361 research outputs found
Seroepidemiology and mathematical modelling of non-polio enteroviruses
No full textEnteroviruses are spread fecal–orally or via respiratory transmission and cause a wide range of diseases. They generally cause mild and self-limited illness but have emerged to cause outbreaks with more severe disease manifestations than previously known. The principal public health needs for enterovirus surveillance include outbreak detection, response and monitoring of enteroviruses associated with severe disease. However, the burden of enterovirus infections is not adequately described due to inadequate systemic surveillance. Here, serum neutralizing antibodies to EV-D68, EV-A71, CVA6 and EV-D111 were measured in samples collected in the UK and four African countries to estimate population-level exposure.
Overall, the serology data showed high antibody levels and seroprevalence that reached 100% in adults indicating extensive exposure and ubiquitous virus circulation. Clinical detection of enteroviruses in the UK showed biennial and annual occurrence of EV-A71 and CVA6, respectively. CVA6 detections were marked by an increasing trend from 2006 to 2017. Model fitting of the seroprevalence data showed possible existence of age-specific transmission or relative risk of infection. The increase in virus detection or clinical occurrence without parallel increase in FOI could be attributed to a change in virus characteristics or pathogenicity leading to pronounced clinical disease even without a change in virus transmissibility. This thesis demonstrates the application of serology and mathematical modelling to estimate pathogen prevalence. The data and inferences will be beneficial for guiding future policies focused on enterovirus epidemiology and disease burden. Certainly, better documentation of enterovirus true prevalence and collective impact on human health is warranted
Characterisation of emergent and emerging human-infective RNA viruses
No full textImproved understanding of the early adaptation of zoonotic, human-infective RNA viruses and the genetic factors leading to spillover will inform public health approaches attempting to limit the morbidity and mortality associated with these events. In this thesis, I use clinical microbiological methods to characterize the intra-host replicative and evolutionary dynamics of SARS-CoV-2 and bioinformatic approaches to investigate genetic factors associated with spillover of arboviruses.
Chapter one broadly reviews the field of virology.
Chapter two reviews the apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC) family of proteins, focusing on their emergence, diversification, and function, and summarizes the bioinformatic and functional evidence of their role in SARS-CoV-2 evolution.
Chapter three details the methods underlying the subsequent results chapters.
Chapter four describes the development and validation of single nucleotide polymorphism-based genotyping assays for identifying variants of concern in COVID-19 clinical samples. Their performance is compared to next-generation sequencing, demonstrating the superiority of the genotyping assays at a wide range of viral loads.
Chapter five uses amplification data generated from two COVID-19 clinical trials to explore factors associated with viral load and within-patient viral load dynamics, uses a novel polymerase chain reaction approach to quantify subgenomic RNA transcripts, and investigates the emergence and spread of the Alpha variant in the United Kingdom and the Zeta, Gamma, and Delta variants in Brazil.
Chapter six investigates the interaction between SARS-CoV-2 virological features and COVID-19 clinical outcomes leveraging patients admitted to intensive care within the REMAP-CAP convalescent plasma clinical trial. The null results in this chapter support severe COVID-19 pathology being primarily immune-mediated.
Chapter seven quantitatively tests the hypothesis that convalescent plasma treatment was responsible for the emergence of SARS-CoV-2 variants of concern using an intensively sampled cohort within the REMAP-CAP convalescent plasma trial. Using a variety of approaches, no evidence in support of convalescent plasma therapy as a general driver of immune-escape substitutions was found.
Chapter eight probes the genetic factors associated with human-human transmissibility of arboviruses, finding strong evidence for the role of CpG suppression in the host optimization of flaviviruses. The strong genetic barriers to spillover enable more focused surveillance of this informal classification of viruses
Emerg Infect Dis
No full textIn England, all blood donations are screened in pools of 24 by nucleic acid test (NAT) for hepatitis E virus (HEV) RNA. During 2016-2020, this screening successfully identified and intercepted 1,727 RNA-positive donations. However, review of previous donations from infected platelet donors identified 9 donations in which HEV RNA detection was missed, of which 2 resulted in confirmed transmission: 1 infection resolved with ribavirin treatment, and 1 proceeded to fatal multiorgan failure within a month from infection. Residual risk calculations predict that over the 5-year study period, HEV RNA detection was missed by minipool NAT in 12-23 platelet and 177-354 whole-blood donations, but transmission risk remains undetermined. Although screening has been able to largely eliminate infectious HEV from the blood supply in England, missed detection of low levels of HEV RNA in donated blood can lead to a severe, even fulminant, infection in recipients and could be prevented by more sensitive screening
HeLI-OTS 1.3
No full textHeLI off-the-shelf language identifier with language models for 200 languages.
