bluuebunny/crossref_metadata_2025 huggingface dataset:
Controlling welding residual stress and distortion by a hybrid technology of transient thermal tensioning and trailing intensive cooling
Authors: Li Mingshen , Ji Shude , Yan Dejun , Yang Zhanpeng
Published: January 2019

A new method of hybrid technology for controlling welding residual stress and distortion is proposed, which contains the transient thermal tensioning with two symmetrical heat sources ahead and the trailing intensive cooling with a cooling source behind the welding heat source during the welding process. Welding temperature, stress and distortion were compared and discussed under different welding processes by experimental and numerical methods. The results reveal that the hybrid technology adjusted the temperature field during welding and redistributed the longitudinal residual stress of welding joint. Thus, the welding residual distortion was reduced. Compared with conventional metal inert gas welding, the reductions of the welding residual stress and distortion of joint by the hybrid technology reached 65% and 58%, respectively.
Multilocus phylogeny and a new classification for African, Asian and Indian supple and writhing skinks (Scincidae: Lygosominae)
Authors: Freitas Elyse S , Datta-Roy Aniruddha , Karanth Praveen , Grismer L Lee , Siler Cameron D
Published: January 2019

The genera Lepidothyris, Lygosoma and Mochlus comprise the writhing or supple skinks, a group of semi-fossorial, elongate-bodied skinks distributed across the Old World Tropics. Due to their generalized morphology and lack of diagnostic characters, species- and clade-level relationships have long been debated. Recent molecular phylogenetic studies of the group have provided some clarification of species-level relationships, but a number of issues regarding higher level relationships among genera still remain. Here we present a phylogenetic estimate of relationships among species in Lygosoma, Mochlus and Lepidothyris generated by concatenated and species tree analyses of multilocus data using the most extensive taxonomic sampling of the group to date. We also use multivariate statistics to examine species and clade distributions in morpho space. Our results reject the monophyly of Lygosoma s.l., Lygosoma s.s. and Mochlus, which highlights the instability of the current taxonomic classification of the group. We, therefore, revise the taxonomy of the writhing skinks to better reflect the evolutionary history of Lygosoma s.l. by restricting Lygosoma for Southeast Asia, resurrecting the genus Riopa for a clade of Indian and Southeast Asian species, expanding the genus Mochlus to include all African species of writhing skinks and describing a new genus in Southeast Asia.
Spatial Associations of Vines Infected With Grapevine Red Blotch Virus in Oregon Vineyards
Authors: Dalton Daniel T. , Hilton Richard J. , Kaiser Clive , Daane Kent M. , Sudarshana Mysore R. , Vo Julia , Zalom Frank G. , Buser Jessica Z. , Walton Vaughn M.
Published: January 2019

Spread and in-field spatial patterns of vines infected with grapevine red blotch virus (GRBV) were documented in Oregon vineyards using field sampling, molecular diagnostics, and spatial analysis. Grapevine petiole tissue collected from 2013 to 2016 was tested using quantitative polymerase chain reaction for GRBV. At Jacksonville in southern Oregon, 3.1% of vines were infected with GRBV in 2014, and GRBV incidence reached 58.5% of study vines by 2016. GRBV-infected plants and GRBV-uninfected plants were spatially aggregated at this site in 2015, and infected plants were spatially associated between years 2015 and 2016. In a southern Oregon vineyard near Talent, 10.4% of vines were infected with GRBV in 2014, and infection increased annually to 21.5% in 2016. At Talent, distribution of the infected vines was spatially associated across all years. GRBV infection was highest at Yamhill, in the Willamette Valley, where 31.7% of the tested vines had GRBV infection in 2014. By 2016, 59.2% of the vines tested positive for GRBV. Areas of aggregation increased and were spatially associated across all years. From 2013 to 2015, GRBV was not detected at Milton-Freewater in eastern Oregon. Spatial patterns of GRBV infection support evidence of spread by a mobile insect vector. GRBV is a significant threat to Oregon wine grape production because of its drastic year-over-year spread in affected vineyards.
The Psychopharmacology Algorithm Project at the Harvard South Shore Program: An Update on Unipolar Nonpsychotic Depression
Authors: Giakoumatos Christoforos Iraklis , Osser David
Published: January 2019

Background

The Psychopharmacology Algorithm Project at the Harvard South Shore Program presents evidence-based recommendations considering efficacy, tolerability, safety, and cost. Two previous algorithms for unipolar nonpsychotic depression were published in 1993 and 1998. New studies over the last 20 years suggest that another update is needed.

Methods

The references reviewed for the previous algorithms were reevaluated, and a new literature search was conducted to identify studies that would either support or alter the previous recommendations. Other guidelines and algorithms were consulted. We considered exceptions to the main algorithm, as for pregnant women and patients with anxious distress, mixed features, or common medical and psychiatric comorbidities.

