bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New General Allometric Biomass Model
Authors: Zeng Wei Sheng , Tang Shou Zheng 
Published: July 2019

AbstractTo implement monitoring and assessment of national forest biomass, it is becoming the trend to develop generalized single-tree biomass models suitable for large scale forest biomass estimation. Considering that the theoretical biomass allometric model developed by West et al. [1,2] was statistically different from the empirical one, the two parameters in the most commonly used biomass equation M=aDb were analyzed in this paper. Firstly, based on the knowledge of geometry, the theoretical value of parameter b was deduced, i.e., b=7/3(&x2248;2.33), and the comparison with many empirical studies conducted throughout the globe indicated that the theoretical parameter could describe soundly the average allometric relationship between aboveground biomass M and D (diameter on breast height). Secondly, using five datasets of aboveground biomass which consisted of 1441 M-D pairs of sample trees, the new general biomass allometric model was validated. Finally, the relationship between parameter a and wood density p was analyzed, and the linear regression was developed. The new model, which is not only simple but also species-specific, offers a feasible approach on establishment of generalized biomass models for regional and national forest biomass estimation.
Optogenetics in primates: monkey see monkey look
Authors: Jazayeri Mehrdad , Lindbloom-Brown Zachary , Horwitz Gregory 
Published: July 2019

AbstractOptogenetics has emerged as a powerful tool for studying the neural basis of simple behaviors in rodents and small animals. In the primate model, however, optogenetics has had limited utility because optical methods have not been able to drive behavior. Here, we report that monkeys reliably shift their gaze toward the receptive field of optically driven channelrhodopsin-2-expressing V1 neurons. This result establishes optogenetics as a viable means for the causal analysis of behavior in the primate model.
CRED: A Deep Residual Network of Convolutional and Recurrent Units for Earthquake Signal Detection
Authors: Mousavi S. Mostafa , Zhu Weiqiang , Sheng Yixiao , Beroza Gregory C. 
Published: July 2019

AbstractEarthquake signal detection is at the core of observational seismology. A good detection algorithm should be sensitive to small and weak events with a variety of waveform shapes, robust to background noise and non-earthquake signals, and efficient for processing large data volumes. Here, we introduce the Cnn-Rnn Earthquake Detector (CRED), a detector based on deep neural networks. CRED uses a combination of convolutional layers and bi-directional long-short-term memory units in a residual structure. It learns the time-frequency characteristics of the dominant phases in an earthquake signal from three component data recorded on individual stations. We train the network using 500,000 seismograms (250k associated with tectonic earthquakes and 250k identified as noise) recorded in Northern California. The robustness of the trained model with respect to the noise level and non-earthquake signals is shown by applying it to a set of semi-synthetic signals. We also apply the model to one month of continuous data recorded at Central Arkansas to demonstrate its efficiency, generalization, and sensitivity. Our model is able to detect more than 800 microearthquakes as small as −1.3 ML induced during hydraulic fracturing far away than the training region. We compare the performance of the model with the STA/LTA, template matching, and FAST algorithms. Our results indicate an efficient and reliable performance of CRED. This framework holds great promise for lowering the detection threshold while minimizing false positive detection rates.
Insight into Fluorocarbon Adsorption in Metal-Organic Frameworks via Experiments and Molecular Simulations
Authors: Barpaga Dushyant , Nguyen Van T. , Medasani Bharat K. , Chatterjee Sayandev , McGrail B. Peter , Motkuri Radha Kishan , Dang Liem X. 
Published: July 2019

