bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gradient‐Based Inverse Estimation for a Rainfall‐Runoff Model
Authors: Krapu Christopher , Borsuk Mark , Kumar Mukesh 
Published: July 2019

AbstractRecent advances in deep learning for neural networks with large numbers of parameters have been enabled by automatic differentiation, an algorithmic technique for calculating gradients of measures of model fit with respect to model parameters. Estimation of high‐dimensional parameter sets is an important problem within the hydrological sciences. Here, we demonstrate the effectiveness of gradient‐based estimation techniques for high‐dimensional inverse estimation problems using a conceptual rainfall‐runoff model. In particular, we compare the effectiveness of Hamiltonian Monte Carlo and automatic differentiation variational inference against two nongradient‐dependent methods, random walk Metropolis and differential evolution Metropolis. We show that the former two techniques exhibit superior performance for inverse estimation of daily rainfall values and are much more computationally efficient on larger data sets in an experiment with synthetic data. We also present a case study evaluating the effectiveness of automatic differentiation variational inference for inverse estimation over 25 years of daily precipitation conditional on streamflow observations at three catchments and show that it is scalable to very high dimensional parameter spaces. The presented results highlight the power of combining hydrological process‐based models with optimization techniques from deep learning for high‐dimensional estimation problems.
Remote Characterization of Dominant Wavelengths From Surface Folding on Lava Flows Using Lidar and Discrete Fourier Transform Analyses
Authors: Deardorff Nicholas , Booth Adam , Cashman Katharine 
Published: July 2019

AbstractSurface folding is common in lava flows of all compositions and is believed to be due to changes in viscosity and flow velocity between the cooling crust and the more fluid flow interior. However, our understanding of the relationship between surface folding and flow rheology is incomplete. In this study we analyze digital terrain models of eight lava flows ranging in composition from basaltic andesite to rhyolite using a discrete Fourier transform analysis to quantitatively determine dominant surface fold wavelengths. Our discrete Fourier transform analyses show that each lava flow has multiple fold generations and that dominant wavelengths are more closely related to calculated effective viscosity than to lava composition. At our Oregon sites, average dominant wavelengths generally increase with viscosity (r2=0.68), and the correlation improves (r2=0.87) when expanded by including previously measured fold wavelengths and viscosities from the global database. However, there are a few exceptions to this positive trend where a few lava flows have lower or higher than expected dominant fold wavelengths, which we infer are due to secondary factors such as differences in eruption conditions (eruption rate, temperature, etc.). Additionally, over a 5 order of magnitude range in viscosity, there is significant overlap between the ranges of fold wavelengths, particularly from 10 to 20m, for lavas from basaltic andesite to rhyolite, making it difficult to determine a numeric correlation between surface folds and lava rheology that would allow remote characterization of lava.
Investigating an Unusually Large 28‐Day Oscillation in Mesospheric Temperature Over Antarctica Using Ground‐Based and Satellite Measurements
Authors: Zhao Yucheng , Taylor M. J. , Pautet P.‐D. , Moffat‐Griffin T. , Hervig M. E. , Murphy D. J. , French W. J. R. , Liu H. L. , Pendleton W. R. , Russell J. M. 
Published: July 2019

AbstractThe Utah State University Advanced Mesospheric Temperature Mapper was deployed at the Amundsen‐Scott South Pole Station in 2010 to measure OH temperature at ~87 km as part of an international network to study the mesospheric dynamics over Antarctica. During the austral winter of 2014, an unusually large amplitude ~28‐day oscillation in mesospheric temperature was observed for ~100 days from the South Pole Station. This study investigates the characteristics and global structure of this exceptional planetary‐scale wave event utilizing ground‐based mesospheric OH temperature measurements from two Antarctic stations (South Pole and Rothera) together with satellite temperature measurements from the Microwave Limb Sounder on the Aura satellite and the Solar Occultation For Ice Experiment on the Aeronomy of Ice in the Mesosphere satellite. Our analyses have revealed that this large oscillation is a wintertime, high‐latitude phenomenon, exhibiting a coherent zonal wave #1 structure below 80‐km altitude. At higher altitudes, the wave was confined in longitude between 180°E and 360°E. The amplitude of this oscillation reached ~15 K at 85 km, and it was observed to grow with altitude as it extended from the stratosphere into the lower thermosphere in the Southern Hemisphere. The satellite data further established the existence of this oscillation in the Northern Hemisphere during the boreal wintertime. The main characteristics and global structure of this event as observed in temperature are consistent with the predicted 28‐day Rossby Wave (1,4) mode.
Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean
Authors: Neupane Surendra , Mathew Febina M. , Varenhorst Adam J. , Nepal Madhav P. 
Published: July 2019