Usage:
java -jar HeLI.jar -r -w
The program will read the and classify the language of each line as one of the 200 languages it knows
and writes the results, one ISO 639-3 code per line, into file .
You can use the -c option to make the program print a confidence score for the identification after each language code.
Usage:
java -jar HeLI.jar -c -r -w
You can give the list of comma-separated ISO 639-3 identifiers for relevant languages after -l option.
Usage:
java -jar HeLI.jar -r -w -l fin,swe,eng
You can give the number of top-scored languages to print after the -t option. (overrides confidence)
Usage:
java -jar HeLI.jar -r -w -l fin,swe,eng -t 2
If you omit both of the filenames, the program will read the standard input one line at a time and write the result to standard output.
It can identify c. 3000 sentences per second using one core on a 2021 laptop and around 3 gigabytes of memory.
If you use this program in producing scientific publications, please refer to:
@inproceedings{jauhiainen-etal-2017-evaluation,
title = "Evaluation of language identification methods using 285 languages",
author = "Jauhiainen, Tommi and
Lind{\'e}n, Krister and
Jauhiainen, Heidi",
booktitle = "Proceedings of the 21st Nordic Conference on Computational Linguistics",
month = may,
year = "2017",
address = "Gothenburg, Sweden",
publisher = "Association for Computational Linguistics",
url = "https://www.aclweb.org/anthology/W17-0221",
pages = "183--191",
}
Producing and publishing this software has been partly supported by The Finnish Research Impact Foundation Tandem Industry Academia -funding in cooperation with Lingsoft
HeLI-OTS 1.4
No full textHeLI off-the-shelf language identifier with language models for 200 languages.
Usage:
java -jar HeLI.jar -r -w
The program will read the and classify the language of each line as one of the 200 languages it knows
and writes the results, one ISO 639-3 code per line, into file .
You can use the -c option to make the program print a confidence score for the identification after each language code.
Usage:
java -jar HeLI.jar -c -r -w
You can give the list of comma-separated ISO 639-3 identifiers for relevant languages after -l option.
Usage:
java -jar HeLI.jar -r -w -l fin,swe,eng
You can give the number of top-scored languages to print after the -t option. (overrides confidence)
Usage:
java -jar HeLI.jar -r -w -l fin,swe,eng -t 2
If you omit both of the filenames, the program will read the standard input one line at a time and write the result to standard output.
It can identify c. 3000 sentences per second using one core on a 2021 laptop and around 3 gigabytes of memory.
