cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.14004q5
title: Data from: Ictal quantitative surface electromyography correlates with postictal EEG suppression

description: Objective: To test the hypothesis that neurophysiological biomarkers of
 muscle activation during convulsive seizures reveal seizure severity, and
 to determine whether automatically computed surface electromyography (EMG)
 parameters during seizures can predict postictal generalized EEG
 suppression (PGES) indicating increased risk for sudden unexpected death
 in epilepsy (SUDEP). Wearable EMG devices have been clinically validated
 for automated detection of generalized tonic-clonic seizures (GTCS). Our
 goal was to use automated EMG measurements for seizure-characterization
 and risk-assessment. Methods: Quantitative parameters were automatically
 computed from surface EMG recorded during convulsive seizures, from
 deltoid and brachial biceps muscles, in patients admitted to long-term
 video-EEG monitoring. Parameters evaluated were: the durations of the
 seizure phases (tonic, clonic), durations of the clonic bursts and silent
 periods, as well as the dynamics of their evolution (slope). We compared
 them with the duration of the PGES. Results: We found significant
 correlations between automatically computed EMG parameters and the
 duration of PGES (p&lt;0.001). Stepwise multiple regression analysis
 identified as independent predictors, in deltoid muscle the duration of
 the clonic phase, and in biceps muscle the duration of the tonic-clonic
 phases, the average silent period, and the slopes of the silent period and
 clonic bursts. An algorithm constructed from these parameters identified
 seizures at increased risk (PGES ≥20s) with an accuracy of 87%.
 Conclusions: Automatically computed ictal EMG parameters correlate with
 PGES and may identify seizures at high risk. Classification of Evidence:
 This study provides Class II evidence that quantitative ictal EMG
 parameters are biomarkers for high-risk convulsive seizures.
description: Supplementary material
 1 Number of seizures with
 long and short PGES (20 seconds threshold) according to seizure
 type   
 Supplementary material
 2 Number of seizures with
 long or short PGES (20 seconds threshold) according to seizure type and
 the presence of oral tonicity     <strong>Supplementary material 3</strong>   PGES duration in patients with single vs multiple seizures   Supplementary material 4 Supplementary material 4: analyses using for each patient average values from all recorded seizures   PGES, seizures Raw data containing patient and seizure ID, seizure type (0 - nonGTCS, 1 - GTCS type 1, 2 - GTCS type 2, 3 - GTCS type 3) and PGES duration (obtained as average of the visual measurements)   P1.1 - P42 EDF containing seizure and postictal phase
DOI: 10.5061/dryad.j008j5h
title: Data from: Macroevolutionary analyses suggest that environmental factors, not venom apparatus, play key role in Terebridae marine snail diversification

description: How species diversification occurs remains an unanswered question in
 predatory marine invertebrates, such as sea snails of the family
 Terebridae. However, the anatomical disparity found throughput the
 Terebridae provides a unique perspective for investigating diversification
 patterns in venomous predators. In this study, a new dated molecular
 phylogeny of the Terebridae is used as a framework for investigating
 diversification of the family through time, and for testing the putative
 role of intrinsic and extrinsic traits, such as shell size, larval
 ecology, bathymetric distribution, and anatomical features of the venom
 apparatus, as drivers of terebrid species diversification.
 Macroevolutionary analysis revealed that when diversification rates do not
 vary across Terebridae clades, the whole family has been increasing its
 global diversification rate since 25 Ma. We recovered evidence for a
 concurrent increase in diversification of depth ranges, while shell size
 appeared to have undergone a fast divergence early in terebrid
 evolutionary history. Our data also confirm that planktotrophy is the
 ancestral larval ecology in terebrids, and evolutionary modeling
 highlighted that shell size is linked to larval ecology of the Terebridae,
 with species with long-living pelagic larvae tending to be larger and have
 a broader size range than lecithotrophic species. Although we recovered
 patterns of size and depth trait diversification through time and across
 clades, the presence or absence of a venom gland (VG) did not appear to
 have impacted Terebridae diversification. Terebrids have lost their venom
 apparatus several times and we confirm that the loss of a VG happened in
 phylogenetically clustered terminal taxa and that reversal is extremely
 unlikely. Our findings suggest that environmental factors, and not venom,
 have had more influence on terebrid evolution.
DOI: 10.5061/dryad.69qg1c0
title: Data from: ApoE is a correlate of phenotypic heterogeneity in Alzheimer’s disease in a national cohort

