Search results for: Mette Bøgh Jensen

Authors: Reena K., Mamatha H. G., Somshekarayya, P. Kumar

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Objectives: The annual proficiency testing of intermediate reference laboratories is conducted by the National Reference Laboratory (NRL) to assess the efficiency of the laboratories to correctly identify Mycobacterium tuberculosis and to determine its drug susceptibility pattern. The proficiency testing results from 2013 to 2017 were analyzed to determine laboratories that were consistent in reporting quality results and those that had difficulty in doing so. Methods: A panel of twenty cultures were sent out to each of these laboratories. The laboratories were expected to grow the cultures in their own laboratories, set up drug susceptibly testing by all the methods they were certified for and report the results within the stipulated time period. The turnaround time for reporting results, specificity, sensitivity positive and negative predictive values and efficiency of the laboratory in identifying the cultures were analyzed. Results: Most of the laboratories had reported their results within the stipulated time period. However, there was enormous delay in reporting results from few of the laboratories. This was mainly due to improper functioning of the biosafety level III laboratory. Only 40% of the laboratories had 100% efficiency in solid culture using Lowenstein Jensen medium. This was expected as a solid culture, and drug susceptibility testing is not used for diagnosing drug resistance. Rapid molecular methods such as Line probe assay and Genexpert are used to determine drug resistance. Automated liquid culture system such as the Mycobacterial growth indicator tube is used to determine prognosis of the patient while on treatment. It was observed that 90% of the laboratories had achieved 100% in the liquid culture method. Almost all laboratories had achieved 100% efficiency in the line probe assay method which is the method of choice for determining drug-resistant tuberculosis. Conclusion: Since the liquid culture and line probe assay technologies are routinely used for the detection of drug-resistant tuberculosis the laboratories exhibited higher level of efficiency as compared to solid culture and drug susceptibility testing which are rarely used. The infrastructure of the laboratory should be maintained properly so that samples can be processed safely and results could be declared on time.

Keywords: annual proficiency testing, drug susceptibility testing, intermediate reference laboratory, national reference laboratory

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Authors: Recep Keşli, Hayriye Tokay, Cengiz Demir, İsmail Ceyhan

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Objective: In many countries, tuberculosis (TB) is still one of the most important diseases. Tuberculosis is among top 10 causes of death worldwide. The early diagnosis of active tuberculosis still depends on the presence of acid resistant bacilli (ARB) in stained smears. In this study, we aimed to investigate the diagnostic performances of Erlich Ziehl Neelsen (EZN), Kinyoun and two different fluorescent stains. Methods: The specimens were obtained from the patients who applied to Chest Diseases Departments of Ankara Atatürk Chest Diseases and Thoracic Surgery Training and Research Hospital, and Afyon Kocatepe University, ANS Research and Practice Hospital. The study was carried out in the Medical Microbiology Laboratory, School of Medicine, Afyon Kocatepe University. All the non-sterile specimens were homogenized and decontaminated according to the EUCAST instructions. Samples were inoculated onto the Löwenstein-Jensen agars (bio-Merieux Marcy l'Etoile, France) and then incubated at 37˚C, for 40 days. Four smears were prepared from each specimen. Slides were stained with commercial EZN (BD, Sparks, USA), Kinyoun (SALUBRIS Istanbul, Turkey), Auramine (SALUBRIS Istanbul, Turkey) and Rhodamine (SALUBRIS Istanbul, Turkey) kit. While EZN and Kinyoun stainings were examined by light microscope, Auramine and Rhodamine slides were examined by fluorescence microscopy. Results: A total of 158 respiratory system samples (sputum, broncho alveolar lavage fluid…etc) were enrolled into the study. A hundred and two of the samples that processed were found as culture positive. The sensitivity, specificity, positive predictive, and negative predictive values were detected as 100%, 67.5%, 73.5%, and 100% for EZN, 100%, 70.9%, 77.4%, and 100% for Kinyoun, 100%,77.8%, 84.3%, 100% for Auramine, and 100%, 80% , 86.3%, and 100% for Rhodamine respectively. Conclusions: According to our study auramine and rhodamine staining methods showed the best diagnostic performance among the four investigated staining methods. In conclusion, the fluorochrome staining method may be accepted as the most reliable, rapid and useful method for diagnosis of the mycobacterial infections truly.