AbstractSoybean aphid (Aphis glycines; SBA) and soybean cyst nematode (Heterodera glycines; SCN) are two major pests of soybean (Glycine max) in the United States of America. This study aims to characterize three-way interactions among soybean, SBA, and SCN using both demographic and genetic datasets. SCN-resistant and SCN-susceptible soybean cultivars with a combination of soybean aphids (biotype 1) and SCN (HG type 0) in a randomized complete block design (RCBD) with six blocks were used to evaluate the three-way interactions in a greenhouse setup. Treatments receiving SCN were infested at planting with 2000 nematode eggs, and the treatments with soybean aphids were infested at second trifoliate growth stage (V2) with 15 soybean aphids. The whole roots were sampled from plants at 5 and 30 days post SBA infestation for RNA sequencing using Illumina Hiseq. 3000. The data comprises of 47 libraries that are useful for further analyses of important genes, which are involved in interaction effects of SBA and SCN on soybean.
TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish
Authors: Gudmundsson Sanna , Wilbe Maria , Filipek-Górniok Beata , Molin Anna-Maja , Ekvall Sara , Johansson Josefin , Allalou Amin , Gylje Hans , Kalscheuer Vera M. , Ledin Johan , Annerén Göran , Bondeson Marie-Louise 
Published: July 2019

AbstractThe TATA-box binding protein associated factor 1 (TAF1) protein is a key unit of the transcription factor II D complex that serves a vital function during transcription initiation. Variants of TAF1 have been associated with neurodevelopmental disorders, but TAF1’s molecular functions remain elusive. In this study, we present a five-generation family affected with X-linked intellectual disability that co-segregated with a TAF1 c.3568C>T, p.(Arg1190Cys) variant. All affected males presented with intellectual disability and dysmorphic features, while heterozygous females were asymptomatic and had completely skewed X-chromosome inactivation. We investigated the role of TAF1 and its association to neurodevelopment by creating the first complete knockout model of the TAF1 orthologue in zebrafish. A crucial function of human TAF1 during embryogenesis can be inferred from the model, demonstrating that intact taf1 is essential for embryonic development. Transcriptome analysis of taf1 zebrafish knockout revealed enrichment for genes associated with neurodevelopmental processes. In conclusion, we propose that functional TAF1 is essential for embryonic development and specifically neurodevelopmental processes.
Normalization of glycosaminoglycan-derived disaccharides detected by tandem mass spectrometry assay for the diagnosis of mucopolysaccharidosis
Authors: Lin Hsiang-Yu , Lo Yun-Ting , Wang Tuan-Jen , Huang Sung-Fa , Tu Ru-Yi , Chen Tzu-Lin , Lin Shuan-Pei , Chuang Chih-Kuang 
Published: July 2019

AbstractMucopolysaccharidosis (MPS) is caused by the deficiency of a specific hydrolytic enzyme that catalyzes the step-wise degradation of glycosaminoglycans (GAGs). In this study, we propose an empirical method to calculate levels of GAG-derived disaccharides based on the quantity (peak areas) of chondroitin sulfate (CS) with the aim of making a diagnosis of MPS more accurate and reducing the occurrence of false positive and false negative results. In this study, levels of urinary GAG-derived disaccharides were measured in 67 patients with different types of MPS and 165 controls without MPS using a tandem mass spectrometry assay. Two different methods of reporting GAG-derived disaccharides were assessed; normalization to urinary CS (in μg/mL), and normalization to μg/mg creatinine. CS-normalization yielded more consistent values than creatinine-normalization. In particular, levels of urinary dermatan sulfate (DS), heparan sulfate (HS), and keratan sulfate (KS) significantly varied because of changes in urine creatinine levels, which were proportional to age but inversely proportional to DS, HS, and KS measurements. Using CS-normalization revealed the actual status of DS, HS, and KS without the influence of factors such as age, urine creatinine, and other physiological conditions. It could discriminate between the patients with MPS and controls without MPS, and also to evaluate changes in GAG levels pre- and post-enzyme replacement therapy.
Ent3 and GGA adaptors facilitate diverse anterograde and retrograde trafficking events to and from the prevacuolar endosome
Authors: Yanguas Francisco , Moscoso-Romero Esteban , Valdivieso M.-Henar 
Published: July 2019