For inpatients with severe melancholic depression and acute safety concerns, electroconvulsive therapy (or ketamine if ECT refused or ineffective) may be the first-line treatment. In the absence of an urgent indication, we recommend trialing venlafaxine, mirtazapine, or a tricyclic antidepressant. These may be augmented if necessary with lithium or T3 (triiodothyronine). For inpatients with non-melancholic depression and most depressed outpatients, sertraline, escitalopram, and bupropion are reasonable first choices. If no response, the prescriber (in collaboration with the patient) has many choices for the second trial in this algorithm because there is no clear preference based on evidence, and there are many individual patient considerations to take into account. If no response to the second medication trial, the patient is considered to have a medication treatment–resistant depression. If the patient meets criteria for the atypical features specifier, a monoamine oxidase inhibitor could be considered. If not, reconsider (for the third trial) some of the same options suggested for the second trial. Some other choices can also considered at this stage. If the patient has comorbidities such as chronic pain, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, or posttraumatic stress disorder, the depression could be secondary; evidence-based treatments for those disorders would then be recommended.
Tenofovir and telbivudine combination therapy rapidly decreases viral loads in immune-tolerant chronic hepatitis B patients awaiting assisted reproduction: an open-label, randomized, controlled study
Authors: Wu Zhi-xian , Chen Feng-sui , Zhou Xiao-ling , Huang Qian , Zhang Shi-an , Wu Hai-cong , Cai Li-rong , Zeng Zhi-yu , Li Ying-hui , Li Dong-liang
Published: January 2019

Background

Immune-tolerant chronic hepatitis B (CHB) patients awaiting assisted reproduction (AR) are required to initiate antiviral therapy because of laboratory safety concerns. The antiviral therapy in this group has not been well assessed. We sought to explore the efficacy and safety of the combination therapy (COM) of tenofovir (TDF) and telbivudine (LdT).

Patients and methods

In this open-label, randomized, controlled study, we enrolled and randomized hepatitis B virus e-antigen (HBeAg)-positive CHB patients awaiting AR into the study COM group and the control (TDF) group. The COM group received combination therapy of TDF and LdT, and the TDF group received a single treatment of TDF. The patients were followed up for at least 48 weeks. The primary endpoint was the proportion of patients with undetectable HBV DNA level at week 12.

Results

A total of 121 patients were recruited into the COM group (n=60) and the TDF group (n=61). The percentages of patients with undetectable HBV DNA levels were 90.0% (54/60) in the COM group and 67.2% (41/61) (P=0.002) in the TDF group at week 12; the percentages were 96.6% (58/60) in the COM group and 85.2% (52/61) in the TDF group at week 48 (P=0.028), respectively. HBeAg seroconversion occurred in 5/60 (8.3%) patients in the COM group and 2/61 (3.3%) patients in the TDF group at week 48 (P=0.233).

Conclusion

TDF and LdT combination therapy shows a rapid antivirological response in immune-tolerant CHB patients awaiting AR, which provide an alternative for this group at AR centers. However, the HBeAg seroconversion rate is unsatisfactory in the short term.
Prognostic predictors for patients with hepatocellular carcinoma receiving adjuvant transcatheter arterial chemoembolization
Authors: Gu Jingxian , Zhang Xing , Cui Ruixia , Zhang Jia , Wang Zhixin , Jia Yifan , Miao Runchen , Dong Yanyan , Ma Xiaohua , Fan Haining , Wang Haijiu , Ren Li , Li Yiming , Niu Wenquan , Zhang Jingyao , Qu Kai , Liu Chang
Published: January 2019

Objectives

We aimed to confirm the clinical effectiveness of postoperative adjuvant transcatheter arterial chemoembolization (PA-TACE) in patients with hepatocellular carcinoma after liver resection, and further identify the patients who could benefit most from PA-TACE.

Patients and methods

Propensity score matching at a ratio of 1 : 2 was used between hepatectomy patients with and without receiving PA-TACE. Kaplan–Meier analysis was performed to compare overall survival and recurrence-free survival between two groups. Univariate COX regression and stratified analyses were performed to screen and identify survival predictors for PA-TACE patients. The identified predictive markers were validated in an external cohort.

Results

The propensity analysis matched 116 patients in PA-TACE group to 232 in the control group. Visible protective effect of PA-TACE was shown by survival curves in matched series (log-rank P=0.009 and 0.008), with hazard ratio of being 0.599 (95% confidence interval: 0.420–0.855) and 0.623 (95% confidence interval: 0.449–0.866), respectively, for overall survival and recurrence-free survival. The identified prognostic predictors for PA-TACE included TNM stage, tumor size and number, hepatitis B infection, spleen diameter, preoperative serum α-fetoprotein, alkaline phosphatase, γ-glutamyl transpeptidase and monocyte, and three risk signatures (aspartate aminotransferase-to-alanine aminotransferase ratio, neutrophil-to-lymphocyte ratio, and systemic immune-inflammation index).

