cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3823902.v3
title: Minimal Tool Set for a Prokaryotic Circadian Clock Raw Data

description: Raw Data from the reciprocal BLAST of circadian clock factors from <i>Synechococcus elongatus</i> PCC 7942 and <i>Synechocystis</i> sp. PCC 6803.<br>
DOI: 10.7910/dvn/v1rjpf/q8rq5f
title: iqa20150515_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823902.v2
title: Minimal Tool Set for a Prokaryotic Circadian Clock Raw Data

description: Raw Data from the reciprocal BLAST of circadian clock factors from <i>Synechococcus elongatus</i> PCC 7942 and <i>Synechocystis</i> sp. PCC 6803.<br>
DOI: 10.7910/dvn/v1rjpf/83mqnw
title: iqa20150401_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823899
title: Minimal Tool Set for a Prokaryotic Circadian Clock Processed Data

description: Processed Data from the reciprocal BLAST of circadian clock factors from <i>Synechococcus elongatus</i> PCC 7942 and <i>Synechocystis</i> sp. PCC 6803.
DOI: 10.7910/dvn/v1rjpf/1lrr3s
title: iqa20160625_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sqwjhf
title: iqa20151230_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823899.v1
title: Processed Data

description: Processed Data from the reciprocal BLAST of circadian clock factors from <i>Synechococcus elongatus</i> PCC 7942 and <i>Synechocystis</i> sp. PCC 6803.
DOI: 10.6084/m9.figshare.3823899.v3
title: Minimal Tool Set for a Prokaryotic Circadian Clock Processed Data

description: Processed Data from the reciprocal BLAST of circadian clock factors from <i>Synechococcus elongatus</i> PCC 7942 and <i>Synechocystis</i> sp. PCC 6803.
DOI: 10.7910/dvn/v1rjpf/2g75gl
title: iqa20151119_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823899.v2
title: Minimal Tool Set for a Prokaryotic Circadian Clock Processed Data

description: Processed Data from the reciprocal BLAST of circadian clock factors from <i>Synechococcus elongatus</i> PCC 7942 and <i>Synechocystis</i> sp. PCC 6803.
DOI: 10.7910/dvn/v1rjpf/9lqkv2
title: iqa20150604_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jsrls1
title: iqa20151024_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sgmxdv
title: iqa20160529_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/nasdxx
title: iqa20150728_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sgekeq
title: iqa20150203_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823806
title: Patent Network Analysis and Quadratic Assignment Procedures to Identify the Convergence of Robot Technologies_Data

description: This dataset is retrieved and collected from KIPO and USPTO patent database. The dataset is utilized to identify the convergence of robot technologies. Variables for quadratic assignment procedures can be used with UCINET software.
DOI: 10.7910/dvn/v1rjpf/iaixvd
title: iqa20150222_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823806.v1
title: Patent Network Analysis and Quadratic Assignment Procedures to Identify the Convergence of Robot Technologies_Data

description: This dataset is retrieved and collected from KIPO and USPTO patent database. The dataset is utilized to identify the convergence of robot technologies. Variables for quadratic assignment procedures can be used with UCINET software.
DOI: 10.7910/dvn/v1rjpf/ig1r4o
title: iqa20161104_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823797
title: Oral intake of added titanium dioxide and its nanofraction from food products, food supplements and toothpaste by the Dutch population

description: Titanium dioxide (TiO<sub>2</sub>) is commonly applied to enhance the white colour and brightness of food products. TiO<sub>2</sub> is also used as white pigment in other products such as toothpaste. A small fraction of the pigment is known to be present as nanoparticles (NPs). Recent studies with TiO<sub>2</sub> NPs indicate that these particles can have toxic effects. In this paper, we aimed to estimate the oral intake of TiO<sub>2</sub> and its NPs from food, food supplements and toothpaste in the Dutch population aged 2 to over 70 years by combining data on food consumption and supplement intake with concentrations of Ti and TiO<sub>2</sub> NPs in food products and supplements. For children aged 2–6 years, additional intake via ingestion of toothpaste was estimated. The mean long-term intake to TiO<sub>2</sub> ranges from 0.06 mg/kg bw/day in elderly (70+), 0.17 mg/kg bw/day for 7–69-year-old people, to 0.67 mg/kg bw/day in children (2–6 year old). The estimated mean intake of TiO<sub>2</sub> NPs ranges from 0.19 μg/kg bw/day in elderly, 0.55 μg/kg bw/day for 7–69-year-old people, to 2.16 μg/kg bw/day in young children. Ninety-fifth percentile (P95) values are 0.74, 1.61 and 4.16 μg/kg bw/day, respectively. The products contributing most to the TiO<sub>2</sub> intake are toothpaste (in young children only), candy, coffee creamer, fine bakery wares and sauces. In a separate publication, the results are used to evaluate whether the presence of TiO<sub>2</sub> NPs in these products can pose a human health risk.
DOI: 10.7910/dvn/v1rjpf/u0etjl
title: iqa20160504_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823794
title: Program to read model output

