bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modularity and predicted functions of the global sponge-microbiome network
Authors: Lurgi Miguel , Thomas Torsten , Wemheuer Bernd , Webster Nicole S. , Montoya Jose M. 
Published: March 2019

AbstractDefining the organisation of species interaction networks and unveiling the processes behind their assembly is fundamental to understanding patterns of biodiversity, community stability and ecosystem functioning. Marine sponges host complex communities of microorganisms that contribute to their health and survival, yet the mechanisms behind microbiome assembly are largely unknown. We present the global marine sponge–microbiome network and reveal a modular organisation in both community structure and function. Modules are linked by a few sponge species that share microbes with other species around the world. Further, we provide evidence that abiotic factors influence the structuring of the sponge microbiome when considering all microbes present, but biotic interactions drive the assembly of more intimately associated ‘core’ microorganisms. These findings suggest that both ecological and evolutionary processes are at play in host-microbe network assembly. We expect mechanisms behind microbiome assembly to be consistent across multicellular hosts throughout the tree of life.
Precipitation strengthening in an ultralight magnesium alloy
Authors: Tang Song , Xin Tongzheng , Xu Wanqiang , Miskovic David , Sha Gang , Quadir Zakaria , Ringer Simon , Nomoto Keita , Birbilis Nick , Ferry Michael 
Published: March 2019

AbstractBody-centred cubic magnesium-lithium-aluminium-base alloys are the lightest of all the structural alloys, with recently developed alloy compositions showing a unique multi-dimensional property profile. By hitherto unrecognised mechanisms, such alloys also exhibit exceptional immediate strengthening after solution treatment and water quenching, but strength eventually decreases during prolonged low temperature ageing. We show that such phenomena are due to the precipitation of semi-coherent D03-Mg3Al nanoparticles during rapid cooling followed by gradual coarsening and subsequent loss of coherency. Physical explanation of these phenomena allowed the creation of an exceptionally low-density alloy that is also structurally stable by controlling the lattice mismatch and volume fraction of the Mg3Al nanoparticles. The outcome is one of highest specific-strength engineering alloys ever developed.
RETRACTED ARTICLE: Atomic insight into hydration shells around facetted nanoparticles
Authors: Thomä Sabrina L. J. , Krauss Sebastian W. , Eckardt Mirco , Chater Phil , Zobel Mirijam 
Published: March 2019

AbstractNanoparticles in solution interact with their surroundings via hydration shells. Although the structure of these shells is used to explain nanoscopic properties, experimental structural insight is still missing. Here we show how to access the hydration shell structures around colloidal nanoparticles in scattering experiments. For this, we synthesize variably functionalized magnetic iron oxide nanoparticle dispersions. Irrespective of the capping agent, we identify three distinct interatomic distances within 2.5 Å from the particle surface which belong to dissociatively and molecularly adsorbed water molecules, based on theoretical predictions. A weaker restructured hydration shell extends up to 15 Å. Our results show that the crystal structure dictates the hydration shell structure. Surprisingly, facets of 7 and 15 nm particles behave like planar surfaces. These findings bridge the large gap between spectroscopic studies on hydrogen bond networks and theoretical advances in solvation science.
A multi-task convolutional deep neural network for variant calling in single molecule sequencing
Authors: Luo Ruibang , Sedlazeck Fritz J. , Lam Tak-Wah , Schatz Michael C. 
Published: March 2019

AbstractThe accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule sequencing, which has a per-nucleotide error rate of ~5–15%. Meeting this demand, we developed Clairvoyante, a multi-task five-layer convolutional neural network model for predicting variant type (SNP or indel), zygosity, alternative allele and indel length from aligned reads. For the well-characterized NA12878 human sample, Clairvoyante achieves 99.67, 95.78, 90.53% F1-score on 1KP common variants, and 98.65, 92.57, 87.26% F1-score for whole-genome analysis, using Illumina, PacBio, and Oxford Nanopore data, respectively. Training on a second human sample shows Clairvoyante is sample agnostic and finds variants in less than 2 h on a standard server. Furthermore, we present 3,135 variants that are missed using Illumina but supported independently by both PacBio and Oxford Nanopore reads. Clairvoyante is available open-source (https://github.com/aquaskyline/Clairvoyante), with modules to train, utilize and visualize the model.
Coexistence of metallic and nonmetallic properties in the pyrochlore Lu2Rh2O7
Authors: Hallas Alannah M. , Sharma Arzoo Z. , Mauws Cole , Chen Qiang , Zhou Haidong D. , Ding Cui , Gong Zizhou , Tachibana Makoto , Sarte Paul M. , Attfield J. Paul , Luke Graeme M. , Wiebe Christopher R. 
Published: March 2019

