Helium and Neon concentration duplicates from station 1 of KN199-04 (GT10) cruise. Station, cast, and Niskin bottle numbers are provided along with CTD pressure.

Please note that some US GEOTRACES data may not be final, pending intercalibration results and further analysis. If you are interested in following changes to US GEOTRACES NAT data, there is an RSS feed available via the BCO-DMO US GEOTRACES project page (scroll down and expand the \"Datasets\" section).

Gene and genome duplication events have created a large number of new genes in plants that can diverge by evolving new expression profiles and functions (neofunctionalization) or dividing extant ones (subfunctionalization). Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or down-regulation of gene expression by transcript decay. Using RNA-seq we investigated the degree to which alternative splicing patterns are conserved between duplicated genes in Arabidopsis thaliana. Our results revealed that 30% of AS events in alpha whole genome duplicates, and 33% of AS events in tandem duplicates, are qualitatively conserved within leaf tissue. Loss of ancestral splice forms, as well as asymmetric gain of new splice forms, may account for this divergence. Conserved events had different frequencies, as only 31% of shared AS events in alpha whole genome duplicates and 41% of shared AS events in tandem duplicates had similar frequencies in both paralogs, indicating considerable quantitative divergence. Analysis of published RNA-seq data from nonsense mediated decay (NMD) mutants indicated that 85% of alpha whole genome duplicates and 89% of tandem duplicates have diverged in their AS-induced NMD. Our results indicate that alternative splicing shows a high degree of divergence between paralogs such that qualitatively conserved alternative splicing events tend to have quantitative divergence. Divergence in AS patterns between duplicates may be a mechanism of regulating expression level divergence.

title: 'BellaBeat Fitbit' author: 'C Romero' date: 'r Sys.Date()' output: html_document: number_sections: true

toc: true

##Installation of the base package for data analysis tool
install.packages("base")

##Installation of the ggplot2 package for data analysis tool
install.packages("ggplot2")

##install Lubridate is an R package that makes it easier to work with dates and times.
install.packages("lubridate")
```{r}

##Installation of the tidyverse package for data analysis tool
install.packages("tidyverse")

##Installation of the tidyr package for data analysis tool
install.packages("dplyr")

##Installation of the readr package for data analysis tool
install.packages("readr")

##Installation of the tidyr package for data analysis tool
install.packages("tidyr")

Importing packages

metapackage of all tidyverse packages

library(base) library(lubridate)# make dealing with dates a little easier library(ggplot2)# create elegant data visialtions using the grammar of graphics library(dplyr)# a grammar of data manpulation library(readr)# read rectangular data text library(tidyr)

## Running code

In a notebook, you can run a single code cell by clicking in the cell and then hitting 
the blue arrow to the left, or by clicking in the cell and pressing Shift+Enter. In a script, 
you can run code by highlighting the code you want to run and then clicking the blue arrow
at the bottom of this window.

## Reading in files


```{r}
list.files(path = "../input")

# load the activity and sleep data set
```{r}
dailyActivity <- read_csv("../input/wellness/dailyActivity_merge.csv")
sleepDay <- read_csv("../input/wellness/sleepDay_merged.csv")

check for duplicates and na

sum(duplicated(dailyActivity)) sum(duplicated(sleepDay)) sum(is.na(dailyActivity)) sum(is.na(sleepDay))

now we will remove duplicate from sleep & create new dataframe

sleepy <- sleepDay %>% distinct() head(sleepy) head(dailyActivity)

count number of id's total sleepy & dailyActivity frames

n_distinct(dailyActivity$Id) n_distinct(sleepy$Id)

get total sum steps for each member id

dailyActivity %>% group_by(Id) %>% summarise(freq = sum(TotalSteps)) %>% arrange(-freq) Tot_dist <- dailyActivity %>% mutate(Id = as.character(dailyActivity$Id)) %>% group_by(Id) %>% summarise(dizzy = sum(TotalDistance)) %>% arrange(-dizzy)

now get total min sleep & lie in bed

sleepy %>% group_by(Id) %>% summarise(Msleep = sum(TotalMinutesAsleep)) %>% arrange(Msleep) sleepy %>% group_by(Id) %>% summarise(inBed = sum(TotalTimeInBed)) %>% arrange(inBed)

plot graph for "inbed and sleep data" & "total steps and distance"

ggplot(Tot_dist) + 
 geom_count(mapping = aes(y= dizzy, x= Id, color = Id, fill = Id, size = 2)) +
 labs(x = "member id's", title = "distance miles" ) +
 theme(axis.text.x = element_text(angle = 90)) 
 ```

