cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1293446.v1
title: Bangor University APCs 2014

description: This spreadsheet contains details of article processing charges (APCs) paid by Bangor University during 2014. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/) and has been released with permission of the Bangor University Library.
DOI: 10.6084/m9.figshare.1293448.v1
title: Cryogenian magmatism and crustal reworking in the Southern Granulite Terrane, India

description: Understanding Neoproterozoic crustal evolution is fundamental to reconstructing the Gondwana supercontinent, which was assembled at this time. Here we report evidence of Cryogenian crustal reworking in the Madurai Block of the Southern Granulite Terrane of India. The study focuses on a garnet-bearing granite–charnockite suite, where the granite shows <i>in situ</i> dehydration into patches and veins of incipient charnockite along the contact with charnockite. The granite also carries dismembered layers of Mg–Al-rich granulite. Micro-textural evidence for dehydration of granite in the presence of CO<sub>2</sub>-rich fluids includes the formation of orthopyroxene by the breakdown of biotite, neoblastic zircon growth in the dehydration zone, at around 870°C and 8 kbar. The zircon U–Pb ages suggest formation of the granite, charnockite, and incipient charnockite at 836 ± 73, 831 ± 31, and 772 ± 49 Ma, respectively. Negative zircon εHf (<i>t</i>) (−5 to −20) values suggest that these rocks were derived from a reworked Palaeoproterozoic crustal source. Zircon grains in the Mg–Al-rich granulite record a spectrum of ages from ca. 2300 to ca. 500 Ma, suggesting multiple provenances ranging from Palaeoproterozoic to mid-Neoproterozoic, with neoblastic zircon growth during high-temperature metamorphism in the Cambrian. We propose that the garnet-bearing granite and charnockite reflect the crustal reworking of aluminous crustal material indicated by the presence of biotite + quartz + aluminosilicate inclusions in the garnet within the granite. This crustal source can be the Mg–Al-rich layers carried by the granite itself, which later experienced high-temperature regional metamorphism at ca. 550 Ma. Our model also envisages that the CO<sub>2</sub> which dehydrated the garnet-bearing granite generating incipient charnockite was sourced from the proximal massive charnockite through advection. These Cryogenian crustal reworking events are related to prolonged tectonic activities prior to the final assembly of the Gondwana supercontinent.
DOI: 10.6084/m9.figshare.1293438
title: Gaussian Job Archive for C13H15N3O2S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1293039
title: Amakihi point transect data

description: Amakihi point transect data<br>=========================== Data used in paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas. Taken from Marques et al (2007) and were provided by Steve Fancy. These are distance sampling point transect observations of 1485 Hawaii Amakihi (Hemignathus virens). Data include distances and covariates (see below). Survey details<br>============== Adapted from the data description in Marques et al (2007): Data were collected as part of a larger survey on the island of Hawaii (Fancy et al. 1997). Multispecies point transect surveys were performed at 7 survey periods between July 1992 and April 1995. There were 41 point count stations, although they were not all surveyed in some survey periods. Data format<br>=========== Comma separated value file with one row for each of the 1485 observations, each with the following 7 columns: survey : Factor with 7 levels giving the date of the survey (e.g. "Apr 93").<br>object : Unique identifier per observation.<br>distance : Exact distances to observed birds in metres.<br>obs : Factor with 3 levels giving observer ("SGF","TJS","TKP")<br>mas : Minutes after sunrise that the observation took place.<br>has : Hours (integer) after sunrise that the observation took place.<br>observed : Column of 1s indicated that the individual was observed (needed for analysis software). References<br>========== Fancy, SG, TJ Snetsinger, and JD Jacoby. Translocation of the Palila, an endangered Hawaiian honeycreeper. Pacific Conservation Biology 3 (1997) 39-46. Marques, TA, L Thomas, SG Fancy, and ST Buckland. Improving Estimates of Bird Density Using Multiple-Covariate Distance Sampling. The Auk 124, no. 4 (2007): 1229–43.
DOI: 10.6084/m9.figshare.1293439.v1
title: Gaussian Job Archive for C13H14BeFN3O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1293447.v2
title: Research Tools: Supporting Research and Publication