If you use this program in producing scientific publications, please refer to:
@inproceedings{heliots2022,
title = "{H}e{LI-OTS}, Off-the-shelf Language Identifier for Text",
author = "Jauhiainen, Tommi and
Jauhiainen, Heidi and
Lind{\'e}n, Krister",
booktitle = "Proceedings of the 13th Conference on Language Resources and Evaluation",
month = june,
year = "2022",
address = "Marseille, France",
publisher = "European Language Resources Association",
url = "http://www.lrec-conf.org/proceedings/lrec2022/pdf/2022.lrec-1.416.pdf",
pages = "3912--3922",
language = "English",
}
Producing and publishing this software has been partly supported by The Finnish Research Impact Foundation Tandem Industry Academia -funding in cooperation with Lingsoft
Assessing the impacts of heli-skiing on the behaviour and spatial distribution of Mountain Cariboo (Rangifer tarandus caribou)
No full textMountain caribou (Rangifer tarandus caribou) are listed as endangered in Canada, with isolated subherds only remaining in British Columbia and parts of northern Idaho. A loss of old-growth forest habitat has caused a decline in their range, making them more likely to be disturbed by backcountry recreational activities such as heli-skiing. This study investigated whether an interaction between heli-skiing and Mountain Caribou could be detected. The detectability of caribou from helicopters indicated that caribou are often not detected when within close proximity to active skiing. Data on the behavioural responses of caribou that were recorded by Mike Wiegele heli-skiing personnel between 1996 and 2010 were analysed. The relationship between the type of responses and the frequency of ski run usage was examined. Responses were not higher in areas subject to more frequent skiing, but overt behavioural responses to heliskiing were documented. Three GIS analyses were performed on GPS data from 25 caribou collared between 1996 and 2007 to determine any spatial effects of skiing activity on how animals use their range. The first test examined habitat use near ski runs. Actual numbers of GPS locations within suitable habitat near ski runs were more than expected. The second test determined the distance established by caribou between themselves and ski runs with different intensities of use. More than an expected number of locations were found close to frequently skied runs; while fewer than expected locations were found close to runs not skied. The third test compared caribou’s rate of movement within zones skied frequently and less often. There was no significant difference in the degree of movement in areas skied heavily or not. Results of these analyses suggest that caribou in the area were not directly displaced by heli-skiing activities during the years studied, but avoidance at finer scales than I measured is possible. It appears as if ‘Best Management Practices’ that enforce closing areas to skiing upon detection of caribou may be helpful in reducing conflicts with caribou; however, mountain caribou in this study area have likely habituated to more than 40 years of skiing. Continued avoidance management, more specific research on short-term reactions to heliskiing and with herds in other areas are suggested to ensure a coexistence of caribou and heli-skiing.Rangifer tarandus caribouheli-skiingbackcountry recreationdisturbancehabitat specialistGI
HeLI-OTS 1.5
No full text<p>HeLI off-the-shelf language identifier with language models for 200 languages.</p><p>In order to use the language identifier, you need only to download the HeLI.jar file which is used as follows.</p><p>Usage:<br>java -jar HeLI.jar -r <infile> -w <outfile></p><p>The program will read the <infile> and classify the language of each line as one of the 200 languages it knows<br>and writes the results, one ISO 639-3 code per line, into file <outfile>.</p><p>You can use the -c option to make the program print a confidence score for the identification after each language code.</p><p>Usage:<br>java -jar HeLI.jar -c -r <infile> -w <outfile></p><p>You can give the list of comma-separated ISO 639-3 identifiers for relevant languages after -l option.</p><p>Usage:<br>java -jar HeLI.jar -r <infile> -w <outfile> -l fin,swe,eng</p><p>You can give the number of top-scored languages to print after the -t option.</p><p>Usage:<br>java -jar HeLI.jar -r <infile> -w <outfile> -l fin,swe,eng -t 2</p><p>You can activate language set identification by -s. You must give the maximum number resulting languages after -s option. (overrides confidence and printing several top-scored languages)</p><p>Usage:<br>java -jar HeLI.jar -r <infile> -w <outfile> -l fin,swe,eng -s 2</p><p>If you omit both of the filenames, the program will read the standard input one line at a time and write the result to standard output.