cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6086/d1h59v
title: Supplemental BOSS Emission Line Catalog

description: This archive contains the emission-line catalog described in Appendix A of
 the paper by Hamann et al., 2016, MNRAS, in press. "Extremely Red
 Quasars in BOSS"Paper Abstract: Red quasars are candidate young
 objects in an early transition stage of massive galaxy evolution. Our team
 recently discovered a population of extremely red quasars (ERQs) in the
 Baryon Oscillation Spectroscopic Survey (BOSS) that has a suite of
 peculiar emission-line properties including large rest equivalent widths
 (REWs), unusual "wingless" line profiles, large NV/Lya, NV/CIV,
 SiIV/CIV and other flux ratios, and very broad and blueshifted [OIII]
 5007. Here we present a new catalog of CIV and NV emission-line data for
 216,188 BOSS quasars to characterize the ERQ line properties further. We
 show that they depend sharply on UV-to-mid-IR color, secondarily on
 REW(CIV), and not at all on luminosity or the Baldwin Effect. We identify
 a “core” sample of 97 ERQs with nearly uniform peculiar properties
 selected via i-W3 &gt; 4.6 (AB) and REW(Civ) &gt; 100 A at
 redshifts 2.0-3.4. A broader search finds 235 more red quasars with
 similar unusual characteristics. The core ERQs have median luminosity
 logL(ergs/s) ~ 47.1, sky density 0.010 deg-2, surprisingly flat/blue UV
 spectra given their red UV-to-mid-IR colors, and common outflow signatures
 including BALs or BAL-like features and large CIV emission-line
 blueshifts. Their SEDs and line properties are inconsistent with normal
 quasars behind a dust reddening screen. We argue that the core ERQs are a
 unique obscured quasar population with extreme physical conditions related
 to powerful outflows across the line-forming regions. Patchy obscuration
 by small dusty clouds could produce the observed UV extinctions without
 substantial UV reddening.
DOI: 10.6071/m3wc7k
title: Reannotation of CCA-ends, initiator tRNAs, and other CAU-anticodon tRNAs of prokaryotic genomes in tRNAdb-CE 0.8

description: Background: While the CCA sequence at the mature 3′ end of tRNAs is
 conserved and critical for translational function, a genetic template for
 this sequence is not always contained in tRNA genes. In eukaryotes and
 archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by
 CCA-adding enzymes. In bacteria, tRNA genes template CCA sporadically.
 Results: In order to understand the variation in how prokaryotic tRNA
 genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database
 version 0.8. Among 132,129 prokaryotic tRNA genes, initiator tRNA genes
 template CCA at the highest average frequency (74.1%) over all functional
 classes except selenocysteine and pyrrolysine tRNA genes (88.1% and 100%
 respectively). Across bacterial phyla and a wide range of genome sizes,
 many lineages exist in which predominantly initiator tRNA genes template
 CCA. Convergent and parallel retention of CCA templating in initiator tRNA
 genes evolved in independent histories of reductive genome evolution in
 Bacteria. Also, in a majority of cyanobacterial and actinobacterial
 genera, predominantly initiator tRNA genes template CCA. We also found
 that a surprising fraction of archaeal tRNA genes template
 CCA.Conclusions: We suggest that cotranscriptional synthesis of initiator
 tRNA CCA 3′ ends can complement inefficient processing of initiator tRNA
 precursors, “bootstrap” rapid initiation of protein synthesis from a
 non-growing state, or contribute to an increase in cellular growth rates
 by reducing overheads of mass and energy to maintain nonfunctional tRNA
 precursors. More generally, CCA templating in structurally non-conforming
 tRNA genes can afford cells robustness and greater plasticity to respond
 rapidly to environmental changes and stimuli.
description: CCA-end reannotation was done by automated sequence comparison to
 annotated 5-prime end. Function of CAU-anticodon tRNAs was computed with
 TFAM (Ardell and Andersson 2006) using the Silva model (Silva et al.
 2007). Reannotations may be applied to prokaryotic genome data through
 genome accession IDs provided in the sequence data identifiers.
DOI: 10.6071/z7wc73
title: Southern Sierra Critical Zone Observatory (SSCZO), Providence Creek meteorological data, soil moisture and temperature, snow depth and air temperature