AbstractCarboxypeptidases Y (Cpy1) and S (Cps1), the receptor Vps10, and the ATPase subunit Vph1 follow the carboxypeptidase Y (CPY) pathway from the trans-Golgi network (TGN) to the prevacuolar endosome (PVE). Using Schizosaccharomyces pombe quantitative live-cell imaging, biochemical and genetic analyses, we extended the previous knowledge and showed that collaboration between Gga22, the dominant Golgi-localized Gamma-ear-containing ARF-binding (GGA) protein, and Gga21, and between Gga22 and the endosomal epsin Ent3, was required for efficient: i) Vps10 anterograde trafficking from the TGN to the PVE; ii) Vps10 retrograde trafficking from the PVE to the TGN; iii) Cps1 exit from the TGN, and its sorting in the PVE en route to the vacuole; and iv) Syb1/Snc1 recycling to the plasma membrane through the PVE. Therefore, monomeric clathrin adaptors facilitated the trafficking of Vps10 in both directions of the CPY pathway, and facilitated trafficking events of Cps1 in different organelles. By contrast, they were dispensable for Vph1 trafficking. Thus, these adaptors regulated the traffic of some, but not all, of the cargo of the CPY pathway, and regulated the traffic of cargoes that do not follow this pathway. Additionally, this collaboration was required for PVE organization and efficient growth under stress.
Prefrontal cortex neuronal ensembles encoding fear drive fear expression during long-term memory retrieval
Authors: Giannotti Giuseppe , Heinsbroek Jasper A. , Yue Alexander J. , Deisseroth Karl , Peters Jamie 
Published: July 2019

AbstractThe prefrontal cortex is an important regulator of fear expression in humans and rodents. Specifically, the rodent prelimbic (PL) prefrontal cortex drives fear expression during both encoding and retrieval of fear memory. Neuronal ensembles have been proposed to function as memory encoding units, and their re-activation is thought to be necessary for memory retrieval and expression of conditioned behavior. However, it remains unclear whether PL cortex neuronal ensembles that encode fear memory contribute to long-term fear expression during memory retrieval. To address this, we employed a viral-mediated TRAP (Targeted Recombination in Active Population) technology to target PL cortex ensembles active during fear conditioning and expressed the inhibitory Gi-DREADD in fear-encoding ensembles. Male and female rats were trained to lever press for food and subjected to Pavlovian delay fear conditioning, then 28 days later, they underwent a fear memory retrieval test. Chemogenetic inhibition of TRAPed PL cortex ensembles reduced conditioned suppression of food seeking in females, but not males. Neither context nor tone freezing behavior was altered by this manipulation during the same retrieval test. Thus, fear-encoding ensembles in PL cortex drive long-term fear expression in a sex and fear modality dependent manner.
Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition
Authors: Tan Mun Hua , Gan Han Ming , Lee Yin Peng , Bracken-Grissom Heather , Chan Tin-Yam , Miller Adam D. , Austin Christopher M. 
Published: July 2019

AbstractThe emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
The MmpL3 interactome reveals a complex crosstalk between cell envelope biosynthesis and cell elongation and division in mycobacteria
Authors: Belardinelli Juan Manuel , Stevens Casey M. , Li Wei , Tan Yong Zi , Jones Victoria , Mancia Filippo , Zgurskaya Helen I. , Jackson Mary 
Published: July 2019

AbstractIntegral membrane transporters of the Mycobacterial Membrane Protein Large (MmpL) family and their interactome play important roles in the synthesis and export of mycobacterial outer membrane lipids. Despite the current interest in the mycolic acid transporter, MmpL3, from the perspective of drug discovery, the nature and biological significance of its interactome remain largely unknown. We here report on a genome-wide screening by two-hybrid system for MmpL3 binding partners. While a surprisingly low number of proteins involved in mycolic acid biosynthesis was found to interact with MmpL3, numerous enzymes and transporters participating in the biogenesis of peptidoglycan, arabinogalactan and lipoglycans, and the cell division regulatory protein, CrgA, were identified among the hits. Surface plasmon resonance and co-immunoprecipitation independently confirmed physical interactions for three proteinsin vitroand/orin vivo. Results are in line with the focal localization of MmpL3 at the poles and septum of actively-growing bacilli where the synthesis of all major constituents of the cell wall core are known to occur, and are further suggestive of a role for MmpL3 in the coordination of new cell wall deposition during cell septation and elongation. This novel aspect of the physiology of MmpL3 may contribute to the extreme vulnerability and high therapeutic potential of this transporter.
Carbon dots with molecular fluorescence and their application as a “turn-off” fluorescent probe for ferricyanide detection
Authors: Wang Tianshu , Wang Ailin , Wang Ruixue , Liu Zhaoyang , Sun Ying , Shan Guiye , Chen Yanwei , Liu Yichun 
Published: July 2019

