Search results for: Renate Ranka

Authors: Alisa Kazarina, Guntis Gerhards, Elina Petersone-Gordina, Ilva Pole, Viktorija Igumnova, Janis Kimsis, Valentina Capligina, Renate Ranka

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Human body is inhabited by a vast number of microorganisms, collectively known as the human microbiome, and there is a tremendous interest in evolutionary changes in human microbial ecology, diversity and function. The field of paleomicrobiology, study of ancient human microbiome, is powered by modern techniques of Next Generation Sequencing (NGS), which allows extracting microbial genomic data directly from archaeological sample of interest. One of the major techniques is 16S rRNA gene sequencing, by which certain 16S rRNA gene hypervariable regions are being amplified and sequenced. However, some limitations of this method exist including the taxonomic precision and efficacy of different regions used. The aim of this study was to evaluate the phylogenetic sensitivity of different 16S rRNA gene hypervariable regions for microbiome studies in the archaeological samples. Towards this aim, archaeological bone samples and corresponding soil samples from each burial environment were collected in Medieval cemeteries in Latvia. The Ion 16S™ Metagenomics Kit targeting different 16S rRNA gene hypervariable regions was used for library construction (Ion Torrent technologies). Sequenced data were analysed by using appropriate bioinformatic techniques; alignment and taxonomic representation was done using Mothur program. Sequences of most abundant genus were further aligned to E. coli 16S rRNA gene reference sequence using MEGA7 in order to identify the hypervariable region of the segment of interest. Our results showed that different hypervariable regions had different discriminatory power depending on the groups of microbes, as well as the nature of samples. On the basis of our results, we suggest that wider range of primers used can provide more accurate recapitulation of microbial communities in archaeological samples. Acknowledgements. This work was supported by the ERAF grant Nr. 1.1.1.1/16/A/101.

Keywords: 16S rRNA gene, ancient human microbiome, archaeology, bioinformatics, genomics, microbiome, molecular biology, next-generation sequencing

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Authors: Prathik Ranka, Sridhar K, Vasanth Daniel, Mithun Shankar

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With growing global food needs and climate uncertainties, informed crop choices are critical for increasing agricultural productivity. Here we propose a machine learning-based crop recommendation system to help farmers in choosing the most proper crops according to their geographical regions and soil properties. We can deploy algorithms like Decision Trees, Random Forests and Support Vector Machines on a broad dataset that consists of climatic factors, soil characteristics and historical crop yields to predict the best choice of crops. The approach includes first preprocessing the data after assessing them for missing values, unlike in previous jobs where we used all the available information and then transformed because there was no way such a model could have worked with missing data, and normalizing as throughput that will be done over a network to get best results out of our machine learning division. The model effectiveness is measured through performance metrics like accuracy, precision and recall. The resultant app provides a farmer-friendly dashboard through which farmers can enter their local conditions and receive individualized crop suggestions.

Keywords: crop recommendation, precision agriculture, crop, machine learning

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Authors: Eric Chabrol, Sidonia B.G. Eckle, Renate de Boer, James McCluskey, Jamie Rossjohn, Mirjam H.M. Heemskerk, Stephanie Gras

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αβ and γδ T-cells are disparate T-cell lineages that, via their use of either αβ or γδ T-cell antigen receptors (TCRs) respectively, can respond to distinct antigens. Here we characterise a new population of human T-cells, term δβ T-cells, that express TCRs comprising a TCR-δ variable gene fused to a Joining-α/Constant-α domain, paired with an array of TCR-β chains. We characterised the cellular, functional, biophysical and structural characteristic feature of this new T-cells population that reveal some new insight into TCR diversity. We provide molecular bases of how δβ T-cells can recognise viral peptide presented by Human Leukocyte Antigen (HLA) molecule. Our findings highlight how components from αβ and γδTCR gene loci can recombine to confer antigen specificity thus expanding our understanding of T-cell biology and TCR diversity.