Keywords: acid resistant bacilli (ARB), auramine, Ehrlich-Ziehl-Neelsen (EZN), Kinyoun, Rhodamine

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Authors: Minwuyelet Maru, Solomon Habtemariam, Endalamaw Gadissa, Abraham Aseffa

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Background: Tuberculosis is a major public health problem in Ethiopia. The burden of TB is aggravated by emergence and expansion of drug resistant tuberculosis and different lineages of Mycobacterium tuberculosis (M. tuberculosis) have been reported in many parts of the country. Describing strains of Mycobacterial isolates and drug susceptibility pattern is necessary. Method: Sputum samples were collected from smear positive pulmonary TB patients age >= 7 years between October 1, 2012 to September 30, 2013 and Mycobacterial strains isolated on Loweensten Jensen (LJ) media. Each strain was characterized by deletion typing and Spoligotyping. Drug sensitivity testing was determined with the indirect proportion method using Middle brook 7H10 media and association to determine possible risk factors to drug resistance was done. Result: A total of 144 smear positive pulmonary tuberculosis patients were enrolled. The age of participants ranged from 7 to 78 with mean age of 29.22 (±10.77) years. In this study 82.2% (n=97) of the isolates were sensitive to the four first line anti-tuberculosis drugs and resistance to any of the four drugs tested was 17.8% (n=21). A high frequency of any resistance was observed in isoniazid, 13.6%, (n=16) followed by streptomycin, 11.8% (n=14). No significant association of isoniazid resistance with HIV, sex and history of previous TB treatment was observed but there was significant association with age, high between 31-35 years of age (p=0.01). Majority, 89.9% (n=128) of participants were new cases and only 11.1% (n=16) had history of previous TB treatment. No MDR-TB from new cases and 2 MDRTB (13.3%) was isolated from re-treatment cases which was significantly associated with previous TB treatment (p<0.01). Thirty two different types of spoligotype patterns were identified and 74.1% were grouped in to 13 clusters. The dominant strains were SIT 25, 18.1% (n=21), SIT 53, 17.2% (n=20) and SIT 149, 8.6% (n=10). Lineage 4 is the predominant lineage followed by lineage 3 and lineage 7 comprising 65.5% (n=76), 28.4% (n=33) and 6% (n=7) respectively. Majority of strains from lineage 3 and 4 were SIT 25 (63.6%) and SIT 53 (26.3%) whereas SIT 343 was the dominant strain from lineage 7 (71.4%). Conclusion: Wide spread of lineage 3 and lineage 4 of the modern lineage and high number of strain cluster indicates high ongoing transmission. The high proportion resistance to any of the first line anti-tuberculosis drugs may be a potential source in the emergence of MDR-TB. Wide spread of SIT 25 and SIT 53 having a tendency of ease transmission and presence of higher resistance of isoniazid in working and mobile age group, 31-35 years of age may increase risk of drug resistant strains transmission.

Keywords: tuberculosis, drug susceptibility, strain diversity, lineage, Ethiopia, spoligotyping

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Authors: Titilope F. Onaolapo, Christiana A. Breed, Maya Pasgaard, Kristine E. Jensen, Peta Brom

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In the face of fast-growing urbanization in most of the world's developing countries, there is a need to understand and address the risk and consequences involved in the indiscriminate use of urban green space. Tshwane city in South Africa has the potential to become one of the world's top biodiversity cities as South Africa is ranked one of the mega countries in biodiversity conservation, and Tshwane metropolitan municipality is the city with the wealthiest biodiversity with grassland biomes. In this study, we focus on the potentials and challenges of urban green transitioning from the Global South perspective with Tshwane city as the case study. We also address the issue of management conflicts that have resulted in informal and illegal activities in and around green spaces, with consequences such as land degradation, loss of livelihoods and biodiversity, and socio-ecological imbalances. A desk study review of eight policy frameworks related to green urban planning and development was done based on four GI principles: multifunctionality, connectivity, interdisciplinary and social inclusion. We interviewed 15 key informants in related departments in the city and administered 200 survey questionnaires among residents. We also had several workshops the other researchers and experts on biodiversity and ecosystem. We found out there is no specific document dedicated to green space management, and where green infrastructure was mentioned, it was focused on as an approach to climate mitigation and adaptation. Also, residents perceive green and open spaces as extra land that could be developed at will. We demonstrated the use of collaborative learning approaches in ecological and development research and the tying research to the existing frameworks, programs, and strategies. Based on this understanding. We outlined the need to incorporate principles of green infrastructure in policy frameworks on spatial planning and environmental development. Furthermore, we develop a model for co-management of green infrastructures by stakeholders, such as residents, developers, policymakers, and decision-makers, to maximize benefits. Our collaborative, interdisciplinary projects pursue SDG multifunctionality of goals 11 and 15 by simultaneously addressing issues around Sustainable Cities and Communities, Climate Action, Life on Land, and Strong Institutions, and halt and reverse land degradation and biodiversity.

