bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tides in the Last Interglacial: insights from notch geometry and palaeo tidal models in Bonaire, Netherland Antilles
Authors: Lorscheid Thomas , Felis Thomas , Stocchi Paolo , Obert J. Christina , Scholz Denis , Rovere Alessio 
Published: November 2017

AbstractThe study of past sea levels relies largely on the interpretation of sea-level indicators. Palaeo tidal notches are considered as one of the most precise sea-level indicators as their formation is closely tied to the local tidal range. We present geometric measurements of modern and palaeo (Marine Isotope Stage (MIS) 5e) tidal notches on Bonaire (southern Caribbean Sea) and results from two tidal simulations, using the present-day bathymetry and a palaeo-bathymetry. We use these two tools to investigate changes in the tidal range since MIS 5e. Our models show that the tidal range changes most significantly in shallow areas, whereas both, notch geometry and models results, suggest that steeper continental shelves, such as the ones bordering the island of Bonaire, are less affected to changes in tidal range in conditions of MIS 5e sea levels. We use our data and results to discuss the importance of considering changes in tidal range while reconstructing MIS 5e sea level histories, and we remark that it is possible to use hydrodynamic modelling and notch geometry as first-order proxies to assess whether, in a particular area, tidal range might have been different in MIS 5e with respect to today.
Driver pattern identification over the gene co-expression of drug response in ovarian cancer by integrating high throughput genomics data
Authors: Lu Xinguo , Lu Jibo , Liao Bo , Li Xing , Qian Xin , Li Keqin 
Published: November 2017

AbstractMultiple types of high throughput genomics data create a potential opportunity to identify driver patterns in ovarian cancer, which will acquire some novel and clinical biomarkers for appropriate diagnosis and treatment to cancer patients. To identify candidate driver genes and the corresponding driving patterns for resistant and sensitive tumors from the heterogeneous data, we combined gene co-expression modules with mutation modulators and proposed the method to identify driver patterns. Firstly, co-expression network analysis is applied to explore gene modules for gene expression profiles through weighted correlation network analysis (WGCNA). Secondly, mutation matrix is generated by integrating the CNV data and somatic mutation data, and a mutation network is constructed from the mutation matrix. Thirdly, candidate modulators are selected from significant genes by clustering vertexs of the mutation network. Finally, a regression tree model is utilized for module network learning, in which the obtained gene modules and candidate modulators are trained for the driving pattern identification and modulators regulatory exploration. Many identified candidate modulators are known to be involved in biological meaningful processes associated with ovarian cancer, such as CCL11, CCL16, CCL18, CCL23, CCL8, CCL5, APOB, BRCA1, SLC18A1, FGF22, GADD45B, GNA15, GNA11, and so on.
Should we screen for the sexually-transmitted infection Mycoplasma genitalium? Evidence synthesis using a transmission-dynamic model
Authors: Birger Ruthie , Saunders John , Estcourt Claudia , Sutton Andrew John , Mercer Catherine H. , Roberts Tracy , White Peter J. 
Published: November 2017

AbstractThere is increasing concern about Mycoplasma genitalium as a cause of urethritis, cervicitis, pelvic inflammatory disease (PID), infertility and ectopic pregnancy. Commercial nucleic acid amplification tests (NAATs) are becoming available, and their use in screening for M. genitalium has been advocated, but M. genitalium’s natural history is poorly-understood, making screening’s effectiveness unclear. We used a transmission-dynamic compartmental model to synthesise evidence from surveillance data and epidemiological and behavioural studies to better understand M. genitalium’s natural history, and then examined the effects of implementing NAAT testing. Introducing NAAT testing initially increases diagnoses, by finding a larger proportion of infections; subsequently the diagnosis rate falls, due to reduced incidence. Testing only symptomatic patients finds relatively little infection in women, as a large proportion is asymptomatic. Testing both symptomatic and asymptomatic patients has a much larger impact and reduces cumulative PID incidence in women due to M. genitalium by 31.1% (95% range:13.0%-52.0%) over 20 years. However, there is important uncertainty in M. genitalium’s natural history parameters, leading to uncertainty in the absolute reduction in PID and sequelae. Empirical work is required to improve understanding of key aspects of M. genitalium’s natural history before it will be possible to determine the effectiveness of screening.
Orthrozanclus elongata n. sp. and the significance of sclerite-covered taxa for early trochozoan evolution
Authors: Zhao Fangchen , Smith Martin R. , Yin Zongjun , Zeng Han , Li Guoxiang , Zhu Maoyan 
Published: November 2017