Conclusion

The treatment effectiveness of adjuvant transcatheter arterial chemoembolization for patients with hepatocellular carcinoma after surgery was validated in this study, and the best candidates for PA-TACE were identified as well, including patients with late-stage tumor, portal hypertension, and high preoperative serum levels of α-fetoprotein, alkaline phosphatase, γ-glutamyl transpeptidase, and monocytes.
Elevated liver enzymes and cardiovascular mortality: a systematic review and dose–response meta-analysis of more than one million participants
Authors: Rahmani Jamal , Miri Ali , Namjoo Iman , Zamaninour Negar , Maljaei Mohammad B. , Zhou Kehua , Cerneviciute Raminta , Mousavi Seyed M. , Varkaneh Hamed K. , Salehisahlabadi Ammar , Zhang Yong
Published: January 2019

Gamma glutamyl transferase (GGT), alanine aminotransferase (ALT), aspartate aminotransferase (AST), and alkaline phosphatase (ALP) are commonly used liver function markers. We performed a dose–response meta-analysis to investigate the association between liver enzymes and cardiovascular disease (CVD) mortality in prospective cohort studies. We conducted a systematic search up to April 2018 in Medline/PubMed, Scopus, Cochrane, and Embase databases. Combined hazard ratios (HRs) with 95% confidence intervals (CIs) were estimated using a random-effects model as described by DerSimonian and Laird. Dose–response analysis was also carried out. Twenty-three studies with 1 067 922 participants reported association between GGT and CVD mortality and were included in our analysis. Pooled results showed a significant association between GGT and risk of CVD mortality (HR: 1.62; 95% CI: 1.47–1.78, P=0.001, P-heterogeneity=0.001) and it was HR: 0.87; 95% CI: 0.73–1.07; P=0.221, P-heterogeneity=0.028, for ALT. There was a direct association between baseline levels of ALP and AST/ALT ratio with CVD mortality (HR: 1.45; 95% CI: 1.11–1.89; P=0.005, P-heterogeneity=0.026, and HR: 2.20; 95% CI: 1.60–3.04; P=0.001, P-heterogeneity=0.540, respectively). Pooled results did not show any significant association between AST and the risk of CVD mortality (HR: 1.20; 95% CI: 0.83–1.73; P=0.313, P-heterogeneity=0.024). Moreover, there was a significant nonlinear association between GGT and ALP levels and the risk of CVD mortality (P=0.008 and 0.016, respectively). Our dose–response meta-analysis revealed a direct relationship between GGT and ALP levels and the risk of CVD mortality. High levels of GGT, ALP and AST/ALT were associated with an increased CVD mortality rate.
The lateral growth and coalesence of magma systems
Authors: Biggs Juliet , Annen Catherine
Published: January 2019

Thermal and mechanical models of magma reservoir growth need to be reconciled with deformation patterns and structural relationships observed at active magma systems. Geophysical observations provide a series of short time-scale snap-shots (10
0
–10
2
years) of the long-term growth of magmatic bodies (10
3
–10
6
years). In this paper, we first review evidence for the growth of magmatic systems along structural features and the associated deformation patterns. We then define three distinct growth stages, (1) aligned melt pockets, (2) coalesced reservoirs, (3) highly evolved systems, which can be distinguished using short-term surface observations. We use two-dimensional thermal models to provide first-order constraints on the time scales and conditions associated with coalescence of individual magma bodies into large-scale reservoirs. We find that closely spaced intrusions (less than 1 km apart) can develop combined viscoelastic shells over time scales of 10s kyr and form laterally extensive mush systems over time scales of 10–100 kyr. The highest temperatures and melt fractions occur during a period of thermal relaxation after melt injection has ceased, suggesting that caldera-forming eruptions may preferentially occur long after the main intrusive activity. The coalescence of eruptible melt-rich chambers only occurs for the highest melt supply rates and deepest systems. Thus, these models indicate that, in most cases, conductive heat transfer alone is not sufficient for a full coalescence of magma chambers and that other processes involving mechanical ruptures and mush mobilization are necessary; individual melt lenses can remain isolated for long periods within growing mush systems, and will only mix during eruption or other catastrophic events. The long-term history of the magmatic system is therefore critical in determining rheological structure and hence short-term behaviour. This framework for the development of magmatic systems in the continental crust provides a mechanical basis for the interpretation of unrest at the world's largest volcanoes.

This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics'.
Magma chambers versus mush zones: constraining the architecture of sub-volcanic plumbing systems from microstructural analysis of crystalline enclaves
Authors: Holness Marian B. , Stock Michael J. , Geist Dennis
Published: January 2019

There are clear microstructural differences between mafic plutonic rocks that formed in a dynamic liquid-rich environment, in which crystals can be moved and re-arranged by magmatic currents, and those in which crystal nucleation and growth are essentiallyin situand static. Crystalline enclaves, derived from deep crustal mushy zones and erupted in many volcanic settings, afford a unique opportunity to use the understanding of microstructural development, established from the study of intrusive plutons, to place constraints on the architecture of sub-volcanic systems. Here, we review the relevant microstructural literature, before applying these techniques to interrogate the crystallization environments of enclaves from the Kameni Islands of Santorini and Rábida Volcano in the Galápagos. Crystals in samples of deep-sourced material from both case studies preserve evidence of at least some time spent in a liquid-rich environment. The Kameni enclaves appear to record an early stage of crystallization during which crystals were free to move, with the bulk of crystallization occurring in a static, mushy environment. By contrast, the Rábida enclaves were sourced from an environment in which hydrodynamic sorting and re-arrangement by magmatic currents were common, consistent with a liquid-rich magma chamber. While presently active volcanoes are thought to be underlain by extensive regions rich in crystal mush, these examples preserve robust evidence for the presence of liquid-rich magma chambers in the geological record.

