ASTMH 2016 in Atlanta | Ken Gavina

I recently had the pleasure of attending my first international conference, the 65th Annual General Meeting for the American Society of Tropical Medicine and Hygiene (ASTMH) in Atlanta, Georgia. The conference was held at the Marriott hotel in the heart of downtown Atlanta. This being my first trip to Georgia, I was absolutely spoiled by the warm weather (+20ºC in the middle of November), the delicious food, and the southern hospitality I received when visiting different venues and walking around the neighborhood. A definite highlight of the trip was visiting the Centers for Disease Control and Prevention and the David J. Sencer Museum.

The conference itself spanned over five days and was easily the largest one I’ve ever attended. The conference started with a pre-meeting course I registered for titled, “The Science of Disease Elimination”, which I found to be quite enlightening. The course featured several different speakers and covered a wide range of topics from statistical modelling to political and financial support. The day only got better as the opening reception and keynote address was given by Dr. Carissa Etienne, director of the Pan American Health Organization (PAHO), who spoke about Zika.

I had the pleasure of presenting my research via a poster presentation. The poster I presented focused on work I am doing as part of my PhD, using molecular diagnostics to survey the burden and clinical impact of submicroscopic malaria in pregnancy in Colombia. I developed an RT-qPCR based method to distinguish submicroscopic malaria infections at the species level (Plasmodium falciparum or P. vivax) and we used this assay to assess the disease burden in pregnant women. We found that submicroscopic malaria occurs frequently in pregnancy but despite this, is not associated with negative birth outcome20161117_145949.jpgs. My poster was well received and generated a lot of interest from other researchers working in a similar field.

What I got most out of the conference was the opportunity to engage with my peers, as well as meeting and discussing my work with some very well respected researchers in the field. Memorable moments included talking about career paths with Dr. Peter Crompton from NIH, listening to a talk by Dr. Kayvan Zainabadi from the University of Maryland about a new highly-sensitive diagnostic method for malaria using dried blood spots, meeting trainees from Dr. Kevin Kane’s lab (one of our lab group’s collaborators) at the University of Toronto, and discussing my research with Dr. Stephen Rogerson from the University of Melbourne. It was a great overall experience and it would not have been possible without the support from HPI which allowed to attend the conference.

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The Innate Lymphoid Cell conference in the heart of Berlin | Edina Szabo

The 2nd EMBO Conference on Innate Lymphoid Cells was held in Berlin, Germany at the end of November, 2016. To support the European scientific communities the European Molecular Biology Organisation (EMBO) holds conferences and conference series that cover different and evolving aspects of important subject areas. The conference was held in a historic building in the heart of the city, called Kalkscheune (Limestone barn). The place was already set for Christmas, and had a great feeling about it.

The first day of the conference started with registration in the afternoon, followed by two intensive full days, and closing with the Gala dinner. Dan Littman from the NYU School of Medicine, New York, gave the keynote lecture, and well introduced the topic with his talk entitled “Role of ILCs in integrating host responses to microbiota”. The keynote lecture was followed by a session on “ILC development and activation” with speakers from the US, Netherlands, from the Institut Pasteur in Paris, and McGill University in Montreal.

The second day started early at 8.30 am with talks on “Regulation of ILC fate and functions”, and continued with “ILCs homeostasis” in the afternoon. I have particularly enjoyed the talk by David Withers from the University of Birmingham. His group is looking at the importance of a particular receptor for cytokine production by ILC3 cells in the small intestine. Another talk that caught my attention during the afternoon session was the “ILCs and immune regulation at barrier surfaces” presented by David Artis from Cornell University, New York. His findings showed that commensal microbes have a significant regulatory influence on lymphocyte, innate lymphoid cell, and granulocyte function. After the talks we had a chance to explore the city a little bit in the evening, and try the local cuisine.

The final day started early as well, and by then most of us were pretty exhausted, but we had great talks and the gala dinner to look forward to. Emily Thornton’s talk from University of Oxford, was very interesting, which was exploring how ILC3s are involved in the initiation of acute intestinal inflammation. In the afternoon also several talks were on intestinal ILCs, including speaker such as Henrique Veiga-Fernandes from Lisboa, Arthur Mortha from New York, and David Voehringer from Germany. My favourite talk of the day and the whole conference was the “Innate lymphoid cells and IL-22: functional analysis in zebrafish” by Pedro Pablo Hernandez, whose project is to investigate the existence of ILCs and the conservation of the function of IL-22, which is produced by ILC3 cells.