Keywords: governance, green infrastructure, South Africa, sustainable development, urban planning, Tshwane

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Authors: Fiona Jensen, Barb Goodwin, Nancy Kleiman, Rhonda Usunier

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Background: Clinical simulation is now a common component in many health profession curricula in preparation for clinical practice. In the Rady Faculty of Health Sciences (RFHS) college leads in simulation and interprofessional (IP) education, planned an eight hour simulated hospital day shift, where seventy students from six health professions across two campuses, learned with each other in a safe, realistic environment. Learning about interprofessional collaboration, an expected competency for many health professions upon graduation, was a primary focus of the simulation event. Method: Faculty representatives from the Colleges of Nursing, Medicine, Pharmacy and Rehabilitation Sciences (Physical Therapy, Occupation Therapy, Respiratory Therapy) and Pharmacy worked together to plan the IP event in a simulation facility in the College of Nursing. Each college provided a faculty mentor to guide the same profession students. Students were placed in interprofessional teams consisting of a nurse, physician, pharmacist, and then sharing respiratory, occupational, and physical therapists across the team depending on the needs of the patients. Eight patient scenarios were role played by health profession students, who had been provided with their patient’s story shortly before the event. Each team was guided by a facilitator. Results and Outcomes: On the morning of the event, all students gathered in a large group to meet mentors and facilitators and have a brief overview of the six competencies for effective collaboration and the session objectives. The students assuming their same profession roles were provided with their patient’s chart at the beginning of the shift, met with their team, and then completed professional specific assessments. Shortly into the shift, IP team rounds began, facilitated by the team facilitator. During the shift, each patient role-played a spontaneous health incident, which required collaboration between the IP team members for assessment and management. The afternoon concluded with team rounds, a collaborative management plan, and a facilitated de-brief. Conclusions: During the de-brief sessions, students responded to set questions related to the session learning objectives and expressed many positive learning moments. We believe that we have a sustainable simulation IP collaborative learning opportunity, which can be embedded into curricula, and has the capacity to grow to include more health profession faculties and students. Opportunities are being explored in the RFHS at the administrative level, to offer this event more frequently in the academic year to reach more students. In addition, a formally structured event evaluation tool would provide important feedback and inform the qualitative feedback to event organizers and the colleges about the significance of the simulation event to student learning.

Keywords: simulation, collaboration, teams, interprofessional

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Authors: Steven Sam, Ximena Schmidt, Hugh Dickinson, Jens Jensen