AbstractGene and genome duplication events have created a large number of new genes in plants that can diverge by evolving new expression profiles and functions (neofunctionalization) or dividing extant ones (subfunctionalization). Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or down-regulation of gene expression by transcript decay. Using RNA-seq we investigated the degree to which alternative splicing patterns are conserved between duplicated genes in Arabidopsis thaliana. Our results revealed that 30% of AS events in alpha whole genome duplicates, and 33% of AS events in tandem duplicates, are qualitatively conserved within leaf tissue. Loss of ancestral splice forms, as well as asymmetric gain of new splice forms, may account for this divergence. Conserved events had different frequencies, as only 31% of shared AS events in alpha whole genome duplicates and 41% of shared AS events in tandem duplicates had similar frequencies in both paralogs, indicating considerable quantitative divergence. Analysis of published RNA-seq data from nonsense mediated decay (NMD) mutants indicated that 85% of alpha whole genome duplicates and 89% of tandem duplicates have diverged in their AS-induced NMD. Our results indicate that alternative splicing shows a high degree of divergence between paralogs such that qualitatively conserved alternative splicing events tend to have quantitative divergence. Divergence in AS patterns between duplicates may be a mechanism of regulating expression level divergence. Usage notesRepo for Tack et al. 2014 GeneticsData and scripts from "Transcriptome Analysis Indicates Considerable Divergence in Alternative Splicing Between Duplicated Genes in Arabidopsis thaliana"Github_Dryad_repo.zip

Robust RSD(r) and RSD(iR) of 2′FL, 3′SL and 6′SL in dog milk from data measured in duplicates during 9 days.

Accession numbers of all protein sequences used in this study. (XLSX 16 kb)

SF6 data from duplicate samples from CTD bottle depths

Methodology:
Law, C.S., Watson, A.J. & Liddicoat, M.I. 1994. Automated vacuum analysis of Sulphur hexafluoride in seawater;
derivation of the atmospheric trend (1970-1993) and potential as a transient tracer. Marine Chemistry, 48 :57-69

This dataset is about: (Table 1) Comparison of interlaboratory results for duplicate analyses of selected ODP Leg 129 basalts. Please consult parent dataset @ https://doi.org/10.1594/PANGAEA.779154 for more information.

IntroductionThis systematic review and meta-analysis aimed to evaluate the success rate of pulpotomy in permanent teeth using ProRoot MTA.MethodsAn unrestricted search was carried out in 6 electronic databases, until August 2024. The selection of studies adhered to the PIOS criteria, encompassing only randomized clinical trials that assessed the success rate of pulpotomy in permanent teeth using ProRoot MTA through clinical and radiographic evaluations. Risk of bias was assessed using the RoB-2 tool, and meta-analyses were conducted through RevMan 5.3 and R software. To determine the quality of evidence, the GRADE tool was employed.ResultsThe initial search yielded 971 studies. After removing duplicates, 468 studies underwent initial screening, and 32 studies were considered for eligibility. In the final selection, 26 studies were included, and among these, 14 were categorized as having high risk of bias. The analysis of pulpotomy in permanent teeth using ProRoot MTA revealed an overall success rate of 96%, 90%, and 96% at 6-, 12-, and 24-month follow-up periods, respectively, and an annual failure rate of 8%. Meta-analyses indicated a significantly higher success rate for pulpotomies in teeth with open apex. Upon applying the GRADE assessment, an overall moderate level of evidence was observed.ConclusionPulpotomy in permanent teeth using ProRoot MTA yields a success rate exceeding 90%, even up to a 24-month follow-up period. Nonetheless, the certainty of evidence supporting these outcomes is moderate, highlighting the requirement for well-designed randomized clinical trials with extended follow-up durations.Registration This systematic review was registered in the PROSPERO database (registration number CRD42023451466).

This dataset is about: (Table 2) Duplicate oxygen-isotope measurements of the planktonic foraminifer Globigerinoides ruber from ODP Hole 133-820A. Please consult parent dataset @ https://doi.org/10.1594/PANGAEA.706033 for more information.

Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared null distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to SWI5 after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication.

RABV: Rabies virus; ;EBLV: European Bat Lyssavirus;neg.: negative control; −: negative result; #: cross-reactivitiy with other Lyssavirus species; ?: doubtful result;*doubtful result was retested; i.h.: in-house assay; dilution series (0), (I), (II), (III); 100, 10−1, 10−2, 10−3; mod.: assay modified; r: RABV-specific detection; e1: EBLV-1 specific; e1+2: EBLV-1+−2 specific; r13, r14, r13/14: R13, R14, duplex R13/14 assay by [17]; fn: false negative results; exp: expected negative results from previous publication; ts: two-step systems; no duplicates for assays D2, D3 and M; 2) Orlowska et al., 2008 [22].

Gene duplication is a key mechanism for the adaptive evolution and neofunctionalization of gene families. Large multi-gene families often exhibit complex evolutionary histories as a result of frequent gene duplication acting in concordance with positive selection pressures. Alterations in the domain structure of genes, causing changes in the molecular scaffold of proteins, can also result in a complex evolutionary history and has been observed in functionally diverse multi-gene toxin families. Here, we investigate the role alterations in domain structure have on the tempo of evolution and neofunctionalization of multi-gene families using the snake venom metalloproteinases (SVMPs) as a model system. Our results reveal that the evolutionary history of viperid (Serpentes: Viperidae) SVMPs is repeatedly punctuated by domain loss, with the single loss of the cysteine-rich domain, facilitating the formation of P-II class SVMPs, occurring prior to the convergent loss of the disintegrin domain to form multiple P-I SVMP structures. Notably, the majority of phylogenetic branches where domain loss was inferred to have occurred exhibited highly significant evidence of positive selection in surface-exposed amino acid residues, resulting in the neofunctionalization of P-II and P-I SVMP classes. These results provide a valuable insight into the mechanisms by which complex gene families evolve and detail how the loss of domain structures can catalyse the accelerated evolution of novel gene paralogues. The ensuing generation of differing molecular scaffolds encoded by the same multi-gene family facilitates gene neofunctionalization, whilst presenting an evolutionary advantage through the retention of multiple genes capable of encoding functionally distinct proteins.

Tissue sections were scored on a scale of 0–7 for combined extent and intensity. The ratios listed are the number of duplicate sections with scores differing by more than 1, divided by the total number of sections scored. Intensity is scored only on the samples for which percentage score is greater than 0.

Please see the file MRDS-with-uncertain-dups.R for full description and instructions for using the code.

Comparative descriptive statistics of useful reads count and duplication rates across the two deduplication strategies.

Medical start-ups (MedTech) significantly contribute to the development and commercialization of innovative healthcare solutions, driving advancements in technology, enhancing treatment effectiveness, and supporting public health. This study explores the main themes and concepts related to MedTech start-ups, examines the research methods used, and identifies major gaps in the literature. A scoping literature review was performed by searching the Scopus, PubMed, and Web of Science databases for publications from 2012 to 2023, focusing on MedTech start-ups in titles, abstracts, and keywords. References were analyzed using the Bibliometrix package in R, and a coupling network analysis was conducted, visualizing results on a Coupling Map to identify key research themes and gaps. The research identified 480 unique articles on MedTech start-ups. After removing duplicates and following a PRISMA-based assessment, 79 articles were included in the review. The studies predominantly focused on organizations, including start-ups and Venture Capital funds (46%). Most articles (60%) used qualitative methods, 25% employed mixed methods, and 15% used quantitative methods. Geographically, 63% of articles focused on a single country, primarily the USA (35%), followed by Iran, Sweden, Switzerland, China, and Japan (2–4% each). Coupling analysis identified five topic clusters: crowdfunding for medical research, innovation in medical technology, new product development, digital start-ups, and the venture capital industry. This review highlights the significant role of MedTech start-ups in advancing healthcare innovations despite challenges like regulatory hurdles and high capital requirements. The literature emphasizes the importance of collaboration among universities, industry, and government for successful commercialization. The geographic concentration in the USA indicates a need for more inclusive research. Crowdfunding and venture capital emerge as crucial funding sources, suggesting strategies to mitigate risks and enhance innovation success.

Genotypic values of a 2-locus duplicate factor model.