bluuebunny/crossref_metadata_2025_split huggingface dataset:
OH/IR stars versus YSOs in infrared photometric surveys
Authors: Loup Cécile , Allen Mark , Lançon Ariane , Oberto Anais 
Published: January 2020

AbstractAGB 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

AbstractThe 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

AbstractThe 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

AbstractModeling 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

AbstractThe 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

AbstractTo 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

AbstractIn 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

AbstractThe 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

AbstractThe 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

AbstractBackgroundLittle 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.MethodsArterial 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.ResultsThree 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).ConclusionsPlasma 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

Abstract
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

Abstract
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

AbstractPreclinical 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

AbstractDuchenne 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.