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Ireland’s Ancient Wild Side: There was once more than just whiskey and stout

17/7/2022

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by Kyle Morrison
​
In today’s world Ireland is famous for vibrant cities, cosy pubs and cold Guinness but, in a simpler time – before us humans got involved, it was once the land of giant deer, grey wolves and grizzly bears. Although, some of these animals can be seen elsewhere, a few sadly cannot and were never seen again. Here I provide you five of the coolest animals that ever roamed the Emerald Isle.  
Number 1 – The Great Auk
Despite being coined the original penguin, great auks were not actually penguins at all but a fine product of convergent evolution. Ironically, the Latin name for the great auk is Pinguinus impennis, and when European explorers found the first penguins in the southern hemisphere, they noticed their uncanny resemblance to the great auk and hence we have modern name for penguins. The great auk had a white belly and a black back, stood around 85cm tall and weighed around 5 kgs. It had small wings for swimming and a large beak for eating fish and krill. The great auk was once a common sight along the Irish coastlines with remains being found in popular tourist spots in Donegal and Galway. Much like penguins, the great auk was utterly defenceless on land which unfortunately contributed to their eventual demise in the 1840’s due to widespread hunting for food and bait.
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​Number 2 – The Irish lynx
Currently, lynxes (or, bobcats) are mainly found across Siberia and North America, but these majestic wildcats were once widespread across the island of Ireland. The presence of Lynx in Ireland wasn’t known until the late 1930’s, when a few hikers found a mandible bone in County Waterford. It’s likely that the Irish lynx roamed the woods and countryside, preying on small deer and hare. Lynxes are known to have survived in the British Isles until the Romans arrived however, there is no indication of when they went extinct in Ireland. Recently, lynx have been considered for a reintroduction project, helping to balance woodland ecosystems and increase biodiversity. The aim is that the introduction of the native lynx will reduce numbers of invasive sika deer, which currently have no natural predator.
​Number 3 – The Irish Wolf
Wolves were a major part of the postglacial fauna in Ireland dating back as long ago as 34,000 BC. The Irish word for wolf is Mac Tíre which means “Son of the Countryside”, which illustrates how important wolves were to the people of Ireland. In fact, many Irish stories, myths and folklore are about wolves and how the Irish gods adored them. Before the great agricultural revolution on the island most of the countryside was clothed with thick forest, which was perfect hunting habitat for wolves. It wasn’t until the arrival of Oliver Cromwell in 1650’s that wolves in Ireland became troubled. Cromwell wanted rid of the wolves in Ireland and shockingly ordered a mass culling of all wolves offering £5 for a male, £6 for a female and 40 shillings for a cub. Unfortunately, the number of wolves began to plummet and the last wolf in Ireland was killed in 1786 in County Carlow. Today, there are only a few reminders of the existence of wolves in Ireland through ring forts that were once used to protect sheep, place names and the great Irish Wolfhound.
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​Number 4 - Irish Bear
For thousands of years brown bears roamed Ireland, preying on deer and fishing in streams for salmon. Much like modern bears in North America, Irish bears hibernated in caves over the long winter months. Amazingly, scientists have revealed DNA evidence that suggests that the Irish bear is the maternal ancestor of Polar bear, which conflicted the previous opinion that North American bears were the ancestors. Additionally, it is thought that the two species may have mated opportunistically during the last 100,000 years which means that they must have interacted during the last ice age. Unfortunately, the Irish brown bear went extinct around 2,500 years ago mostly due to great deforestation and hunting in Ireland. There is a famous Irish myth about a sleeping bear god who will rise from hibernation and come to the aid of their people when called. The summoners of the bear god were called the Mahon’s, the son of the bears. Ironically, the Mahons later became the McMahons which is now a common surname around the world. Today, all that remains to remember the Irish bears are a few sculptures and a Guinness poster.
​Number 5 – The Irish Elk
Megaloceros giganteus, the Irish elk, is one of the largest deer that ever lived. It stood at seven feet tall at the shoulder and its antlers spanned an impressive 12 feet wide. Their enormous antlers are thought to be due to sexual selection, a trait to impress females. It had long been thought that their antlers were purely for display but recently scientist have indicated that they may have also been for contests. At their largest males weighed a massive 1,500 lbs, roughly the size of the modern Alaskan moose. Strangely, the Irish elk is not an elk at all but a deer, the name was coined due to its sheer size and the original excavators believed they found the remains of an extinct species of elk.  The Irish elk was not exclusive to Ireland but was named so due to their most famous and well-preserved fossils were found in peat bogs across the island. Although impressive, their wide antlers became a maladaptation, and contributed to their eventual extinction in 7,700 BC.
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Image sources:
  • Auk image: https://www.bbc.com/news/science-environment-50563953
  • Irish Lynx Image: https://www.breakingnews.ie/lifestyle/four-amazing-animals-that-could-be-reintroduced-to-ireland-1019270.html
  • Ring fort image : https://www.amazing-grace.ie/an-grianan-of-aileach
  • Irish wolves’ mythology Image: https://earthandstarryheaven.com/2015/05/13/irish-werewolves/
  • Guinness Bear Image : https://commons.wikimedia.org/wiki/File:Guinness_StoreHouse,_Dublin._Advertising_Exhibit._-_geograph.org.uk_-_626611.jpg
  • Elk Image: http://news.bbc.co.uk/2/hi/uk_news/northern_ireland/8316262.stm

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What a beautiful hypothesis! It explains a lot!

