1,423 results on '"Rokka A"'
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2. Low-power light irradiation based plasmonic photoresponse on quasi-freestanding monolayer/AuNPs hybrid system
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Khadka, Ishwor Bahadur, Rai, Krishna Bahadur, and Rokka, Dilip
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- 2024
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3. Contrastive Credibility Propagation for Reliable Semi-supervised Learning.
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Brody Kutt, Pralay Ramteke, Xavier Mignot, Pamela Toman, Nandini Ramanan, Sujit Rokka Chhetri, Shan Huang, Min Du, and William Hewlett
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- 2024
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4. Contrastive Credibility Propagation for Reliable Semi-Supervised Learning
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Kutt, Brody, Ramteke, Pralay, Mignot, Xavier, Toman, Pamela, Ramanan, Nandini, Chhetri, Sujit Rokka, Huang, Shan, Du, Min, and Hewlett, William
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Computer Science - Machine Learning - Abstract
Producing labels for unlabeled data is error-prone, making semi-supervised learning (SSL) troublesome. Often, little is known about when and why an algorithm fails to outperform a supervised baseline. Using benchmark datasets, we craft five common real-world SSL data scenarios: few-label, open-set, noisy-label, and class distribution imbalance/misalignment in the labeled and unlabeled sets. We propose a novel algorithm called Contrastive Credibility Propagation (CCP) for deep SSL via iterative transductive pseudo-label refinement. CCP unifies semi-supervised learning and noisy label learning for the goal of reliably outperforming a supervised baseline in any data scenario. Compared to prior methods which focus on a subset of scenarios, CCP uniquely outperforms the supervised baseline in all scenarios, supporting practitioners when the qualities of labeled or unlabeled data are unknown., Comment: Accepted to AAAI '24
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- 2022
5. Estrogen deprivation and estrogen receptor α antagonism decrease DSS colitis in female mice
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Anja Hjelt, Santeri Anttila, Anu Wiklund, Anne Rokka, Darin Al‐Ramahi, Diana M. Toivola, Lauri Polari, and Jorma Määttä
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colitis ,dextran sulfate ,estradiol ,estrogen receptor modulators ,inflammatory bowel diseases ,receptors ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Abstract The association of hormonal contraception with increased risk of inflammatory bowel disease (IBD) observed in females suggests involvement of ovarian hormones, such as estradiol, and the estrogen receptors in the progression of intestinal inflammation. Here, we investigated the effects of prophylactic SERM2 and estradiol supplementation in dextran sulfate sodium‐induced colitis using mice with intact ovaries and ovariectomized (OVX) female mice. We found that graded colitis score was threefold reduced in the OVX mice, compared to mice with intact ovaries. Estradiol supplementation, however, aggravated the colitis in OVX mice, increasing the colitis score to a similar level than what was observed in the intact mice. Further, we observed that immune infiltration and gene expression of inflammatory interleukins Il1b, Il6, and Il17a were up to 200‐fold increased in estradiol supplemented OVX colitis mice, while a mild but consistent decrease was observed by SERM2 treatment in intact animals. Additionally, cyclo‐oxygenase 2 induction was increased in the colon of colitis mice, in correlation with increased serum estradiol levels. Measured antagonist properties of SERM2, together with the other results presented here, indicates an exaggerating role of ERα signaling in colitis. Our results contribute to the knowledge of ovarian hormone effects in colitis and encourage further research on the potential use of ER antagonists in the colon, in order to alleviate inflammation.
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- 2024
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6. Synthesis and evaluation of fluorine-18 labelled tetrazines as pre-targeting imaging agents for PET
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Eva Schlein, Johanna Rokka, Luke R. Odell, Sara Lopes van den Broek, Matthias M. Herth, Umberto M. Battisti, Stina Syvänen, Dag Sehlin, and Jonas Eriksson
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Inverse electron demand Diels–Alder reaction ,IEDDA ,Pre-targeting ,Tetrazine ,Trans-cyclooctene ,TCO ,Medical physics. Medical radiology. Nuclear medicine ,R895-920 ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Abstract Background The brain is a challenging target for antibody-based positron emission tomography (immunoPET) imaging due to the restricted access of antibody-based ligands through the blood–brain barrier (BBB). To overcome this physiological obstacle, we have previously developed bispecific antibody ligands that pass through the BBB via receptor-mediated transcytosis. While these radiolabelled ligands have high affinity and specificity, their long residence time in the blood and brain, typical for large molecules, poses another challenge for PET imaging. A viable solution could be a two-step pre-targeting approach which involves the administration of a tagged antibody that accumulates at the target site in the brain and then clears from the blood, followed by administration of a small radiolabelled molecule with fast kinetics. This radiolabelled molecule can couple to the tagged antibody and thereby make the antibody localisation visible by PET imaging. The in vivo linkage can be achieved by using the inverse electron demand Diels–Alder reaction (IEDDA), with trans-cyclooctene (TCO) and tetrazine groups participating as reactants. In this study, two novel 18F-labelled tetrazines were synthesized and evaluated for their potential use as pre-targeting imaging agents, i.e., for their ability to rapidly enter the brain and, if unbound, to be efficiently cleared with minimal background retention. Results The two compounds, a methyl tetrazine [18F]MeTz and an H-tetrazine [18F]HTz were radiolabelled using a two-step procedure via [18F]F-Py-TFP synthesized on solid support followed by amidation with amine-bearing tetrazines, resulting in radiochemical yields of 24% and 22%, respectively, and a radiochemical purity of > 96%. In vivo PET imaging was performed to assess their suitability for in vivo pre-targeting. Time-activity curves from PET-scans showed [18F]MeTz to be the more pharmacokinetically suitable agent, given its fast and homogenous distribution in the brain and rapid clearance. However, in terms of rection kinetics, H-tetrazines are advantageous, exhibiting faster reaction rates in IEDDA reactions with dienophiles like trans-cyclooctenes, making [18F]HTz potentially more beneficial for pre-targeting applications. Conclusion This study demonstrates a significant potential of [18F]MeTz and [18F]HTz as agents for pre-targeted PET brain imaging due to their efficient brain uptake, swift clearance and appropriate chemical stability.
