Search results for: cluster analysis

Authors: Annika Stechemesser, Rachel Pounds, Emma Lucas, Chris Dawson, Julia Lipecki, Pavle Vrljicak, Jan Brosens, Sean Kehoe, Jason Yap, Lawrence Young, Sascha Ott

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Advances in technology make it now possible to retrieve the genetic information of thousands of single cancerous cells. One of the key challenges in single cell analysis of cancerous tissue is to determine the number of different cell types and their characteristic genes within the sample to better understand the tumors and their reaction to different treatments. For this analysis to be possible, it is crucial to filter out background noise as it can severely blur the downstream analysis and give misleading results. In-depth analysis of the state-of-the-art filtering methods for single cell data showed that they do, in some cases, not separate noisy and normal cells sufficiently. We introduced an algorithm that filters and clusters single cell data simultaneously without relying on certain genes or thresholds chosen by eye. It detects communities in a Shared Nearest Neighbor similarity network, which captures the similarities and dissimilarities of the cells by optimizing the modularity and then identifies and removes vertices with a weak clustering belonging. This strategy is based on the fact that noisy data instances are very likely to be similar to true cell types but do not match any of these wells. Once the clustering is complete, we apply a set of evaluation metrics on the cluster level and accept or reject clusters based on the outcome. The performance of our algorithm was tested on three datasets and led to convincing results. We were able to replicate the results on a Peripheral Blood Mononuclear Cells dataset. Furthermore, we applied the algorithm to two samples of ovarian cancer from the same patient before and after chemotherapy. Comparing the standard approach to our algorithm, we found a hidden cell type in the ovarian postchemotherapy data with interesting marker genes that are potentially relevant for medical research.

Keywords: cancer research, graph theory, machine learning, single cell analysis

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Authors: Elham Taghizade Sigarodi, Ani Mirzakhanian

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Journalism atmosphere in present era is highly competitive so that what matters the most is “the speed of news broadcasting”. The first newspaper that lets out the news is therefore of higher validity. The value of the news is in fact in its truthfulness. Expressing the facts and reality is an accepted norm in professional media arena and it is as well considered the acceptable and trustworthy language for journalism. However, different conditions generate self-censorship. The present study seeks to explore the relationship between self-censorship and satisfaction of Iran newspaper’s readers. Thus, the statistical population including journalists of Iran newspaper for Tehran’s readers was estimated 384 persons based on Morgan table. Through cluster sampling, 50 journalists were selected so that totally the sample size was 434 persons and questionnaire was applied for data analysis and based on Alpha Chronbache, it was supported. Through Pierson correlation, the main and all subsidiary hypotheses were supported except the forth one.

Keywords: newspaper, satisfaction of audiences, self-censorship, journalists

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Authors: Maria Anjelica P. Ancheta, Roberto S. Soriano, Erickson L. Llaguno

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The main purpose of this study is to examine whether there is a significant relationship between socio-economic class and household water supply demand, through determining or verifying the factors governing water use consumption patterns of households from a sampling from different socio-economic classes in Metro Manila, the national capital region of the Philippines. This study is also an opportunity to augment the lack of local academic literature due to the very few publications on urban household water demand after 1999. In over 600 Metro Manila households, a rapid survey was conducted on their average monthly water consumption and habits on household water usage. The questions in the rapid survey were based on an extensive review of literature on urban household water demand. Sample households were divided into socio-economic classes A-B and C-D. Cluster analysis, dummy coding and outlier tests were done to prepare the data for regression analysis. Subsequently, backward stepwise regression analysis was used in order to determine different statistical models to describe the determinants of water consumption. The key finding of this study is that the socio-economic class of a household in Metro Manila is a significant factor in water consumption. A-B households consume more water in contrast to C-D families based on the mean average water consumption for A-B and C-D households are 36.75 m3 and 18.92 m3, respectively. The most significant proxy factors of socio-economic class that were related to household water consumption were examined in order to suggest improvements in policy formulation and household water demand management.