description: “Research Tools” can be defined as vehicles that broadly facilitate research and related activities. Scientific tools enable researchers to collect, organize, analyze, visualize and publicized research outputs. Dr. Nader has collected over 700 tools that enable students to follow the correct path in research and to ultimately produce high-quality research outputs with more accuracy and efficiency. It is assembled as an interactive Web-based mind map, titled “Research Tools”, which is updated periodically. “Research Tools” consists of a hierarchical set of nodes. It has four main nodes: (1) Searching the literature, (2) Writing a paper, (3) Targeting suitable journals, and (4) Enhancing visibility and impact of the research, and six auxiliary nodes. Several free tools can be found in the child nodes. Some paid tools are also included. In this workshop some tools as examples from the four main nodes will be described. The e-skills learned from the workshop are useful across various research disciplines and research institutions.
DOI: 10.6084/m9.figshare.1293039.v1
title: Amakihi point transect data

description: Amakihi point transect data<br>=========================== Data used in paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas. Taken from Marques et al (2007) and were provided by Steve Fancy. These are distance sampling point transect observations of 1485 Hawaii Amakihi (Hemignathus virens). Data include distances and covariates (see below). Survey details<br>============== Adapted from the data description in Marques et al (2007): Data were collected as part of a larger survey on the island of Hawaii (Fancy et al. 1997). Multispecies point transect surveys were performed at 7 survey periods between July 1992 and April 1995. There were 41 point count stations, although they were not all surveyed in some survey periods. Data format<br>=========== Comma separated value file with one row for each of the 1485 observations, each with the following 7 columns: survey : Factor with 7 levels giving the date of the survey (e.g. "Apr 93").<br>object : Unique identifier per observation.<br>distance : Exact distances to observed birds in metres.<br>obs : Factor with 3 levels giving observer ("SGF","TJS","TKP")<br>mas : Minutes after sunrise that the observation took place.<br>has : Hours (integer) after sunrise that the observation took place.<br>observed : Column of 1s indicated that the individual was observed (needed for analysis software). References<br>========== Fancy, SG, TJ Snetsinger, and JD Jacoby. Translocation of the Palila, an endangered Hawaiian honeycreeper. Pacific Conservation Biology 3 (1997) 39-46. Marques, TA, L Thomas, SG Fancy, and ST Buckland. Improving Estimates of Bird Density Using Multiple-Covariate Distance Sampling. The Auk 124, no. 4 (2007): 1229–43.
DOI: 10.6084/m9.figshare.1293041
title: Data used in paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas

description: Line and point transect distance sampling data used as examples in the paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas. Each file has a corresponding README which gives further details.
DOI: 10.6084/m9.figshare.1293447.v1
title: Research Tools: Supporting Research and Publication

description: “Research Tools” can be defined as vehicles that broadly facilitate research and related activities. Scientific tools enable researchers to collect, organize, analyze, visualize and publicized research outputs. Dr. Nader has collected over 700 tools that enable students to follow the correct path in research and to ultimately produce high-quality research outputs with more accuracy and efficiency. It is assembled as an interactive Web-based mind map, titled “Research Tools”, which is updated periodically. “Research Tools” consists of a hierarchical set of nodes. It has four main nodes: (1) Searching the literature, (2) Writing a paper, (3) Targeting suitable journals, and (4) Enhancing visibility and impact of the research, and six auxiliary nodes. Several free tools can be found in the child nodes. Some paid tools are also included. In this workshop some tools as examples from the four main nodes will be described. The e-skills learned from the workshop are useful across various research disciplines and research institutions.
DOI: 10.6084/m9.figshare.1293038
title: Humpback whale line transect data