AbstractOrthrozanclus is a shell-bearing, sclerite covered Cambrian organism of uncertain taxonomic affinity, seemingly representing an intermediate between its fellow problematica Wiwaxia and Halkieria. Attempts to group these slug-like taxa into a single ‘halwaxiid’ clade nevertheless present structural and evolutionary difficulties. Here we report a new species of Orthrozanclus from the early Cambrian Chengjiang Lagerstätte. The scleritome arrangement and constitution in this material corroborates the link between Orthrozanclus and Halkieria, but not with Wiwaxia — and calls into question its purported relationship with molluscs. Instead, the tripartite construction of the halkieriid scleritome finds a more compelling parallel in the camenellan tommotiids, relatives of the brachiopods and phoronids. Such a phylogenetic position would indicate the presence of a scleritome in the common ancestor of the three major trochozoan lineages, Mollusca, Annelida and Brachiozoa. On this view, the absence of fossil Ediacaran sclerites is evidence against any ‘Precambrian prelude’ to the explosive diversification of these phyla in the Cambrian, c. 540–530 million years ago.
Pulsed Corona Discharge Induced Hydroxyl Radical Transfer Through the Gas-Liquid Interface
Authors: Ajo Petri , Kornev Iakov , Preis Sergei 
Published: November 2017

AbstractThe highly energetic electrons in non-thermal plasma generated by gas phase pulsed corona discharge (PCD) produce hydroxyl (OH) radicals via collision reactions with water molecules. Previous work has established that OH radicals are formed at the plasma-liquid interface, making it an important location for the oxidation of aqueous pollutants. Here, by contacting water as aerosol with PCD plasma, it is shown that OH radicals are produced on the gas side of the interface, and not in the liquid phase. It is also demonstrated that the gas-liquid interfacial boundary poses a barrier for the OH radicals, one they need to cross for reactive affinity with dissolved components, and that this process requires a gaseous atomic H scavenger. For gaseous oxidation, a scavenger, oxygen in common cases, is an advantage but not a requirement. OH radical efficiency in liquid phase reactions is strongly temperature dependent as radical termination reaction rates increase with temperature.
The microbiomes of blowflies and houseflies as bacterial transmission reservoirs
Authors: Junqueira Ana Carolina M. , Ratan Aakrosh , Acerbi Enzo , Drautz-Moses Daniela I. , Premkrishnan Balakrishnan N. V. , Costea Paul I. , Linz Bodo , Purbojati Rikky W. , Paulo Daniel F. , Gaultier Nicolas E. , Subramanian Poorani , Hasan Nur A. , Colwell Rita R. , Bork Peer , Azeredo-Espin Ana Maria L. , Bryant Donald A. , Schuster Stephan C. 
Published: November 2017

AbstractBlowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.
Visualising the 3D microstructure of stained and native intervertebral discs using X-ray microtomography
Authors: Disney C. M. , Madi K. , Bodey A. J. , Lee P. D. , Hoyland J. A. , Sherratt M. J. 
Published: November 2017

AbstractIntervertebral disc degeneration (IVDD) is linked to low back pain. Microstructural changes during degeneration have previously been imaged using 2D sectioning techniques and 3D methods which are limited to small specimens and prone to inducing artefacts from sample preparation. This study explores micro computed X-ray tomography (microCT) methods with the aim of resolving IVD 3D microstructure whilst minimising sample preparation artefacts. Low X-ray absorption contrast in non-mineralised tissue can be enhanced using staining and phase contrast techniques. A step-wise approach, including comparing three stains, was used to develop microCT for bovine tail IVD using laboratory and synchrotron sources. Staining successfully contrasted collagenous structures; however not all regions were stained and the procedure induced macroscopic structural changes. Phase contrast microCT of chemically fixed yet unstained samples resolved the nucleus pulposus, annulus fibrosus and constituent lamellae, and finer structures including collagen bundles and cross-bridges. Using the same imaging methods native tissue scans were of slightly lower contrast but free from sample processing artefacts. In the future these methods may be used to characterise structural remodelling in soft (non-calcified) tissues and to conduct in situ studies of native loaded tissues and constructs to characterise their 3D mechanical properties.
No evidence for social immunity in co-founding queen associations
Authors: Brütsch Timothée , Avril Amaury , Chapuisat Michel 
Published: November 2017