27/6/2022

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by Lorenzo Ricolfi
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The Italian version of Charles Darwin's The Origin of Species opens with a preface by Luca and Francesco Cavalli-Sforza. They are two of the four children of Luigi Luca Cavalli-Sforza, an Italian geneticist, academic, researcher, and professor emeritus at Stanford University in California, who died in 2018 and became known for his research activities in population genetics. He was also involved in anthropology and history in his studies of human migration.
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From https://www.nytimes.com/2018/09/19/obituaries/luigi-cavalli-sforza-dies.html
Since I could not find the English version of the preface anywhere, I would like to translate and summarize it in this article. Therefore, the following text is a summary and translation of the preface written by Luca and Francesco Cavalli-Sforza.

Translation: "It is said that when Laplace, the great French astronomer, presented Napoleon with a copy of his Celestial Mechanics, in which he described universal gravitation and advanced hypotheses on the formation of the solar system, Napoleon remarked: "Mr Laplace, they tell me that you have written this big book on the design of the universe, without ever mentioning its Creator". "This is a hypothesis I did not need", replied Laplace. When Napoleon, amused, reported this conviction to the mathematician Lagrange, he exclaimed: "What a beautiful hypothesis! It explains a lot! ". Two hundred years later, modern texts on astronomy continue to describe the behaviour of celestial bodies without the need for a God creator. In science, no unnecessary hypotheses are introduced to explain events. While no one nowadays argues about divine intervention in the history of the cosmos, a similar question resurfaces from time to time in biology. Since Darwin's time, the theory of evolution has made enormous progress and can explain a great deal of the history of life. Today, our relationship with primates is no longer in question. It has been proven beyond any reasonable doubt.
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From Stutz, 2014: https://www.researchgate.net/publication/264417273_Embodied_Niche_Construction_in_the_Hominin_Lineage_Semiotic_Structure_and_Sustained_Attention_in_Human_Embodied_Cognition/citations
Nevertheless, it still meets with the most vigorous resistance from the ultra-conservative fringes of Baptist Christians (a powerful political force in the south of the United States) and ultra-orthodox Jews. On the other hand, it does not seem to create any difficulties for either Catholicism or Islam. What is questioned today is whether evolution is sufficient to explain the extraordinary complexity of life: how is it possible that living beings have developed such a variety of forms? How can an organ such as the eye have achieved its extreme complexity only under natural forces?
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From: https://www.phos.co.uk/journal/the-evolution-of-sight
​Someone says there must be an Intelligent Design guiding the history of life, intervening in the mechanisms of evolution (with a view to some goal, it is assumed, but this is not stated). The Intelligent Design movement was born as a political fact in the United States; it is promoted by foundations financed by ultra-conservative billionaires and engaged in specific activities, such as supporting those who sue state schools to have the biblical account of creation taught alongside the theory of evolution as an equal alternative. The extreme right-wing label with which the movement was born does not help its spread in Europe, where there has been enough ideology. The absence of scientific arguments makes it fiddly to counter directly. An organism can only live if it interacts with its living environment to obtain food and can only pass on its DNA to the next generation if it becomes an adult and reproduces. However, the environment is constantly changing. Only those who remain 'adapted' to their environment can continue to live. Natural selection acts by automatically filtering, like a rigid sieve, the best types to survive and reproduce, environment by environment and circumstance by circumstance.
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From: https://www.britannica.com/science/evolution-scientific-theory/Adaptive-radiation
The theory of evolution by mutation and natural selection says precisely this: living species evolve under the impetus of chance and necessity. Darwin's theory of evolution provides an excellent key to interpreting what we see around us and deepening our knowledge of the molecules that make life possible." - End of translation.
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Science and religion have always had harsh disagreements about explaining the existence of the observable universe from the earliest known periods through its subsequent large-scale evolution (of both abiotic and biotic factors). My opinion is that science should not be concerned with the beliefs of others if the views of others do not limit science. But, at the same time, religions should help scientists find the right path following moral rules and ethics. Both science and religion are great powers that give humankind its singularity. Therefore, they should work together to make our species more just, educated and happy.
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Farewell and welcome

31/5/2022

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by Shinichi
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Last week, the I-DEEL lab gathered to have a farewell party for Cat who worked on the "PFAS project" for the last 2 years. This project is our lab’s first research synthesis project in environmental sciences, and Cat played a major role. Now she is in Europe and travelling around the world for the next several months (detoxifying PFAS, I presume).

We also welcomed 4 new PhD students to our lab: Lorenzo, Kyle, Coralie and Jess. Lorenzo will further synthesize the PFAS literature while Kyle will work on the pesticide pollution literature. Coralie will develop new meta-analytic tools, working with Prof David Warton. Jess, who did Honours degree with us already, will apply deep learning methods to Australian wildlife image data, working with Prof Richard Kingsford, people from Taronga Zoo, and NSW Wildlife and National Parks.

