bluuebunny/crossref_metadata_2025 huggingface dataset:
Economic and Social Interactions in the Piedmont Village Tradition-Mississippian Boundarylands of Southeastern North America, AD 1200–1600
Authors: Jones Eric E. , Krause Maya B. , Watson Caroline R. , O'Saile Grayson N.
Published: November 2019

This research seeks to understand the economic and social interaction patterns among dispersed Piedmont Village Tradition communities in the North American Southeast, AD 1200–1600. Piedmont Village Tradition communities lived adjacent to Mississippian societies and have been categorized as a peripheral society because of this spatial relationship. We examine economic behaviors by constructing fall-off curves of local versus nonlocal lithic material proportions at settlement sites and examining the reduction behaviors and tool types at sites. The results support a possible gateway model for the acquisition and distribution of nonlocal materials that linked spatially proximate communities. To examine social interaction patterns, we conducted a Brainerd-Robinson analysis of ceramic attributes from six sites and combined our results with work by Rogers (1993). The results show sites with stylistic similarities are not the same sites that share lithic resources. We conclude that these spatially non-overlapping artifact patterns result from a heterarchical social organization with a high degree of independence between economic and social interactions. Finally, we contextualize our results within the current knowledge of Mississippian and Piedmont Village Tradition societies in the region to broaden the discussion of gateways in reciprocity-based economies, societies traditionally thought of as peripheral to complex societies, and coalescence.
Special Issue: Psychosis from early intervention to treatment resistance
Authors: McDonald C. , Cotter D.R.
Published: November 2019

Psychotic disorders are central to mental health service provision and a common theme of academic research programmes in Ireland, which explore the neurobiological and psychosocial risk factors underpinning the development and progression of these illnesses. While we await the discovery of novel pharmacological treatment targets for psychotic disorders, it is important to employ our existing management strategies to optimal effect. In this special issue on psychosis, a selection of clinical research studies and reviews from Irish researchers, and often of Irish populations, are brought together which span the trajectory of psychotic illness from early intervention to treatment resistance. The topics include the characteristics and course of first episode psychosis cohorts, real-world evaluation of early intervention services, management strategies for treatment resistant schizophrenia and neurobiological research into social stress. The current editorial provides an overview of these papers and highlights the initial steps of the Irish Psychosis Research Network towards developing an integrated clinical research network focusing on the treatment and research into psychotic disorders.
Famine, Memory, and Politics in the Post-Soviet Space: Contrasting Echoes of Collectivization in Ukraine and Kazakhstan
Authors: Richter James
Published: November 2019

Stalin’s collectivization campaigns and the associated famine killed millions in Ukraine and Kazakhstan, yet the two countries commemorate the events quite differently. In Ukraine, the Holodomor (death by hunger) occupies a prominent place in the public sphere and is remembered most frequently as a genocidal policy against the Ukrainian nation. In Kazakhstan, the famine takes up little space in the public arena, and officials remain reluctant to call it a genocide. This article explores these differences using two models explaining variation in the politics of memory: one emphasizing the instrumental calculations of political elites and the other emphasizing the historical and cultural constraints that frame contemporary debates. These two models complement each other rather than compete. The contest over the famine in Ukraine was in part a consequence of eastern and western Ukraine’s differing histories, but it intensified when governing politicians deployed the memory of the famine instrumentally in the 2000s. In Kazakhstan, political calculations led the regime to emphasize unity and stability over divisive debates about the past, but historical factors made depoliticizing the famine feasible.
The Falkland Islands (Malvinas) as sub-Antarctic foraging, migratory and wintering habitat for southern right whales
Authors: Weir Caroline R. , Stanworth Andrew
Published: November 2019

The historical and contemporary presence of southern right whales (SRWs;Eubalaena australis) around the Falkland Islands (Malvinas) has received little recognition. We assessed SRW occurrence in the Falklands via whaling records, a literature review, systematic surveys (boat, aerial and shore-based), and citizen science sightings. The combined data sources indicated a year-round (peaking in austral summer) presence of SRWs in pelagic areas around the Falklands. In contrast, most nearshore records originated in the austral late autumn and winter (May to August), including a marked increase in sightings along the north-east coast during 2017 compared with previous years. The data support spatio-temporal variation in the use of Falklands waters by SRWs. Pelagic waters appear to comprise summer foraging habitat, and may also be used by animals migrating between the Patagonian shelf and feeding grounds located further south and east. The peak numbers observed in nearshore waters occurred earlier in the winter (July) than those on the Argentinean or Brazilian calving grounds (Aug–Oct). Consequently, some whales may have continued migrating northwards to established breeding areas after departing Falklands waters. A component of the south-west Atlantic population could also be using the islands as a novel wintering destination, for mating and/or socializing (no calving has been confirmed to date). The importance of Falklands waters as a multi-use SRW habitat appears to be increasing. The region is important in the context of addressing current knowledge gaps regarding feeding grounds and migratory corridors highlighted in international SRW conservation and management plans for the wider South-west Atlantic.
Social media and social wellbeing in later life
Authors: Quinn Kelly
Published: November 2019

