bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian Poroelastic Aquifer Characterization From InSAR Surface Deformation Data. Part I: Maximum A Posteriori Estimate
Authors: Alghamdi Amal , Hesse Marc A. , Chen Jingyi , Ghattas Omar 
Published: July 2020

AbstractCharacterizing the properties of groundwater aquifers is essential for predicting aquifer response and managing groundwater resources. In this work, we develop a high‐dimensional scalable Bayesian inversion framework governed by a three‐dimensional quasi‐static linear poroelastic model to characterize lateral permeability variations in groundwater aquifers. We determine the maximum a posteriori (MAP) point of the posterior permeability distribution from centimeter‐level surface deformation measurements obtained from Interferometric Synthetic Aperture Radar (InSAR). The scalability of our method to high parameter dimension is achieved through the use of adjoint‐based derivatives, inexact Newton methods to determine the MAP point, and a Matérn class sparse prior precision operator. Together, these guarantee that the MAP point is found at a cost, measured in number of forward/adjoint poroelasticity solves, that is independent of the parameter dimension. We apply our methodology to a test case for a municipal well in Mesquite, Nevada, in which InSAR and GPS surface deformation data are available. We solve problems with up to320,824state variable degrees of freedom (DOFs) and16,896parameter DOFs. A consistent treatment of noise level is employed so that the aquifer characterization result does not depend on the pixel spacing of surface deformation data. Our results show that the use of InSAR data significantly improves characterization of lateral aquifer heterogeneity, and the InSAR‐based aquifer characterization recovers complex lateral displacement trends observed by independent daily GPS measurements.
The mevalonate pathway is an actionable vulnerability of t(4;14)-positive multiple myeloma
Authors: Longo Joseph , Smirnov Petr , Li Zhihua , Branchard Emily , van Leeuwen Jenna E. , Licht Jonathan D. , Haibe-Kains Benjamin , Andrews David W. , Keats Jonathan J. , Pugh Trevor J. , Trudel Suzanne , Penn Linda Z. 
Published: July 2020

AbstractMultiple myeloma (MM) is a plasma cell malignancy that is often driven by chromosomal translocations. In particular, patients with t(4;14)-positive disease have worse prognosis compared to other MM subtypes. Herein, we demonstrated that t(4;14)-positive cells are highly dependent on the mevalonate (MVA) pathway for survival. Moreover, we showed that this metabolic vulnerability is immediately actionable, as inhibiting the MVA pathway with a statin preferentially induced apoptosis in t(4;14)-positive cells. In response to statin treatment, t(4;14)-positive cells activated the integrated stress response (ISR), which was augmented by co-treatment with bortezomib, a proteasome inhibitor. We identified that t(4;14)-positive cells depend on the MVA pathway for the synthesis of geranylgeranyl pyrophosphate (GGPP), as exogenous GGPP fully rescued statin-induced ISR activation and apoptosis. Inhibiting protein geranylgeranylation similarly induced the ISR in t(4;14)-positive cells, suggesting that this subtype of MM depends on GGPP, at least in part, for protein geranylgeranylation. Notably, fluvastatin treatment synergized with bortezomib to induce apoptosis in t(4;14)-positive cells and potentiated the anti-tumor activity of bortezomib in vivo. Our data implicate the t(4;14) translocation as a biomarker of statin sensitivity and warrant further clinical evaluation of a statin in combination with bortezomib for the treatment of t(4;14)-positive disease.
Giant photothermoelectric effect in silicon nanoribbon photodetectors
Authors: Dai Wei , Liu Weikang , Yang Jian , Xu Chao , Alabastri Alessandro , Liu Chang , Nordlander Peter , Guan Zhiqiang , Xu Hongxing 
Published: July 2020

