cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10528947
title: Dataset related to article "Genetic Deficiency of the Long Pentraxin 3 Affects Osteogenesis and Osteoclastogenesis in Homeostatic and Inflammatory Conditions "

description: This record contains raw data related to article “Genetic Deficiency of the Long Pentraxin 3 Affects Osteogenesis and Osteoclastogenesis in Homeostatic and Inflammatory Conditions"

Abstract



The long pentraxin 3 (PTX3) is a soluble glycoprotein made by immune and nonimmune cells endowed with pleiotropic functions in innate immunity, inflammation, and tissue remodeling. PTX3 has recently emerged as a mediator of bone turnover in both physiological and pathological conditions, with direct and indirect effects on osteoblasts and osteoclasts. This notwithstanding, its role in bone biology, with major regard to the osteogenic potential of osteoblasts and their interplay with osteoclasts, is at present unclear. Here, we investigated the contribution of this pentraxin to bone deposition in the osteogenic lineage by assessing collagen production, mineralization capacity, osteoblast maturation, extracellular matrix gene expression, and inflammatory mediators' production in primary osteoblasts from the calvaria of wild-type (WT) and Ptx3-deficient (Ptx3-/-) mice. Also, we evaluated the effect of PTX3 on osteoclastogenesis in cocultures of primary osteoblasts and bone marrow-derived osteoclasts. Our investigations were carried out both in physiological and inflammatory conditions to recapitulate in vitro aspects of inflammatory diseases of the bone. We found that primary osteoblasts from WT animals constitutively expressed low levels of the protein in osteogenic noninflammatory conditions, and genetic ablation of PTX3 in these cells had no major impact on collagen and hydroxyapatite deposition. However, Ptx3-/- osteoblasts had an increased RANKL/OPG ratio and CD44 expression, which resulted in in enhanced osteoclastogenesis when cocultured with bone marrow monocytes. Inflammation (modelled through administration of tumor necrosis factor-α, TNF-α) boosted the expression and accumulation of PTX3 and inflammatory mediators in WT osteoblasts. In these conditions, Ptx3 genetic depletion was associated with reduced collagen deposition and immune modulators' production. Our study shed light on the role of PTX3 in osteoblast and osteoclast biology and identified a major effect of inflammation on the bone-related properties of this pentraxin, which might be relevant for therapeutic and/or diagnostic purposes in musculoskeletal pathology.
DOI: 10.57992/nmrxiv.p56.s307
title: VS-20220603-Diterpen4
DOI: 10.57992/nmrxiv.p56.s301.d1753
title: VS-20221020-Diterpen10[15]
DOI: 10.6073/pasta/dbf98d8ddc5f48c4bc074ae4293d8d7c
title: Santa Barbara Channel Marine BON: Nearshore kelp forest integrated fish, 1981-ongoing

description: The Santa Barbara Channel Marine Biodiversity Observation Network
 (SBCMBON) tracks long-term patterns in species abundance and
 diversity. This dataset contains counts of fish (including cryptic
 fish, which are deliberately sought out) produced by integrating data
 from four contributing projects working in the kelp forests of the
 Santa Barbara Channel, USA.

 
 The four contributing projects are two research projects, the Santa
 Barbara Coastal LTER (SBC LTER) and the Partnership for
 Interdisciplinary Studies of Coastal Oceans (PISCO), and the kelp
 forest monitoring program of the Santa Barbara Channel National Park,
 and the San Nicolas Island monitoring program supported by USGS.
 Together, these projects have recorded data for more than 200 species
 at approximately 100 sites on both the mainland coast and on the Santa
 Barbara Channel Islands. Sampling began in 1980 and is ongoing. Data
 were collected by human observation (divers using SCUBA) during
 regular surveys.

 
 This dataset includes five entities, three data tables and two R
 scripts. The main data table contains counts of organisms, the
 bottom-area and height of the water column over which the fish were
 surveyed. The column labeled “count” records the number of organisms
 found in each plot/transect at a given timestamp. A second data table
 contains place names and geolocation for sampling sites. Information
 is sufficient for the calculation of fish density, which is left to
 the user. The third data table contains the depths of each transect
 the for the fish survey. Sample R script is included to illustrate
 generation of a basic table of areal density by taxa and sampling
 site. A second R script is included to convert these data from their
 primary MBON structure to a Darwin Core Archive (and available through
 multiple sources).

 
 MBON is funded by National Aeronautics and Space Administration
 (NASA), Bureau of Ocean Energy Management (BOEM), and National Oceanic
 and Atmospheric Administration (NOAA).