AbstractTransition metal oxides of the 4d and 5d block have recently become the targets of materials discovery, largely due to their strong spin–orbit coupling that can generate exotic magnetic and electronic states. Here, we report the high-pressure synthesis of Lu2Rh2O7, a new cubic pyrochlore oxide based on 4d5 Rh4+, and characterizations via thermodynamic, electrical transport, and muon spin relaxation measurements. Magnetic susceptibility measurements reveal a large temperature-independent Pauli paramagnetic contribution, while heat capacity shows an enhanced Sommerfeld coefficient, γ = 21.8(1) mJ/mol-Rh K2. Muon spin relaxation measurements confirm that Lu2Rh2O7 remains paramagnetic down to 2 K. Taken in combination, these three measurements suggest that Lu2Rh2O7 is a correlated paramagnetic metal with a Wilson ratio of RW = 2.5. However, electric transport measurements present a striking contradiction as the resistivity of Lu2Rh2O7 is observed to monotonically increase with decreasing temperature, indicative of a nonmetallic state. Furthermore, although the magnitude of the resistivity is that of a semiconductor, the temperature dependence does not obey any conventional form. Thus, we propose that Lu2Rh2O7 may belong to the same novel class of non-Fermi liquids as the nonmetallic metal FeCrAs.
Direct stimulation of somatosensory cortex results in slower reaction times compared to peripheral touch in humans
Authors: Caldwell David J. , Cronin Jeneva A. , Wu Jing , Weaver Kurt E. , Ko Andrew L. , Rao Rajesh P. N. , Ojemann Jeffrey G. 
Published: March 2019

AbstractDirect cortical stimulation (DCS) of primary somatosensory cortex (S1) could help restore sensation and provide task-relevant feedback in a neuroprosthesis. However, the psychophysics of S1 DCS is poorly studied, including any comparison to cutaneous haptic stimulation. We compare the response times to DCS of human hand somatosensory cortex through electrocorticographic grids with response times to haptic stimuli delivered to the hand in four subjects. We found that subjects respond significantly slower to S1 DCS than to natural, haptic stimuli for a range of DCS train durations. Median response times for haptic stimulation varied from 198 ms to 313 ms, while median responses to reliably perceived DCS ranged from 254 ms for one subject, all the way to 528 ms for another. We discern no significant impact of learning or habituation through the analysis of blocked trials, and find no significant impact of cortical stimulation train duration on response times. Our results provide a realistic set of expectations for latencies with somatosensory DCS feedback for future neuroprosthetic applications and motivate the study of neural mechanisms underlying human perception of somatosensation via DCS.
Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings
Authors: Hwang Kyu-Baek , Lee In-Hee , Li Honglan , Won Dhong-Geon , Hernandez-Ferrer Carles , Negron Jose Alberto , Kong Sek Won 
Published: March 2019

AbstractComprehensive and accurate detection of variants from whole-genome sequencing (WGS) is a strong prerequisite for translational genomic medicine; however, low concordance between analytic pipelines is an outstanding challenge. We processed a European and an African WGS samples with 70 analytic pipelines comprising the combination of 7 short-read aligners and 10 variant calling algorithms (VCAs), and observed remarkable differences in the number of variants called by different pipelines (max/min ratio: 1.3~3.4). The similarity between variant call sets was more closely determined by VCAs rather than by short-read aligners. Remarkably, reported minor allele frequency had a substantial effect on concordance between pipelines (concordance rate ratio: 0.11~0.92; Wald tests, P < 0.001), entailing more discordant results for rare and novel variants. We compared the performance of analytic pipelines and pipeline ensembles using gold-standard variant call sets and the catalog of variants from the 1000 Genomes Project. Notably, a single pipeline using BWA-MEM and GATK-HaplotypeCaller performed comparable to the pipeline ensembles for ‘callable’ regions (~97%) of the human reference genome. While a single pipeline is capable of analyzing common variants in most genomic regions, our findings demonstrated the limitations and challenges in analyzing rare or novel variants, especially for non-European genomes.
Prospects for Bioinspired Single-Photon Detection Using Nanotube-Chromophore Hybrids
Authors: Léonard François , Foster Michael E. , Spataru Catalin D. 
Published: March 2019

