cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.47d7wm3d0
title: Critical angle reflection imaging for quantification of molecular interactions on glass surface

description: Quantification of molecular interactions on a surface is typically
 achieved via label-free techniques such as surface plasmon resonance
 (SPR). The sensitivity of SPR originates from the characteristic that the
 SPR angle is sensitive to the surface refractive index change.
 Analogously, in another interfacial optical phenomenon, total internal
 reflection, the critical angle is also refractive index dependent.
 Therefore, surface refractive index change can also be quantified by
 measuring the reflectivity near critical angle. Based on this concept, we
 develop a method called critical angle reflection (CAR) imaging to
 quantify molecular interactions on glass surface. CAR imaging can be
 performed on SPR imaging setups. Through a side-by-side comparison, we
 show that CAR is capable of most molecular interaction measurements that
 SPR does, including proteins, nucleic acids and cell-based detections. In
 addition, we show that CAR can detect small molecule bindings and
 intracellular signals beyond SPR sensing range. CAR exhibits several
 distinct characteristics over SPR, including tunable sensitivity and
 dynamic range, deeper vertical sensing range, fluorescence compatibility,
 broader wavelength and polarization of light selection, and glass surface
 chemistry. We anticipate CAR can expand SPR capability in small molecule
 detection, whole cell-based detection, simultaneous fluorescence imaging,
 and broader conjugation chemistry.
description: The dataset include binding kinetics data measured by CAR and SPR
 imaging techniques.
description: Please use Winspall to open WSP file, and use Fiji (ImageJ) to
 open image files.
DOI: 10.5061/dryad.kd51c5b5k
title: Melting curve analysis for detection and identification of ghost parasitoids in host carcasses a month after host death-fluorescence data

description: 1. Incidence of parasitism is often underestimated because ‘ghost’
 parasitoids (deadnunemerged parasitoids or those that have emerged leaving
 the host carcasses) are difficult to detect and identify. This study
 demonstrates that the use of melting curve analysis (MCA) of host
 carcasses can detect and identify DNA of ghost parasitoids even a month
 after host death. 2. The coccinellid hosts Cycloneda sanguinea, Eriopis
 connexa, Harmonia axyridis and Hippodamia convergens were sampled
 from cole crops in 2017 and 2018 in the Midwest of Brazil, and reared and
 observed daily for parasitoid emergence. Dead coccinellids were held for
 30 days after death before storage and only host carcasses with parasitoid
 emergence observed were analysed. Species-specific primers were designed
 for the identification of the parasitoid species that emerged during host
 rearing: Dinocampus coccinellae, Homalotylus mirabilis, Ho.
 terminalis, Strongygaster triangulifera and Phalacrotophora sp.
 The melting temperatures (Tm) of their amplicons were used as positive
 controls in MCA post-amplification in qPCR. 3. Detection of parasitoid DNA
 in host carcasses was possible for D. coccinellae, Ho. mirabilis and
 Phalacrotophora sp. with a limit of detection (LOD) for all the
 parasitoids &lt;1 pg of DNA, except for Phalacroptopthora sp. (LOD =
 1.9 ng). Parasitoids were detected in 31 out of 70 host carcasses (44.3%)
 with detection ranging from 0% to 71%, depending on the parasitoid
 species. 4. Synthesis and applications. This work demonstrates that MCA
 could be used to detect and rapidly identify the DNA of some parasitoid
 species (e.g. Ho. mirabilis, D. coccinellae and Phalacrotophora
 sp.) in host carcasses up to a month after parasitoid emergence with high
 sensitivity and specificity. MCA can be used on any field-collected host
 and, for some parasitoid species, it should lead to more accurate
 estimates of the incidence of parasitism. Our approach can be easily
 adapted and applied to study other parasitoid–host interactions.
description: qPCR with a Roche 480 (details in published manuscript). Melt
 curves were constructed using the raw fluorescence data and diffQ in the
 library MBmca in R (R Core Team 2013) as in the associated R
 script.
description: Usage notes are described in Code Book sheet of data file.
 Software file makes melting curve graphs (-dF/dT), but needs to be
 modified to accept files in formats different from that
 described.
DOI: 10.5061/dryad.stqjq2c3j
title: Data from: Transgenerational plasticity responses of oysters to ocean acidification differ with habitat