Social wellbeing is important to health, but maintaining social relations often becomes difficult in later life due to retirement, chronic disease, and the death of spouses and friends. Social media platforms, such as Facebook and Twitter, present accessible and low-cost communication technologies that have been demonstrated to enhance feelings of social connection and reduce loneliness in younger age groups. This exploratory study uses a four-week social media training workshop as an intervention in a randomised controlled study to examine whether similar social benefits might be realised for those at older ages, aged 65+ years. Social wellbeing measures of social capital, loneliness, social connectedness and social provisions were examined, revealing only small differences in social integration. As these findings seemingly contradict studies conducted with younger persons, the contexts of social media use in older adulthood are discussed, along with proposals for future research directions.
Variation of the algebraic λ-invariant over a solvable extension
Authors: DELBOURGO DANIEL
Published: November 2019

Fix an odd primep. Let$\mathcal{D}_n$denote a non-abelian extension of a number fieldKsuch that$K\cap\mathbb{Q}(\mu_{p^{\infty}})=\mathbb{Q}, $and whose Galois group has the form$ \text{Gal}\big(\mathcal{D}_n/K\big)\cong \big(\mathbb{Z}/p^{n'}\mathbb{Z}\big)^{\oplus g}\rtimes \big(\mathbb{Z}/p^n\mathbb{Z}\big)^{\times}\ $whereg> 0 and$0 \lt n'\leq n$. Given a modular Galois representation$\overline{\rho}:G_{\mathbb{Q}}\rightarrow \text{GL}_2(\mathbb{F})$which isp-ordinary and alsop-distinguished, we shall write$\mathcal{H}(\overline{\rho})$for the associated Hida family. Using Greenberg’s notion of Selmer atoms, we prove an exact formula for the algebraic λ-invariant\begin{equation} \lambda^{\text{alg}}_{\mathcal{D}_n}(f) \;=\; \text{the number of zeroes of } \text{char}_{\Lambda}\big(\text{Sel}_{\mathcal{D}_n^{\text{cy}}}\big(f\big)^{\wedge}\big) \end{equation}at all$f\in\mathcal{H}(\overline{\rho})$, under the assumption$\mu^{\text{alg}}_{K(\mu_p)}(f_0)=0$for at least one formf0. We can then easily deduce that$\lambda^{\text{alg}}_{\mathcal{D}_n}(f)$is constant along branches of$\mathcal{H}(\overline{\rho})$, generalising a theorem of Emerton, Pollack and Weston for$\lambda^{\text{alg}}_{\mathbb{Q}(\mu_{p})}(f)$.

For example, if$\mathcal{D}_{\infty}=\bigcup_{n\geq 1}\mathcal{D}_n$has the structure of ap-adic Lie extension then our formulae include the cases where: either (i)$\mathcal{D}_{\infty}/K$is ag-fold false Tate tower, or (ii)$\text{Gal}\big(\mathcal{D}_{\infty}/K(\mu_p)\big)$has dimension ≤ 3 and is a pro-p-group.
Establishing a sustainable open heart surgery programme in Nigeria, a low-income country: which is the best model?
Authors: Nwafor Ikechukwu A. , Eze John C. , Nwafor Maureen N. ,   National Cardiothoracic Center of Excellence (NCTCE), University of Nigeria Teaching Hospital (UNTH), Ituku-Ozalla, Enugu, Nigeria
Published: November 2019

Background:

In any country, the development of open heart surgery programme parallels stable political climate, economic growth, good leadership, and prudent fiscal management. This is lacking in a country like Nigeria without a functional cardiac hospital.

Objective:

To review and compare the various models being adopted towards establishing a sustainable open heart surgery programme in Nigeria.

Materials and Methods:

For ethnic and cultural reasons, Nigeria is divided into six geopolitical regions. Each region has one or more Federal Teaching Hospitals including medical centres. The hospitals have trained cardiothoracic surgeons and cardiologists as well as other auxiliary staff. After attainment of democratic rule in 1999, individual hospitals have devised various models to establish sustainable open heart surgery programme. The number of hospitals in each region, the models devised, and the limitations including the outcome were studied and analysed.

Results:

Each geopolitical zone has about three to four centres, either public or private, trying to establish the programme. There are six different models. Each centre has been trying the different models since the year 2000. The oldest of the model is cardiac mission and the newest is employment of highly skilled retired expatriate consultant cardiac surgeon to help develop the local team. Inadequate funds, lack of governmental support, and brain drain syndrome have largely affected the programme.
The broad autism phenotype in real-life: clinical and functional correlates of autism spectrum symptoms and rumination among parents of patients with autism spectrum disorder
Authors: Carpita Barbara , Carmassi Claudia , Calderoni Sara , Muti Dario , Muscarella Alessia , Massimetti Gabriele , Cremone Ivan M. , Gesi Camilla , Conti Eugenia , Muratori Filippo , Dell’Osso Liliana
Published: November 2019

Objective

Increasing literature reported higher rates of psychiatric disorders in parents of children with autism spectrum disorder (ASD), as well as of autistic-like features in social and cognitive functioning. However, little attention has been paid to the association between autistic traits (AT) and global functioning in this population. The aim of the present work was to investigate clinical and functional correlates of AT among parents of ASD children, with a specific focus on ruminative thinking.

Methods

One hundred and twenty parents of ASD children were assessed by the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders (DSM-5), the Adult Autism Subthreshold Spectrum (AdAS Spectrum), the Ruminative Response Scale (RRS), the Social and Occupational Functioning Assessment Scale (SOFAS).

