bluuebunny/crossref_metadata_2025 huggingface dataset:
Imaging the dust and the gas around Mira using ALMA and SPHERE/ZIMPOL
Authors: Khouri Theo , Vlemmings Wouter H. T. , Olofsson Hans , Ginski Christian , De Beck Elvire , Maercker Matthias , Ramstedt Sofia
Published: January 2020

The mass-loss mechanism of asymptotic giant branch stars has long been thought to rely on two processes: stellar pulsations and dust formation. The details of the mass-loss mechanism have remained elusive, however, because of the overall complexity of the dust formation process in the very dynamical pulsation-enhanced atmosphere. Recently, our understanding of AGB stars and the associated mass loss has evolved significantly, thanks both to new instruments which allow sensitive and high-angular-resolution observations and the development of models for the convective AGB envelopes and the dust formation process. ALMA and SPHERE/ZIMPOL on the VLT have been very important instruments in driving this advance in the last few years by providing high-angular resolution images in the sub-mm and visible wavelengths, respectively. I will present observations obtained using these instruments at the same epoch (2.5 weeks apart) of the AGB star Mira that resolve even the stellar disk. The ALMA data reveals the distribution and dynamics of the gas around the star, while the polarised light imaged using SPHERE shows the distribution of the dust grains expected to drive the outflows. Moreover, the observations show a central source surrounded by asymmetric distributions of gas and dust, with complementary structures seen in the two components. We model the observed CO v = 1, J = 3−2 line to determine the density, temperature and velocity of gas close to the star. This model is then used to estimate the abundance of AlO. Our results show that only a very small fraction of aluminium (≲0.1%) is locked in AlO molecules. We also calculate models to fit the observed polarised light based on the gas densities we find. The low level of visible-light polarisation detected using ZIMPOL implies that, at the time of the observations, aluminium atoms are either not efficiently depleted into dust or the aluminium-oxide grains are relatively small (≲0.02μm).
Separation of gas and dust in the winds of AGB stars
Authors: Mattsson Lars , Sandin Christer , Ventura Paolo
Published: January 2020

We present first results from a project aiming at a better understanding of how gas and dust interact in dust-driven winds from Asymptotic Giant Branch (AGB) stars. We are at the final stage of developing a new parallelised radiation-hydrodynamics (RHD) code for AGB-wind modelling including a new generalised implementation of drift. We also discuss first results from high-resolution box simulations of forced turbulence intended to give quantitative “3D corrections” to dust-driven winds from AGB stars. It is argued that modelling of dust-driven winds of AGB stars is a problem that may need to be treated in a less holistic way, where some parts of the problem are treated separately in detailed simulations and are parameterised back into a less detailed (1D spherically symmetric) model describing the entire picture.
Spectroscopic binaries among AGB stars from HERMES/Mercator: the case of V Hya
Authors: Jorissen Alain , Van Eck Sophie , Merle Thibault , Van Winckel Hans
Published: January 2020

We report on our search for spectroscopic binaries among a sample of AGB stars. Observations were carried out in the framework of the monitoring of radial velocities of (candidate) binary stars performed at the Mercator 1.2m telescope, using the HERMES spectrograph. We found evidence for duplicity in UV Cam, TU Tau, BL Ori, VZ Per, T Dra, and V Hya.
Near-Infrared Stellar Populations in the metal-poor, Dwarf irregular Galaxies Sextans A and Leo A
Authors: Jones Olivia C. , Maclay Matthew T. , Boyer Martha L. , Meixner Margaret , McDonald Iain
Published: January 2020

We present JHK observations of the metal-poor $$(\left[ {{\rm{Fe}}/{\rm{H}}} \right] < - 1.40)$$ dwarf-irregular galaxies, Leo A and Sextans A, obtained with the WIYN High-resolution Infrared Camera. Their near-IR stellar populations are characterized by using a combination of color-magnitude diagrams and by identifying long-period variable (LPV) stars. We detected red giant and asymptotic giant branch (AGB) stars, consistent with membership of the galaxy’s intermediate-age populations (2-8 Gyr old). We identify 32 dusty evolved stars in Leo A and 101 dusty stars in Sextans A, confirming that metal-poor stars can form substantial amounts of dust. We also find tentative evidence for oxygen-rich dust formation at low metallicity, contradicting previous models that suggest oxygen-rich dust production is inhibited in metal-poor environments. The majority of this dust is produced by a few very dusty evolved stars.
AGB stars and the cosmic dust cycle
Authors: Zhukovska Svitlana
Published: January 2020

Theoretical and observational studies of dust condensed in outflows of AGB stars have substantially advanced the understanding of dust mixture from individual stars. This detailed information incorporated in models of the lifecycle of interstellar grains provides a flexible tool to study the contribution of AGB stars to the galactic dust budget. The role of these stars in dust production depends on the morphological type and age of galaxy. While AGB stars are sub-dominant dust sources in evolved systems as the Milky Way, the observed relation between the dust-to-gas ratio and metallicity suggests that the dust input in young dwarf galaxies with 7≲12+log(O/H)≲8 can be dominated by the AGB stars. In application to post-starburst and early-type galaxies, the models for stardust evolution in combination with modern infrared observations give insights in the origin of their high dust content and its implications for their evolutionary scenarios.
SWAG: Distribution and Kinematics of an Obscured AGB Population toward the Galactic Center
Authors: Ott Jürgen , Meier David S. , Ginsburg Adam , Yusef-Zadeh Farhad , Krieger Nico , Jäschke Cornelia
Published: January 2020