description: This dataset contains data from a two-part experiment described in the
 paper: Transgenerational plasticity responses of oysters to ocean
 acidification differ with habitat, J Exp Biol jeb.239269. This paper
 assessed the role of tidal habitat on the existing and transgenerational
 response of larvae of the Sydney rock oyster, Saccostrea glomerata to
 ocean acidification caused by elevated carbon dioxide (CO2). In experiment
 1, gravid Sydney rock oysters were collected from the subtidal and high
 intertidal zone and brought into the hatchery. Their gametes were
 collected and fertilized and the size of eggs, shell length of D-veliger
 larvae, percentage of D-veliger larvae, and percentage of D-veliger larvae
 that were abnormal, was determined after 48 hours of exposure to ambient
 (400 µatm) and elevated (1000 µatm) CO2. In experiment
 2, non-gravid adult Sydney rock oysters were collected from the subtidal
 and high intertidal zone and brought into the hatchery. Adults were
 conditioned in the hatchery under two different tidal cycles (subtidal and
 intertidal) and two different CO2 treatments (ambient or elevated) until
 reaching gravid stage. Gametes from gravid adults were collected and
 fertilized, and the size of eggs, shell length of D-veliger larvae,
 percentage of D-veliger larvae, percentage of D-veliger larvae that were
 abnormal, and respiration rate of larvae was determined after 48 hours of
 exposure to ambient and elevated CO2. Main results of the experiment were
 that larvae from parents conditioned in an intertidal habitat had a
 greater existing tolerance to elevated CO2 than larvae from parents
 conditioned in a subtidal habitat but had a lower capacity for beneficial
 transgenerational plasticity following adult exposure to elevated CO2.
      
description: Details of how the measurements were taken can be found in the
 methods section of the associated manuscript that is referenced
 above.
description: The ReadMe file describes
 the variables that were measured and the measurement units that were
 used.
DOI: 10.5061/dryad.d51c5b034
title: Transfer efficiency of carbon, nutrients, and PUFAs in planktonic food webs under different environmental conditions

description: We investigated the transfer of essential substances (carbon, nutrients,
 and polyunsaturated fatty acids) through plankton communities in 30 Polish
 lakes with different trophic status in the middle of summer. The results
 of our study revealed that different essential substances were transferred
 from phytoplankton to zooplankton with varying efficiencies. The average
 TTE of C, N, P, and the sum of ω-3 PUFA were 6.55%, 9.82%, 15.82%, 20.90%,
 respectively. Our results also show a large mismatch between the elemental
 and biochemical compositions of zooplankton and their food during the peak
 of the summer stagnation, which may further promote the accumulation of
 essential substances. There were also large differences in TTEs between
 trophic conditions, with the highest efficiencies in oligotrophic lakes
 and the lowest in dystrophic and eutrophic lakes. Therefore, our study
 indicates that disturbances like eutrophication and dystrophication
 similarly decrease the TTE of essential substances between phytoplankton
 and zooplankton in freshwater food webs.
DOI: 10.5061/dryad.wstqjq2m1
title: Patient-reported outcomes among people living with HIV on single- versus multi-tablet regimens

