cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n2z34tmwr
title: Associations of fully-automated CSF and novel plasma biomarkers with Alzheimer's disease neuropathology at autopsy

description: The objective of this study was to study cerebrospinal fluid
 (CSF) biomarkers of Alzheimer’s disease (AD) analyzed by fully automated
 Elecsys immunoassays in comparison to neuropathologic gold standards, and
 compare their accuracy to plasma phosphorylated tau (p-tau181) measured
 using a novel Simoa method. We studied ante-mortem Elecsys-derived CSF
 biomarkers in 45 individuals who underwent standardized post-mortem
 assessments of AD and non-AD neuropathologic changes at autopsy. In a
 subset of 26 participants, we also analysed ante-mortem levels of plasma
 p-tau181 and neurofilament light (NfL). Reference biomarker values were
 obtained from 146 amyloid-PET-negative healthy controls (HC). All
 CSF biomarkers clearly distinguished pathology-confirmed AD dementia
 (N=27) from HC (AUCs=0.86-1.00). CSF total-tau (t-tau), p-tau181, and
 their ratios with Aβ1-42, also accurately distinguished
 pathology-confirmed AD from non-AD dementia (N=8; AUCs=0.94-0.97). In
 pathology-specific analyses, intermediate-to-high Thal amyloid phases were
 best detected by CSF Aβ1-42 (AUC[95% CI]=0.91[0.81-1]), while
 intermediate-to-high CERAD neuritic plaques and Braak tau stages were best
 detected by CSF p-tau181 (AUC=0.89[0.79-0.99] and 0.88[0.77-0.99],
 respectively). Optimal Elecsys biomarker cut-offs were derived at
 1097/229/19 pg/ml for Aβ1-42, t-tau, and p-tau181. In the plasma
 subsample, both plasma p-tau181 (AUC=0.91[0.86-0.96]) and NfL
 (AUC=0.93[0.87-0.99]) accurately distinguished pathology-confirmed AD
 (N=14) from HC. However, only p-tau181 distinguished AD from non-AD
 dementia cases (N=4; AUC=0.96[0.88-1.00]), and showed a similar, though
 weaker, pathologic specificity for neuritic plaques (AUC=0.75[0.52-0.98])
 and Braak stage (AUC=0.71[0.44-0.98]) as CSF p-tau181. Elecsys-derived CSF
 biomarkers detect AD neuropathologic changes with very high discriminative
 accuracy in-vivo. Preliminary findings support the use of plasma p-tau181
 as an easily accessible and scalable biomarker of AD
 pathology. This study provides Class II evidence that
 fully-automated CSF t-tau and p-tau181measurements discriminate between
 autopsy-confirmed Alzheimer's disease and other dementias.
DOI: 10.5061/dryad.280gb5mq6
title: Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control

description: The genus Spodoptera (Lepidoptera: Noctuidae) includes some of the most
 infamous insect pests of cultivated plants including Spodoptera
 frugiperda, Spodoptera litura and Spodoptera exigua. To effectively
 develop targeted pest control strategies for diverse Spodoptera species,
 genomic resources are highly desired. To this aim, we provide the genome
 assembly and developmental transcriptome comprising all major life stages
 of S. exigua, the beet armyworm. Spodoptera exigua is a polyphagous
 herbivore that can feed from &gt; 130 host plants including several
 economically important crops. The 419 Mb beet armyworm genome was
 sequenced from a female S. exigua pupa. Using a hybrid genome sequencing
 approach (Nanopore long read data and Illumina short read), a high-quality
 genome assembly was achieved (N50=1.1 Mb). An official gene set (OGS,
 18,477 transcripts) was generated by automatic annotation and by using
 transcriptomic RNA-seq data sets of 18 S. exigua samples as supporting
 evidence. In-depth analyses of developmental stage-specific expression in
 combination with gene tree analyses of identified homologous genes across
 Lepidoptera genomes revealed four potential genes of interest (three of
 them Spodoptera-specific) upregulated during 1st and 3rd instar larval
 stages for targeted pest-outbreak management. The beet armyworm genome
 sequence and developmental transcriptome covering all major developmental
 stages provides critical insights into the biology of this devastating
 polyphagous insect pest species with a worldwide distribution. In
 addition, comparative genomic analyses across Lepidoptera significantly
 advance our knowledge to further control other invasive Spodoptera species
 and reveals potential lineage-specific target genes for pest control
 strategies.
DOI: 10.5061/dryad.hhmgqnkgr
title: Data from: Dietary stress unmasks cryptic genetic variation regulating lifespan in outbred Drosophila