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The goal of this study is to explore the potential of data science and citizen science approaches to develop an interactive, digital, open infrastructure that pulls together African indigenous agriculture and food systems data from multiple sources, making it accessible and reusable for policy, research and practice in modern food production efforts. The World Bank has recognised that African Indigenous Knowledge (AIK) is innovative and unique among local and subsistent smallholder farmers, and it is central to sustainable food production and enhancing biodiversity and natural resources in many poor, rural societies. AIK refers to tacit knowledge held in different languages, cultures and skills passed down from generation to generation by word of mouth. AIK is a key driver of food production, preservation, and consumption for more than 80% of citizens in Africa, and can therefore assist modern efforts of reducing food insecurity and hunger. However, the documentation and dissemination of AIK remain a big challenge confronting librarians and other information professionals in Africa, and there is a risk of losing AIK owing to urban migration, modernisation, land grabbing, and the emergence of relatively small-scale commercial farming businesses. There is also a clear disconnect between the AIK and scientific knowledge and modern efforts for sustainable food production. The study combines data science and citizen science approaches through active community participation to generate and share AIK for facilitating learning and promoting knowledge that is relevant for policy intervention and sustainable food production through a curated digital platform based on FAIR principles. The study adopts key informant interviews along with participatory photo and video elicitation approach, where farmers are given digital devices (mobile phones) to record and document their every practice involving agriculture, food production, processing, and consumption by traditional means. Data collected are analysed using the UK Science and Technology Facilities Council’s proven methodology of citizen science (Zooniverse) and data science. Outcomes are presented in participatory stakeholder workshops, where the researchers outline plans for creating the platform and developing the knowledge sharing standard framework and copyrights agreement. Overall, the study shows that learning from AIK, by investigating what local communities know and have, can improve understanding of food production and consumption, in particular in times of stress or shocks affecting the food systems and communities. Thus, the platform can be useful for local populations, research, and policy-makers, and it could lead to transformative innovation in the food system, creating a fundamental shift in the way the North supports sustainable, modern food production efforts in Africa.

Keywords: Africa indigenous agriculture knowledge, citizen science, data science, sustainable food production, traditional food system

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Authors: Patrick Cormier, Cesar Meylan, Matt Jensen, Dana Agar-Newman, Chloe Werle, Ming-Chang Tsai, Marc Klimstra

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Sprint-derived horizontal force-velocity-power (FVP) profiles can be developed with adequate validity and reliability with satellite (GPS/GNSS) systems. However, FVP metrics are sensitive to small nuances in data processing procedures such that minor differences in defining the onset and end of the sprint could result in different FVP metric outcomes. Furthermore, in team-sports, there is a requirement for rapid analysis and feedback of results from multiple athletes, therefore developing standardized and automated methods to improve the speed, efficiency and reliability of this process are warranted. Thus, the purpose of this study was to compare different methods of sprint end detection on the development of FVP profiles from 10Hz GPS/GNSS data through goodness-of-fit and intertrial reliability statistics. Seventeen national team female soccer players participated in the FVP protocol which consisted of 2x40m maximal sprints performed towards the end of a soccer specific warm-up in a training session (1020 hPa, wind = 0, temperature = 30°C) on an open grass field. Each player wore a 10Hz Catapult system unit (Vector S7, Catapult Innovations) inserted in a vest in a pouch between the scapulae. All data were analyzed following common procedures. Variables computed and assessed were the model parameters, estimated maximal sprint speed (MSS) and the acceleration constant τ, in addition to horizontal relative force (F₀), velocity at zero (V₀), and relative mechanical power (Pmax). The onset of the sprints was standardized with an acceleration threshold of 0.1 m/s². The sprint end detection methods were: 1. Time when peak velocity (MSS) was achieved (zero acceleration), 2. Time after peak velocity drops by -0.4 m/s, 3. Time after peak velocity drops by -0.6 m/s, and 4. When the integrated distance from the GPS/GNSS signal achieves 40-m. Goodness-of-fit of each sprint end detection method was determined using the residual sum of squares (RSS) to demonstrate the error of the FVP modeling with the sprint data from the GPS/GNSS system. Inter-trial reliability (from 2 trials) was assessed utilizing intraclass correlation coefficients (ICC). For goodness-of-fit results, the end detection technique that used the time when peak velocity was achieved (zero acceleration) had the lowest RSS values, followed by -0.4 and -0.6 velocity decay, and 40-m end had the highest RSS values. For intertrial reliability, the end of sprint detection techniques that were defined as the time at (method 1) or shortly after (method 2 and 3) when MSS was achieved had very large to near perfect ICC and the time at the 40 m integrated distance (method 4) had large to very large ICCs. Peak velocity was reached at 29.52 ± 4.02-m. Therefore, sport scientists should implement end of sprint detection either when peak velocity is determined or shortly after to improve goodness of fit to achieve reliable between trial FVP profile metrics. Although, more robust processing and modeling procedures should be developed in future research to improve sprint model fitting. This protocol was seamlessly integrated into the usual training which shows promise for sprint monitoring in the field with this technology.