AbstractThe human eye is an exquisite photodetection system with the ability to detect single photons. The process of vision is initiated by single-photon absorption in the molecule retinal, triggering a cascade of complex chemical processes that eventually lead to the generation of an electrical impulse. Here, we analyze the single-photon detection prospects for an architecture inspired by the human eye: field-effect transistors employing carbon nanotubes functionalized with chromophores. We employ non-equilibrium quantum transport simulations of realistic devices to reveal device response upon absorption of a single photon. We establish the parameters that determine the strength of the response such as the magnitude and orientation of molecular dipole(s), as well as the arrangements of chromophores on carbon nanotubes. Moreover, we show that functionalization of a single nanotube with multiple chromophores allows for number resolution, whereby the number of photons in an incoming light packet can be determined. Finally, we assess the performance prospects by calculating the dark count rate, and we identify the most promising architectures and regimes of operation.
Genetic and evolutionary analysis of a new Asia-4 lineage and naturally recombinant canine distemper virus strains from Thailand
Authors: Piewbang Chutchai , Radtanakatikanon Araya , Puenpa Jiratchaya , Poovorawan Yong , Techangamsuwan Somporn 
Published: March 2019

AbstractCanine distemper virus (CDV), a pathogen causing fatal disease in a wide range of carnivores, can be classified into several geographically-related lineages. It is unclear how genetic recombination contributed to the evolution and emergence of the novel CDV strains and the evolutions of these strains are not fully yet investigated. In this study, the complete genome sequences of eight CDV viruses, isolated from domestic dogs in Thailand, were investigated. Interestingly, most of the identified CDV strains (CDV1-3, -5, -8 TH/2014) clustered as a novel Asia-4 lineage, while the CDV4, -6, -7 TH/2014 belonged to the Asia-1 lineage. Recombination analysis revealed that the CDV4 TH/2014 is a putative recombinant virus from the Asia-1 and America-2 parent viruses. In contrast, no recombination events were detected in the Asia-4 lineage, indicating that it is a distinctive lineage. Evolutionary analysis suggested that the CDV Asia-4 lineage had emerged since 1924 and shared common ancestor with the America-2 lineage. Pressure analysis revealed that CDV nucleotides were under negative selection pressure for its rapid adaptation. These findings demonstrate the evolution of CDV Asia-4 lineage and identified the Asia-1 recombination event. The information regarding genetic diversity of CDVs is essential for further CDV’s research and monitoring.
Dynamic Concatenation of Quantum Error Correction in Integrated Quantum Computing Architecture
Authors: Sohn Ilkwon , Bang Jeongho , Heo Jun 
Published: March 2019

AbstractResource overhead problem caused by concatenation in quantum error correction (QEC) is of significant importance for the realization of fault-tolerant quantum computation (FTQC). To attack this problem, we propose a novel scheme by considering integrated FTQC architecture where the concatenation level is controlled dynamically; i.e., less (or more) concatenation levels are imposed by good (or poor) performance gates—we call this scheme “dynamic concatenation” in this sense. Such a dynamic concatenation is realizable in an integrated structure of FTQC, as the information of the concatenation can be communicated between classical system elements (e.g., compiler and system organizer) and the logical qubits in real-time. We derive the effective lower and upper bounds of the length of gate decomposition in order to achieve the practical advantage, namely of reduction of the overall operation time. By considering two non-trivial examples, it is shown that the aforementioned advantage can indeed be achieved in the presented scheme. Our result also provides an important scientific message, i.e., the interplay between “classical” and “quantum” can be helpful in QEC.
Metabolic effects of leptin receptor knockdown or reconstitution in adipose tissues
Authors: Pereira Sandra , O’Dwyer Shannon M. , Webber Travis D. , Baker Robert K. , So Victor , Ellis Cara E. , Yoon Ji Soo , Mojibian Majid , Glavas Maria M. , Karunakaran Subashini , Clee Susanne M. , Covey Scott D. , Kieffer Timothy J. 
Published: March 2019