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- 2024
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7. Altered amyloid-β structure markedly reduces gliosis in the brain of mice harboring the Uppsala APP deletion
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María Pagnon de la Vega, Stina Syvänen, Vilmantas Giedraitis, Monique Hooley, Evangelos Konstantinidis, Silvio R. Meier, Johanna Rokka, Jonas Eriksson, Ximena Aguilar, Tara L. Spires-Jones, Lars Lannfelt, Lars N. G. Nilsson, Anna Erlandsson, Greta Hultqvist, Martin Ingelsson, and Dag Sehlin
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Alzheimer’s disease (AD) ,Amyloid precursor protein (APP) ,Amyloid-beta (Aβ) ,PET imaging ,Microglia ,Astrocytes ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract Deposition of amyloid beta (Aβ) into plaques is a major hallmark of Alzheimer’s disease (AD). Different amyloid precursor protein (APP) mutations cause early-onset AD by altering the production or aggregation properties of Aβ. We recently identified the Uppsala APP mutation (APPUpp), which causes Aβ pathology by a triple mechanism: increased β-secretase and altered α-secretase APP cleavage, leading to increased formation of a unique Aβ conformer that rapidly aggregates and deposits in the brain. The aim of this study was to further explore the effects of APPUpp in a transgenic mouse model (tg-UppSwe), expressing human APP with the APPUpp mutation together with the APPSwe mutation. Aβ pathology was studied in tg-UppSwe brains at different ages, using ELISA and immunohistochemistry. In vivo PET imaging with three different PET radioligands was conducted in aged tg-UppSwe mice and two other mouse models; tg-ArcSwe and tg-Swe. Finally, glial responses to Aβ pathology were studied in cell culture models and mouse brain tissue, using ELISA and immunohistochemistry. Tg-UppSwe mice displayed increased β-secretase cleavage and suppressed α-secretase cleavage, resulting in AβUpp42 dominated diffuse plaque pathology appearing from the age of 5–6 months. The γ-secretase cleavage was not affected. Contrary to tg-ArcSwe and tg-Swe mice, tg-UppSwe mice were [11C]PiB-PET negative. Antibody-based PET with the 3D6 ligand visualized Aβ pathology in all models, whereas the Aβ protofibril selective mAb158 ligand did not give any signals in tg-UppSwe mice. Moreover, unlike the other two models, tg-UppSwe mice displayed a very faint glial response to the Aβ pathology. The tg-UppSwe mouse model thus recapitulates several pathological features of the Uppsala APP mutation carriers. The presumed unique structural features of AβUpp42 aggregates were found to affect their interaction with anti-Aβ antibodies and profoundly modify the Aβ-mediated glial response, which may be important aspects to consider for further development of AD therapies.
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- 2024
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8. The 'Motivational Climate in Physical Education Scale' in Greek Educational Context: Psychometric Properties and Gender Effects
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Masadis, Gregory, Filippou, Filippos, Kouli, Olga, Gargalianos, Dimitris, Rokka, Stella, Bebetsos, Evangelos, Derri, Vasiliki, Damianidou, Sofia, Koupani, Aikaterini, Samara, Eleni, Siarenou, Dafni, and Filippou, Dafni-Anastasia
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The aim of this study was to carry out a preliminary validation of "Motivational Climate in Physical Education Scale" in Greek educational context and specifically in relation to elementary school students. The participants of the research were 184 (101 male and 83 female) students of grades 5th and 6th from four elementary schools, in different geographical areas of Greece. The Greek version of Motivational Climate in Physical Education Scale was used for the data collection. The statistical analyses that were applied included: descriptive analysis, exploratory factor analysis, reliability analysis and the One-way ANOVA analysis. The results showed that the questionnaire retains the structure of the four factors that its designers have recommended and the internal cohesion of the four factors was high (.85 the lowest and .90 the highest). Survey data revealed that the Greek version of the "Motivational Climate in Physical Education Scale" is a reliable tool for the measurement of motivational climate in the Greek educational elementary school environment, and the gender determines the climate of motivation with male students scoring higher in task involving and autonomy factors whereas female students perform better in task involving and relatedness.
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- 2020
9. Mapping Research on Bambara Groundnut (Vigna subterranea (L.) Verdc.) in Africa: Bibliometric, Geographical, and Topical Perspectives
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Hamid El Bilali, Zakaria Kiebre, Romaric Kiswendsida Nanema, Iro Dan Guimbo, Veli-Matti Rokka, Maria Gonnella, Sheirita Reine Fanta Tietiambou, Lawali Dambo, Jacques Nanema, Francesca Grazioli, and Filippo Acasto
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neglected and underutilised species ,NUS ,orphan crops ,Bambara nut ,Bambara bean ,legume ,Agriculture (General) ,S1-972 - Abstract
While Bambara groundnut (Vigna subterranea (L.) Verdc.) originates from Africa and the list of producers is topped by African countries, it is not clear whether research is developed enough to support crop promotion in the continent. Thus, this systematic review of 180 articles presents a comprehensive summary of research on Bambara groundnut (BGN) in Africa. The paper addresses bibliographical metrics, the geographic distribution of the research and themes covered (viz., food and nutrition security, climate resilience, and livelihoods). The analysis shows that BGN can help address different challenges in Africa, such as food and nutrition insecurity and poverty. However, it also highlights gaps in the research from geographical and thematic standpoints. Geographically speaking, the most important producers of BGN in Africa are not sufficiently covered in the research; instead, it is mainly carried out in Nigeria and South Africa. Thematically speaking, the gaps are related to economics and social sciences, the use of BGN in animal production, processing and marketing, irrigation, contribution to climate resilience and livelihoods, and health benefits. Collaborative research and knowledge sharing, including among producing countries and those leading the research field, are highly needed to unlock the potential of BGN and boost its contribution to sustainable development in Africa.