AbstractThe improvement in adsorption/desorption of hydrofluorocarbons has implications for many heat transformation applications such as cooling, refrigeration, heat pumps, power generation, etc. The lack of chlorine in hydrofluorocarbons minimizes the lasting environmental damage to the ozone, with R134a (1,1,1,2-tetrafluoroethane) being used as the primary industrial alternative to commonly used Freon-12. The efficacy of novel adsorbents used in conjunction with R134a requires a deeper understanding of the host-guest chemical interaction. Metal-organic frameworks (MOFs) represent a newer class of adsorbent materials with significant industrial potential given their high surface area, porosity, stability, and tunability. In this work, we studied two benchmark MOFs, a microporous Ni-MOF-74 and mesoporous Cr-MIL-101. We employed a combined experimental and simulation approach to study the adsorption of R134a to better understand host-guest interactions using equilibrium isotherms, enthalpy of adsorption, Henry’s coefficients, and radial distribution functions. The overall uptake was shown to be exceptionally high for Cr-MIL-101, >140 wt% near saturation while >50 wt% at very low partial pressures. For both MOFs, simulation data suggest that metal sites provide preferable adsorption sites for fluorocarbon based on favorable C-F ··· M+ interactions between negatively charged fluorine atoms of R134a and positively charged metal atoms of the MOF framework.
Global impact of diet and temperature over aquaculture of Octopus vulgaris paralarvae from a transcriptomic approach
Authors: García-Fernández P. , Prado-Alvarez M. , Nande M. , Garcia de la serrana D. , Perales-Raya C. , Almansa E. , Varó I. , Gestal C. 
Published: July 2019

AbstractCommon octopus, Octopus vulgaris, is an economically important cephalopod species. However, its rearing under captivity is currently challenged by massive mortalities previous to their juvenile stage due to nutritional and environmental factors. Dissecting the genetic basis and regulatory mechanism behind this mortality requires genomic background knowledge. A transcriptomic sequencing of 10 dph octopus paralarvae from different experimental conditions was constructed via RNA-seq. A total of 613,767,530 raw reads were filtered and de novo assembled into 363,527 contigs of which 82,513 were annotated in UniProt carrying also their GO and KEGG information. Differential gene expression analysis was carried out on paralarvae reared under different diet regimes and temperatures, also including wild paralarvae. Genes related to lipid metabolism exhibited higher transcriptional levels in individuals whose diet includes crustacean zoeas, which had an impact over their development and immune response capability. High temperature induces acclimation processes at the time that increase metabolic demands and oxidative stress. Wild individuals show an expression profile unexpectedly similar to Artemia fed individuals. Proteomic results support the hypothesis revealed by transcriptional analysis. The comparative study of the O. vulgaris transcriptomic profiles allowed the identification of genes that deserve to be further studied as candidates for biomarkers of development and health. The results obtained here on the transcriptional variations of genes caused by diet and temperature will provide new perspectives in understanding the molecular mechanisms behind nutritional and temperature requirements of common octopus that will open new opportunities to deepen in paralarvae rearing requirements.
Label-free time- and space-resolved exometabolite sampling of growing plant roots through nanoporous interfaces
Authors: Patabadige Damith E. W. , Millet Larry J. , Aufrecht Jayde A. , Shankles Peter G. , Standaert Robert F. , Retterer Scott T. , Doktycz Mitchel J. 
Published: July 2019

AbstractSpatial and temporal profiling of metabolites within and between living systems is vital to understanding how chemical signaling shapes the composition and function of these complex systems. Measurement of metabolites is challenging because they are often not amenable to extrinsic tags, are diverse in nature, and are present with a broad range of concentrations. Moreover, direct imaging by chemically informative tools can significantly compromise viability of the system of interest or lack adequate resolution. Here, we present a nano-enabled and label-free imaging technology using a microfluidic sampling network to track production and distribution of chemical information in the microenvironment of a living organism. We describe the integration of a polyester track-etched (PETE) nanofluidic interface to physically confine the biological sample within the model environment, while allowing fluidic access via an underlying microfluidic network. The nanoporous interface enables sampling of the microenvironment above in a time-dependent and spatially-resolved manner. For demonstration, the diffusional flux through the PETE membrane was characterized to understand membrane performance, and exometabolites from a growing plant root were successfully profiled in a space- and time-resolved manner. This method and device provide a frame-by-frame description of the chemical environment that maps to the physical and biological characteristics of the sample.
Palaeo-tsunami inundation distances deduced from roundness of gravel particles in tsunami deposits
Authors: Ishimura Daisuke , Yamada Keitaro 
Published: July 2019