</p><p>It can identify c. 2000 sentences (averaging c. 150 characters) per second from a file using one core and around 4,3 gigabytes of memory on a 2021 laptop.</p><p>If you use this program in producing scientific publications, please refer to: <br> @inproceedings{heliots2022,<br> title = "{H}e{LI-OTS}, Off-the-shelf Language Identifier for Text",<br> author = "Jauhiainen, Tommi and<br> Jauhiainen, Heidi and<br> Lind{\'e}n, Krister",<br> booktitle = "Proceedings of the 13th Conference on Language Resources and Evaluation",<br> month = june,<br> year = "2022",<br> address = "Marseille, France",<br> publisher = "European Language Resources Association",<br> url = "http://www.lrec-conf.org/proceedings/lrec2022/pdf/2022.lrec-1.416.pdf",<br> pages = "3912--3922",<br> language = "English",<br> }</p><p>HeLI-OTS-1.5.zip includes the complete source code for the software.</p><p>Producing and publishing this software has been partly supported by the University of Helsinki, the Academy of Finland, the Kone Foundation, and the Finnish Research Impact Foundation Tandem Industry Academia -funding in cooperation with Lingsoft.</p>
HeLI-OTS 2.0
No full text<div>
<div># HeLI-OTS 2.0</div>
<br>
<div>HeLI off-the-shelf language identifier with language models for 220 languages.</div>
<br>
<div># Performance</div>
<br>
<div>It can identify c. 600-1700 sentences (averaging c. 150 characters) per second from a file using one core and around 4,3 gigabytes of memory on a modern laptop.</div>
<br>
<div># Requirements</div>
<br>
<div>Java</div>
<div>The software has been created and tested on MacOS and Windows 11.</div>
<br>
<div># Setting up HeLI-OTS</div>
<br>
<div>The github repository does not include pre-compiled version of HeLI.jar. The .jar file can be downloaded from:</div>
<div>https://zenodo.org/doi/10.5281/zenodo.4780897</div>
<br>
<div>Note that you need Java Developement Kit 'JDK' in order to create .jar files. Java Runtime Enviroment 'JRE' does NOT include jar program.</div>
<br>
<div>The HeLI.jar can be created from command-line within the src folder using:</div>
<div>```</div>
<div>jar cmf HeLI.mf HeLI.jar HeLI.class HeLI.java languagelist LanguageModels confidenceThresholds</div>
<div>```</div>
<br>
<div># Command line use</div>
</div>
<div> </div>
<div>In order to use the language identifier, you need only to download the HeLI.jar file which is used as follows.</div>
<div><br>
<div>These examples are for the jar file. The program can be used directly as the GitHub version by leaving out ```-jar``` and ```.jar```.</div>
<br>
<div>Please note that loading the language models takes the same amount of time (up to one minute) regardless of the size of the text file.</div>
<br>
<div>Usage:</div>
<div>```</div>
<div>java -jar HeLI.jar -r <infile> -w <outfile></div>
<div>```</div>
<br>
<div>The program will read the <infile> and classify the language of each line as one of the 220 languages it knows</div>
<div>and writes the results, one ISO 639-3 code per line, into file <outfile>.</div>
<br>
<div>You can use the -c option to make the program print a confidence score for the identification after each language code.</div>
<div>The lower the 'confidence score' the more sure the identification is.</div>
<br>
<div>Usage:</div>
<div>```</div>
<div>java -jar HeLI.jar -c -r <infile> -w <outfile></div>
<div>```</div>
<br>
<div>You can give the list of comma-separated ISO 639-3 identifiers for relevant languages after -l option.</div>
<br>
<div>Usage:</div>
<div>```</div>
<div>java -jar HeLI.jar -r <infile> -w <outfile> -l fin,swe,eng</div>
<div>```</div>
<br>
<div>You can give the number of top-scored languages to print after the -t option.</div>
<br>
<div>Usage:</div>
<div>```</div>
<div>java -jar HeLI.jar -r <infile> -w <outfile> -l fin,swe,eng -t 2</div>
<div>```</div>
<br>
<div>You can activate language set identification by -s. If a row contains longer passages in multiple languages, all the detected languages in the row will be returned. You must give the maximum number of resulting languages after -s option. (overrides confidence and printing several top-scored languages)</div>
<br>
<div>Usage:</div>
<div>```</div>
<div>java -jar HeLI.jar -r <infile> -w <outfile> -l fin,swe,eng -s 2</div>
<div>```</div>
<br>
<div>If you omit both of the filenames, the program will read the standard input one line at a time and write the result to standard output.</div>
<br>
<div># Citations</div>
<br>
<div>If you use this program in producing scientific publications, please refer to:</div>
<div>```</div>
<div> @inproceedings{heliots2022,</div>
<div> title = "{H}e{LI-OTS}, Off-the-shelf Language Identifier for Text",</div>
<div> author = "Jauhiainen, Tommi and</div>
<div> Jauhiainen, Heidi and</div>
<div> Lind{\'e}n, Krister",</div>