 
 For users who are interested in using all or part of this integrated
 datasets, please contact data owners to discuss your research
 interests, data-related issues or any other questions. A recommended
 citation for the data package is available from the download page. In
 addition, any manuscript generated using this dataset is expected to
 be sent to the data owners before publication so we can be sure the
 data is used in the proper context and methods are reported
 accurately:

 
 Santa Barbara Coastal LTER (LTER):

 
 Dan Reed dan.reed@lifesci.ucsb.edu

 
 Robert Miller miller@msi.ucsb.edu

 
 Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO):

 
 Jenn Caselle caselle@ucsb.edu

 
 Kelp forest monitoring (KFM):

 
 David Kushner david_kushner@nps.gov

 
 Joshua Sprague joshua_sprague@nps.gov

 
 San Nicolas Island monitoring (SNI):

 
 Kevin Lafferty Klafferty@usgs.gov

 
 Mike Kenner mkenner@ucsc.edu
DOI: 10.6073/pasta/1aed976cbe5c1fef745fc50e3d217747
title: SBC LTER: Reef: Kelp Forest Community Dynamics: Transect depth data

description: The data table provides summaries of depth information (mean,
 standard deviation and coefficient of variation) for all of the
 transects surveyed as part of the SBC LTER Kelp Forest Monitoring
 program. All data are expressed in meters, reference to mean lower
 low water (MLLW). Each value is the result of 160 observations, four
 at each meter (n=160). The sampling locations in this dataset are 40
 meter transects at nine reef sites along the mainland coast of the
 Santa Barbara Channel and at two sites on the north side of Santa
 Cruz Island. The PDF document provides descriptive information of
 the transect such as headings and relative locations of the points
 along the transect. Data were recorded in 2010 and 2011.
DOI: 10.5281/zenodo.10520259
title: NOAA GML and CIRES/Uni. of Colorado-Boulder Ceilometer Cloud Data Products at Brush Creek (CBC) for SPLASH

description: Cloud base height / vertical visibility and attenuated backscatter coefficient profiles from NOAA GML's Vaisala CL51 ceilometer deployed at Brush Creek (CBC). Data have been sampled to nearest 1-min. See Readme document for details.
DOI: 10.5281/zenodo.10520258
title: NOAA GML and CIRES/Uni. of Colorado-Boulder Ceilometer Cloud Data Products at Brush Creek (CBC) for SPLASH

description: Cloud base height / vertical visibility and attenuated backscatter coefficient profiles from NOAA GML's Vaisala CL51 ceilometer deployed at Brush Creek (CBC). Data have been sampled to nearest 1-min. See Readme document for details.
DOI: 10.17630/4975c6ad-8e73-46af-a477-c1643c4efdf4
title: "Antibiotics under our feet" Bioinformatics Taxonomic and Functional Profiling

description: The attached data files are from the bioinformatics taxonomic and functional profiling of soil samples collected during the University of St Andrews "Antibiotics under our feet" citizen science project funded by a ScotPEN Wellcome Engagement Award to Clarissa Melo Czekster, University of St Andrews. The taxonomic classifications are in the form of html files that can be opened in a browser. The functional profiling has three output files searchable to determine desired pathways. The README explains the pipeline used and the output files.
DOI: 10.6073/pasta/da35d83d200341c27ce50348e1835971
title: SBC LTER: Reef: Kelp Forest Community Dynamics: Invertebrate and algal density

description: These data describe the density and size of a select group of
 about 50 species of benthic invertebrates and understory algae in
 fixed plots (either 1m x 1m or 20m x 1m) along permanent
 transects. These data are part of SBCLTER’s kelp forest monitoring
 program to track long-term patterns in species abundance and
 diversity of reef-associated organisms in the Santa Barbara
 Channel, California, USA. The sampling locations in this dataset
 are at nine reef sites along the mainland coast of the Santa
 Barbara Channel and at two sites on the north side of Santa Cruz
 Island. These sites reflect several oceanographic regimes in the
 channel and vary in distance from sources of terrestrial runoff.
 Sampling began in 2000, and these data are updated annually.
 
 
 The time period of data collection varied among the 11 kelp forest
 sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at
 the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK)
 began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in
 2011). Data collection at the two Santa Cruz Island sites (SCTW
 and SCDI) began in 2004. See Methods for more information.  
 
