cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0kh1f8j
title: Data from: A review of protocols for the experimental release of kelp (Laminariales) zoospores

description: Kelps (order Laminariales) are foundation species in temperate and arctic
 seas globally, but they are in decline in many places. Laminarian kelp
 have an alternation of generations and this poses challenges for
 experimental studies due to the difficulties in achieving zoospore release
 and gametophyte growth. Here we review and synthesize the protocols that
 have been used to induce zoospore release in kelps to identify
 commonalities and provide guidance on best practices. We found 171 papers,
 where zoospore release was induced in four kelp families from 35 different
 ecoregions. The most commonly treated family was Laminariaceae, followed
 by Lessoniaceae and the most studied ecoregion was Central Chile, followed
 by the Southern California Bight. Zoospore release generally involved
 three steps: a pre-treatment which included cleaning of the reproductive
 tissue to eliminate epiphytic organisms, followed by desiccation of the
 tissue, and finally a post-desiccation immersion of the reproductive
 material in a seawater medium for zoospore release. Despite these
 commonalities, there was a high degree of variation in the detail within
 each of these steps, even among studies within genera and from the same
 ecoregions. This suggests that zoospore release may be relatively
 insensitive across the Laminariales. Nevertheless, greater attention to
 standardisation of protocols would facilitate comparisons of kelp zoospore
 release across species and locations. Based on practicality and most
 common practices, we suggest zoospore release should be achieved through
 1) wiping clean the reproductive material, 2) desiccating the reproductive
 material by wrapping in moist paper towels for 12 hours at room
 temperature in darkness, and 3) submerging the tissue in seawater medium
 for one hour at room temperature in darkness. The choice of seawater
 medium should depend on the actual experiment conducted. Standardized
 protocols will facilitate broad scale comparative studies across this key
 taxa.
description: Comprehensive list of
 the journal articles examining the microscopic stages on
 LaminarialesThe data table available
 through this link contains a comprehensive list of the journal articles
 examining the microscopic stages on Laminariales, displaying the full
 description of the species studied; geographic location (GPS position) and
 ecoregion; collection date; sea surface temperature; details concerning
 the protocol used to induce zoospore release; aim of the research; and the
 reference.Alsuwaiyan et al spore release
 Dryad raw data table.docx
DOI: 10.5061/dryad.245j1p8
title: Data from: Predicted tracking error triggers catch-up saccades during smooth pursuit

description: For foveated animals, visual tracking of moving stimuli requires the
 synergy between saccades and smooth pursuit eye movements. Deciding to
 trigger a catch-up saccade during pursuit influences the quality of visual
 input. This decision is a trade-off between tolerating sustained position
 error when no saccade is triggered or a transient loss of vision during
 the saccade due to saccadic suppression. Although catch-up saccades have
 been extensively investigated, it remains unclear how the trigger decision
 is made by the brain. de Brouwer et al (2002) demonstrated that catch-up
 saccades were less likely to occur when the expected time to foveate a
 target using pursuit alone is between 40 and 180ms into the future,
 referred to as the smooth zone. However, this descriptive result lacks a
 mechanistic explanation for how the trigger decision is made. More
 recently, we proposed a decision model (Coutinho et al., 2018) that relies
 on a probabilistic estimation of predicted position error (PEpred) during
 visual tracking. To test the model predictions, we investigated how human
 participants combined predicted position error, retinal slip, and the
 uncertainty in those estimates to make trigger decisions. We found a
 significant effect of the pre-saccadic magnitude of PEpred on trigger time
 and occurrence of catch-up saccades. To test the role of uncertainty, we
 blurred the moving target which led to longer and more variable saccade
 trigger times and more smooth pursuit trials, consistent with model
 predictions. As predicted by our model, large PEpred (&gt;10deg)
 produced early saccades regardless of the level of uncertainty while
 saccades preceded by small PEpred (&lt;10deg) were significantly
 modulated by high uncertainty. Our model also predicted increased signal
 dependent noise as retinal slip increases, which resulted in longer
 saccade trigger times and more smooth trials. In conclusion, the data
 supports our hypothesized role of PEpred in deciding when to trigger a
 catch-up saccade during smooth pursuit while taking into account
 uncertainty in sensory estimates.
description: RawRaw double-step ramp
 eye-tracking data of 15 subjects from EyeLink 1000 and
 Matlab.LabeledS1-S5Labeled data file for subjects 1-5LabeledS7-S11Labeled data for subjects 7-11LabeledS12-S16Labeled data for subjects 12-16Data Collection Log
DOI: 10.7272/q6kw5cxv
title: Predicting Cognitive Decline