description: Evolutionary theory suggests that lifespan-associated alleles should be
 purged from the gene pool, and yet decades of GWAS and model organism
 studies have shown they persist. Here, we address one potential
 explanation, the idea that the alleles that regulate lifespan do so only
 in certain contexts. We exposed thousands of outbred Drosophila
 to a standard and a high sugar diet. We then sequenced over 10,000
 individuals and track genome-wide allele frequency changes over time, as
 these populations aged. We mapped thousands of lifespan-altering alleles,
 some associated with early- vs late-life tradeoffs, late-onset effects,
 and genotype-by-environment interactions. We find that lifespan-reducing
 alleles are most likely to be recently derived and have stronger effects
 on a high-sugar diet, consistent with the hypothesis that historically
 neutral or beneficial alleles can become detrimental in novel conditions.
 We also show that the gene midway, a regulator of lipid storage and
 ortholog of the lifespan-associated gene DGAT1 in mice, also regulates
 lifespan in Drosophila. Our results provide insight into the
 highly polygenic and context-dependent genetic architecture of lifespan,
 as well as the evolutionary processes that shape this key trait.
description: There are three main data types: 
 counts of reads that mapped to the alternate and reference
 allele for each sample (data were generated through next-generation
 sequencing of individually barcoded DNA-seq libraries);
 metadata for the individually barcoded libraries;
 SNP-level summary tables (e.g., describing allele frequencies or
 other properties for various SNP sets).
description: Missing values are denoted by NA.
DOI: 10.6084/m9.figshare.31166257
title: Additional file 7 of Spatial and temporal dynamics of cancer-associated fibroblast niches in breast cancer

description: Supplementary Material 7.
DOI: 10.6084/m9.figshare.31166257.v1
title: Additional file 7 of Spatial and temporal dynamics of cancer-associated fibroblast niches in breast cancer

description: Supplementary Material 7.
DOI: 10.5061/dryad.mpg4f4r06
title: Erectile Dysfunction and Penile Rehabilitation after Pelvic Fracture – a Systematic Review and Meta-Analysis

description: Objective To investigate the rate of erectile dysfunction (ED) after
 pelvic ring fracture (PRF). Design Systematic review, and meta-analysis.
 Methods A systematic literature search of the Cochrane, EMBASE, MEDLINE,
 Scopus and Web of Science Library databases was conducted in January 2020.
 Included were original studies performed on humans assessing ED after PRF
 according the 5-item International Index of Erectile Function (IIEF-5)
 questionnaire and fracture classification following Young &
 Burgess, Tile or AO/OTA (Arbeitsgemeinschaft für Osteosynthesefragen /
 Orthopedic Trauma Association). Further, interventional cohort studies
 assessing the effect of penile rehabilitation therapy with
 phosphodiesterase-5-inhibitors (PDE-5-I) on IIEF-5 scores compared before
 and after treatment were included. Results were presented as forest plots
 of proportions of patients with ED after PRF or mean changes on IIEF-5
 questionnaires before and after penile rehabilitation. Studies not
 included in the quantitative analysis were narratively summarized. Risk of
 bias assessment was conducted using the revised tool for the Quality
 Assessment on Diagnostic Accuracy studies (QUADAS-2). Results The
 systematic literature search retrieved 617 articles. Seven articles were
 included in the qualitative analysis and the meta-analysis. Pooled
 proportions revealed 37% of patients with ED after suffering any form of
 PRF (result on probability scale pr = 0.37, 95% CI: 0.26 to 0.50).
 Patients after 3 months of penile rehabilitation therapy reported a higher
 IIEF-5 score than before (change score [CS] = 6.5 points, 95% CI: 2.54 to
 10.46, p-value = 0.0013). Conclusion Despite some heterogeneity and
 limited high quality research, this study concludes that patients
 suffering from any type of PRF have an increased risk of developing ED.
 Oral intake of PDE-5-I for the purpose of penile rehabilitation therapy
 increases IIEF-5 scores and may relevantly influence Quality of Life (QoL)
 in these patients.
DOI: 10.5061/dryad.xksn02vg4
title: Antibiotic phase transition curves

