first characterization of exosomes miRNAs from human synovial fluid. The synovial fluid exosomes share similar characteristics (size, surface marker, miRNA content) with previously described exosomes in other body fluids. MiRNA microarray analysis showed OA specific exosomal miRNA of male and female OA. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified gender-specific target genes/signaling pathways. These pathway analyses showed that female OA specific miRNAs are estrogen responsive and target TLR (toll-like receptor) signaling pathways. Furthermore, articular chondrocytes treated with OA derived extracellular vesicles had decreased expression of anabolic genes and elevated expression of catabolic and inflammatory genes. In conclusion, synovial fluid exosomal miRNA content is altered in patients with OA and these changes are gender specific.
Genetic diversity of armored scales (Hemiptera: Diaspididae) and soft scales (Hemiptera: Coccidae) in Chile
Authors: Amouroux P. , Crochard D. , Germain J.-F. , Correa M. , Ampuero J. , Groussier G. , Kreiter P. , Malausa T. , Zaviezo T. 
Published: May 2017

AbstractScale insects (Sternorrhyncha: Coccoidea) are one of the most invasive and agriculturally damaging insect groups. Their management and the development of new control methods are currently jeopardized by the scarcity of identification data, in particular in regions where no large survey coupling morphological and DNA analyses have been performed. In this study, we sampled 116 populations of armored scales (Hemiptera: Diaspididae) and 112 populations of soft scales (Hemiptera: Coccidae) in Chile, over a latitudinal gradient ranging from 18°S to 41°S, on fruit crops, ornamental plants and trees. We sequenced the COI and 28S genes in each population. In total, 19 Diaspididae species and 11 Coccidae species were identified morphologically. From the 63 COI haplotypes and the 54 28S haplotypes uncovered, and using several DNA data analysis methods (Automatic Barcode Gap Discovery, K2P distance, NJ trees), up to 36 genetic clusters were detected. Morphological and DNA data were congruent, except for three species (Aspidiotus nerii, Hemiberlesia rapax and Coccus hesperidum) in which DNA data revealed highly differentiated lineages. More than 50% of the haplotypes obtained had no high-scoring matches with any of the sequences in the GenBank database. This study provides 63 COI and 54 28S barcode sequences for the identification of Coccoidea from Chile.
Observational Evidence for Desert Amplification Using Multiple Satellite Datasets
Authors: Wei Nan , Zhou Liming , Dai Yongjiu , Xia Geng , Hua Wenjian 
Published: May 2017

AbstractDesert amplification identified in recent studies has large uncertainties due to data paucity over remote deserts. Here we present observational evidence using multiple satellite-derived datasets that desert amplification is a real large-scale pattern of warming mode in near surface and low-tropospheric temperatures. Trend analyses of three long-term temperature products consistently confirm that near-surface warming is generally strongest over the driest climate regions and this spatial pattern of warming maximizes near the surface, gradually decays with height, and disappears in the upper troposphere. Short-term anomaly analyses show a strong spatial and temporal coupling of changes in temperatures, water vapor and downward longwave radiation (DLR), indicating that the large increase in DLR drives primarily near surface warming and is tightly associated with increasing water vapor over deserts. Atmospheric soundings of temperature and water vapor anomalies support the results of the long-term temperature trend analysis and suggest that desert amplification is due to comparable warming and moistening effects of the troposphere. Likely, desert amplification results from the strongest water vapor feedbacks near the surface over the driest deserts, where the air is very sensitive to changes in water vapor and thus efficient in enhancing the longwave greenhouse effect in a warming climate.
Kv3.4 is modulated by HIF-1α to protect SH-SY5Y cells against oxidative stress-induced neural cell death
Authors: Song Min Seok , Ryu Pan Dong , Lee So Yeong 
Published: May 2017