Results

Subjects with at least 1 psychiatric disorder (39.2%) showed significantly higher AdAS Spectrum and RRS scores. Subjects with a history of school difficulties and with language development alterations scored significantly higher on specific AdAS Spectrum domains. A significant negative correlation was found between SOFAS and AdAS Spectrum scores, as well as between SOFAS and RRS scores. AdAS Spectrum nonverbal communication domain score was identified has a statistically predictive variable for the presence of psychiatric disorders and lower SOFAS scores. Finally, we found a significant indirect effect of AdAS total score on SOFAS score, which was fully mediated by RRS total score.

Conclusions

AT in parents of ASD children seem to be associated with a higher vulnerability toward psychopathology and with a lower global functioning. Ruminative thinking may play a role in the relationship between AT and functional outcome.
Active and passive: two ways party systems influence electoral outcomes
Authors: Nemčok Miroslav
Published: November 2019

Parties can not onlyactivelyadjust the electoral rules to reach more favourable outcomes, as is most often recognized in political science, but they alsopassivelycreate an environment that systematically influences electoral competition. This link is theorized and included in the wider framework capturing the mutual dependence of electoral systems and party systems. The impact of passive influence is successfully tested on one out of two factors closely related to party systems: choice set size (i.e., number of options provided to voters) and degree of ideological polarization. The research utilizes established datasets (i.e., Constituency-Level Elections Archive, Party System Polarization Index, Chapel Hill Expert Survey, and Manifesto Project Database) and via regression analysis with clustered robust standard errors concludes that the choice set size constitutes an attribute with passive influence over electoral systems. Thus, it must be reflected when outcomes of electoral systems are estimated or compared across various contexts.
The Swedish Twin Registry: Content and Management as a Research Infrastructure
Authors: Zagai Ulrika , Lichtenstein Paul , Pedersen Nancy L. , Magnusson Patrik K. E.
Published: November 2019

The Swedish Twin Registry functions as research infrastructure containing information on 216,258 twins born between 1886 and 2015, of whom 86,199 pairs have zygosity determined by DNA, an intrapair similarity algorithm, or being of opposite sex. In essence, practically all twins alive and currently 9 years or older have been invited for participation and donation of DNA on which genomewide single nucleotide polymorphisms array genotyping has been performed. Content, management and alternatives for future improvements are discussed.
Instantaneous Antarctic ice sheet mass loss driven by thinning ice shelves
Authors: Gudmundsson G. Hilmar , Paolo Fernando S. , Adusumilli Susheel , Fricker Helen A.
Published: November 2019

Recent observations show that the rate at which the Antarctic ice sheet (AIS) is contributing to sea level rise is increasing. Increases in ice‐ocean heat exchange have the potential to induce substantial mass loss through the melting of its ice shelves. Lack of data and limitations in modeling, however, has made it challenging to quantify the importance of ocean‐induced changes in ice shelf thickness as a driver for ongoing mass loss. Here, we use a numerical ice sheet model in combination with satellite observations of ice shelf thinning from 1994 to 2017 to quantify instantaneous changes in ice flow across all AIS grounding lines, resulting from changes in ice shelf buttressing alone. Our process‐based predictions are in good agreement with observed spatial patterns of ice loss, providing support for the notion that a significant portion of the current ice loss of the AIS is ocean driven and caused by a reduction in ice shelf buttressing.
Differential Heating Drives Downslope Flows that Accelerate Mixed‐Layer Warming in Ice‐Covered Waters
Authors: Ulloa Hugo N. , Winters Kraig B. , Wüest Alfred , Bouffard Damien
Published: November 2019

In ice‐covered lakes, penetrative radiation warms fluid beneath a diffusive boundary layer, thereby increasing its density and providing energy for convection in a diurnally active, deepening mixed layer. Shallow regions are differentially heated to warmer temperatures, driving turbulent gravity currents that transport warm water downslope and into the basin interior. We examine the energetics of these processes, focusing on the rate at which penetrative radiation supplies energy that is available to drive fluid motion. Using numerical simulations that resolve convective plumes, gravity currents, and the secondary instabilities leading to entrainment, we show that advective fluxes due to differential heating contribute to the evolution of the mixed layer in waterbodies with significant shallow areas. A heat balance is used to assess the relative importance of differential heating to the one‐dimensional effects of radiative heating and diffusive cooling at the ice‐water interface in lakes of varying morphologies.
Observation of a Large‐Amplitude Slow Magnetosonic Wave in the Magnetosheath
Authors: Zhao S. Q. , Xiao C. J. , Wang X. G. , Pu Z. Y. , Shi M. J. , Liu T. Z.
Published: November 2019

Using the Magnetospheric Multiscale spacecraft, we report observations of the pressure‐balanced structures in the form of slow magnetosonic waves rather than the mirror mode description in the Earth's magnetosheath. The slow magnetosonic waves are identified with three criteria: (1) The significant inverse correlation coefficients between the plasma thermal pressure (Pplasma) and the magnetic pressure (Pmag) with the constant total pressure (Ptot = Pplasma+Pmag); (2) the wave frequency Doppler shifted to the plasma flow frame is not zero to within the measurement error, which distinguishes the slow magnetosonic mode from the mirror mode; and (3) the observational dispersion relation is in a reasonable agreement with the linear theoretical result of slow magnetosonic waves. We find that slow magnetosonic waves can propagate over many wavelengths with negligible decay due to their transverse propagation which dramatically decreases their kinetic damping rate. Furthermore, we propose a possible generation mechanism that a high‐speed ion beam resonates with the local ion acoustic mode contributing to the inverse Landau damping process that converts particle energy into waves.
Transition Zone Radiative Effects in Shortwave Radiation Parameterizations: Case of Weather Research and Forecasting Model
Authors: Jahani Babak , Calbó Josep , González Josep‐Abel
Published: November 2019