description: Background: Single-tablet regimens (STR) have become the golden
 standard in antiretroviral therapy. However, there are calls to
 reintroduce (generic) components as multi-tablet regimens (MTR) because of
 cost-savings. Patient-reported outcome measures (PROs) are an important
 touchstone to support or to renounce this proposal. As such, our aim was
 to compare PROs of people living with HIV taking an STR versus a MTR in a
 real world setting. Materials and methods: 188 people living with
 HIV participated in a longitudinal study. 132 remained on their MTR and 56
 switched to an STR. At baseline, months 1-3-6-12-18 and 24, participants
 filled in questionnaires on health-related quality of life (HRQoL),
 depressive symptoms, HIV symptoms, neurocognitive complaints (NCC)
 treatment satisfaction and adherence. Generalized linear mixed models and
 generalized estimation equations mixed models were built.
 Results: At baseline, the two groups did not differ in clinical
 parameters and PROs. The mixed models revealed differences among the
 groups regarding neurocognitive complaints and treatment satisfaction. The
 odds of having NCC increased by 4,1% per month in the STR-group as
 compared to the MTR-group (p=0.035). Nonetheless, treatment satisfaction
 also increased in the STR-group: at month 6, median change score was
 highly positive: 24 (IQR 7,5-29). Treatment satisfaction showed a
 significantly different evolution in the groups: the estimated state score
 increased by 3,3 in the STR-group while it decreased by 0,2 in the
 MTR-group (p=0.003). HRQoL measures, HIV symptoms, depressive symptoms and
 adherence did not differ between the groups over time.
 Conclusions: Neurocognitive complaints and treatment satisfaction
 differed between the two groups. More people on an STR reported NCC over
 time compared to the MTR-group. Contrarily, treatment satisfaction in the
 STR-group increased significantly over time. It should be further
 investigated to which extent treatment satisfaction is a predictor for
 long-term treatment persistence and health outcomes.
DOI: 10.5061/dryad.cjsxksn5p
title: Data on: contrasting manual and automated assessment of larval body size and thermal stress responses in black soldier flies and houseflies

description: The data files described below contains information on larval body size
 traits and stress tolerance traits obtained using contrasting methods
 (manual and automated). The species investigated are black soldier flies
 (Hermetia illucens) and houseflies (Musca domestica). Larval body size is
 estimated using manual weighing and imaging analysis software (Noldus
 EthoVision XT 15.0.1418, Wageningen, the Netherlands). Stress tolerance
 traits are obtained using manual observations of traditional thermal
 tolerance assays and by using software for video analysis (Noldus
 EthoVision XT).
DOI: 10.5061/dryad.s4mw6m969
title: Data From: Fit and fatty freshwater fish: Contrasting polyunsaturated fatty acid phenotypes between hybridizing stickleback lineages

description: Long-chain polyunsaturated fatty acids are biologically important lipids
 that are unevenly distributed between and throughout environments. This
 heterogeneity can affect the evolution of metabolic processes, as
 populations adapt to the resource landscape that they encounter. Here, we
 compare fatty acid phenotypes of stickleback over two time scales of
 evolutionary divergence: between two lineages with different metabolic
 capacities for fatty acid synthesis (i.e. different copy number of the
 fatty acid desaturase gene; FADS2) that independently colonized European
 freshwaters during the Pleistocene and Holocene; and between two ecotypes
 within each lineage that have diverged more recently (~150 years) in
 different habitats (i.e. lake and stream). We measured fatty acid profiles
 of wild-caught and lab-reared fish for each lineage and ecotype
 combination after rearing lab fish on a diet deficient in omega-3
 long-chain polyunsaturated fatty acids. Since these lineages hybridize in
 nature, we also measured profiles of lab-reared hybrids and backcrosses
 raised on the same deficient diet. Wild fish showed strong compositional
 differences in fatty acids between habitats, lineages, and sexes. Common
 garden fish had generally lower polyunsaturated fatty acid levels than
 wild fish, and females had lower omega-6:omega-3 than males. Fish from the
 lineage with fewer FADS2 copies also had lower levels of docosahexaenoic
 acid. Overall, we document divergence in fatty acid phenotypes between
 stickleback lineages with different histories of freshwater colonization,
 and between ecotypes in the early stages of adaptive population
 divergence.
description: This dataset is split into five parts. Parts one and two are
 composed of data on the omega-3 fatty acid content of invertebrate prey
 (part one), and <em>FADS2</em> copy number variation of
 threespine stickleback (part two) collected from previously published
 works. Part three is the main dataset used in the manuscript, containing
 fatty acid profiles of lab raised and wild caught threespine stickleback.
 These fatty acid profiles were produced from GC-MS of lipids extracted
 from freeze dried muscle tissue. Parts four and five are subsets of the
 main dataset that were used in analysis and the production of figures for
 the manuscript.
DOI: 10.5061/dryad.r4xgxd2cc
title: Community composition of tree and palm species in a forest with bamboo in southwestern Amazonia

