bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hotspot motion caused the Hawaiian-Emperor Bend and LLSVPs are not fixed
Authors: Bono Richard K. , Tarduno John A. , Bunge Hans-Peter 
Published: July 2019

AbstractControversy surrounds the fixity of both hotspots and large low shear velocity provinces (LLSVPs). Paleomagnetism, plate-circuit analyses, sediment facies, geodynamic modeling, and geochemistry suggest motion of the Hawaiian plume in Earth’s mantle during formation of the Emperor seamounts. Herein, we report new paleomagnetic data from the Hawaiian chain (Midway Atoll) that indicate the Hawaiian plume arrived at its current latitude by 28 Ma. A dramatic decrease in distance between Hawaiian-Emperor and Louisville chain seamounts between 63 and 52 Ma confirms a high rate of southward Hawaiian hotspot drift (~47 mm yr−1), and excludes true polar wander as a relevant factor. These findings further indicate that the Hawaiian-Emperor chain bend morphology was caused by hotspot motion, not plate motion. Rapid plume motion was likely produced by ridge-plume interaction and deeper influence of the Pacific LLSVP. When compared to plate circuit predictions, the Midway data suggest ~13 mm yr−1 of African LLSVP motion since the Oligocene. LLSVP upwellings are not fixed, but also wander as they attract plumes and are shaped by deep mantle convection.
Mitofusins regulate lipid metabolism to mediate the development of lung fibrosis
Authors: Chung Kuei-Pin , Hsu Chia-Lang , Fan Li-Chao , Huang Ziling , Bhatia Divya , Chen Yi-Jung , Hisata Shu , Cho Soo Jung , Nakahira Kiichi , Imamura Mitsuru , Choi Mary E. , Yu Chong-Jen , Cloonan Suzanne M. , Choi Augustine M. K. 
Published: July 2019

AbstractAccumulating evidence illustrates a fundamental role for mitochondria in lung alveolar type 2 epithelial cell (AEC2) dysfunction in the pathogenesis of idiopathic pulmonary fibrosis. However, the role of mitochondrial fusion in AEC2 function and lung fibrosis development remains unknown. Here we report that the absence of the mitochondrial fusion proteins mitofusin1 (MFN1) and mitofusin2 (MFN2) in murine AEC2 cells leads to morbidity and mortality associated with spontaneous lung fibrosis. We uncover a crucial role for MFN1 and MFN2 in the production of surfactant lipids with MFN1 and MFN2 regulating the synthesis of phospholipids and cholesterol in AEC2 cells. Loss of MFN1, MFN2 or inhibiting lipid synthesis via fatty acid synthase deficiency in AEC2 cells exacerbates bleomycin-induced lung fibrosis. We propose a tenet that mitochondrial fusion and lipid metabolism are tightly linked to regulate AEC2 cell injury and subsequent fibrotic remodeling in the lung.
The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs
Authors: Lingaraju Mahesh , Johnsen Dennis , Schlundt Andreas , Langer Lukas M. , Basquin Jérôme , Sattler Michael , Heick Jensen Torben , Falk Sebastian , Conti Elena 
Published: July 2019

AbstractThe nuclear exosome and its essential co-factor, the RNA helicase MTR4, play crucial roles in several RNA degradation pathways. Besides unwinding RNA substrates for exosome-mediated degradation, MTR4 associates with RNA-binding proteins that function as adaptors in different RNA processing and decay pathways. Here, we identify and characterize the interactions of human MTR4 with a ribosome processing adaptor, NVL, and with ZCCHC8, an adaptor involved in the decay of small nuclear RNAs. We show that the unstructured regions of NVL and ZCCHC8 contain short linear motifs that bind the MTR4 arch domain in a mutually exclusive manner. These short sequences diverged from the arch-interacting motif (AIM) of yeast rRNA processing factors. Our results suggest that nuclear exosome adaptors have evolved canonical and non-canonical AIM sequences to target human MTR4 and demonstrate the versatility and specificity with which the MTR4 arch domain can recruit a repertoire of different RNA-binding proteins.
Meiosis I progression in spermatogenesis requires a type of testis-specific 20S core proteasome
Authors: Zhang Qianting , Ji Shu-Yan , Busayavalasa Kiran , Shao Jingchen , Yu Chao 
Published: July 2019