This is going to be a huge variety of research work - just like the food on the table (see picture above - this is a potluck party where everybody brings a dish!). As they say: “Variety is the spice of life”.
​I am very much looking forward to what the future will bring to I-DEEL!
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Vegan food guide - Sydney edition

30/4/2022

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By Patrice Pottier

​Being vegan for nearly five years, I have noticed drastic changes in the accessibility and fanciness of vegan food. The days when people thought vegan food only consist of salads and seeds are far behind! Plant-based foods can take all shapes and forms, and I guarantee you that you may not be able to tell some meals are vegan in a blind taste.

Let me introduce you to 10 vegan restaurants you must try in Sydney. Forget the old dry veggie patty - I guarantee you won’t be skeptical about vegan food after trying those places.
1.   I Should be Souvlaki
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Fan of mock meats, garlicky sauces and delicious wraps? Souvlaki got you covered! I swear even the hardest “carnivores” will succumb to the flavours of the signature Souvlaki.
​Recommendation: Mix (Soy-based “lamb” and “chicken”) Signature Souvlaki.
Address: 399 King St, Newtown
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​2.   Golden Lotus
Probably the best Vietnamese vegan restaurant in Sydney. Impressive variety of dishes, great service, and delicious.
Recommendation: Laksa, chef’s recommendations.
Address: 341 King St, Newtown
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3.   Yulli’s
While Yulli’s is mostly known for their brewery, they also make delicious food!
The dishes are delicate, beautifully presented, and flavourful (especially with a freshly brewed beer).
Recommendation: San Choy Bow, Pizza
Address: 417 Crown St, Surry Hills
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4.   Shift Eatery
Who doesn’t like toasties? These ones taste like no other! The whole staff is vegan, and the food is fresh and flavourful.
Recommendation: The Reuben’s vegan brother, Steve
Address: 2/241 Commonwealth St, Surry Hills
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5.   Nutie
Craving sweets? Nutie has the best treats around the area.
Recommendation: Strawberry cheesecake, Donuts
Address: 44 Holt St, Surry Hills
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6.   Lonely Mouth
Have you tried RaRa ramen and loved it? Well, folks from RaRa made a fully-vegan version of their restaurant – Lonely Mouth. There are not many options in the menu, but even to fulfill your stomach!
Recommendation: TanTanmen, Sunflower & Hempseed Shoyu
Address: 275 Australia St, Newtown
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7.   Gigi Pizzeria
Authentic Napoletana-style, woodfired pizza. I don’t think I need to say anything else!
Recommendation: Calzone con Melanzane, Lasagna
Address: 379 King St, Newtown
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8.   La Petite Fauxmagerie
Before you say that “Vegan cheese is boring” – try this place! Fetta, mozzarella, ricotta, blue, brie, halloumi – options are endless, and they will blow your mind!
Recommendation: I am not of big fan of cheese, so I haven’t tried this place myself. It is, however, highly recommended by cheese-lovers!
​Address: 412 King St, Newtown

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9.   Oh My Days
Being French, I used to miss croissants and other pastries. Not anymore! Oh My Days has a great variety of pastries and they taste really authentic.
Recommendation: “Bacon” & “cheese” croissant, Almond croissant
Address: 99 Glebe Point Rd, Glebe

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10.  Soul Burger
Soul Burger is probably the best option around campus if you are craving for burgers. Ingredients are fresh, and the burgers blook and taste amazing!
Recommendation: Sydney Sider, Southern Fried “chicken”
Address: 49 Perouse Rd, Randwick

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This are, of course, only a short sample of the amazing range of options Sydney has to offer.  Want to find more vegan places? Check out HappyCow – an app that list vegetarian and vegan restaurants worldwide.
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I hope you enjoy this culinary discovery! 😊
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The endless fight for acclimatization

31/3/2022

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by Lorenzo Ricolfi

"It is not the strongest of the species that survives, nor the most intelligent; it is the one most adaptable to change.”

​This quote is cool but it is often associated with Charles Darwin's Origin of Species when Charles never wrote that! Instead, it was formulated by Leon C. Megginson, Professor of Management and Marketing at Louisiana State University. (To read about this anecdote, click on this link).
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Anyway, adaptation is a capacity that plays an essential role in evolutionary biology; it is a dynamic process that adapts organisms to their environment, improving their evolutionary fitness. Similarly, but on a different time scale, an individual's acclimatization capacity to a change in its environment enables it to maintain fitness across various environmental conditions. My name is Lorenzo Ricolfi, and, like anyone who has survived these two years of the pandemic, I struggle every day to acclimatize to change.
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The COVID-19 pandemic has dramatically upset our habits and daily routines. Moreover, it has presented us with a tough challenge: to cope with dramatic and sudden changes. I lived my life in Italy, studying and working as a researcher at the University of Rome, until January 2020, when I took a plane to Brisbane. Study and work followed each other without a gap year, and I needed a breath of fresh air and an adventure before returning to Italy six months later. It was a good plan.

Well, it never came true. The World Health Organization declared the outbreak a Public Health Emergency of International Concern on the 30th of January 2020, 21 days after my landing in Australia. On the 31st of January, two Chinese tourists in Rome tested positive for the virus, and Italy was the first country in Europe to be affected by the pandemic. A month and a half later, the Italian army vehicles had to transport the dead out of the city of Bergamo as its crematorium struggled to cope. This disaster happened only a week after the World Health Organization officially declared COVID-19 a pandemic. That was the situation.