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- 2024
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10. Effect of Dance Aerobic Programs on Intrinsic Motivation and Perceived Task Climate in Secondary School Students
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Rokka, Stella, Kouli, Olga, Bebetsos, Evangelos, Goulimaris, Dimitrios, and Mavridis, George
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The aim of the present study was to investigate the effect of a dance aerobic intervention program on intrinsic motivation and perceived motivation climate in 7th grade middle school students. The sample of the study consisted of 160 healthy students, of the first grade of middle school. Of these, 91 students was the experimental group and the remaining 69 was the control. The experimental group followed an aerobic dance intervention program for ten weeks, three times per week, with 45-minute sessions while the control group only followed the typical physical education program of the school. In order to conduct the study the following instruments were used: a) the Intrinsic Motivation Inventory (??? -- McAuley, Duncan & Tammen, 1989) and the Perceived Oriented Climate (LAPOPECQ; Papaioannou, 1998).
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- 2019
11. Traditional Dances as a Means of Teaching Social Skills to Elementary School Students
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Masadis, Grigorios, Filippou, Filippos, Derri, Vasiliki, Mavridis, Georgios, and Rokka, Stella
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The aim of this study was to investigate: a. the effect of an interdisciplinary program of Greek traditional dance by the means of the teamwork method of teaching social skills to students. b. whether this effect was similar for boys and girls. The sample of the study constituted of 206 elementary school pupils (4th, 5th, and 6th class). The intervention program lasted for two months. There were a total of sixteen lessons (2 per week) which concerned the acquisition of social skills through Greek traditional dance (the experimental group). The method in use was either the group divided work or teamwork. The Greek version (Masadis et al., 2016) of Matson Evaluation of Social Skills with Youngsters (MESSY-II) (Matson et al., 2012) was applied to collect the research data. This in order to be analysed required the following statistical analysis: a. Descriptive statistics b. t-test for independent sample c. Reliability analysis (Cronbach's a) and d. Repeated Measures ANOVA. The findings and the evaluation of the study suggest that the teamwork method is the most appropriate to adopt in social skills learning for the last 3 grades of primary school and traditional dancing the best choice to make.
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- 2019
12. Knowledge, attitudes, and conservation challenges for the Lesser Adjutant in Nepal
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Katuwal, Hem Bahadur, Sharma, Hari Prasad, Rokka, Prashant, Das, Nitesh Kumar, and Quan, Rui-Chang
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- 2024
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13. Characterization of Immune Cell Populations of Cutaneous Neurofibromas in Neurofibromatosis 1
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Kallionpää, Roope A., Peltonen, Sirkku, Le, Kim My, Martikkala, Eija, Jääskeläinen, Mira, Fazeli, Elnaz, Riihilä, Pilvi, Haapaniemi, Pekka, Rokka, Anne, Salmi, Marko, Leivo, Ilmo, and Peltonen, Juha
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- 2024
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14. Imaging of fibrogenesis in the liver by [18F]TZ-Z09591, an Affibody molecule targeting platelet derived growth factor receptor β
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Olivia Wegrzyniak, Bo Zhang, Johanna Rokka, Maria Rosestedt, Bogdan Mitran, Pierre Cheung, Emmi Puuvuori, Sofie Ingvast, Jonas Persson, Helena Nordström, John Löfblom, Fredrik Pontén, Fredrik Y. Frejd, Olle Korsgren, Jonas Eriksson, and Olof Eriksson
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PET imaging ,Platelet derived growth factor receptor ,Hepatic stellate cells ,Fibrogenesis ,Liver fibrosis ,Medical physics. Medical radiology. Nuclear medicine ,R895-920 ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Abstract Background Platelet-derived growth factor receptor beta (PDGFRβ) is a receptor overexpressed on activated hepatic stellate cells (aHSCs). Positron emission tomography (PET) imaging of PDGFRβ could potentially allow the quantification of fibrogenesis in fibrotic livers. This study aims to evaluate a fluorine-18 radiolabeled Affibody molecule ([18F]TZ-Z09591) as a PET tracer for imaging liver fibrogenesis. Results In vitro specificity studies demonstrated that the trans-Cyclooctenes (TCO) conjugated Z09591 Affibody molecule had a picomolar affinity for human PDGFRβ. Biodistribution performed on healthy rats showed rapid clearance of [18F]TZ-Z09591 through the kidneys and low liver background uptake. Autoradiography (ARG) studies on fibrotic livers from mice or humans correlated with histopathology results. Ex vivo biodistribution and ARG revealed that [18F]TZ-Z09591 binding in the liver was increased in fibrotic livers (p = 0.02) and corresponded to binding in fibrotic scars. Conclusions Our study highlights [18F]TZ-Z09591 as a specific tracer for fibrogenic cells in the fibrotic liver, thus offering the potential to assess fibrogenesis clearly. Graphical abstract
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- 2023
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15. Knowledge, attitudes, and conservation challenges for the Lesser Adjutant in Nepal
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Hem Bahadur Katuwal, Hari Prasad Sharma, Prashant Rokka, Nitesh Kumar Das, and Rui-Chang Quan
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Conservation ,Farmland ,Nesting colonies ,Pesticides ,Interviews ,Wetland ,Ecology ,QH540-549.5 - Abstract
The knowledge and attitudes of local communities are essential for understanding the distribution, ecology, and pertinent threats to bird species, particularly those existing beyond protected areas. Despite the reliance of large waterbirds like storks on human-dominated landscapes, research in this domain is limited across its range. To address this knowledge gap, we conducted semi-structured interviews with 546 local people across seven districts in the lowlands of Nepal from 2021 to 2022 to insights into people’s knowledge, attitudes, and the conservation challenges faced by the Lesser Adjutant (Leptoptilos javanicus). Our findings showed that people possessed substantial knowledge about the species name and ecology. A majority of the people (89%), agreed with the statement that the Lesser Adjutant contributes to ecosystem services in farmlands, whereas they disagreed with the notions that it is a pest, unattractive species, or possess medicinal values, with 84%, 82%, and 67% respectively holding these views. In addition, 65% of people reported a significant decline in its population, with 67% noting a decrease in distribution range and 49% observing a decline in nesting sites over the past decade, primarily due to food scarcity, habitat loss, the felling of nesting trees, wetland degradation, pesticide use, and hunting, among other factors. A striking knowledge gap was evident, with approximately two-thirds of people unaware of its conservation status, and over 80% highlighting the absence of local awareness initiatives. Nonetheless, majority of the people (95%) expressed strong support for its conservation, emphasizing the need for intensified awareness programs, habitat conservation and management, and the protection of large trees, among other measures, to ensure the well-being of this iconic species beyond the confines of protected areas. Our study provides essential baseline data for researchers and conservation managers to design effective plans and policies for the research and conservation of the Lesser Adjutant.