AbstractSpermatogenesis is tightly regulated by ubiquitination and proteasomal degradation, especially during spermiogenesis, in which histones are replaced by protamine. However, the functions of proteasomal activity in meiosis I and II remain elusive. Here, we show that PSMA8-associated proteasomes are essential for the degradation of meiotic proteins and the progression of meiosis I during spermatogenesis. PSMA8 is expressed in spermatocytes from the pachytene stage, and assembles a type of testis-specific core proteasome. Deletion of PSMA8 decreases the abundance of proteasome in testes. Meiotic proteins that are normally degraded at late prophase I, such as RAD51 and RPA1, remain stable in PSMA8-deleted spermatocytes. Moreover, PSMA8-null spermatocytes exhibit delayed M-phase entry and are finally arrested at this stage, resulting in male infertility. However, PSMA8 is neither expressed nor required for female meiotic progression. Thus, meiosis I progression in spermatogenesis, particularly entry into and exit from M-phase, requires the proteasomal activity of PSMA8-associated proteasomes.
Long-term and persistent vocal plasticity in adult bats
Authors: Genzel Daria , Desai Janki , Paras Elana , Yartsev Michael M. 
Published: July 2019

AbstractBats exhibit a diverse and complex vocabulary of social communication calls some of which are believed to be learned during development. This ability to produce learned, species-specific vocalizations – a rare trait in the animal kingdom – requires a high-degree of vocal plasticity. Bats live extremely long lives in highly complex and dynamic social environments, which suggests that they might also retain a high degree of vocal plasticity in adulthood, much as humans do. Here, we report persistent vocal plasticity in adult bats (Rousettus aegyptiacus) following exposure to broad-band, acoustic perturbation. Our results show that adult bats can not only modify distinct parameters of their vocalizations, but that these changes persist even after noise cessation – in some cases lasting several weeks or months. Combined, these findings underscore the potential importance of bats as a model organism for studies of vocal plasticity, including in adulthood.
High performance III-V photoelectrodes for solar water splitting via synergistically tailored structure and stoichiometry
Authors: Lim Haneol , Young James L. , Geisz John F. , Friedman Daniel J. , Deutsch Todd G. , Yoon Jongseung 
Published: July 2019

AbstractCatalytic interface of semiconductor photoelectrodes is critical for high-performance photoelectrochemical solar water splitting because of its multiple roles in light absorption, electrocatalysis, and corrosion protection. Nevertheless, simultaneously optimizing each of these processes represents a materials conundrum owing to conflicting requirements of materials attributes at the electrode surface. Here we show an approach that can circumvent these challenges by collaboratively exploiting corrosion-resistant surface stoichiometry and structurally-tailored reactive interface. Nanoporous, density-graded surface of ‘black’ gallium indium phosphide (GaInP2), when combined with ammonium-sulfide-based surface passivation, effectively reduces reflection and surface recombination of photogenerated carriers for high efficiency photocatalysis in the hydrogen evolution half-reaction, but also augments electrochemical durability with lifetime over 124 h via strongly suppressed kinetics of corrosion. Such synergistic control of stoichiometry and structure at the reactive interface provides a practical pathway to concurrently enhance efficiency and durability of semiconductor photoelectrodes without solely relying on the development of new protective materials.
Time-resolved NMR monitoring of tRNA maturation
Authors: Barraud Pierre , Gato Alexandre , Heiss Matthias , Catala Marjorie , Kellner Stefanie , Tisné Carine 
Published: July 2019

AbstractAlthough the biological importance of post-transcriptional RNA modifications in gene expression is widely appreciated, methods to directly detect their introduction during RNA biosynthesis are rare and do not easily provide information on the temporal nature of events. Here, we introduce the application of NMR spectroscopy to observe the maturation of tRNAs in cell extracts. By following the maturation of yeast tRNAPhe with time-resolved NMR measurements, we show that modifications are introduced in a defined sequential order, and that the chronology is controlled by cross-talk between modification events. In particular, we show that a strong hierarchy controls the introduction of the T54, Ψ55 and m1A58 modifications in the T-arm, and we demonstrate that the modification circuits identified in yeast extract with NMR also impact the tRNA modification process in living cells. The NMR-based methodology presented here could be adapted to investigate different aspects of tRNA maturation and RNA modifications in general.
Activity-controlled annealing of colloidal monolayers
Authors: Ramananarivo Sophie , Ducrot Etienne , Palacci Jeremie 
Published: July 2019

AbstractMolecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium.
Correlating dynamic strain and photoluminescence of solid-state defects with stroboscopic x-ray diffraction microscopy
Authors: Whiteley S. J. , Heremans F. J. , Wolfowicz G. , Awschalom D. D. , Holt M. V. 
Published: July 2019

AbstractControl of local lattice perturbations near optically-active defects in semiconductors is a key step to harnessing the potential of solid-state qubits for quantum information science and nanoscale sensing. We report the development of a stroboscopic scanning X-ray diffraction microscopy approach for real-space imaging of dynamic strain used in correlation with microscopic photoluminescence measurements. We demonstrate this technique in 4H-SiC, which hosts long-lifetime room temperature vacancy spin defects. Using nano-focused X-ray photon pulses synchronized to a surface acoustic wave launcher, we achieve an effective time resolution of ~100 ps at a 25 nm spatial resolution to map micro-radian dynamic lattice curvatures. The acoustically induced lattice distortions near an engineered scattering structure are correlated with enhanced photoluminescence responses of optically-active SiC quantum defects driven by local piezoelectric effects. These results demonstrate a unique route for directly imaging local strain in nanomechanical structures and quantifying dynamic structure-function relationships in materials under realistic operating conditions.
Development of bifunctional organocatalysts and application to asymmetric total synthesis of naucleofficine I and II
Authors: Yuan Yong-Hai , Han Xue , Zhu Fu-Ping , Tian Jin-Miao , Zhang Fu-Min , Zhang Xiao-Ming , Tu Yong-Qiang , Wang Shao-Hua , Guo Xiang 
Published: July 2019

AbstractThe proline-type organocatalysts has been efficiently employed to catalyze a wide range of asymmetric transformations; however, there are still many synthetically useful and challenging transformations that remain unachievable in an asymmetric fashion. Herein, a chiral bifunctional organocatalyst with a spirocyclic pyrrolidine backbone-derived containing fluoro-alkyl and aryl sulfonamide functionalities, are designed, prepared, and examined in the asymmetric Mannich/acylation/Wittig reaction sequence of 3,4-dihydro-β-carboline with acetaldehyde, acyl halides, and Wittig reagents. As a result, the spirocyclic pyrrolidine trifluoromethanesulfonamide catalyst can facilitate this versatile sequence as demonstrated by 18 examples displaying excellent enantioselectivity (up to 94% ee), as well as moderate to good yields (up to 54% over 3 steps). As a practical application, the asymmetric total synthesis of naucleofficine I (1a) and II (1b) in ten steps have been accomplished.
Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards
Authors: Lind Abigail L. , Lai Yvonne Y. Y. , Mostovoy Yulia , Holloway Alisha K. , Iannucci Alessio , Mak Angel C. Y. , Fondi Marco , Orlandini Valerio , Eckalbar Walter L. , Milan Massimo , Rovatsos Michail , Kichigin Ilya G. , Makunin Alex I. , Johnson Pokorná Martina , Altmanová Marie , Trifonov Vladimir A. , Schijlen Elio , Kratochvíl Lukáš , Fani Renato , Velenský Petr , Rehák Ivan , Patarnello Tomaso , Jessop Tim S. , Hicks James W. , Ryder Oliver A. , Mendelson Joseph R. , Ciofi Claudio , Kwok Pui-Yan , Pollard Katherine S. , Bruneau Benoit G. 
Published: July 2019