The highlight of the day was the Gala dinner in the Natural History Museum, right by the dinosaur exhibition.

I would like to take the opportunity to thank NSERC CREATE HPI for funding to attend this conference. I had a great time at the conference, and learnt a lot about ILCs, as well as I had a chance to visit some of my family in Berlin.

 

NALMS | By Michelle Gordy

Two men walk into a bar. The first man tells the bartender “I’d like some good ‘ol H2O”. The second man says “I’ll have some H2O too”. The second man died.

Despite this horribly punny joke, I think it’s safe to say, we can all agree that water quality is important, whether it is your drinking water, or the water used for recreational purposes, like lakes. In consideration of our changing climate, our increasing demand and use of freshwater sources, and our ever-expanding anthropogenic impact on the environment around us, it is pertinent that we work to protect the fresh water we have and make sure it is sustainable for generations to come. Such a task cannot be done in isolation, but requires the collaborative efforts of everyone. Hence, this year’s theme of the North American Lake Management Society’s (NALMS) International Symposium was “Science to Stewardship: Balancing Economic Growth with Lake Sustainability”.

I recently had the pleasure to attend the annual NALMS meeting in Banff, Alberta. Held at the Banff Springs Hotel, the conference literally took place in a castle in the mountains, and the views were outstanding! (Insert pics here)

The conference started out on a high note—literally—as the pub crawl on the first night ended at a karaoke bar with a mechanical bull, and yes, I rode it. Let me just give big props to all the cowboys out there and to NALMS for really knowing how to get a conference off to a good start!

Of all the conferences I’ve attended, this one was quite unique, in that the attendees were a conglomerate of scientists, government representatives, lake managers, members of watershed associations and stewardships, and environmental consultants. Topics spanned all areas of lake health and management, from the molecular level to the involvement of stakeholders and citizen scientists. The conference provided a unique perspective into applied research and all levels of opportunity to be involved in protecting our lakes. It was particularly interesting and encouraging to see the level of community involvement in accomplishing much of the data collection for many studies.

What I found most appealing about many of the talks was the practicality around them. I learned some useful things about how to best use maps to communicate data to the public, as well as how not to use maps…probably a much more important skill. I learned about the importance of involving the community in lake-based monitoring projects early on, to attain a common ground and understanding about the importance of the data collection on top of maintaining a healthy lake ecosystem.

While this conference was not parasite-focused, and perhaps the only talk about parasites was the one I gave, it was such a great opportunity to gain a new perspective outside of the little box that is my research. I am incredibly thankful to HPI for funding my attendance to this conference.

 

NIPGIT 2016 in Banff | By: Christina Amat

I was fortunate to be able to attend the NeuroImmunoPhysiology of the Gastrointestinal Tract (NIPGIT) conference this year, taking place in the beautiful mountains of Banff, Alberta. The conference took place at the Banff Centre – our meeting room featured the beautiful Rocky Mountains as our backdrop and we enjoyed our meals in the awesome Vistas Dining Room. Such an amazing view to start off the morning and end the day!

The conference was one of the smaller ones I’ve been at, and with only about 100 people in attendance, it was easy to get to know the fellow attendees and spend some time talking with researchers who are amongst the best in their field. Some of my personal highlights included learning how virulent strains of bacteria can switch on or off genomic “hot spots” to hide from the host immune response by Dr. Eugene Chang from the University of Chicago, how the microbiota of human irritable bowel syndrome patients can alter the behaviour of mice by Dr. Permysl Bercik from McMaster University, and also how the microbiome is a key regulator of behaviour in IBS patients from Dr. John Cryan at the University of Cork, how the inflammasome may regulate mucus secretion from Dr. Bruce Vallance at the University of British Columbia, and lastly, how enteropathogens (including parasites!) can induce inflammation by altering microbiota biofilms from the University of Calgary’s very own HPI researcher Dr. Andre Buret. All in all, it was a great conference full of exciting talks and I’m incredibly grateful to HPI for allowing me the opportunity to attend.