<div> booktitle = "Proceedings of the 13th Conference on Language Resources and Evaluation",</div>
<div> month = june,</div>
<div> year = "2022",</div>
<div> address = "Marseille, France",</div>
<div> publisher = "European Language Resources Association",</div>
<div> url = "http://www.lrec-conf.org/proceedings/lrec2022/pdf/2022.lrec-1.416.pdf",</div>
<div> pages = "3912--3922",</div>
<div> language = "English",</div>
<div> }</div>
<div>```</div>
HeLI-OTS-2.0.zip includes the complete source code for the software.</div>
<div><br>
<div># Acknowledgements</div>
<br>
<div>Producing and publishing this software has been partly supported by The Finnish Research Impact Foundation Tandem Industry Academia -funding in cooperation with Lingsoft, by the Kone Foundation, by the European Union – NextGenerationEU instrument, and by the Research Council of Finland under grant number 358720 (FIN-CLARIAH – Developing a Common RI for CLARIAH Finland).</div>
</div>
Assessing the impacts of heli-skiing on the behaviour and spatial distribution of Mountain Cariboo (Rangifer tarandus caribou)
No full textMountain caribou (Rangifer tarandus caribou) are listed as endangered in Canada, with isolated subherds only remaining in British Columbia and parts of northern Idaho. A loss of old-growth forest habitat has caused a decline in their range, making them more likely to be disturbed by backcountry recreational activities such as heli-skiing. This study investigated whether an interaction between heli-skiing and Mountain Caribou could be detected. The detectability of caribou from helicopters indicated that caribou are often not detected when within close proximity to active skiing. Data on the behavioural responses of caribou that were recorded by Mike Wiegele heli-skiing personnel between 1996 and 2010 were analysed. The relationship between the type of responses and the frequency of ski run usage was examined. Responses were not higher in areas subject to more frequent skiing, but overt behavioural responses to heliskiing were documented. Three GIS analyses were performed on GPS data from 25 caribou collared between 1996 and 2007 to determine any spatial effects of skiing activity on how animals use their range. The first test examined habitat use near ski runs. Actual numbers of GPS locations within suitable habitat near ski runs were more than expected. The second test determined the distance established by caribou between themselves and ski runs with different intensities of use. More than an expected number of locations were found close to frequently skied runs; while fewer than expected locations were found close to runs not skied. The third test compared caribou’s rate of movement within zones skied frequently and less often. There was no significant difference in the degree of movement in areas skied heavily or not. Results of these analyses suggest that caribou in the area were not directly displaced by heli-skiing activities during the years studied, but avoidance at finer scales than I measured is possible. It appears as if ‘Best Management Practices’ that enforce closing areas to skiing upon detection of caribou may be helpful in reducing conflicts with caribou; however, mountain caribou in this study area have likely habituated to more than 40 years of skiing. Continued avoidance management, more specific research on short-term reactions to heliskiing and with herds in other areas are suggested to ensure a coexistence of caribou and heli-skiing.Rangifer tarandus caribouheli-skiingbackcountry recreationdisturbancehabitat specialistGI
Heli maastikuarhitektuuris: Rotterdami linna Slinge tänava juhtumianalüüs
No full textMaster’s thesis
Curriculum in Landscape architectureNowadays the audio and visual landscape as a part of the urban landscape is neglected in urban planning and
planning. This is while today's cities are rapidly expanding and, as a result, the emergence of traffic and other
environmental contaminants has created a disturbing landscape. In order to achieve high quality and enjoyable
recording spaces, this position needs to be addressed. The research provides a comprehensive overview of the
concept, dimensions, and factors affecting the sound landscape and its methods of study. The method
described pleasing and unpleasing sounds in urban spaces is the result of extensive research and studies in
the field of view. Positive soundscape design is the key step. Complex design requires that you take steps each
step simultaneously. In order to achieve high quality and positive soundscape, this position needs to be
addressed. The method described by the author in the direction of designing and redesigning a pleasing sound
landscape in urban spaces is the result of extensive research and studies in the field of view. Positive
soundscape design is the key.