Outflows from AGB stars enrich the Galactic environment with metals and inject mechanical energy into the ISM. Radio spectroscopy can recover both properties through observations of molecular lines. We present results from SWAG: “Survey of Water and Ammonia in the Galactic Center”. The survey covers the entire Central Molecular Zone (CMZ), the inner 3.35° × 0.9° (∼480 × 130 pc) of the Milky Way that contains 5 × 107 M⊙ of molecular gas. Although our survey primarily targets the CMZ, we observe across the entire sightline through the Milky Way. AGB stars are revealed by their signature of double peaked 22 GHz water maser lines. They are distinguished by their spectral signatures and their luminosities, which reach up to 10−7 L⊙. Higher luminosities are usually associated with Young Stellar Objects located in CMZ star forming regions. We detect a population of ∼600 new water masers that can likely be associated with AGB outflows.
Circumstellar molecular maser emission of AGB and post-AGB stars
Authors: Rudnitskij Georgij , Ashimbaeva Nuriya , Colom Pierre , Lekht Evgeny , Pashchenko Mikhail , Tolmachev Alexander
Published: January 2020

Results of long-term studies of circumstellar molecular maser emission of late-type giant and supergiant variable stars are reported. In the 1.35-cm H2O line, the peak flux density correlates with the optical brightness lagging behind it by 0.3–0.4 P (P is the stellar period). “Superperiods” of 10 to 15 P are visible in several stars, demonstrated as high maxima in the visible light curve and associated flares in the H2O maser line. In the 18-cm OH lines, full polarization of the maser emission has been measured. Variable Zeeman patterns suggesting a changing magnetic field of a few milligauss have been detected.
Abundance Estimates in Carbon Star Envelopes
Authors: Massalkhi S. , Agúndez M. , Cernicharo J.
Published: January 2020

The synthesis of dust grains mostly takes place in the circumstellar envelopes (CSEs) of asymptotic giant branch (AGB) stars. What are the precursor seeds of condensation nuclei and how do these particles evolve toward the micrometer sized grains that populate the interstellar medium? These are key questions of the NANOCOSMOS project. In this study, we carried out an observational study to constrain what the main gas-phase precursors of dust in C-rich AGB stars are.
OH/IR stars versus YSOs in infrared photometric surveys
Authors: Loup Cécile , Allen Mark , Lançon Ariane , Oberto Anais
Published: January 2020

AGB stars play a major role in the chemical evolution of the galaxies. It thus is important to establish reliable photometric selection criteria to count them, especially AGB stars at the last stages of AGB evolution like OH/IR stars. Here, we have identified about 1500 OH/IR stars and 500 YSOs with methanol masers, in all major mid– and far–infrared surveys (IRAS, MSX, AKARI, WISE, GLIMPSE, and Hi–Gal). We show that AGB stars with high mass-loss rates cannot be disentagled from YSOs with only mid–infrared photometry; far–infrared photometry is essential. In the region observed by GLIMPSE, we show that the proportion of AGB stars has been severely underestimated in previous works: about 70% of “intrinsically” red objects in GLIMPSE are AGB stars rather than YSOs.
Rawinsonde‐Based Analysis of the Urban Boundary Layer in the Metropolitan Region of São Paulo, Brazil
Authors: Piñero Sánchez Maciel , de Oliveira Amauri Pereira , Varona Ramón Pérez , Tito Janet Valdés , Codato Georgia , Ribeiro Flávia Noronha Dutra , Marques Filho Edson Pereira , Silveira Lucas Cardoso da
Published: January 2020

The main features of the urban boundary layer in the metropolitan region of São Paulo are estimated based on rawinsondes carried out (a) every 3 hr in two 10‐day field campaigns of the MCITY BRAZIL Project during the summer and winter of 2013 and (b) regularly once per day and continuously for 4 years from 2009 to 2013. On average, the boundary layer height showed a daytime maximum of 1476 ± 149 m in summer and 1122 ± 168 m in winter campaigns. The differences are related to seasonal variations in the (a) buoyancy flux at the surface, which was 30% larger in summer (4.7 ± 0.6 MJ m−2 day−1), and the (b) static stability of the free atmosphere, which was 15% smaller in summer (3.3 ± 0.1 K km−1). The average nighttime boundary layer height, estimated from equilibrium empirical expression, indicated maximum of 126 ± 13 m in summer and 122 ± 10 m in winter campaigns. The presence of a low‐level jet was identified in 80% of the field campaign nights, with intensity varying from 2.7 to 14 m s−1 and height ranging from 95 to 962 m. The nighttime residual‐mixing layer is well estimated using the air temperature gradient method and is a good indication of the maximum vertical evolution of the previous daytime boundary layer. The monthly average maximum boundary layer height varied from a minimum of 1,061 ± 77 m in September to maximum of 1,632 ± 96 m in May.
On the Derivation of Geometric Optical Kernels for Directional Thermal Radiation
Authors: Liu Xiangyang , Tang Bo‐Hui , Li Zhao‐Liang , Zhang Xia , Shang Guofei
Published: January 2020

The derivation of widely used geometric optical (GO) kernels in bidirectional reflectance distribution function models, that is, LiSparseReciprocal kernel (KGOLSR) and LiDenseReciprocal kernel, was based on two important assumptions: (1) The shaded components are perfect black and (2) the contributions of two sunlit components are identical. Different from the bidirectional reflectance, thermal radiation directionality effect mainly results from component temperature differences, suggesting the above assumptions are not applicable in most situations. Therefore, this study derived GO kernels for thermal radiation based on temperature differences rather than illumination differences. Specifically, four GO kernels, that is, KGO4 with considering sunlit/shaded vegetation and sunlit/shaded soil, KGO3 with considering sunlit/shaded soil and vegetation, KGO2 with considering vegetation and soil, and KGOg only considering the hottest sunlit soil, have been developed. By using a comprehensive simulated data set, their performances have been thoroughly evaluated and the comparison with KGOLSR has also been analyzed in depth. Results showed that (1) KGO4 had the highest accuracy and KGO3 was the second; in the case of only two available angles, KGOg performed best. (2) Variables such as component temperature, component emissivity, solar zenith angle, and the percentage of tree crown cover mainly affected the comparison result between KGOLSR and KGO2; KGOLSR would have a better performance for a scene with a stronger vegetation effect. Moreover, the best values of two structure characteristics, that is, the crown shape parameter b/r and relative height h/b, for these five kernels have been determined, which can provide instruction for practical application.
Improving Mass Conservation With the Tracer Ratio Method: Application to Thermochemical Mantle Flows
Authors: Trim S. J. , Lowman J. P. , Butler S. L.
Published: January 2020

