DeepTract: A Probabilistic Deep Learning Framework for White Matter Fiber Tractography

We present DeepTract, a deep-learning framework for estimating white matter fibers orientation and streamline tractography. We adopt a data-driven approach for fiber reconstruction from diffusion weighted images (DWI), which does not assume a specific diffusion model. We use a recurrent neural network for mapping sequences of DWI values into probabilistic fiber orientation distributions. Based on these estimations, our model facilitates both deterministic and probabilistic streamline tractography. We quantitatively evaluate our method using the Tractometer tool, demonstrating competitive performance with state-of-the art classical and machine learning based tractography algorithms. We further present qualitative results of bundle-specific probabilistic tractography obtained using our method. The code is publicly available at: https://github.com/itaybenou/DeepTract.git

Segregation of in to dislocations in InGaN

Dislocations are one-dimensional topological defects that occur frequently in functional thin film materials and that are known to degrade the performance of InxGa1-xN-based optoelectronic devices. Here, we show that large local deviations in alloy composition and atomic structure are expected to occur in and around dislocation cores in InxGa1-xN alloy thin films. We present energy-dispersive X-ray spectroscopy data supporting this result. The methods presented here are also widely applicable for predicting composition fluctuations associated with strain fields in other inorganic functional material thin films

Millennial-Scale Instability in the Geomagnetic Field Prior to the Matuyama-Brunhes Reversal

Changes in the Earth's magnetic field have global significance that reach from the outer core extending out to the uppermost atmosphere. Paleomagnetic records derived from sedimentary and volcanic sequences provide important insights into the geodynamo processes that govern the largest geomagnetic changes (polarity reversals), but dating uncertainties have hindered progress in this understanding. Here, we report a paleomagnetic record from multiple lava flows on Tahiti that bracket the Matuyama‐Brunhes (M‐B) polarity reversal ∼771,000 years ago. Our high‐precision ^(40)Ar/^(39)Ar ages constrain several rapid and short‐lived changes in field orientation up to 33,000 years prior to the M‐B reversal. These changes are similar to ones identified in other less well‐dated lava flows in Maui, Chile, and La Palma that occurred during an extended period of reduced field strength recorded in sediments. We use a simple stochastic model to show that these rapid polarity changes are highly attenuated in sediment records with low sedimentation rates. This prolonged 33,000 year period of reduced field strength and increased geomagnetic instability supports models that show frequent centennial‐to‐millennial‐scale polarity changes in the presence of a strongly weakened dipole field

"Petit spot" rejuvenated volcanism superimposed on plume-derived Samoan shield volcanoes: Evidence from a 645-m drill core from Tutuila Island, American Samoa

Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 20(3), (2019): 1485-1507, doi:10.1029/2018GC007985.In 2015 a geothermal exploration well was drilled on the island of Tutuila, American Samoa. The sample suite from the drill core provides 645 m of volcanic stratigraphy from a Samoan volcano, spanning 1.45 million years of volcanic history. In the Tutuila drill core, shield lavas with an EM2 (enriched mantle 2) signature are observed at depth, spanning 1.46 to 1.44 Ma. These are overlain by younger (1.35 to 1.17 Ma) shield lavas with a primordial “common” (focus zone) component interlayered with lavas that sample a depleted mantle component. Following ~1.15 Myr of volcanic quiescence, rejuvenated volcanism initiated at 24.3 ka and samples an EM1 (enriched mantle 1) component. The timing of the initiation of rejuvenated volcanism on Tutuila suggests that rejuvenated volcanism may be tectonically driven, as Samoan hotspot volcanoes approach the northern terminus of the Tonga Trench. This is consistent with a model where the timing of rejuvenated volcanism at Tutuila and at other Samoan volcanoes relates to their distance from the Tonga Trench. Notably, the Samoan rejuvenated lavas have EM1 isotopic compositions distinct from shield lavas that are geochemically similar to “petit spot” lavas erupted outboard of the Japan Trench and late stage lavas erupted at Christmas Island located outboard of the Sunda Trench. Therefore, like the Samoan rejuvenated lavas, petit spot volcanism in general appears to be related to tectonic uplift outboard of subduction zones, and existing geochemical data suggest that petit spots share similar EM1 isotopic signatures.Reviews from Kaj Hoernle and three anonymous reviewers are gratefully acknowledged. M. G. J. acknowledges support from the American Samoa Power Authority and National Science Foundation grants OCE‐1736984 and EAR‐1624840. The Tutuila drill core was the brainchild of Tim Bodell, without whom we would still have no stratigraphic record of Tutuila volcanism. The support of Utu Abe Malae and Matamua Katrina Mariner was instrumental to the project's success. We dedicate this paper to the memory of Abe Malae and his efforts to support science and education in American Samoa. Images of the entire drill core are available online (escholarship.org/uc/item/6gg6p61w). All data presented are either part of this study or previously published and are referenced in text.2019-08-1