AbstractHighly fluorescent carbon dots (CDs) exhibiting molecular fluorescence were synthesized and successfully used for sensing ferricyanide based on fluorescence quenching. We conducted dialysis to purify the CDs and found that the dialysate is also fluorescent. From the mass spectra and quantum yield analyses of the dialysate, it is demonstrated that molecular fluorophores were also synthesized during the synthesis of CDs. By the comparison of fluorescence spectra between CDs and dialysate, it is established that the fluorescence emission of CDs partly originates from fluorophores that are attached to CDs’ surface. The fluorescence quenching caused by ferricyanide is proved to be the overlap of absorption spectra between ferricyanide and CDs. The changes of the absorbance and fluorescence spectra are combined to enhance the detection sensitivity, and the limit of detection is calculated to be 1.7 μM. A good linear response of fluorescence-absorbance combined sensing toward ferricyanide is achieved in the range of 5–100 µM. This method is highly selective to ferricyanide among other common cations and anions, and it is also successfully applied in detecting ferricyanide in real water samples.
Precise and systematic survey of the efficacy of multicomponent drugs against functional dyspepsia
Authors: Wei Junying , Man Qiong , Guo Feifei , Xian Minghua , Wang Tingting , Tang Chunyu , Zhang Yi , Li Defeng , Tang Daifeng , Yang Hongjun , Huang Luqi 
Published: July 2019

AbstractFunctional dyspepsia (FD) is one of the most prevalent functional gastrointestinal disorders, and more and more multicomponent drugs represented by traditional Chinese medicines have provided a favorable therapeutic effect in its treatment. However, their precise localization in the clinic, as well as corresponding mechanism, is ambiguous, thus hindering their widespread use. To meet this requirement, a precise and systematic approach based on a restriction of special disease-related molecules and the following network pharmacology analysis was developed and applied to a multicomponent conventional drug, XiaoErFuPi (XEFP) granules. Experimental verification of the results indicates that this approach can facilitate the prediction, and the precise and systematic efficacy of XEFP could be easily revealed, which shows that XEFP has an advantage over the positive control drug on lactate, gastrin, interleukin 4 and calcitonin gene-related peptide. Moreover, by the proteomics analysis, its superposition of multi-target effects was revealed and a new candidate target for the treatment of FD, striatin, was obtained and verified. This study provides a practicable precise approach for the investigation of the efficacy of multicomponent drugs against FD and offers a promising alternative for the systematical management of FD.
Strong interlayer hybridization in the aligned SnS2/WSe2 hetero-bilayer structure
Authors: Zribi Jihene , Khalil Lama , Zheng Biyuan , Avila José , Pierucci Debora , Brulé Thibault , Chaste Julien , Lhuillier Emmanuel , Asensio Maria C. , Pan Anlian , Ouerghi Abdelkarim 
Published: July 2019

AbstractThe combination of monolayers of different two-dimensional (2D) materials into van der Waals hetero-bilayer structures creates unprecedented physical phenomena, acting as a powerful tool for future devices. Understanding and exploiting these phenomena hinge on knowing the electronic structure and the hybridization of hetero-bilayer structures. Here, we show strong hybridization effects arising between the constitutive single layers of a SnS2/WSe2 hetero-bilayer structure grown by chemical vapor deposition. Surprisingly, the valence band maximum position of WSe2 is moved from the K point for the single layer WSe2 to the Γ point for the aligned SnS2/WSe2 hetero-bilayer. Additionally, a significant photoluminescence quenching is observed for the SnS2/WSe2 hetero-bilayer structure with respect to the WSe2 monolayer. Using photoluminescence spectroscopy and nano-angle-resolved photoemission spectroscopy techniques, we demonstrate that the SnS2/WSe2 heterostructure present a type-II band alignment. These findings directly answer many outstanding questions about the electronic band structure and the band offset of SnS2/WSe2 hetero-bilayers for envisaging their applications in nanoelectronics.
Congenital goitrous hypothyroidism is caused by dysfunction of the iodide transporter SLC26A7
Authors: Ishii Jun , Suzuki Atsushi , Kimura Toru , Tateyama Michihiro , Tanaka Tatsushi , Yazawa Takuya , Arimasu Yu , Chen I-Shan , Aoyama Kohei , Kubo Yoshihiro , Saitoh Shinji , Mizuno Haruo , Kamma Hiroshi 
Published: July 2019

AbstractIodide transport and storage in the thyroid follicles is crucial for thyroid hormone synthesis. Pendrin, the iodide exporter that transports iodide to thyroid follicles, is responsible for Pendred syndrome, a disorder characterized by congenital hypothyroidism and hearing loss. However, thyroid hormone levels are basically normal in patients with Pendred syndrome, indicating the presence of another unknown iodide transporter. Here, we show that SLC26A7 is a novel iodide transporter in the thyroid. We observe that SLC26A7 is specifically expressed in normal thyroid tissues and demonstrate its function in iodide transport. Using whole-exome sequencing, we also find a homozygous nonsense mutation in SLC26A7 (c.1498 C > T; p.Gln500Ter) in two siblings with congenital goitrous hypothyroidism. The mutated SLC26A7 protein shows an abnormal cytoplasmic localisation and lacks the iodide transport function. These results reveal that SLC26A7 functions as a novel iodide transporter in the thyroid and its dysfunction affects thyroid hormonogenesis in humans and causes congenital goitrous hypothyroidism.