Keywords: new delta-beta TCR, HLA, viral peptide, structural immunology

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Authors: Renate Krassnig, Gloria M. Hohenberger, Uldis Berzins, Stefen Fischerauer

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Background: Only a few reports discuss the effectiveness of intraoperative radiographs for placing femoral components. Therefore there is no international standard in using intraoperative imaging in the proceeding of total hip replacement. Method: Case report; an 84-year-old female patient underwent changing the components of the Total hip arthroplasty (THA) because of aseptic loosening. Due to circumstances, the surgeon decided to implant a cemented femoral component. The procedure was without any significant abnormalities. The first postoperative radiograph was planned after recovery – as usual. The x-ray imaging showed a misplaced femoral component. Therefore a CT-scan was performed additionally and the malposition of the cemented femoral component was confirmed. The patient had to undergo another surgery – removing of the cemented femoral component and implantation of a new well placed one. Conclusion: Intraoperative imaging of the femoral component is not a common standard but this case shows that intraoperative imaging is a useful method for detecting errors and gives the surgeon the opportunity to correct errors intraoperatively.

Keywords: femoral component, intraoperative imaging, malplacement, revison

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Authors: Ar.Abhishek Ranka

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Cultural landscapes are a part of a nation’s heritage, which represent the exquisite combination of Natural (Ecological) & Built (Architectural) fabric, consisting of many historic gardens, water management system, sustainable planning, and designed framework. The use of landscape and topography with Tangible &Intangible heritage components (forts, temples, tombs, mosques, etc.) are locally, regionally, and nationally significant. The paper speaks about the contribution of Bahmani Sultanate to military architecture in the Deccan region. It is a study of the series of seven land forts as a cultural landscape, which plays an important role in shaping the knowledge systems in the form of typologies of military architecture, water management system, and the administrative setups, which are presently located in the cultural region, Marathwada of the Deccan. Conservation of Culturall and scapeasan approach offers opportunities to better integrate natural and cultural heritage conservation. Conserving of Seven Land forts could act as an inspirational model for other sites.

Keywords: bahmani sultanate, deccan region, land forts, culture landscape, military architecture, tradational knowledge system, architectural conservation

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Authors: Katarina Lazarević, Mirjana Todosijević, Tijana Vulević, Natalija Momirović, Ranka Erić

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Due to increasing demand, climate change, and world population growth, natural resources are getting exploit fast. One of the most important natural resources is soil, which is susceptible to degradation. Erosion as one of the forms of land degradation is also one of the most global environmental problems. Ecosystem services are often defined as benefits that nature provides to humankind. Soil, as the foundation of basic ecosystem functions, provides benefits to people, erosion control, water infiltration, food, fuel, fibers… This research is using the ecosystem approach as a strategy for natural resources management for promoting sustainability and conservation. The research was done on the Topčiderska River basin (Belgrade, Serbia). The InVEST Sediment Delivery Ratio model was used, to quantify erosion intensity with a spatial distribution output map of overland sediment generation and delivery to the stream. InVEST SDR, a spatially explicit model, is using a method based on the concept of hydrological connectivity and (R) USLE model. This, combined with socio-economic and law and policy analysis, gives a full set of information to decision-makers helping them to successfully manage and deliver sustainable ecosystems.

Keywords: ecosystem services, InVEST model, soil erosion, sustainability

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Authors: Renate Gericke, Carol Long

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Despite the robust empirical support of attachment, advancement in the description and conceptualization of attachment has been slow and has not significantly advanced beyond the identification of attachment security or type (namely, secure, avoidant, ambivalent and disorganized). This has continued despite papers arguing for theoretical refinement in the classification of attachment presentations. For thinking and practice to advance, it is critically important that these categories and their assessment be interrogated in different contexts and across developmental age. To achieve this, a quantitative design was used with descriptive and inferential statistics, and general linear models were employed to analyze the data. The Attachment Story Completion Test (ASCT) was administered to 105 children between the ages of eight and twelve from socio-economically deprived contexts with high exposure to trauma. A staggering 93% of the children had insecure attachments (specifically, avoidant 37%, disorganized 34% and ambivalent 22%) and attachment was more complex than currently conceptualized in the attachment literature. Primary attachment did not only present as one of four discreet categories, but 70% of the sample had a complex attachment with more than one type of maternal attachment style. Attachment intensity also varied along a continuum (between 1 and 5). The findings have implications for a) research that has not considered the potential complexity of attachment or attachment intensity, b) policy to more actively support mother-infant dyads, particularly in high-risk contexts and c) question the applicability of a western conceptualization of a primary maternal attachment figure in non-western collectivist societies.