AbstractThe photothermoelectric (PTE) effect enables efficient harvesting of the energy of photogenerated hot carriers and is a promising choice for high-efficiency photoelectric energy conversion and photodetection. Recently, the PTE effect was reported in low-dimensional nanomaterials, suggesting the possibility of optimizing their energy conversion efficiency. Unfortunately, the PTE effect becomes extremely inefficient in low-dimensional nanomaterials, owing to intrinsic disadvantages, such as low optical absorption and immature fabrication methods. In this study, a giant PTE effect was observed in lightly doped p-type silicon nanoribbons caused by photogenerated hot carriers. The open-circuit photovoltage responsivity of the device was 3-4 orders of magnitude higher than those of previously reported PTE devices. The measured photovoltage responses fit very well with the proposed photothermoelectric multiphysics models. This research proposes an application of the PTE effect and a possible method for utilizing hot carriers in semiconductors to significantly improve their photoelectric conversion efficiency.
Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation
Authors: Reyes Carolina , Hodgskiss Logan H , Kerou Melina , Pribasnig Thomas , Abby Sophie S , Bayer Barbara , Kraemer Stephan M , Schleper Christa 
Published: July 2020

Abstract
Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.
Prediction of breeding values for group-recorded traits including genomic information and an individually recorded correlated trait
Authors: Ma Xiang , Christensen Ole F. , Gao Hongding , Huang Ruihua , Nielsen Bjarne , Madsen Per , Jensen Just , Ostersen Tage , Li Pinghua , Shirali Mahmoud , Su Guosheng 
Published: July 2020

AbstractRecords on groups of individuals could be valuable for predicting breeding values when a trait is difficult or costly to measure on single individuals, such as feed intake and egg production. Adding genomic information has shown improvement in the accuracy of genetic evaluation of quantitative traits with individual records. Here, we investigated the value of genomic information for traits with group records. Besides, we investigated the improvement in accuracy of genetic evaluation for group-recorded traits when including information on a correlated trait with individual records. The study was based on a simulated pig population, including three scenarios of group structure and size. The results showed that both the genomic information and a correlated trait increased the accuracy of estimated breeding values (EBVs) for traits with group records. The accuracies of EBV obtained from group records with a size 24 were much lower than those with a size 12. Random assignment of animals to pens led to lower accuracy due to the weaker relationship between individuals within each group. It suggests that group records are valuable for genetic evaluation of a trait that is difficult to record on individuals, and the accuracy of genetic evaluation can be considerably increased using genomic information. Moreover, the genetic evaluation for a trait with group records can be greatly improved using a bivariate model, including correlated traits that are recorded individually. For efficient use of group records in genetic evaluation, relatively small group size and close relationships between individuals within one group are recommended.
Spatial domain analysis predicts risk of colorectal cancer recurrence and infers associated tumor microenvironment networks
Authors: Uttam Shikhar , Stern Andrew M. , Sevinsky Christopher J. , Furman Samantha , Pullara Filippo , Spagnolo Daniel , Nguyen Luong , Gough Albert , Ginty Fiona , Lansing Taylor D. , Chakra Chennubhotla S. 
Published: July 2020

AbstractAn unmet clinical need in solid tumor cancers is the ability to harness the intrinsic spatial information in primary tumors that can be exploited to optimize prognostics, diagnostics and therapeutic strategies for precision medicine. Here, we develop a transformational spatial analytics computational and systems biology platform (SpAn) that predicts clinical outcomes and captures emergent spatial biology that can potentially inform therapeutic strategies. We apply SpAn to primary tumor tissue samples from a cohort of 432 chemo-naïve colorectal cancer (CRC) patients iteratively labeled with a highly multiplexed (hyperplexed) panel of 55 fluorescently tagged antibodies. We show that SpAn predicts the 5-year risk of CRC recurrence with a mean AUROC of 88.5% (SE of 0.1%), significantly better than current state-of-the-art methods. Additionally, SpAn infers the emergent network biology of tumor microenvironment spatial domains revealing a spatially-mediated role of CRC consensus molecular subtype features with the potential to inform precision medicine.
Avoiding dynastic, assortative mating, and population stratification biases in Mendelian randomization through within-family analyses
Authors: Brumpton Ben , Sanderson Eleanor , Heilbron Karl , Hartwig Fernando Pires , Harrison Sean , Vie Gunnhild Åberge , Cho Yoonsu , Howe Laura D. , Hughes Amanda , Boomsma Dorret I. , Havdahl Alexandra , Hopper John , Neale Michael , Nivard Michel G. , Pedersen Nancy L. , Reynolds Chandra A. , Tucker-Drob Elliot M. , Grotzinger Andrew , Howe Laurence , Morris Tim , Li Shuai ,   The Within-family Consortium, Brumpton Ben , Sanderson Eleanor , Heilbron Karl , Hartwig Fernando Pires , Harrison Sean , Vie Gunnhild Åberge , Cho Yoonsu , Howe Laura D. , Hughes Amanda , Boomsma Dorret I. , Havdahl Alexandra , Hopper John , Neale Michael , Nivard Michel G. , Pedersen Nancy L. , Reynolds Chandra A. , Tucker-Drob Elliot M. , Grotzinger Andrew , Howe Laurence , Morris Tim , Li Shuai , Auton Adam , Windmeijer Frank , Chen Wei-Min , Bjørngaard Johan Håkon , Hveem Kristian , Willer Cristen , Evans David M. , Kaprio Jaakko , Smith George Davey , Åsvold Bjørn Olav , Hemani Gibran , Davies Neil M. ,   The 23andMe Research Team, Heilbron Karl , Auton Adam , Auton Adam , Windmeijer Frank , Chen Wei-Min , Bjørngaard Johan Håkon , Hveem Kristian , Willer Cristen , Evans David M. , Kaprio Jaakko , Davey Smith George , Åsvold Bjørn Olav , Hemani Gibran , Davies Neil M. 
Published: July 2020

