cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cvdncjt2w
title: Pearls and oy-sters: Primary pineal melanoma with leptomeningeal carcinomatosis - Supplemental figures

description: Pearls: Pineal masses commonly present with Parinaud syndrome, a triad
 consisting of upgaze restriction, convergenceretraction nystagmus, and
 pupillary light-near dissociation from compression of the quadrigeminal
 plate. The differential diagnosis for pineal region tumors includes germ
 cell tumors, pineal parenchymal tumors, glioma, atypical teratoid rhabdoid
 tumor and metastatic disease. While exceedingly uncommon, primary pineal
 melanoma is also a known histopathologic entity that is suspected to arise
 from melanocytes in the pia mater of the pineal gland. Primary pineal
 melanoma is often treated with surgical resection, radiation, and either
 chemotherapy or immunotherapy. Some patients have received targeted
 therapy (such as vemurafenib in patients with BRAF V600E mutation) with
 varying degrees of success. Oy-sters: Cerebrospinal fluid (CSF) sampling
 can assist in the diagnosis of pineal tumor, specifically to test for germ
 cell tumor markers (alphafetoprotein, beta human chorionic gonadotropin,
 placental alkaline phosphatase), systemic tumor markers such as
 carcinoembryonic antigen, cell-free DNA or malignant cells on
 cytopathology.  Pineal tumors can result in obstructive
 hydrocephalus, therefore lumbar puncture is not always a feasible option
 due to the risk of herniation. In patients with melanoma of the central
 nervous system (CNS), a careful survey consisting of systemic imaging and
 total body skin examination are warranted to exclude a separate primary
 melanoma lesion. The differential diagnosis for rapidly progressive
 bilateral sensorineural hearing loss includes meningitis, superficial
 siderosis, ototoxicity and leptomeningeal disease. Difficulty in speech
 comprehension in excess of pure tone audiometry may suggest involvement or
 compression of the inferior colliculus.
description: <b>Supplementary
 Figure 2. </b>Image taken during endoscopic biopsy demonstrating
 dark material (melanin) lining the third ventricle. <b>Supplementary Figure
 3.</b> Pathologic specimens. H&E (A) stained section
 demonstrating high-grade pigmented epithelioid neoplasm. Differentiation
 marker immunophenotyping (B) with staining for HMB45, MART1, tyrosinase)
 consistent with melanoma.
DOI: 10.5061/dryad.3tx95x6dt
title: Female and male song exhibit both parallel and divergent patterns of cultural evolution: a long-term study of song structure and diversity in tropical wrens

description: Animal culture changes over time through processes that include drift,
 immigration, selection, and innovation. Cultural change has been
 particularly well-studied for animal vocalizations, especially for the
 vocalizations of male animals in the temperate zone. Here we examine
 cultural change in the vocalizations of tropical Rufous-and-white Wrens
 (Thryophilus rufalbus), quantifying temporal variation in song structure,
 song type diversity, and population-level distribution of song types in
 both males and females. We use data from 10 microsatellite loci to
 quantify patterns of immigration and neutral genetic differentiation over
 time, to investigate whether cultural diversity changes with rates of
 immigration. Based on 11 years of data, we show that the spectro-temporal
 features of several widely-used persistent song types maintain a
 relatively high level of consistency for both males and females, whereas
 the distribution and frequency of particular song types change over time
 for both sexes. Males and females exhibit comparable levels of cultural
 diversity (i.e. the diversity of song types across the population),
 although females exhibit greater rates of cultural change over time. We
 found that female changes in cultural diversity increased when immigration
 is high, whereas male cultural diversity did not change with immigration.
 Our study is the first long-term study to explore cultural evolution for
 both male and female birds and suggests that cultural patterns exhibit
 notable differences between the sexes.
DOI: 10.15468/dl.9hfrnx
title: Occurrence Download

description: A dataset containing 610 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "Geometry POLYGON((-99.734375 16.09814453125,-95.734375 16.09814453125,-95.734375 20.09814453125,-99.734375 20.09814453125,-99.734375 16.09814453125))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Iguana"
 ]
}