 
 See Methods for more information.
DOI: 10.5258/soton/d1900
title: Dataset in support of the article 'Control of fatigue failure mechanisms in multilayer coatings by varying the architectural parameters of an intermetallic interlayer

description: Raw data in support of the figures in the article Control of fatigue failure mechanisms in multilayer coatings by varying the architectural parameters of an intermetallic interlayer' published in Fatigue & Fracture in Engineering Materials & Structures
DOI: 10.25934/pr00009350
title: Evaluation of epilepsy-DOOR (Desirability of outcome ranking) as an outcome measure for therapeutic trials in drug resistant epilepsy

description: Epilepsy is a common neurological disorder which causes seizures and affects ~1% of the general population. Despite the availability of numerous anti-seizure medications, a significant proportion of patients are not well controlled by the currently available treatments and continue to have seizures. Epilepsy is not only associated with ongoing seizures, but people with epilepsy can also experience anxiety and depression and cognitive deficits (the ability to clearly think, learn and remember). 

Current clinical trials in people with epilepsy who haven’t responded to existing treatments (drug resistant epilepsy) are commonly powered to detect a 50% reduction in seizure frequency, without consideration for other impacts that may be experienced by patients when commencing a new treatment such as side effects and worsening of cognitive deficits or mood disturbances. 

The epilepsy-DOOR (Desirability of outcome ranking) is a new methodology which evaluates seizure frequency, side effects and overall quality of life measures to provide a more holistic measure of potential benefits and harms and reflects the preferences of people with epilepsy when considering trade-offs between these aspects of patient outcomes.

It aims to provide a more comprehensive measure of potential benefits and harms associated with a new therapy for people with epilepsy. 

This study seeks to use data collected from previous clinical trials to evaluate the feasibility of epilepsy-DOOR as a potential new outcome measure for use in future therapeutic trials in drug resistant epilepsy.
DOI: 10.5281/zenodo.10528558
title: data and analysis files for "Vanishing bulk heat flow in the ν=0 quantum Hall ferromagnet in monolayer graphene"

description: RsT21: 2-terminal heat transport, aligned. March-April 2021.

FS41-4-3: Corbino heat transport. November 2021.
DOI: 10.5281/zenodo.10528559
title: data and analysis files for "Vanishing bulk heat flow in the ν=0 quantum Hall ferromagnet in monolayer graphene"

description: RsT21: 2-terminal heat transport, aligned. March-April 2021.

FS41-4-3: Corbino heat transport. November 2021.
DOI: 10.6073/pasta/7d7b640d5cafd29c00a647f6016e165d
title: SBC LTER: Reef: Kelp Forest Community Dynamics: Abundance and size of Giant Kelp (Macrocystis Pyrifera), ongoing since 2000

description: These data describe the abundance of giant kelp,
 Macrocystis pyrifera, and are part of the
 SBCLTER kelp forest monitoring program. The study was initiated in
 2000, in the Santa Barbara Channel, California, USA, and this
 dataset is updated once per year. The number and size (number of
 fronds and diameter of holdfasts) of plants were recorded along
 permanent transects at nine reef sites located along the mainland
 coast of the Santa Barbara Channel and at two sites on the north
 side Santa Cruz Island. These sites reflect several oceanographic
 regimes in the channel and vary in distance from sources of
 terrestrial runoff.
 
 
 The time period of data collection varied among the 11 kelp forest
 sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at
 the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK)
 began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in
 2011). Data collection at the two Santa Cruz Island sites (SCTW
 and SCDI) began in 2004. See Methods for more information.
DOI: 10.6073/pasta/1dcf59ef5a7ec3fd7c90203e3a2c171a
title: SBC LTER: REEF: Net primary production, growth and standing crop of Macrocystis pyrifera in Southern California

description: The giant kelp Macrocystis pyrifera forms
 subtidal forests on shallow reefs in temperate regions of the
 world. It is one of the fastest-growing multicellular autotrophs
 on Earth and its high productivity supports diverse marine food
 webs. In 2008, we published a method for estimating biomass and
 net primary production (NPP) of giant kelp along with five years
 of data, to provide a more integrated measure of NPP than those
 yielded by previous methods. Our method combines monthly field
 measurements of standing crop and loss rates with a model of kelp
 biomass dynamics to estimate instantaneous mass-specific growth
 rates and NPP for each season of each year. We have since improved
 our approach to account for several previously unresolved sources
 of biomass loss. These improvements have led to a near doubling of
 our prior estimates of growth and NPP. At our site with the most
 persistent stand of giant kelp, NPP averages ~5.2 kg dry mass
 m-2 y-1 and
 results from the rapid growth (~3.5% per day) of a relatively
 small standing biomass (~ 0.4 kg dry mass
 m-2 on average) that turns over ~ 12
 times annually. Here we provide revised estimates of seasonal
 biomass, growth and NPP for the five years covered by our previous
 publication (2002-2006), along with an additional decade of data
 (2007-2017). We also present updated relationships for predicting
 giant kelp biomass and NPP from much more easily obtained
 measurements of frond density. These data can be used to
 understand the mechanisms that drive variation in giant kelp NPP
 at a wide range of temporal scales.
DOI: 10.6073/pasta/6af4cc3b0e63b887baf1ae9201e1cd1d
title: SBC LTER: Sea urchin foraging rates on giant kelp