AbstractThe Kv3.4 channel is characterized by fast inactivation and sensitivity to oxidation. However, the physiological role of Kv3.4 as an oxidation-sensitive channel has yet to be investigated. Here, we demonstrate that Kv3.4 plays a pivotal role in oxidative stress-related neural cell damage as an oxidation-sensitive channel and that HIF-1α down-regulates Kv3.4 function, providing neuroprotection. MPP+ and CoCl2 are reactive oxygen species (ROS)-generating reagents that induce oxidative stress. However, only CoCl2 decreases the expression and function of Kv3.4. HIF-1α, which accumulates in response to CoCl2 treatment, is a key factor in Kv3.4 regulation. In particular, mitochondrial Kv3.4 was more sensitive to CoCl2. Blocking Kv3.4 function using BDS-II, a Kv3.4-specific inhibitor, protected SH-SY5Y cells against MPP+-induced neural cell death. Kv3.4 inhibition blocked MPP+-induced cytochrome c release from the mitochondrial intermembrane space to the cytosol and mitochondrial membrane potential depolarization, which are characteristic features of apoptosis. Our results highlight Kv3.4 as a possible new therapeutic paradigm for oxidative stress-related diseases, including Parkinson’s disease.
The complex tibial organ of the New Zealand ground weta: sensory adaptations for vibrational signal detection
Authors: Strauß Johannes , Lomas Kathryn , Field Laurence H. 
Published: May 2017

AbstractIn orthopteran insects, a complex tibial organ has evolved to detect substrate vibrations and/or airborne sound. Species of New Zealand weta (Anostostomatidae) with tympanal ears on the foreleg tibia use this organ to communicate by sound, while in atympanate species (which communicate by substrate drumming) the organ is unstudied. We investigated the complex tibial organ of the atympanate ground weta, Hemiandrus pallitarsis, for vibration detection adaptations. This system contains four sensory components (subgenual organ, intermediate organ, crista acustica homolog, accessory organ) in all legs, together with up to 90 scolopidial sensilla. Microcomputed tomography shows that the subgenual organ spans the hemolymph channel, with attachments suggesting that hemolymph oscillations displace the organ in a hinged-plate fashion. Subgenual sensilla are likely excited by substrate oscillations transmitted within the leg. Instead of the usual suspension within the middle of the tibial cavity, we show that the intermediate organ and crista acustica homolog comprise a cellular mass broadly attached to the anterior tibial wall. They likely detect cuticular vibrations, and not airborne sound. This atympanate complex tibial organ shows elaborate structural changes suggesting detection of vibrational stimuli by parallel input pathways, thus correlating well with the burrowing lifestyle and communication by substrate-transmitted vibration.
HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
Authors: Jäger Daniela , Barth Thomas F. E. , Brüderlein Silke , Scheuerle Angelika , Rinner Beate , von Witzleben Adrian , Lechel André , Meyer Patrick , Mayer-Steinacker Regine , Baer Alexandra von , Schultheiss Markus , Wirtz Christian R. , Möller Peter , Mellert Kevin 
Published: May 2017

AbstractChordomas are rare tumours of the bone arising along the spine from clivus to sacrum. We compared three chordoma cell lines of the clivus region including the newly established clivus chordoma cell line, U-CH14, with nine chordoma cell lines originating from sacral primaries by morphology, on genomic and expression levels and with patient samples from our chordoma tissue bank. Clinically, chordomas of the clivus were generally smaller in size at presentation and patients with sacral chordomas had more metastases and more often recurrent disease. All chordoma cell lines had a typical physaliphorous morphology and expressed brachyury, S100-protein and cytokeratin. By expression analyses we detected differentially expressed genes in the clivus derived cell lines as compared to the sacral cell lines. Among these were HOXA7, HOXA9, and HOXA10 known to be important for the development of the anterior-posterior body axis. These results were confirmed by qPCR. Immunohistologically, clivus chordomas had no or very low levels of HOXA10 protein while sacral chordomas showed a strong nuclear positivity in all samples analysed. This differential expression of HOX genes in chordomas of the clivus and sacrum suggests an oncofetal mechanism in gene regulation linked to the anatomic site.