AbstractMonitor lizards are unique among ectothermic reptiles in that they have high aerobic capacity and distinctive cardiovascular physiology resembling that of endothermic mammals. Here, we sequence the genome of the Komodo dragon Varanus komodoensis, the largest extant monitor lizard, and generate a high-resolution de novo chromosome-assigned genome assembly for V. komodoensis using a hybrid approach of long-range sequencing and single-molecule optical mapping. Comparing the genome of V. komodoensis with those of related species, we find evidence of positive selection in pathways related to energy metabolism, cardiovascular homoeostasis, and haemostasis. We also show species-specific expansions of a chemoreceptor gene family related to pheromone and kairomone sensing in V. komodoensis and other lizard lineages. Together, these evolutionary signatures of adaptation reveal the genetic underpinnings of the unique Komodo dragon sensory and cardiovascular systems, and suggest that selective pressure altered haemostasis genes to help Komodo dragons evade the anticoagulant effects of their own saliva. The Komodo dragon genome is an important resource for understanding the biology of monitor lizards and reptiles worldwide.
Easy-to-use clinical tool for survival estimation in Ewing sarcoma at diagnosis and after surgery
Authors: Bosma S. E. , Lancia C. , Rueten-Budde A. J. , Ranft A. , Gelderblom H. , Fiocco M. , van de Sande M. A. J. , Dijkstra P. D. S. , Dirksen U. 
Published: July 2019

AbstractAccurate survival estimations in Ewing sarcoma are necessary to develop risk- and response adaptive treatment strategies allowing for early decision-making. We aim to develop an easy-to-use survival estimation tool from diagnosis and surgery. A retrospective study of 1314 Ewing sarcoma patients was performed. Associations between prognostic variables at diagnosis/surgery and overall survival (OS), were investigated using Kaplan-Meier and multivariate Cox models. Predictive accuracy was evaluated by cross-validation and Harrell C-statistics. Median follow-up was 7.9 years (95%CI 7.6–8.3). Independent prognostic factors at diagnosis were age, volume, primary tumor localization and disease extent. 5 risk categories (A-E) were identified with 5-year OS of 88% (86–94), 69% (64–74), 57% (50–64), 51% (42–60) and 28% (22–34) respectively. Harrell C-statistic was 0.70. Independent prognostic factors from surgery were age, volume, disease extent and histological response. In categories A-B, 5y OS increased to 92% (87–97) and 79% (71–87) respectively for 100% necrosis and decreased to 76% (67–85) and 62% (55–69) respectively for <100% necrosis. In categories C-E, 5y OS increased to 65% (55–75), 65% (52–78) and 52% (38–66) respectively for ≥90% necrosis and decreased to 38% (22–54), 11% (0–26) and 7% (0–19) respectively for <90% necrosis. We present an easy-to-use survival estimation tool from diagnosis in Ewing sarcoma based on age, volume, primary tumor localization and disease extent. Histological response is a strong additional prognostic factor for OS.
Drought-induced soil microbial amino acid and polysaccharide change and their implications for C-N cycles in a climate change world
Authors: Kakumanu Madhavi L. , Ma Li , Williams Mark A. 
Published: July 2019

AbstractHigh microbial carbon (MBC) demand, a proxy for energy demand (cost), during soil microbial response to stressors such as drought are a major gap in understanding global biogeochemical cycling of carbon (C) and nitrogen (N). The dynamics of two dominant microbial pools (amino acids; AA and exopolymeric substances; EPS) in soils exposed to drying and C and N amendment to mimic both low and high nutrient soil habitats were examined. It was hypothesized that dynamics of EPS and AA (osmolytes) would be greater when soil drying was preceded by a pulse of bioavailable C and N. Drying reduced AA content, even as overall soil MBC increased (~35%). The increase in absolute amounts and mol% of certain AA (eg: Taurine, glutamine, tyrosine, phenylalanine) in the driest treatment (−10 MPa) were similar in both soils regardless of amendment suggesting a common mechanism underlying the energy intensive acclimation across soils. MBC and EPS, both increased ~1.5X and ~3X due to drying and especially drying associated with amendment. Overall major pools of C and N based microbial metabolites are dynamic to drying (drought), and thus have implications for earth’s biogeochemical fluxes of C and N, perhaps costing 4–7% of forest fixed photosynthetic C input during a single drying (drought) period.
In vivo evaluation of the effect of lithium on peripheral circadian clocks by real-time monitoring of clock gene expression in near-freely moving mice
Authors: Sawai Yuka , Okamoto Takezo , Muranaka Yugo , Nakamura Rino , Matsumura Ritsuko , Node Koichi , Akashi Makoto 
Published: July 2019

