cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4067r78
title: Data from: Cyclin dependent kinase 5 (CDK5) regulates the circadian clock

description: Circadian oscillations emerge from transcriptional and post-translational
 feedback loops. An important step in generating rhythmicity is the
 translocation of clock components into the nucleus, which is regulated in
 many cases by kinases. In mammals, the kinase promoting the nuclear import
 of the key clock component Period 2 (PER2) is unknown. We observed that
 the cyclin-dependent kinase 5 (CDK5) regulates the mammalian clock
 involving phosphorylation of PER2. Knock-down of Cdk5 in the
 suprachiasmatic nuclei (SCN), the main coordinator site of the mammalian
 circadian system, shortened the free-running period in mice. CDK5
 phosphorylated PER2 at serine 394 (S394) in a diurnal fashion. This
 facilitated interaction with Cryptochrome 1 (CRY1) and nuclear entry of
 the PER2-CRY1 complex. Taken together, we found that CDK5 drives nuclear
 entry of PER2, which is critical for establishing an adequate circadian
 period of the circadian cycle. Therefore, CDK5 is critically involved in
 the regulation of the circadian clock.
description: Source data In the excel file all the raw
 data is provided in each tab labeled with the figure number of the
 manuscript.
DOI: 10.5061/dryad.n1qq6v3
title: Data from: Diet-based assortative mating through sexual imprinting

description: Speciation is facilitated by ‘magic traits’, where divergent natural
 selection on such traits also results in non-random mating. In animal
 populations, diet is a potential magic trait because selection for
 divergence in consumed food may contribute to assortative mating and
 therefore sexual isolation. However, the mechanisms causing positive
 diet-based assortment are largely unknown. Here, using diet manipulations
 in a sexually imprinting species of mouse, Peromyscus gossypinus (the
 cotton mouse), we tested the hypothesis that sexual imprinting on
 divergent diets could be a mechanism that generates rapid and significant
 sexual isolation. We provided breeding pairs with novel garlic- or
 orange-flavored water and assessed whether their offspring, exposed to
 these flavors in utero and in the nest before weaning, later preferred
 mates that consumed the same flavored water as their parents. While males
 showed no preference, females preferred males of their parental diet,
 which is predicted to yield moderate sexual isolation. Thus, our
 experiment demonstrates that sexual imprinting on dietary cues learned in
 utero and/or postnatally could facilitate reproductive isolation and
 potentially speciation.
description: Diet behavioral trial
 dataThese data are from
 trials with P. gossypinus in an electronically-gated mate choice assay.
 Choosers and stimulus mice were raised on garlic- or orange-flavored
 water, and tested for preferences for these mice. (Unflavored water was
 used during the trials).Diet_data_supplement_forDryad.csv
DOI: 10.5061/dryad.h8t823r
title: Data from: Molecular biogeography and host relations of a parasitoid fly

description: Successful geographic range expansion by parasites and parasitoids may
 also require host range expansion. Thus the evolutionary advantages of
 host specialization may trade off against the ability to exploit new host
 species encountered in new geographic regions. Here we use molecular
 techniques and confirmed host records to examine biogeography, population
 divergence, and host flexibility of the parasitoid fly, Ormia ochracea
 (Bigot). Gravid females of this fly find their cricket hosts acoustically
 by eavesdropping on male cricket calling songs; these songs vary greatly
 among the known host species of crickets. Using both nuclear and
 mitochondrial genetic markers, we (1) describe the geographical
 distribution and sub-division of genetic variation in O. ochracea from
 across the continental United States, the Mexican states of Sonora and
 Oaxaca, and populations introduced to Hawaii; (2) demonstrate that the
 distribution of genetic variation among fly populations is consistent with
 a single widespread species with regional host specialization, rather than
 locally differentiated cryptic species, (3) identify the more-probable
 source populations for the flies introduced to the Hawaiian islands; (4)
 examine genetic variation and sub-structure within Hawaii; (5) show that
 among-population geographic, genetic, and host song distances are all
 correlated, and (6) discuss specialization and lability in host-finding
 behavior in light of the diversity of cricket songs serving as host cues
 in different geographically separate populations.
description: Song Distance Matrix
 CalculationExample of calculation
 of a song distance matrix, from raw data.
DOI: 10.5061/dryad.0g22962
title: Data from: Density-dependence and persistence of Morogoro arenavirus transmission in a fluctuating population of its reservoir host