description: A forest inventory was conducted in August 2016 in the
 municipality of Rio Branco, Acre, Brazil. This data was used in
 "Community composition of tree and palm species following disturbance
 in a forest with bamboo in southwestern Amazonia, Brazil" (Ziccardi
 et al., 2021). The dataset is composed by 5 variables and 1224 cases
 (rows). It presents data for species identified in a total of 24 plots
 distributed in three treatments: Fire + Logging (1); Fire (2) and Control
 (3). The second dataset is composed by 41 variables and 25 cases (rows).
 It combines data collected by a remote piloted aircraft (RPA) and
 variables sampled in the field. The abundance bamboo was
 represented by the density of culms at the ground level and the
 canopy area occupied by bamboo.
DOI: 10.5061/dryad.4mw6m9098
title: Driving cell response through deep learning, a study in simulated 3D cell cultures

description: Computational simulations are becoming increasingly relevant in biomedical
 research, providing strategies to reproduce experimental results, improve
 the resolution of in-vitro experiments, and predict the system’s behavior
 in untested conditions. The study of how each simulated variable
 influences measurable outcomes, however, has received little attention. To
 bridge this gap, we here propose a deep learning framework capable of
 reliably classify simulated time series data and identify class-defining
 features. This information will be shown to be useful for the
 determination of which changes in the experimental conditions elicit a
 desired cellular response. This analysis pipeline will be initially tested
 on a synthetic dataset created ad-hoc to identify its accuracy in
 identifying the most relevant portion of the signals. Successively this
 method will be applied to simulations describing the behaviors of
 populations of cancer cells treated with either one or two drugs in
 different concentrations. The proposed method will be shown to be
 effective in identifying which changes in the treatment protocol leads to
 a more extensive response to treatment. While lacking direct experimental
 validation, this result holds great potential for the integration of
 in-silico and in-vitro analyses and the effective optimization of
 experimental conditions in complex experimental set-ups.
DOI: 10.5061/dryad.q2bvq83jh
title: Sleep/wake transitions in sheep

description: Sleep disturbance is a common and disruptive symptom of neurodegenerative
 diseases such as Alzheimer’s and Huntington’s disease (HD). In HD
 patients, sleep fragmentation appears at an early stage of disease,
 although features of the earliest sleep abnormalities in presymptomatic HD
 are not fully established. Here we used novel automated analysis of
 quantitative electroencephalography to study transitions between wake and
 non-rapid eye movement sleep in a sheep model of presymptomatic HD. We
 found that while the number of transitions between sleep and wake were
 similar in normal and HD sheep, the dynamics of transitions from
 sleep-to-wake differed markedly between genotypes. Rather than the gradual
 changes in EEG power that occurs during transitioning from sleep-to-wake
 in normal sheep, transition into wake was abrupt in HD sheep. Furthermore,
 transitions to wake in normal sheep were preceded by a significant
 reduction in slow wave power, whereas in HD sheep this prior reduction in
 slow wave power was far less pronounced. This suggests an impaired ability
 to prepare for waking in HD sheep. The abruptness of awakenings may also
 have the potential to disrupt sleep-dependent processes if they are
 interrupted in an untimely and disjointed manner. We propose that not only
 could these abnormal dynamics of sleep transitions be useful as an early
 biomarker of HD, but also that our novel methodology would be useful for
 studying transition dynamics in other sleep disorders.
DOI: 10.5061/dryad.5x69p8d2t
title: Data from: Clinical correlation of multiple sclerosis immunopathological subtypes