Geochemical evidence in the northeast Lau Basin for subduction of the Cook-Austral volcanic chain in the Tonga Trench

Author Posting. © American Geophysical Union, 2016. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry, Geophysics, Geosystems 17 (2016): 1694–1724, doi:10.1002/2015GC006237.Lau Basin basalts host an array of geochemical signatures that suggest incorporation of enriched mantle source material often associated with intraplate hotspots, but the origin of these signatures remain uncertain. Geochemical signatures associated with mantle material entrained from the nearby Samoan hotspot are present in northwest Lau Basin lavas, and subducted seamounts from the Louisville hotspot track may contribute geochemical signatures to the Tonga Arc. However, lavas in the northeast Lau Basin (NELB) have unique enriched geochemical signatures that cannot be related to these hotspots, but can be attributed to the subduction of seamounts associated with the Cook-Austral volcanic lineament. Here we present geochemical data on a new suite of NELB lavas—ranging in 40Ar/39Ar age from 1.3 Ma to 0.365 ka—that have extreme signatures of geochemical enrichment, including lavas with the highest 206Pb/204Pb (19.580) and among the lowest 143Nd/144Nd (0.512697) encountered in the Lau Basin to date. These signatures are linked to the canonical EM1 (enriched mantle 1) and HIMU (high-μ = 238U/204Pb) mantle end-members, respectively. Using a plate reconstruction model, we show that older portions of the traces of two of the Cook-Austral hotspots that contributed volcanism to the Cook-Austral volcanic lineament—the Rarotonga and Rurutu hotspots—were potentially subducted in the Tonga Trench beneath the NELB. The geochemical signatures of the Rarotonga, Rurutu, and Samoan hotspots provide a compelling match to the extreme geochemical components observed in the new NELB lavas.NSF. Grant Number OCE-1153894, EAR-1347377, EAR-1145202, and EAR-1348082; French Agence Nationale de la Recherche Grant Number: ANR-10-BLANC-0603; NSF Grant Numbers: OCE-1154070, OCE-1232985, OCE-1153959 and OCE-14330972016-11-1

Bovine Herpesvirus Type 1 (BHV-1) UL49.5 Luminal Domain Residues 30 to 32 Are Critical for MHC-I Down-Regulation in Virus-Infected Cells

Bovine herpesvirus type 1 (BHV-1) UL49.5 inhibits transporter associated with antigen processing (TAP) and down-regulates cell-surface expression of major histocompatibility complex (MHC) class I molecules to promote immune evasion. We have constructed a BHV-1 UL49.5 cytoplasmic tail (CT) null and several UL49.5 luminal domain mutants in the backbone of wild-type BHV-1 or BHV-1 UL49.5 CT- null viruses and determined their relative TAP mediated peptide transport inhibition and MHC-1 down-regulation properties compared with BHV-1 wt. Based on our results, the UL49.5 luminal domain residues 30–32 and UL49.5 CT residues, together, promote efficient TAP inhibition and MHC-I down-regulation functions. In vitro, BHV-1 UL49.5 Δ30–32 CT-null virus growth property was similar to that of BHV-1 wt and like the wt UL49.5, the mutant UL49.5 was incorporated in the virion envelope and it formed a complex with gM in the infected cells