description: These data were acquired with the overall goal of determining the regional
 and longitudinal pattern of changes in the brain which best predict future
 cognitive decline and dementia due to Alzheimer's disease (AD). The
 data set includes longitudinal clinical evaluation, cognitive testing, and
 neuroimaging assessments from a non-demented study population aged 65 and
 up who complain of memory problems and show some indication of memory
 and/or executive functioning below age/gender/education adjusted norm.
description: Data Acquisition Location: San Francisco VA Medical Center;
 Scanner Type: Siemens Vision 1.5T; Coronal T1 MPRAGE: TR=9ms, TE=4ms,
 TI=300ms, 1x1mm2, 3mm slice thickness; Axial double spin echo PD &
 T2: TR=5000ms, TE=20/85ms, 1x1.25mm2, 3mm slice thickness
DOI: 10.5061/dryad.86qh1tm
title: Data from: Fine-scale substrate heterogeneity in green roof plant communities: the constraint of size

description: Heterogeneity-diversity relationship (HDR) is commonly shown to be
 positive in accordance with classic niche processes. However, recent
 soil-based studies have often found neutral and even negative HDRs. Some
 of the suggested reasons for this discrepancy include the lack of
 resemblance between manipulated substrate and natural settings, the
 treated areas not being large enough to contain species' root span
 and finally limited-sized plots may not sustain focal species’ populations
 over time. V egetated green roofs are a growing phenomenon in many cities
 that could be an ideal testing ground for this problem. Recent studies
 have focused on the ability of these roofs to sustain stable and diverse
 plant communities and substrate heterogeneity that would increase niches
 on the roof has been proposed as a method to attain this goal. We
 constructed an experimental design using green roof experimental modules
 (4 m²) where we manipulated mineral and organic substrate component
 heterogeneity in different subplots (0.25 m²) within the experimental
 module while maintaining the total sum of mineral and organic components.
 A local annual plant community was seeded in the modules and monitored
 over three growing seasons. We found that plant diversity and biomass were
 not affected by experimentally created substrate heterogeneity. In
 addition, we found that different treatments, as well as specific subplot
 substrates, had an effect on plant community assemblages during the first
 year but not during the second and third years. Substrate heterogeneity
 levels were mostly unchanged over time. The inability to retain plant
 community composition over the years despite the maintenance of substrate
 differences supports the hypothesis that maintenance of diversity is
 constrained at these spatial scales by unfavorable dispersal and increased
 stochastic events as opposed to predictions of classic niche processes.
description: species_monthThis file details the FHD total counts (touch of live plant tissue) of the different species in each of the plots each month.Species_germination_3_yearsThis file details the total germination of each of the species in the different plots over each of the 3 years of the experiment.Speies_germination_3_years.xlsxsoil_sample_weight_3_yearsThis file details the weight of the soil samples within the plots over the years of the experiment.substrate_organic_matter_over_3_yearsThis file details the organic matter in the different samples over the 3 years.jan_moisture_plot-subplot_3_yrsThis file details the moisture results for plots and subplots in January samples over 3 years. samples werein a transect and moisture 2 is always in the plot and 1+3 are subplots. grey - organic treated subplot, yellow - mineral treated plot.
DOI: 10.5061/dryad.fc0qr81
title: Data from: Sequence specificity despite intrinsic disorder: how a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein

description: The role of electrostatic interactions and mutations that change charge
 states in intrinsically disordered proteins (IDPs) is well-established,
 but many disease-associated mutations in IDPs are charge-neutral. The
 Val66Met single nucleotide polymorphism (SNP) in precursor brain-derived
 neurotrophic factor (BDNF) is one of the earliest SNPs to be associated
 with neuropsychiatric disorders, and the underlying molecular mechanism is
 unknown. Here we report on over 250 μ s of fully-atomistic, explicit
 solvent, temperature replica exchange molecular dynamics (MD) simulations
 of the 91 residue BDNF prodomain, for both the V66 and M66 sequence. The
 simulations were able to correctly reproduce the location of both local
 and non-local secondary changes due to the Val66Met mutation when compared
 with NMR spectroscopy. We find that the change in local structure is
 mediated via entropic and sequence specific effects. We developed a
 hierarchical sequence-based framework for analysis and conceptualization,
 which first identifies “blobs” of 5-15 residues representing local
 globular regions or linkers. We use this framework within a novel test for
 enrichment of higher-order (tertiary) structure in disordered proteins;
 the size and shape of each blob is extracted from MD simulation of the
 real protein (RP), and used to parameterize a self-avoiding heterogenous
 polymer (SAHP). The SAHP version of the BDNF prodomain suggested a protein
 segmented into three regions, with a central long, highly disordered
 polyampholyte linker separating two globular regions. This effective
 segmentation was also observed in full simulations of the RP, but the
 Val66Met substitution significantly increased interactions across the
 linker, as well as the number of participating residues. The Val66Met
 substitution replaces β -bridging between Val66 and Val94 (on either side
 of the linker) with specific side-chain interactions between Met66 and
 Met95.The protein backbone in the vicinity of Met95 is then free to form β
 -bridges with residues 31-41 near the N-terminus, which condenses the
 protein. A significant role for Met/Met interactions is consistent with
 previously-observed non-local effects of the Val66Met SNP, as well as
 established interactions between the Met66 sequence and a Met-rich
 receptor that initiates neuronal growth cone retraction.
description: bdnf-val66met_trajectoriesThe directory includes MD trajectories for V66 prodomain sequence (folder V_hid_11) and M66 prodomain sequence (folder M_hid_11) simulations as described in the manuscript. Replica id 0 corresponds to simulations at 300K and is used for bulk of the calculations in the manuscript.Val66Met_trajectories.tar.gzsetup_scripts_bdnf-val66metContains simulation setup scripts, input coordinates, topologies, mdp and force field files.setup_scripts.tar.gz
DOI: 10.5061/dryad.28n8d6t
title: Data from: Quantitative PCR primer design affects quantification of dsRNA-mediated gene knockdown

description: RNA interference (RNAi) is a powerful tool for studying functions of
 candidate genes in both model and non-model organisms and a promising
 technique for therapeutic applications. Successful application of this
 technique relies on the accuracy and reliability of methods used to
 quantify gene knockdown. With the limitation in the availability of
 antibodies for detecting proteins, quantitative PCR (qPCR) remains the
 preferred method for quantifying target gene knockdown after dsRNA
 treatment . We evaluated how qPCR primer binding site and target gene
 expression levels affect quantification of intact mRNA transcripts
 following dsRNA-mediated RNAi. The use of primer pairs targeting the mRNA
 sequence within the dsRNA target region failed to reveal a significant
 decrease in target mRNA transcripts for genes with low expression levels,
 but not for a highly expressed gene. By contrast, significant knockdown
 was detected in all cases with primer pairs targeting the mRNA sequence
 extending beyond the dsRNA target region, regardless of the expression
 levels of the target gene. Our results suggest that at least for genes
 with low expression levels, quantifying the efficiency of dsRNA-mediated
 RNAi with primers amplifying sequences completely contained in the dsRNA
 target region should be avoided due to the risk of false negative results.
 Instead, primer pairs extending beyond the dsRNA target region of the mRNA
 transcript sequences should be used for accurate and reliable
 quantification of silencing efficiency.
description: SupplementaryFile_GeneExpressionRawDataGene expression raw data measurements for Defensins, c-type-lysozyme, and 18s rRNA
DOI: 10.5281/zenodo.8231172
title: GUI Testing in Practice: An Interview-Based Study of Approaches and Challenges in the Brazilian Software Industry