Modeling the evolution of composition in a convecting mantle is difficult since the associated chemical diffusivity is very small. Consequently, compositional evolution is often modeled using the advection equation which is prone to overdiffusion and spurious oscillations unless special numerical schemes are employed. Similar errors can also occur while modeling the evolution of temperature, since mantle convection is advection dominated. One numerical scheme designed to minimize such errors is the tracer ratio method, in which Lagrangian tracers are used to track each composition in the system in addition to carrying local temperature values that are time dependent. However, tracer spacing may become very uneven during evolution, which can contribute to errors in mass and energy conservation. In this study, a tracer repositioning algorithm designed to promote even tracer coverage is presented and tested using over 400 calculations in a large thermal Rayleigh number/buoyancy ratio parameter space. In particular, the effect of tracer repositioning on mass and energy conservation errors is examined. In most cases, we find that energy errors are roughly an order of magnitude less than mass errors, regardless of tracer repositioning. However, in situations with substantial entrainment of compositionally distinct material, mass errors can be reduced by up to an order of magnitude if tracers are repositioned during model evolution. We also find that for a fixed buoyancy ratio, entrainment of basal material decreases as the thermal Rayleigh number increases.
Diurnal Variation of Meiyu Rainfall in the Yangtze Plain During Atypical Meiyu Years
Authors: Zhang A. Q. , Chen Y. L. , Zhou S. N. , Cui C. G. , Wan R. , Fu Y. F.
Published: January 2020

The diurnal variation of precipitation reflects the influence of atmospheric heat and dynamic processes on the water cycle. Using multiple data sets, we carried out case studies and statistical analysis of the diurnal variation in Meiyu rainfall in atypical Meiyu years. Our results show that the morning precipitation was induced by strong southwesterly moisture transport and was mainly composed of stratiform pixels, whereas the precipitation occurring in the afternoon was mainly composed of convective pixels affected by updrafts. The diurnal variation in precipitation in the atypical Meiyu years appeared as a bimodal structure with peaks in early morning (06:30 LST) and afternoon (16:00 LST), which was different from the single morning peak (09:30 LST) in the normal Meiyu years and reported previously. Further research indicated that the morning peak is related to the low‐level water vapor flux, whereas the afternoon peak is related to the local solar heating. In addition, the water vapor flux in the Yangtze Plain was characterized by strong morning and weak afternoon fluxes during both normal and atypical Meiyu periods. The diurnal variation in the low‐level water vapor flux is thought to be influenced by the intensity of, and distance from, the subtropical high.
Similarities and Differences of Global Dust Storms in MY 25, 28, and 34
Authors: Wolkenberg P. , Giuranna M. , Smith M. D. , Grassi D. , Amoroso M.
Published: January 2020

To better understand the dust cycle on Mars during years with planet‐encircling dust storms, we analyze the last three events that took place in Mars Year (MY) 25, MY 28, and MY 34. Global dust storms that occurred in MY 25 and MY 34 (June 2018) were taking place during equinox, while the MY 28 storm had an onset after perihelion. Before the expansion phase of the MY 25 and MY 34 storms, we find similar regions (northern rim of Hellas, Arabia Terra, and Utopia Planitia) where dust is present. Possible precursor dust storms over Hellas and the southern polar cap edges were observed during MY 28 as a component of background dust activity. These features are not found in equinoctial dust storms on this scale. Dust during the MY 25 and MY 34 storms encircled the entire planet by the similar season (Ls = 193°). The MY 34 storm is characterized by a shorter decay phase compared to the events in MY 25 and MY 28. Dust opacity is correlated with atmospheric temperatures at 0.5 mbar and nighttime surface temperatures, while daytime surface temperatures are anticorrelated with dust opacity.
Regional Correlations in the Layered Deposits of Arabia Terra, Mars
Authors: Annex Andrew M. , Lewis Kevin W.
Published: January 2020

In the mid‐equatorial region of Arabia Terra, Mars, dozens of moderately sized impact craters (10 to 100 km diameter) contain layered sedimentary deposits. Previous work has found that these layers are resolvable at the meter scale and that they are quasiperiodic in expression. However, the interrelationships of these deposits, along with their formative depositional process, has not yet been determined. Proposed formation mechanisms include fluviolacustrine deposition, groundwater upwelling and evaporation, and aeolian or distal volcanic air fall. For this study, we measured layer thicknesses from stereo image‐derived topography within nine craters. We find two regionally extensive layered units with characteristic average bed thicknesses of 12 and 3.5 m and a possible third unit of intermediate thickness. Each unit was identified in a number of craters forming regionally consistent groups. These proposed units represent the first regional correlations of isolated sedimentary deposits in Arabia Terra and point to blanketing regional deposition over at least two separate geologic periods.
CD93 is expressed on chronic myeloid leukemia stem cells and identifies a quiescent population which persists after tyrosine kinase inhibitor therapy
Authors: Kinstrie Ross , Horne Gillian A. , Morrison Heather , Irvine David , Munje Chinmay , Castañeda Eduardo Gómez , Moka Hothri A. , Dunn Karen , Cassels Jennifer E. , Parry Narissa , Clarke Cassie J. , Scott Mary T. , Clark Richard E. , Holyoake Tessa L. , Wheadon Helen , Copland Mhairi
Published: January 2020