Microbiota and Mucosal Immunity |by Aralia León

The Society for Mucosal Immunology held this year’s symposium “Microbiota and Mucosal Immunity: Rules of Engagement in Health and Disease”. Attending this meeting was a unique opportunity since my work is focused in elucidating the role of microbiota and mucus layer in gastrointestinal health, so by participating in this meeting I got amazing feedback about my work, got to talk with experts on the field as well as with trainees from labs all over the world and more importantly share my results to an audience of experts. One of the things I liked the most was the high quality of research that was presented in this meeting, they had clinical work, basic science work, work done in animal models, all kinds of different approaches to microbiota study.

This year, the symposium was held in the city of Toronto, at the Westin Harbour Castle Hotel with a magnificent view to the Marina and Lake Ontario.  It was my first time in Toronto, so I took advantage of the hotel location and went from knowing a bit about this city to finally falling in love with Toronto´s vibe, markets and multiculturalism!

The first day we had a keynote lecture at the University of Toronto where Dr. Relman from Stanford talked about stability and resilience in the human microbiome.

The second day started early with sessions about I) Influence of microbiota in asthma and allergies, II) Secretory IgA and regulation of mucosal microbiota and III) Microbiota and gut immune system development, all these plenary sessions were given by experts on the field, in between plenary sessions we had concurrent sessions where I had the chance to present my work. The day ended with a poster session where I presented my poster and received very valuable feedback about my experiments.

On the third day the plenary sessions included: I) Intestinal microbiota and IBD and II) Mucosal immunity of the urogenital tract microbiota, with an afternoon trainee networking reception and the last poster session.

The last day was only half day where we had a session about therapeutic modulation of the human gut microbiota and ended with a Rising Star session where the organizers chose the top 4 work done by trainees, giving them the chance to present at the plenary session. It was a nice opportunity for listening to peers who are working on my same field and are having amazing results and using the most advanced technology.

This symposium was one of a kind in terms of relevance for my work, the knowledge I got from it will help to move forward my work and gave me a personal perspective of where is the microbiota field moving to.

I want to thanks NSERC-CREATE HPI program and the Society for Mucosal Immunology for providing with the funds for this trip.

American Association of Veterinary Parasitologists 61st Annual Meeting (August 6-9th, 2016) | By Russel Avramenko

I recently had the pleasure of attending the 61st Annual Meeting of the American Association of Veterinary Parasitologists in San Antonio, Texas. This is my third time attending this conference, having attended every year since 2014. This year, like every one before, did not disappoint.

Getting to the AAVP this year, was definitely more of a challenge than it has been in the past. Just before the AAVP this year, I was on vacation at my in-laws’ cabin in Northern Saskatchewan, which is a 2.5 hour drive from the nearest airport in Saskatoon. I had to get up at 6AM (a feat for me!), to drive to Saskatoon, then I had flights from Saskatoon to Calgary, Calgary to Houston, and then finally Houston to San Antonio. I finally arrived at ~10:30PM, a very long day of travel.

I must say, San Antonio in August is HOT! The high each day was ~38oC, but it cooled down to a breezy 31oC at night. Needless to say, I mainly stayed in the hotel, as a born and raised Canadian, I would have probably died of heat exhaustion if I had stayed out too long!

I had the pleasure of giving two oral presentations at this conference, which was a first for me. The first presentation that I gave focused on part of my PhD thesis work, which I have currently drafted into a publication. It focuses on applying a new sequencing assay to assess parasitic gastrointestinal nematode species proportions. I have used this assay to assess parasite species prevalence in Canadian cattle, as well as cattle in both the United States and Brazil. We have also used the assay to assess changes in species proportions following drug treatment (which gives us an idea of which species are surviving drug treatment, indicating a lack of drug efficacy). My presentation was well received, and I got multiple interesting questions and further discussions after my presentation.

After giving my first presentation, I discovered that I was giving the second presentation later that afternoon, rather than the next day as I had mistakenly thought! Oops! I managed to make the last minute changes to the presentation that I needed, as well as run through it a couple times, so it all worked out just fine.

