cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.v92cd6
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"USA.37.45_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 13 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009672-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/bfz2b49dw9
title: plants-Elucidating the Molecular Mechanisms of Physiological Fruit Abscission in Actinidia arguta through Comparative Transcriptomics and Transient Genetic Transformation-Supplementary data

description: Supplemental figures and tables for the Article "Elucidating the Molecular Mechanisms of Physiological Fruit Abscission in Actinidia arguta through Comparative Transcriptomics and Transient Genetic Transformation"
DOI: 10.17632/bfz2b49dw9.1
title: plants-Elucidating the Molecular Mechanisms of Physiological Fruit Abscission in Actinidia arguta through Comparative Transcriptomics and Transient Genetic Transformation-Supplementary data

description: Supplemental figures and tables for the Article "Elucidating the Molecular Mechanisms of Physiological Fruit Abscission in Actinidia arguta through Comparative Transcriptomics and Transient Genetic Transformation"
DOI: 10.17632/bk6p72jnk5.1
title: LINF_160018000

description: Cullin-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/s2yrd362sd.1
title: LINF_160018600

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/jw242rsfzf.1
title: LINF_160018700

description: Diacylglycerol kinase (ATP); Leishmania infantum (strain JPCM5)
DOI: 10.15468/dl.hhse9y
title: Occurrence Download

description: A dataset containing 591 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Larix gmelinii (Rupr.) Kuzen."
 ]
}

 The dataset includes 591 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002227-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/zg2268xzwv.2
title: Replication Package for "The Impact of Prices on Analyst Cash Flow Expectations: Reconciling Subjective Beliefs Data with Rational Discount Rate Variation"

description: Replication Package for "The Impact of Prices on Analyst Cash Flow Expectations: Reconciling Subjective Beliefs Data with Rational Discount Rate Variation" by Aditya Chaudhry.
DOI: 10.17632/vpcd66r3n4.1
title: LINF_160018800

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/hvyxmrpsz2.1
title: LINF_160019200

description: Leucine-rich repeat-containing protein; Leishmania infantum (strain JPCM5)
DOI: 10.15468/dl.5u7wyh
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lonchophylla mordax Thomas, 1903"
 ]
}

 The dataset includes 99 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002550-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14288/1.0373458
title: Replication Data for: Users’ guide to SI-MAB biodiversity monitoring plot 01 at Bamfield, British Columbia, Canada

description: In 1997 the Bamfield Marine Station (now Bamfield Marine Sciences Centre) established a one-hectare second growth forest plot for long-term monitoring of trees following the Smithsonian Institution / Man and Biosphere Program (now Monitoring and Assessment of Biodiversity) or SI/MAB protocol. Permanent plots such as this one provide an inventory of plant diversity and long-term data on the growth, mortality, regeneration and dynamics of forest trees. &lt;p/&gt; The SI/MAB plot is located on the north side of Grappler Inlet near Bamfield, British Columbia on property owned and administered by the research station. The centre of the plot has GPS coordinates 48°50’19.00”N, 125°08’02.00”W (48.83861111, -125.13388889). The plot includes both mid-seral forest dominated by Western Hemlock and late seral forest dominated by Western red cedar, Sitka spruce, Amabilis fir and Douglas fir. &lt;p/&gt; The plot was divided into 25 quadrats (20m x 20m), and trees with a DBH (diameter at breast height) ≥ 4 cm (including dead and epiphytic trees) were mapped and censused for species, DBH and class (physical condition). Quadrats were renumbered for north/south discrepancies in 2001 and subsequent studies. &lt;p/&gt; The SI/MAB plot was established, and tree data was collected by students in the Coastal Biodiversity and Conservation course taught by Dr. Tom Berman July 21-Aug 29, 1997. In addition a species list of macrofungi observed in the plot was compiled by students in the Field Mycology course taught by Dr. Kathy Fuller July 21-August 29, 1997.
DOI: 10.14288/1.0374297
title: Replication data for: Barkley Sound intertidal long-term monitoring: rocky substrate methodology