description: Background A key aim in wildlife disease ecology is to understand how host
 and parasite characteristics influence parasite transmission and
 persistence. Variation in host population density can have strong impacts
 on transmission and outbreaks, and theory predicts particular
 transmission-density patterns depending on how parasites are transmitted
 between individuals. Here, we present the results of a study on the
 dynamics of Morogoro arenavirus in a population of multimammate mice
 (Mastomys natalensis). This widespread African rodent, which is also the
 reservoir host of Lassa arenavirus in West Africa, is known for its strong
 seasonal density fluctuations driven by food availability. Goal We
 investigated to what degree virus transmission changes with host
 population density and how the virus might be able to persist during
 periods of low host density. Methods A seven-year capture-mark-recapture
 study was conducted in Tanzania where rodents were trapped monthly and
 screened for the presence of antibodies against Morogoro virus. Observed
 seasonal seroprevalence patterns were compared with those generated by
 mathematical transmission models to test different hypotheses regarding
 the degree of density-dependence and the role of chronically infected
 individuals. Results We observed that Morogoro virus seroprevalence
 correlates positively with host density with a lag of one to four months.
 Model results suggest that the observed seasonal seroprevalence dynamics
 can be best explained by a combination of vertical and horizontal
 transmission, and that a small number of animals needs to be infected
 chronically to ensure viral persistence. Broad context Transmission
 dynamics and viral persistence were best explained by the existence of
 both acutely and chronically infected individuals, and by seasonally
 changing transmission rates. Due to the presence of chronically infected
 rodents, rodent control is unlikely to be a feasible approach for
 eliminating arenaviruses such as Lassa virus from Mastomys populations.
description: serology data Mastomys
 natalensis CMR MorogoroThis is all the data
 needed to calculate the monthly seroprevalence as analysed in the main
 article. Each line corresponds to an individual Mastomys natalensis that
 was captured in the field in Morogoro (Tanzania). Although not used in
 this article, information about the individual sex, body weight,
 reproductive and recapture state is available upon reasonable request
 (email: herwig.leirs@uantwerpen.be).MN serology data CMR
 Morogoro_19_08_2019.txt
DOI: 10.5281/zenodo.18393556
title: FARG'ONA VILOYATIDA EKOLOGIK OMILLARNING QARISH JARAYONIGA TA'SIRI

description: Ushbu maqolada Farg‘ona viloyati sharoitida yashash muhitining asosiy komponentlari — atmosfera havosi, ichimlik suvi va tuproqning gigiyenik holati inson organizmida qarish jarayoniga ko‘rsatadigan ta’siri ilmiy-nazariy va amaliy jihatdan tahlil qilindi. Tadqiqotda ekologik omillarning qarish mexanizmlariga ta’siri (oksidlovchi stress, surunkali yallig‘lanish, metabolik buzilishlar, yurak-qon tomir va nafas tizimi kasalliklari kuchayishi) yoritildi. Shuningdek, hududiy xususiyatlar nuqtayi nazaridan shahar va qishloq muhitida ustuvor xavf omillari farqlanishi asoslandi. Natijalar shuni ko‘rsatadiki, shahar hududlarida atmosfera havosining ifloslanishi va shovqin darajasi, qishloq hududlarida esa ichimlik suvi sifati keksalar salomatligi va erta qarish jarayoniga sezilarli ta’sir ko‘rsatadi. Tuproqning pestitsidlar va agroximikatlar bilan ifloslanishi oziq-ovqat zanjiri orqali organizmga kirib, surunkali intoksikatsiya va endokrin-metabolik buzilishlar orqali qarish tezligini oshirishi mumkin. Olingan xulosalar faol uzoq umrni ta’minlash bo‘yicha hududiy profilaktik dasturlarni ishlab chiqishda amaliy ahamiyatga ega.
DOI: 10.5281/zenodo.18393555
title: FARG'ONA VILOYATIDA EKOLOGIK OMILLARNING QARISH JARAYONIGA TA'SIRI