Keywords: attachment, children at risk, middle childhood, non-western context

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Authors: Abhishek Ranka

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Rock-cut Architecture is a manifestation of human endurance in constructing magnificent structures by sculpting and cutting entire hills. Cave Architecture in India form an important part of rock-cut development and is among the most prolific examples of rock-cut architecture in the world. There are more than 1500 rock-cut caves in various regions of India. Among them mostly are located in western India, more particularly in the state of Maharashtra. Some of the rock-cut caves are located in the central region of India, which is presently known as Malawa (Madhya Pradesh). The region is dominated by the vidhyachal hill ranges toward the west, dotted with the coarse laterite rock. Dhamnar Caves have been excavated in the central region of Mandsaur Dist. With a combination of shared sacred faiths. The earliest rock-cut activity began in the north, in Bihar, where caves were excavated in the Barabar and the Nagarjuni hills during the Mauryan period (3rd century BCE). The rock-cut activity then shifts to the central part of India in Madhya Pradesh, where the caves at Dhamnar, Bagh, Udayagiri, Poldungar, etc. excavated between 3rdto 9ᵗʰ CE. The rock-cut excavation continued to flourish in Madhya Pradesh till 10ᵗʰ century CE, simultaneously with monolithic Hindu temples. Dhamnar caves fall into four architectural typologies: the Lena caves, Chaitya caves, Viharas & Lena-Chaityagriha caves. The Buddhist rock-cutting activity in central India is divisible into two phases. In the first phase (2ndBCE-3rd CE), the Buddha image is conspicuously absent. After a lapse of about three centuries, activity begins again, and the Buddha images this time are carved. The former group belongs to the Hinayana (Lesser Vehicle) phase and the latter to the Mahayana (Greater Vehicle). Dhamnar caves has an elaborate facades, pillar capitals, and many more creative sculptures in various postures. These caves were excavated against the background of invigorating trade activities and varied socio-religious or Socio Cultural contexts. These caves also highlights the wealthy and varied patronage provided by the dynasties of the past. This paper speaks about the appraisal of the rock cut mechanisms, design strategies, and approaches while promoting a scope for further research in conservation practices. Rock-cut sites, with their physical setting and various functional spaces as a sustainable habitat for centuries, has a heritage footprint with a researchquotient.

Keywords: rock-cut architecture, buddhism, hinduism, Iconography, and architectural typologies, Jainism

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Authors: Renate Verkaik, Mieke Rijken, Hennie Boeije

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Elderly who are living alone and who are having one or more impairments are vulnerable for a loss of wellbeing and institutionalization. Physical exercise and social activities together with peers have the potential to make them more resilient. The Dutch program ‘More Resilience, Longer at Home’ initiated by FNO funded 126 local projects to stimulate vulnerable older citizens to participate in exercise and social activities, and as such to improve wellbeing and independent living. The program evaluation addressed the following questions: (1) what are the effects of the program on older (65+) participants exercise behavior, social activities and what is the relationship with wellbeing?, (2) which factors contribute to successful implementation of the projects and their outcomes? A mixed method approach was used. Effects on participants were assessed with a short survey, containing questions on exercise, social engagement, daily functioning, loneliness and life satisfaction. Results of the participants were compared with those of a reference group from the Dutch national population. Perceived influencing factors were investigated with a questionnaire for project leaders. This questionnaire was based on site visits and interviews with project leaders, volunteers and participating elderly. Preliminary results show that social engagement of the participating elderly rises significantly (p ≤ .05) as do their exercise levels and daily functioning. They experience less social loneliness, but not less emotional loneliness. Additionally, there is a positive association between daily functioning and life satisfaction and between exercise and life satisfaction. Perceived influencing factors that contribute to successful implementation of the projects can be categorized in 4 types: (1) characteristics of the activities; (2) profiles of the involved staff (professionals and volunteers), (3) characteristics of the organization, (4) the social political environment. Conclusions are that local projects have been successful in stimulating older citizens to participate in exercise and social activities. Multiple factors need to be addressed to ensure sustainability and scaling-up of the good practices.