description: In 1997 the Bamfield Marine Station (now Bamfield Marine Sciences Centre) established a long-term monitoring project to collect baseline data on the distribution and abundance of macroorganisms at three intertidal sites in Barkley Sound. Data is presented here for seaweed cover (%), understory cover (%) and invertebrate density for two sites on Wizard Islet. The third site located at the mouth of Grappler Inlet is discussed in the study report. &lt;p/&gt; Wizard Islet (48°51’29.5”N, 125°09’31”W) is located within the Deer Group Islands in Barkley Sound and has an area of 1.73 hectares at low tide. The sheltered site (with less wave exposure) is located on a 50m stretch of fixed rocky shore on the northeast side and is characterized by Fucus and Phyllospadix (seagrass). The exposed site is located on a 50m stretch of fixed rocky shore on the southwest side and is characterized by Egregia (feather-boa kelp), goose-necked barnacles and Alaria (brown alga). &lt;p/&gt; At both sites, a line of numbered tags spaced at 1m intervals at the same tidal height was installed. The tags denote the upper origin for 50 vertical transects. Fifteen tag numbers were chosen randomly, and transects were extended from the tags to the water. At the sheltered site, the tag numbers were 8, 9, 11, 15, 17, 19, 23, 24, 28, 35, 36, 40, 42, 48, 49. At the exposed site, they were 4, 9, 12, 13, 15, 16, 18, 23, 26, 31, 32, 36, 42, 44, 45, 49. &lt;p/&gt; Sampling was done at tidal heights 0.2, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0 and 3.5m. To maintain consistency, all quadrats were positioned to the left and above each point on the transect (when facing away from the water). &lt;p/&gt; Algal canopy cover (%) which includes seaweeds and one grass was estimated using a 25x25cm quadrat divided into 100 squares or 1%. A square was counted if it contained &gt;=50% canopy cover. If a species was present but &lt;50%, abundance was recorded as 0.5%. &lt;p/&gt; Understory species cover (%) which includes algal species, encrusting invertebrates and rocks was estimated using the point intercept method for 20 random points in a 25x25cm quadrat of 100 squares. Since 20 of 100 possible intersections were marked, each point represented 5%. Each point could contain multiple organisms (layers), e.g. Balanus growing on Mytilus. &lt;p/&gt; Invertebrates were counted if &gt;=50% of the organism occurred within the quadrat. Quadrat size depended on the density of the organism (e.g. 12.5x12.5cm for Littorina, 25x25cm for Hemigrapsus, 50x50cm for Pisaster). &lt;p/&gt; Data was collected by students in the Coastal Biodiversity and Conservation course taught by Dr. Tom Berman with Teaching Assistant Russ Markel July 21-Aug 29, 1997.
DOI: 10.14288/1.0363900
title: Analysis of strain and regional variation in gene expression in mouse brain

description: &lt;p&gt;BACKGROUND:&lt;br&gt; We performed a statistical analysis of a previously published set of gene expression microarray data from six different brain regions in two mouse strains. In the previous analysis, 24 genes showing expression differences between the strains and about 240 genes with regional differences in expression were identified. Like many gene expression studies, that analysis relied primarily on ad hoc 'fold change' and 'absent/present' criteria to select genes. To determine whether statistically motivated methods would give a more sensitive and selective analysis of gene expression patterns in the brain, we decided to use analysis of variance (ANOVA) and feature selection methods designed to select genes showing strain- or region-dependent patterns of expression.&lt;p&gt; &lt;p&gt;RESULTS:&lt;br&gt; Our analysis revealed many additional genes that might be involved in behavioral differences between the two mouse strains and functional differences between the six brain regions. Using conservative statistical criteria, we identified at least 63 genes showing strain variation and approximately 600 genes showing regional variation. Unlike ad hoc methods, ours have the additional benefit of ranking the genes by statistical score, permitting further analysis to focus on the most significant. Comparison of our results to the previous studies and to published reports on individual genes show that we achieved high sensitivity while preserving selectivity.&lt;p&gt; &lt;p&gt;CONCLUSIONS:&lt;br&gt; Our results indicate that molecular differences between the strains and regions studied are larger than indicated previously. We conclude that for large complex datasets, ANOVA and feature selection, alone or in combination, are more powerful than methods based on fold-change thresholds and other ad hoc selection criteria.&lt;p&gt;
DOI: 10.14288/1.0373456
title: Replication data for: The Bamfield SI/MAB plot 01: monitoring biodiversity in a coastal hemlock forest