description: Objective: To compare the proportion of APOEε4 genotype carriers in
 aphasic versus amnestic variants of Alzheimer’s disease (AD). Method: The
 proportion of APOEε4 carriers was compared among 3 groups. 1) Forty-two
 patients with primary progressive aphasia (PPA) and AD pathology (PPA/AD)
 enrolled in the Northwestern Alzheimer Disease Center Clinical Core. 2)
 1,418 patients with autopsy confirmed AD and amnestic dementia of the
 Alzheimer-type (DAT/AD); 3) 2,608 cognitively normal controls (NC). The
 latter two groups were compiled from the National Alzheimer Coordinating
 Center (NACC) database. Logistic regression models analyzed the
 relationship between groups and APOEε4 carrier status, adjusting for age
 of onset and sex as needed. Results: Using NC as the reference and
 adjusting for sex and age, the DAT/AD group was 3.97 times more likely to
 be APOEε4 carriers. Adjusting for sex and age at symptom onset, the DAT/AD
 group was 2.46 times as likely to be carriers compared to PPA/AD. There
 was no significant difference in the proportion of APOEε4 carriers for
 PPA/AD compared to NC. PPA subtypes included 24 logopenic, 10 agrammatic
 nonfluent, and eight either mixed (n=5) or too severe (n=3) to subtype.
 The proportion of carriers and non carriers was similar for logopenic and
 agrammatic subtypes, both having fewer carriers. Conclusion: The
 proportion of APOEε4 carriers was elevated in amnestic but not aphasic
 manifestations of AD. These results suggest that APOEε4 is an anatomically
 selective risk factor that preferentially increases the vulnerability to
 AD pathology of memory-related medial temporal areas rather that
 language-related neocortices.
description: APOE4 PPA Supplementary
 Materials 04-08-19This file contains
 information about additional data analysis that was completed in response
 to reviewer's comments but not necessary to include in the
 manuscript. There are tables reporting the age makeup of the samples and
 also an analysis using a matched sample technique that showed no
 differences from the original analysis in which the samples were not
 matched and sample numbers were uneven.
DOI: 10.5061/dryad.n80c2g0
title: Data from: Sleep duration, midday napping and sleep quality and incident stroke: the Dongfeng-Tongji cohort

description: Objective: To investigate the associations of sleep duration, midday
 napping and sleep quality, and change in sleep duration with risk of
 incident stroke and stroke subtypes. Methods: Among 31750 participants
 aged 61.7 years on average at baseline from the Dongfeng-Tongji cohort, we
 used Cox regression models to estimate hazard ratios (HRs) and 95%
 confidence intervals (CIs) for incident stroke. Results: Compared with
 sleeping 7-&lt;8 h/night, those reporting longer sleep duration (≥9
 h/night) had a greater risk of total stroke (HR, 1.23; 95% CI, 1.07-1.41),
 while shorter sleep (&lt;6 h/night) had no significant effect on
 stroke risk. The HR (95% CI) of total stroke was 1.25 (1.03-1.53) for
 midday napping &gt;90 min vs 1-30 min. The results were similar for
 ischemic stroke. Compared with good sleep quality, those with poor sleep
 quality showed a 29%, 28% and 56% higher risk of total, ischemic, and
 hemorrhagic stroke, respectively. Moreover, we observed significant joint
 effects of sleeping ≥9 h/night and midday napping &gt;90 min (HR,
 1.85; 95% CI, 1.28-2.66), and sleeping ≥9 h/night and poor sleep quality
 (HR, 1.82; 95% CI, 1.33-2.48) on risks of total stroke. Furthermore,
 compared with persistently sleeping 7-9 h/night, those persistently slept
 ≥9 h/night or switched from 7-9 h to ≥9 h/night had a higher risk of total
 stroke. Conclusions: Long sleep duration, long midday napping and poor
 sleep quality were independently and jointly associated with higher risks
 of incident stroke. Persistently long sleep duration or switch from
 average to long sleep duration increased the risk of stroke.
description: Supplemental
 data_revised_20190626
DOI: 10.5061/dryad.6nq98f5
title: Data from: Burrowing detritivores regulate nutrient cycling in a desert ecosystem