 The dataset includes 610 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002615-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bnzs7h48r
title: Do heterogeneous seascapes of carbonate conditions across biogeographic breaks influence divergent phenotypic plasticity in natural populations?

description: Aim: Understanding how environmental variability influences stress
 tolerance, local adaptation, and phenotypic variation among populations is
 a key challenge for evolutionary ecology and climate change biology.
 Coastal biogeographic breaks are natural laboratories to explore this
 fundamental research question due to the contrasting environmental
 conditions experienced by natural populations across these regions.
 Location: In the South East Pacific (SEP) coast a major break (30º-32ºS)
 is characterized by extreme natural variability in seawater carbonate
 chemistry parameters related to temporal and spatial dynamics in upwelling
 events. Mollusk species that reach their range limit at this zone are
 exposed to naturally acidified waters that can be corrosive and impact
 their calcification, physiology, and fitness, making them particularly
 prone to the effects of ocean acidification (OA). We investigated to what
 extent the interplay between biogeographic breaks and local variability of
 seawater carbonate conditions influences the tolerances and sensitivity of
 populations of the limpet Scurria araucana to OA. Methods: During two
 years, we conducted field surveys of limpet populations at sites across
 the SEP break (27ºS, 30ºS and 32ºS). We collected individuals from each
 population to test for geographic differences in morphometric (e.g., total
 buoyancy weight, shell length) and physiological (e.g., oxygen consumption
 rate, cardiac activity, and thermal performance curves; TPC) responses to
 local conditions and to simulated OA scenarios. Results: Analysis of the
 cardiac activity indicates that limpets from the central part of the break
 (30ºS) exhibit higher thermal performance compared to limpets from
 populations at both sides of the break. Thus, heterogeneous seascape of
 carbonate conditions and sea surface temperature across a biogeographic
 break in the SEP coast influence phenotypic differences among populations
 of this ecosystem engineer. Main Conclusions: Natural environmental
 variation might be the underpinning driver of the high tolerance to OA
 evidenced by populations of the limpet Scurria araucana along the SEP.
description: This dataset was obtained directly by measurementes in the lab as
 well as in the field.
DOI: 10.5061/dryad.pzgmsbcjm
title: One comprehensive clinical neurologic examination is sufficient to declare brain death

description: Objective: To fill
 the evidence gap on the value of a single (SBD)
 or dual brain death (DBD) exam by
 providing data on irreversibility of brain function,
 organ donation consent and
 transplantation  
 Methods: 12-year tertiary
 hospital and organ procurement
 organization data on brain death (BD) were
 combined and outcomes, including consent rate for organ
 donation and organs recovered and
 transplanted after SBD and DBD were
 compared after multiple adjustments for co-variates 
 Results: two-hundred sixty-six patients were
 declared BD, 122 after SBD and 144 after DBD. Time from
 event to BD declaration was longer by an
 average of 20.9 hours after
 DBD (p=0.003). Seventy-five (73%) families of patients with SBD and 86 (72%) with DBD consented for organ donation (p=0.79). The number of BD exams was not a predictor for consent. No patient regained brain function during the periods following BD. Patients with SBD were more likely to have at least one lung transplanted (p = 0.033). The number of organs transplanted was associated with the number of exams [beta coefficient, (95% CI) -0.5 (-0.97 to -0.02), p=0.044], along with age (for 5 year increase, -0.36 (-0.43 to -0.29), p&lt;0.001) and PaO2 level (for 10 mmHg increase, 0.026 (0.008 to 0.044), p=0.005) and decreased as the elapsed time to BD declaration increased (p=0.019).  Conclusions:  A single neurologic examination to determine brain death is sufficient in patients with non-anoxic catastrophic brain injuries. A second examination is without additional yield in this group and its delay reduces the number of organs transplanted. 
description: Table that shows difference between a single brain
 death exam and dual brain death exams Figure that
 shows yearly trends over 12 years regarding single and dual brain death
 exams Figure showing who is performing the exams over
 the same time period Figure showing the decline of
 Organs transplanted based on the delay of brain death
 evaluation
DOI: 10.5061/dryad.0rxwdbrxx
title: The checklist of spiders in tea plantations of China