AbstractEstimates from Mendelian randomization studies of unrelated individuals can be biased due to uncontrolled confounding from familial effects. Here we describe methods for within-family Mendelian randomization analyses and use simulation studies to show that family-based analyses can reduce such biases. We illustrate empirically how familial effects can affect estimates using data from 61,008 siblings from the Nord-Trøndelag Health Study and UK Biobank and replicated our findings using 222,368 siblings from 23andMe. Both Mendelian randomization estimates using unrelated individuals and within family methods reproduced established effects of lower BMI reducing risk of diabetes and high blood pressure. However, while Mendelian randomization estimates from samples of unrelated individuals suggested that taller height and lower BMI increase educational attainment, these effects were strongly attenuated in within-family Mendelian randomization analyses. Our findings indicate the necessity of controlling for population structure and familial effects in Mendelian randomization studies.
Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing
Authors: Sadegh Sepideh , Matschinske Julian , Blumenthal David B. , Galindez Gihanna , Kacprowski Tim , List Markus , Nasirigerdeh Reza , Oubounyt Mhaned , Pichlmair Andreas , Rose Tim Daniel , Salgado-Albarrán Marisol , Späth Julian , Stukalov Alexey , Wenke Nina K. , Yuan Kevin , Pauling Josch K. , Baumbach Jan 
Published: July 2020

AbstractCoronavirus Disease-2019 (COVID-19) is an infectious disease caused by the SARS-CoV-2 virus. Various studies exist about the molecular mechanisms of viral infection. However, such information is spread across many publications and it is very time-consuming to integrate, and exploit. We develop CoVex, an interactive online platform for SARS-CoV-2 host interactome exploration and drug (target) identification. CoVex integrates virus-human protein interactions, human protein-protein interactions, and drug-target interactions. It allows visual exploration of the virus-host interactome and implements systems medicine algorithms for network-based prediction of drug candidates. Thus, CoVex is a resource to understand molecular mechanisms of pathogenicity and to prioritize candidate therapeutics. We investigate recent hypotheses on a systems biology level to explore mechanistic virus life cycle drivers, and to extract drug repurposing candidates. CoVex renders COVID-19 drug research systems-medicine-ready by giving the scientific community direct access to network medicine algorithms. It is available at https://exbio.wzw.tum.de/covex/.
Atmospheric transport is a major pathway of microplastics to remote regions
Authors: Evangeliou N. , Grythe H. , Klimont Z. , Heyes C. , Eckhardt S. , Lopez-Aparicio S. , Stohl A. 
Published: July 2020