description: Nutrient cycling in most terrestrial ecosystems is thought to be
 controlled by moisture-dependent decomposer activity. In arid ecosystems,
 plant litter cycling exceeds rates predicted based on precipitation
 amounts, suggesting that additional factors are involved in these systems.
 Attempts to reveal these factors have predominantly focused on abiotic
 degradation, precipitation frequency, soil-litter mixing, and alternative
 moisture sources. Our aim was to explore an additional hypothesis that
 macro-detritivores control litter cycling in deserts. We quantified the
 role different organisms play in clearing plant detritus from the desert
 surface, using litter-baskets with different mesh sizes that allow
 selective entry of micro-, meso- or macro-fauna. We also measured soil
 nutrient concentrations in increasing distances from the burrows of a
 highly abundant macro-detritivore, the desert isopod Hemilepistus
 reaumuri, in the field and in laboratory microcosms. Macro-detritivores
 controlled the clearing of plant litter in our field site. The highest
 rates of litter removal were measured during the hot and dry summer when
 isopod activity peaks and microbial activity is minimal. We also found
 substantial enrichment of inorganic nitrogen and phosphorous in the
 vicinity of isopod burrows. We conclude that burrowing macro-detritivores
 are important regulators of litter cycling in this arid ecosystem,
 providing a plausible general mechanism that explains the unexpectedly
 high rates of plant-litter cycling in deserts.
description: The contribution of
 macro-detritivores to surface litter removalData used in analysis of
 the litter baskets experiment.Soil characteristics
 around isopod burrows in the fieldData used in analysis of
 soil characteristics around isopod burrows.Nitrogen distribution
 around isopod burrows - laboratory microcosmsData used in analysis of
 lab microcosms experiment
DOI: 10.5061/dryad.23h5195
title: Data from: Genome duplication effects on functional traits and fitness are genetic context and species dependent: studies of synthetic polyploid Fragaria

description: PREMISE OF THE STUDY Divergence in functional traits and adaptive
 responses to environmental change underlies the ecological advantage of
 polyploid plants in the wild. While established polyploids may benefit
 from combined outcomes of genome doubling, hybridization and
 polyploidy-enabled adaptive evolution, it remains less clear whether
 genome doubling alone can drive ecological divergence or whether the
 outcome is genetically variable.METHODS Using synthetic,
 colchicine-induced, autotetraploid (4x) plants derived from
 self-pollinated diploid (2x) seeds, and their colchicine-treated but
 unconverted diploid (2x.nc) full sibs from two diploid wild strawberry
 taxa (Fragaria vesca ssp. vesca and F. vesca ssp. bracteata), we examined
 the effects of genome doubling on functional traits, heat stress tolerance
 and fitness components across taxa and maternal families (i.e. genetic
 families) within taxa.KEY RESULTS Comparisons between 2x and 2x.nc plants
 indicated a negligible effect of colchicine treatment on functional
 traits. Genome doubling increased stomatal length, and decreased stomatal
 density, specific leaf area and leaf vein density, recapitulating patterns
 observed in wild polyploid Fragaria. Trichome density, heat stress
 tolerance and relative growth rate were not significantly affected by
 genome doubling. Although a reduction in clonal reproduction was observed
 in response to genome doubling, this effect was strongly genetic family
 dependent.CONCLUSIONS The results suggest that genome doubling during
 incipient speciation alone can generate ecological divergence and
 variation among genetic lineages. This response potentially allows for
 rapid short-term evolutionary adaptation and fuels genomic diversity and
 independent origins of polyploidy.
description: Wei_AJB_data
DOI: 10.5061/dryad.gv57c8j
title: Data from: Functional connectivity and structural analysis of trial spinal cord stimulation responders in failed back surgery syndrome

description: [No abstract provided]
description: sub01_restsub02_restsub03_restsub04_restsub05_restsub06_restsub08_restsub09_restsub10_restsub11_rest
DOI: 10.5061/dryad.kp8pb51
title: Data from: Targeted next-generation sequencing panels in the diagnosis of Charcot Marie Tooth disease