AbstractInformation on palaeo-tsunami magnitude is scientifically and socially essential to mitigate tsunami risk. However, estimating palaeo-tsunami parameters (e.g., inundation distance) from sediments is not simple because tsunami deposits reflect complex transport processes. Here, we show a new approach to estimate tsunami inundation distance based on the mixture ratio of gravels from several sources in tsunami deposits. We measured the roundness of source gravels in modern beach and fluvial deposits in a coastal valley in Japan through image analysis and then calculated the mixture ratio of both sediment types in tsunami deposits. Normalising the mixture ratios by inundation distances revealed an abrupt change in the mixture ratio at a constant percentile, regardless of tsunami magnitude. This relation allowed estimation of the inundation distance of palaeo-tsunamis during the last 4000 years.
Genomic non-redundancy of the mir-183/96/182 cluster and its requirement for hair cell maintenance
Authors: Fogerty Joseph , Stepanyan Ruben , Cianciolo Lauren T. , Tooke Benjamin P. , Perkins Brian D. 
Published: July 2019

AbstractmicroRNAs are important regulators of gene expression. In the retina, the mir-183/96/182 cluster is of particular interest due to its robust expression and studies in which loss of the cluster caused photoreceptor degeneration. However, it is unclear which of the three miRNAs in the cluster are ultimately required in photoreceptors, whether each may have independent, contributory roles, or whether a single miRNA from the cluster compensates for the loss of another. These are important questions that will not only help us to understand the role of these particular miRNAs in the retina, but will deepen our understanding of how clustered microRNAs evolve and operate. To that end, we have developed a complete panel of single, double, and triple mir-183/96/182 mutant zebrafish. While the retinas of all mutant animals were normal, the triple mutants exhibited acute hair cell degeneration which corresponded with impaired swimming and death at a young age. By measuring the penetrance of this phenotype in each mutant line, we determine which of the three miRNAs in the cluster are necessary and/or sufficient to ensure normal hair cell development and function.
Relationship of reduced glomerular filtration rate with alterations in plasma free amino acids and uric acid evaluated in healthy control and hypertensive subjects
Authors: Mahbub M. H. , Yamaguchi Natsu , Takahashi Hidekazu , Hase Ryosuke , Yamamoto Hiroshi , Kikuchi Shinya , Tanabe Tsuyoshi 
Published: July 2019

AbstractThe potential association between altered levels of plasma free amino acids (PFAAs) and uric acid (UA) with estimated glomerular filtration rate (eGFR) remains unknown among patients with hypertension. A total of 2804 healthy controls and 2455 hypertensive patients were included in the current analysis. eGFR was defined as reduced when it was <60 ml/min/1.73 m2. The associations between reduced eGFR and individual PFAAs and UA in the healthy control and hypertension groups were explored by logistic regression analyses adjusted for potential confounding variables. Results show that UA had a significant positive association with reduced eGFR in both healthy control and hypertension groups (P < 0.001). Among the PFAAs, citrulline, glycine and phenylalanine showed significant positive associations with reduced eGFR in both healthy control (P < 0.01 to 0.001) and hypertension (P < 0.001) groups. Moreover, alanine, asparagine and methionine achieved significant positive associations with reduced eGFR only in the hypertension group (P < 0.01 to 0.001). Conversely, serine showed significant inverse associations with reduced eGFR in the hypertension group only (P < 0.001). Our findings provide first evidence for a strong relationship between distinct patterns of PFAAs and elevated UA with reduced eGFR in hypertension. The findings may appear useful in developing effective strategies for the prevention or early detection and treatment of declined kidney function in hypertension.
Deep-dose: a voxel dose estimation method using deep convolutional neural network for personalized internal dosimetry
Authors: Lee Min Sun , Hwang Donghwi , Kim Joong Hyun , Lee Jae Sung 
Published: July 2019