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- 2024
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16. Imaging of fibrogenesis in the liver by [18F]TZ-Z09591, an Affibody molecule targeting platelet derived growth factor receptor β
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Wegrzyniak, Olivia, Zhang, Bo, Rokka, Johanna, Rosestedt, Maria, Mitran, Bogdan, Cheung, Pierre, Puuvuori, Emmi, Ingvast, Sofie, Persson, Jonas, Nordström, Helena, Löfblom, John, Pontén, Fredrik, Frejd, Fredrik Y., Korsgren, Olle, Eriksson, Jonas, and Eriksson, Olof
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- 2023
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17. Research on Moringa (Moringa oleifera Lam.) in Africa
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Hamid El Bilali, Iro Dan Guimbo, Romaric Kiswendsida Nanema, Hamidou Falalou, Zakaria Kiebre, Veli-Matti Rokka, Sheirita Reine Fanta Tietiambou, Jacques Nanema, Lawali Dambo, Francesca Grazioli, Abdel Kader Naino Jika, Maria Gonnella, and Filippo Acasto
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neglected and underutilized species ,NUS ,orphan crops ,M. oleifera ,drumstick tree ,horseradish tree ,Botany ,QK1-989 - Abstract
While Moringa oleifera Lam. is gaining importance in Africa, especially sub-Saharan Africa, it is unclear whether research is following the quick pace of its development on the continent. Therefore, this article analyzes the landscape of research dealing with moringa in Africa. This systematic review draws upon 299 eligible articles identified through a search carried out on the Web of Science in April 2023. Research on M. oleifera is rather recent in Africa but interest is increasing among scholars. While the research field is multidisciplinary and cross-sectoral, the literature seems to focus on biological and environmental sciences. Moreover, research is performed mainly in South Africa, Nigeria, Egypt, and Ghana. The analysis suggests a significant potential contribution of moringa to food security and nutrition, climate change mitigation/adaptation, farming systems resilience, and livelihoods. Its versatility and diverse applications and uses make moringa particularly interesting for developing countries, such as African ones. However, this review also underscores some factors hindering its development. Therefore, there is a need to strengthen research on moringa to unlock its potential in Africa. Investments in research, innovation, and development can help address the many challenges that Africa faces and contribute to the transition towards sustainable and resilient food systems.
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- 2024
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18. Interdisciplinary Greek Traditional Dance Course: Impact on Student Satisfaction and Anxiety
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Filippou, Filippos, Rokka, Stella, Pitsi, Athena, Gargalianos, Dimitrios, Bebetsos, Evangelos, and Filippou, Dafni-Anastasia
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The aim of this study was to investigate the effect of an interdisciplinary program of Greek folk dance music and sociology on 8th grade Middle school student satisfaction and anxiety level. To evaluate students' anxiety and satisfaction the Competitive State Anxiety Inventory-2 and Duda and Nicholls' Satisfaction questionnaire were used respectively. The reliability analysis showed that indicators of internal cohesion of subscales in both instruments were at satisfactory levels. The results showed that the experimental group enhanced significantly the levels of satisfaction, and self-confidence and decreased significantly the levels of somatic and cognitive anxiety. The satisfaction of students was positively related to self-confidence and negatively related to cognitive anxiety. The improvement observed in the experimental group concerned both boys and girls. In conclusion, we can say that an interdisciplinary program of traditional Greek dance reduces the rates of somatic and cognitive anxiety while simultaneously increasing students' satisfaction and self-confidence.
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- 2018
19. Lipid-related thiamine deficiency cause mortality of river lampreys (Lampetra fluviatilis) during pre-spawning fasting
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Vuorinen, Pekka J., Juntunen, Esa-Pekka, Iivari, Juha, Koski, Perttu, Nikonen, Soili, Rokka, Mervi, Ritvanen, Tiina, Pakkala, Jukka, Heinimaa, Petri, and Keinänen, Marja
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- 2023
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20. Synaptic density in aging mice measured by [18F]SynVesT-1 PET
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Xiong, Mengfei, Roshanbin, Sahar, Sehlin, Dag, Hansen, Hanne D., Knudsen, Gitte M., Rokka, Johanna, Eriksson, Jonas, and Syvänen, Stina
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- 2023
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21. Graph Representation Ensemble Learning
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Goyal, Palash, Huang, Di, Chhetri, Sujit Rokka, Canedo, Arquimedes, Shree, Jaya, and Patterson, Evan
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Computer Science - Social and Information Networks ,Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
Representation learning on graphs has been gaining attention due to its wide applicability in predicting missing links, and classifying and recommending nodes. Most embedding methods aim to preserve certain properties of the original graph in the low dimensional space. However, real world graphs have a combination of several properties which are difficult to characterize and capture by a single approach. In this work, we introduce the problem of graph representation ensemble learning and provide a first of its kind framework to aggregate multiple graph embedding methods efficiently. We provide analysis of our framework and analyze -- theoretically and empirically -- the dependence between state-of-the-art embedding methods. We test our models on the node classification task on four real world graphs and show that proposed ensemble approaches can outperform the state-of-the-art methods by up to 8% on macro-F1. We further show that the approach is even more beneficial for underrepresented classes providing an improvement of up to 12%.