description: Humpback whale line transect data<br>================================= Data used in paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas. Taken from Williams and Thomas (2007) and were provided by Rob Williams. Data are line transect observations of 76 humpback whales (Megaptera novaeangliae) in British Columbia. Survey details<br>============== Survey design and protocol are detailed in Thomas et al 2007. Multi-species small boat surveys were conducted along the coastline of British Columbia, Canada during the summers of 2004 and 2005. Data format<br>=========== Comma separated value file with one row for each of the 76 observations, each with the following 3 columns: distance : Exact perpendicular distances to observed humpbacks in metres.<br>object : Unique observation identifier.<br>detected : Column of 1s indicated that the individual was observed (needed for analysis software). References<br>========== Williams, R, and L Thomas. Distribution and Abundance of Marine Mammals in the Coastal Waters of British Columbia, Canada. Journal of Cetacean Research and Management 9, no. 1 (2007): 15. Thomas, L, R Williams, and D Sandilands. Designing Line Transect Surveys for Complex Survey Regions. Journal of Cetacean Research and Management 9, no. 1 (2007): 1.
DOI: 10.6084/m9.figshare.1293438.v1
title: Gaussian Job Archive for C13H15N3O2S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1293037
title: Wood ant line transect data

description: Wood ant line transect data<br>=========================== Data used in paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas. Taken from Borkin et al (2012) and provided by Kerry Borkin. Data are line transect observations of 144 wood ant (Formica lugubris and Formica aquilonia) nests in Abernethy Forest, Scotland. Both distance to ant nests and other covariates were collected. Survey details<br>============== Adapted from Borkin et al (2012): Surveys took place on 13 days between between 22 August and 9 September 2003 using a line transect protocol on 17 transects in the Abernethy Forest, Scotland (57°15 ́N, 3°40 ́W). Data format<br>=========== Comma separated value file with one row for each of the 144 observations, each with the following 7 columns: habitat : 4 level stand type: "stand initiation", "stem exclusion", "understorey re-initiation" and "old-growth".<br>transect : ID of the transect where the observation was made.<br>distance : Exact perpendicular distances to observed ant nests in metres.<br>nest.size : Size of nest, calculated as half-width multiplied by height.<br>species : Factor with 2 levels ("aqu" and "lug") giving the ant species.<br>object : Unique observation identifier.<br>detected : Column of 1s indicated that the individual was observed (needed for analysis software). References<br>========== Borkin, KM, RW Summers, and L Thomas. Surveying Abundance and Stand Type Associations of Formica Aquilonia And F. Lugubris (Hymenoptera: Formicidae) Nest Mounds Over an Extensive Area: Trialing a Novel Method. European Journal of Entomology 109, no. 1 (2012): 47–53.
DOI: 10.23645/epacomptox.6062533
title: ReadMe for ToxCast and Tox21 high-throughput assay information

description: ReadMe file for the ToxCast and Tox21 high-throughput assay information
DOI: 10.6084/m9.figshare.1293033
title: Harbour porpoise line transect data

description: Harbour porpoise line transect data<br>=================================== Data used in paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas. Taken from Williams and Thomas (2007) and were provided by Rob Williams. Data are line transect observations of 68 harbour porpoise clusters (Phocoena phocoena) in British Columbia. Both distance to animal and group/cluster size were collected. Survey details<br>============== Survey design and protocol are detailed in Thomas et al 2007. Multi-species small boat surveys were conducted along the coastline of British Columbia, Canada during the summers of 2004 and 2005. Data format<br>=========== Comma separated value file with one row for each of the 68 observations, each with the following 5 columns: distance : Exact perpendicular distances to observed harbour porpoise groups in metres.<br>size : Number of animals observed (i.e. group/cluster size).<br>object : Unique observation identifier.<br>observer : Factor with 13 levels giving observer ID.<br>detected : Column of 1s indicated that the individual was observed (needed for analysis software). References<br>========== Williams, R, and L Thomas. Distribution and Abundance of Marine Mammals in the Coastal Waters of British Columbia, Canada. Journal of Cetacean Research and Management 9, no. 1 (2007): 15. Thomas, L, R Williams, and D Sandilands. Designing Line Transect Surveys for Complex Survey Regions. Journal of Cetacean Research and Management 9, no. 1 (2007): 1.
DOI: 10.6084/m9.figshare.1293035
title: Harbour seal line transect data