Keywords: elderly living alone in the community, exercise and social activities, resilience, quality of life

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Authors: Pieter De Vries, Renate Klaassen, Maria Ioannides

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This paper is about an explorative research into the use of emerging technologies for teaching and learning in higher engineering education. The assumption is that these technologies and applications, which are not yet widely adopted, will help to improve education and as such actively work on the ability to better deal with the mismatch of skills bothering our industries. Technologies such as 3D printing, the Internet of Things, Virtual Reality, and others, are in a dynamic state of development which makes it difficult to grasp the value for education. Also, the instruments in current educational research seem not appropriate to assess the value of such technologies. This explorative research aims to foster an approach to better deal with this new complexity. The need to find out is urgent, because these technologies will be dominantly present in the near future in all aspects of life, including education. The methodology used in this research comprised an inventory of emerging technologies and tools that potentially give way to innovation and are used or about to be used in technical universities. The inventory was based on both a literature review and a review of reports and web resources like blogs and others and included a series of interviews with stakeholders in engineering education and at representative industries. In addition, a number of small experiments were executed with the aim to analyze the requirements for the use of in this case Virtual Reality and the Internet of Things to better understanding the opportunities and limitations in the day-today learning environment. The major findings indicate that it is rather difficult to decide about the value of these technologies for education due to the dynamic state of change and therefor unpredictability and the lack of a coherent policy at the institutions. Most decisions are being made by teachers on an individual basis, who in their micro-environment are not equipped to select, test and ultimately decide about the use of these technologies. Most experiences are being made in the industry knowing that the skills to handle these technologies are in high demand. The industry though is worried about the inclination and the capability of education to help bridge the skills gap related to the emergence of new technologies. Due to the complexity, the diversity, the speed of development and the decay, education is challenged to develop an approach that can make these technologies work in an integrated fashion. For education to fully profit from the opportunities, these technologies offer it is eminent to develop a pro-active strategy and a sustainable approach to frame the emerging technologies development.

Keywords: emerging technologies, internet of things, pro-active strategy, virtual reality

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Authors: M. A. C. S. Sampath Fernando, James M. Curran, Renate Meyer

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Forensic DNA analysis has received much attention over the last three decades, due to its incredible usefulness in human identification. The statistical interpretation of DNA evidence is recognised as one of the most mature fields in forensic science. Peak heights in an Electropherogram (EPG) are approximately proportional to the amount of template DNA in the original sample being tested. A stutter is a minor peak in an EPG, which is not masking as an allele of a potential contributor, and considered as an artefact that is presumed to be arisen due to miscopying or slippage during the PCR. Stutter peaks are mostly analysed in terms of stutter ratio that is calculated relative to the corresponding parent allele height. Analysis of mixture profiles has always been problematic in evidence interpretation, especially with the presence of PCR artefacts like stutters. Unlike binary and semi-continuous models; continuous models assign a probability (as a continuous weight) for each possible genotype combination, and significantly enhances the use of continuous peak height information resulting in more efficient reliable interpretations. Therefore, the presence of a sound methodology to distinguish between stutters and real alleles is essential for the accuracy of the interpretation. Sensibly, any such method has to be able to focus on modelling stutter peaks. Bayesian nonparametric methods provide increased flexibility in applied statistical modelling. Mixture models are frequently employed as fundamental data analysis tools in clustering and classification of data and assume unidentified heterogeneous sources for data. In model-based clustering, each unknown source is reflected by a cluster, and the clusters are modelled using parametric models. Specifying the number of components in finite mixture models, however, is practically difficult even though the calculations are relatively simple. Infinite mixture models, in contrast, do not require the user to specify the number of components. Instead, a Dirichlet process, which is an infinite-dimensional generalization of the Dirichlet distribution, is used to deal with the problem of a number of components. Chinese restaurant process (CRP), Stick-breaking process and Pólya urn scheme are frequently used as Dirichlet priors in Bayesian mixture models. In this study, we illustrate an infinite mixture of simple linear regression models for modelling stutter ratio and introduce some modifications to overcome weaknesses associated with CRP.

Keywords: Chinese restaurant process, Dirichlet prior, infinite mixture model, PCR stutter

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Authors: Hennie Boeije, Renate Verkaik, Joke Korevaar