The second presentation was on data generated with a collaborator, rather than myself. Over the past year, the Gilleard Lab has had a PhD student, Murilo Bichuette, visiting from Brazil. Murilo and I have been working closely together over the past year to apply the sequencing techniques that I have developed to various samples that he collected from back home in Brazil. I had the opportunity to present a small fraction of the work that Murilo has been working on, on his behalf. This was a good opportunity for me, as I have never had the opportunity to present work that I was not been completely familiar with before. Overall, the presentation went very well!

I was also invited to moderate the “Large Animal: Diagnosis/Epidemiology” session in the afternoon on August 7th (in between giving my first and second presentations). So the first full day of the conference was definitely busy to say the least!

After the very busy first day, I was able to relax a bit and enjoy the rest of the conference. I was able to attend numerous interesting talks, and was able to reconnect with numerous students, professors and industry professionals that I had met previously. The conference is a fantastic place to network and make connections. Previous AAVP meeting have sparked numerous collaborative opportunities for the lab, so it will be interesting to see what comes from this meeting!

After another successful AAVP, it was time to head home. Coming home was also an adventure! I was travelling with both my supervisor Dr. John Gilleard and another PhD student in the lab, Camila Queiroz. Our layover in Houston before heading home to Calgary was very short to begin with (~1 hour), but our flight leaving San Antonio ended up being 40 minutes late on departure (leaving just 20 minutes from the time we landed in Houston, till takeoff of the plane to Calgary!) When the plane landed in Houston, I immediately took off to try and catch the flight, as both John and Camila were seated further back in the plane (every man for themselves?). I found out that the connecting flight was on the other side of the airport, which you have to take to take a shuttle train to get to. Ugh! I managed to make it just in time! I then saw John make it on to the plane. A moment later, I get a text from Camila, saying she’s on her way. I tell her to hurry! She should only be a minute or two behind us! Moments later, I see the jetway pull away from the plane. Camila is still not on board; uh oh. Unfortunately, Camila got left behind. It all worked out in the end, as the airline set her up in a hotel, so at least she wasn’t stranded. But I definitely felt a little guilty (sorry Camila)!

Overall, I really enjoyed my experience at the AAVP this year. Thank you to HPI for providing me with the funds necessary to attend the conference. It would not be possible without your continued support.

Bioinformatics in Toronto

139322084-lysanyqu-_dsc21070001In May of this year the University of Toronto hosted the first Canadian Computational Biology Conference, and bioinformatics geeks like myself flocked to their beautiful campus from all over the continent and across the pond. There was a lot of cool new work being presented, and it’s always interesting to get an update on the current state of our art. It was especially striking as the conference took place at Victoria College, which is essentially a castle sitting on on the U of T campus. I’ve never before heard about new applications of set cover machines or the pitfalls of failing to treat metagenomics data as compositional, while the speaker is being framed by beautiful 180 year old stained glass windows.

me_presenting_2I was fortunate enough to be able to present my work in a talk, which was somewhat nerve-wracking as my session was chaired by Dannie Durand, the very researcher whose work I have adapted and modified for my own purposes. She spoke about their recent work analyzing gene families by considering the evolution of each domain separately. We also heard about the staggering complexity involved in trying to predict transcription factor binding behavior, about how representing bacterial genomes as profiles of k-mers yields better phenotypic information than standard phylogenetic analyses, and how disordered regions on eukaryotic proteins are vital to their functions (especially transcription factors).

In addition, we heard about several projects out of Greg Gloor’s group, with his talk titled “We’ve been analyzing high throughput sequence data in the wrong geometric space”. It raised a fundamental problem with how abundance sequencing data is commonly handled, essentially suggesting that most of the metagenomics field have been analyzing their data incorrectly. It boils down to the fact that 10% of one sample can’t be assumed to be the same as 10% of an independent sample, when you have no idea about how many total data you have in each sample. If your data are ratios, you can’t treat them the same as if they were actual counts. Spurious correlations will absolutely appear simply due to the structure of the data, and even simple operations like addition and subtraction no longer really work. Researchers have not really properly respected this fundamental issue, but there is now a tool available called CoDaSeq to help them handle it in the future.

Overall I found the conference very valuable, and I am very grateful to the HPI for the funding and support that sent me there. Hopefully this conference will continue in the future!