Australia at that time was in a bubble of its own, far removed from what was happening overseas. I was reading the news on the web, and it all seemed absurdly surreal. Virus? Wheezing and difficulty breathing? Social distancing? Masks? It was hard to assess and assimilate the news with reason and objectivity. And I had to take a decision now and immediately: return to my country or keep staying in Australia. How could I take such a decision lightly?

​There were many factors to consider and the implications too. Italy was in full lockdown, and although I was worried about my loved ones, I decided to stay, not knowing when I would return. I would return when the situation improved and the pandemic had passed. Days turned into weeks and weeks into months, and I began to need work. I held about ten different jobs in the time that followed. I worked as a dishwasher, a waiter, a kitchen hand, a warehouse worker, a driver, a delivery guy and a carpenter. I had never done any of these jobs before in my life. Months turned into years, and I realized that I wasn't coming back anytime soon. Australia closed its borders. There were no more planes in the sky.
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Suddenly, my life was completely different, and the sense of nostalgia was strong. If I couldn't go home, I wanted at least to get back to what I was passionate about. I decided to take the English exam necessary to apply for a research project at the university level. I studied and passed the exam with flying colours.

Meanwhile, while surfing the websites of various Australian universities, I found an exciting laboratory at the University of New South Wales in Sydney. As luck would have it, the lab was looking for a PhD student with my background. I immediately got in touch and, after devising a research proposal that matched my interests and the knowledge and skills of the lab, I applied for a scholarship from the Australian government to cover the PhD.

It is now the beginning of April 2022, it has been two years and three months since I landed in Australia, and I started my PhD a couple of months ago. The pandemic situation has improved thanks to vaccines, although the pandemic is not over. And I have still never returned home. Over the last two years, the changes in my life have been massive, but I am thrilled with where they have taken me, even though they were unplanned and presented me with some callous times and challenges.
The point of all of this is that although we constantly try to categorize, order, and simplify reality, it is permeated by the chaos in which change is the engine. We need order and stillness in our environment and minds, but we cannot avoid change. Instead, we must learn to be flexible enough to shape ourselves without breaking or losing our identity. It is a challenging game based on compromise and sometimes on acceptance and letting go.

The pandemic has abruptly put reality before us, where not everything goes as planned. But it also reminded us of one thing: there is nothing wrong with that. Plans in life are necessary, but their implementation is not to achieve a state of happiness. Instead, an idea and a plan can evolve into something completely different. This turning point may initially be seen as a failure, a crack in the wall of our lives. However, it is only after time that we realize that the plan was but one of many steps, rather than the dividing line between success and failure.
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Around meta-analysis (14): deduplicating bibliographic records

28/2/2022

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by Losia Lagisz
 
Removing duplicated records can be cumbersome. When collating bibliographic records from   multiple literature databases both the total number of records and the proportion of duplicates can be high making manual removal of duplicates extremely time-consuming. Manual resolution of each set of potentially duplicated records is required when using reference managers such as Zotero or EndNote, and especially a screening platform Rayyan (note that deduplication algorithms available in all these are reasonably good at detecting (flagging) duplicating records (exact and non-exact duplicates), but not perfect, so combining different approaches is recommended anyway).
 
Here, I present an efficient workflow in which records from multiple sources (literature databases) are combined in Rayyan (https://rayyan.ai/), then automatically deduplicated using an R script (www.r-project.org), and finally uploaded into Rayyan again for the final round of deduplication and screening. Importantly, apart from Rayyan and R no other software is needed (but, at any stage, you can import/export lists of records into your reference manager to see the records or convert file formats). I assume you are already quite familiar with Rayyan and R.
​ 
The workflow:

​1. Gather the bibliographic files. 

​Download lists of bibliographic references (with abstracts) from databases used to run the literature searches. Most of the time, exporting thema as a .ris file would work best. Rayyan has guidelines for the most commonly used databases on its upload page (see the screenshot below).
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2. Upload files into Rayan.
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Create a new project in Rayyan and upload all files into it. This will create a combined list of records.

3. Run deduplication algorithm in Rayan (optional).

This will give you an idea on how many duplicated records you have in the combined set of records (if less <200 you may want to resolve them manually in Rayyan). To run the algorithm, press a “Detect duplicates” button close to the top right corner of the view with the list of combined references in Rayyan.
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4. Export combined list of records from Rayan.

​This will create one .csv with all references in the same format. To export the records, press a “Export” button close to the top right corner of the view with the list of combined references in Rayyan. In the pop-up window select “All” and “CSV” format (you can include all the fields listed below these options). Note that Rayyan will send you a link via email to download a compressed file. After decompressing, rename the .csv file to something usable (e.g., "FILENAME.csv") and place it in your R project folder.
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5. Upload combined .csv file into R.