A number of studies have stated that the shift from a cloud‐free to cloudy atmosphere (and vice versa) contains an additional phase, named “Transition (or twilight) Zone”. However, the information available about radiative effects of this phase is very limited. Consequently, in most meteorological and climate studies, the area corresponding to the transition zone is considered as an area containing aerosol or optically thin clouds. This study investigates the differences in shortwave radiative effects driven from different treatments of the transition zone. To this aim, three of the shortwave radiation parameterizations (NewGoddard, Rapid Radiative Transfer Model for Global circulation models, and Fu‐Liou‐Gu) included in the Advanced Research Weather Research and Forecasting Model (WRF‐ARW) were isolated and adapted for one‐dimensional vertical simulations. These parameterizations were then utilized to perform simulations under ideal “cloud” and “aerosol” modes, for different values of (i) cloud optical depths resulting from different sizes of ice crystals or liquid droplets and mixing ratios; and (ii) different aerosol optical depths combined with various aerosol types. The resulting shortwave broadband total, direct, and diffuse irradiances at the Earth surface were analyzed. The uncertainties originated from different assumptions of a situation regarding to the transition zone are quite substantial for all the parameterizations. For all the parameterizations, direct and total irradiances are the least and most sensitive irradiances to different treatments of the transition zone, respectively. Differences in the radiative effects of transition zone dominantly result from the difference between the radiative effects of clouds and aerosols (different types), not from cloud type or droplet/crystal size.
Low-loss silicon core fibre platform for mid-infrared nonlinear photonics
Authors: Ren Haonan , Shen Li , Runge Antoine F. J. , Hawkins Thomas W. , Ballato John , Gibson Ursula , Peacock Anna C.
Published: November 2019

Broadband mid-infrared light sources are highly desired for wide-ranging applications that span free-space communications to spectroscopy. In recent years, silicon has attracted great interest as a platform for nonlinear optical wavelength conversion in this region, owing to its low losses (linear and nonlinear) and high stability. However, most research in this area has made use of small core waveguides fabricated from silicon-on-insulator platforms, which suffer from high absorption losses of the use of silica cladding, limiting their ability to generate light beyond 3 µm. Here, we design and demonstrate a compact silicon core, silica-clad waveguide platform that has low losses across the entire silicon transparency window. The waveguides are fabricated from a silicon core fibre that is tapered to engineer mode properties to ensure efficient nonlinear propagation in the core with minimal interaction of the mid-infrared light with the cladding. These waveguides exhibit many of the benefits of fibre platforms, such as a high coupling efficiency and power handling capability, allowing for the generation of mid-infrared supercontinuum spectra with high brightness and coherence spanning almost two octaves (1.6–5.3 µm).
Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
Authors: Doud Devin F R , Bowers Robert M , Schulz Frederik , De Raad Markus , Deng Kai , Tarver Angela , Glasgow Evan , Vander Meulen Kirk , Fox Brian , Deutsch Sam , Yoshikuni Yasuo , Northen Trent , Hedlund Brian P , Singer Steven W , Ivanova Natalia , Woyke Tanja
Published: November 2019

Assigning a functional role to a microorganism has historically relied on cultivation of isolates or detection of environmental genome-based biomarkers using a posteriori knowledge of function. However, the emerging field of function-driven single-cell genomics aims to expand this paradigm by identifying and capturing individual microbes based on their in situ functions or traits. To identify and characterize yet uncultivated microbial taxa involved in cellulose degradation, we developed and benchmarked a function-driven single-cell screen, which we applied to a microbial community inhabiting the Great Boiling Spring (GBS) Geothermal Field, northwest Nevada. Our approach involved recruiting microbes to fluorescently labeled cellulose particles, and then isolating single microbe-bound particles via fluorescence-activated cell sorting. The microbial community profiles prior to sorting were determined via bulk sample 16S rRNA gene amplicon sequencing. The flow-sorted cellulose-bound microbes were subjected to whole genome amplification and shotgun sequencing, followed by phylogenetic placement. Next, putative cellulase genes were identified, expressed and tested for activity against derivatives of cellulose and xylose. Alongside typical cellulose degraders, including members of the Actinobacteria, Bacteroidetes, and Chloroflexi, we found divergent cellulases encoded in the genome of a recently described candidate phylum from the rare biosphere, Goldbacteria, and validated their cellulase activity. As this genome represents a species-level organism with novel and phylogenetically distinct cellulolytic activity, we propose the name Candidatus ‘Cellulosimonas argentiregionis’. We expect that this function-driven single-cell approach can be extended to a broad range of substrates, linking microbial taxonomy directly to in situ function.
NAD+ augmentation restores mitophagy and limits accelerated aging in Werner syndrome
Authors: Fang Evandro F. , Hou Yujun , Lautrup Sofie , Jensen Martin Borch , Yang Beimeng , SenGupta Tanima , Caponio Domenica , Khezri Rojyar , Demarest Tyler G. , Aman Yahyah , Figueroa David , Morevati Marya , Lee Ho-Joon , Kato Hisaya , Kassahun Henok , Lee Jong-Hyuk , Filippelli Deborah , Okur Mustafa Nazir , Mangerich Aswin , Croteau Deborah L. , Maezawa Yoshiro , Lyssiotis Costas A. , Tao Jun , Yokote Koutaro , Rusten Tor Erik , Mattson Mark P. , Jasper Heinrich , Nilsen Hilde , Bohr Vilhelm A.
Published: November 2019

