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"Andrew Newman"
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The CAMELS data set: catchment attributes and meteorology for large-sample studies
We present a new data set of attributes for 671 catchments in the contiguous United States (CONUS) minimally impacted by human activities. This complements the daily time series of meteorological forcing and streamflow provided by Newman et al. (2015b). To produce this extension, we synthesized diverse and complementary data sets to describe six main classes of attributes at the catchment scale: topography, climate, streamflow, land cover, soil, and geology. The spatial variations among basins over the CONUS are discussed and compared using a series of maps. The large number of catchments, combined with the diversity of the attributes we extracted, makes this new data set well suited for large-sample studies and comparative hydrology. In comparison to the similar Model Parameter Estimation Experiment (MOPEX) data set, this data set relies on more recent data, it covers a wider range of attributes, and its catchments are more evenly distributed across the CONUS. This study also involves assessments of the limitations of the source data sets used to compute catchment attributes, as well as detailed descriptions of how the attributes were computed. The hydrometeorological time series provided by Newman et al. (2015b, https://doi.org/10.5065/D6MW2F4D) together with the catchment attributes introduced in this paper (https://doi.org/10.5065/D6G73C3Q) constitute the freely available CAMELS data set, which stands for Catchment Attributes and MEteorology for Large-sample Studies.
Journal Article
Allegories of encounter : colonial literacy and Indian captivities
\"Presenting an innovative, interdisciplinary approach to colonial America's best-known literary genre, Andrew Newman analyzes depictions of reading, writing, and recollecting texts in Indian captivity narratives. While histories of literacy and colonialism have emphasized the experiences of Native Americans, as students in missionary schools or as parties to treacherous treaties, captivity narratives reveal what literacy meant to colonists among Indians. Colonial captives treasured the written word in order to distinguish themselves from their Native captors and to affiliate with their distant cultural communities. Their narratives suggest that Indians recognized this value, sometimes with benevolence: repeatedly, they presented colonists with books\"-- Provided by publisher.
Book
A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation
During exon ligation, the Saccharomyces cerevisiae spliceosome recognizes the 3′-splice site (3′SS) of precursor messenger RNA (pre-mRNA) through non–Watson-Crick pairing with the 5′SS and the branch adenosine, in a conformation stabilized by Prp18 and Prp8. Here we present the 3.3-angstrom cryo–electron microscopy structure of a human postcatalytic spliceosome just after exon ligation. The 3′SS docks at the active site through conserved RNA interactions in the absence of Prp18. Unexpectedly, the metazoan-specific FAM32A directly bridges the 5′-exon and intron 3′SS of pre-mRNA and promotes exon ligation, as shown by functional assays. CACTIN, SDE2, and NKAP—factors implicated in alternative splicing—further stabilize the catalytic conformation of the spliceosome during exon ligation. Together these four proteins act as exon ligation factors. Our study reveals how the human spliceosome has co-opted additional proteins to modulate a conserved RNA-based mechanism for 3′SS selection and to potentially fine-tune alternative splicing at the exon ligation stage.
Journal Article
Global Nuclear Explosion Discrimination Using a Convolutional Neural Network
Using P‐wave seismograms, we trained a seismic source classifier using a Convolutional Neural Network. We trained for three classes: earthquake P‐wave, underground nuclear explosion (UNE) P‐wave, and noise. With the current absence of nuclear testing by countries that have signed the Comprehensive Test Ban Treaty, high quality seismic data from UNEs is limited. Even with limited training data, our model can accurately characterize most events recorded at regional and teleseismic distances, finding over 95% signals in the validation set. We applied the model on holdout datasets of the North Korean test explosions to evaluate the performance on unique region and station‐source pairs, with promising results. Additionally, we tested on the Source Physics Experiment events to investigate the potential for chemical explosions to act as a surrogate for nuclear explosions. We anticipate that machine‐learning models like our classifier system can have broad application for other seismic signals including volcanic and non‐volcanic tremor, anomalous earthquakes, ice‐quakes or landslide‐quakes. Plain Language Summary We train a global seismic event classifier using machine learning on underground nuclear test explosion seismic data. Our classifier model can successfully discriminate (with over 95% accuracy) between underground nuclear explosion, earthquake, and noise signals from stations both regionally and far‐field. Since this model was trained on a relatively small data set (for machine learning applications) we expect that similar methods can be applied to event or discrimination of other unique seismic sources like those from volcanoes, landslides, or glaciers. Key Points We successfully discriminate underground nuclear explosions with a Convolutional Neural network (CNN) trained on P‐wave seismograms Robust global seismic event discrimination is possible with machine learning trained on regional and teleseismic data A CNN trained with historical nuclear explosion data can be applied with high accuracy to other regions, like the six Democratic People's Republic of Korea's test explosions
Journal Article
الحقبة التأسيسية للتشيع الاثنى عشري : خطاب الحديث بين قم وبغداد
يتناول كتاب آندرو نيومان (متخصص في الدراسات الإسلامية في جامعة أدنبره) تاريخ متون الحديث الشيعية في القرون التأسيسية للمذهب الإمامي وأثر النهجين الفكريين المعروفين عند علماء الأمامية : النهج الأصولي الذي يمثله علماء بغداد والنهج الإخباري الذي تمثله علماء قم آنذاك في تدوين اقدام ثلاث مجاميع روائية عند الشيعة الأمامية : المحاسن للبرقي وبصائر الدرجات للصفار القمي والكافي في علم الدين للكليني على وفق منهج التحليل التاريخي والاستقرائي للنصوص التاريخية والروائية.