description: Software testing is an important activity in the software development cycle, which seeks to ensure the quality of software created. When software does not meet its users' implicit and explicit needs, one can say that it lacks quality. The lack of quality in software can generate several problems for the software development project, such as friction between supplier and clients/users, financial losses, legal problems due to breach of contracts, and even risk to the life of its users in critical contexts.

Along these lines, different levels of testing have been developed to ensure quality in different aspects of the software. A popular approach is functional interface testing, which evaluates software by executing events on the software screen, such as filling in a text field or clicking in a button. GUI (Graphical User Interface) functional testing can be executed either manually, with the tester interacting directly with the software, or automatically, by running the software through a programmed script.

In recent years, one can find several solutions and techniques proposed to deal with GUI testing in the literature. However, they usually do not analyze how industry professionals perform this type of testing, leaving a gap in the area. Therefore, this study investigates how testers perform interface testing on their projects. Then, we conducted a semi-structured interview with 20 testing professionals. The results indicated that testers who only perform manual GUI tests do not create automated GUI tests due to the context of the project in which they work, their professional preferences and also for educational reasons, such as difficulty in programming. In addition, distinct limitations were observed for manual and automated GUI tests that negatively impact the activities performed by professionals, such as difficulties related to the company's culture and technical problems related to the software under test. The combined results provide a general overview of GUI testing available in the Brazilian software industry.
DOI: 10.5281/zenodo.8231171
title: GUI Testing in Practice: An Interview-Based Study of Approaches and Challenges in the Brazilian Software Industry

description: Software testing is an important activity in the software development cycle, which seeks to ensure the quality of software created. When software does not meet its users' implicit and explicit needs, one can say that it lacks quality. The lack of quality in software can generate several problems for the software development project, such as friction between supplier and clients/users, financial losses, legal problems due to breach of contracts, and even risk to the life of its users in critical contexts.

Along these lines, different levels of testing have been developed to ensure quality in different aspects of the software. A popular approach is functional interface testing, which evaluates software by executing events on the software screen, such as filling in a text field or clicking in a button. GUI (Graphical User Interface) functional testing can be executed either manually, with the tester interacting directly with the software, or automatically, by running the software through a programmed script.

In recent years, one can find several solutions and techniques proposed to deal with GUI testing in the literature. However, they usually do not analyze how industry professionals perform this type of testing, leaving a gap in the area. Therefore, this study investigates how testers perform interface testing on their projects. Then, we conducted a semi-structured interview with 20 testing professionals. The results indicated that testers who only perform manual GUI tests do not create automated GUI tests due to the context of the project in which they work, their professional preferences and also for educational reasons, such as difficulty in programming. In addition, distinct limitations were observed for manual and automated GUI tests that negatively impact the activities performed by professionals, such as difficulties related to the company's culture and technical problems related to the software under test. The combined results provide a general overview of GUI testing available in the Brazilian software industry.
DOI: 10.5061/dryad.65j00m3
title: Data from: The effects of vessel noise on the communication network of humpback whales