description: Trees in the one-hectare second growth SI/MAB plot were recensused in 2001. Data were also collected for shrubs and small trees, coarse woody debris (CWD), and small mammals, and are presented here. For results on canopy cover, dwarf mistletoe, and slugs, see the 2001 student report. &lt;p/&gt; The SI/MAB plot was established in 1997 following the Smithsonian Institution / Man and Biosphere Program (now Monitoring and Assessment of Biodiversity) or SI/MAB protocol. It is located on the north side of Grappler Inlet near Bamfield, British Columbia on property owned and administered by the Bamfield Marine Sciences Centre. The centre of the plot has GPS coordinates 48°50’19.00”N, 125°08’02.00”W (48.83861111, -125.13388889). &lt;p/&gt; The SI/MAB plot is divided into 25 quadrats (20m x 20m). In 2001 quadrats were renumbered for north/south discrepancies. Trees with a DBH (diameter at breast height) ≥ 4 cm were recensused for species, DBH and status (physical condition). For the 2001 census, dead fallen trees were counted as coarse woody debris instead of trees. &lt;p/&gt; Shrubs and small trees (maximum DBH of 4cm) were identified and tagged following the Ecological Monitoring and Assessment Network (EMAN) protocol for Shrub and Small Tree Sampling. In 1999, 11 5x5m quadrats were randomly chosen in corners of randomly chosen 20mx20m quadrats in the SI/MAB plot. In 2001, the 11 quadrats were resampled, and 4 more quadrats were sampled. A species list of shrubs and small trees is presented here. &lt;p/&gt; Coarse woody debris was measured along three 90m transects within the SI/MAB plot (labeled site A = wet; site B = steep slope; site C = flat, stem exclusion). Methodology is described in the Vegetation Resources Inventory: Ground Sampling Procedures (2007) with decay classes 1-5 defined on page 196. The methodology was modified such that each 90m transect consisted of an equilateral triangle with sides of 30m each (vs. two transects at 90 degrees to each other). Triangles were used to ensure that any orientation biases were accounted for as pieces may have a dominant direction of fall. Data for coarse woody debris and volume calculations are presented here. &lt;p/&gt; Three days of live trapping of small mammals (i.e. deer mice) was done using two edge transects parallel but 3m from south and east edges of plot to minimize disturbance. Data is presented here. &lt;p/&gt; The majority of data was collected by students in the Coastal Biodiversity and Conservation course taught by Dr. Tom Berman July 23-Aug 31, 2001 with Teaching Assistant Dana Haggarty. Shrub and small tree data from 1999 was collected by students in the Coastal Biodiversity and Conservation course taught by Dr. Tom Berman and Dr. Andre Martel June 7-July 16, 1999.
DOI: 10.14288/1.0374294
title: Replication data for: Rocky intertidal monitoring: a protocol for assessing human impact in Barkley Sound