Metabolic dysfunction is a primary feature of Werner syndrome (WS), a human premature aging disease caused by mutations in the gene encoding the Werner (WRN) DNA helicase. WS patients exhibit severe metabolic phenotypes, but the underlying mechanisms are not understood, and whether the metabolic deficit can be targeted for therapeutic intervention has not been determined. Here we report impaired mitophagy and depletion of NAD+, a fundamental ubiquitous molecule, in WS patient samples and WS invertebrate models. WRN regulates transcription of a key NAD+ biosynthetic enzyme nicotinamide nucleotide adenylyltransferase 1 (NMNAT1). NAD+ repletion restores NAD+ metabolic profiles and improves mitochondrial quality through DCT-1 and ULK-1-dependent mitophagy. At the organismal level, NAD+ repletion remarkably extends lifespan and delays accelerated aging, including stem cell dysfunction, in Caenorhabditis elegans and Drosophila melanogaster models of WS. Our findings suggest that accelerated aging in WS is mediated by impaired mitochondrial function and mitophagy, and that bolstering cellular NAD+ levels counteracts WS phenotypes.
Plasmon-enhanced stimulated Raman scattering microscopy with single-molecule detection sensitivity
Authors: Zong Cheng , Premasiri Ranjith , Lin Haonan , Huang Yimin , Zhang Chi , Yang Chen , Ren Bin , Ziegler Lawrence D. , Cheng Ji-Xin
Published: November 2019

Stimulated Raman scattering (SRS) microscopy allows for high-speed label-free chemical imaging of biomedical systems. The imaging sensitivity of SRS microscopy is limited to ~10 mM for endogenous biomolecules. Electronic pre-resonant SRS allows detection of sub-micromolar chromophores. However, label-free SRS detection of single biomolecules having extremely small Raman cross-sections (~10−30 cm2 sr−1) remains unreachable. Here, we demonstrate plasmon-enhanced stimulated Raman scattering (PESRS) microscopy with single-molecule detection sensitivity. Incorporating pico-Joule laser excitation, background subtraction, and a denoising algorithm, we obtain robust single-pixel SRS spectra exhibiting single-molecule events, verified by using two isotopologues of adenine and further confirmed by digital blinking and bleaching in the temporal domain. To demonstrate the capability of PESRS for biological applications, we utilize PESRS to map adenine released from bacteria due to starvation stress. PESRS microscopy holds the promise for ultrasensitive detection and rapid mapping of molecular events in chemical and biomedical systems.
The genome of a subterrestrial nematode reveals adaptations to heat
Authors: Weinstein Deborah J. , Allen Sarah E. , Lau Maggie C. Y. , Erasmus Mariana , Asalone Kathryn C. , Walters-Conte Kathryn , Deikus Gintaras , Sebra Robert , Borgonie Gaetan , van Heerden Esta , Onstott Tullis C. , Bracht John R.
Published: November 2019

The nematode Halicephalobus mephisto was originally discovered inhabiting a deep terrestrial aquifer 1.3 km underground. H. mephisto can thrive under conditions of abiotic stress including heat and minimal oxygen, where it feeds on a community of both chemolithotrophic and heterotrophic prokaryotes in an unusual ecosystem isolated from the surface biosphere. Here we report the comprehensive genome and transcriptome of this organism, identifying a signature of adaptation: an expanded repertoire of 70 kilodalton heat-shock proteins (Hsp70) and avrRpt2 induced gene 1 (AIG1) proteins. The expanded Hsp70 genes are transcriptionally induced upon growth under heat stress, and we find that positive selection is detectable in several members of this family. We further show that AIG1 may have been acquired by horizontal gene transfer (HGT) from a rhizobial fungus. Over one-third of the genes of H. mephisto are novel, highlighting the divergence of this nematode from other sequenced organisms. This work sheds light on the genomic basis of heat tolerance in a complete subterrestrial eukaryotic genome.
Phenotypic transitions enacted by simulated microgravity do not alter coherence in gene transcription profile
Authors: Po Agnese , Giuliani Alessandro , Masiello Maria Grazia , Cucina Alessandra , Catizone Angela , Ricci Giulia , Chiacchiarini Martina , Tafani Marco , Ferretti Elisabetta , Bizzarri Mariano
Published: November 2019

Cells in simulated microgravity undergo a reversible morphology switch, causing the appearance of two distinct phenotypes. Despite the dramatic splitting into an adherent-fusiform and a floating-spherical population, when looking at the gene-expression phase space, cell transition ends up in a largely invariant gene transcription profile characterized by only mild modifications in the respective Pearson’s correlation coefficients. Functional changes among the different phenotypes emerging in simulated microgravity using random positioning machine are adaptive modifications—as cells promptly recover their native phenotype when placed again into normal gravity—and do not alter the internal gene coherence. However, biophysical constraints are required to drive phenotypic commitment in an appropriate way, compatible with physiological requirements, given that absence of gravity foster cells to oscillate between different attractor states, thus preventing them to acquire a exclusive phenotype. This is a proof-of-concept of the adaptive properties of gene-expression networks supporting very different phenotypes by coordinated ‘profile preserving’ modifications.
A large-scale dataset for mitotic figure assessment on whole slide images of canine cutaneous mast cell tumor
Authors: Bertram Christof A. , Aubreville Marc , Marzahl Christian , Maier Andreas , Klopfleisch Robert
Published: November 2019