description: Snow depth, soil moisture and soil temperature are measured at lower
 Providence South facing (LowMetS) and North facing (LowMetN), Upper
 Providence South facing (UpMetS), North facing (UpMetN) and Flat aspect
 (UpMetF), and Subcatchment basin P301 (P301) with a wireless sensor
 network, using a Campbell Scientific logger to control peripheral devices.
 Snow depth is measured in the open, at the drip edge and under canopies.
 Soil moisture and temperature are measured at 10, 30, 60 and 90 cm depths
 coincident with the snow depth nodes. 10 watt solar panels provides power
 for monitoring at 10 minute intervals. Raw data have been processed to
 level 1 (QA/QC) and level 2 (gap-filled, derived) data. Time period: water
 year 2008 through water year 2012 (version 1), 2013 to 2016 (version 2,
 zip files), 2017 to 2021 (version 3, zip files).
description: Soil volumetric water content (VWC) and soil temperature measured
 using Decagon Devices ECHO-TM at depths of 10, 30, 60, an 90 cm below the
 mineral soil surface. Sensor now equivalent to 5TM (http://www.decagon.com/soil-moisture-sensors/). Distance to snow/soil surface and air temperature measured with Judd Communications ultrasonic depth sensor, using analog control ( http://www.juddcom.com/ ). Data control and storage on Campbell Scientific CR1000 datalogger, using AM16/32B multiplexer ( http://www.campbellsci.com ). Program for data acquisition are located on UC Merced-SNRI digital library ( https://sndl.ucmerced.edu/files/MHWG/Field/Southern...)
description: Lower and upper Providence Creek, Subcatchment basin P301.acde:
 white fir drip edge; acuc: white fir under canopy; cdde: incense-cedar
 drip edge; cduc: incense-cedar under canopy; open: open canopy; plde:
 sugar pine drip edge; pluc: sugar pine under canopy; ppde: Ponderosa pine
 drip; edge ppde: Ponderosa pine drip edge; ppuc: Ponderosa pine under
 canopy; ppuc: Ponderosa pine under canopy; qkde: black oak drip edge;
 qkuc: black oak under canopy. SSCZOKREW-Providence.gdb:
 boundaries, met stations, sensor nodes, stream gauging.
 Please see README and Providence_met_soil_snow_metadata.xml for
 additional information
DOI: 10.15468/dl.r2xhq4
title: Occurrence Download

description: A dataset containing 8792 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ips sexdentatus"
 ]
}

 The dataset includes 8792 records from 184 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001858-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.54s0mn2
title: Data from: Physical properties and bonding quality of laminated veneer lumber produced with veneers peeled from small-diameter rubberwood log

description: The peeling of small diameter rubber logs from the current short-rotation
 practices, undoubtedly will produced lower-grade veneers compared to the
 veneers from the conventional planting rotation. Hence, this raises the
 question of the properties of the produced laminated veneer lumber (LVL)
 from veneers peeled from small diameter rubber logs using spindleless
 lathe technology. Different thickness of rubberwood veneers were peeled
 from rubber logs with diameter less than 20 cm using spindleless lathe.
 Three layer LVLs were prepared using phenol formaldehyde (PF) adhesive and
 hot pressed at different temperature. During the peeling of veneer, lathe
 checks as deep as 30 to 60% of the veneer thickness are formed. This study
 showed that deep lathe check of 3 mm rubberwood veneer significantly
 reduced the gluebond shear strength of PF bonded LVL. In addition, lathe
 checks frequency were also shown to influence bond strengths. The presence
 of higher lathe check frequency on 2 mm veneer increased the wettability,
 thus, facilitated optimum penetration of adhesive for stronger bonding.
 These findings stress the importance of measuring and considering the
 lathe check depth and frequency during lamination process to get a better
 understanding of bonding quality in veneer-based products.
description: Physical properties and
 gluebond shear strength Specific gravity, water
 absorption, tangential swelling, longitudinal swelling, radial swelling,
 volumetric swelling, and gluebond shear strength
DOI: 10.5061/dryad.bv10m57
title: Data from: Phosphorus release from unamended and gypsum-or biochar-amended soils under simulated spring snowmelt and summer flooding conditions