Keywords: household water uses, socio-economic classes, urban planning, urban water demand management

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Authors: Thiru Vandeyar

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This study sets out to explore how teachers’ beliefs and attitudes about ICT policy influence a consensus approach to the formulation of a school ICT policy. This case study proposes Q- methodology as an innovative method to facilitate a school’s capacity to develop policy reflecting teacher beliefs and attitudes. Q-methodology is used as a constructivist approach to the formulation of an ICT policy. Data capture was a mix of Q-methodology and qualitative principles. Data was analyzed by means of document, content and cluster analysis methods. Findings were threefold: First, teachers’ beliefs and attitudes about ICT policy influenced a consensus approach by including teachers as policy decision-makers. Second, given the opportunity, teachers have the inherent ability to deconstruct and critically engage with policy statements according to their own professional beliefs and attitudes. And third, an inclusive approach to policy formulation may inform the practice of school leaders and policymakers alike on how schools may develop their own policy.

Keywords: ICT, policy, teacher beliefs, consensus

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Authors: Ksenija Taški-Ajdukovic, Nevena Nagl, Živko Ćurčić, Dario Danojević

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Information about genetic diversity of sugar beet parental populations is of a great importance for hybrid breeding programs. The aim of this research was to evaluate genetic diversity among and within populations and lines of diploid sugar beet pollinators, by using SSR markers. As plant material were used eight pollinators originating from three USDA-ARS breeding programs and four pollinators from Institute of Field and Vegetable Crops, Novi Sad. Depending on the presence of self-fertility gene, the pollinators were divided into three groups: autofertile (inbred lines), autosterile (open-pollinating populations), and group with partial presence of autofertility gene. A total of 40 SSR primers were screened, out of which 34 were selected for the analysis of genetic diversity. A total of 129 different alleles were obtained with mean value 3.2 alleles per SSR primer. According to the results of genetic variability assessment the number and percentage of polymorphic loci was the maximal in pollinators NS1 and tester cms2 while effective number of alleles, expected heterozygosis and Shannon’s index was highest in pollinator EL0204. Analysis of molecular variance (AMOVA) showed that 77.34% of the total genetic variation was attributed to intra-varietal variance. Correspondence analysis results were very similar to grouping by neighbor-joining algorithm. Number of groups was smaller by one, because correspondence analysis merged IFVCNS pollinators with CZ25 into one group. Pollinators FC220, FC221 and C 51 were in the next group, while self-fertile pollinators CR10 and C930-35 from USDA-Salinas were separated. On another branch were self-sterile pollinators ЕL0204 and ЕL53 from USDA-East Lansing. Sterile testers cms1 and cms2 formed separate group. The presented results confirmed that SSR analysis can be successfully used in estimation of genetic diversity within and among sugar beet populations. Since the tested pollinator differed considering the presence of self-fertility gene, their heterozygosity differed as well. It was lower in genotypes with fixed self-fertility genes. Since the most of tested populations were open-pollinated, which rarely self-pollinate, high variability within the populations was expected. Cluster analysis grouped populations according to their origin.

Keywords: auto fertility, genetic diversity, pollinator, SSR, sugar beet

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Authors: Sajed Yaghoubnezhad, Mina Karimi, Seyede Marjan Modirkhazeni

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The goal of this research was to study the relationship between codependency, perceived social support and depression in mothers of children with intellectual disability (ID). The correlational method was used in this study. The research population is comprised of mothers of educable children with ID in the age range of 25 to 61 years. From among this, a sample of 251 individuals, in the multistage cluster sampling method, was selected from educational districts in Tehran, who responded to the Spann-Fischer Codependency Scale (SFCDS), the Social Support Questionnaire and the Beck Depression Inventory (BDI). The findings of this study indicate that among mothers of children with ID depression has a positive and significant correlation with codependency (P<0.01, r=0.4) and a negative and significant correlation with the total score of social support (P<0.01, r=-0.34). Moreover, the results of stepwise multiple regression analysis showed that codependency is allocated a higher variance than social support in explaining depression (R²=0.023).