AbstractIn recent years, marine, freshwater and terrestrial pollution with microplastics has been discussed extensively, whereas atmospheric microplastic transport has been largely overlooked. Here, we present global simulations of atmospheric transport of microplastic particles produced by road traffic (TWPs – tire wear particles and BWPs – brake wear particles), a major source that can be quantified relatively well. We find a high transport efficiencies of these particles to remote regions. About 34% of the emitted coarse TWPs and 30% of the emitted coarse BWPs (100 kt yr−1 and 40 kt yr−1 respectively) were deposited in the World Ocean. These amounts are of similar magnitude as the total estimated direct and riverine transport of TWPs and fibres to the ocean (64 kt yr−1). We suggest that the Arctic may be a particularly sensitive receptor region, where the light-absorbing properties of TWPs and BWPs may also cause accelerated warming and melting of the cryosphere.
Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming
Authors: Zheng Zhen-Zhen , Zheng Li-Wei , Xu Min Nina , Tan Ehui , Hutchins David A. , Deng Wenchao , Zhang Yao , Shi Dalin , Dai Minhan , Kao Shuh-Ji 
Published: July 2020

AbstractIn the context of continuously increasing anthropogenic nitrogen inputs, knowledge of how ammonia oxidation (AO) in the ocean responds to warming is crucial to predicting future changes in marine nitrogen biogeochemistry. Here, we show divergent thermal response patterns for marine AO across a wide onshore/offshore trophic gradient. We find ammonia oxidizer community and ambient substrate co-regulate optimum temperatures (Topt), generating distinct thermal response patterns with Topt varying from ≤14 °C to ≥34 °C. Substrate addition elevates Topt when ambient substrate is unsaturated. The thermal sensitivity of kinetic parameters allows us to predict responses of both AO rate and Topt at varying substrate and temperature below the critical temperature. A warming ocean promotes nearshore AO, while suppressing offshore AO. Our findings reconcile field inconsistencies of temperature effects on AO, suggesting that predictive biogeochemical models need to include such differential warming mechanisms on this key nitrogen cycle process.
Transplacental transmission of SARS-CoV-2 infection
Authors: Vivanti Alexandre J. , Vauloup-Fellous Christelle , Prevot Sophie , Zupan Veronique , Suffee Cecile , Do Cao Jeremy , Benachi Alexandra , De Luca Daniele 
Published: July 2020

AbstractSARS-CoV-2 outbreak is the first pandemic of the century. SARS-CoV-2 infection is transmitted through droplets; other transmission routes are hypothesized but not confirmed. So far, it is unclear whether and how SARS-CoV-2 can be transmitted from the mother to the fetus. We demonstrate the transplacental transmission of SARS-CoV-2 in a neonate born to a mother infected in the last trimester and presenting with neurological compromise. The transmission is confirmed by comprehensive virological and pathological investigations. In detail, SARS-CoV-2 causes: (1) maternal viremia, (2) placental infection demonstrated by immunohistochemistry and very high viral load; placental inflammation, as shown by histological examination and immunohistochemistry, and (3) neonatal viremia following placental infection. The neonate is studied clinically, through imaging, and followed up. The neonate presented with neurological manifestations, similar to those described in adult patients.
Telomere-to-telomere assembly of a complete human X chromosome
Authors: Miga Karen H. , Koren Sergey , Rhie Arang , Vollger Mitchell R. , Gershman Ariel , Bzikadze Andrey , Brooks Shelise , Howe Edmund , Porubsky David , Logsdon Glennis A. , Schneider Valerie A. , Potapova Tamara , Wood Jonathan , Chow William , Armstrong Joel , Fredrickson Jeanne , Pak Evgenia , Tigyi Kristof , Kremitzki Milinn , Markovic Christopher , Maduro Valerie , Dutra Amalia , Bouffard Gerard G. , Chang Alexander M. , Hansen Nancy F. , Wilfert Amy B. , Thibaud-Nissen Françoise , Schmitt Anthony D. , Belton Jon-Matthew , Selvaraj Siddarth , Dennis Megan Y. , Soto Daniela C. , Sahasrabudhe Ruta , Kaya Gulhan , Quick Josh , Loman Nicholas J. , Holmes Nadine , Loose Matthew , Surti Urvashi , Risques Rosa ana , Graves Lindsay Tina A. , Fulton Robert , Hall Ira , Paten Benedict , Howe Kerstin , Timp Winston , Young Alice , Mullikin James C. , Pevzner Pavel A. , Gerton Jennifer L. , Sullivan Beth A. , Eichler Evan E. , Phillippy Adam M. 
Published: July 2020