description: Harbour seal line transect data<br>=============================== Data used in paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas. Taken from Williams and Thomas (2007) and were provided by Rob Williams. Data are line transect observations of 232 harbour seal clusters in water (Phoca vitulina) in British Columbia. Survey details<br>============== Survey design and protocol are detailed in Thomas et al 2007. Multi-species small boat surveys were conducted along the coastline of British Columbia, Canada during the summers of 2004 and 2005. Note that the data analysed in Williams and Thomas (2007) included harbour seals that were hauled-out as well as in water, we do not include the hauled-out animals here. Data format<br>=========== Comma separated value file with one row for each of the 232 observations, each with the following 3 columns: distance : Exact perpendicular distances to observed harbour seals in metres.<br>object : Unique observation identifier.<br>detected : Column of 1s indicated that the individual was observed (needed for analysis software). References<br>========== Williams, R, and L Thomas. Distribution and Abundance of Marine Mammals in the Coastal Waters of British Columbia, Canada. Journal of Cetacean Research and Management 9, no. 1 (2007): 15. Thomas, L, R Williams, and D Sandilands. Designing Line Transect Surveys for Complex Survey Regions. Journal of Cetacean Research and Management 9, no. 1 (2007): 1.
DOI: 10.6084/m9.figshare.1293038.v1
title: Humpback whale line transect data

description: Humpback whale line transect data<br>================================= Data used in paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas. Taken from Williams and Thomas (2007) and were provided by Rob Williams. Data are line transect observations of 76 humpback whales (Megaptera novaeangliae) in British Columbia. Survey details<br>============== Survey design and protocol are detailed in Thomas et al 2007. Multi-species small boat surveys were conducted along the coastline of British Columbia, Canada during the summers of 2004 and 2005. Data format<br>=========== Comma separated value file with one row for each of the 76 observations, each with the following 3 columns: distance : Exact perpendicular distances to observed humpbacks in metres.<br>object : Unique observation identifier.<br>detected : Column of 1s indicated that the individual was observed (needed for analysis software). References<br>========== Williams, R, and L Thomas. Distribution and Abundance of Marine Mammals in the Coastal Waters of British Columbia, Canada. Journal of Cetacean Research and Management 9, no. 1 (2007): 15. Thomas, L, R Williams, and D Sandilands. Designing Line Transect Surveys for Complex Survey Regions. Journal of Cetacean Research and Management 9, no. 1 (2007): 1.
DOI: 10.6084/m9.figshare.1293041.v1
title: Data used in paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas

description: Line and point transect distance sampling data used as examples in the paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas. Each file has a corresponding README which gives further details.
DOI: 10.23645/epacomptox.6062533.v4
title: ReadMe for ToxCast and Tox21 high-throughput assay information

description: ReadMe file for the ToxCast and Tox21 high-throughput assay information
DOI: 10.6084/m9.figshare.1293029
title: Alignments for phylogeny inference

description: ZIP file with alignments used for phylogeny inference (Fig. 2 in paper) – contains alignments of separate genes as well as final concatenated dataset
DOI: 10.6084/m9.figshare.1293029.v1
title: Alignments for phylogeny inference

description: ZIP file with alignments used for phylogeny inference (Fig. 2 in paper) – contains alignments of separate genes as well as final concatenated dataset
DOI: 10.6084/m9.figshare.1293033.v1
title: Harbour porpoise line transect data