description: Prolonged flooding changes the oxidation–reduction status of soils, often
 enhancing phosphorus (P) release to overlying floodwater. We studied P
 release from unamended, gypsum-amended and biochar- amended soils under
 simulated snowmelt flooding (previously frozen, cold flooding at +4°C) and
 summer flooding (unfrozen, warm flooding at +22°C), using two soils, Fyala
 clay (FYL-Cl) and Neuenberg sandy loam (NBG-SL) from Manitoba, Canada.
 Amended and unamended soils were packed into vessels and flooded under
 cold and warm temperatures in the laboratory. Pore water and floodwater
 samples were taken weekly for 6 weeks after flooding (WAF) and thereafter
 biweekly for 10 WAF, and analyzed for dissolved reactive P (DRP), pH and
 cation concentrations. NBG-SL showed a significantly higher DRP
 concentration in pore water and floodwater despite its low Olsen P
 content. Redox potential (Eh) decreased slowly under cold compared to warm
 flooding; hence redox-induced P release was substantially lower under cold
 flooding. Gypsum amendment significantly decreased the floodwater DRP
 concentrations in NBG-SL by 38% and 35% under cold and warm flooding,
 respectively, but had no significant effect in FYL-Cl, which had low DRP
 concentrations (&lt;1.2 mg L-1) throughout flooding period. Biochar
 amendment significantly increased floodwater DRP concentrations by 27 to
 68% in FYL-Cl under cold and warm flooding, respectively, but had no
 significant effect in NBG-SL. The results indicate substantially less P
 release under cold, than under warm flooding. Gypsum was effective in
 reducing floodwater DRP concentrations only at high DRP concentrations;
 thus the effectiveness was greater under warm, than under cold flooding
 conditions.
description: Pore water and
 floodwater DRP, pH, Ca, Mg, Fe and Mn with flooding time
 Pore water and
 floodwater collected and analyzed from a laboratory incubation study using
 packed soils. Soils were unamended, or amended with gypsum or biochar.
 Incubation conditions were simulated snow melt and simulated summer
 conditions. Dharmakeerthi_Datadryad.xlsx
DOI: 10.5061/dryad.7p3p8j3
title: Data from: Topological DNA-binding of SMC-like RecN promotes RecA-mediated DNA double-strand break repair

description: Bacterial RecN, closely related to the structural maintenance of
 chromosomes (SMC) family of proteins, functions in the repair of DNA
 double-strand breaks (DSBs) by homologous recombination. However, the
 understanding of how RecN acts in concert with the RecA recombinase to
 promote DSB repair remains limited. Here, we demonstrated that the
 purified Escherichia coli RecN protein topologically loads onto both
 single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) that has a
 preference for ssDNA. RecN topologically bound to dsDNA slides off the end
 of linear dsDNA, but this is prevented by RecA nucleoprotein filaments on
 ssDNA, thereby allowing RecN to translocate to DSBs. Furthermore, we found
 that, once RecN is recruited onto ssDNA, it can topologically capture a
 second dsDNA substrate in an ATP-dependent manner, suggesting a role in
 synapsis. Indeed, RecN stimulates RecA-mediated D-loop formation and
 subsequent strand exchange activities. Our findings provide mechanistic
 insights into the recruitment of RecN to DSBs and sister chromatid
 interactions by RecN, both of which function in RecA-mediated DSB repair.
description: Source data file contains numerical values that were used to
 plots graphs from Figures.
DOI: 10.5061/dryad.n7353s9
title: Data from: Brachiopods from the Byrd Group (Cambrian Series 2, Stage 4), Central Transantarctic Mountains, East Antarctica

description: Brachiopods from Cambrian Series 2, Stage 4 carbonate strata of the Byrd
 Group in the Central Transantarctic Mountains, East Antarctica, are
 described for the first time. These include six lingulate, one paterinate,
 and one rhynchonelliform taxa, including the new lingulate brachiopod
 Plicarmus wildi gen. et sp. nov. The assemblage correlates closely to the
 brachiopods recently reported from the Xinji Formation (Shuiyu section) in
 North China, as well as brachiopods recovered from the Dailyatia odyssei
 Zone across the Arrowie Basin of South Australia. The first unambiguous
 example of the acrotretid brachiopod Eohadrotreta zhenbaensis Li and
 Holmer 2004 outside South China is also identified in the context of its
 ontogenetic stages. Well preserved specimens of the acrotheloid
 Schizopholis yorkensis (Holmer and Ushatinskaya in Gravestock et al.,
 2001) facilitates a new reconstruction of its musculature and visceral
 region. This data is synthesised into a new cladistic analysis that
 resolves Acrotheloidea as a well-supported monophyletic clade and supports
 previous notions of a morphocline in acrotheloid evolution.
description: S1
 CountsNumbers of dorsal and
 ventral valves from each fossil-bearing localityS2
 MeasurementsMeasurements and summary
 statistics of valves' morphologyS3 List of characters
 and their statesDetield list of
 characters and character states used in taxon-character
 metrixS4 Character
 matrixDetailed character
 matrix in excel formatS5 Character matrix
 reference listList of references for
 taxa described in the matrix, where those from published literature are
 used.S6 Cladistic analysis
 nexus fileTaxa-character matrix in
 nexus format, used in cladistic analysisS5 Character matrix
 reference listList of references used
 for constructing the taxon-character matrix
DOI: 10.5061/dryad.d5hg2tv
title: Data from: Defence versus defence: are crucian carp trading off immune function against predator-induced morphology?