description: SAS program to read model output
DOI: 10.6084/m9.figshare.3823794.v1
title: Program to read model output

description: SAS program to read model output
DOI: 10.7910/dvn/v1rjpf/thpu7z
title: iqa20150523_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zi0zbq
title: iqa20150309_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823788.v1
title: The State of European Forest Resources metadata

description: Metadata about all of the datasets in the collection.
DOI: 10.7910/dvn/v1rjpf/q61ydb
title: iqa20150925_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/p0mtfx
title: iqa20150531_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/cbewkz
title: iqa20151108_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gtehfm
title: iqa20151118_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823779
title: Maastrichtian_turtle_PBDBdata from Modelling the climatic niche of turtles: a deep-time perspective

description: Ectotherms have close physiological ties with the thermal environment; consequently, the impact of future climate change on their biogeographic distributions is of major interest. Here, we use the modern and deep-time fossil record of testudines (turtles, tortoises and terrapins) to provide the first test of climate on the niche limits of both extant and extinct (Late Cretaceous, Maastrichtian) taxa. Ecological niche models are used to assess niche overlap in model projections for key testudine ecotypes and families. An ordination framework is applied to quantify metrics of niche change (stability, expansion and unfilling) between the Maastrichtian and present-day. Results indicate that niche stability over evolutionary timescales varies between testudine clades. Groups that originated in the Early Cretaceous show climatic niche stability, whereas those diversifying towards the end of the Cretaceous display larger niche expansion towards the modern. Temperature is the dominant driver of modern and past distributions, whereas precipitation is important for freshwater turtle ranges. Our findings demonstrate that testudines were able to occupy warmer climates than present day in the geological record. However, the projected rate and magnitude of future environmental change, in concert with other conservation threats, presents challenges for acclimation or adaptation.
DOI: 10.6084/m9.figshare.3823779.v1
title: Maastrichtian_turtle_PBDBdata from Modelling the climatic niche of turtles: a deep-time perspective

description: Ectotherms have close physiological ties with the thermal environment; consequently, the impact of future climate change on their biogeographic distributions is of major interest. Here, we use the modern and deep-time fossil record of testudines (turtles, tortoises and terrapins) to provide the first test of climate on the niche limits of both extant and extinct (Late Cretaceous, Maastrichtian) taxa. Ecological niche models are used to assess niche overlap in model projections for key testudine ecotypes and families. An ordination framework is applied to quantify metrics of niche change (stability, expansion and unfilling) between the Maastrichtian and present-day. Results indicate that niche stability over evolutionary timescales varies between testudine clades. Groups that originated in the Early Cretaceous show climatic niche stability, whereas those diversifying towards the end of the Cretaceous display larger niche expansion towards the modern. Temperature is the dominant driver of modern and past distributions, whereas precipitation is important for freshwater turtle ranges. Our findings demonstrate that testudines were able to occupy warmer climates than present day in the geological record. However, the projected rate and magnitude of future environmental change, in concert with other conservation threats, presents challenges for acclimation or adaptation.
DOI: 10.7910/dvn/v1rjpf/tlmrqk
title: iqa20150817_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/umatq8
title: iqa20150919_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/b1gftr
title: iqa20150627_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823770
title: Modelling of adherence monitoring interventions

description: File of model outputs
DOI: 10.7910/dvn/v1rjpf/9yx4zf
title: iqa20150922_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823770.v1
title: Modelling of adherence monitoring interventions