The introduction of BCR-ABL tyrosine kinase inhibitors has revolutionized the treatment of chronic myeloid leukemia (CML). A major clinical aim remains the identification and elimination of low-level disease persistence, termed “minimal residual disease”. The phenomenon of disease persistence suggests that despite targeted therapeutic approaches, BCR-ABL-independent mechanisms exist which sustain the survival of leukemic stem cells (LSCs). Although other markers of a primitive CML LSC population have been identified in the preclinical setting, only CD26 appears to offer clinical utility. Here we demonstrate consistent and selective expression of CD93 on a lin−CD34+CD38−CD90+CML LSC population and show in vitro and in vivo data to suggest increased stem cell characteristics, as well as robust engraftment in patient-derived xenograft models in comparison with a CD93−CML stem/progenitor cell population, which fails to engraft. Through bulk and single-cell analyses of selected stem cell and cell survival-specific genes, we confirmed the quiescent character and demonstrate their persistence in a population of CML patient samples who demonstrate molecular relapse on TKI withdrawal. Taken together, our results identify that CD93 is consistently and selectively expressed on a lin−CD34+CD38−CD90+CML LSC population with stem cell characteristics and may be an important indicator in determining poor TKI responders.
The clinical mutatome of core binding factor leukemia
Authors: Opatz Sabrina , Bamopoulos Stefanos A. , Metzeler Klaus H. , Herold Tobias , Ksienzyk Bianka , Bräundl Kathrin , Tschuri Sebastian , Vosberg Sebastian , Konstandin Nikola P. , Wang Christine , Hartmann Luise , Graf Alexander , Krebs Stefan , Blum Helmut , Schneider Stephanie , Thiede Christian , Middeke Jan Moritz , Stölzel Friedrich , Röllig Christoph , Schetelig Johannes , Ehninger Gerhard , Krämer Alwin , Braess Jan , Görlich Dennis , Sauerland Maria Cristina , Berdel Wolfgang E. , Wörmann Bernhard J. , Hiddemann Wolfgang , Spiekermann Karsten , Bohlander Stefan K. , Greif Philipp A.
Published: January 2020

The fusion genes CBFB/MYH11 and RUNX1/RUNX1T1 block differentiation through disruption of the core binding factor (CBF) complex and are found in 10–15% of adult de novo acute myeloid leukemia (AML) cases. This AML subtype is associated with a favorable prognosis; however, nearly half of CBF-rearranged patients cannot be cured with chemotherapy. This divergent outcome might be due to additional mutations, whose spectrum and prognostic relevance remains hardly defined. Here, we identify nonsilent mutations, which may collaborate with CBF-rearrangements during leukemogenesis by targeted sequencing of 129 genes in 292 adult CBF leukemia patients, and thus provide a comprehensive overview of the mutational spectrum (‘mutatome’) in CBF leukemia. Thereby, we detected fundamental differences between CBFB/MYH11- and RUNX1/RUNX1T1-rearranged patients with ASXL2, JAK2, JAK3, RAD21, TET2, and ZBTB7A being strongly correlated with the latter subgroup. We found prognostic relevance of mutations in genes previously known to be AML-associated such as KIT, SMC1A, and DHX15 and identified novel, recurrent mutations in NFE2 (3%), MN1 (4%), HERC1 (3%), and ZFHX4 (5%). Furthermore, age >60 years, nonprimary AML and loss of the Y-chromosomes are important predictors of survival. These findings are important for refinement of treatment stratification and development of targeted therapy approaches in CBF leukemia.
Plasma ammonia concentrations in extremely low birthweight infants in the first week after birth: secondary analysis from the ProVIDe randomized clinical trial
Authors: Cormack Barbara E. , Jiang Yannan , Harding Jane E. , Crowther Caroline A. , Lynn Adrienne , Nair Arun , Hewson Michael , Meyer Mike , Broadbent Roland , Webster Dianne , Glamuzina Emma , Ryder Bryony , Bloomfield Frank H.
Published: January 2020

Background

Little is known about normative ammonia concentrations in extremely low birthweight (ELBW) babies and whether these vary with birth characteristics. We aimed to determine ammonia concentrations in ELBW babies in the first week after birth and relationships with neonatal characteristics and protein intake.

Methods

Arterial blood samples for the measurement of plasma ammonia concentration were collected within 7 days of birth from ProVIDe trial participants in six New Zealand neonatal intensive care units.

Results

Three hundred and twenty-two babies were included. Median (range) gestational age was 25.7 (22.7–31.6) weeks. Median (interquartile range (IQR)) ammonia concentration was 102 (80–131) µg/dL. There were no statistically significant associations between ammonia concentrations and birthweight or sex. Ammonia concentrations were weakly correlated with mean total (Spearman’srs = 0.11,P = 0.047) and intravenous (rs = 0.13,P = 0.02) protein intake from birth, gestational age at birth (rs = −0.13,P = 0.02) and postnatal age (rs = −0.13,P = 0.02).