Keywords: codependency, social support, depression, mothers of children with ID

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Authors: Hajar Mohafezatkar Abadi

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The family foundation is formed by marriage, and each couple, with their unique attitudes and personalities, takes a step into marriage. The more efficient and flexible these variables are, the more stable the marriage will be predicted. This group of couples sees their conflicts as an opportunity for growth, not as a threat to their shared life. Regarding family issue importance, a lot of research has been done around this topic which can be an effective step toward improving couples' life quality. The aim of the present study was to determine the role of personality and attitude on marital conflict. 306 couples (153 females, 153 males) were selected using multistage cluster sampling. The participants completed the personality Questionnaire (16PF, Cattell, 1975), marital conflict Questionnaire (MCQ-R, Sanaee Zaker, 1387), and dysfunctional attitude Questionnaire (DAS-26, Weissman & beck. 1987). The regression analysis results indicated that some personality traits and dysfunctional attitudes had a significant positive correlation with marital conflict.

Keywords: marital conflict, dysfunctional attitude, personality, personality questionnaire (16PF)

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Authors: Vijay Meena, Arup Kumar Sarma, Chandan Mahanta

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The environment has been getting contaminated by anthropogenic processes including those that discharge heavy metals to air, soil and water. The present work emphasizes the spatial distribution and vertical profile of six heavy metals (Cu, Zn, Mn, Ni, Fe, Cr) in three layers of mid sand bars (bed surface layer, 50 cm and 100 cm depth) at 42 sampling stations covering around 600 km stretch of the Brahmaputra River, India. Heavy metal analysis was conducted on the sample collected from mid-sand bars in the river stretch to examine the impact of dredging for various hydrological operations in the future. Sediment quality was assessed by calculating six different indices viz., EF, CF, CD, PLI, Igeo, and PERI. In all sediment layers, heavy metal concentrations have been observed to be the same as listed, Fe > Mn > Zn > Ni > Cr > Cu in μg/g. The average concentration of Cu, Mn, and Fe was found in the middle layer while Zn, Ni, and Cr were in the Surface layer. EF indicates higher enrichment in reach 2 which is likely to be due to anthropogenic sources of industrial and urbanized effluents. The sediment of the mid-sand bar was generally found moderately polluted possessing low risk to aquatic lives and the environment. Suggesting, Dredging can be possible in the future. An examination of correlation matrices, principal components analysis, and cluster analyses indicated that these heavy metals possess similar anthropogenic origins for their enrichment.

Keywords: heavy metal contamination, risk assessment, anthropogenic impacts, sediment

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Authors: Aleksandra Bylinska, Samantha Slight-Webb, Kevin Thomas, Miles Smith, Susan Macwana, Nicolas Dominguez, Eliza Chakravarty, Joan T. Merrill, Judith A. James, Joel M. Guthridge