description: File of model outputs
DOI: 10.7910/dvn/v1rjpf/ggh5zy
title: iqa20160829_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ajnual
title: iqa20151026_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ynymk2
title: iqa20160708_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/nncuwh
title: iqa20160506_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qv2euu
title: iqa20151016_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hijcsi
title: iqa20150501_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/rtce6o
title: iqa20160614_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/2kkruu
title: iqa20161015_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/61bcpd
title: iqa20160613_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/pjpcvs
title: iqa20160627_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gyhg5i
title: iqa20150701_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qjk9ja
title: iqa20150507_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qtzvx9
title: iqa20150807_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/dap7li
title: iqa20151005_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hqqfzg
title: iqa20150921_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ylcfmo
title: iqa20150516_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qqeu8g
title: iqa20150207_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/etgzqi
title: iqa20151022_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823728
title: Table S3. OM profile of WT and ΔpldA strains from The outer membrane phospholipase A is essential for membrane integrity and type III secretion in <i>Shigella flexneri</i>

description: Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in <i>Escherichia coli</i> and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in <i>Shigella flexneri</i>, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the <i>ΔpldA</i> mutant strain. Furthermore, the <i>ΔpldA</i> mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support PldA, which is widespread across Gram-negative bacteria, as an important factor for the bacterial life cycle, particularly in human pathogens.
DOI: 10.7910/dvn/v1rjpf/tfdjur
title: iqa20150324_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823728.v1
title: Table S3. OM profile of WT and ΔpldA strains from The outer membrane phospholipase A is essential for membrane integrity and type III secretion in <i>Shigella flexneri</i>

description: Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in <i>Escherichia coli</i> and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in <i>Shigella flexneri</i>, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the <i>ΔpldA</i> mutant strain. Furthermore, the <i>ΔpldA</i> mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support PldA, which is widespread across Gram-negative bacteria, as an important factor for the bacterial life cycle, particularly in human pathogens.
DOI: 10.7910/dvn/v1rjpf/z3sea6
title: iqa20151231_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/darxct
title: iqa20151003_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823722
title: Data_Cerebellar_Inpsired_Adaptive_Control_for_Nonlinear_Artificial_Muscle from Cerebellar inspired algorithm for adaptive control of nonlinear dielectric elastomer based artificial muscle

description: Electroactive polymer actuators are important for soft robotics, but can be difficult to control because of compliance, creep, and nonlinearities. Since biological control mechanisms have evolved to deal with such problems, we investigated whether a control scheme based on the cerebellum would be useful for controlling a nonlinear dielectric elastomer actuator, a class of artificial muscle. The cerebellum was represented by the adaptive filter model, and acted in parallel with a brainstem, an approximate inverse plant model. The recurrent connections between the two allowed for direct use of sensory error to adjust motor commands. Accurate tracking of a displacement command in the actuator's nonlinear range was achieved by either semi-linear basis functions in the cerebellar model, or semi-linear functions in the brainstem corresponding to recruitment in biological muscle. In addition, allowing transfer of training between cerebellum and brainstem as has been observed in the vestibulo-ocular reflex prevented the steady increase in cerebellar output otherwise required to deal with creep. The extensibility and relative simplicity of the cerebellar-based adaptive-inverse control scheme suggests it is a plausible candidate for controlling this type of actuator. Moreover, its performance highlights important features of biological control, particularly nonlinear basis functions, recruitment, and transfer of training.
DOI: 10.7910/dvn/v1rjpf/jbibrl
title: iqa20151226_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823722.v1
title: Data_Cerebellar_Inpsired_Adaptive_Control_for_Nonlinear_Artificial_Muscle from Cerebellar inspired algorithm for adaptive control of nonlinear dielectric elastomer based artificial muscle