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- 2019
22. Benchmarks for Graph Embedding Evaluation
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Goyal, Palash, Huang, Di, Goswami, Ankita, Chhetri, Sujit Rokka, Canedo, Arquimedes, and Ferrara, Emilio
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Computer Science - Social and Information Networks ,Computer Science - Machine Learning - Abstract
Graph embedding is the task of representing nodes of a graph in a low-dimensional space and its applications for graph tasks have gained significant traction in academia and industry. The primary difference among the many recently proposed graph embedding methods is the way they preserve the inherent properties of the graphs. However, in practice, comparing these methods is very challenging. The majority of methods report performance boosts on few selected real graphs. Therefore, it is difficult to generalize these performance improvements to other types of graphs. Given a graph, it is currently impossible to quantify the advantages of one approach over another. In this work, we introduce a principled framework to compare graph embedding methods. Our goal is threefold: (i) provide a unifying framework for comparing the performance of various graph embedding methods, (ii) establish a benchmark with real-world graphs that exhibit different structural properties, and (iii) provide users with a tool to identify the best graph embedding method for their data. This paper evaluates 4 of the most influential graph embedding methods and 4 traditional link prediction methods against a corpus of 100 real-world networks with varying properties. We organize the 100 networks in terms of their properties to get a better understanding of the embedding performance of these popular methods. We use the comparisons on our 100 benchmark graphs to define GFS-score, that can be applied to any embedding method to quantify its performance. We rank the state-of-the-art embedding approaches using the GFS-score and show that it can be used to understand and evaluate novel embedding approaches. We envision that the proposed framework (https://www.github.com/palash1992/GEM-Benchmark) will serve the community as a benchmarking platform to test and compare the performance of future graph embedding techniques.
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- 2019
23. Tracking Temporal Evolution of Graphs using Non-Timestamped Data
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Chhetri, Sujit Rokka, Goyal, Palash, and Canedo, Arquimedes
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Computer Science - Social and Information Networks - Abstract
Datasets to study the temporal evolution of graphs are scarce. To encourage the research of novel dynamic graph learning algorithms we introduce YoutubeGraph-Dyn (available at https://github.com/palash1992/YoutubeGraph-Dyn), an evolving graph dataset generated from YouTube real-world interactions. YoutubeGraph-Dyn provides intra-day time granularity (with 416 snapshots taken every 6 hours for a period of 104 days), multi-modal relationships that capture different aspects of the data, multiple attributes including timestamped, non-timestamped, word embeddings, and integers. Our data collection methodology emphasizes the creation of time evolving graphs from non-timestamped data. In this paper, we provide various graph statistics of YoutubeGraph-Dyn and test state-of-the-art graph clustering algorithms to detect community migration, and time series analysis and recurrent neural network algorithms to forecast non-timestamped data.
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- 2019
24. Pykg2vec: A Python Library for Knowledge Graph Embedding
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Yu, Shih Yuan, Chhetri, Sujit Rokka, Canedo, Arquimedes, Goyal, Palash, and Faruque, Mohammad Abdullah Al
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Computer Science - Artificial Intelligence ,Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
Pykg2vec is an open-source Python library for learning the representations of the entities and relations in knowledge graphs. Pykg2vec's flexible and modular software architecture currently implements 16 state-of-the-art knowledge graph embedding algorithms, and is designed to easily incorporate new algorithms. The goal of pykg2vec is to provide a practical and educational platform to accelerate research in knowledge graph representation learning. Pykg2vec is built on top of TensorFlow and Python's multiprocessing framework and provides modules for batch generation, Bayesian hyperparameter optimization, mean rank evaluation, embedding, and result visualization. Pykg2vec is released under the MIT License and is also available in the Python Package Index (PyPI). The source code of pykg2vec is available at https://github.com/Sujit-O/pykg2vec., Comment: 5 pages, 5 figures, few code snippets
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- 2019
25. Dynamics of convivial affective atmospheres
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Rokka, Joonas, Auriacombe, Brigitte, Arnould, Eric, and Sitz, Lionel
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- 2023
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26. Determination of Bioactive Compounds, Antioxidant Capacities and Safety of the Somatic Hybrid Potatoes
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Kammoun, Mariem, Jeddou, Khaoula Ben, Rokka, Veli-Matti, Pihlava, Juha-Matti, Hellström, Jarkko, Gutiérrez-Quequezana, Liz, Essid, Mohamed Farouk, Gargouri-Bouzid, Radhia, and Nouri-Ellouz, Oumèma
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- 2022
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27. The effects of climate and land use change on the potential distribution and nesting habitat of the Lesser Adjutant in Nepal
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Katuwal, Hem Bahadur, Sharma, Hari Prasad, Rokka, Prashant, Bhusal, Krishna Prasad, Bhattarai, Bishnu Prasad, Koirala, Sabina, Luitel, Sandeep Chhetri, Yadav, Shailendra, Sah, Ganesh, Baral, Hem Sagar, Poudyal, Laxman Prasad, Wang, Lin, and Quan, Rui-Chang
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- 2023
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28. The 'Unknown' Greek Paleoenvironment: Curriculum Proposals through an Infusion Model for Elementary School, Using Ammonite Fossils
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Fragouli, Stiliani and Rokka, Aggeliki
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In this study we introduce an infusion model to "inject" ammonites and ammonite fossils in current subjects of Greek primary curriculum. Paleontology and mainly fossils attract more and more elementary students and teachers, yet in Greece this trend is solely about dinosaurs, despite the fact that the most common Greek fossils are not dinosaurs, but ammonites. Ammonites can be found in large population and diversity inside Greek rocks, as these rocks were part of Tethys' seafloor at their geological time. Apart from the informal sources of education, these science topics are excluded from elementary national curriculum, and leave the regional paleoenvironment and geological history practically "unknown" to students. Data collected through a pre-test study, in 558 students of 4th, 5th, and 6th grade confirmed the above belief. A post-test at the original sample, using an open ended questionnaire and students' drawings, evaluated positively the infusion teaching model, whose core were the ammonite fossils.