description: Harbour porpoise line transect data<br>=================================== Data used in paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas. Taken from Williams and Thomas (2007) and were provided by Rob Williams. Data are line transect observations of 68 harbour porpoise clusters (Phocoena phocoena) in British Columbia. Both distance to animal and group/cluster size were collected. Survey details<br>============== Survey design and protocol are detailed in Thomas et al 2007. Multi-species small boat surveys were conducted along the coastline of British Columbia, Canada during the summers of 2004 and 2005. Data format<br>=========== Comma separated value file with one row for each of the 68 observations, each with the following 5 columns: distance : Exact perpendicular distances to observed harbour porpoise groups in metres.<br>size : Number of animals observed (i.e. group/cluster size).<br>object : Unique observation identifier.<br>observer : Factor with 13 levels giving observer ID.<br>detected : Column of 1s indicated that the individual was observed (needed for analysis software). References<br>========== Williams, R, and L Thomas. Distribution and Abundance of Marine Mammals in the Coastal Waters of British Columbia, Canada. Journal of Cetacean Research and Management 9, no. 1 (2007): 15. Thomas, L, R Williams, and D Sandilands. Designing Line Transect Surveys for Complex Survey Regions. Journal of Cetacean Research and Management 9, no. 1 (2007): 1.
DOI: 10.6084/m9.figshare.1293035.v1
title: Harbour seal line transect data

description: Harbour seal line transect data<br>=============================== Data used in paper "Mixture models for distance sampling detection functions" by David L. Miller and Len Thomas. Taken from Williams and Thomas (2007) and were provided by Rob Williams. Data are line transect observations of 232 harbour seal clusters in water (Phoca vitulina) in British Columbia. Survey details<br>============== Survey design and protocol are detailed in Thomas et al 2007. Multi-species small boat surveys were conducted along the coastline of British Columbia, Canada during the summers of 2004 and 2005. Note that the data analysed in Williams and Thomas (2007) included harbour seals that were hauled-out as well as in water, we do not include the hauled-out animals here. Data format<br>=========== Comma separated value file with one row for each of the 232 observations, each with the following 3 columns: distance : Exact perpendicular distances to observed harbour seals in metres.<br>object : Unique observation identifier.<br>detected : Column of 1s indicated that the individual was observed (needed for analysis software). References<br>========== Williams, R, and L Thomas. Distribution and Abundance of Marine Mammals in the Coastal Waters of British Columbia, Canada. Journal of Cetacean Research and Management 9, no. 1 (2007): 15. Thomas, L, R Williams, and D Sandilands. Designing Line Transect Surveys for Complex Survey Regions. Journal of Cetacean Research and Management 9, no. 1 (2007): 1.
DOI: 10.23645/epacomptox.6062533.v3
title: ReadMe for ToxCast and Tox21 high-throughput assay information

description: ReadMe file for the ToxCast and Tox21 high-throughput assay information
DOI: 10.6084/m9.figshare.1293028
title: Alignments for species delimitation

description: ZIP file with the rbcL and tufA alignments used to infer species boundaries (Supplement S1 of paper)
DOI: 10.6084/m9.figshare.1293028.v1
title: Alignments for species delimitation

description: ZIP file with the rbcL and tufA alignments used to infer species boundaries (Supplement S1 of paper)
DOI: 10.6084/m9.figshare.1293027
title: Instrumental Variables Estimation With Some Invalid Instruments and its Application to Mendelian Randomization

description: Instrumental variables have been widely used for estimating the causal effect between exposure and outcome. Conventional estimation methods require complete knowledge about all the instruments’ validity; a valid instrument must not have a direct effect on the outcome and not be related to unmeasured confounders. Often, this is impractical as highlighted by Mendelian randomization studies where genetic markers are used as instruments and complete knowledge about instruments’ validity is equivalent to complete knowledge about the involved genes’ functions. In this article, we propose a method for estimation of causal effects when this complete knowledge is absent. It is shown that causal effects are identified and can be estimated as long as less than 50% of instruments are invalid, without knowing which of the instruments are invalid. We also introduce conditions for identification when the 50% threshold is violated. A fast penalized ℓ<sub>1</sub> estimation method, called sisVIVE, is introduced for estimating the causal effect without knowing which instruments are valid, with theoretical guarantees on its performance. The proposed method is demonstrated on simulated data and a real Mendelian randomization study concerning the effect of body mass index(BMI) on health-related quality of life (HRQL) index. An R package <i>sisVIVE</i> is available on CRAN. Supplementary materials for this article are available online.