AbstractThe relative contribution of peripheral and central leptin signalling to the regulation of metabolism and the mechanisms through which leptin affects glucose homeostasis have not been fully elucidated. We generated complementary lines of mice with either leptin receptor (Lepr) knockdown or reconstitution in adipose tissues using Cre-lox methodology. Lepr knockdown mice were modestly lighter and had lower plasma insulin concentrations following an oral glucose challenge compared to controls, despite similar insulin sensitivity. We rendered male mice diabetic using streptozotocin (STZ) and found that upon prolonged leptin therapy, Lepr knockdown mice had an accelerated decrease in blood glucose compared to controls that was associated with higher plasma concentrations of leptin and leptin receptor. Mice with transcriptional blockade of Lepr (LeprloxTB/loxTB) were obese and hyperglycemic and reconstitution of Lepr in adipose tissues of LeprloxTB/loxTB mice resulted in males reaching a higher maximal body weight. Although mice with adipose tissue Lepr reconstitution had lower blood glucose levels at several ages, their plasma insulin concentrations during an oral glucose test were elevated. Thus, attenuation or restoration of Lepr in adipocytes alters the plasma insulin profile following glucose ingestion, modifies the glucose-lowering effect of prolonged leptin therapy in insulin-deficient diabetes, and may modulate weight gain.
Optimized pupal age of Tenebrio molitor L. (Coleoptera: Tenebrionidae) enhanced mass rearing efficiency of Chouioia cunea Yang (Hymenoptera: Eulophidae)
Authors: Li Tian-Hao , Che Peng-Fei , Yang Xiangbing , Song Li-Wei , Zhang Chao-Ran , Benelli Giovanni , Desneux Nicolas , Zang Lian-Sheng 
Published: March 2019

AbstractChouioia cunea Yang (Hymenoptera: Eulophidae) has been widely used for biological control of the fall webworm, Hyphantria cunea (Drury) (Lepidoptera: Arctiidae), in China. The yellow mealworm, Tenebrio molitor L. (Coleoptera: Tenebrionidae), an important resource insect species distributed worldwide, is considered to be a potential alternative host for mass rearing of C. cunea to the Chinese oak silkworm, Antheraea pernyi (Guerin-Meneville) (Lepidoptera: Saturniidae), which is currently used. In this study, we investigated the effects of host age on C. cunea mass rearing by measuring parasitism, development and adult fertility of C. cunea on T. molitor pupae of different ages. The results showed no significant differences in the percentage of parasitized hosts and developmental time of C. cunea in pupae of different ages. However, the number of C. cunea adults (137.2–154.7 adults per host) that emerged from 0, 1, and 2-day-old pupae was significantly higher than that from 4-day-old pupae. The lowest percentages of unemerged adults were found in 2-day-old (1.2%) and 3-day-old (1.4%) pupae, which were significantly lower than that of 4-day-old pupae (10.3%). The emergence of adult females from 0 to 2-day-old pupae (120.2–142.3 per pupa) was significantly higher than that from 4-day-old hosts (64.6). Adult females emerging from 2-day-old pupae carried significantly more eggs (258.2 eggs/female) than those from 0 and 1-day-old pupae (178.4–178.9 eggs/female). Our findings indicated that 2-day-old pupae of T. molitor were most suitable to rear C. cunea. Overall, this research provided valuable information to optimize pupae for the mass rearing of C. cunea on host T. molitor.
Temporal relationship between perceptual and physiological events triggered by nociceptive heat stimuli
Authors: Castellote J. M. , Valls-Solé J. 
Published: March 2019

AbstractA combined assessment tool for the perceptual-motor aspects of pain processing will be valuable to clinicians. Fifteen healthy subjects were exposed to contact-heat stimulation (Pathway, Medoc, Israel) to assess perception through a simple task (motor response or conscious appraisal of the time the stimulus was felt) or with a dual task (both responses). The outcome measure was the temporal relationship between contact heat evoked potentials (CHEPS), reaction time (RT) and conscious awareness (AW). There were different temporal profiles for CHEPs, RT and AW to changes in stimulus intensity, AW being the least affected. Performing the dual task led to a significantly more pronounced effect on RT than on AW, while CHEPS were not influenced by task performance. Our results support the dissociation between physiological, behavioral and cognitive events elicited by nociceptive stimuli. The time of conscious appraisal of stimulus occurrence is a complementary information to other responses such as evoked potentials or behavioral tasks. The combined assessment of physiological and behavioral aspects of pain processing may provide clinicians with information on the different paths followed by nociceptive afferent inputs in the central nervous system.
Pelota-interacting G protein Hbs1 is required for spermatogenesis in Drosophila
Authors: Li Zhaohui , Yang Fu , Xuan Yang , Xi Rongwen , Zhao Rui 
Published: March 2019