AbstractLithium has been used as a mood stabilizer to treat human bipolar disorders for over half a century. Several studies have suggested the possibility that the efficacy of lithium treatment results in part from the amelioration of circadian dysfunction. However, the effect of lithium on clock gene expression has not yet been investigated in vivo because continuous measurement of gene expression in organs with high time resolution over a period of several days is difficult. To resolve this issue, we attached a small photo multiplier tube (PMT) tightly to the body surface of transgenic mice carrying a reporter gene such that the photon input window faced target organs such as the liver and kidney and succeeded in long-term continuous measurement of circadian gene expression in semi-freely moving mice over periods of several weeks. Using this simple method, we clearly showed that lithium causes circadian period elongation in peripheral clock gene expression rhythms in vivo. Further development of our detection system to maturity will aid a wide range of research fields in medicine and biology.
Prognostic Performance of Kidney Volume Measurement for Polycystic Kidney Disease: A Comparative Study of Ellipsoid vs. Manual Segmentation
Authors: Shi Beili , Akbari Pedram , Pourafkari Marina , Iliuta Ioan-Andrei , Guiard Elsa , Quist Crystal F. , Song Xuewen , Hillier David , Khalili Korosh , Pei York 
Published: July 2019

AbstractTotal kidney volume (TKV) is a validated prognostic biomarker for risk assessment in autosomal dominant polycystic kidney disease (ADPKD). TKV by manual segmentation (MS) is the “gold standard” but is time-consuming and requires expertise. The purpose of this study was to compare TKV-based prognostic performance by ellipsoid (EL) vs. MS in a large cohort of patients. Cross-sectional study of 308 patients seen at a tertiary referral center; all had a standardized MRI with typical imaging of ADPKD. An experienced radiologist blinded to patient clinical results performed all TKV measurements by EL and MS. We assessed the agreement of TKV measurements by intraclass correlation(ICC) and Bland-Altman plot and also how the disagreement of the two methods impact the prognostic performance of the Mayo Clinic Imaging Classification (MCIC). We found a high ICC of TKV measurements (0.991, p < 0.001) between EL vs. MS; however, 5.5% of the cases displayed disagreement of TKV measurements >20%. We also found a high degree of agreement of the individual MCIC risk classes (i.e. 1A to 1E) with a Cohen’s weighted-kappa of 0.89; but 42 cases (13.6%) were misclassified by EL with no misclassification spanning more than one risk class. The sensitivity and specificity of EL in distinguishing low-risk (1A-B) from high-risk (1C-E) MCIC prognostic grouping were 96.6% and 96.1%, respectively. Overall, we found an excellent agreement of TKV-based risk assessment between EL and MS. However, caution is warranted for patients with MCIC 1B and 1C, as misclassification can have therapeutic consequence.
Probing conformational changes of monomeric transthyretin with second derivative fluorescence
Authors: Jazaj Denisa , Ghadami Seyyed Abolghasem , Bemporad Francesco , Chiti Fabrizio 
Published: July 2019

AbstractWe have studied the intrinsic fluorescence spectra of a monomeric variant of human transthyretin (M-TTR), a protein involved in the transport of the thyroid hormone and retinol and associated with various forms of amyloidosis, extending our analysis to the second order derivative of the spectra. This procedure allowed to identify three peaks readily assigned to Trp41, as the three peaks were also visible in a mutant lacking the other tryptophan (Trp79) and had similar FRET efficiency values with an acceptor molecule positioned at position 10. The wavelength values of the three peaks and their susceptibility to acrylamide quenching revealed that the three corresponding conformers experience different solvent-exposure, polarity of the environment and flexibility. We could monitor the three peaks individually in urea-unfolding and pH-unfolding curves. This revealed changes in the distribution of the corresponding conformers, indicating conformational changes and alterations of the dynamics of the microenvironment that surrounds the associated tryptophan residue in such transitions, but also native-like conformers of such residues in unfolded states. We also found that the amyloidogenic state adopted by M-TTR at mildly low pH has a structural and dynamical microenvironment surrounding Trp41 indistinguishable from that of the fully folded and soluble state at neutral pH.