Omics analysis of educated platelets in cancer and benign disease of the pancreas

Pancreatic ductal adenocarcinoma (PDAC) is traditionally associated with thrombocy-tosis/hypercoagulation and novel insights on platelet-PDAC “dangerous liaisons” are warranted. Here we performed an integrative omics study investigating the biological processes of mRNAs and expressed miRNAs, as well as proteins in PDAC blood platelets, using benign disease as a refer-ence for inflammatory noise. Gene ontology mining revealed enrichment of RNA splicing, mRNA processing and translation initiation in miRNAs and proteins but depletion in RNA transcripts. Remarkably, correlation analyses revealed a negative regulation on SPARC transcription by isomiRs involved in cancer signaling, suggesting a specific ”education” in PDAC platelets. Platelets of benign patients were enriched for non-templated additions of G nucleotides (#ntaG) miRNAs, while PDAC presented length variation on 3′ (lv3p) as the most frequent modification on miRNAs. Additionally, we provided an actionable repertoire of PDAC and benign platelet-ome to be exploited for future studies. In conclusion, our data show that platelets change their biological repertoire in patients with PDAC, through dysregulation of miRNAs and splicing factors, supporting the presence of de novo protein machinery that can “educate” the platelet. These novel findings could be further exploited for innovative liquid biopsies platforms as well as possible therapeutic targets

Thermochronology of the modern Indus River bedload: New insight into the controls on the marine stratigraphic record

The Indus River is the only major drainage in the western Himalaya and delivers a long geological record of continental erosion to the Arabian Sea, which may be deciphered and used to reconstruct orogenic growth if the modern bedload can be related to the mountains. In this study we collected thermochronologic data from river sediment collected near the modern delta. U-Pb ages of zircons spanning 3 Gyr show that only ∼5% of the eroding crust has been generated since India-Asia collision. The Greater Himalaya are the major source of zircons, with additional contributions from the Karakoram and Lesser Himalaya. The 39Ar/40Ar dating of muscovites gives ages that cluster between 10 and 25 Ma, differing from those recorded in the Bengal Fan. Biotite ages are generally younger, ranging 0–15 Ma. Modern average exhumation rates are estimated at ∼0.6 km/m.y. or less, and have slowed progressively since the early Miocene (∼20 Ma), although fission track (FT) dating of apatites may indicate a recent moderate acceleration in rates since the Pliocene (∼1.0 km/m.y.) driven by climate change. The 39Ar/40Ar and FT techniques emphasize the dominance of high topography in controlling the erosional flux to the ocean. Localized regions of tectonically driven, very rapid exhumation (e.g., Nanga Parbat, S. Karakoram metamorphic domes) do not dominate the erosional record

Millennial-Scale Instability in the Geomagnetic Field Prior to the Matuyama-Brunhes Reversal

Changes in the Earth's magnetic field have global significance that reach from the outer core extending out to the uppermost atmosphere. Paleomagnetic records derived from sedimentary and volcanic sequences provide important insights into the geodynamo processes that govern the largest geomagnetic changes (polarity reversals), but dating uncertainties have hindered progress in this understanding. Here, we report a paleomagnetic record from multiple lava flows on Tahiti that bracket the Matuyama‐Brunhes (M‐B) polarity reversal ∼771,000 years ago. Our high‐precision ^(40)Ar/^(39)Ar ages constrain several rapid and short‐lived changes in field orientation up to 33,000 years prior to the M‐B reversal. These changes are similar to ones identified in other less well‐dated lava flows in Maui, Chile, and La Palma that occurred during an extended period of reduced field strength recorded in sediments. We use a simple stochastic model to show that these rapid polarity changes are highly attenuated in sediment records with low sedimentation rates. This prolonged 33,000 year period of reduced field strength and increased geomagnetic instability supports models that show frequent centennial‐to‐millennial‐scale polarity changes in the presence of a strongly weakened dipole field