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- 2017
29. Synaptic density in aging mice measured by [18F]SynVesT-1 PET
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Mengfei Xiong, Sahar Roshanbin, Dag Sehlin, Hanne D. Hansen, Gitte M. Knudsen, Johanna Rokka, Jonas Eriksson, and Stina Syvänen
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Synaptic density ,Aging ,Positron emission tomography (PET) ,Mice ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Synaptic alterations in certain brain structures are related to cognitive decline in neurodegeneration and in aging. Synaptic loss in many neurodegenerative diseases can be visualized by positron emission tomography (PET) imaging of synaptic vesicle glycoprotein 2A (SV2A). However, the use of SV2A PET for studying synaptic changes during aging is not particularly explored. Thus, in the present study, PET ligand [18F]SynVesT-1, which binds to SV2A, was used to investigate synaptic density at different ages in healthy mice.Wild type C57BL/6 mice divided into three age groups (4–5 months (n = 7), 12–14 months (n = 11), 17–19 months (n = 7)) were PET scanned with [18F]SynVesT-1. Brain retention of [18F]SynVesT-1 expressed as the volume of distribution (VIDIF) was calculated using an image-derived input function. Estimates of VIDIF were derived using either a one-tissue compartment model (1TCM), a two-tissue compartment model (2TCM), or the Logan plot with blood input to find the best-fit model for [18F]SynVesT-1. After the PET scans, tissue sections were immunostained for the detection of SV2A and neuronal markers.We found that [18F]SynVesT-1 data acquired 60 min post intravenously injection and analyzed with 1TCM described the brain pharmacokinetics of the radioligand in mice well. [18F]SynVesT-1 brain retention was lower in the oldest group of mice, indicating a decrease in synaptic density in this age group. However, no gradual age-dependent decrease in synaptic density at a region-specific level was observed. Immunostaining indicated that SV2A expression and neuron numbers were similar across all three age groups. In general, these data obtained in healthy aging mice are consistent with previous findings in humans where synaptic density appeared stable during aging up to a certain age, after which a small decrease is observed.
- Published
- 2023
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30. Thiamine Deficiency M74 Developed in Salmon (Salmo salar) Stocks in Two Baltic Sea Areas after the Hatching of Large Year-Classes of Two Clupeid Species—Detected by Fatty Acid Signature Analysis
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Pekka J. Vuorinen, Reijo Käkelä, Tapani Pakarinen, Petri Heinimaa, Tiina Ritvanen, Soili Nikonen, Mervi Rokka, and Marja Keinänen
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Atlantic salmon (Salmo salar) ,Baltic Sea ,docosahexaenoic acid (DHA, 22:6n−3) ,free thiamine in eggs ,herring (Clupea harengus) ,M74 syndrome ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Lipid-related thiamine (vitamin B1) deficiency of Baltic salmon (Salmo salar), the M74 syndrome, is generally caused by feeding on abundant young sprat (Sprattus sprattus) in the Baltic Proper, the main foraging area of these salmon. In 2014, a strong year-class of sprat was hatched in the Baltic Proper, and a strong herring (Clupea harengus) year-class was hatched in the Gulf of Bothnia, where herring is the dominant salmon prey. The fatty acid (FA) signatures of prey fish in muscle or eggs of second sea-year spawners suggested that 27% of wild River Simojoki and 68% of reared River Dal salmon remained in the Gulf of Bothnia in 2014 instead of continuing to the Baltic Proper. In 2016, 23% of the M74 females of the River Simojoki and 58% of the River Dal originated from the Gulf of Bothnia, and 13% and 16%, respectively, originated from the Baltic Proper. Some salmon from the River Neris in the southern Baltic Proper had also been feeding in the Gulf of Bothnia. In general, low free thiamine (THIAM) concentration in eggs was associated with high lipid content and high docosahexaenoic acid (DHA, 22:6n−3) and n−3 polyunsaturated FA (n−3 PUFA) concentrations in muscle but not in eggs. A higher THIAM concentration and lower proportions of DHA and n−3 PUFAs in Arctic Ocean salmon eggs, despite higher egg lipid content, indicated that their diet contained fewer fatty fish than the Baltic salmon diet. Hence, M74 originated by foraging heavily on young fatty sprat in the Baltic Proper or herring in the Gulf of Bothnia.
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- 2024
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31. Efficacy of water and methanol potato peel extracts from a somatic hybrid line in sunflower oil stability
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Jeddou, Khawla Ben, Rokka, Veli-Matti, Chaabane, Mariem, Gargouri-Bouzid, Radhia, Ellouz-Chaabouni, Semia, and Nouri-Ellouz, Oumèma
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- 2022
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32. DynamicGEM: A Library for Dynamic Graph Embedding Methods
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Goyal, Palash, Chhetri, Sujit Rokka, Mehrabi, Ninareh, Ferrara, Emilio, and Canedo, Arquimedes
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Computer Science - Social and Information Networks ,Statistics - Machine Learning - Abstract
DynamicGEM is an open-source Python library for learning node representations of dynamic graphs. It consists of state-of-the-art algorithms for defining embeddings of nodes whose connections evolve over time. The library also contains the evaluation framework for four downstream tasks on the network: graph reconstruction, static and temporal link prediction, node classification, and temporal visualization. We have implemented various metrics to evaluate the state-of-the-art methods, and examples of evolving networks from various domains. We have easy-to-use functions to call and evaluate the methods and have extensive usage documentation. Furthermore, DynamicGEM provides a template to add new algorithms with ease to facilitate further research on the topic.
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- 2018
33. dyngraph2vec: Capturing Network Dynamics using Dynamic Graph Representation Learning
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Goyal, Palash, Chhetri, Sujit Rokka, and Canedo, Arquimedes
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Computer Science - Social and Information Networks ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
Learning graph representations is a fundamental task aimed at capturing various properties of graphs in vector space. The most recent methods learn such representations for static networks. However, real world networks evolve over time and have varying dynamics. Capturing such evolution is key to predicting the properties of unseen networks. To understand how the network dynamics affect the prediction performance, we propose an embedding approach which learns the structure of evolution in dynamic graphs and can predict unseen links with higher precision. Our model, dyngraph2vec, learns the temporal transitions in the network using a deep architecture composed of dense and recurrent layers. We motivate the need of capturing dynamics for prediction on a toy data set created using stochastic block models. We then demonstrate the efficacy of dyngraph2vec over existing state-of-the-art methods on two real world data sets. We observe that learning dynamics can improve the quality of embedding and yield better performance in link prediction.