Sound and soundscape are emotional stimuli that overshadow the quality of urban spaces. Sound as an
inseparable part of the urban atmosphere affects the behavior of pedestrians, the choice of space to stay or
pass, the pedestrians' perception of the urban space, and in general, the quality of the urban space. Nowadays,
the increase and redistribution of sound sources, such as traffic noise, human activities, and disturbing sounds,
creates an unpleasant acoustic perspective and creates a disturbing audiovisual perception for the citizens.
These alternatives show the importance of addressing the audio landscape in urban spaces. The purpose of
this research was to investigate the quantitative and qualitative aspects of the soundscape on the people in
Slinge street(South Rotterdam). The present study is applied and descriptive and analytical in nature. The
quantitative and qualitative complementary method has been used for evaluation purposes. Physical Sound
Index (LA eq) Study the literature and explain it in the study area by the sound sensor Evaluated and for
qualitative evaluation, Questionnaires were used. In order to collect the required data, field acoustic harvesting
from 13 points with distances of 250m and Questionnaires were filled out by those present in the range. In the
end, there are some suggestions to use landscape design to manage and control the quality of the sound and
sound pollution in this area. Research of this part shows that Landscape Architects can control sound pollution
by natural materials and vegetation.the second part of the design part started by 3 different study cases in 3
different countries. In the End, compounding the design part and results of databases can change sound
pollution of Slinge sound to be a better neighborhood for the people of this area.Tänapäeval on unarusse jäetud linnamaastikuplaneerimises audio-visuaalne maastik. Seda ajal, kui linnaruum
on aina kasvamas, ning liiklus ja muud analoogne keskkonna saaste on tekitamas häirivat maastikku.
Saavutamaks kõrgekvaliteetset, nauditavat salvestusruumi tuleb selle probleemiga tegeleda. Uurimustöö pakub
põhjaliku ülevaate kontseptsioonidest, mõõtmetest ja teistest faktoritest, mis mõjutavad heliruumi, ning
meetoditest selle uurimiseks. Antud vallas tehtud tööst tuuakse välja metodoloogiline lähenenine meeldiva, ning
ebameeldiva heliruumi loomiseks. Positiivse heliruumi tekitamine on antud töö peaasjalik mõte. Autori poolt
kirjeldatud meetod saavutamaks positiivne heliruum läbi linnaruumi kujundamise ja ümberkujundamise on
pikaajalise ja põhjaliku uurimistöö antud valdkonnas.
Heli ja heliruum on emotsionaalsed stiimulid, mis varjutavad linnaruumi kvaliteeti. Heli, olles lahutamatu osa
linnaruumist mõjutab näiteks jalakäiate käitumismustreid, valikuid vaba aja veetmiseks valitud kohtades,
linnaelaniku taju üleüldisest linnaruumist ja selle kvaliteedist. Tänapäeval, tulenevalt heli allikate asukoha ja
arvukuse kasvust, nagu näiteks liiklusmüra, inimtegevuslik müra, ja muud häirivad helid tekitavad ebameeldiva
akustilise ja visuaalse pildi üleüldisest linnaruumist. Alternatiivide olemasolu näitlikustab heliruumiga tegelemise
vajadust. Töö eesmärk oli uurida kvantitatiivseid ja kvalitatiivseid aspekte Slinge tänava (Lõuna-Rotterdam)
heliruumi mõjust inimestele. Töö on rakendusliku iseloomuga, kirjeldav ja iseloomult analüütiline. Kvantitatiivkvalitatiivkomplementaarset meetodit on kasutatud hinnagute andmiseks. Füüsilise heli indeksit ja helisensorit
kasutati mõõtmisteks. Kvalitatiivsete hinnangute andmiseks kasutati küsimustikke, mis viidi läbi mõõtekohtades.
Mõõtekohti oli kokku 12, 250m distantsiga ja küsimustikke täitsid parasjagu kohal viibivad linnaelanikud. Töös
on välja pakutud võimalikku lahendusi kuidas kujundada ümber linnamaastikku, et parandada helisaasted
looduslike vahenditega, ning taimedega. Teine osa tööst viidi läbi kolme eri uuringuga kolmes eri maal.
Lõpptulemusena saab koondandmestikku ja kogutud andmebaasi kasutada Slinge tänava elanike elukvaliteedi
parandamiseks
- …