Keywords: automated, biomechanics, team-sports, sprint

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Authors: Azeem Tariq, Stephane De Tourdonnet, Lars Stoumann Jensen, Reiner Wassmann, Bjoern Ole Sander, Quynh Duong Vu, Trinh Van Mai, Andreas De Neergaard

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Rice growing area is increasing to meet the food demand of increasing population. Mostly, rice is growing on lowland, small landholder fields in most part of the world, which is one of the major sources of greenhouse gases (GHG) emissions from agriculture fields. The strategies such as, altering water and residues (carbon) management practices are assumed to be essential to mitigate the GHG emissions from flooded rice system. The actual implementation and potential of these measures on small farmer fields is still challenging. A field study was conducted on red river delta in Northern Vietnam to identify the potential challenges and barriers to the small rice farmers for implementation of climate smart rice practices. The objective of this study was to develop and access the feasibility of climate smart rice prototypes under actual farmer conditions. Field and scientific oriented framework was used to meet our objective. The methodological framework composed of six steps: i) identification of stakeholders and possible options, ii) assessment of barrios, drawbacks/advantages of new technologies, iii) prototype design, iv) assessment of mitigation potential of each prototype, v) scenario building and vi) scenario assessment. A farm survey was conducted to identify the existing farm practices and major constraints of small rice farmers. We proposed the two water (pre transplant+midseason drainage and early+midseason drainage) and one straw (full residue incorporation) management option keeping in views the farmers constraints and barriers for implementation. To test new typologies with existing prototypes (midseason drainage, partial residue incorporation) at farmer local conditions, a participatory field experiment was conducted for two consecutive rice seasons at farmer fields. Following the results of each season a workshop was conducted with stakeholders (farmers, village leaders, cooperatives, irrigation staff, extensionists, agricultural officers) at local and district level to get feedbacks on new tested prototypes and to develop possible scenarios for climate smart rice production practices. The farm analysis survey showed that non-availability of cheap labor and lacks of alternatives for straw management influence the small farmers to burn the residues in the fields except to use for composting or other purposes. Our field results revealed that application of early season drainage significantly mitigates (40-60%) the methane emissions from residue incorporation. Early season drainage was more efficient and easy to control under cooperate manage system than individually managed water system, and it leads to both economic (9-11% high rice yield, low cost of production, reduced nutrient loses) and environmental (mitigate methane emissions) benefits. The participatory field study allows the assessment of adaptation potential and possible benefits of climate smart practices on small farmer fields. If farmers have no other residue management option, full residue incorporation with early plus midseason drainage is adaptable and beneficial (both environmentally and economically) management option for small rice farmers.

Keywords: adaptation, climate smart agriculture, constrainsts, smallholders

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Authors: Enya Trenholm-Jensen

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This paper employs various semiotic methodologies to examine the mechanism of soft power. Soft power refers to a country’s global reputation and their ability to leverage that reputation to achieve certain aims. South Korea has invested heavily in their soft power strategy for a multitude of predominantly historical and geopolitical reasons. On account of this investment and the global prominence of their strategy, South Korea was considered to be the optimal candidate for the aims of this investigation. Having isolated the entertainment industry as one of the most heavily funded segments of the South Korean soft power strategy, the analysis restricted itself to this sector. Within this industry, two entertainment products were selected as case studies. The case studies were chosen based on commercial success according to metrics such as streams, purchases, and subsequent revenue. This criterion was deemed to be the most objective and verifiable indicator of the products general appeal. The entertainment products which met the chosen criterion were Netflix’ “Squid Game” and BTS’ hit single “Butter”. The methodologies employed were chosen according to the medium of the entertainment products. For “Squid Game,” an aesthetic analysis was carried out to investigate how multi- layered meanings were mobilized in a show popularized by its visual grammar. To examine “Butter”, both music semiology and linguistic analysis were employed. The music section featured an analysis underpinned by denotative and connotative music semiotic theories borrowing from scholars Theo van Leeuwen and Martin Irvine. The linguistic analysis focused on stance and semantic fields according to scholarship by George Yule and John W. DuBois. The aesthetic analysis of the first case study revealed intertextual references to famous artworks, which served to augment the emotional provocation of the Squid Game narrative. For the second case study, the findings exposed a set of musical meaning units arranged in a patchwork of familiar and futuristic elements to achieve a song that existed on the boundary between old and new. The linguistic analysis of the song’s lyrics found a deceptively innocuous surface level meaning that bore implications for authority, intimacy, and commercial success. Whether through means of visual metaphor, embedded auditory associations, or linguistic subtext, the collective findings of the three analyses exhibited a desire to conjure a form of positive arousal in the spectator. In the synthesis section, this process is likened to that of branding. Through an exploration of branding, the entertainment products can be understood as cogs in a larger operation aiming to create positive associations to Korea as a country and a concept. Limitations in the form of a timeframe biased perspective are addressed, and directions for future research are suggested. This paper employs semiotic methodologies to examine two entertainment products as mechanisms of soft power. Through means of visual metaphor, embedded auditory associations, or linguistic subtext, the findings reveal a desire to conjure positive arousal in the spectator. The synthesis finds similarities to branding, thus positioning the entertainment products as cogs in a larger operation aiming to create positive associations to Korea as a country and a concept.