Load the R packages needed:
 
library(tidyverse) # https://www.tidyverse.org/
library(synthesisr) # https://CRAN.R-project.org/package=synthesisr
library(revtools) # https://revtools.net/
dat <- read.csv("FILENAME.csv") #load the file
dim(dat) #see the initial number of uploaded references

 
6. Prepare data for deduplication in R.

We will deduplicate by comparing titles. Before doing so, it is good to tidy them up by bring them to the same case, removing extra white spaces and punctuation. We save these “processed” titles in a new column.
 
dat$title2 <- stringr::str_replace_all(dat$title,"[:punct:]","") %>% str_replace_all(.,"[ ]+", " ") %>% tolower() # Removing all punctuation and extra white spaces

 
7. Remove exact title matches in R.

This step uses processed titles to create a new smaller list of references with exact duplicates removed. It will save computational time for the next step (detection of non-exact duplicates).
 
dat2 <- distinct(dat, title2, .keep_all = TRUE) #reduce to records with unique titles
(removes exact duplicates)
 
dim(dat2) #see the new number of records
#View(arrange(dat2, title2)$title2) #an optional visual check - sorted titles

 
8. Deduplicate by fuzzy matching the remaining titles in R.

This step uses string distances to identify likely duplicates - it may take a while for long lists of references.
 
duplicates_string <- synthesisr::find_duplicates(dat2$title2, method = "string_osa", to_lower = TRUE, rm_punctuation = TRUE, threshold = 7)
 
#dim(manual_checks) #number of duplicated records found
#View( review_duplicates(dat2$title2, duplicates_string) # optional visual check of the list of duplicates detected. If needed, you can manually mark some records as unique (not duplicates) by providing their new record number from duplicates_string (duplicates have the same record number), e.g.
#new_duplicates <- synthesisr::override_duplicates(duplicates_string, 34)
 
dat3 <- extract_unique_references(dat2, duplicates_string) #extract unique references (i.e. remove fuzzy duplicates)
dim(dat3) #new number of unique records

 
9. Prepare the data for exporting from R.

Modify the data frame into a format that can be imported to Rayyan (the files saved as .bib or .ris for .csv files cannot be directly uploaded to Rayyan due to some formatting changes happening during processing them in R). This is done by first selecting only the key columns, saving them into a BibTex format (.bib file) and them changing the record labels into the desired format.
 
dat3 %>% select(key, title, authors, journal, issn, volume, issue, pages, day, month, year, publisher, pmc_id, pubmed_id, url, abstract, language) -> dat4 #select the key columns
 
write_refs(dat4, format = "bib", file = "FILENAME_deduplicated.bib") #save into a bib file
 
readLines("FILENAME_deduplicated.bib") %>%
  stringr::str_replace(
    pattern = "@ARTICLE",
    replace = "@article") %>%
  writeLines(con = " FILENAME_deduplicated.bib") #fix the record labels and save again as a .bib file
 

10. Import deduplicated records into Rayyan.

Create a new project in Rayyan and import the modified .bib file. Run the algorithm for detecting duplicates in Rayyan (see Point 3 above). This will reveal potential duplicates that were below the similarity threshold used in R (or have lots of formatting differences). These will need to be resolved manually in Rayyan (usually it is not a big number and some will require human intelligence to tell what counts as a real “duplicate”). After resolving these duplicates you are ready to start screening your deduplicated records in Rayyan.
 
Note: Unfortunately, record fields with authors and keyword information (and many other fields) are stripped from the original records in the above workflow, mostly by Rayyan. For this reason, records exported from Rayyan are usually not suitable for direct use in bibliometric analyses. But, at least, you can claim that your screening of bibliographic records in Rayyan was blinded to the authors’ identity.
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Embrace the destination, but be sure to enjoy the journey

31/1/2022

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by Hamza Anwer

One would have heard the following quote at some stage in their life: “The journey of a thousand miles begins with the first step”. However, you don’t hear too much relating to how that journey went or how it ended.
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Chapter 1 (2018) - Rollercoaster

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When I first started my PhD, I was armed with an optimism that one feels when they hear that quote, a sense of dipping into the unknown willingly. I wasn’t quite sure what to expect. My first year could only be described as a rollercoaster. It felt like it flew and there were plenty of moments where I thought I would not make it out alive. The learning curve was a lot steeper than I thought and I had to master it, fast, otherwise I would be left behind. I look back now, and I can’t understate how valuable that year was. I learnt a lot about myself and was able to sharpen my skillset as well as my mentality and approach. I learnt to drop bad habits and develop new ones. I took criticism on board and told myself to see every opportunity, good and bad, as a learning opportunity. It set the stage for a very exciting Chapter 2.
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Chapter 2 (2019) - Foundation

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This was the year everything really started to take shape. I had a good sense of direction and the work I achieved in this year really set the ultimate foundation. While I had several other tasks in the background, my major milestone was completing my zebrafish work. It was long. It was gruelling. Nailing down the tiniest details was crucial to ensure everything didn’t fall apart. There was no room for significant error although I came horrendously close several times. Whilst the process was by no means smooth, the times in the lab during this year were some of my favourites. I had a great support group and grew in confidence each day. Thankfully, I was able to complete my experiments before we entered the era of Covid-19. Out of the frying pan and into the fire I went.
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Chapter 3 (2020) – Knuckling down

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My time at Garvan Institute of Medical Research was over. Covid-19 was sweeping across the world and soon enough, we had entered the lockdown phase. Working from home and online meetings became the norm. I embraced every moment. I looked at it as an opportunity for growth. I had to adapt and focus on moving forward. I embraced a good rhythm while working from home but there was still plenty of work that needed to be done, even when I got back to campus and was grinding away at my desk. I had completed the foundations, but it was all about putting it together in coherent pieces of writing to be published. Slowly but surely, it was all coming together but I was 3/4 into my PhD and still had not published a single paper or completed a single chapter. It was worrying but I pressed on. I still had time. I just needed to use my time wisely. I had everything I needed. I just needed to finish strong.  