Conclusions

Plasma ammonia concentrations in ELBW babies are similar to those of larger and more mature babies and only weakly correlated with protein intake. Currently, recommended thresholds for investigation of hyperammonaemia are appropriate for ELBW babies. Protein intake should not be limited by concerns about potential hyperammonaemia.
Syntrophus conductive pili demonstrate that common hydrogen-donating syntrophs can have a direct electron transfer option
Authors: Walker David J F , Nevin Kelly P , Holmes Dawn E , Rotaru Amelia-Elena , Ward Joy E , Woodard Trevor L , Zhu Jiaxin , Ueki Toshiyuki , Nonnenmann Stephen S , McInerney Michael J , Lovley Derek R
Published: January 2020

Syntrophic interspecies electron exchange is essential for the stable functioning of diverse anaerobic microbial communities. Hydrogen/formate interspecies electron transfer (HFIT), in which H2 and/or formate function as diffusible electron carriers, has been considered to be the primary mechanism for electron transfer because most common syntrophs were thought to lack biochemical components, such as electrically conductive pili (e-pili), necessary for direct interspecies electron transfer (DIET). Here we report that Syntrophus aciditrophicus, one of the most intensively studied microbial models for HFIT, produces e-pili and can grow via DIET. Heterologous expression of the putative S. aciditrophicus type IV pilin gene in Geobacter sulfurreducens yielded conductive pili of the same diameter (4 nm) and conductance of the native S. aciditrophicus pili and enabled long-range electron transport in G. sulfurreducens. S. aciditrophicus lacked abundant c-type cytochromes often associated with DIET. Pilin genes likely to yield e-pili were found in other genera of hydrogen/formate-producing syntrophs. The finding that DIET is a likely option for diverse syntrophs that are abundant in many anaerobic environments necessitates a reexamination of the paradigm that HFIT is the predominant mechanism for syntrophic electron exchange within anaerobic microbial communities of biogeochemical and practical significance.
Regulation of fungal decomposition at single-cell level
Authors: Op De Beeck Michiel , Troein Carl , Siregar Syahril , Gentile Luigi , Abbondanza Giuseppe , Peterson Carsten , Persson Per , Tunlid Anders
Published: January 2020

Filamentous fungi play a key role as decomposers in Earth’s nutrient cycles. In soils, substrates are heterogeneously distributed in microenvironments. Hence, individual hyphae of a mycelium may experience very different environmental conditions simultaneously. In the current work, we investigated how fungi cope with local environmental variations at single-cell level. We developed a method based on infrared spectroscopy that allows the direct, in-situ chemical imaging of the decomposition activity of individual hyphal tips. Colonies of the ectomycorrhizal Basidiomycete Paxillus involutus were grown on liquid media, while parts of colonies were allowed to colonize lignin patches. Oxidative decomposition of lignin by individual hyphae growing under different conditions was followed for a period of seven days. We identified two sub-populations of hyphal tips: one with low decomposition activity and one with much higher activity. Active cells secreted more extracellular polymeric substances and oxidized lignin more strongly. The ratio of active to inactive hyphae strongly depended on the environmental conditions in lignin patches, but was further mediated by the decomposition activity of entire mycelia. Phenotypic heterogeneity occurring between genetically identical hyphal tips may be an important strategy for filamentous fungi to cope with heterogeneous and constantly changing soil environments.
Patient-derived explants (PDEs) as a powerful preclinical platform for anti-cancer drug and biomarker discovery
Authors: Powley Ian R. , Patel Meeta , Miles Gareth , Pringle Howard , Howells Lynne , Thomas Anne , Kettleborough Catherine , Bryans Justin , Hammonds Tim , MacFarlane Marion , Pritchard Catrin
Published: January 2020

Preclinical models that can accurately predict outcomes in the clinic are much sought after in the field of cancer drug discovery and development. Existing models such as organoids and patient-derived xenografts have many advantages, but they suffer from the drawback of not contextually preserving human tumour architecture. This is a particular problem for the preclinical testing of immunotherapies, as these agents require an intact tumour human-specific microenvironment for them to be effective. In this review, we explore the potential of patient-derived explants (PDEs) for fulfilling this need. PDEs involve the ex vivo culture of fragments of freshly resected human tumours that retain the histological features of original tumours. PDE methodology for anti-cancer drug testing has been in existence for many years, but the platform has not been widely adopted in translational research facilities, despite strong evidence for its clinical predictivity. By modifying PDE endpoint analysis to include the spatial profiling of key biomarkers by using multispectral imaging, we argue that PDEs offer many advantages, including the ability to correlate drug responses with tumour pathology, tumour heterogeneity and changes in the tumour microenvironment. As such, PDEs are a powerful model of choice for cancer drug and biomarker discovery programmes.
TCTEX1D1 is a genetic modifier of disease progression in Duchenne muscular dystrophy
Authors:   CINRG Investigators, Spitali Pietro , Zaharieva Irina , Bohringer Stefan , Hiller Monika , Chaouch Amina , Roos Andreas , Scotton Chiara , Claustres Mireille , Bello Luca , McDonald Craig M. , Hoffman Eric P. , Koeks Zaida , Eka Suchiman H. , Cirak Sebahattin , Scoto Mariacristina , Reza Mojgan , ‘t Hoen Peter A. C. , Niks Erik H. , Tuffery-Giraud Sylvie , Lochmüller Hanns , Ferlini Alessandra , Muntoni Francesco , Aartsma-Rus Annemieke
Published: January 2020