AbstractAnt queens often associate to found new colonies, yet the benefits of this behaviour remain unclear. A major hypothesis is that queens founding in groups are protected by social immunity and can better resist disease than solitary queens, due to mutual grooming, sharing of antimicrobials, or higher genetic diversity among their workers. We tested this hypothesis by manipulating the number of queens in incipient colonies of Lasius niger and measuring their resistance to the fungal entomopathogen Metarhizium brunneum. We found no evidence for social immunity in associations of founding queens. First, co-founding queens engaged in self-grooming, but performed very little allo-grooming or trophallaxis. Second, co-founding queens did not exhibit higher pathogen resistance than solitary queens, and their respective workers did not differ in disease resistance. Finally, queens founding in groups increased their investment in a component of individual immunity, as expected if they do not benefit from social immunity but respond to a higher risk of disease. Overall, our results provide no evidence that joint colony founding by L. niger queens increases their ability to resist fungal pathogens.
The responses of cancer cells to PLK1 inhibitors reveal a novel protective role for p53 in maintaining centrosome separation
Authors: Smith Linda , Farzan Raed , Ali Simak , Buluwela Laki , Saurin Adrian T. , Meek David W. 
Published: November 2017

AbstractPolo-like kinase-1 (PLK1) plays a major role in driving mitotic events, including centrosome disjunction and separation, and is frequently over-expressed in human cancers. PLK1 inhibition is a promising therapeutic strategy and works by arresting cells in mitosis due to monopolar spindles. The p53 tumour suppressor protein is a short-lived transcription factor that can inhibit the growth, or stimulate the death, of developing cancer cells. Curiously, although p53 normally acts in an anti-cancer capacity, it can offer significant protection against inhibitors of PLK1, but the events underpinning this effect are not known. Here, we show that functional p53 reduces the sensitivity to PLK1 inhibitors by permitting centrosome separation to occur, allowing cells to traverse mitosis and re-enter cycle with a normal complement of 2N chromosomes. Protection entails the activation of p53 through the DNA damage-response enzymes, ATM and ATR, and requires the phosphorylation of p53 at the key regulatory site, Ser15. These data highlight a previously unrecognised link between p53, PLK1 and centrosome separation that has therapeutic implications for the use of PLK1 inhibitors in the clinic.
Micro-gun based on laser pulse propulsion
Authors: Yu Haichao , Li Hanyang , Cui Lugui , Liu Shuangqiang , Yang Jun 
Published: November 2017

AbstractThis paper proposes a novel “micro-gun” structure for laser pulse propulsion. The “micro-bullets” (glass microspheres) are irradiated by a laser pulse with a 10 ns duration in a dynamic process. Experimental parameters such as the microsphere diameter and the laser pulse energy are varied to investigate their influence on laser pulse propulsion. The energy field and spatial intensity distribution in the capillary tube were simulated using a three-dimensional finite-difference time-domain method. The experimental results demonstrate that the propulsion efficiency is dependent on the laser pulse energy and the microsphere size. The propulsion modes and sources of the propelling force were confirmed through direct observation and theoretical calculation. Waves also generated by light-pressure and thermal expansions assisted the propulsion.
Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide
Authors: Cadby Ian T. , Faulkner Matthew , Cheneby Jeanne , Long Justine , van Helden Jacques , Dolla Alain , Cole Jeffrey A. 
Published: November 2017

AbstractThe sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative electron acceptors to sulfate to support growth. Like other sulphate reducing bacteria, it can also protect itself against nitrosative stress caused by NO generated when nitrite accumulates. By combining in vitro experiments with bioinformatic and RNA-seq data, metabolic responses to nitrate or NO and how nitrate and nitrite reduction are coordinated with the response to nitrosative stress were revealed. Although nitrate and nitrite reduction are tightly regulated in response to substrate availability, the global responses to nitrate or NO were largely regulated independently. Multiple NADH dehydrogenases, transcription factors of unknown function and genes for iron uptake were differentially expressed in response to electron acceptor availability or nitrosative stress. Amongst many fascinating problems for future research, the data revealed a YtfE orthologue, Ddes_1165, that is implicated in the repair of nitrosative damage. The combined data suggest that three transcription factors coordinate this regulation in which NrfS-NrfR coordinates nitrate and nitrite reduction to minimize toxicity due to nitrite accumulation, HcpR1 serves a global role in regulating the response to nitrate, and HcpR2 regulates the response to nitrosative stress.
A rapid flow strategy for the oxidative cyanation of secondary and tertiary amines via C-H activation
Authors: Tadele Kidus , Verma Sanny , Nadagouda Mallikarjuna N. , Gonzalez Michael A. , Varma Rajender S. 
Published: November 2017

AbstractAn efficient continuous flow protocol has been developed for bond C-H activation which promotes the α-cyanation of secondary and tertiary amines using magnetic nano-ferrites.
The steady enhancement of the Australian Summer Monsoon in the last 200 years
Authors: Gallego David , García-Herrera Ricardo , Peña-Ortiz Cristina , Ribera Pedro 
Published: November 2017