Chapter 4 (2021) – Finish line

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“There are better starters than me, but I'm a strong finisher.” -Usain Bolt

I think this quote by Usain Bolt really sums up my PhD. If I was running a marathon, my start would be akin to one stumbling and landing face first on the ground. However, knowing I can make up for lost ground if I push that extra bit harder. Which is what I did. I started the year strong with my first publication (can read about that here). The first publication formed the first chapter of my thesis. Slowly but steadily, I worked on putting more components together. The next achievement was publishing my meta-analysis which would form the final chapter of my thesis as well as my general introduction. Two chapters down, two to go. The final two chapters were the most difficult because they comprised the bulk of my zebrafish data. In addition, they complimented one another so I had to ensure a lot of things were consistent. The final few months were intense, but after plenty of deliberation, I managed to piece all the components together. I could finally see the finish line. It looked glorious.

Fast forward to 2022, my thesis has been successfully submitted. The final two chapters have been sent in for publication. I am working full-time at Cure Brain Cancer Foundation and am better placed than ever.

To finish, I can’t emphasize enough how important my lab was in this journey. From my supervisors to lab members, everyone played a crucial part in where I am now. I thank you all.

“The way a team plays as a whole determines its success. You may have the greatest bunch of individual stars in the world, but if they don't play together, the club won't be worth a dime” – Babe Ruth
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Reflecting on 2021

29/12/2021

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by Shinichi (he/his)

I used to do the end-of-the-year blog but last few years I have not done it, which is a shame. It is always good to have time to reflect on the past year. So here I am.
 
I-DEEL did remarkably well despite the pandemic limiting our interactions and slowing down empirical work we planned to do. Twelve of our members (including former members) published their first-author papers in 2021. I congratulate them as it takes a lot of work and patience to publish. This is especially so as I demand high quality and open practice, and transparency, all of which take time to do. Also, for 3 of these members (Dom, Hamza & Patrice), this was their very first lead-authored paper, so I am very happy for them. The first paper is something very special which I can give to my students as a supervisor.
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And we were lucky to have the end of year BBQ party to celebrate our success. And we congratulated Hamza submitting his PhD thesis and getting a job as a research manager at a non-profit. I am relieved as last 3 PhD fledglings have managed to secure a job – and I am very proud.
 
Certainly, 2021 has been another difficult year, but I believe that it is up to us to see whether this as an opportunity or not. An opportunity to time to start something new or which we always wanted to do. Or just keep doing what we are supposed to do, which is remarkably difficult.

​I am looking forward to 2022 – hopefully some overseas trips to catch up with friends and family and new challenges from which I can grow with I-DEEL members and my collaborators around the world. A Happy New Year to you all!
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How to be a better ally to transgender folks in academia

28/11/2021

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by Jess (they / them)

This year marks one of the worst years so far for transgender1 (trans) folks. So far in 2021, violent hate crimes have taken the lives of at least 48 trans people in the US alone, while more deaths either go unreported or that individuals took their own lives. While our society has become more accepting, there is still strong stigma against those who challenge the existing gender norms. In addition to the lack of proper education, this stigma has led to a lack of support from family and friends of some trans individuals.

The idea that there are more than 2 genders might sound contemporary for some. On the other hand, many First Nations and Polynesian cultures have long embraced gender fluidity. For example, ‘māhū’ in Hawaiian culture represents someone ‘in between’, or someone of the third gender. The western concept of the gender binary was not introduced until colonialism, as foreign missionaries considered indigenous believes immoral. Since they were developed separately, indigenous believes of gender and the modern LGBTQIA+ framework are not identical to each other. However, both can help us describe and understand gender and its fluid-nature.

As a research student who is trans and non-binary2, I often find my identity being a source of contention among academics and graduate students. I have been a spectator of many debates surrounding trans issues, from whether or not J. K. Rowling is transphobic (she is, because she is a keen supporter of transphobic policies in the UK), to whether or not the ban on trans women, who have not undergone gender reassignment surgery, of McIver’s Ladies Bath is discriminatory (it is, because not all trans people opt for surgery). Although it is obvious to me where the problems lie within these debates, I often forget that some trans issues can be complex for those who are cisgender3 to fully understand them. Unfortunately, I find it quite jarring when these conversations are happening. To prevent myself from being emotionally triggered, I shy away from actively participating and thus failing to point out the transphobia right away.