Duchenne muscular dystrophy (DMD) is caused by pathogenic variants in the DMD gene leading to the lack of dystrophin. Variability in the disease course suggests that other factors influence disease progression. With this study we aimed to identify genetic factors that may account for some of the variability in the clinical presentation. We compared whole-exome sequencing (WES) data in 27 DMD patients with extreme phenotypes to identify candidate variants that could affect disease progression. Validation of the candidate SNPs was performed in two independent cohorts including 301 (BIO-NMD cohort) and 109 (CINRG cohort of European ancestry) DMD patients, respectively. Variants in the Tctex1 domain containing 1 (TCTEX1D1) gene on chromosome 1 were associated with age of ambulation loss. The minor alleles of two independent variants, known to affect TCTEX1D1 coding sequence and induce skipping of its exon 4, were associated with earlier loss of ambulation. Our data show that disease progression of DMD is affected by a new locus on chromosome 1 and demonstrate the possibility to identify genetic modifiers in rare diseases by studying WES data in patients with extreme phenotypes followed by multiple layers of validation.
Engineering grain boundaries at the 2D limit for the hydrogen evolution reaction
Authors: He Yongmin , Tang Pengyi , Hu Zhili , He Qiyuan , Zhu Chao , Wang Luqing , Zeng Qingsheng , Golani Prafful , Gao Guanhui , Fu Wei , Huang Zhiqi , Gao Caitian , Xia Juan , Wang Xingli , Wang Xuewen , Zhu Chao , Ramasse Quentin M. , Zhang Ao , An Boxing , Zhang Yongzhe , Martí-Sánchez Sara , Morante Joan Ramon , Wang Liang , Tay Beng Kang , Yakobson Boris I. , Trampert Achim , Zhang Hua , Wu Minghong , Wang Qi Jie , Arbiol Jordi , Liu Zheng
Published: January 2020

Atom-thin transition metal dichalcogenides (TMDs) have emerged as fascinating materials and key structures for electrocatalysis. So far, their edges, dopant heteroatoms and defects have been intensively explored as active sites for the hydrogen evolution reaction (HER) to split water. However, grain boundaries (GBs), a key type of defects in TMDs, have been overlooked due to their low density and large structural variations. Here, we demonstrate the synthesis of wafer-size atom-thin TMD films with an ultra-high-density of GBs, up to ~1012 cm−2. We propose a climb and drive 0D/2D interaction to explain the underlying growth mechanism. The electrocatalytic activity of the nanograin film is comprehensively examined by micro-electrochemical measurements, showing an excellent hydrogen-evolution performance (onset potential: −25 mV and Tafel slope: 54 mV dec−1), thus indicating an intrinsically high activation of the TMD GBs.
Gut stem cell aging is driven by mTORC1 via a p38 MAPK-p53 pathway
Authors: He Dan , Wu Hongguang , Xiang Jinnan , Ruan Xinsen , Peng Peike , Ruan Yuanyuan , Chen Ye-Guang , Wang Yibin , Yu Qiang , Zhang Hongbing , Habib Samy L. , De Pinho Ronald A. , Liu Huijuan , Li Baojie
Published: January 2020

Nutrients are absorbed solely by the intestinal villi. Aging of this organ causes malabsorption and associated illnesses, yet its aging mechanisms remain unclear. Here, we show that aging-caused intestinal villus structural and functional decline is regulated by mTORC1, a sensor of nutrients and growth factors, which is highly activated in intestinal stem and progenitor cells in geriatric mice. These aging phenotypes are recapitulated in intestinal stem cell-specific Tsc1 knockout mice. Mechanistically, mTORC1 activation increases protein synthesis of MKK6 and augments activation of the p38 MAPK-p53 pathway, leading to decreases in the number and activity of intestinal stem cells as well as villus size and density. Targeting p38 MAPK or p53 prevents or rescues ISC and villus aging and nutrient absorption defects. These findings reveal that mTORC1 drives aging by augmenting a prominent stress response pathway in gut stem cells and identify p38 MAPK as an anti-aging target downstream of mTORC1.
Linoleic acid–good or bad for the brain?
Authors: Taha Ameer Y.
Published: January 2020

Increased intake of omega-6 rich plant oils such as soybean and corn oil over the past few decades has inadvertently tripled the amount of n-6 linoleic acid (LA, 18:2n-6) in the diet. Although LA is nutritionally “essential”, very little is known about how it affects the brain when present in excess. This review provides an overview on the metabolism of LA by the brain and the effects of excess dietary LA intake on brain function. Pre-clinical evidence suggests that excess dietary LA increases the brain’s vulnerability to inflammation and likely acts via its oxidized metabolites. In humans, excess maternal LA intake has been linked to atypical neurodevelopment, but underlying mechanisms are unknown. It is concluded that excess dietary LA may adversely affect the brain. The potential neuroprotective role of reducing dietary LA merits clinical evaluation in future studies.
The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe
Authors: Martínez-Sancho Elisabet , Slámová Lenka , Morganti Sandro , Grefen Claudio , Carvalho Barbara , Dauphin Benjamin , Rellstab Christian , Gugerli Felix , Opgenoorth Lars , Heer Katrin , Knutzen Florian , von Arx Georg , Valladares Fernando , Cavers Stephen , Fady Bruno , Alía Ricardo , Aravanopoulos Filippos , Avanzi Camilla , Bagnoli Francesca , Barbas Evangelos , Bastien Catherine , Benavides Raquel , Bernier Frédéric , Bodineau Guillaume , Bastias Cristina C. , Charpentier Jean-Paul , Climent José M. , Corréard Marianne , Courdier Florence , Danusevicius Darius , Farsakoglou Anna-Maria , del Barrio José M. García , Gilg Olivier , González-Martínez Santiago C. , Gray Alan , Hartleitner Christoph , Hurel Agathe , Jouineau Arnaud , Kärkkäinen Katri , Kujala Sonja T. , Labriola Mariaceleste , Lascoux Martin , Lefebvre Marlène , Lejeune Vincent , Le-Provost Grégoire , Liesebach Mirko , Malliarou Ermioni , Mariotte Nicolas , Matesanz Silvia , Michotey Célia , Milesi Pascal , Myking Tor , Notivol Eduardo , Pakull Birte , Piotti Andrea , Plomion Christophe , Pringarbe Mehdi , Pyhäjärvi Tanja , Raffin Annie , Ramírez-Valiente José A. , Ramskogler Kurt , Robledo-Arnuncio Juan J. , Savolainen Outi , Schueler Silvio , Semerikov Vladimir , Spanu Ilaria , Thévenet Jean , Mette Tollefsrud Mari , Turion Norbert , Veisse Dominique , Vendramin Giovanni Giuseppe , Villar Marc , Westin Johan , Fonti Patrick
Published: January 2020