BOOK
Crystal structure of Prp8 reveals active site cavity of the spliceosome
The active centre of the spliceosome consists of an intricate network formed by U5, U2 and U6 small nuclear RNAs, and a pre-messenger-RNA substrate. Prp8, a component of the U5 small nuclear ribonucleoprotein particle, crosslinks extensively with this RNA catalytic core. Here we present the crystal structure of yeast Prp8 (residues 885–2413) in complex with Aar2, a U5 small nuclear ribonucleoprotein particle assembly factor. The structure reveals tightly associated domains of Prp8 resembling a bacterial group II intron reverse transcriptase and a type II restriction endonuclease. Suppressors of splice-site mutations, and an intron branch-point crosslink, map to a large cavity formed by the reverse transcriptase thumb, and the endonuclease-like and RNaseH-like domains. This cavity is large enough to accommodate the catalytic core of group II intron RNA. The structure provides crucial insights into the architecture of the spliceosome active site, and reinforces the notion that nuclear pre-mRNA splicing and group II intron splicing have a common origin.
The crystal structure of yeast Prp8 bound to a U5 small nuclear ribonucleoprotein particle assembly factor Aar2 is solved, offering insight into the architecture of the spliceosome active site, and supporting a possible common origin of eukaryotic pre-messenger-RNA splicing and group II intron splicing.
Spliceosome mechanism revealed
The core of the spliceosome, a complex that removes introns from precursor mRNA transcripts prior to their expression, consists of several RNA–protein complexes arranged on the pre-mRNA. Prp8 is a protein in one such core complex, the U5 snRNP, and it contains the active site where cleavage occurs. Kiyoshi Nagai and colleagues have solved the structure of a large fragment of Prp8 bound to a U5 snRNP assembly factor, Aar2. This structure offers insight into how the splice sites might fit into the active site, and supports a possible unified evolutionary origin of eukaryotic pre-mRNA and bacterial group II intron-splicing mechanisms.
Journal Article
Knaves over queens
As the alien Xenovirus reaches Britain, Prime Minister Sir Winston Churchill, now gifted with extraordinary longevity, joins with Alan Turing to set up a special organization, the Order of the Silver Helix, to outmaneuver the terrifying mutations of the virus in Britain.
BOOK
Cryo-EM structure of the spliceosome immediately after branching
Precursor mRNA (pre-mRNA) splicing proceeds by two consecutive transesterification reactions via a lariat–intron intermediate. Here we present the 3.8 Å cryo-electron microscopy structure of the spliceosome immediately after lariat formation. The 5′-splice site is cleaved but remains close to the catalytic Mg
2+
site in the U2/U6 small nuclear RNA (snRNA) triplex, and the 5′-phosphate of the intron nucleotide G(+1) is linked to the branch adenosine 2′OH. The 5′-exon is held between the Prp8 amino-terminal and linker domains, and base-pairs with U5 snRNA loop 1. Non-Watson–Crick interactions between the branch helix and 5′-splice site dock the branch adenosine into the active site, while intron nucleotides +3 to +6 base-pair with the U6 snRNA
ACAG
AGA sequence. Isy1 and the step-one factors Yju2 and Cwc25 stabilize docking of the branch helix. The intron downstream of the branch site emerges between the Prp8 reverse transcriptase and linker domains and extends towards the Prp16 helicase, suggesting a plausible mechanism of remodelling before exon ligation.
Cryo-EM reveals the configuration of substrate pre-mRNA within the active spliceosome and suggests how remodelling occurs prior to exon ligation.
Structure of the branched splicing complex
The excision of introns from RNA is not a concerted process, but is rather an ordered one involving two transesterification reactions by the spliceosome. In the first step, the 5′-splice site is cleaved and the intron end is joined to make a lariat structure. Kiyoshi Nagai and colleagues have captured the
Saccharomyces cerevisiae
spliceosome stalled immediately after this first transesterification (branching) reaction by cryo-electron microscopy single-particle reconstruction at an overall resolution of 3.8 Å. The configuration of the RNA within the complex suggests that remodelling occurs before the second step, exon ligation.
Journal Article