This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics'.
Melt movement through the Icelandic crust
Authors: White Robert S. , Edmonds Marie , Maclennan John , Greenfield Tim , Agustsdottir Thorbjorg
Published: January 2019

We use both seismology and geobarometry to investigate the movement of melt through the volcanic crust of Iceland. We have captured melt in the act of moving within or through a series of sills ranging from the upper mantle to the shallow crust by the clusters of small earthquakes it produces as it forces its way upward. The melt is injected not just beneath the central volcanoes, but also at discrete locations along the rift zones and above the centre of the underlying mantle plume. We suggest that the high strain rates required to produce seismicity at depths of 10–25 km in a normally ductile part of the Icelandic crust are linked to the exsolution of carbon dioxide from the basaltic melts. The seismicity and geobarometry provide complementary information on the way that the melt moves through the crust, stalling and fractionating, and often freezing in one or more melt lenses on its way upwards: the seismicity shows what is happening instantaneously today, while the geobarometry gives constraints averaged over longer time scales on the depths of residence in the crust of melts prior to their eruption.

This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics'.
On the hydrodynamics of crystal clustering
Authors: McIntire Michael Z. , Bergantz George W. , Schleicher Jillian M.
Published: January 2019

The formation of crystal clusters may influence the mechanical behaviour of magmas. However, whether clusters form largely from physical contact in a mobile state during sedimentation and stirring, or require residence in a crystal mush, is not well understood. In this paper, we use discrete-element fluid dynamics numerical experiments to illuminate the potential for clustering from both sedimentation and open-system mixing in a model olivine basalt reservoir for three different initial solid volume per cents. Crystal clustering is quantified using both bulk measures of clustering such as the
R
index and Ripley's
L(r)
and
g(r)
functions and with a variable scale technique called Voronoi tessellations, which also provide orientation data. Probability density functions for the likelihood of crystal clustering under freely circulating conditions indicate that there is nearly an equal likelihood for clustering and non-clustered textures in natural examples. A crystal cargo in igneous rock suites exhibiting a dominance of crystal clusters may be largely sampling magmatic materials formed in a crystal mush.

This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics’.
How do volatiles escape their shallow magmatic hearth?
Authors: Degruyter Wim , Parmigiani Andrea , Huber Christian , Bachmann Olivier
Published: January 2019

Only a small fraction (approx. 1–20%) of magmas generated in the mantle erupt at the surface. While volcanic eruptions are typically considered as the main exhaust pipes for volatile elements to escape into the atmosphere, the contribution of magma reservoirs crystallizing in the crust is likely to dominate the volatile transfer from depth to the surface. Here, we use multiscale physical modelling to identify and quantify the main mechanisms of gas escape from crystallizing magma bodies. We show that most of the outgassing occurs at intermediate to high crystal fraction, when the system has reached a mature mush state. It is particularly true for shallow volatile-rich systems that tend to exsolve volatiles through second boiling, leading to efficient construction of gas channels as soon as the crystallinity reaches approximately 40–50 vol.%. We, therefore, argue that estimates of volatile budgets based on volcanic activity may be misleading because they tend to significantly underestimate the magmatic volatile flux and can provide biased volatile compositions. Recognition of the compositional signature and volumetric dominance of intrusive outgassing is, therefore, necessary to build robust models of volatile recycling between the mantle and the surface.

This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics’.
Identifying the ingredients of hydrous arc magmas: insights from Mt Lamington, Papua New Guinea
Authors: Humphreys M. C. S. , Zhang J. , Cooper G. F. , Macpherson C. G. , Ottley C. J.
Published: January 2019

Volcanism is the surface expression of magma intrusion, crystallization, assimilation and hybridization processes operating throughout the crust over a range of time periods. Many magmas, including those erupted at subduction zones, have complex textures that reflect these processes. Here, we use textural and geochemical characteristics of calcic amphiboles to help identify multiple ingredients of subduction zone magmatism at Mt Lamington volcano, Papua New Guinea. Our approach uses existing trace element partitioning schemes to calculate the compositions of amphibole equilibrium melts (AEMs). The AEM compositions show that Mt Lamington andesites and plutonic enclaves are dominated by fractionation of amphibole + plagioclase + biotite, with assimilation of plagioclase and zircon. Magnesiohastingsite crystals in the andesite and diktytaxitic mafic enclaves reflect multiple episodes of recharge by more primitive, geochemically variable melts. The andesite also contains clots with rounded grains and melt on grain boundaries. These features indicate slow crystallization, and the retention of melt films could significantly enhance the potential for remobilization of crystals by infiltrating melts or during magma mixing. Variations in crystallization conditions could thus significantly affect the mush microstructure. We suggest that this could result in a significant bias of the volcanic record towards the preferential incorporation of more slowly cooled plutonic material from the lower crust or from more thermally mature plumbing systems.