AbstractHbs1, which is homologous to the GTPase eRF3, is a small G protein implicated in mRNA quality control. It interacts with a translation-release factor 1-like protein Dom34/Pelota to direct decay of mRNAs with ribosomal stalls. Although both proteins are evolutionarily conserved in eukaryotes, the biological function of Hbs1 in multicellular organisms is yet to be characterized. In Drosophila, pelota is essential for the progression through meiosis during spermatogenesis and germline stem cell maintenance. Here we show that homozygous Hbs1 mutant flies are viable, female-fertile, but male-sterile, which is due to defects in meiosis and spermatid individualization, phenotypes that are also observed in pelota hypomorphic mutants. In contrast, Hbs1 mutants have no obvious defects in germline stem cell maintenance. We show that Hbs1 genetically interacts with pelota during spermatid individualization. Furthermore, Pelota with a point mutation on the putative Hbs1-binding site cannot substitute the wild type protein for normal spermatogenesis. These data suggest that Pelota forms a complex with Hbs1 to regulate multiple processes during spermatogenesis. Our results reveal a specific requirement of Hbs1 in male gametogenesis in Drosophila and indicate an essential role for the RNA surveillance complex Pelota-Hbs1 in spermatogenesis, a function that could be conserved in mammals.
A Portion of the Apomixis Locus of Paspalum Simplex is Microsyntenic with an Unstable Chromosome Segment Highly Conserved Among Poaceae
Authors: Galla Giulio , Siena Lorena A. , Ortiz Juan Pablo A. , Baumlein Helmut , Barcaccia Gianni , Pessino Silvina C. , Bellucci Michele , Pupilli Fulvio 
Published: March 2019

AbstractThe introgression of apomixis in major seed crops, would guarantee self-seeding of superior heterotic seeds over generations. In the grass speciesPaspalum simplex, apomixis is controlled by a single locus in which recombination is blocked. In the perspective of isolating the genetic determinants of apomixis, we report data on sequencing,in silicomapping and expression analysis of some of the genes contained in two cloned genomic regions of the apomixis locus ofP.simplex.In silicomapping allowed us to identify a conserved synteny group homoeologous to the apomixis locus, located on a telomeric position of chromosomes 12, 8, 3 and 4 of rice,Sorghum bicolor,Setaria italicaandBrachypodium distachyum, respectively, and on a more centromeric position of maize chromosome 1. Selected genes of the apomixis locus expressed sense and antisense transcripts in reproductively committed cells of sexual and apomictic ovules. Some of the genes considered here expressed apomixis-specific allelic variants which showed partial non-overlapping expression patterns with alleles shared by sexual and apomictic reproductive phenotypes. Our findings open new routes for the isolation of the genetic determinants of apomixis and, in perspective, for its introgression in crop grasses.
Evaluation of focal damage in the retinal pigment epithelium layer in serous retinal pigment epithelium detachment
Authors: Miura Masahiro , Makita Shuichi , Azuma Shinnosuke , Yasuno Yoshiaki , Ueda Shunichiro , Sugiyama Satoshi , Mino Toshihiro , Yamaguchi Tatsuo , Sandhu Harpal S. , Kaplan Henry J. , Iwasaki Takuya , Goto Hiroshi 
Published: March 2019

AbstractThe purpose of this study was to evaluate focal damage in the retinal pigment epithelium (RPE) layer in serous retinal pigment epithelium detachment (PED) with multi-contrast optical coherence tomography (OCT), which is capable of simultaneous measurement of OCT angiography, polarization-sensitive OCT and standard OCT images. We evaluated 37 eyes with age-related macular degeneration that had serous PED. Focal RPE damage was indicated by hyper-transmission beneath the RPE-Bruch’s membrane band in standard OCT images. Distribution of RPE melanin was calculated using the dataset from multi-contrast OCT. Twenty-four points with hyper-transmission were detected in 21 of the 37 eyes. Standard OCT images failed to show disruption of the RPE-Bruch’s membrane band at 5 of the 24 hyper-transmission points. Conversely, multi-contrast OCT images clearly showed melanin defects in the RPE-Bruch’s membrane band at all points. Areas of melanin defects with disruption of the RPE-Bruch’s membrane band were significantly larger than those without disruption. The volume of intraretinal hyper-reflective foci was significantly larger in eyes with hyper-transmission than that in eyes without hyper-transmission. Multi-contrast OCT is more sensitive than standard OCT for displaying changes at the RPE-Bruch’s membrane band when there are small areas of RPE damage.