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.
PGxCorpus, a manually annotated corpus for pharmacogenomics
Authors: Legrand Joël , Gogdemir Romain , Bousquet Cédric , Dalleau Kevin , Devignes Marie-Dominique , Digan William , Lee Chia-Ju , Ndiaye Ndeye-Coumba , Petitpain Nadine , Ringot Patrice , Smaïl-Tabbone Malika , Toussaint Yannick , Coulet Adrien
Published: January 2020

Pharmacogenomics (PGx) studies how individual gene variations impact drug response phenotypes, which makes PGx-related knowledge a key component towards precision medicine. A significant part of the state-of-the-art knowledge in PGx is accumulated in scientific publications, where it is hardly reusable by humans or software. Natural language processing techniques have been developed to guide experts who curate this amount of knowledge. But existing works are limited by the absence of a high quality annotated corpus focusing on PGx domain. In particular, this absence restricts the use of supervised machine learning. This article introduces PGxCorpus, a manually annotated corpus, designed to fill this gap and to enable the automatic extraction of PGx relationships from text. It comprises 945 sentences from 911 PubMed abstracts, annotated with PGx entities of interest (mainly gene variations, genes, drugs and phenotypes), and relationships between those. In this article, we present the corpus itself, its construction and a baseline experiment that illustrates how it may be leveraged to synthesize and summarize PGx knowledge.
Single-cell RNA sequencing of human kidney
Authors: Liao Jinling , Yu Zhenyuan , Chen Yang , Bao Mengying , Zou Chunlin , Zhang Haiying , Liu Deyun , Li Tianyu , Zhang Qingyun , Li Jiaping , Cheng Jiwen , Mo Zengnan
Published: January 2020

A comprehensive cellular anatomy of normal human kidney is crucial to address the cellular origins of renal disease and renal cancer. Some kidney diseases may be cell type-specific, especially renal tubular cells. To investigate the classification and transcriptomic information of the human kidney, we rapidly obtained a single-cell suspension of the kidney and conducted single-cell RNA sequencing (scRNA-seq). Here, we present the scRNA-seq data of 23,366 high-quality cells from the kidneys of three human donors. In this dataset, we show 10 clusters of normal human renal cells. Due to the high quality of single-cell transcriptomic information, proximal tubule (PT) cells were classified into three subtypes and collecting ducts cells into two subtypes. Collectively, our data provide a reliable reference for studies on renal cell biology and kidney disease.
P3-type layered K0.48Mn0.4Co0.6O2: a novel cathode material for potassium-ion batteries
Authors: Sada Krishnakanth , Barpanda Prabeer
Published: January 2020

A P3-type K0.48Mn0.4Co0.6O2 oxide forms a 3 V economical cathode for potassium-ion batteries, having a discharge capacity of 64 mA h g−1 coupled with excellent cycling stability.
An exceptionally long-lived triplet state of red light-absorbing compact phenothiazine-styrylBodipy electron donor/acceptor dyads: a better alternative to the heavy atom-effect?
Authors: Hou Yuqi , Liu Qingyun , Zhao Jianzhang
Published: January 2020

Heavy atom-free dyads showing a red light-absorbing and exceptionally long-lived triplet state based on a spin–orbital charge transfer intersystem crossing mechanism.
C–H activations of methanol and ethanol and C–C couplings into diols by zinc–indium–sulfide under visible light
Authors: Zhang Haikun , Xie Shunji , Hu Jinyuan , Wu Xuejiao , Zhang Qinghong , Cheng Jun , Wang Ye
Published: January 2020

Use of few-layer Zn2In2S5 nanosheets as an environmentally friendly visible-light photocatalyst for directly transforming methanol to ethylene glycol with high selectivity.
Strong hydrophilicity NiS2/Fe7S8 heterojunctions encapsulated in N-doped carbon nanotubes for enhanced oxygen evolution reaction
Authors: Wang Jing-Yu , Liu Wen-Ting , Li Xiao-Peng , Ouyang Ting , Liu Zhao-Qing
Published: January 2020

The construction of active sites with excellent water oxidation activity is of great significance in the design of OER electrocatalysts.
para-Selective copper-catalyzed C(sp2)–H amidation/dimerization of anilides via a radical pathway
Authors: Viveki Amol B. , Garad Dnyaneshwar N. , Gonnade Rajesh G. , Mhaske Santosh B.
Published: January 2020

A unique process for para-selective C–H functionalization leading to amidation/dimerization of anilide derivatives via a radical pathway has been demonstrated.
On the delocalization length in RNA single strands of cytosine: how many bases see the light?
Authors: Jones Nykola C. , Nielsen Steen Brøndsted , Hoffmann Søren Vrønning
Published: January 2020

The interplay between multiple chromophores in nucleic acids and photosynthetic proteins gives rise to complex electronic phenomena and largely governs the de-excitation dynamics.
Biomimetic ultra-broadband perfect absorbers optimised with reinforcement learning
Authors: Badloe Trevon , Kim Inki , Rho Junsuk
Published: January 2020

The reinforcement learning method of double deep-Q learning is used to design moth-eye structure-based ultra-broadband perfect absorbers with a variety of transition metals, using transfer learning to share knowledge between different environments.
Three-dimensional docking of alcohols to ketones: an experimental benchmark based on acetophenone solvation energy balances
Authors: Zimmermann C. , Gottschalk H. C. , Suhm M. A.
Published: January 2020