This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics’.
Magma chambers: what we can, and cannot, learn from volcano geodesy
Authors: Segall Paul
Published: January 2019

Geodetic observations on volcanoes can reveal important aspects of crustal magma chambers. The rate of decay of deformation with distance reflects the centroid depth of the chamber. The amplitude of the deformation is proportional to the product of the pressure change and volume of the reservoir. The ratio of horizontal to vertical displacement is sensitive to chamber shape: sills are efficient at generating vertical displacement, while stocks produce more horizontal deformation. Geodesy alone cannot constrain important parameters such as chamber volume or pressure; furthermore, kinematic models have no predictive power. Elastic response combined with influx proportional to pressure gradient predicts an exponentially decaying flux, leading to saw-tooth inflation cycles observed at some volcanoes. Yet many magmatic systems exhibit more complex temporal behaviour. Wall rock adjacent to magma reservoirs cannot behave fully elastically. Modern conceptual models of magma chambers also include cumulate and/or mush zones, with potentially multi-level melt lenses. A viscoelastic shell surrounding a spherical magma chamber significantly modifies the predicted time-dependent response; post-eruptive inflation can occur without recharge if the magma is sufficiently incompressible relative to the surrounding crust (Segall P. 2016
J. Geophys. Res. Solid Earth
,
121
, 8501–8522). Numerical calculations confirm this behaviour for both oblate and prolate ellipsoidal chambers surrounded by viscoelastic aureoles. Interestingly, the response to a nearly instantaneous pressure drop during an explosive eruption can be non-monotonic as the rock around the chamber relaxes at different rates. Pressure-dependent recharge of a non-Newtonian magma in an elastic crust leads to an initially high rate of inflation which slows over time; behaviour that has been observed in some magmatic systems. I close by discussing future challenges in volcano geodesy.

This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics’.
Architecture and dynamics of magma reservoirs
Authors: Edmonds Marie , Cashman Katharine V. , Holness Marian , Jackson Matthew
Published: January 2019

This introductory article provides a synopsis of our current understanding of the form and dynamics of magma reservoirs in the crust. This knowledge is based on a range of experimental, observational and theoretical approaches, some of which are multidisclipinary and pioneering. We introduce and provide a contextual background for the papers in this issue, which cover a wide range of topics, encompassing magma storage, transport, behaviour and rheology, as well as the timescales on which magma reservoirs operate. We summarize the key findings that emerged from the meeting and the challenges that remain. The study of magma reservoirs has wide implications not only for understanding geothermal and magmatic systems, but also for natural oil and gas reservoirs and for ore deposit formation.

This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics’.
DO-MS: Data-Driven Optimization of Mass Spectrometry Methods
Authors: Huffman Gray , Specht Harrison , Chen Albert , Slavov Nikolai
Published: January 2019

The performance of ultrasensitive LC-MS/MS methods, such as Single-Cell Proteomics by Mass Spectrometry (SCoPE-MS), depends on multiple interdependent parameters. This interdependence makes it challenging to specifically pinpoint bottlenecks in the LC-MS/MS methods and approaches for resolving them. For example, low signal at MS2 level can be due to poor LC separation, ionization, apex targeting, ion transfer, or ion detection. We sought to specifically diagnose such bottlenecks by interactively visualizing data from all levels of bottom-up LC-MS/MS analysis. Many search engines, such as MaxQuant, already provide such data, and we developed an open source platform for their interactive visualization and analysis: Data-driven Optimization of MS (DO-MS). We found that in many cases DO-MS not only specifically diagnosed bottlenecks but also enabled us to rationally optimize them. For example, we used DO-MS to diagnose poor sampling of the elution peak apex and to optimize it, which increased the efficiency of delivering ions for MS2 analysis by 370%. DO-MS is easy to install and use, and its GUI allows for interactive data subsetting and high-quality figure generation. The modular design of DO-MS facilitates customization and expansion. DO-MS is available for download from GitHub: github.com/SlavovLab/DO-MS
scSVA: an interactive tool for big data visualization and exploration in single-cell omics
Authors: Tabaka Marcin , Gould Joshua , Regev Aviv
Published: January 2019

We present scSVA (single-cell Scalable Visualization and Analytics), a lightweight R package for interactive two- and three-dimensional visualization and exploration of massive single-cell omics data. Building in part of methods originally developed for astronomy datasets, scSVA is memory efficient for more than hundreds of millions of cells, can be run locally or in a cloud, and generates high-quality figures. In particular, we introduce a numerically efficient method for single-cell data embedding in 3D which combines an optimized implementation of diffusion maps with a 3D force-directed layout, enabling generation of 3D data visualizations at the scale of a million cells. To facilitate reproducible research, scSVA supports interactive analytics in a cloud with containerized tools. scSVA is available online at https://github.com/klarman-cell-observatory/scSVA.
Microtubule plus-end dynamics link wound repair to the innate immune response
Authors: Taffoni Clara , Omi Shizue , Huber Caroline , Mailfert Sebastien , Fallet Matthieu , Ewbank Jonathan J. , Pujol Nathalie
Published: January 2019