 

Ethiopia Short Course 2016 | By Joel Bowron and Timothy Jayme

I had the unique privilege to aid Drs. Guido van Marle and Lashitew Gedamu along with fellow graduate student Tim Jayme to travel to Africa and teach a workshop on molecular biology and bioinformatics. I was honoured to be chosen for the trip, and was not disappointed in the thrilling opportunity that awaited me in Africa – the birthplace of humanity.  In the months that led up to the trip itself, there were many meetings, many workshops, and lots of brushing up on rusty molecular microbiology techniques. Tim and I were tasked with developing assignments for the workshop. For my part, the assignment included a number of bioinformatics and virtual molecular biology tools, many of which are available freely on the internet. But how do you access these types of tools in a rural area in a country where the electrical infrastructure is sometimes as simple two exposed live wires that you connect and disconnect when/if you require power (this is how our hotel was powered off the main grid)? This was one of the first challenges that presented itself to me. The short answer to this question is you have a back-up plan, and a back-up plan for your back-up plan, and so on. With internet being even more sporadic than the power grid, you download offline tools, and, when all else fails, you resort to good old fashioned pen and paper. I worked and polished my assignment until I felt I had accounted for almost any contingent.

In addition to working on physical assignments, we were also tasked to act as teaching assistants (TAs) to run the wet lab portion of the workshop. In the wet labs we were running different types of PCR, including sequence specific PCR and qPCR (or real-time PCR). Here we reinforced concepts learned from the lecture portion of the workshop to really enable the students achieve a thorough understanding of the work that they would be doing. This, in my eyes, was one of the most applicable and fundamental lessons for the students. The connection between theory and practical application is where you would see so many of those “lightbulb” moments where you see the students connect the concepts and really start to grasp the power of these types of molecular techniques.

image3-1This experience was unique, not only in its professional challenges, but for me on a more personal level as well. Born and raised in Calgary, Alberta, I have never set foot outside the continent. On this trip alone, I had tripled the amount of continents I have set foot on, adding Europe and Africa to the list. With a short 12-hour layover in London, England, Tim and I decided to make the most of it and take a quick tour of the sites. After a grueling couple days of travel, we finally arrived in Addis Ababa, Ethiopia. Addis was startling to someone like me, and definitely took some getting used to. Traffic is chaotic, there truly appear to be few observed rules of the road. You push, you shove, and eventually you get to where you’re going. During our stay in Addis, we toured around the city, saw some sites, and met with various people from AHRI (Armauer Hansen Research Institute). Here we toured a facility that was being built as a Tuberculosis research lab, as well as the current research laboratories. It was truly amazing and inspiring to see the amount and quality of research being carried out in the labs we toured, and it made me appreciate more fully the amenities of my own lab.

After spending one week in Addis, we flew to Gonder, a rural city up in the north of the country, where we carried out three of the five days of our workshop. It was in Gonder that we met up with Drs. Dylan Pillai and Bonnie Meatherall who were teaching an infectious disease workshop in parallel to ours. The workshops were definitely a resounding success and I think were appreciated by all parties involved. Now, when I say we carried out three of the five days of our workshop, I feel I must admit that our workshop was regrettably cut short in Gonder due to unforeseen protests, that had unfortunately turned violent. I begrudgingly admit this because, while we did end up flying out of Gonder early for safety reasons, I never felt like my safety was in jeopardy. I should further explain that both the University of Gonder and Dr. Gedamu never hesitated when they felt the situation warranted action and were commendable on the mitigation of any possible risks. Furthermore the president of the University of Gonder personally escorted us to the airport and facilitated our departure from the city. I also feel obliged to point out that Dr. van Marle and Dr. Gedamu have never witnessed this type of activity in the 7+ years these types of workshops have been held in Ethiopia.

While the situation during our trip was not ideal, I feel confident in stating that I have walked away from this trip with hundreds of positive experiences and would recommend this experience to anyone remotely interested without hesitation. I can only say positive things about my time in Africa, and wouldn’t skip a beat if asked to return. Africa is such a beautiful place, and the citizens of Ethiopia were warm, welcoming and extremely courteous. I met so many amazing people on this trip and cannot fully express my gratitude towards everyone involved in making this experience a reality for me. For my part, I would like to thank the NSERC-CREATE Host Parasite Interactions groups for facilitating my trip, as well as personally thank Drs. Guido van Marle and Lashitew Gedamu. I would also like to thank our contacts in Ethiopia, at the University of Gonder, who truly made us feel welcomed and comfortable and were always around for us. Finally, I cannot recommend this program enough, and encourage anyone who is thinking about it, to apply. It is a unique and amazing experience, and has opened my eyes to a more global perspective which I believe will help shape my career aspirations in the future.