In light of Trans Awareness Week (November 13-19) and Transgender Day of Remembrance (November 20), I would like to offer some advice as a trans and non-binary person and hopefully spark meaningful conversations around LGBTQIA+ issues. However, my perspectives are likely to differ from others of the trans community since we all live different lives and have different struggles. This is therefore based solely on my personal lived experience4 in academia. Other forms of phobias, such as homophobia, and biphobia, will not be directly covered here today. Perhaps another time! The following are some tips on how to create safer spaces for your trans colleagues:
1. Share your pronouns. 
Even if you are someone in the gender binary, i.e. a man or a woman, it signals to us that it is safe to approach you without having to hide our identities. For example, adding your pronouns to your twitter profile and presentation slides is a good start.
2. Use our pronouns. 
Adjusting to someone’s new pronouns can take time, especially if you’ve known them for a while. If you have unintentionally misgendered someone, be kind to yourself and make efforts to correctly gender them in the rest of the conversation. There is no need to feel overly guilty about it. In fact, I misgendered myself a lot when I first came out as non-binary and am still learning.
3. Use gender-neutral language. 
For example, instead of saying ‘ladies and gentlemen’, try using ‘folks’, ‘friends’, ‘everyone’, ‘distinguished guests’, etc., to accommodate all crowds.
4. Do not ask us about our genitals, surgeries, or hormonal treatments without consent. 
Although not all trans people experience gender dysphoria5, mentions of genitals, surgeries, or hormonal therapies could trigger negative emotions towards one’s body. Discussions of surgeries and treatments can also be difficult for those who require them but are unable to access them. Having trouble accessing healthcare can be caused by financial hardship, living with transphobic family members, etc. If you are curious, the internet can be a very helpful resource. Only ask these questions if you have established a trusting relationship with said trans person and/or have their consent. Personally, I am quite open to share my experience, but would also really appreciate a heads up as I struggle with gender dysphoria.
5. Know the difference between ‘sex’ and ‘gender’.
I have in the past come across numerous journal articles, books, and surveys incorrectly using the terms ‘sex’ and ‘gender’. ‘Sex’ refers to someone’s anatomical makeup, or assigned gender at birth, i.e. male, female, or intersex. While ‘gender’ refers to someone’s gender identity – one’s internal sense of their gender. Some examples of gender identities include man, woman, non-binary, agender6, and bigender7. ‘Sex’ and ‘gender’ refer to different aspects of our identities and are not interchangeable.
6. Include gender-diverse peoples in addition to women when ‘addressing gender equity’.
I have, in 2021 alone, stumbled upon job listings of 2 respective ecology labs from reputable Australian universities that had set aside certain positions for candidates who identify as women, to ‘address goals for gender equity’. While we need more women in academia, including gender-diverse peoples is a nod to our existence. Being inclusive will also show your potential candidates that your research group is a safe space for members of the queer community.
7. Invite queer and trans colleagues into conversations on LGBTQIA+ issues.
As with all discussions surrounding social issues, it is vital that we listen to the concerns and needs of the targeted communities, e.g. actively listening to people of colour on their views towards racial issues and injustices. If you are cisgender, you are unlikely to experience active forms of transphobia. Include us in your conversations to gain new perspectives on issues that directly affect us.
8. Being an academic doesn’t mean that you must flex your academic muscles in all situations.
It might seem ‘fun’ or ‘challenging’ for you looking for evidence to validate our existence, but being constantly questioned and doubted can cause us unnecessary emotional stress. While discussions about queer issues are important, we must also learn to listen and understand. After all, knowledge and experience can be mutually exclusive.
9. Call out transphobia.
Although scientists are generally quite open-minded and accepting, academia isn’t immune to transphobia. While I have not personally experienced any active forms of transphobia, I have heard comments such as ‘that’s really weird’, or others discuss certain issues with a negative tone. It is therefore a good idea for us all to regularly challenge and unlearn our assumptions about gender and educate ourselves. Actively help one another and raise questions gently. If you have been called out for making transphobic comments, instead of taking it as an offence, actively listen and learn from the point of view of trans people.
10. Show empathy when a trans colleague has experienced transphobia.
Instead of listing all your Equity, Diversity, and Inclusion (EDI) awards and policies, be human and express compassion. Receiving harassment for simply being our true selves is a very distressing situation. It makes us feel unsafe and rejected. Let them know that you will work on providing a safer environment, actively listen to their concerns, and take actual steps to improve existing policies to create a safer workplace.
​
This might seem like a long list of etiquettes, but with time and practice, things will come naturally. I’m sure if I think hard enough, I can come up with even more tips, but this will suffice for the time-being. Although Trans Awareness Week only lasts for a single week, it doesn’t mean that our education ends here. Even as a trans person, I find myself gaining new insights all the time. Transgender people experience transphobia everyday around the world. If we can comprehend complicated models and equations, surely, we can accept those who are different from us. Actively listen, learn, and lift each other up.
​
To end this article, please enjoy this lovely comic that my good friend Mira had shared with me, created by the artist Aaron Billings on Instagram (@dillings).
Footnotes
1  transgender – describes a person whose assigned gender at birth does not align with their inner sense of gender
2  non-binary – describes a person who identify as neither man nor woman
3  cisgender – describes a person whose assigned gender at birth is aligned with their inner sense of gender
4  lived experience – a representation of the experiences and choices of a given person, and the knowledge that they gain from these experiences and choices (Wikipedia)
5  gender dysphoria – emotional distress caused by a mismatch between one’s body and gender
6  agender – describes a person who does not have a gender
7  bigender – describes a person who identify as a man and woman simultaneously
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Staying on top of your mental health