As a first line of defence against the environment, the epidermis protect animals from infection and physical damage. In C. elegans, wounding the epidermal epithelium triggers both an immune reaction and a repair response. Exactly how these are controlled, and the degree to which they are inter-connected remains unclear. To address these questions, we established a simple system for simultaneously inflicting precise laser wounds and imaging at high spatial and temporal resolution. We show that in C. elegans, wounding provokes a rapid sealing of the plasma membrane, involving reorganisation of phosphatidylinositol 4,5- bisphosphate domains. This is followed by a radial recruitment at the wound site of EBP-2/EB1, a protein that binds the plus ends of microtubules. EB1 recruitment is accompanied by a reorganisation of microtubules, required for the subsequent recruitment of actin and wound closure. It is also required for the directed trafficking towards the site of injury of the key signalling protein SNF-12. In the absence of SNF-12 recruitment, there is an abrogation of the immune response. Our results suggest that microtubule dynamics coordinate the cytoskeletal changes required for wound repair and the concomitant activation of the innate immune response.
Colonial ascidians strongly preyed upon, yet dominate the substrate in a subtropical fouling community
Authors: Hiebert Laurel Sky , Vieira Edson A. , Dias Gustavo M. , Tiozzo Stefano , Brown Federico D.
Published: January 2019

Higher diversity and dominance at lower latitudes has been suggested for colonial species. We verified the latitudinal pattern in species richness of ascidians, finding that higher colonial-to-solitary species ratios occur in the tropics and subtropics. At the latitudinal region with the highest ratio, in south-eastern Brazil, we confirmed that colonial species dominate the space on artificial plates in two independent studies of five fouling communities. We manipulated settlement plates to measure effects of predation and competition on growth and survivorship of colonial vs. solitary ascidians. Eight ascidian species were subjected to a predation treatment, i.e. caged vs. exposed to predators, and a competition treatment, i.e. leaving vs. removing competitors, to assess main and interactive effects. Predation had a greater effect on growth and survivorship of colonial compared to solitary species, whereas competition did not show consistent patterns between the two life histories. We hypothesize that colonial ascidians dominate at this subtropical site despite being highly preyed upon because they regrow when partially consumed and can adjust in shape and space to grow into refuges. We contend that these means of avoiding mortality from predation can have large influences on the diversification patterns of colonial species at low latitudes, where predation intensity is greater.
A Preliminary Occurrence of Extended-Spectrum and AmpC Beta-Lactamases in Clinical Isolates of EnteropathogenicEscherichia coliin Najaf, Iraq
Authors: Alsherees Hashim Ali Abdulameer , Ali Sumaya Najim Abed
Published: January 2019

Extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase producing enteropathogenicEscherichia coli(EPEC) have become an important clinical problem due to their resistance to multiple antibiotics. The purpose of this study was to evaluate the multi-drug resistant (MDR) and β-lactamases producing EPEC isolated from children with diarrhea. Twenty two EPEC strains were gathered from another study performed from September to November 2009. Antibiotic susceptibilities against 20 antibiotics determined by the agar disk diffusion according to the protocol recommended by Clinical and Laboratory Standards Institute guidelines (CLSI). Phenotypic confirmatory tests carried out for screening of ESBLs and AmpC β-lactamase. The isolates subjected to PCR assays with specific primers forbla-genes (blaSHV,blaTEM,blaCTX-MandblaOXA,blaPER,blaVEBandblaGES). Only 22 (3.4%) EPEC isolates recovered from clinical infections. MDR rate in EPEC was 90.9%. Phenotypic confirmatory tests showed that 13.6% and 20.0% of isolates were ESBL and AmpC β-lactamase producers, respectively. Among the EPEC isolates, percent recovery ofblaSHV,blaTEM,blaCTX-MandblaOXAgenes was 100%, 81.8%, 77.3% and 9.1%, respectively. Only 2 (9.1%) isolates hadblaAmpCgene and none of the isolates carriedblaPER,blaVEBandblaGESgenes. The results of our study showed that the ESBLs were common among EPEC isolates. Such high dissemination of ESBLs is a serious problem for public health and therefore, it is necessary to seek a program for monitoring ESBLs in Najaf hospitals. This study is the first report on the presence of thebla-genes in EPEC isolates in Najaf.
Cdc42 promotes epithelial morphogenesis by coupling Par-complex and Crumbs recruitment via Par6-aPKC
Authors: Nunes de Almeida Francisca , Walther Rhian F. , Pressé Mary , Vlassaks Evi , Pichaud Franck
Published: January 2019

Epithelial morphogenesis depends on Cdc42, which acts in part through the Par-complex (Baz/Par3-Par6-aPKC), and Crumbs (Crb/CRB3). However, how these proteins come together and interact during morphogenesis is not well understood. Here we show that inDrosophilacells, Cdc42 is active at the apical membrane and cell-cell contacts, and couples apical recruitment of Par6-aPKC and Crb to promote apical identify. This coupling depends on Cdc42 and aPKC binding to Par6, and is mediated by Par6 binding to Crb. Conversely, Crb promotes the apical retention of Par6-aPKC, and thus Cdc42-Par6-aPKC and Crb promote each other’s apical accumulation to specify the apical membrane andZonula Adherens (ZA). Altogether, our work shows that epithelial morphogenesis relies on a two tiered-mechanism whereby Cdc42 coordinates Par-complex assembly and apical recruitment of Crb through Par6-aPKC.
Hypoxia induces rapid changes to histone methylation reprogramming chromatin for the cellular response
Authors: Batie Michael , Frost Julianty , Frost Mark , Wilson James W. , Schofield Pieta , Rocha Sonia
Published: January 2019

Molecular dioxygenases include JmjC-containing histone demethylases and PHD enzymes, but only PHDs are considered to be molecular oxygen sensors in cells. Although, it is known that hypoxia can alter chromatin, whether this is a direct effect on histone demethylases or due to hypoxia induced HIF-dependent transcriptional changes is not known. Here, we report that hypoxia induces a rapid and HIF-independent alteration to a variety of histone methylation marks. Genomic locations of H3K4me3 and H3K36me3 following short hypoxia predict the hypoxia gene signature observed several hours later in cells. We show that KDM5A inactivation mimics hypoxic changes to H3K4me3 in its targets and is required for the cellular response to hypoxia. Our results demonstrate a direct link between oxygen sensing and chromatin changes via KDM inhibition.