description: Objective: To investigate the effectiveness of targeted NGS panels in
 achieving a molecular diagnosis in CMT and related disorders in a clinical
 setting Methods: We prospectively enrolled 220 patients from two tertiary
 referral centres, one in London, UK (n=120) and one in Iowa, US (n=100) in
 whom a targeted CMT NGS panel had been requested as a diagnostic test.
 PMP22 duplication/deletion was previously excluded in demyelinating cases.
 We reviewed the genetic and clinical data upon completion of the
 diagnostic process. Results: After targeted NGS sequencing a definite
 molecular diagnosis, defined as a pathogenic or likely pathogenic variant,
 was reached in 30% of cases (n=67). The diagnostic rate was similar in
 London (32%) and Iowa (29%). Variants of unknown significance were found
 in an additional 33% of cases. Mutations in GJB1, MFN2, MPZ accounted for
 39% of cases who received genetic confirmation, while the remainder of
 positive cases had mutations in diverse genes, including SH3TC2, GDAP1,
 IGHMBP2, LRSAM1, FDG4, GARS and another 12 less common genes. Copy number
 changes in PMP22, MPZ, MFN2, SH3TC2 and FDG4 were also accurately
 detected. A definite genetic diagnosis was more likely in cases with an
 early onset, a positive family history of neuropathy or consanguinity and
 a demyelinating neuropathy. Conclusions: NGS panels are effective tools in
 the diagnosis of CMT leading to the genetic confirmation in one third
 cases negative for PMP22 duplication/deletion, thus highlighting how rarer
 and previously undiagnosed subtypes represent today a relevant part of the
 genetic landscape of CMT.
description: Supplementary_table_1-2-3_31.01.2022 Supplementary Tables 1-3
DOI: 10.5061/dryad.4913978
title: Data from: Dynamic expressions of hypothalamic genes regulate seasonal breeding in a natural rodent population

description: Seasonal breeding is a universal reproductive strategy in many animals.
 Hypothalamic genes, especially type 2 and 3 iodothyronine deiodinases
 (Dio2/3), RFamide-related peptide 3 (Rfrp-3), kisspeptin (Kiss-1), and
 gonadotropin-releasing hormone (GnRH), are involved in a photoperiodic
 pathway that encodes seasonal signals from day length in many vertebrate
 species. However, the seasonal expression patterns of these genes in wild
 mammals are less studied. Here, we present a four-year field investigation
 to reveal seasonal rhythm and age-dependent reproductive activity in male
 Brandt’s voles (Lasiopodomys brandtii) and to detect relationships among
 seasonal expression profiles of hypothalamic genes, testicular activity,
 age, and annual day length. From breeding season (April) to non-breeding
 season (October), adult male voles displayed a synchronous peak in gonadal
 activity with annual day length around summer solstice, which was jointly
 caused by age structure shifts and age-dependent gonadal development
 patterns. Overwintered males maintained reproductive activity until late
 in the breeding season, whereas most newborn males terminated gonadal
 development completely, except for a minority of males born early in
 spring. Consistently, the synchronous and opposite expression profiles of
 Dio2/3 suggest their central function to decode photoperiodic signals and
 to predict the onset of the non-breeding season. Moreover, changes in
 Dio2/3 signals may guide the actions of Kiss-1 and Rfrp-3 to regulate the
 age-dependent divergence of reproductive strategy in wild Brandt’s vole.
 Our results provide evidence on how hypothalamic photoperiod genes
 regulate seasonal breeding in a natural rodent population.
description: Data for seasonal
 breeding of Brandt's voleData in this file
 contain all data to make the figures and tables and to do analysis in this
 paper, including seasonal variatoins of age structure, body mass, gonadal
 mass, testosterone, hypothalamic gene expression.
DOI: 10.5061/dryad.3h1d321
title: Data from: Effect of organic matters on anammox coupled denitrification system: when nitrite nitrogen was sufficient