31/10/2021

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by Szymek Drobniak
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​The 2021 Mental Health Month has just ended – in October we gave special attention to people suffering from all sorts of mental health issues. This was also a perfect opportunity to emphasize the importance of support and respect towards any mental health problems, no matter how big or small they might seem. The general attitude towards psychological disorders has changed tremendously over the past decades. The dynamics of this change varied a lot between countries and social groups but overall, there seem to be greater awareness of the importance of caring for one’s mental health, and deeper understanding of psychological challenges other people around us may be facing.
In academia, the issue of mental health is still largely neglected. Many institutions often offer specialist counselling services to their employees or organize events aimed at alleviating some of the psychological impact academic lifestyle can have on scientists (like, e.g., two Recharge Weeks organized at UNSW during the last COVID-19 lockdown). We still, however, lack universal acknowledgment of psychological difficulties so tightly linked to an academic career. The current research culture, by incentivizing productivity and overachievement as core characteristics of a successful academic, lacks mechanisms that would protect the mental wellbeing of scientists. In 2018, Evans et al. published a report in Nature Biotechnology that painted a bleak image of the mental wellbeing of graduate students: with roughly 40% of them suffering from various forms of anxiety or depression, the report concluded that this group was more than six time as likely to experience these psychological disorders than the general population. Independent researchers and faculty members may be similarly affected, although precise numbers are more difficult to extract. Towering piles of to-dos, faculty meetings, supervision of students that we would like to see excel and shine, and grant proposals only add to the constant pressure exerted by the community that seems to value unrealistically productive publishing activity, and that places more emphasis on one’s citation scores than on all aspects of the academic life. At times we are almost convinced the culture has moved away from traditionally valued h-indices and impact factors, only to realise it is like that all over again when we try to submit our next grant application.
​Throughout my academic life, I always struggled to navigate this narrow labyrinth of expectations, having to tackle my own mental health issues. Mine were of the kind that could easily stop my scientific career to a grind: severe social anxiety has always prevented me from taking full advantage of conferences and meetings, and my attention deficit disorder (ADD) constantly makes it difficult to stay on top of my tasks and to-dos. For people that have never experienced ADD it may seem bizarre not to be able to focus on one task and lead it to successful fruition: it should be so easy to just sit and work your way through it, right? The key thing to understand is that in case of all similar psychological conditions we are trying to fight our own  mind. In the same way as we would not expect anyone to be able to “will” one’s broken limb to suddenly heal and mend itself, it is impossible to wield one’s brain to repair mental illness or neurological differences. Also, as we would expect someone with a broken arm to seek specialist’s help, the same should be true for those struggling with their own mental wellbeing. Thus, in spite of still occasionally heard encouragements to “put oneself together” or “it’s only in your head” – we should never underestimate the importance of good mental health, and we should never delay seeking professional help if our mind makes our life difficult. Psychotherapy and medication are no longer a stigma – and your mind will thank you tremendously for the love and care you can provide it with.
​Having said that – it is worth having a few tricks in your toolkit, to ward off the negative impacts of mental conditions you may be experiencing. Procrastination – a milder form of what people with ADD are experiencing – can be managed in everyday life by following a few simple rules:
  • Define small, manageable goals (instead of “write the introduction” try breaking it down into smaller tasks, ideally achievable within short, e.g., 1 hour, chunks of time);
  • Consider embarking on a journey with a Pomodoro technique – a work management tool that makes large swaths of to-do lists controllable by forcing you to work in small, 20-minute chunks;
  • ADD sufferers love to endlessly scroll through social media as it relieves lack-of-focus tension – consider timing your social media attention (nowadays most phone operating systems offer such functionality; be realistic! – if you use social media for 4 hours a day, cutting down to 30 minutes won’t happen and you’ll be more tempted to cheat and override the time limits);
  • Be easy on yourself and do not mentally punish yourself for not achieving your goals for the day;
  • Try meditation – you can find lots of guiding videos in the web, I can also recommend the Headspace app; meditating regularly is not easy and requires commitment – but it can work wonders for your mind;
  • Be honest with your supervisor – they likely have their own mental struggles too!; working together to find the routine that works best for you will benefit both parties.
​You are probably wondering – what about social anxiety? For a long time, it has defined my life and the way I participated in conferences and similar meetings. With some surprise, I also learned a while ago that it is a much bigger issue than I expected and that many more people experience similar limitations. Although I have never fully overcome mine – there are some tricks you can use to help you push yourself a tiny bit out of your comfort zone:
  • Again – be realistic J If mild social anxiety marks your life, you probably won’t jump into a loud, chatting group of people to meet an academic you’d love to talk to; instead – try planning ahead, e.g., send him/her/them an email beforehand asking for a chat, or try to catch them in a bit less socially heavy contexts (e.g., browsing through exhibitors’ stalls or attending a less crowded talk); such pre-emption requires some strategic planning (e.g., browsing through the program beforehand) but it pays-off!
  • If you take part in organising a conference – consider suggesting a mixer or other social gather-up for shy people – believe me, this helps to break ice very quickly and empowers participants with much more self-confidence elsewhere during the meeting;
  • If asking a question terrifies you (some may recognize this: you’ve just seen a wonderful talk, your head is buzzing with questions, but you just sit there trying to overcome anxiety, observing with horror all your best ones being asked by others) – make a contract with yourself: choose one question, and on the count of three just rise your hand – whatever happens after that will anyway drown in your excitement and you’ll do great, trust me.
​Above all – if you feel overwhelmed – do not stay at home. Meet or call your friends, or just go for a walk. Nothing clears head better than mixing with a crowd of strangers or exploring a quiet forest path – whatever suits you better.
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Created by Losia Lagisz, last modified on June 24, 2015