description: In 1997 the Bamfield Marine Sciences Centre established a long-term monitoring project to collect baseline data on the distribution and abundance of macroorganisms at two intertidal sites on Wizard Islet in Barkley Sound. The sites were resampled in 2001, and data is presented here for algal and invertebrate cover (%) and invertebrate density. &lt;p/&gt; Wizard Islet (48°51’29.5”N, 125°09’31”W) is located within the Deer Group Islands in Barkley Sound and has an area of 1.73 hectares at low tide. The sheltered site (with less wave exposure) is located on a 50m stretch of fixed rocky shore on the northeast side and is characterized by Fucus and Phyllospadix (seagrass). The exposed site is located on a 50m stretch of fixed rocky shore on the southwest side and is characterized by Egregia (feather-boa kelp), goose-necked barnacles and Alaria (brown alga). &lt;p/&gt; Fifteen vertical transects at each site were sampled by randomly selecting 15 of the 50 numbered tags (actual tag numbers unknown). Sampling was done at tidal heights of 0.2 (exposed site only), 0.5, 1, 1.5, 2, 2.5, 3 and 3.5m. Quadrats of 25x25cm were used to determine species percent cover and abundance for floral and faunal macroorganisms. Quadrats of 50x50cm were used for larger organisms such as Astroidea and Pisaster. To maintain consistency, all quadrats were positioned to the left and above each point on the transect (when facing away from the water). &lt;p/&gt; Spreadsheets contain columns labelled EH1Q1 to EH8Q15 and SH2Q1 to SH8Q15. It is assumed that E and S refer to Exposed and Sheltered, H1-8 refers to tidal height and Q1-15 refers to transect. Sheltered columns start at SH2 because 0.2m was not sampled. &lt;p/&gt; Data was collected by students in the Coastal Biodiversity and Conservation course taught by Dr. Tom Berman with Teaching Assistant Dana Haggarty and support from Russ Markel July 23-Aug 31, 2001.
DOI: 10.14288/1.0374295
title: Rocky intertidal monitoring of Wizard Islet in 2002

description: In 1997 the Bamfield Marine Sciences Centre established a long-term monitoring project to collect baseline data on the distribution and abundance of macroorganisms at two intertidal sites on Wizard Islet in Barkley Sound. Both sites were resampled in 2001. In 2002 ten transects at the exposed site only were resampled (tag numbers unknown), and data is presented here for algal cover (%), invertebrate cover (%), and invertebrate density including sea stars. &lt;p/&gt; Wizard Islet (48°51’29.5”N, 125°09’31”W) is located within the Deer Group Islands in Barkley Sound and has an area of 1.73 hectares at low tide. The sheltered site (with less wave exposure) is located on a 50m stretch of fixed rocky shore on the northeast side and is characterized by Fucus and Phyllospadix (seagrass). The exposed site is located on a 50m stretch of fixed rocky shore on the southwest side and is characterized by Egregia (feather-boa kelp), goose-necked barnacles and Alaria (brown alga).
DOI: 10.14288/1.0363895
title: Using ANOVA for gene selection from microarray studies of the nervous system

description: Methods are presented for detecting differential expression using statistical hypothesis testing methods including analysis of variance (ANOVA). Practicalities of experimental design, power, and sample size are discussed. Methods for multiple testing correction and their application are described. Instructions for running typical analyses are given in the R programming environment. R code and the sample data set used to generate the examples are available at http://microarray.cpmc.columbia.edu/pavlidis/pub/aovmethods/.
DOI: 10.14288/1.0363898
title: The effect of replication on gene expression microarray experiments

description: &lt;p&gt;MOTIVATION:&lt;br&gt; We examine the effect of replication on the detection of apparently differentially expressed genes in gene expression microarray experiments. Our analysis is based on a random sampling approach using real data sets from 16 published studies. We consider both the ability to find genes that meet particular statistical criteria as well as the stability of the results in the face of changing levels of replication.&lt;p&gt; &lt;p&gt;RESULTS:&lt;br&gt; While dependent on the data source, our findings suggest that stable results are typically not obtained until at least five biological replicates have been used. Conversely, for most studies, 10-15 replicates yield results that are quite stable, and there is less improvement in stability as the number of replicates is further increased. Our methods will be of use in evaluating existing data sets and in helping to design new studies.&lt;p&gt;
DOI: 10.14288/1.0374293
title: Rocky intertidal monitoring of Wizard Islet in 2003