description: Spiders are the most dominant predatory natural enemies of insect pests in
 the tea plantation ecosystem. There has been a large amount of literature
 published about the investigation of spider species in Chinese tea
 plantations from 1982 to 2020. Here, the spider species in Chinese tea
 plantations has been summarised and the dominant spider species in each
 regional tea plantation recorded. To date, there were 535 spider
 species from 40 families reported in Chinese tea plantations, with a total
 of 13 families and 245 species now being added. A total of 89
 spider species from 19 families were the dominant species, amongst
 them, Agelena labyrinthica, Allagelena
 difficilis, Neoscona theisi, Clubiona
 deletrix, Clubiona japonicola, Hylyphantes
 graminicola, Pardosa laura, Oxyopes
 sertatus, Evarcha albaria, Plexippus
 paykulli, Coleosoma octomaculatum, Ebrechtella
 tricuspidata and Xysticus ephippiatus were
 recorded in many tea plantations. The checklist will provide
 important data for the biodiversity and distribution of spiders in tea
 plantations of China.
DOI: 10.5061/dryad.qv9s4mwcz
title: SNPs markers of Trypoxylus dichotomus developed by using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques

description: The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest
 beetle species in the world and is commonly used in traditional chinese
 medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species
 (T. kanamorii) have been described throughout Asia, but their taxonomic
 delimitations remain problematic. To clarify issues such as taxonomy, and
 the degree of genetic differentiation of Trypoxylus populations, we
 investigated the genetic structure, genetic variability and phylogeography
 of 53 specimens of Trypoxylus species from 44 locations in five Asian
 countries (China, Japan, Korea, Thailand, and Myanmar). Using
 specific‐locus amplified fragment sequencing (SLAF‐seq) techniques, we
 developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939
 high-resolution single nucleotide polymorphisms (SNPs) for genotyping.
description: For SLAF-seq analysis, DNA concentration was quantified using a
 NanoDrop-2000 spectrophotometer, and all DNA samples were diluted to 50
 ng/μL. SLAF library construction was carried out following Sun et al.
 (2013) with minor modifications. To obtain evenly distributed SLAF tags
 and to avoid repetitive SLAF tags for maximum SLAF-seq efficiency,
 simulated restriction enzyme digestion was carried out in silico. Genomic
 DNA was digested using RsaI-HaeIII restriction enzyme and the reference
 genome of Dendroctonus ponderosae
 (https://www.ncbi.nlm.nih.gov/genome/?term=Dendroctonus+ponderosae) was
 used to predict enzyme digestion. DNA fragments of 264–364 bp were
 selected as SLAFs and prepared for paired-end sequencing on the Illumina
 High-Seq 2500 sequencing platform (Illumina, Inc.; San Diego, CA) at
 Biomarker Technologies Corporation (Beijing, China). 
 Raw pair-end reads were clustered based on sequence similarity.
 Sequences with over 90% identity were grouped in one SLAF tag, SLAFs with
 low-depth coverage were filtered out (Sun et al. 2013; Huang et al. 2016;
 Wang et al. 2019). Only groups with higher depth and four tags or fewer
 were identified as high-quality SLAFs with SLAFs possessing two, three, or
 four tags identified as polymorphic. In this study, depth was 17.63 × on
 average, and a total of 1, 374, 985 high‐quality unique SLAF tags were
 obtained with 330,799 of those tags considered polymorphic.
 Development of SNP markers was based on reference sequence with
 very high depth in each SLAF tag. SAMtools and GATK were used for mapping
 and SNP calling (McKenna et al., 2010; Li et al., 2009; Wang et al. 2019).
 A total of 46, 939 SNPs with minor allele frequencies (MAF) of ≥ 0.05 and
 an integrity score of ≥80% were employed in downstream analyses.
DOI: 10.5061/dryad.9kd51c5fk
title: Unique mode of cell division by the mycobacterial genetic resister clones emerging de novo from the antibiotic surviving population