description: Ushbu maqolada Farg‘ona viloyati sharoitida yashash muhitining asosiy komponentlari — atmosfera havosi, ichimlik suvi va tuproqning gigiyenik holati inson organizmida qarish jarayoniga ko‘rsatadigan ta’siri ilmiy-nazariy va amaliy jihatdan tahlil qilindi. Tadqiqotda ekologik omillarning qarish mexanizmlariga ta’siri (oksidlovchi stress, surunkali yallig‘lanish, metabolik buzilishlar, yurak-qon tomir va nafas tizimi kasalliklari kuchayishi) yoritildi. Shuningdek, hududiy xususiyatlar nuqtayi nazaridan shahar va qishloq muhitida ustuvor xavf omillari farqlanishi asoslandi. Natijalar shuni ko‘rsatadiki, shahar hududlarida atmosfera havosining ifloslanishi va shovqin darajasi, qishloq hududlarida esa ichimlik suvi sifati keksalar salomatligi va erta qarish jarayoniga sezilarli ta’sir ko‘rsatadi. Tuproqning pestitsidlar va agroximikatlar bilan ifloslanishi oziq-ovqat zanjiri orqali organizmga kirib, surunkali intoksikatsiya va endokrin-metabolik buzilishlar orqali qarish tezligini oshirishi mumkin. Olingan xulosalar faol uzoq umrni ta’minlash bo‘yicha hududiy profilaktik dasturlarni ishlab chiqishda amaliy ahamiyatga ega.
DOI: 10.5061/dryad.249rk92
title: Data from: Validation of COI metabarcoding primers for terrestrial arthropods

description: Metabarcoding can rapidly determine the species composition of bulk
 samples and thus aids biodiversity and ecosystem assessment. However, it
 is essential to use primer sets that minimize amplification bias among
 taxa to maximize species recovery. Despite this fact, the performance of
 primer sets employed for metabarcoding terrestrial arthropods has not been
 sufficiently evaluated. This study tests the performance of 36 primer sets
 on a mock community containing 374 insect species. Amplification success
 was assessed with gradient PCRs and the 21 most promising primer sets
 selected for metabarcoding. These 21 primer sets were also tested by
 metabarcoding a Malaise trap sample. We identified eight primer sets,
 mainly those including inosine and/or high degeneracy, that recovered more
 than 95% of the species in the mock community. Results from the Malaise
 trap sample were congruent with the mock community, but primer sets
 generating short amplicons produced potential false positives. Taxon
 recovery from both mock community and Malaise trap sample metabarcoding
 were used to select four primer sets for additional evaluation at
 different annealing temperatures (40–60 °C) using the mock community. The
 effect of temperature varied by primer pair but overall it only had a
 minor effect on taxon recovery. This study reveals the weak performance of
 some primer sets employed in past studies. It also demonstrates that
 certain primer sets can recover most taxa in a diverse species assemblage.
 Thus, based our experimental set up, there is no need to employ several
 primer sets targeting the same gene region. We identify several suitable
 primer sets for arthropod metabarcoding, and specifically recommend BF3 +
 BR2, as it is not affected by primer slippage and provides maximal
 taxonomic resolution. The fwhF2 + fwhR2n primer set amplifies a shorter
 fragment and is therefore ideal when targeting degraded DNA (e.g., from
 gut contents).
description: PrimerMiner sequence alignments fasta files,
 as generated in Vamos et al. 2017
 _ALIGNMENTS.zip Project folder
 Archive of project planning, laboratory notes and scripts. Large
 files where removed, to reduce file sizes. As is, not extensively
 documented. 2018 Primer testing.zip
DOI: 10.5061/dryad.d39b44r
title: Data from: A re-evaluation of the chemical composition of avian urinary excreta

description: Osmoregulation in birds is complicated, with different organs acting
 concurrently to regulate this physiological process. Of particular
 interest is how the urinary excretions of birds can remove excess nitrogen
 while minimizing the need for dietary water and balancing the
 physiological demands of oviparity. It has long been concluded from
 chemical analyses, and more recently from genetic studies, that uric acid
 is the principal constituent of urine in Aves. However, research has also
 demonstrated that waste material may be modified in the ceca immediately
 prior to it being expelled. Here, we quantify the chemical composition of
 the urine component of excreta of six avian species using X-ray
 diffraction techniques to test the hypothesis that it is principally
 composed of uric acid, as commonly reported. None of the analyzed samples
 were found to contain uric acid. Instead, a variety of compounds including
 ammonium urate, struvite (magnesium ammonium phosphate), and two unknown
 compounds, were found. Our results show that the uric acid pathway is
 indeed the system by which nitrogen is removed in these birds, but that
 additional modification occurs in the urine prior to excretion. These
 results raise questions for future research on the urinary excretions of
 birds, including identification of the unknown compounds found in the
 present study.
description: urine-raw-dataREADMEInformation on file names and viewing the data
DOI: 10.5061/dryad.f8q4350
title: Data from: Development of an adrenocortical cancer humanized mouse model to characterize anti-PD1 effects on tumor microenvironment