description: These data describe the foraging rates of two sea urchin species
 (Strongylocentrotus purpuratus and
 Mesocentrotus franciscanus) on giant kelp
 (Macrocystis pyrifera) in laboratory mesocosms.
 Data are contained in two tables: 1) a data file describing the
 foraging rates of sea urchins as a function of urchin biomass where
 biomass was varied by manipulating the number of urchins in a
 foraging trial, and 2) a data file describing the foraging rates of
 sea urchins as a function of urchin biomass where biomass was varied
 by manipulating the size of urchins in a foraging trial.
DOI: 10.57992/nmrxiv.p56.s315.d1824
title: of_20220706_MF_DT9[20]
DOI: 10.17630/54781f80-3c71-48a2-aed7-45381cab7683
title: Structural diversity in layered hybrid perovskites, A2PbBr4 or AA′PbBr4, templated by small disc-shaped amines (dataset)

description: Data underpinning article
DOI: 10.6073/pasta/d1107107e7c9ebc6476dfbe9e64eb6cb
title: Kelp metapopulations: Semi-annual time series of spore dispersal times among giant kelp patches in southern California, 1996 - 2006

description: These data describe the estimated dispersal duration of spores of giant kelp, Macrocystis
 pyrifera, among patches in southern California, USA, from 1996 to 2006. Asymmetrical and dynamic
 estimates of giant kelp spore dispersal durations among patches were estimated for 6-month
 periods (January - June and July - Dececember, 1996 - 2006) using minimum mean transit times
 connecting source and destination connectivity cells in a high-resolution, three-dimensional,
 spatiotemporally-explicit ocean circulation model (Regional Oceanic Modeling System, ROMS).
 Minimum transport times between giant kelp patches were assumed to be proportional to minimum
 transport times between ROMS cells and the alongshore distance between giant kelp patches
DOI: 10.6073/pasta/4c5a27154458ece5585384339eb0c2ee
title: Kelp metapopulations: Semi-annual time series of giant kelp patch area, biomass and fecundity in southern California, 1996 - 2006

description: These data describe the patch-scale canopy biomass and population fecundity of giant kelp,
 Macrocystis pyrifera, in southern California, USA, from 1996¬ to 2007. Biomass of the surface
 canopy was estimated using diver-calibrated Landsat 5 Thematic Mapper and Landsat 7 Enhanced
 Thematic Mapper Plus satellite imagery. Fecundity was estimated from canopy biomass pixel data
 using a seasonally-adjusted relationship between the diver-measured density of giant kelp
 spore-bearing tissue and the Landsat estimate of canopy biomass density using data collected
 across five years at the San Clemente Artificial Reef, located offshore of San Clemente,
 California, USA. Landsat pixel-scale estimates of giant kelp biomass and fecundity were summed
 across space for each giant kelp patch and averaged across time separately with two semesters
 each year (January–June and July–December). The location and area of each giant kelp patch are
 also provided. 
 These data were described in Castorani, M.
 C., D. C. Reed, F. Alberto, T. W. Bell, R. D. Simons, K. C. Cavanaugh, D. A. Siegel and P. T.
 Raimondi. Connectivity structures local populations dynamics: a long-term empirical test in a
 large metapopulation system. Ecology. DOI: 10.1890/15-0283.1
 
 These data are part of the NSF collaborative project: The effect of inbreeding on
 metapopulation dynamics of the giant kelp, Macrocystis pyrifera (funded wholly or part by NSF
 Awards OCE-1233283, 1233288, 1233839).
DOI: 10.6073/pasta/97ef540ba3fc62dff50779533bb39466
title: SBC LTER: Spatial definitions of giant kelp (Macrocystis pyrifera) patches in southern and central California