One Sentence Summary

Rapid oxygen sensing by chromatin
Intrinsic plasticity of cerebellar Purkinje cells in motor learning circuits
Authors: Jang Dong Cheol , Shim Hyun Geun , Kim Sang Jeong
Published: January 2019

Intrinsic plasticity of cerebellar Purkinje cells (PCs) is recently highlighted in the cerebellar local circuits, however, its physiological impact on the cerebellar learning and memory remains elusive. Using a mouse model of memory consolidation deficiency, we found that the intrinsic plasticity of PCs may be involved in motor memory consolidation. Gain-up training of the vestibulo-ocular reflex produced a decrease in the synaptic weight of PCs in both the wild-type and knockout groups. However, intrinsic plasticity was impaired only in the knockout mice. Furthermore, the observed defects in the intrinsic plasticity of PCs led to the formation of improper neural plasticity in the vestibular nucleus (VN) neurons. Our results suggest that the synergistic modulation of intrinsic and synaptic plasticity in PCs is required for the changes in following plasticity in the VN, thereby contributes to the long-term storage of motor memory.
Integrated multi-omics analysis to study the effects of simulated weightlessness on rhesus macaques (Macaca mulatta)
Authors: Zhang Peng , Shao Libin , Zhang Jie , Li Wenjiong , Fan Guangyi , Zhou Ying , Kan Guanghan , Liu Hongju , Li Weidong , Wang Fei , Chu Xixia , Han Peng , Peng Ling , Liu Xingmin , Chen Jianwei , Liang Xinming , Ji Jingkai , Du Shiyi , Mei Zhanlong , Li Ronghui , Xu Xun , Chen Shanguang , Liu Xin , Chen Xiaoping
Published: January 2019

Safety and health of astronauts in space is one of the most important aspects of space exploration, however, the genomic research about how a weightless space can affect astronaut’s health was limited. In this study, we sequenced 25 transcriptomic, 42 metabolomic and 35 metagenomic data of 15 rhesus macaques (Macaca mulatta) spanning seven simulated weightlessness experiment stages. We identified 84 genes, 1911 features and 55 genera which are significantly changed in blood and muscle, hippocampal region, dorsomedial prefrontal cortex as well as fecal, respectively. Furthermore, performing the integrated analysis of three omics data, we found several pathways which were related to regulation of immune system process, glucose uptake, reaction to threatens, neurotoxic and bone or joints damage, such as tyrosine metabolism and tryptophan metabolism. Our results provided an initial attempt of “multi-omics” approaches which combined transcriptomics, metabolomics and metagenomics to illustrate some molecular clues for simulated weightlessness effect on the rhesus macaques and potential sight of microgravity’s effect on astronauts’ health.
Range-wide variation in local adaptation and phenotypic plasticity of fitness-related traits in Fagus sylvatica and their implications under climate change
Authors: Gárate-Escamilla Homero , Hampe Arndt , Vizcaíno-Palomar Natalia , Robson T. Matthew , Garzón Marta Benito
Published: January 2019

Aim

To better understand and more realistically predict future species distribution ranges, it is critical to account for local adaptation and phenotypic plasticity in populations’ responses to climate. This is challenging because local adaptation and phenotypic plasticity are trait-dependent and traits co-vary along climatic gradients, with differential consequences for fitness. Our aim is to quantify local adaptation and phenotypic plasticity of vertical and radial growth, leaf flushing and survival across Fagus sylvatica range and to estimate each trait contribution to explain the species occurrence.

Location

Europe

Time period

1995 – 2014; 2070

Major taxa studied

Fagus sylvatica L.

Methods

We used vertical and radial growth, flushing phenology and mortality of Fagus sylvatica L. recorded in BeechCOSTe52 (>150,000 trees). Firstly, we performed linear mixed-effect models that related trait variation and co-variation to local adaptation (related to the planted populations’ climatic origin) and phenotypic plasticity (accounting for the climate of the plantation), and we made spatial predictions under current and RCP 8.5 climates. Secondly, we combined spatial trait predictions in a linear model to explain the occurrence of the species.

Results

The contribution of plasticity to intra-specific trait variation is always higher than that of local adaptation, suggesting that the species is less sensitive to climate change than expected; different traits constrain beech’s distribution in different parts of its range: the northernmost edge is mainly delimited by flushing phenology (mostly driven by photoperiod and temperature), the southern edge by mortality (mainly driven by intolerance to drought), and the eastern edge is characterised by decreasing radial growth (mainly shaped by precipitation-related variables in our model); considering trait co-variation improved single-trait predictions.