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Background: Systemic Lupus Erythematosus (SLE) is an interferon-related autoimmune disease characterized by B cell dysfunction. One of the main hallmarks is a loss of tolerance to self-antigens leading to increased levels of autoantibodies against nuclear components (ANAs). However, up to 20% of healthy ANA+ individuals will not develop clinical illness. SLE is more prevalent among women and minority populations (African, Asian American and Hispanics). Moreover, African Americans have a stronger interferon (IFN) signature and develop more severe symptoms. The exact mechanisms involved in ethnicity-dependent B cell dysregulation and the progression of autoimmune disease from ANA+ healthy individuals to clinical disease remains unclear. Methods: Peripheral blood mononuclear cells (PBMCs) from African (AA) and European American (EA) ANA- (n=12), ANA+ (n=12) and SLE (n=12) individuals were assessed by multimodal scRNA-Seq/CITE-Seq methods to examine differential gene signatures in specific B cell subsets. Library preparation was done with a 10X Genomics Chromium according to established protocols and sequenced on Illumina NextSeq. The data were further analyzed for distinct cluster identification and differential gene signatures in the Seurat package in R and pathways analysis was performed using Ingenuity Pathways Analysis (IPA). Results: Comparing all subjects, 14 distinct B cell clusters were identified using a community detection algorithm and visualized with Uniform Manifold Approximation Projection (UMAP). The proportion of each of those clusters varied by disease status and ethnicity. Transitional B cells trended higher in ANA+ healthy individuals, especially in AA. Ribonucleoprotein high population (HNRNPH1 elevated, heterogeneous nuclear ribonucleoprotein, RNP-Hi) of proliferating Naïve B cells were more prevalent in SLE patients, specifically in EA. Interferon-induced protein high population (IFIT-Hi) of Naive B cells are increased in EA ANA- individuals. The proportion of memory B cells and plasma cells clusters tend to be expanded in SLE patients. As anticipated, we observed a higher signature of cytokine-related pathways, especially interferon, in SLE individuals. Pathway analysis among AA individuals revealed an NRF2-mediated Oxidative Stress response signature in the transitional B cell cluster, not seen in EA individuals. TNFR1/2 and Sirtuin Signaling pathway genes were higher in AA IFIT-Hi Naive B cells, whereas they were not detected in EA individuals. Interferon signaling was observed in B cells in both ethnicities. Oxidative phosphorylation was found in age-related B cells (ABCs) for both ethnicities, whereas Death Receptor Signaling was found only in EA patients in these cells. Interferon-related transcription factors were elevated in ABCs and IFIT-Hi Naive B cells in SLE subjects of both ethnicities. Conclusions: ANA+ healthy individuals have altered gene expression pathways in B cells that might drive apoptosis and subsequent clinical autoimmune pathogenesis. Increases in certain regulatory pathways may delay progression to SLE. Further, AA individuals have more elevated activation pathways that may make them more susceptible to SLE.

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Authors: Jiahao Tian, Michael D. Porter

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Law enforcement agencies are tasked with crime prevention and crime reduction under limited resources. Having an accurate temporal estimate of the crime rate would be valuable to achieve such a goal. However, estimation is usually complicated by the interval-censored nature of crime data. We cast the problem of intensity estimation as a Poisson regression using an EM algorithm to estimate the parameters. Two special penalties are added that provide smoothness over the time of day and day of the week. This approach presented here provides accurate intensity estimates and can also uncover day-of-week clusters that share the same intensity patterns. Anticipating where and when crimes might occur is a key element to successful policing strategies. However, this task is complicated by the presence of interval-censored data. The censored data refers to the type of data that the event time is only known to lie within an interval instead of being observed exactly. This type of data is prevailing in the field of criminology because of the absence of victims for certain types of crime. Despite its importance, the research in temporal analysis of crime has lagged behind the spatial component. Inspired by the success of solving crime-related problems with a statistical approach, we propose a statistical model for the temporal intensity estimation of crime with censored data. The model is built on Poisson regression and has special penalty terms added to the likelihood. An EM algorithm was derived to obtain maximum likelihood estimates, and the resulting model shows superior performance to the competing model. Our research is in line with the smart policing initiative (SPI) proposed by the Bureau Justice of Assistance (BJA) as an effort to support law enforcement agencies in building evidence-based, data-driven law enforcement tactics. The goal is to identify strategic approaches that are effective in crime prevention and reduction. In our case, we allow agencies to deploy their resources for a relatively short period of time to achieve the maximum level of crime reduction. By analyzing a particular area within cities where data are available, our proposed approach could not only provide an accurate estimate of intensities for the time unit considered but a time-variation crime incidence pattern. Both will be helpful in the allocation of limited resources by either improving the existing patrol plan with the understanding of the discovery of the day of week cluster or supporting extra resources available.