description: These data describe the spatial definitions of patches of giant kelp,
 Macrocystis pyrifera, in central and southern California, USA, using a
 27-year time series of giant kelp canopy biomass from Landsat 5
 Thematic Mapper satellite imagery (1984-2011). Giant kelp patches were
 delineated using a spatial synchrony-based method that avoids the
 consolidation of adjacent, independently fluctuating local populations
 into "megapatches". The method uses a network theory
 modularity approach to optimally cluster Landsat pixels into patches
 based on suitable habitat area (i.e., all areas containing giant kelp,
 1984-2011) and the spatial synchrony of canopy biomass. These data
 were described in Cavanaugh, K. C., D. A. Siegel, P. T. Raimondi, and
 F. A. Alberto. 2014. Patch definition in metapopulation analysis: a
 graph theory approach to solve the mega-patch problem. Ecology
 95:316-328. doi:10.1890/13-0221.1
DOI: 10.3886/e113174
title: Replication data for: 'Acting Wife': Marriage Market Incentives and Labor Market Investments

description: Do single women avoid career-enhancing actions because these actions signal undesirable traits, like ambition, to the marriage market? While married and unmarried female MBA students perform similarly when their performance is unobserved by classmates (on exams and problem sets), unmarried women have lower participation grades. In a field experiment, single female students reported lower desired salaries and willingness to travel and work long hours on a real-stakes placement questionnaire when they expected their classmates to see their preferences. Other groups' responses were unaffected by peer observability. A second experiment indicates the effects are driven by observability by single male peers.
DOI: 10.3886/e113174v1-145405
title: Replication data for: 'Acting Wife': Marriage Market Incentives and Labor Market Investments

description: Do single women avoid career-enhancing actions because these actions signal undesirable traits, like ambition, to the marriage market? While married and unmarried female MBA 
students perform similarly when their performance is unobserved by classmates (on exams and problem sets), unmarried women have lower participation grades. In a field 
experiment, single female students reported lower desired salaries and willingness to travel and work long hours on a real-stakes placement questionnaire when they expected 
their classmates to see their preferences. Other groups' responses were unaffected by peer observability. A second experiment indicates the effects are driven by observability by 
single male peers.
DOI: 10.17630/c5629cc7-02f4-480c-907e-e1a01d9b99bf
title: Growth Speeds and Growth Modes of Sodium Chloride: a Quantitative Two-Dimensional Phase-Field Study (thesis data)

description: Research data output from the precipitation Phase-field model simulate during the PhD. The data files are embargoed until 13/04/2026
DOI: 10.7927/6s2a-9r49
title: U.S. Social Vulnerability Index Grids
title: U.S. Social Vulnerability Index, v1 (2000, 2010, 2014, 2016, 2018)

description: The U.S. Social Vulnerability Index Grids data set contains gridded layers for the overall Centers for Disease Control and Prevention (CDC) Social Vulnerability Index (SVI) using four sub-category themes (Socioeconomic, Household Composition Disability, Minority Status Language, and Housing Type Transportation) based on census tract level inputs from 15 variables for the years 2000, 2010, 2014, 2016, and 2018. SVI values range between 0 and 1 based on their percentile position among all census tracts in the U.S., with 0 representing lowest vulnerability census tracts and 1 representing highest vulnerability census tracts. SEDAC has gridded these vector inputs to create 1 km spatial resolution raster surfaces allowing users to obtain vulnerability metrics for any user-defined area within the U.S. Utilizing inputs from CIESIN's Gridded Population of the World, Version 4, Revision 11 (GPWv4.11), a mask is applied for water, and optionally, for no population. The data are provided in two different projection formats, NAD83 as a U.S. specific standard, and WGS84 as a global standard. The goal of the SVI is to help identify vulnerable communities by ranking them on these inputs across the U.S.
DOI: 10.17630/4b1c9e3d-7787-40c8-aade-1dcf1af62315
title: Nanoscale heterogeneity in CsPbBr3 and CsPbBr3:KI perovskite films revealed by cat hodoluminescence hyperspectral imaging (dataset)
DOI: 10.57745/0dgc6s
title: FAIRCHAIN_Assessment indicators_CS Austria.tab

description: :unav
DOI: 10.6073/pasta/26eddd56405e041fb81ccb50c8eb447a
title: Microclimatic data trials for various fabrics

description: Data from lab trials examining various microclimatic parameters such as humidity, light intensity, and temperature under various fabrics such as nursery, canvas, and burlap. Data was collected using pendant loggers.
DOI: 10.57745/hnv8v0/r4ddqg
title: FAIRCHAIN_Assessment_Indicators_CS_Austria.tab

description: :unav
DOI: 10.17630/723d7ab4-1ee6-40ec-899c-4e5ce0a67060
title: Nature of quasiparticle interference in three dimensions (dataset)