We introduce a novel, large-scale dataset for microscopy cell annotations. The dataset includes 32 whole slide images (WSI) of canine cutaneous mast cell tumors, selected to include both low grade cases as well as high grade cases. The slides have been completely annotated for mitotic figures and we provide secondary annotations for neoplastic mast cells, inflammatory granulocytes, and mitotic figure look-alikes. Additionally to a blinded two-expert manual annotation with consensus, we provide an algorithm-aided dataset, where potentially missed mitotic figures were detected by a deep neural network and subsequently assessed by two human experts. We included 262,481 annotations in total, out of which 44,880 represent mitotic figures. For algorithmic validation, we used a customized RetinaNet approach, followed by a cell classification network. We find F1-Scores of 0.786 and 0.820 for the manually labelled and the algorithm-aided dataset, respectively. The dataset provides, for the first time, WSIs completely annotated for mitotic figures and thus enables assessment of mitosis detection algorithms on complete WSIs as well as region of interest detection algorithms.
Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos
Authors: Yin ZhongTao , Zhang Fan , Smith Jacqueline , Kuo Richard , Hou Zhuo-Cheng
Published: November 2019

Duck (Anas platyrhynchos), one of the most economically important waterfowl, is an ideal model for studying the immune protection mechanism of birds. An incomplete duck reference genome and very limited availability of full-length cDNAs has hindered the identification of alternatively spliced transcripts and slowed down many basic studies in ducks. We applied PacBio Iso-Seq technologies to multiple tissues from duck for use in transcriptome sequencing. We obtained 199,993 full-length transcripts and comprehensively annotated these transcripts. 23,755 lncRNAs were predicted from all identified transcripts and 35,031 alternative splicing events, which divided into 5 models, were accurately predicted from 3,346 genes. Our data constitute a large increase in the known number of both lncRNA, and alternatively spliced transcripts of duck and plays an important role in improving current genome annotation. In addition, the data will be extremely useful for functional studies in other birds.
Diversified Floral Resource Plantings Support Bee Communities after Apple Bloom in Commercial Orchards
Authors: Heller Sarah , Joshi Neelendra K. , Leslie Timothy , Rajotte Edwin G. , Biddinger David J.
Published: November 2019

Natural habitats, comprised of various flowering plant species, provide food and nesting resources for pollinator species and other beneficial arthropods. Loss of such habitats in agricultural regions and in other human-modified landscapes could be a factor in recent bee declines. Artificially established floral plantings may offset these losses. A multi-year, season-long field study was conducted to examine how wildflower plantings near commercial apple orchards influenced bee communities. We examined bee abundance, species richness, diversity, and species assemblages in both the floral plantings and adjoining apple orchards. We also examined bee community subsets, such as known tree fruit pollinators, rare pollinator species, and bees collected during apple bloom. During this study, a total of 138 species of bees  were collected, which included 100 species in the floral plantings and 116 species in the apple orchards. Abundance of rare bee species was not significantly different between apple orchards and the floral plantings. During apple bloom, the known tree fruit pollinators were more frequently captured in the orchards than the floral plantings. However, after apple bloom, the abundance of known tree fruit pollinating bees increased significantly in the floral plantings, indicating potential for floral plantings to provide additional food and nesting resources when apple flowers are not available.
Two Quenchers Formed During Photodamage of Phostosystem II and The Role of One Quencher in Preemptive Photoprotection
Authors: Zavafer Alonso , Iermak Ievgeniia , Cheah Mun Hon , Chow Wah Soon
Published: November 2019

The quenching of chlorophyll fluorescence caused by photodamage of Photosystem II (qI) is a well recognized phenomenon, where the nature and physiological role of which are still debatable. Paradoxically, photodamage to the reaction centre of Photosystem II is supposed to be alleviated by excitation quenching mechanisms which manifest as fluorescence quenchers. Here we investigated the time course of PSII photodamage in vivo and in vitro and that of picosecond time-resolved chlorophyll fluorescence (quencher formation). Two long-lived fluorescence quenching processes during photodamage were observed and were formed at different speeds. The slow-developing quenching process exhibited a time course similar to that of the accumulation of photodamaged PSII, while the fast-developing process took place faster than the light-induced PSII damage. We attribute the slow process to the accumulation of photodamaged PSII and the fast process to an independent quenching mechanism that precedes PSII photodamage and that alleviates the inactivation of the PSII reaction centre.
Impact of Sex on Office White Coat Effect Tail: Investigating Two Italian Residential Cohorts
Authors: Humbert Xavier , Fedrizzi Sophie , Alexandre Joachim , Menotti Alessandro , Manrique Alain , Laurenzi Martino , Touzé Emmanuel , Puddu Paolo E.
Published: November 2019