description: Electroactive polymer actuators are important for soft robotics, but can be difficult to control because of compliance, creep, and nonlinearities. Since biological control mechanisms have evolved to deal with such problems, we investigated whether a control scheme based on the cerebellum would be useful for controlling a nonlinear dielectric elastomer actuator, a class of artificial muscle. The cerebellum was represented by the adaptive filter model, and acted in parallel with a brainstem, an approximate inverse plant model. The recurrent connections between the two allowed for direct use of sensory error to adjust motor commands. Accurate tracking of a displacement command in the actuator's nonlinear range was achieved by either semi-linear basis functions in the cerebellar model, or semi-linear functions in the brainstem corresponding to recruitment in biological muscle. In addition, allowing transfer of training between cerebellum and brainstem as has been observed in the vestibulo-ocular reflex prevented the steady increase in cerebellar output otherwise required to deal with creep. The extensibility and relative simplicity of the cerebellar-based adaptive-inverse control scheme suggests it is a plausible candidate for controlling this type of actuator. Moreover, its performance highlights important features of biological control, particularly nonlinear basis functions, recruitment, and transfer of training.
DOI: 10.6084/m9.figshare.3823719
title: Table S5. Secretome of S. flexneri WT and related strains in the presence of Congo Red from The outer membrane phospholipase A is essential for membrane integrity and type III secretion in <i>Shigella flexneri</i>

description: Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in <i>Escherichia coli</i> and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in <i>Shigella flexneri</i>, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the <i>ΔpldA</i> mutant strain. Furthermore, the <i>ΔpldA</i> mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support PldA, which is widespread across Gram-negative bacteria, as an important factor for the bacterial life cycle, particularly in human pathogens.
DOI: 10.7910/dvn/v1rjpf/e6ktd6
title: iqa20160920_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823719.v1
title: Table S5. Secretome of S. flexneri WT and related strains in the presence of Congo Red from The outer membrane phospholipase A is essential for membrane integrity and type III secretion in <i>Shigella flexneri</i>

description: Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in <i>Escherichia coli</i> and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in <i>Shigella flexneri</i>, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the <i>ΔpldA</i> mutant strain. Furthermore, the <i>ΔpldA</i> mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support PldA, which is widespread across Gram-negative bacteria, as an important factor for the bacterial life cycle, particularly in human pathogens.
DOI: 10.7910/dvn/v1rjpf/d6foue
title: iqa20150116_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/avou08
title: iqa20161116_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/rybaw7
title: iqa20160901_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xu8rpc
title: iqa20160824_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/93kudp
title: iqa20160903_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/lrpzm0
title: iqa20161113_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3823707
title: Fish Data from Using collision cones to assess biological deconfliction methods

description: Biological systems consistently outperform autonomous systems governed by engineered algorithms in their ability to reactively avoid collisions. To better understand this discrepancy, a collision avoidance algorithm was applied to frames of digitized video trajectory data from bats, swallows, and fish (<i>Myotis velifer</i>, <i>Petrochelidon pyrrhonota</i>, and <i>Danio aequipinnatus</i>). Information available from visual cues, specifically relative position and velocity, was provided to the algorithm which used this information to define collision cones that allowed the algorithm to find a safe velocity requiring minimal deviation from the original velocity. The subset of obstacles provided to the algorithm was determined by the animal's sensing range in terms of metric and topological distance. The algorithmic calculated velocities showed good agreement with observed biological velocities, indicating that the algorithm was an informative basis for comparison with the three species and could potentially be improved for engineered applications with further study.
DOI: 10.6084/m9.figshare.3823707.v1
title: Fish Data from Using collision cones to assess biological deconfliction methods

description: Biological systems consistently outperform autonomous systems governed by engineered algorithms in their ability to reactively avoid collisions. To better understand this discrepancy, a collision avoidance algorithm was applied to frames of digitized video trajectory data from bats, swallows, and fish (<i>Myotis velifer</i>, <i>Petrochelidon pyrrhonota</i>, and <i>Danio aequipinnatus</i>). Information available from visual cues, specifically relative position and velocity, was provided to the algorithm which used this information to define collision cones that allowed the algorithm to find a safe velocity requiring minimal deviation from the original velocity. The subset of obstacles provided to the algorithm was determined by the animal's sensing range in terms of metric and topological distance. The algorithmic calculated velocities showed good agreement with observed biological velocities, indicating that the algorithm was an informative basis for comparison with the three species and could potentially be improved for engineered applications with further study.
DOI: 10.7910/dvn/v1rjpf/ttt7oy
title: iqa20150905_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/d1uio1
title: iqa20150319_03.txt.gz

description: :unav