Jet FTIR spectroscopy of acetophenone–methanol balances reveals subtle solvation energy preferences by dispersion-tuning of the alkyl groups.
A first principles study of the spin–orbit coupling effect in LiM (M = Na, K, Rb, Cs) molecules
Authors: Kozlov S. V. , Bormotova E. A. , Medvedev A. A. , Pazyuk E. A. , Stolyarov A. V. , Zaitsevskii A.
Published: January 2020

Both fully relativistic and scalar-state based perturbation models provided the spin–orbit functions of the LiM (M = Na, K, Rb, Cs) molecules at almost experimental level of confidence.
NH3/H2O-mediated proton conductivity and photocatalytic behaviour of Fe(ii)-hydroxyphosphonoacetate and M(ii)-substituted derivatives
Authors: Salcedo Inés R. , Bazaga-García Montse , Cuesta Ana , Losilla Enrique R. , Demadis Konstantinos D. , Olivera-Pastor Pascual , Colodrero Rosario M. P. , Cabeza Aurelio
Published: January 2020

Multifunctional Fe(ii)-hydroxyphosphonoacetate and M(ii)-substituted derivatives exhibit ammonia-tunable proton conductivity and photo-Fenton catalytic properties.
New 1,2,3-triazole based bis- and trisphosphine ligands: synthesis, transition metal chemistry and catalytic studies
Authors: Radhakrishna Latchupatula , Kunchur Harish S. , Namdeo Pavan K. , Butcher Ray J. , Balakrishna Maravanji S.
Published: January 2020

This paper describes a novel synthetic methodology for the preparation of 1,2,3-triazole based phosphines and their transition metal chemistry and preliminary catalytic studies.
The one-pot synthesis of CuNi nanoparticles with a Ni-rich surface for the electrocatalytic methanol oxidation reaction
Authors: An Yajing , Ijaz Hamza , Huang Ming , Qu Jianqiang , Hu Shi
Published: January 2020

Polyhedral Cu–Ni alloy nanoparticles with a Ni-rich surface were synthesized, and they exhibit very high activity during the methanol oxidation reaction.
Enhancement of mainstream nitrogen removal via simultaneous partial nitrification, anammox and denitrification by the gel entrapment technique
Authors: Zeng Ming , Yang Junfeng , Li Xiaofang , Wu Nan , Pan Peng , Wang Chang
Published: January 2020

A BSgel system was prepared by integrating the gel entrapment technique with a traditional biofilm carrier to realize the SNAD process under mainstream conditions.
Charge transfer between lead halide perovskite nanocrystals and single-walled carbon nanotubes
Authors: Bansal Parul , Zhang Xiangtong , Wang Hua , Kar Prasenjit , Yu William W.
Published: January 2020

A charge transfer study between lead halide-based perovskite nanocrystals and single-walled carbon nanotubes (PNC@CNT nanocomposite) was performed.
Remarkable improvement of TiO2 for dye photocatalytic degradation by a facile post-treatment
Authors: Sun Qiong , Li Kaijing , Wu Songhao , Han Bing , Sui Lina , Dong Lifeng
Published: January 2020

A neutral, facile and universal hydrothermal post-treatment of TiO2 was developed to significantly improve its photocatalytic activity.
Preparation of ZnO quantum dots@SiO2/PVA for multifunctional coating on PET
Authors: Ding Lei , Chen YiFan , Hua Zibo , Liu Li , Chen Haixu , Zhong Zhengxiang , Du Yunzhe , Huang Yudong
Published: January 2020

A durable, highly transparent and ultraviolet shielded inkjet printing coating was successfully prepared using ZnO QDs@SiO2.
Black arsenic: a new synthetic method by catalytic crystallization of arsenic glass
Authors: Antonatos Nikolas , Luxa Jan , Sturala Jiri , Sofer Zdeněk
Published: January 2020

Arsenic analogue of black phosphorus was synthesized by crystallization of arsenic glass in presence of mercury catalyst.
Surface reconstruction of AgPd nanoalloy particles during the electrocatalytic formate oxidation reaction
Authors: Guo Longfei , Chen Fuyi , Jin Tao , Liu Huazhen , Zhang Nan , Jin Yachao , Wang Qiao , Tang Quan , Pan Bowei
Published: January 2020

Ag49Pd51 nanoalloys undergo surface reconstruction on graphene where Pd surface coverage increases from 51.87 to 62.42% during the FOR, and the catalytic activity increases from 2.32 to 6.03 A mg−1Pd.
Self-assembly of amphiphilic aryl-squaramides in water driven by dipolar π–π interactions
Authors: Bujosa Sergi , Castellanos Eduardo , Frontera Antonio , Rotger Carmen , Costa Antonio , Soberats Bartolome
Published: January 2020

Amphiphilic aryl-squaramides self-assembleviaunprecedented dipolar π–π interactions forming well-defined supramolecular aggregates and self-consistent hydrogels in water
Cationic iron porphyrins with sodium dodecyl sulphate for micellar catalysis of cyclopropanation reactions
Authors: Maaskant Ruben V. , Polanco Ehider A. , van Lier Roos C. W. , Roelfes Gerard
Published: January 2020

Here, we report that the combination of cationic iron porphyrins with sodium dodecyl sulphate (SDS) gives rise to efficient micellar catalysis of cyclopropanation reactions of styrene derivatives, using diazoacetates as carbene precursors.
Staphylococcus aureuscapsular polysaccharides: a structural and synthetic perspective
Authors: Visansirikul Satsawat , Kolodziej Stephen A. , Demchenko Alexei V.
Published: January 2020

This review surveys known structures of staphylococcal polysaccharides and summarizes all synthetic efforts to obtain these sequences.