description: Live cell and timelapse microscopic images of the cells
 taken from different time points post antibiotic (Rifampicin and
 Moxifloxacin) exposure. The cells post antibiotic exposure, during their
 regrowth, showed multiple constriction to divide and
 generate sister antibiotic resister daughter cells with abrupt increased
 cell number within less division time by multiple septation. The phenomena
 of  multiple septation can be seen in Miscellaneous Figures (MF.
 1-4) and Miscellaneous Movies (MF. 1-4). 
description: Agarose pad method was used
 for the Live-cell time-lapse microscopy of <i>Msm </i>regrowth
 phase cells. In brief, Agarose pad was prepared by 1.75% low melting point
 agarose on a clean glass slide using s<em>pent media of
 90<sup> </sup>hr</em> rifampicin (25 µg/ml); 60 hr and
 54 hr of moxifloxacin (1.5 µg/ml) exposed cultures. After the
 solidification of the agarose, for the introduction of rifampicin into the
 agarose pad, a portion of the agarose (about 1/5<sup>th
 </sup>of the total agarose pad area) was cut out using a blade to
 make a well. A tip was attached towards one side of the well, which was
 connected to a syringe for the removal of rifampicin containing medium. On
 top of the agarose pad,10 µl of <em>90<sup>
 </sup>hr</em> rifampicin (25 µg/ml); 60 and 54 hr of
 moxifloxacin (1.5 µg/ml) exposed <i>Msm</i> cells were placed
 and by tilting the slide the cells were spread evenly. Leaving a portion
 of the well open for the introduction of rifampicin with<sub>
 </sub>a syringe, the slide was covered by a cover slip at 45º angle
 from the base of the glass slide. To facilitate cell adhesion, the agarose
 pad with the cells was kept at 37ºC for 1 hr. Under Carl Zeiss AxioVision
 4 microscope this slide was observed. We have used a live cell imaging
 option, at 100x magnification (DIC), with 0.2 µm slice distance Z-stacking
 at 37ºC. DIC images were taken at every 10 min time interval. The
 parameters like cell length and cell constriction, data analysis of  the
 images was performed using AxioVision 4 and ImageJ software.
DOI: 10.5061/dryad.547d7wm6m
title: Data from: Smart bracelet to assess physical activity after cardiac surgery: a prospective study

description: Objectives: Little is known about the physical activity of
 patients after cardiac surgery. This study was designed to assess this
 activity using a connected bracelet.  Methods: In this
 prospective, monocentric study, patients scheduled for cardiac surgery
 were offered to wear an electronic bracelet. The main objective was to
 measure the physical activity recovery. Secondary objectives were the
 predictors of the correct use of the monitoring system, of the physical
 recovery and, if any, the relationship between physical activity and
 out-of-hospital morbidity.  Results: One hundred
 patients were included. Most patients (86%) were interested in
 participating in the study. The compliance to the device and to the study
 protocol was good (94%). At discharge, the mean number of daily steps was
 1454 ± 145 steps, increasing quite homogeneously, reaching 5801±1151 steps
 at Day 60. The best fit regression curve gave a maximum number of steps at
 5897±119 (r²=0.97). The 85% level of activity was achieved at Day
 30±3.  No predictor of noncompliance was found. At
 discharge, age was independently associated with a lower number of daily
 steps (p &lt;0.001). At Day 60, age, peripheral arterial disease and
 cardio-pulmonary bypass duration were independently associated with a
 lower number of daily steps (p=0.039, p=0.041 and p=0.033,
 respectively).  Conclusions: After cardiac surgery,
 wearing a smart bracelet recording daily steps is simple, well tolerated
 and suitable for measuring physical activity. Standard patients achieved
 around 6000 daily steps 2 months after discharge. 85% of this activity is
 reached in the first month.
DOI: 10.5061/dryad.bzkh1896z
title: Data from: Tolerability and efficacy of long-term medical therapy in primary aldosteronism