description: Objective: To compare clinical characteristics across immunopathological
 subtypes of patients with multiple sclerosis. Methods: Immunopathological
 subtyping was performed on specimens from 547 patients with biopsy and/or
 autopsy confirmed CNS demyelination. Results: The frequency of
 immunopathological subtypes were pattern I (23%), II (56%), and III (22%).
 Immunopatterns were similar in terms of age at autopsy/biopsy (median age
 41 years, range 4-83 years, p=0.16) and proportion female (54%, p=0.71).
 Median follow-up after symptom onset was 2.3 years (range 0-38y). In
 addition to being overrepresented among autopsy cases (45% vs. 19% in
 biopsy cohort, p&lt;0.001), index attack-related disability was higher
 in pattern III vs. pattern II (median EDSS 4 vs. 3, p=0.02). Monophasic
 clinical course was more common in patients with pattern III than pattern
 I or II (59% vs. 33% vs. 32%, p&lt;0.001). Similarly, patients with
 pattern III pathology were likely to have progressive disease compared to
 patients with patterns I or II, when followed for ≥5 years (24% overall,
 p=0.49), with no differences in long-term survival, despite a more
 fulminant attack presentation. Conclusion: All three immunopatterns can be
 detected in active lesions, although they are found less frequently later
 into the disease due to the lower number of active lesions. Pattern III is
 associated with a more fulminant initial attack than either pattern I or
 II. Biopsied patients appear to have similar long-term outcomes
 irrespective of their immunopatterns. Progressive disease is less
 associated with the initial immunopattern and suggests convergence into a
 final common pathway related to the chronically denuded axon.
DOI: 10.5061/dryad.1c59zw3vb
title: Identification of thresholds for accuracy comparisons of heart rate and respiratory rate in neonates

description: Background: Heart rate (HR) and respiratory rate (RR) can be challenging
 to measure accurately and reliably in neonates. The introduction of
 innovative, non-invasive measurement technologies suitable for
 resource-constrained settings is limited by the lack of appropriate
 clinical thresholds for accuracy comparison studies. Methods: We collected
 measurements of photoplethysmography-recorded HR and capnography-recorded
 exhaled carbon dioxide across multiple 60-second epochs (observations) in
 enrolled neonates admitted to the neonatal care unit at Aga Khan
 University Hospital in Nairobi, Kenya. Trained study nurses manually
 recorded HR, and the study team manually counted individual breaths from
 capnograms. For comparison, HR and RR also were measured using an
 automated signal detection algorithm. Clinical measurements were analyzed
 for repeatability. Results: A total of 297 epochs across 35 neonates were
 recorded. Manual HR showed a bias of -2.4 (-1.8%) and a spread between the
 95% limits of agreement (LOA) of 40.3 (29.6%) compared to the
 algorithm-derived median HR. Manual RR showed a bias of -3.2 (-6.6%) and a
 spread between the 95% LOA of 17.9 (37.3%) compared to the
 algorithm-derived median RR, and a bias of -0.5 (1.1%) and a spread
 between the 95% LOA of 4.4 (9.1%) compared to the algorithm-derived RR
 count. Manual HR and RR showed repeatability of 0.6 (interquartile range
 (IQR) 0.5-0.7), and 0.7 (IQR 0.5-0.8), respectively. Conclusions:
 Appropriate clinical thresholds should be selected a priori when
 performing accuracy comparisons for HR and RR. Automated measurement
 technologies typically use a smoothing or averaging filter, which
 significantly impacts accuracy. A wider spread between the LOA, as much as
 30%, should be considered to account for the observed physiological
 nuances and within- and between-neonate variability and different
 averaging methods. Wider adoption of thresholds by data standards
 organizations and technology developers and manufacturers will increase
 the robustness of clinical comparison studies.
description: We collected measurements of photoplethysmography-recorded heart
 rate (HR) and capnography-recorded exhaled carbon dioxide across multiple
 60-second epochs (observations) in enrolled neonates. Trained study nurses
 manually recorded HR, and the study team manually counted individual
 breaths from capnograms. For comparison, HR and respiratory rate also were
 measured using an automated signal detection algorithm. Clinical
 measurements were analyzed for repeatability.