Keywords: BTS, cognitive semiotics, entertainment, soft power, south korea, squid game

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Authors: Heather E. Ewart, Keith Jensen, Rebecca N. Cliffe

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Fragmentation and changes in the structural composition of tropical forests – as a result of intensifying anthropogenic disturbance – are increasing pressures on local biodiversity. Species with low dispersal abilities have some of the highest extinction risks in response to environmental change, as even small-scale environmental variation can substantially impact their space use and energetic balance. Understanding the implications of forest disturbance is therefore essential, ultimately allowing for more effective and targeted conservation initiatives. Here, the impact of different levels of forest disturbance on the space use, energetics, movement and behavior of 18 brown-throated sloths (Bradypus variegatus) were assessed in the South Caribbean of Costa Rica. A multi-scale framework was used to measure forest disturbance, including large-scale (landscape-level classifications) and fine-scale (within and surrounding individual home ranges) forest composition. Three landscape-level classifications were identified: primary forests (undisturbed), secondary forests (some disturbance, regenerating) and urban forests (high levels of disturbance and fragmentation). Finer-scale forest composition was determined using measurements of habitat structure and quality within and surrounding individual home ranges for each sloth (home range estimates were calculated using autocorrelated kernel density estimation [AKDE]). Measurements of forest quality included tree connectivity, density, diameter and height, species richness, and percentage of canopy cover. To determine space use, energetics, movement and behavior, six sloths in urban forests, seven sloths in secondary forests and five sloths in primary forests were tracked using a combination of Very High Frequency (VHF) radio transmitters and Global Positioning System (GPS) technology over an average period of 120 days. All sloths were also fitted with micro data-loggers (containing tri-axial accelerometers and pressure loggers) for an average of 30 days to allow for behavior-specific movement analyses (data analysis ongoing for data-loggers and primary forest sloths). Data-loggers included determination of activity budgets, circadian rhythms of activity and energy expenditure (using the vector of the dynamic body acceleration [VeDBA] as a proxy). Analyses to date indicate that home range size significantly increased with the level of forest disturbance. Female sloths inhabiting secondary forests averaged 0.67-hectare home ranges, while female sloths inhabiting urban forests averaged 1.93-hectare home ranges (estimates are represented by median values to account for the individual variation in home range size in sloths). Likewise, home range estimates for male sloths were 2.35 hectares in secondary forests and 4.83 in urban forests. Sloths in urban forests also used nearly double (median = 22.5) the number of trees as sloths in the secondary forest (median = 12). These preliminary data indicate that forest disturbance likely heightens the energetic requirements of sloths, a species already critically limited by low dispersal ability and rates of energy acquisition. Energetic and behavioral analyses from the data-loggers will be considered in the context of fine-scale forest composition measurements (i.e., habitat quality and structure) and are expected to reflect the observed home range and movement constraints. The implications of these results are far-reaching, presenting an opportunity to define a critical index of habitat connectivity for low dispersal species such as sloths.

Keywords: biodiversity conservation, forest disturbance, movement ecology, sloths

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