description: Context: While the development of immune checkpoint inhibitors has
 transformed treatment strategies of several human malignancies, research
 models to study immunotherapy in ACC are lacking. Objective: To explore
 the effect of anti-PD1 immunotherapy on the alteration of the immune
 milieu in ACC in a newly generated preclinical model and correlate with
 the response of the matched patient. Design, Setting and Intervention: To
 characterize the CU-ACC2-M2B patient-derived xenograft in a humanized
 mouse model, evaluate the effect of a PD-1 inhibitor therapy and compare
 to the CU-ACC2 patient with metastatic disease. Results: Characterization
 of the CU-ACC2-hu-CB-BRGS model confirmed ACC origin and match with the
 original human tumor. Treatment of the mice with pembrolizumab
 demonstrated significant tumor growth inhibition (TGI = 60%) compared to
 controls, which correlated with increased tumor infiltrating lymphocyte
 activity, with an increase of human CD8+ T cells (p&lt;0.05), HLA-DR+
 T cells (p&lt;0.05) as well as Granzyme B+ CD8+ T cells
 (&lt;0.001). In parallel, treatment of the CU-ACC2 patient, who had
 progressive disease, demonstrated a partial response with 79%-100%
 reduction in the size of target lesions, and no new sites of metastasis.
 Pre-treatment analysis of the patient’s metastatic liver lesion
 demonstrated abundant intra-tumoral CD8+ T cells by immunohistochemistry.
 Conclusions: Our study reports the first humanized ACC PDX mouse model
 which may be useful to define mechanisms and biomarkers of response and
 resistance to immune-based therapies, to ultimately provide more
 personalized care for patients with ACC.
description: Supplementary
 figuresJCEM-2019-00297 Supplementary
 figs.pdf
DOI: 10.5061/dryad.0ck07n7
title: Data from: Field-realistic antidepressant exposure disrupts group foraging dynamics in mosquitofish

description: Psychoactive pollutants, such as antidepressants, are increasingly
 detected in the environment. Mounting evidence suggests that such
 pollutants can disrupt the behaviour of non-target species. Despite this,
 few studies have considered how the response of exposed organisms might be
 mediated by social context. To redress this, we investigated impacts of
 two environmentally realistic concentrations of a pervasive antidepressant
 pollutant, fluoxetine, on foraging behaviour in fish (Gambusia holbrooki),
 tested individually or in a group. Fluoxetine did not alter behaviour of
 solitary fish. However, in a group setting, fluoxetine exposure disrupted
 the frequency of aggressive interactions and food consumption, with
 observed effects being contingent on both the mean weight of group members
 and the level of within-group variation in weight. Our results suggest
 that behavioural tests in social isolation may not accurately predict the
 environmental risk of chemical pollutants for group-living species, and
 highlight the potential for social context to mediate the effects of
 psychoactive pollutants in exposed wildlife.
description: Martin 2019 Biology
 letters forage morphThe morphological data
 for all fish used in the experiment.Martin 2019 Biology
 letters forage groupExperimental data from
 group foraging trials. Where fish have been exposed to one of three
 conditions, a freshwater control, low-fluoxetine (nominal: 30 ng/L), or
 high-fluoxetine (nominal: 300 ng/L).Martin 2019 Biology
 letters forage singleExperimental data from
 indivudal foraging trials. Where fish have been exposed to one of three
 conditions, a freshwater control, low-fluoxetine (nominal: 30 ng/L), or
 high-fluoxetine (nominal: 300 ng/L).
DOI: 10.5061/dryad.50dh670
title: Data from: Effect of coupled reduced irrigation and nitrogen fertilizer on soil mite community composition in a wheat field