description: 1. Numerous species adopt inducible defence strategies, i.e. they have
 phenotypically plastic traits that decrease the risk of capture and
 consumption by potential predators. The benefits of expressing alternative
 phenotypes in high- versus low-risk environments are well documented.
 However, inducible anti-predator traits are also expected to incur costs,
 as they are not expressed when predators are absent, yet empirical
 evidence of such costs remains scarce. 2. Virtually all animals in nature
 are simultaneously under strong selection to evade both capture by
 predators and infection by parasites or pathogens, and, hence, display a
 diverse arsenal of defences to combat these threats, raising the
 possibility of trade-offs between defences. A classic example of a
 predator-induced morphological defence is the deep-bodied shape of crucian
 carp that reduces risk of predation from gape-size limited predators. The
 goal of this study was to examine if predator exposure affects also immune
 function in crucian carp, and if the degree of expressed morphological
 defence is traded off against immune function in individuals. 3. Following
 exposure to manipulations of perceived risk (predator presence/absence) in
 a long-term experiment (eight months), key aspects of innate immune
 function and individual differences in the expression of inducible
 morphological defence were quantified. 4. Predator-exposed individuals
 showed lower haptoglobin levels and complement activity, but higher
 natural antibody titres than fish from predator-free conditions. When
 experimentally challenged with a mimicked bacterial infection (LPS
 injection), fish reared in the presence of a natural predator showed a
 weaker immune response. Moreover, among predator-exposed individuals, the
 magnitude of morphological defence expression correlated with both
 baseline immune function and the ability to mount an immune response.
 However, these relationships were not consistently supportive of a general
 trade-off among defences. 5. Our results suggest that fish exposed to
 predators on average reduce investment in immune function and, further,
 the observed relationships among defences in predator-exposed individuals
 can best be explained from individual fitness and pace-of-life
 perspectives.
description: Data on morphology and
 immune function variables in predator-exposed and predator-free crucian
 carpData
 defence versus defence.xlsx
DOI: 10.5068/d1cc7x
title: 14c dates from Taraco, Peru

description: Carbon dates from excavated contexts at the site of Taraco, Peru
description: Ran through UC-Irvine
DOI: 10.5068/d1h59v
title: Lensfree On-chip Microscopy for Telemedicine

description: Conventional optical microscopes image cells by use of objective lenses
 that work together with other lenses and optical components. While quite
 effective, this classical approach has certain limitations for
 miniaturization of the imaging platform to make it compatible with the
 advanced state of the art in microfluidics. In this thesis, we introduce
 experimental details of a lensless on-chip imaging concept termed LUCAS
 (Lensless Ultra-wide field-of-view Cell monitoring Array platform based on
 Shadow imaging) that does not require any microscope objectives or other
 bulky optical components to image a heterogeneous cell solution over an
 ultra-wide field of view that can span as large as ~18 cm2. Moreover,
 unlike conventional microscopes, LUCAS can image a heterogeneous cell
 solution of interest over a depth-of-field of ~5 mm without the need for
 refocusing v vi which corresponds to up to ~9 mL sample volume. This
 imaging platform records the shadows (i.e., lensless digital holograms) of
 each cell of interest within its field of view, and automated digital
 processing of these cell shadows can determine the type, the count and the
 relative positions of cells within the solution. Because it does not
 require any bulky optical components or mechanical scanning stages it
 offers a significantly miniaturized platform that at the same time reduces
 the cost, which is quite important for especially point of care diagnostic
 tools. Furthermore, the imaging throughput of this platform is orders of
 magnitude better than conventional optical microscopes, which could be
 exceedingly valuable for high-throughput cell-biology experiments.
DOI: 10.5068/d1rp49
title: Live cell interferometry cell division tracking data files