description: Humpback whales likely rely on acoustic communication to mediate social
 interactions. The distance to which these social signals propagate from
 the signaller defines its communication space, and therefore communication
 network (number of potential receivers). As humpback whales migrate along
 populated coastlines, they are likely to encounter noise from vessel
 traffic which will mask their social signals. Since no empirical data
 exists on baleen whale hearing, the consequences of this are usually
 assumed, being the modelled reduction in their communication space. Here,
 the communication space and network of migrating humpback whales was
 compared in increasing wind-dominated and vessel noise. Behavioural data
 on their social interactions were then used to inform these models. In
 typical wind noise, a signaller’s communication space was estimated to
 extend to 4 km, which agreed with the maximum separation distance between
 groups that socially interacted. An increase in vessel noise reduced the
 modelled communication area by a factor of four, along with a significant
 reduction in group social interactions, likely due to a reduction in their
 communication network. However, signal masking did not fully explain this
 change in social behaviour, implying there was also an additional effect
 of the physical presence of the vessel on signaller and receiver
 behaviour. Though these observed changes in communication space and social
 behaviour were likely to be short-term and localised, an increase in
 vessel activity due to tourism and coastal population growth may cause
 more sustained changes along the humpback whale migration paths.
description: all.vocalsignal measures in boat and wind noise
DOI: 10.5061/dryad.82557c0
title: Data from Native adiponectin in serum binds to mammalian cells expressing T-cadherin, but not AdipoRs or calreticulin

description: Adiponectin is an adipocyte-derived atypically abundant circulating factor
 that protects various organs and tissues through its receptors, AdipoRs,
 calreticulin, and T-cadherin. To identify the major binding partner of
 circulating native adiponectin, we expressed these receptors on the
 surface of HEK293 cells. Adiponectin, either that in mouse or human serum,
 purified from serum, or produced by mammalian cells, bound to cells
 expressing T-cadherin, but not to those expressing AdipoR1 or
 calreticulin. The stable introduction of T-cadherin and AdipoR1 into CHO
 cells resulted in the cell surface localization of these receptors. Native
 adiponectin in serum bound to cells expressing T-cadherin, not to those
 expressing AdipoR1. The knockdown of T-cadherin, but not AdipoRs resulted
 in the significant attenuation of native adiponectin binding to C2C12
 myotubes. Therefore, native adiponectin binding depended on the amount of
 T-cadherin expressed in HEK293 cells, CHO cells, and C2C12 myotubes.
 Collectively, our mammalian cell-based studies suggest that T-cadherin is
 the major binding partner of native adiponectin in serum.  
description: Binding of
 APN Native APN binding
 study qPCR
 absolute quantification_2018-11-05 185355 (version 1).xlsx
 
 2018-11-05
 185355     
 2018-12-10
 172652     
 2018-12-10
 204623     
 human moouse serum HMW
 binding_2018-11-01 13h06m07s 10.400s Chemiluminescence   
 mAPN mSerum on mAPN
 recpetors 2018-10-30 13h43m23s 12.460s Chemiluminescence
 Figure 1C_mSerum
 to HEK OE   
 T-cad mSerum hSerum on
 APN-receptors 2018-10-30 13h29m33s 7.243s Chemiluminescence
  
 
 T-cad mSerum
 hSerum on APN-receptors 2018-10-30 13h29m33s 7.243s
 Chemiluminescence Figure 1C_mSerum to HEK
 OE   
 Tubulin_mSerum on
 mAPN-receptors 293a 2018-10-30 13h24m42s 6.647s
 Chemiluminescence Figure 1C_mSerum to HEK
 OE   
 human moouse serum HMW
 binding_2018-11-01 13h06m07s 10.400s Chemiluminescence Figure 1C_mSerum to HEK
 OE     
 2018-10-30 13h24m42s
 6.647s Chemiluminescence Figure 1C_mSerum to HEK
 OE raw data   
 2018-10-30 13h24m42s
 6.647s Chemiluminescence+2018-10-30 13h25m23s 0.123s
 Colorimetric Figure 1C_mSerum to HEK
 OE raw data   
 data deposit for
 eLife All data files including
 raw data compressed. Pass word is 3737. Data deposit.7z
 
 Native
 adiponectin in serum binds to cells expressing T-cadherin, but not AdipoRs
 or calreticulin All raw and calculated
 data compressed. Data deposit for
 eLife.zip