AbstractPersonalized dosimetry with high accuracy is crucial owing to the growing interests in personalized medicine. The direct Monte Carlo simulation is considered as a state-of-art voxel-based dosimetry technique; however, it incurs an excessive computational cost and time. To overcome the limitations of the direct Monte Carlo approach, we propose using a deep convolutional neural network (CNN) for the voxel dose prediction. PET and CT image patches were used as inputs for the CNN with the given ground truth from direct Monte Carlo. The predicted voxel dose rate maps from the CNN were compared with the ground truth and dose rate maps generated voxel S-value (VSV) kernel convolution method, which is one of the common voxel-based dosimetry techniques. The CNN-based dose rate map agreed well with the ground truth with voxel dose rate errors of 2.54% ± 2.09%. The VSV kernel approach showed a voxel error of 9.97% ± 1.79%. In the whole-body dosimetry study, the average organ absorbed dose errors were 1.07%, 9.43%, and 34.22% for the CNN, VSV, and OLINDA/EXM dosimetry software, respectively. The proposed CNN-based dosimetry method showed improvements compared to the conventional dosimetry approaches and showed results comparable with that of the direct Monte Carlo simulation with significantly lower calculation time.
Bioactive Thymosin Alpha-1 Does Not Influence F508del-CFTR Maturation and Activity
Authors: Armirotti Andrea , Tomati Valeria , Matthes Elizabeth , Veit Guido , Cholon Deborah M. , Phuan Puay-Wah , Braccia Clarissa , Guidone Daniela , Gentzsch Martina , Lukacs Gergely L. , Verkman Alan S. , Galietta Luis J. V. , Hanrahan John W. , Pedemonte Nicoletta 
Published: July 2019

AbstractDeletion of phenylalanine 508 (F508del) in the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel is the most frequent mutation causing cystic fibrosis (CF). F508del-CFTR is misfolded and prematurely degraded. Recently thymosin a-1 (Tα-1) was proposed as a single molecule-based therapy for CF, improving both F508del-CFTR maturation and function by restoring defective autophagy. However, three independent laboratories failed to reproduce these results. Lack of reproducibility has been ascribed by the authors of the original paper to the use of DMSO and to improper handling. Here, we address these potential issues by demonstrating that Tα-1 changes induced by DMSO are fully reversible and that Tα-1 peptides prepared from different stock solutions have equivalent biological activity. Considering the negative results here reported, six independent laboratories failed to demonstrate F508del-CFTR correction by Tα-1. This study also calls into question the autophagy modulator cysteamine, since no rescue of mutant CFTR function was detected following treatment with cysteamine, while deleterious effects were observed when bronchial epithelia were exposed to cysteamine plus the antioxidant food supplement EGCG. Although these studies do not exclude the possibility of beneficial immunomodulatory effects of thymosin α-1, they do not support its utility as a corrector of F508del-CFTR.
Magnetic Resonance Spectroscopy-based Metabolomic Biomarkers for Typing, Staging, and Survival Estimation of Early-Stage Human Lung Cancer
Authors: Berker Yannick , Vandergrift Lindsey A. , Wagner Isabel , Su Li , Kurth Johannes , Schuler Andreas , Dinges Sarah S. , Habbel Piet , Nowak Johannes , Mark Eugene , Aryee Martin J. , Christiani David C. , Cheng Leo L. 
Published: July 2019

AbstractLow-dose CT has shown promise in detecting early stage lung cancer. However, concerns about the adverse health effects of radiation and high cost prevent its use as a population-wide screening tool. Effective and feasible screening methods to triage suspicious patients to CT are needed. We investigated human lung cancer metabolomics from 93 paired tissue-serum samples with magnetic resonance spectroscopy and identified tissue and serum metabolomic markers that can differentiate cancer types and stages. Most interestingly, we identified serum metabolomic profiles that can predict patient overall survival for all cases (p = 0.0076), and more importantly for Stage I cases alone (n = 58, p = 0.0100), a prediction which is significant for treatment strategies but currently cannot be achieved by any clinical method. Prolonged survival is associated with relative overexpression of glutamine, valine, and glycine, and relative suppression of glutamate and lipids in serum.
Olfactory response of Mahanarva spectabilis (Hemiptera: Cercopidae) to volatile organic compounds from forage grasses
Authors: Silva Sandra E. B. , Auad Alexander M. , Moraes Jair C. , Alvarenga Roberta , Fonseca Marcy G. , Marques Francisco A. , Santos Nayana C. S. , Nagata Noemi 
Published: July 2019