AbstractAfter two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no single chromosome has been finished end to end, and hundreds of unresolved gaps persist1,2. Here we present a human genome assembly that surpasses the continuity of GRCh382, along with a gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. Focusing our efforts on the human X chromosome3, we reconstructed the centromeric satellite DNA array (approximately 3.1 Mb) and closed the 29 remaining gaps in the current reference, including new sequences from the human pseudoautosomal regions and from cancer-testis ampliconic gene families (CT-X and GAGE). These sequences will be integrated into future human reference genome releases. In addition, the complete chromosome X, combined with the ultra-long nanopore data, allowed us to map methylation patterns across complex tandem repeats and satellite arrays. Our results demonstrate that finishing the entire human genome is now within reach, and the data presented here will facilitate ongoing efforts to complete the other human chromosomes.
High-resolution terrestrial climate, bioclimate and vegetation for the last 120,000 years
Authors: Beyer Robert M. , Krapp Mario , Manica Andrea 
Published: July 2020

AbstractThe variability of climate has profoundly impacted a wide range of macroecological processes in the Late Quaternary. Our understanding of these has greatly benefited from palaeoclimate simulations, however, high-quality reconstructions of ecologically relevant climatic variables have thus far been limited to a few selected time periods. Here, we present a 0.5° resolution bias-corrected dataset of global monthly temperature, precipitation, cloud cover, relative humidity and wind speed, 17 bioclimatic variables, annual net primary productivity, leaf area index and biomes, covering the last 120,000 years at a temporal resolution of 1,000–2,000 years. We combined medium-resolution HadCM3 climate simulations of the last 120,000 years with high-resolution HadAM3H simulations of the last 21,000 years, and modern-era instrumental data. This allows for the temporal variability of small-scale features whilst ensuring consistency with observed climate. Our data make it possible to perform continuous-time analyses at a high spatial resolution for a wide range of climatic and ecological applications - such as habitat and species distribution modelling, dispersal and extinction processes, biogeography and bioanthropology.
Diversity of a bacterial community associated with Cliona lobata Hancock and Gelliodes pumila (Lendenfeld, 1887) sponges on the South-East coast of India
Authors: Meenatchi Ramu , Brindangnanam Pownraj , Hassan Saqib , Rathna Kumarasamy , Kiran G. Seghal , Selvin Joseph 
Published: July 2020

AbstractMarine sponges are sources of various bioactive metabolites, including several anticancer drugs, produced mainly by sponge-associated microbes. Palk Bay, on the south-east coast of India, is an understudied, highly disturbed reef environment exposed to various anthropogenic and climatic stresses. In recent years, Palk Bay suffered from pollution due to the dumping of untreated domestic sewage, effluents from coastal aquaculture, tourism, salt pans, cultivation of exotic seaweeds, and geogenic heavy-metal pollution, especially arsenic, mercury, cadmium, and lead. Low microbial-abundant sponge species, such asGelliodes pumilaandCliona lobata, were found to be ubiquitously present in this reef environment. Triplicate samples of each of these sponge species were subjected to Illumina MiSeq sequencing using V3–V4 region-specific primers. In bothC. lobataandG. pumila,there was an overwhelming dominance (98 and 99%) of phylum Candidatus SaccharibacteriaandProteobacteria,respectively.The overall number of operational taxonomic units (OTUs) was 68 (40 and 13 OTUs unique toG. pumilaandC. lobata, respectively; 15 shared OTUs).Alphaproteobacteriawas the most abundant class in both the sponge species. Unclassified species of phylum Candidatus SaccharibacteriafromC. lobataandChelotivorans compostifromG. pumilawere the most abundant bacterial species. The predominance ofAlphaproteobacteriaalso revealed the occurrence of various xenobiotic-degrading, surfactant-producing bacterial genera in both the sponge species, indirectly indicating the possible polluted reef status of Palk Bay. Studies on sponge microbiomes at various understudied geographical locations might be helpful in predicting the status of reef environments.