To assess the impact of sex on office white-coat effect tail (OWCET), the waning of systolic blood pressure (SBP) after its waxing during office visit, on the incidence of long-term major fatal and non-fatal events in two Italian residential cohorts [from the Gubbio Study and the Italian Rural Areas of the Seven Countries Study (IRA)]. There were 3565 persons (92 with missing data, 44% men, 54 ± 11 years) included in the Gubbio and 1712 men (49 ± 5 years) in the IRA studies. OWCET was defined as a decrease of ≥10 mmHg in SBP between successive measurements with slight measurement differences between the two cohorts. Cardiovascular (CVD), coronary heart disease (CHD) and stroke (STR) incidences were considered. Over an approximately 20-year follow-up, women with OWCET had an increased risk of CVD [HR: 1.591 (95%CI: 1.204–2.103)], CHD [HR: 1.614 (95%CI: 1.037–2.512)] and STR [HR: 1.696 (95%CI: 1.123–2.563)] events independently of age, serum and HDL cholesterol, cigarettes, BMI and SBP in the Gubbio study. However, there was no increased risk of CVD, CHD or STR in men with OWCET neither in the Gubbio 20-year follow-up nor in the IRA 50-year follow-up. These results were not modified significantly by the correction of the regression dilutions bias between the first and the subsequent SBP measurements. Thus, in primary care, OWCET should be actively evaluated in women as it can improve stratification of long-term CVD, CHD and STR risks.
Chern and Z2 topological insulating phases in perovskite-derived 4d and 5d oxide buckled honeycomb lattices
Authors: Köksal Okan , Pentcheva Rossitza
Published: November 2019

Based on density functional theory calculations including a Coulomb repulsion parameter U, we explore the topological properties of (LaXO3)2/(LaAlO3)4 (111) with X = 4d and 5d cations. The metastable ferromagnetic phases of LaTcO3 and LaPtO3 with preserved P321 symmetry emerge as Chern insulators (CI) with C = 2 and 1 and band gaps of 41 and 38 meV at the lateral lattice constant of LaAlO3, respectively. Berry curvatures, spin textures as well as edge states provide additional insight into the nature of the CI states. While for X = Tc the CI phase is further stabilized under tensile strain, for X = Pd and Pt a site disproportionation takes place when increasing the lateral lattice constant from aLAO to aLNO. The CI phase of X = Pt shows a strong dependence on the Hubbard U parameter with sign reversal for higher values associated with the change of band gap opening mechanism. Parallels to the previously studied (X2O3)1/(Al2O3)5 (0001) honeycomb corundum layers are discussed. Additionally, non-magnetic systems with X = Mo and W are identified as potential candidates for Z2 topological insulators at aLAO with band gaps of 26 and 60 meV, respectively. The computed edge states and Z2 invariants underpin the non-trivial topological properties.
Genome Wide Analysis Approach Suggests Chromosome 2 Locus to be Associated with Thiazide and Thiazide Like-Diuretics Blood Pressure Response
Authors: Singh Sonal , McDonough Caitrin W. , Gong Yan , Bailey Kent R. , Boerwinkle Eric , Chapman Arlene B. , Gums John G. , Turner Stephen T. , Cooper-DeHoff Rhonda M. , Johnson Julie A.
Published: November 2019

Chlorthalidone (CTD) is more potent than hydrochlorothiazide (HCTZ) in reducing blood pressure (BP) in hypertensive patients, though both are plagued with BP response variability. However, there is a void in the literature regarding the genetic determinants contributing to the variability observed in BP response to CTD. We performed a discovery genome wide association analysis of BP response post CTD treatment in African Americans (AA) and European Americans (EA) from the Pharmacogenomic Evaluation of Antihypertensive Responses-2 (PEAR-2) study and replication in an independent cohort of AA and EA treated with HCTZ from the PEAR study, followed by a race specific meta-analysis of the two studies. Successfully replicated SNPs were further validated in beta-blocker treated participants from PEAR-2 and PEAR for opposite direction of association. The replicated and validated signals were further evaluated by protein-protein interaction network analysis. An intronic SNP rs79237970 in the WDR92 (eQTL for PPP3R1) was significantly associated with better DBP response to CTD (p = 5.76 × 10−6, β = −15.75) in the AA cohort. This SNP further replicated in PEAR (p = 0.00046, β = −9.815) with a genome wide significant meta-analysis p-value of 8.49 × 10−9. This variant was further validated for opposite association in two β-blockers treated cohorts from PEAR-2 metoprolol (p = 9.9 × 10−3, β = 7.47) and PEAR atenolol (p = 0.04, β = 4.36) for association with DBP. Studies have implicated WDR92 in coronary artery damage. PPP3R1 is the regulatory subunit of the calcineurin complex. Use of calcineurin inhibitors is associated with HTN. Studies have also shown polymorphisms in PPP3R1 to be associated with ventricular hypertrophy in AA hypertensive patients. Protein-protein interaction analysis further identified important hypertension related pathways such as inositol phosphate-mediated signaling and calcineurin-NFAT signaling cascade as important biological process associated with PPP3R1 which further strengthen the potential importance of this signal. These data collectively suggest that WDR92 and PPP3R1 are novel candidates that may help explain the genetic underpinnings of BP response of thiazide and thiazide-like diuretics and help identify the patients better suited for thiazide and thiazide-like diuretics compared to β-blockers for improved BP management. This may further help advance personalized approaches to antihypertensive therapy.
Phosphorylation of PD-1-Y248 is a marker of PD-1-mediated inhibitory function in human T cells
Authors: Bardhan Kankana , Aksoylar Halil-Ibrahim , Le Bourgeois Thibault , Strauss Laura , Weaver Jessica D. , Delcuze Bethany , Charest Alain , Patsoukis Nikolaos , Boussiotis Vassiliki A.
Published: November 2019