description: Overuse of groundwater and nitrogen fertilizer constitute a severe threat
 to crop production, thus, low inputs of irrigation and nitrogen fertilizer
 were required in current ecological agriculture. The effects of combined
 reduced irrigation and nitrogen fertilizer addition on soil organism
 (e.g., mite) community and biodiversity remain poorly understood. We
 analyzed soil mite community composition, wheat grain yields, and soil
 characteristics in a ten-year manipulation experiment with two levels of
 irrigation (reduced irrigation and conventional irrigation) and five
 levels of nitrogen fertilizer (0, 70, 140, 210, 280 kg N ha-1). The study
 showed that reduced irrigation (20% reduction, from 280 to 220 mm) and
 nitrogen fertilizer (25% reduction, from 280 to 210 kg N ha-1) addition
 did not significantly influence soil mite community and wheat yields. The
 relative abundances of fungivore and predator showed negative quadratic
 relationships with wheat yields, while that of plant parasite was
 positive. The relationships between soil mite trophic groups and wheat
 yields revealed that we can elevated the impacts of reduced irrigation and
 nitrogen fertilizer addition from the perspective of soil fauna. The soil
 mite community composition was altered by soil abiotic factors prior to
 reduced irrigation and nitrogen fertilizer addition. On the whole,
 moderate reductions of irrigation and nitrogen fertilizer may not threaten
 to soil mite community and diversity or decrease crop production, on the
 contrary, it will benefit to the development of mite community and the
 sustainable agriculture.
description: Soil mite taxon
 abundance
DOI: 10.15468/dl.btp4ys
title: Occurrence Download

description: A dataset containing 246 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Castanopsis concinna, Cyclobalanopsis sichourensis, Fagus hayatae, Formanodendron doichangensis, Quercus bawanglingensis, Quercus oxyphylla, Annamocarya sinensis, Carya kweichowensis, Carpinus putoensis, Carpinus tientaiensis, Ostrya rehderiana, Cucumis sativus xishuangbannanensis, Tetrameles nudiflora, Begonia arachnoidea, Begonia coptidifolia, Begonia ferox, Begonia gulinqingensis, Begonia gulongshanensis, Begonia hainanensis, Begonia hongkongensis)"
 ]
}

 The dataset includes 246 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001906-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3vyuzz
title: Occurrence Download

description: A dataset containing 912 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Potential prey of Rice's whales based on seawater eDNA 2019"
 ]
}

 The dataset includes 912 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001903-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4231/46px-0772
title: Resonant scattering, metallicity, and redshift (Cloudy scripts)

description: &lt;p&gt;The warmer gaseous component of the Large Scale Structure of the Universe emits primarily in the X-ray portion of the electromagnetic spectrum, mostly through thermal emission. Resonant scattering of X-ray background radiation by the Warm-Hot Intergalactic Medium (10&lt;sup&gt;5 &lt;/sup&gt;K &lt; T &lt; 10&lt;sup&gt;7&lt;/sup&gt; K), however, can contribute significantly to the amplitude of the resonant emission lines of selected ions (with an increment of more than a factor 30).&lt;/p&gt;

&lt;p&gt;Tables for the emission (thermal and resonant scattering) at different temperature, density, metallicity, and redshift are generated with Cloudy. The comparison between thermal emission and resonant scattering contributions is performed with Jupyter Notebooks.&lt;/p&gt;

&lt;p&gt;All the material related to the published paper is stored in four sets: &ldquo;Cloudy scripts&rdquo;, &ldquo;Jupyter scripts&rdquo;, &ldquo;Data&rdquo;, and &ldquo;Figures&rdquo;. Additional material, that extends beyond the initial investigation, will be stored at a later time (the description will be updated accordingly).&lt;/p&gt;

&lt;p&gt;Cloudy Scripts.&lt;/p&gt;

&lt;p&gt;The Cloudy script &ldquo;runcloudy&rdquo; is the basic script to launch cloudy activities.&lt;/p&gt;

&lt;p&gt;The Cloudy script &ldquo;runbatchcloudy&rdquo; is called by &ldquo;runcloudy&rdquo; and runs all simulations.&lt;/p&gt;

&lt;p&gt;The Cloudy scripts &ldquo;*.in&rdquo; are called by runbatchcloudy and contain the instructions for each simulation. Input files ending with the tags &quot;01HM&quot;, &quot;02HM&quot;, &quot;05HM&quot;, &quot;HM12&quot;, and &quot;KS19&quot; are used to compare the different CXB models.&lt;/p&gt;

&lt;p&gt;The output is very large, each simulation generating about 30 GB of data (not included in this repository). One simulation runs in about 1 hour.&lt;/p&gt;
description: Investigation of the contribution of resonant scattering to the emission of the Warm-Hot gas (10^5 K &lt; T &lt; 10^7 K) in the large scale structure of the Universe. Assessment of the effect of metallicity and redshift.