description: Introduction: Patients with primary aldosteronism (PA) have increased
 cardiovascular risk and studies have found that medical therapy fails to
 ameliorate this. This may be due to side effects and limited efficacy of
 medications at tolerable doses. Methods: We conducted a retrospective
 study on 201 patients with PA treated with medical therapy
 (spironolactone, eplerenone or amiloride) for PA from 2000-2020 at two
 tertiary centres. Patients were assessed for efficacy to achieve clinical
 and biochemical control, and for side effects. Results: 53.7% of patients
 achieved blood pressure &lt;140/90mmHg, 44.6% achieved potassium
 ≥4.3mmol/L, 63.2% achieved renin &gt;1ng/ml/hr, and only 24.6%
 achieved all three. Concordance of biochemical control using potassium and
 renin levels was 49%. 45.3% of patients experienced side effects, with
 8.5% switching to another medication, 18.9% decreasing dose, and 10.0%
 stopping medications altogether. Risk factors for side effects
 were spironolactone use, dose ≥50mg, duration of treatment ≥1year, male
 gender and unilateral PA. Patients with unilateral PA, compared to
 bilateral PA, used higher median doses of spironolactone, 75mg vs 50mg,
 P&lt;0.001, but more had persistent hypokalemia, 20.5% vs 6.4%,
 P=0.007. 44 patients with unilateral PA underwent surgery after initial
 medical therapy, which further improved systolic and diastolic BP, from
 142 to 134mmHg, P&lt;0.001, and from 85 to 79mmHg, P&lt;0.001,
 respectively. Conclusion: Dose-dependent side effects limit the efficacy
 of medical therapy in PA. Future prospective studies should assess the
 best monitoring strategy for biochemical control during long-term medical
 therapy. In patients with unilateral PA, surgery remains a better option
 compared to life-long medications.
DOI: 10.5061/dryad.jwstqjq7g
title: Fish abundance data in forest steppe and grassland river networks in Mongolia

description: Fish abundance data (fish per m) collected during the MACRO project in
 Mongolia. We collected fish assemblages in river networks of two different
 ecoregions, the Forest Steppe (FS) and Grassland (G), in 2017 and 2019.
description: We established reaches for fish collections measuring at least 20
 times the mean wetted width of the river at the sampling area. We
 collected fishes by single-pass backpack electrofishing supplemented with
 angling (Ball State University IACUC #126193) following the American
 Fisheries Society standard collection protocols (Bonar, Hubert, &
 Willis, 2009), and reported fish abundance as fish-per-meter
 sampled. We sampled fishes during one month expeditions
 in each of the river networks during the month of August in 2017 for the
 FS and 2019 for the G.
DOI: 10.5061/dryad.q2bvq83hd
title: VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species

description: Domestication is a human-induced selection process that imprints the
 genomes of domesticated populations over a short evolutionary time scale,
 and that occurs in a given demographic context. Reconstructing historical
 gene flow, effective population size changes and their timing is therefore
 of fundamental interest to understand how plant demography and human
 selection jointly shape genomic divergence during domestication. Yet, the
 comparison under a single statistical framework of independent
 domestication histories across different crop species has been little
 evaluated so far. Thus, it is unclear whether domestication leads to
 convergent demographic changes that similarly affect crop genomes. To
 address this question, we used existing and new transcriptome data on
 three crop species of Solanaceae (eggplant, pepper and tomato), together
 with their close wild relatives. We fitted twelve demographic models of
 increasing complexity on the unfolded joint allele frequency spectrum for
 each wild/crop pair, and we found evidence for both shared and
 species-specific demographic processes between species. A convergent
 history of domestication with gene-flow was inferred for all three
 species, along with evidence of strong reduction in the effective
 population size during the cultivation stage of tomato and pepper. The
 absence of any reduction in size of the crop in eggplant stands out from
 the classical view of the domestication process; as does the existence of
 a “protracted period” of management before cultivation. Our results also
 suggest divergent management strategies of modern cultivars among species
 as their current demography substantially differs. Finally, the timing of
 domestication is species-specific and supported by the few historical
 records available.