PD-1 is a target of cancer immunotherapy but responses are limited to a fraction of patients. Identifying patients with T cells subjected to PD-1-mediated inhibition will allow selection of suitable candidates for PD-1-blocking therapy and will improve the therapeutic success. We sought to develop an approach to detect PD-1-mediated inhibitory signaling. The cytoplasmic tail of PD-1 contains an immunoreceptor tyrosine-based inhibitory motif (ITIM) encompassing Y223 and an immunoreceptor tyrosine-based switch motif (ITSM) encompassing Y248, which is indispensable for interaction of SHP-2 and delivery of PD-1 inhibitory function. We generated an antibody specific for phosphorylated PD-1-Y248 and examined PD-1pY248+ (pPD-1) expression in human T cells. pPD-1 was upregulated by TCR/CD3 + CD28 stimulation and simultaneous PD-1 ligation. pPD-1+CD8+ T cells were identified in human peripheral blood and had impaired effector function. pPD-1+ T cells were also detected in tumor-draining lymph nodes of tumor bearing mice and in biopsies of patients with glioblastoma multiform. Detection of pPD-1+ T cells might serve as a biomarker for identification of T cells subjected to PD-1-mediated immunosuppression.
Micro-scale patchiness enhances trophic transfer efficiency and potential plankton biodiversity
Authors: Priyadarshi Anupam , Smith S. Lan , Mandal Sandip , Tanaka Mamoru , Yamazaki Hidekatsu
Published: November 2019

Rather than spatial means of biomass, observed overlap in the intermittent spatial distributions of aquatic predators and prey is known to be more important for determining the flow of nutrients and energy up the food chain. A few previous studies have separately suggested that such intermittency enhances phytoplankton growth and trophic transfer to sustain zooplankton and ultimately fisheries. Recent observations have revealed that phytoplankton distributions display consistently high degrees of mm scale patchiness, increasing along a gradient from estuarine to open ocean waters. Using a generalized framework of plankton ecosystem models with different trophic configurations, each accounting for this intermittency, we show that it consistently enhances trophic transfer efficiency (TE), i.e. the transfer of energy up the food chain, and expands the model stability domain. Our results provide a new explanation for observation-based estimates of unexpectedly high TE in the vast oligotrophic ocean and suggest that by enhancing the viable trait space, micro-scale variability may potentially sustain plankton biodiversity.
Effects of sampling strategy and DNA extraction on human skin microbiome investigations
Authors: Bjerre Rie Dybboe , Hugerth Luisa Warchavchik , Boulund Fredrik , Seifert Maike , Johansen Jeanne Duus , Engstrand Lars
Published: November 2019

The human skin is colonized by a wide array of microorganisms playing a role in skin disorders. Studying the skin microbiome provides unique obstacles such as low microbial biomass. The objective of this study was to establish methodology for skin microbiome analyses, focusing on sampling technique and DNA extraction. Skin swabs and scrapes were collected from 9 healthy adult subjects, and DNA extracted using 12 commercial kits. All 165 samples were sequenced using the 16S rRNA gene. Comparing the populations captured by eSwabs and scrapes, 99.3% of sequences overlapped. Using eSwabs yielded higher consistency. The success rate of library preparation applying different DNA extraction kits ranged from 39% to 100%. Some kits had higher Shannon alpha-diversity. Metagenomic shotgun analyses were performed on a subset of samples (N = 12). These data indicate that a reduction of human DNA from 90% to 57% is feasible without lowering the success of 16S rRNA library preparation and without introducing taxonomic bias. Using swabs is a reliable technique to investigate the skin microbiome. DNA extraction methodology is crucial for success of sequencing and adds a substantial amount of variation in microbiome analyses. Reduction of host DNA is recommended for interventional studies applying metagenomics.
Terminal fucose mediates progression of human cholangiocarcinoma through EGF/EGFR activation and the Akt/Erk signaling pathway
Authors: Indramanee Somsiri , Sawanyawisuth Kanlayanee , Silsirivanit Atit , Dana Paweena , Phoomak Chatchai , Kariya Ryusho , Klinhom-on Nathakan , Sorin Supannika , Wongkham Chaisiri , Okada Seiji , Wongkham Sopit
Published: November 2019

Aberrant glycosylation is recognized as a cancer hallmark that is associated with cancer development and progression. In this study, the clinical relevance and significance of terminal fucose (TFG), by fucosyltransferase-1 (FUT1) in carcinogenesis and progression of cholangiocarcinoma (CCA) were demonstrated. TFG expression in human and hamster CCA tissues were determined using Ulex europaeus agglutinin-I (UEA-I) histochemistry. Normal bile ducts rarely expressed TFG while 47% of CCA human tissues had high TFG expression and was correlated with shorter survival of patients. In the CCA-hamster model, TFG was elevated in hyperproliferative bile ducts and gradually increased until CCA was developed. This evidence indicates the involvement of TFG in carcinogenesis and progression of CCA. The mechanistic insight was performed in 2 CCA cell lines. Suppression of TFG expression using siFUT1 or neutralizing the surface TFG with UEA-I significantly reduced migration, invasion and adhesion of CCA cells in correlation with the reduction of Akt/Erk signaling and epithelial-mesenchymal transition. A short pulse of EGF could stimulate Akt/Erk signaling via activation of EGF-EGFR cascade, however, decreasing TFG using siFUT1 or UEA-I treatment reduced the EGF-EGFR activation and Akt/Erk signaling. This evidence provides important insight into the relevant role and molecular mechanism of TFG in progression of CCA.