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- 2018
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34. Future Automation Engineering using Structural Graph Convolutional Neural Networks
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Wan, Jiang, Pollard, Blake S., Chhetri, Sujit Rokka, Goyal, Palash, Faruque, Mohammad Abdullah Al, and Canedo, Arquimedes
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Computer Science - Artificial Intelligence - Abstract
The digitalization of automation engineering generates large quantities of engineering data that is interlinked in knowledge graphs. Classifying and clustering subgraphs according to their functionality is useful to discover functionally equivalent engineering artifacts that exhibit different graph structures. This paper presents a new graph learning algorithm designed to classify engineering data artifacts -- represented in the form of graphs -- according to their structure and neighborhood features. Our Structural Graph Convolutional Neural Network (SGCNN) is capable of learning graphs and subgraphs with a novel graph invariant convolution kernel and downsampling/pooling algorithm. On a realistic engineering-related dataset, we show that SGCNN is capable of achieving ~91% classification accuracy., Comment: ICCAD 2018
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- 2018
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35. IoT-Enabled Living Digital Twin Modeling
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Rokka Chhetri, Sujit, Al Faruque, Mohammad Abdullah, Rokka Chhetri, Sujit, and Al Faruque, Mohammad Abdullah
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- 2020
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36. Non-euclidean Data-Driven Modeling Using Graph Convolutional Neural Networks
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Rokka Chhetri, Sujit, Al Faruque, Mohammad Abdullah, Rokka Chhetri, Sujit, and Al Faruque, Mohammad Abdullah
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- 2020
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37. Data-Driven Security Analysis Using Generative Adversarial Networks
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Rokka Chhetri, Sujit, Al Faruque, Mohammad Abdullah, Rokka Chhetri, Sujit, and Al Faruque, Mohammad Abdullah
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- 2020
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38. Dynamic Data-Driven Digital Twin Modeling
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Rokka Chhetri, Sujit, Al Faruque, Mohammad Abdullah, Rokka Chhetri, Sujit, and Al Faruque, Mohammad Abdullah
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- 2020
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39. Dynamic Graph Embedding
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Rokka Chhetri, Sujit, Al Faruque, Mohammad Abdullah, Rokka Chhetri, Sujit, and Al Faruque, Mohammad Abdullah
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- 2020
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40. Aiding Data-Driven Attack Model with a Compiler Modification
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Rokka Chhetri, Sujit, Al Faruque, Mohammad Abdullah, Rokka Chhetri, Sujit, and Al Faruque, Mohammad Abdullah
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- 2020
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41. Data-Driven Kinetic Cyber-Attack Detection
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Rokka Chhetri, Sujit, Al Faruque, Mohammad Abdullah, Rokka Chhetri, Sujit, and Al Faruque, Mohammad Abdullah
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- 2020
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42. Data-Driven Attack Modeling Using Acoustic Side-Channel
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Rokka Chhetri, Sujit, Al Faruque, Mohammad Abdullah, Rokka Chhetri, Sujit, and Al Faruque, Mohammad Abdullah
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- 2020
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43. Introduction
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Rokka Chhetri, Sujit, Al Faruque, Mohammad Abdullah, Rokka Chhetri, Sujit, and Al Faruque, Mohammad Abdullah
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- 2020
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44. Data-Driven Defense Through Leakage Minimization
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Rokka Chhetri, Sujit, Al Faruque, Mohammad Abdullah, Rokka Chhetri, Sujit, and Al Faruque, Mohammad Abdullah
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- 2020
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45. Editorial: Deep learning with limited labeled data for vision, audio, and text
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Marko Orescanin, Leslie N. Smith, Saurabh Sahu, Palash Goyal, and Sujit Rokka Chhetri
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deep learning ,few shot learning ,semi-supervised ,neural network ,active learning ,semantic segmentation ,Electronic computers. Computer science ,QA75.5-76.95 - Published
- 2023
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46. Illegal trapping and local trade of farmland birds in Madhesh Province, Nepal
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Hem Bahadur Katuwal, Hari Prasad Sharma, Roshan Kumar Thakur, Prashant Rokka, Dev Narayan Mandal, Hem Sagar Baral, and Rui-Chang Quan
- Subjects
Hunting ,Bunting ,Bush meat ,Farmland bird ,Wild bird ,Conservation ,Ecology ,QH540-549.5 - Abstract
Worldwide defaunation is being accelerated by wildlife hunting, trapping, and trade. However, there is little knowledge of bird hunting or trapping in South Asia, including Nepal. Despite being illegal, trapping and eating wild birds (locally called Bagedi, i.e., bunting species - small passerine birds that are declining globally) is popular in lowland Nepal. However, it has received little research interest. We identified the potential bird species that could be trapped under the name Bagedi. We also interviewed 24 trappers, 26 middlemen, 65 hoteliers, and 105 customers to understand the trapping, trade, and eating practices of Bagedi and the impacts on the farmland bird population in Madhesh Province, Nepal. By following trappers and middlemen and based on our Farmland Bird Survey Program in lowland Nepal, we identified 25 farmland bird species that are most likely to be trapped, killed, and sold in the name of Bagedi. We confirmed six of them including true buntings, such as Black-headed Bunting (Emberiza melanocephala), Crested Bunting (Emberiza lathami) and other similar-sized species like Scaly-breasted Munia (Lonchura punctulata) and Baya Weaver (Ploceus philippinus), among others. Trade in Bagedi has increased over the past ten years due to high prices and the customers’ belief that consuming Bagedi produces heat in the body in winter and has aphrodisiac properties. Winter (December–February) is the peak Bagedi eating season and based on interviews with hoteliers (n = 55) during the survey period, we estimated that 115,200 to 129,600 birds were killed. During this period, the surveyed hoteliers would make an estimated business of around Nepalese Rupees 7488,000 to 8424,000 (USD 65,113–73,252). More than 70% of the people interviewed claimed that they did not know that trapping, trading, or eating wild birds is illegal. Around 50% of the trappers, 92% of the middlemen, 56% of the hoteliers, and 54% of the customers showed an unwillingness to stop this activity. Our study shows that bird trapping in our study area is highly market-driven and is a serious, understudied, and overlooked conservation threats to farmland birds in Nepal.