AbstractA new bicentennial series of the Australian monsoon strength based on historical wind observations has allowed for the assessment of the variability of this system since the early 19th century. Our series covers a period in which the scarcity of meteorological observations in the area had precluded the evaluation of long-term climatic trends. Results indicate that the increase in precipitation over Northern Australia reported for the last 60 years is just a manifestation of a much longer lasting trend related to the strengthening of the Australian monsoon that has been occurring since at least 1816.
Different diversity-dependent declines in speciation rate unbalances species richness in terrestrial slugs
Authors: Cunha Regina L. , Patrão Cláudia , Castilho Rita 
Published: November 2017

AbstractTwo genera of terrestrial slugs (Arion and Geomalacus) display a striking disproportion in species richness in the Iberian Peninsula. While there are 17 Iberian endemic species in Arion, morphological criteria only recognize four species within Geomalacus. Sequence data were used to test whether these differences could result from: (1) cryptic diversity within Geomalacus; (2) an earlier origin for Arion (older clades are expected to accumulate more species); (3) distinct patterns of diversification rates (higher initial speciation rates in Arion), and (4) some combination of the above factors (e.g., an older clade with higher speciation rates). Species delimitation tests based on mitochondrial and nuclear data revealed eight cryptic lineages within Geomalacus that lessened the asymmetry; nevertheless, the disparity required further investigation. No meaningful differences in crown group ages of each recovered clade were found. Regardless the different premises of the two equally plausible diversification models (similar initial speciation rates vs. higher initial speciation rates in Geomalacus), both coincide on diversity-dependent diversification for the two groups but weaker rate declines in Arion best explains the observed asymmetry in species richness. Also, the broader environmental tolerance combined with a faster dispersal and wider distribution may have represented an evolutionary advantage for Arion.
Reduced loss aversion in pathological gambling and alcohol dependence is associated with differential alterations in amygdala and prefrontal functioning
Authors: Genauck Alexander , Quester Saskia , Wüstenberg Torsten , Mörsen Chantal , Heinz Andreas , Romanczuk-Seiferth Nina 
Published: November 2017

AbstractDiagnostic criteria for pathological gambling and alcohol dependence (AD) include repeated addictive behavior despite severe negative consequences. However, the concept of loss aversion (LA) as a facet of value-based decision making has not yet been used to directly compare these disorders. We hypothesized reduced LA in pathological gamblers (PG) and AD patients, correlation of LA with disorder severity, and reduced loss-related modulation of brain activity. 19 PG subjects, 15 AD patients and 17 healthy controls (HC) engaged in a LA task in a functional magnetic resonance imaging setting. Imaging analyses focused on neural gain and loss sensitivity in the meso-cortico-limbic network of the brain. Both PG and AD subjects showed reduced LA. AD subjects showed altered loss-related modulation of activity in lateral prefrontal regions. PG subjects showed indication of altered amygdala-prefrontal functional connectivity. Although we observed reduced LA in both a behavioral addiction and a substance-related disorder our neural findings might challenge the notion of complete neuro-behavioral congruence of substance-use disorders and behavioral addictions.
Species composition and environmental adaptation of indigenous Chinese cattle
Authors: Gao Yahui , Gautier Mathieu , Ding Xiangdong , Zhang Hao , Wang Yachun , Wang Xi , Faruque MD Omar , Li Junya , Ye Shaohui , Gou Xiao , Han Jianlin , Lenstra Johannes A. , Zhang Yi 
Published: November 2017

AbstractIndigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.
Disrupted Brain Network in Children with Autism Spectrum Disorder
Authors: Zeng Ke , Kang Jiannan , Ouyang Gaoxiang , Li Jingqing , Han Junxia , Wang Yao , Sokhadze Estate M. , Casanova Manuel F. , Li Xiaoli 
Published: November 2017

AbstractAlterations in brain connectivity have been extensively reported in autism spectrum disorder (ASD), while their effects on the topology of brain network are still unclear. This study investigated whether and how the brain networks in children with ASD were abnormally organized with resting state EEG. Temporal synchronization analysis was first applied to capture the aberrant brain connectivity. Then brain network topology was characterized by three graph analysis methods including the commonly-used weighted and binary graph, as well as minimum spanning tree (MST). Whole brain connectivity in ASD group was found to be significantly reduced in theta and alpha band compared to typically development children (TD). Weighted graph found significantly decreased path length together with marginally significantly decreased clustering coefficient in ASD in alpha band, indicating a loss of small-world architecture to a random network. Such abnormal network topology was also demonstrated in the binary graph. In MST analysis, children with ASD showed a significant lower leaf fractions with a decrease trend of tree hierarchy in the alpha band, suggesting a shift towards line-like decentralized organization in ASD. The altered brain network may offer an insight into the underlying pathology of ASD and possibly serve as a biomarker that may aid in diagnosis of ASD.