Main conclusions

Population responses to climate across large geographical gradients are trait-dependent, indicating that multi-trait combinations are needed to understand species’ sensitivity to climate change and its variation across distribution ranges.
The “I” in government archives: the individual as stakeholder
Authors: Peterson Trudy Huskamp
Published: January 2019

Purpose

The purpose of this paper is to discuss the critical reasons why citizens need government archives, with an elaboration on why managing electronic records is crucial.

Design/methodology/approach

The paper offers a philosophical framework that argues that not managing records harms individuals. Examples from several countries are reviewed to find the relevance of the records relationships between people and governments, and the nexus between human rights and archives through an examination of the first three articles of the Universal Declaration of Human Rights is analyzed.

Findings

The paper identifies a strong relationship between human rights and archives and the way lives are reflected in the records in government archives. This reinforces the argument that governments need clearly established and legally empowered archival institutions.

Originality/value

Critical examination of the “I” in government archives is relatively rare in the literature, particularly when linked to the human rights implications of government records. The study is a constructive beginning for further academic discussions to explore this dimension, which in turn is related to both the efficiency of governance and the public trust in government.
Social and psychological determinants of value co-creation behavior for South Korean firms
Authors: Yoon Sungjoon , Lee Eun-Mi
Published: January 2019

Purpose

In view of the increasing importance of creating values that require shared societal responsibilities to be borne by not just firms but customers as well, the purpose of this paper is to empirically investigate whether customers’ social capital plays a role in creating shared values for South Korean firms directly or indirectly through social identity and corporate authenticity.

Design/methodology/approach

To understand the effects of social capital on value co-creation, the authors conducted a face-to-face questionnaire survey with a selected group of 400 adult respondents aged more than 20 years. To verify precision in wording and sentence structure and the validity of questions in reflecting the study objective, the authors conducted a pretest on 40 respondents before administering the main survey. Ultimately, 50 questionnaires considered inappropriate and with inconsistent response patterns were discarded, leaving 350 questionnaires for the statistical analysis.

Findings

This research adopts the consumer-centric as well as societal perspectives to conceptualize value co-creation behavior, and tests the moderating roles of psychometric measures of self-monitoring and corporate trust. Next, the research confirms whether social identity and perceived corporate authenticity mediate the relationship between social capital and value co-creation.

Originality/value

The study results shed new insights into the societal, psychological and normative aspects of value co-creation.
Extending a TAM–TTF model with perceptions toward telematics adoption
Authors: Chen Nai-Hua
Published: January 2019

Purpose

The purpose of this paper is to examine a framework integrating the technology acceptance model (TAM), individuals’ task–technology fit (TTF) and perceptions toward adopting automobile telematics devices.

Design/methodology/approach

This study integrated the TAM with TTF to understand individual perceptions of a technology’s value. In addition, the intrinsic motivational factors toward technology usage, including positive perceptions (perceived enjoyment, personal innovation and perceived uniqueness) and negative perceptions (perceived risk and performance gap), were considered in the model. Furthermore, the moderating effect of driving experience was examined.

Findings

The perceived usefulness (PU) of telematics as well as perceived ease of use (PEOU) affected drivers’ adoption intentions. PEOU had a greater effect on adoption intentions than PU, and technology characteristics had a greater effect on TTF than task characteristics. Moreover, individuals’ perceptions of perceived enjoyment and uniqueness affected PU and PEOU. The negative perceptions of perceived risk and performance gap affected PU and PEOU, respectively. Furthermore, driving experience significantly weakened the relationship between PU and intentions.

Originality/value

Telematics is a niche market due to the development of the Internet of Things, but users’ adoption intentions remain unknown. This study constructed a more comprehensive model and tested the impacts of certain variables on telematics adoption, with driving experience as a crucial moderator.
Food insecurity amongst older people in the UK
Authors: Purdam Kingsley , Esmail Aneez , Garratt Elisabeth
Published: January 2019

Purpose

The purpose of this paper is to present findings from research into food insecurity amongst older people aged 50 years and older in the UK.

Design/methodology/approach

This paper uses secondary analysis of national-level survey data and semi-structured interviews with older people receiving emergency food from foodbanks.

Findings

There is a forgotten care gap in the UK where a substantial number of older people are living in food insecurity. Many older people live alone and in poverty, and increasing numbers are constrained in their spending on food and are skipping meals. Food insecurity amongst older people can be hidden. Within families a number of older people were trying to ensure that their children and grandchildren had enough to eat, but were reluctant to ask for help themselves.

Research limitations/implications

The broad categorisation of older people aged 50 and above comprises people in very different circumstances. The qualitative component of the research was undertaken across various sites in a single city in England. Despite these limitations, the analysis provides important insights into the experiences of the many older people enduring food insecurity.

Practical implications

An increased public and professional awareness of food insecurity amongst older people is needed. Increased routine screening for under-nutrition risk is a priority. Policy initiatives are needed that are multifaceted and which support older people across a range of age groups, particularly those living alone.

Social implications

Food insecurity amongst older people in the UK raises questions about the present policy approach and the responsibilities of the government.

Originality/value

The research provides important new insights into the experiences of the many older people experiencing food insecurity in the UK by drawing on survey data and interviews with older people using foodbanks.