AbstractSeveral herbivorous insects utilize plant chemical cues to identify hosts for feeding. The role of smell in host plant detection by Mahanarva spectabilis (Distant) remains largely unknown. In this study, assays were applied to assess M. spectabilis olfactory responses to forage grasses (Pennisetum purpureum cvs. Roxo Botucatu and Pioneiro; Panicum maximum cvs. Makueni and Tanzânia; Hyparrhenia rufa cv. Jaraguá; Melinis minutiflora; Cynodon dactylon cv. Tifton; Brachiaria brizantha cv. Marandú; and Brachiaria decumbens cv. Basilisk). Bioassays were performed using a Y-olfactometer to evaluate the behavior of adult M. spectabilis to forage damaged and undamaged by insects. M. spectabilis preferred volatiles of undamaged Basilisk and Pioneiro. Repellent behavior by M. spectabilis to cospecifics was recorded for plant volatiles from damaged Marandú. The mixture of volatiles from undamaged forage grasses differed from that of forage grasses damaged by insects. Forage grasses showed a greater diversity of compounds after damage, including menthone, eucalyptol and camphor, which are compounds likely to cause loss of attractiveness or repellence. Our results demonstrate that M. spectabilis employs plant chemical cues in its choice of hosts. This fact may contribute to strategies of integrated management against this pest.
A role for ABCB1 in prognosis, invasion and drug resistance in ependymoma
Authors: Sabnis Durgagauri H. , Storer Lisa C. D. , Liu Jo-Fen , Jackson Hannah K. , Kilday J. P. , Grundy Richard G. , Kerr Ian D. , Coyle Beth 
Published: July 2019

AbstractThree of the hallmarks of poor prognosis in paediatric ependymoma are drug resistance, local invasion and recurrence. We hypothesised that these hallmarks were due to the presence of a sub-population of cancer stem cells expressing the multi-drug efflux transporter ABCB1. ABCB1 gene expression was observed in 4 out of 5 paediatric ependymoma cell lines and increased in stem cell enriched neurospheres. Functional inhibition of ABCB1 using vardenafil or verapamil significantly (p ≤ 0.05–0.001) potentiated the response to three chemotherapeutic drugs (vincristine, etoposide and methotrexate). Both inhibitors were also able to significantly reduce migration (p ≤ 0.001) and invasion (p ≤ 0.001). We demonstrate that ABCB1 positive patients from an infant chemotherapy-led trial (CNS9204) had a shorter mean event free survival (EFS) (2.7 versus 8.6 years; p = 0.007 log-rank analysis) and overall survival (OS) (5.4 versus 12 years; p = 0.009 log-rank analysis). ABCB1 positivity also correlated with reduced event free survival in patients with incompletely resected tumours who received chemotherapy across CNS9204 and CNS9904 (a radiotherapy-led SIOP 1999-04 trial cohort; p = 0.03). ABCB1 is a predictive marker of chemotherapy response in ependymoma patients and vardenafil, currently used to treat paediatric pulmonary hypertension in children, could be repurposed to reduce chemoresistance, migration and invasion in paediatric ependymoma patients at non-toxic concentrations.
Elevated aerosol layer over South Asia worsens the Indian droughts
Authors: Fadnavis Suvarna , Sabin T. P. , Roy Chaitri , Rowlinson Matthew , Rap Alexandru , Vernier Jean-Paul , Sioris Christopher E. 
Published: July 2019

AbstractDroughts have become more severe and recurrent over the Indian sub-continent during the second half of the twentieth century, leading to more severe hydro-climatic and socio-economic impacts over one of the most densely populated parts of the world. So far, droughts have mostly been connected to circulation changes concomitant with the abnormal warming over the Pacific Ocean, prevalently known as “El Niño”. Here, exploiting observational data sets and a series of dedicated sensitivity experiments, we show that the severity of droughts during El Niño is amplified (17%) by changes in aerosols. The model experiments simulate the transport of boundary layer aerosols from South Asian countries to higher altitudes (12–18 km) where they form the Asian Tropopause Aerosol Layer (ATAL) (~ 60–120°E, 20–40°N). During El Niño, the anomalous overturning circulation from the East Asian region further enriches the thickness of aerosol layers in the ATAL over the northern part of South Asia. The anomalous aerosol loading in the ATAL reduces insolation over the monsoon region, thereby exacerbating the severity of drought by further weakening the monsoon circulation. Future increases in industrial emissions from both East and South Asia will lead to a wider and thicker elevated aerosol layer in the upper troposphere, potentially amplifying the severity of droughts.