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- 2023
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47. From ‘Mayday’ to #MeToo: Sexual Harassment in Margaret Atwood’s Dystopian Workplaces in The Handmaid’s Tale, The Testaments and The Heart Goes Last
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Rokka, Susanna, Henry, Alastair, editor, and Persson, Åke, editor
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- 2021
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48. The effects of climate and land use change on the potential distribution and nesting habitat of the Lesser Adjutant in Nepal
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Hem Bahadur Katuwal, Hari Prasad Sharma, Prashant Rokka, Krishna Prasad Bhusal, Bishnu Prasad Bhattarai, Sabina Koirala, Sandeep Chhetri Luitel, Shailendra Yadav, Ganesh Sah, Hem Sagar Baral, Laxman Prasad Poudyal, Lin Wang, and Rui-Chang Quan
- Subjects
Agricultural landscapes ,Bombax ceiba ,Ensemble modeling ,Farmland bird ,IBA ,Nest site ,Zoology ,QL1-991 - Abstract
Climate change and land use change pose a threat to the world's biodiversity and have significant impacts on the geographic distribution and composition of many bird species, but little is known about how they affect threatened large-sized waterbird species that rely on agricultural landscapes. To address this gap, we investigated how climate and land use changes influence the distribution and nesting habitats of the globally vulnerable Lesser Adjutant (Leptoptilos javanicus) in Nepal. Between 2012 and 2023, we collected distribution data from 24 districts and nesting site information from 18 districts. In a nation-wide breeding survey conducted in 2020, we documented a total of 581 fledglings from 346 nests in 109 colonies. The ensemble model predicted a current potential distribution of 15% (21,637 km2) and a potential nesting habitat of 13% (19,651 km2) for the species in Nepal. The highest predicted current suitable distribution and nesting habitat was in Madhesh Province, while none was predicted in Karnali Province. The majority of this predicted distributional and nesting habitat falls on agricultural landscapes (>70%). Our model showed a likely range expansion of up to 15% (21,573 km2) for the distribution and up to 12% (17,482 km2) for the nesting habitat under SSP5–8.5 scenarios for the 2070s. The range expansion is expected to occur mainly within the current distribution and breeding range (Tarai and some regions of Siwalk), particularly in Lumbini and Sudurpashchim provinces, and extend to the northern portions (Siwalik and Mid-hill regions) in other provinces. However, the current Protected Areas and Important Bird and Biodiversity Areas are inadequate for providing optimal habitats for the species. Although the model suggests range expansion, the use of such novel habitats is primarily contingent on the availability and protection of large-sized trees (particularly Bombax ceiba, observed in 65% of colonies) in agricultural regions where nesting occurs. Therefore, our research suggests that agricultural landscapes should be prioritized in management plans for the conservation of the Lesser Adjutant in Nepal.
- Published
- 2023
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49. Low circulation of respiratory syncytial and influenza viruses during autumn-winter 2021 in the industrial workplace and long-term healthcare facilities in Athens, Greece
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Eleni Papachristou, Chrysoula Rokka, Triantafyllia Sotiriadou, Leukothea Maneka, Alexandros Vassilakis, Spyros Sapounas, Dimitrios Paraskevis, Eddison Jahaj, Anastasia Kotanidou, Pagona Lagiou, and Gkikas Magiorkinis
- Subjects
COVID-19 ,RSV ,SARS-CoV-2 ,influenza ,non-pharmaceutical interventions ,Medicine (General) ,R5-920 - Abstract
The emergence of SARS-CoV-2 has pinpointed the importance of non-pharmaceutical interventions (NPIs), which have been traditionally used for the prevention of the spread of respiratory viruses among individuals. The aim of our study was to capture the level of circulation of respiratory syncytial and influenza viruses during a period of medium severity NPIs due to SARS-CoV-2 pandemics in Greece. A total of 2,225 nasopharyngeal samples were received during the year 2021 as a part of the routine diagnostic service and were divided into two study groups: (a) January to September 2021 and (b) October to the end of December 2021. The latter is the time of the year when there is a peak of infections from most respiratory viruses, and thus, most of the samples were tested in that period. The samples were taken from three different sites, i.e., (a) industrial workers in a factory, (b) elderly homecare facilities, and c) people who actively asked to be tested for SARS-CoV-2. All the samples were tested simultaneously for SARS-CoV2, RSV, and influenza virus. A total of 2,110 samples were negative for either of the three viruses, 106 were SARS-CoV-2-positive, and 9 were RSV-positive from which 7 were found in the workers’ group. None of the samples was found to be positive for the influenza virus, and no sample had co-infection. Our study shows the low-level circulation of RSV and influenza viruses during autumn-winter 2021 and will provide a reference for future studies of RSV and influenza in Greece.
- Published
- 2023
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50. Research on Moringa (Moringa oleifera Lam.) in Africa
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El Bilali, Hamid, primary, Dan Guimbo, Iro, additional, Nanema, Romaric Kiswendsida, additional, Falalou, Hamidou, additional, Kiebre, Zakaria, additional, Rokka, Veli-Matti, additional, Tietiambou, Sheirita Reine Fanta, additional, Nanema, Jacques, additional, Dambo, Lawali, additional, Grazioli, Francesca, additional, Naino Jika, Abdel Kader, additional, Gonnella, Maria, additional, and Acasto, Filippo, additional
- Published
- 2024
- Full Text
- View/download PDF
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