description: In 1997 the Bamfield Marine Sciences Centre established a long-term monitoring project to collect baseline data on the distribution and abundance of macroorganisms at two intertidal sites on Wizard Islet in Barkley Sound. Both sites were resampled in 2001, and the exposed site was resampled in 2002. In 2003 fifteen transects at the exposed site only were sampled again. Tag numbers were 7, 9, 10, 11, 12, 13, 18, 20, 25, 26, 27, 34, 44, 45. Data presented here for algal cover (%), invertebrate cover (%), invertebrate density and seastar density was obtained from a 2009 Microsoft Access database. &lt;p/&gt; Wizard Islet (48°51’29.5”N, 125°09’31”W) is located within the Deer Group Islands in Barkley Sound and has an area of 1.73 hectares at low tide. The sheltered site (with less wave exposure) is located on a 50m stretch of fixed rocky shore on the northeast side and is characterized by Fucus and Phyllospadix (seagrass). The exposed site is located on a 50m stretch of fixed rocky shore on the southwest side and is characterized by Egregia (feather-boa kelp), goose-necked barnacles and Alaria (brown alga).
DOI: 10.14288/1.0363901
title: Altered Hippocampal Transcript Profile Accompanies an Age-Related Spatial Memory Deficit in Mice

description: We have carried out a global survey of age-related changes in mRNA levels in the C57BL/6NIA mouse hippocampus and found a difference in the hippocampal gene expression profile between 2-month-old young mice and 15-month-old middle-aged mice correlated with an age-related cognitive deficit in hippocampal-based explicit memory formation. Middle-aged mice displayed a mild but specific deficit in spatial memory in the Morris water maze. By using Affymetrix GeneChip microarrays, we found a distinct pattern of age-related change, consisting mostly of gene overexpression in the middle-aged mice, suggesting that the induction of negative regulators in the middle-aged hippocampus could be involved in impairment of learning. Interestingly, we report changes in transcript levels for genes that could affect synaptic plasticity. Those changes could be involved in the memory deficits we observed in the 15-month-old mice. In agreement with previous reports, we also found altered expression in genes related to inflammation, protein processing, and oxidative stress.
DOI: 10.14288/1.0364309
title: Coexpression Analysis of Human Genes Across Many Microarray Data Sets

description: We present a large-scale analysis of mRNA coexpression based on 60 large human data sets containing a total of 3924 microarrays. We sought pairs of genes that were reliably coexpressed (based on the correlation of their expression profiles) in multiple data sets, establishing a high-confidence network of 8805 genes connected by 220,649 “coexpression links” that are observed in at least three data sets. Confirmed positive correlations between genes were much more common than confirmed negative correlations. We show that confirmation of coexpression in multiple data sets is correlated with functional relatedness, and show how cluster analysis of the network can reveal functionally coherent groups of genes. Our findings demonstrate how the large body of accumulated microarray data can be exploited to increase the reliability of inferences about gene function.
DOI: 10.14288/1.0363893
title: Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms

description: The growth in popularity of RNA expression microarrays has been accompanied by concerns about the reliability of the data especially when comparing between different platforms. Here, we present an evaluation of the reproducibility of microarray results using two platforms, Affymetrix GeneChips and Illumina BeadArrays. The study design is based on a dilution series of two human tissues (blood and placenta), tested in duplicate on each platform. The results of a comparison between the platforms indicate very high agreement, particularly for genes which are predicted to be differentially expressed between the two tissues. Agreement was strongly correlated with the level of expression of a gene. Concordance was also improved when probes on the two platforms could be identified as being likely to target the same set of transcripts of a given gene. These results shed light on the causes or failures of agreement across microarray platforms. The set of probes we found to be most highly reproducible can be used by others to help increase confidence in analyses of other data sets using these platforms.