description: Cell tracking data from quantitative phase microscopy experiments
 generated by Matlab analysis of raw image data.
description: Data is stored as x-position, y-position (pixels), cell dry mass
 (pg), time (h), cell number, area (pixels^2). Cell numbers in the
 pairtracks array follow the following convention: daughter 1 cell number =
 parent cell number*1000 + 1 daughter 2 cell number = parent cell
 number*1000 + 2
DOI: 10.5061/dryad.4j9n25d
title: Data from: Education Research: An experiential outpatient teleneurology curriculum for residents

description: Background: Telemedicine is rapidly becoming a major vehicle of delivering
 neurologic care to patients who have limited access to subspecialists and
 exaggerated travel hardship. However, neurology residents receive
 little-to-no training in telemedicine in outpatient clinics. Methods: We
 piloted, to our knowledge, the first formalized, experiential outpatient
 teleneurology curriculum. Neurology residents in their third and fourth
 postgraduate years (PGY3 and PGY4) at the University of California San
 Francisco (UCSF) completed an interactive lecture and 4 weeks of
 teleneurology clinics at the San Francisco Veterans Affairs Medical Center
 (SFVAMC). Change in residents’ telemedicine knowledge and perspectives on
 the utility, challenges, benefits, and future practice implementation of
 teleneurology were evaluated in 11 residents using precurriculum and
 postcurriculum quizzes and surveys after 2 of 4 weeks on the rotation.
 Results: Residents’ performance on quizzes improved from 53% to 88% (p =
 0.002). Residents’ impression of video visits compared to in-person visits
 changed, with more individuals indicating video visits to be the “same” if
 not “somewhat superior” with regards to obtaining a focused history,
 formulating a focused assessment and plan, communicating recommendations,
 and the overall care provided (p ≤ 0.04). All residents felt more
 competent using telemedicine for patient care in their eventual career.
 Conclusion: Our formal didactic and clinic-based teleneurology curriculum
 for neurology residents, which shared core themes suggested by the 2017
 American Academy of Neurology (AAN) Telemedicine Work Group’s published
 recommendations, showed a statistically significant improvement in
 knowledge and perspectives about the promise and limitations of
 teleneurology practice, as well as increased comfort levels in future
 implementation.
description: Table e-1:
 Teleneurologic examination tipsTeleneurologic
 examination tipsTableE1_AfshariEtAl.pdfTable e-2: Recommended “webside manners”Recommended “webside manners”TableE2_AfshariEtAl.pdfTable e-3: Teleneurology knowledge quiz questionsTeleneurology knowledge quiz questionsTableE3_AfshariEtAl.pdfFigure e-1: Shift in resident perspectives on video visits compared to in-person visits.Shift in resident perspectives on video visits compared to in-person visits.FigureE1_AfshariEtAl.pdfFigure e-2: Shift in resident perspectives on challenges of teleneurology.Shift in resident perspectives on challenges of teleneurology.TableE3_AfshariEtAl.pdf
DOI: 10.6084/m9.figshare.31161250
title: Neighbourhood models reveal Common cuckoo parasitism decisions depend on social information

description: 1. Individuals inadvertently provide a rich source of information about the local environment, influencing resource acquisition and breeding decisions, as well as how selection operates within and between species.2. In theory, the availability and utility of this social information should depend on proximity in time and space, as well as variation in traits between the information source and potential users. However, it remains challenging to combine these data and model how ‘neighbourhood information’ affects behavioural decisions.3. Here we adopt a common approach from plant ecology, neighbourhood models with maximum likelihood approach, to evaluate whether laying decisions of brood-parasitic Common cuckoos are influenced by variation in the availability and quality of the local host environment.4. We used a georeferenced 9-year dataset to model parasitism probability of redstart hosts depending on the characteristics of surrounding nests (neighbourhood density and variation in clutch size as a proxy for quality) and found that neighbourhoods were more informative of parasitism risk than attributes of the nest where the cuckoo deposited her egg. Although hosts of higher quality were slightly more likely to be parasitised, any given nest was less likely to be parasitised if neighbours were closer, and/or of higher quality.5. Our results therefore reveal that cuckoos gain information from patrolling host neighbourhoods beyond just monitoring for egg-laying opportunities and may make strategic decisions based on host quality. This highlights the potential for neighbourhood models to improve understanding more broadly of systems where risk or decision-making may be influenced by the social environment.