description: Anaerobic ammonia oxidation (ANAMMOX) and denitrification can work
 together to weaken the influence of organic matter on anaerobic ammonia
 oxidation bacteria (AAOB) and improve nitrogen removal performance. As the
 common substrate of ANAMMOX and denitrification, nitrite nitrogen will
 also affect nitrogen removal performance when it is insufficient, which is
 not conducive to reflect the endurance of ANAMMOX reactor to organic
 matter. The UASB continuous flow experiment was carried out to investigate
 the effect of the concentration of glucose and sodium acetate on nitrogen
 removal performance of ANAMMOX reactor under the condition of sufficient
 nitrite nitrogen. With glucose as the organic matter, when the COD
 concentration increased to 200 mg/L, nitrogen removal performance of the
 system began to decrease significantly, and the anammox activity was
 significantly inhibited. With sodium acetate as the organic substance, the
 anammox activity was affected when the COD was 20 mg/L. Adequate nitrite
 nitrogen could relieve the inhibition of the coupling system by a low
 concentration (COD&lt;200mg/L) of glucose organic matter. However, it
 could not relieve the inhibitory effect of sodium acetate. With the
 increase of organic concentration, the biological density of AAOB in
 granular sludge gradually decreased, while the biological density of
 denitrifying bacteria increased gradually.
description:
DOI: 10.5061/dryad.230s5h0
title: Data from: Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation in BEAST

description: Markov models of character substitution on phylogenies form the foundation
 of phylogenetic inference frameworks. Early models made the simplifying
 assumption that the substitution process is homogeneous over time and
 across sites in the molecular sequence alignment. While standard practice
 adopts extensions that accommodate heterogeneity of substitution rates
 across sites, heterogeneity in the process over time in a site-specific
 manner remains frequently overlooked. This is problematic, as evolutionary
 processes that act at the molecular level are highly variable, subjecting
 different sites to different selective constraints over time, impacting
 their substitution behaviour. We propose incorporating time variability
 through Markov-modulated models (MMMs), which extend covarion-like models
 and allow the substitution process (including relative character exchange
 rates as well as the overall substitution rate) at individual sites to
 vary across lineages. We implement a general MMM framework in BEAST, a
 popular Bayesian phylogenetic inference software package, allowing
 researchers to compose a wide range of MMMs through flexible XML
 specification. Using examples from bacterial, viral and plastid genome
 evolution, we show that MMMs impact phylogenetic tree estimation and can
 substantially improve model fit compared to standard substitution models.
 Through simulations, we show that marginal likelihood estimation
 accurately identifies the generative model and does not systematically
 prefer the more parameter-rich MMMs. To mitigate the increased
 computational demands associated with MMMs, our implementation exploits
 recent developments in BEAGLE, a high-performance computational library
 for phylogenetic inference.
description: 16 data files
 accompanying main manuscript All 16 data files
 accompanying our submitted Markov-modulated model manuscript: the
 supplementary text in PDF format, 5 nexus files and 10 BEAST 1.10 XML
 files. Baele_et_al-AllDataFiles.zip
DOI: 10.5061/dryad.tf8440h
title: Data from: Long-term employment outcomes after epilepsy surgery in childhood

description: Objective: To analyse long-term employment outcomes in a population-based
 cohort of adults who underwent epilepsy surgery in childhood or
 adolescence and to compare the results to general population reference
 data. Methods: Prospective data on epilepsy surgery procedures performed
 on patients &lt;19 years of age between 1995 and 2012 were extracted
 from the Swedish National Epilepsy Surgery Register. Five-, 10-, 15- and
 20-year follow-up data were analysed. Patients aged ≥19 years at follow-up
 were eligible for inclusion. Educational attainment and employment status
 were analysed in relation to seizure outcome. Education and employment
 outcomes of seizure-free patients with a preoperative IQ of ≥70 were
 compared to general population reference data. Results: A total of 203
 patients were included. The mean age at surgery was 13.6 years and 66% had
 IQ≥70. Of these, a majority had attained at least high school education
 five years after surgery. Employment rates were 44%, 69%, 71% and 77% at
 the 5-, 10-, 15- and 20-year follow-ups, respectively. Seizure-free
 patients were significantly more likely to work full-time. Educational
 attainment and rates of full-time employment of seizure-free patients were
 similar to the general population. A majority of patients with
 IQ&lt;70 had attended special education and were reliant on social
 benefits. Conclusion: Long-term overall employment rates were higher
 compared to most previous studies on surgery in adults. Seizure-free
 patients with a preoperative IQ≥70 showed rates of full-time employment
 similar to the general population. Further research is needed to determine
 whether this also applies for occupational complexity and wages.
description: Baseline characteristics
 of included and lost patients at each follow-upThis table (excel file)
 contains detailed baseline characteristics of included and lost patients
 at the five, 10, 15 and 20-year follow-ups including tests for
 significance. There is also a legend detailing the statistical tests used
 and explaining all acronyms.Table
 e1.xlsx