description: Phase transitions are an important and extensively studied concept in
 physics. The insights derived from understanding phase transitions in
 physics have also recently and successfully been applied to a number of
 different phenomena in biological systems. Here, we provide a brief review
 of phase transitions and their role in explaining biological processes
 ranging from collective behavior in animal flocks to neuronal firing. We
 also highlight a new and exciting area where phase transition theory is
 particularly applicable: population collapse and extinction.  We
 discuss how phase transition theory can give insight into a range of
 extinction events such as population decline due to climate change or
 microbial responses to environmental stressors such as antibiotic
 treatment.
description: This data was collected by using a BioTek Epoch 2
 spectrophotometer. The data is absorbance at OD600nm.
DOI: 10.6084/m9.figshare.31166271
title: Additional file 2 of Allogeneic MHC-mismatched microglia-like cell replacement as a therapeutic approach for multiple sclerosis

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.31166271.v1
title: Additional file 2 of Allogeneic MHC-mismatched microglia-like cell replacement as a therapeutic approach for multiple sclerosis

description: Supplementary Material 2
DOI: 10.5061/dryad.41ns1rndc
title: Food availability and long-term predation risk interactively affect antipredator response

description: Food availability and temporal variation in predation risk are both
 important determinants of the magnitude of antipredator responses, but
 their effects have rarely been examined simultaneously, particularly in
 wild prey. Here, we determine how food availability and long-term
 predation risk affect antipredator responses to acute predation risk by
 monitoring the foraging response of free-ranging snowshoe hares (Lepus
 americanus) to an encounter with a Canada lynx Lynx canadensis) in Yukon,
 Canada, over 4 winters (from 2015-2016 to 2018-2019). We examined how this
 response was influenced by natural variation in long-term predation risk
 (two-month mortality rate of hares) while providing some individuals with
 supplemental food. On average, snowshoe hares reduced foraging time up to
 10 hours after coming into close proximity (≤ 75 m) with lynx, and reduced
 foraging time an average of 15.28 ± 7.08 minutes per lynx encounter. Hares
 tended to respond more strongly when the distance to lynx was shorter.
 More importantly, the magnitude of hares’ antipredator response to a lynx
 encounter was affected by the interaction between food-supplementation and
 long-term predation risk. Food-supplemented hares reduced foraging time
 more than control hares after a lynx encounter under low long-term risk,
 but decreased the magnitude of the response as long-term risk increased.
 In contrast, control hares increased the magnitude of their response as
 long-term risk increased. Our findings show that food availability and
 long-term predation risk interactively drive the magnitude of reactive
 antipredator response to acute predation risk. Determining the factors
 driving the magnitude of antipredator responses would contribute to a
 better understanding of the indirect effects of predators on prey
 populations.
description: Snowshoe hare-lynx encounter events were identified by
 simultaneous GPS fixes, and foraging time of snowshoe hares before and
 after lynx encounter was calculated from accelerometer data. To estimate
 two-month mortality rate of control hares, we first estimated two-month
 (November-December, January-February, March-April) survival rate of
 hares for each winter using the Kaplan-Meier method accounting for
 left-truncation with <i>survival</i> package in R (Therneau
 2015), and then calculated mortality rate by subtracting survival rate
 from 1. Hares that survived were censored on the last day for each
 monitoring period (2 months), and lost hares were censored on the day they
 went missing.
DOI: 10.5061/dryad.bnzs7h4bd
title: Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition

description: When organisms experience secondary contact after allopatric divergence,
 genomic regions can introgress differentially depending on their
 relationships with adaptation, reproductive isolation, recombination, and
 drift. Analyses of genome-wide patterns of divergence and introgression
 could provide insight into the outcomes of hybridization and the potential
 relationship between allopatric divergence and reproductive isolation.
 Here, we generate population genetic data (26,262 SNPs; 353 individuals)
 using a reduced-representation sequencing approach to quantify patterns of
 ancestry, differentiation, and introgression between a pair of
 ecologically distinct mammals – the desert woodrat (N. lepida) and
 Bryant’s woodrat (N. bryanti) – that hybridize at a sharp ecotone in
 southern California. Individual ancestry estimates confirmed that hybrids
 were rare in this bimodal hybrid zone, and entirely consisted of a few
 F1 individuals and a broad range of multigenerational
 backcrosses. Genomic cline analyses indicated more than half of loci had
 elevated introgression from one genomic background into the other.
 However, introgression was not associated with relative or absolute
 measures of divergence, and loci with extreme values for both were not
 typically found near detoxification enzymes previously implicated in
 dietary specialization for woodrats. The decoupling of differentiation and
 introgression suggests that processes other than adaptation, such as
 drift, may underlie the extreme clines at this contact zone.
description: neotoma_gprobs.txt.gz -- Matrix of genotype probabilities for the
 353 individuals included in the final analyses. First column contains
 individual ids. The file has been compressed with gzip.
 neotoma_fastqs.tar.gz -- Directory containing fastq files for all
 383 individuals analyzed in the paper. This directory has been compressed
 as a tar archive.
DOI: 10.6084/m9.figshare.31166275
title: Additional file 5 of Computational decoding of cell-cycle phase effects on cancer hallmarks across breast cancer subtypes

description: Additional file 5 (XLSX 546 KB)
DOI: 10.6084/m9.figshare.31166275.v1
title: Additional file 5 of Computational decoding of cell-cycle phase effects on cancer hallmarks across breast cancer subtypes

description: Additional file 5 (XLSX 546 KB)
DOI: 10.6084/m9.figshare.31166278
title: Additional file 6 of Computational decoding of cell-cycle phase effects on cancer hallmarks across breast cancer subtypes

description: Additional file 6 (XLSX 34 KB)
DOI: 10.6084/m9.figshare.31166278.v1
title: Additional file 6 of Computational decoding of cell-cycle phase effects on cancer hallmarks across breast cancer subtypes

description: Additional file 6 (XLSX 34 KB)
DOI: 10.5061/dryad.p5hqbzkpn
title: Selection in males purges the mutation load on female fitness

description: Theory predicts that the ability of selection and recombination to purge
 mutation load is enhanced if selection against deleterious genetic
 variants operates more strongly in males than females. However, direct
 empirical support for this tenet is limited, in part because traditional
 quantitative genetic approaches allow dominance and intermediate-frequency
 polymorphisms to obscure the effects of the many rare and partially
 recessive deleterious alleles that make up the main part of a population’s
 mutation load. Here, we exposed the partially recessive genetic load of a
 population of Callosobruchus maculatus seed beetles via successive
 generations of inbreeding, and quantified its effects by measuring
 heterosis – the increase in fitness experienced when masking the effects
 of deleterious alleles by heterozygosity – in a fully factorial
 sex-specific diallel cross among 16 inbred strains. Competitive lifetime
 reproductive success (i.e. fitness) was measured in male and female
 outcrossed F1s as well as inbred parental ‘selfs’, and we estimated the
 4×4 male-female inbred-outbred genetic covariance matrix for fitness using
 Bayesian Markov chain Monte Carlo simulations of a custom-made general
 linear mixed effects model. We found that heterosis estimated
 independently in males and females was highly genetically correlated among
 strains, and that heterosis was strongly negatively genetically correlated
 to outbred male, but not female, fitness. This suggests that genetic
 variation for fitness in males, but not in females, reflects the amount of
 (partially) recessive deleterious alleles segregating at
 mutation-selection balance in this population. The population’s mutation
 load therefore has greater potential to be purged via selection in males.
 These findings contribute to our understanding of the prevalence of sexual
 reproduction in nature and the maintenance of genetic variation in
 fitness-related traits.
description: See Methods
description: All analyses, procedures, figures and tables can be reproduced
 using the provided data and R scripts (annotated with
 instructions).
DOI: 10.5061/dryad.34tmpg4k7
title: Emergence of structures from parasitic species in a spatially distributed molecular system