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In Dutch national policy, it is promoted that the elderly remain living at home longer. They are less often admitted to a nursing home or only later in life. While living at home, it is important that they experience a good quality of life. Care providers in primary care support this. In this study, it was investigated what quality of life means for the elderly and which characteristics care should have that supports living at home longer with quality of life. To explore this topic, a qualitative methodology was used. Four focus groups were conducted: two with elderly people who live at home and their family caregivers, one with district nurses employed in-home care services and one with elderly care physicians working in primary care. Next to this individual interviews were employed with general practitioners (GPs). In total 32 participants took part in the study. The data were thematically analysed with MaxQDA software for qualitative analysis and reported. Quality of life is a multi-faceted term for elderly. The essence of their description is that they can still undertake activities that matter to them. Good physical health, mental well-being and social connections enable them to do this. Own control over their life is important for some. They are of opinion that how they experience life and manage old age is related to their resilience and coping. Key terms in the definitions of quality of life by GPs are also physical and mental health and social contacts. These are the three pillars. Next, to this elderly care, physicians mention security and safety and district nurses add control over their own life and meaningful daily activities. They agree that with frail elderly people, the balance is delicate and a change in one of the three pillars can cause it to collapse like a house of cards. When discussing what support is needed, professionals agree on access to care with a low threshold, prevention, and life course planning. When care is provided in a timely manner, a worsening of the situation can be prevented. They agree that hospital care often is not needed since most of the problems with the elderly have to do with care and security rather than with a cure per se. GPs can consult elderly care physicians to lower their workload and to bring in specific knowledge. District nurses often signal changes in the situation of the elderly. According to them, the elderly predominantly need someone to watch over them and provide them with a feeling of security. Life course planning and advance care planning can contribute to uniform treatment in line with older adults’ wishes. In conclusion, all stakeholders, including elderly persons, agree on what entails quality of life and the quality of care that is needed to support that. A future challenge is to shape conditions for the right skill mix of professionals, cooperation between the professions and breaking down differences in financing and supply. For the elderly, the challenge is preparing for aging.

Keywords: elderly living at home, quality of life, quality of care, professional cooperation, life course planning, advance care planning

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Authors: M. A. C. S. Sampath Fernando, James M. Curran, Renate Meyer

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Model assessment, in the Bayesian context, involves evaluation of the goodness-of-fit and the comparison of several alternative candidate models for predictive accuracy and improvements. In posterior predictive checks, the data simulated under the fitted model is compared with the actual data. Predictive model accuracy is estimated using information criteria such as the Akaike information criterion (AIC), the Bayesian information criterion (BIC), the Deviance information criterion (DIC), and the Watanabe-Akaike information criterion (WAIC). The goal of an information criterion is to obtain an unbiased measure of out-of-sample prediction error. Since posterior checks use the data twice; once for model estimation and once for testing, a bias correction which penalises the model complexity is incorporated in these criteria. Cross-validation (CV) is another method used for examining out-of-sample prediction accuracy. Leave-one-out cross-validation (LOO-CV) is the most computationally expensive variant among the other CV methods, as it fits as many models as the number of observations. Importance sampling (IS), truncated importance sampling (TIS) and Pareto-smoothed importance sampling (PSIS) are generally used as approximations to the exact LOO-CV and utilise the existing MCMC results avoiding expensive computational issues. The reciprocals of the predictive densities calculated over posterior draws for each observation are treated as the raw importance weights. These are in turn used to calculate the approximate LOO-CV of the observation as a weighted average of posterior densities. In IS-LOO, the raw weights are directly used. In contrast, the larger weights are replaced by their modified truncated weights in calculating TIS-LOO and PSIS-LOO. Although, information criteria and LOO-CV are unable to reflect the goodness-of-fit in absolute sense, the differences can be used to measure the relative performance of the models of interest. However, the use of these measures is only valid under specific circumstances. This study has developed 11 models using normal, log-normal, gamma, and student’s t distributions to improve the PCR stutter prediction with forensic data. These models are comprised of four with profile-wide variances, four with locus specific variances, and three which are two-component mixture models. The mean stutter ratio in each model is modeled as a locus specific simple linear regression against a feature of the alleles under study known as the longest uninterrupted sequence (LUS). The use of AIC, BIC, DIC, and WAIC in model comparison has some practical limitations. Even though, IS-LOO, TIS-LOO, and PSIS-LOO are considered to be approximations of the exact LOO-CV, the study observed some drastic deviations in the results. However, there are some interesting relationships among the logarithms of pointwise predictive densities (lppd) calculated under WAIC and the LOO approximation methods. The estimated overall lppd is a relative measure that reflects the overall goodness-of-fit of the model. Parallel log-likelihood profiles for the models conditional on equal posterior variances in lppds were observed. This study illustrates the limitations of the information criteria in practical model comparison problems. In addition, the relationships among LOO-CV approximation methods and WAIC with their limitations are discussed. Finally, useful recommendations that may help in practical model comparisons with these methods are provided.

Keywords: cross-validation, importance sampling, information criteria, predictive accuracy

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