American Association of Veterinary Parasitologists | By: Camila Almeida Queiroz

Hello everybody! My name is Camila Queiroz, I have just arrived to University of Calgary so maybe few people from NSERC CREATE Host-Parasite Interactions (HPI) group know me. I am a first year PhD student at the UofC, working on sheep nematodes under the supervision of Dr. John Gilleard and Dr. Michel Levy. My project focuses on investigate sheep nematodes benzimidazole resistance in Western Canadian farms.

The last month I had the opportunity to attend the 61st American Association of Veterinary Parasitologists (AAVP) annual Meeting at the Westin Riverwalk, in San Antonio, Texas, US. The AAVP annual meeting is one of the most important gatherings of researchers, students, and clinicians for the dissemination of the new information and insightful perspectives on the biology and control of parasites of veterinary importance. The conference was held for four days from August 6-9, 2016.

I was excited because this was my first time attending the AAVP Meeting, and I have only attended the UofC for 3 months, and I was going to present my PhD project in an oral talk. The Meeting exceeded expectations, the student talks were excellent and covered a variety of topics including New vistas in HPI; Ectoparasites; Heartworm; Molecular and Biochemical; Treatment, control, diagnosis and epidemiology for dogs, cats and large animal; Anthelmintic resistance and Immunology of Haemonchus contortus.

Overall, it was a really friendly environment, and I was so impressed with having the chance to meet and talk with other students and professors whose articles I had read many times! The many social sessions provided opportunities for networking and sharing knowledge. I enjoyed a lot this Meeting! I also got free time to explore the city, visiting the Alamo and the Riverwalk region.

NSERC CREATE HPI supported all the expenses associated with the trip. I therefore want to highly thank my supervisors, Dr. John Gilleard Dr. Michel Levy, our program coordinator, Teresa Emmett and HPI executives for providing me this opportunity.

 

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Canadian Computational Biology Conference 2016, Toronto, Canada | By Shruti Srivastava

torontoHi, I am Shruti. Most of all my friends in the NSERC CREATE Host-Parasite Interactions (HPI) group know me but for my new friends I want to let them know: who am I and what my business is here. I am a second year M.Sc student at the University of Calgary, working on helminths under the supervision of Dr. James Wasmuth and Dr. Derek McKay. My work in the lab focuses on identification of HPI through bioinformatics approaches. Yes, I use computers to solve biological questions relevant to HPI.

Recently I had a chance to attend a conference at the University of Toronto (U of T), Canada. It was called the Canadian Computational Biology Conference which is one of the first of its kind in Canada. It was co-hosted by the Great Lakes Bioinformatics Consortium (GLBC) and the International Society for Computational Biology (ISCB). The conference was actively held for four days from May 16-19, 2016. Victoria College at U of T, one of the most beautiful buildings around the campus, was chosen as its venue.

viccollege
Victoria College

GLBIO CCBC’16 was a way to reach out to the bioinformatics community across North America. Around 270 people attended this very first computational biology conference here in Canada. All four days were packed with outstanding keynote talks, original research and flash talks, workshops and poster sessions. The various sessions provided the delegates with opportunities for networking. Career building sessions were organized to help budding scientists and many students. Each day started with an opening keynote talk followed by either 15 or five minutes’ flash talks. An ice-breaking session happened at the welcoming reception at the Duke of York Pub. It was an interesting evening, hearing renowned scientists talking about varied research topics in casual setting.

I managed to attend a workshop on best practices used in programming amidst those interesting talks. I also got an opportunity to present my research in front of some inquisitive minds in research. I enjoyed this conference to the fullest!

shruti
Victoria College

I got ample time to roam around in the city. Since we were staying at the most happening street of Toronto, the Yonge street, exploration became easy. I ended this wonderful trip by visiting Niagara Falls.

NSERC CREATE HPI supported all the expenses associated with the trip. I therefore want to highly thank my supervisors, Dr. James Wasmuth and Dr. Derek McKay, our program coordinator, Teresa Emmett and HPI executives for providing me this opportunity.