description: This dataset contains microscopy images from a microfluidic setup
 implementing a localized autocatalytic molecular system based on
 the PEN DNA toolbox. Due to the enzymatic nature of the catalytic process,
 a variety of parasitic species eventually emerge and compete with the
 legitimate molecular process for fuel. The behaviors observed range from
 the creation of large stable structures to that of small diffusing
 particles. Those results, along with the modularity of the molecular
 system, show that the proposed experimental setup can be used safely for
 further study of the evolution of parasitic behaviors at the molecular
 scale.
description: Reaction chambers were kept at 42C and monitored by an Olympus
 IX71 inverted microscope. <br> We used two fluorescence sources:
 EvaGreen, a non-specific DNA-binding dye attaching to double-stranded
 species and Atto633 (red fluorophore, attached to minority
 beads). We used an XY stage to take pictures of 30
 regions of interest (10 per experimental settings) at 5-minute intervals.
 The regions of interest were manually selected by using the Atto633
 fluorescence. We picked regions with at least one minority bead and 2 or
 more majority beads in close proximity to trigger a reasonably sized zone
 of enzymatic activity.
description: It is recommended to use a software like Fiji to enhance the raw
 images.
DOI: 10.6084/m9.figshare.31166310
title: Additional file 3 of Unveiling dental diagnostic dilemmas: a national survey of US dentists

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.31166310.v1
title: Additional file 3 of Unveiling dental diagnostic dilemmas: a national survey of US dentists

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.31166311
title: Additional file 1 of Transporters, an important but poorly studied area of Toxoplasma gondii

description: Supplementary material 1. Additional file 1. Potential transporters screened out from ToxoDB
DOI: 10.6084/m9.figshare.31166311.v1
title: Additional file 1 of Transporters, an important but poorly studied area of Toxoplasma gondii

description: Supplementary material 1. Additional file 1. Potential transporters screened out from ToxoDB
DOI: 10.5061/dryad.wwpzgmsk0
title: Lack of lipid accumulation in two species of Chalcidoid wasps with secondarily evolved phytophagy

description: Stable co-evolutionary relationships between species can result in the
 loss of autonomous synthesis of essential nutrients when these can be
 obtained from the ecological partner. Parasitoid insects obtain the
 majority of their nutrients from their host, and contain multiple,
 independently-evolved lineages that do not increase their adult lipid
 reserves despite feeding on a surplus of dietary sugars, although some
 parasitoid species in these lineages were found to have reactivated adult
 lipogenesis. Several clades within the parasitoid insects have lost the
 parasitoid lifestyle and switched to either a predatory or a phytophagous
 lifestyle. Here, we test whether adult lipid accumulation is reactivated
 in two species that independently evolved a phytophagous lifestyle from
 parasitoid ancestors. The larvae of Megastigmus aculeatus (Hymenoptera:
 Chalcidoidea: Torymidae) and Bruchophagus platypterus (Hymenoptera:
 Chalcidoidea: Eurytomidae) obligatorily feed on seeds of specific plants.
 Seeds of wild host plants were collected and the emerging wasps were
 tested for their lipogenic abilities by comparing their lipid content upon
 emergence and after feeding on sugar. The lipid content of both species
 after ad libitum access to sugars was equal to or lower than at emergence,
 indicating lack of lipogenesis. Therefore the secondary switch to
 phytophagy was not associated with recovery of lipid accumulation in these
 species. We discuss these results in relation to the lipid content of the
 host seeds and the reversibility of the lipid accumulation phenotype. We
 infer that the close relationship between seed-feeding insects and their
 hosts allow the seed-feeders to rely on a predictable amount of lipids in
 their diet which relaxes the need for autonomous lipid synthesis.
DOI: 10.5061/dryad.gb5mkkwpw
title: DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species: supplementary data and code

description: Alternative pathways of energy transfer guarantee the functionality and
 productivity in marine food webs that experience strong
 seasonality. Nevertheless, the complexity of zooplankton
 interactions is rarely considered in trophic studies because of the lack
 of detailed information about feeding interactions in nature. In this
 study, we used DNA metabarcoding to highlight the diversity of trophic
 niches in a wide range of micro- and mesozooplankton including ciliates,
 rotifers, cladocerans, copepods, and their prey, by
 sequencing 16- and 18S rRNA genes. Our study demonstrates that the zooplankton trophic niche partitioning goes beyond both phylogeny and size and reinforces the importance of diversity in resource use for stabilizing food web efficiency by allowing for several different pathways of energy transfer. We further highlight that small rarely studied zooplankton (rotifers and ciliates) fill an important role in the pathways of the Baltic Sea pelagic primary production, and the potential of ciliates, rotifers, and crustaceans in the utilization of filamentous and picocyanobacteria within the pelagic food web. The approach used in this study is a suitable entry point to ecosystem-wide food web modeling considering species-specific resource use of key consumers.
description: For information on sampling and analysis, see
 DOI: 10.1098/rspb.2021.0908