Keywords: cluster detection, EM algorithm, interval censoring, intensity estimation

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Authors: Ni Wayan Sinthia Widiastuti, Komang Rahayu Indrawati

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The increasing number of tourists coming to Bali, causing accommodation facilities, such as hotels have increased. The existence of hotel needs will be the source of labor and cost efficiency, so that hotel management employs employees with different working status. The hospitality industry is one of the sectors that require organizational citizenship behavior because, the main goal of every hotel, in general, was to provide the best service and quality to tourists. The purpose of this study was to determine the differences in organizational citizenship behavior based on work status of employees at the Hotel in Bali in terms of quality of work life. Research sample was chosen randomly through two-stage cluster sampling which succeeds to obtain 126 samples from 11 hotels in Denpasar, Bali. The subjects consisted of 64 employees with Employment Agreement of Uncertain Time or who is often called a permanent employee and 62 employees with Employment Agreement of Certain Time or better known as contract employees, outsourcing, and daily workers. Instruments in this study were the scale of organizational citizenship behavior and the scale of quality of work life. The results of ANCOVA analysis showed there were differences in organizational citizenship behavior based on employee work status in terms of quality of work life. Differences in organizational citizenship behavior and quality of work life based on work status of employees using comparative test was analysis by independent sample t-test shows there were differences in organizational citizenship behavior and quality of work life between employees with different working status in hotels in Bali. The result of the regression analysis showed the functional relationship between quality of work life and organizational citizenship behavior.

Keywords: hotel in Bali, organizational citizenship behavior, quality of work life, work status of employees

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Authors: Xu Yifei, Le Yining, Yang Qingluan, Tu Yanjie

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Objective: This study aims to investigate the distribution features of Traditional Chinese Medicine (TCM) syndromes and syndrome elements in Epstein-Barr virus-associated diseases and then explores the relations between TCM syndromes or syndrome elements and laboratory indicators of Epstein-Barr virus-associated diseases. Methods: A cross-sectional study of 70 patients with EBV infection was described. We assessed the diagnostic information and laboratory indicators of these patients from Huashan Hospital Affiliated to Fudan University between November 2017 and July 2019. The disease diagnosis and syndrome differentiation were based on the diagnostic criteria of EBV-associated diseases and the theory of TCM respectively. Confidence correlation analysis, logistic regression analysis, cluster analysis, and the Sankey diagram were used to analyze the correlation between the data. Results: The differentiation of the 4 primary TCM syndromes in the collected patients was correlated with the indexes of immune function, liver function, inflammation, and anemia, especially the relationship between Qifen syndrome and high lactic acid dehydrogenase level. The common 11 TCM syndrome elements were associated with the increased CD3+ T cell rate, low hemoglobin level, high procalcitonin level, high lactic acid dehydrogenase level, and low albumin level. Conclusion: The changes in immune function indexes, procalcitonin, and liver function-related indexes in patients with EBV-associated diseases were consistent with the evolution law of TCM syndromes. This study provides a reference for judging the pathological stages of these kinds of diseases, predicting their prognosis, and guiding subsequent treatment strategies based on TCM syndrome type.

Keywords: EBV-associated diseases, traditional Chinese medicine syndrome, syndrome element, diagnostics

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Authors: K. Umbleja, M. Ichino

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Symbolic data mining has been developed to analyze data in very large datasets. It is also useful in cases when entry specific details should remain hidden. Symbolic data mining is quickly gaining popularity as datasets in need of analyzing are becoming ever larger. One type of such symbolic data is a histogram, which enables to save huge amounts of information into a single variable with high-level of granularity. Other types of symbolic data can also be described in histograms, therefore making histogram a very important and general symbolic data type - a method developed for histograms - can also be applied to other types of symbolic data. Due to its complex structure, analyzing histograms is complicated. This paper proposes a method, which allows to compare two histogram-valued variables and therefore find a dissimilarity between two histograms. Proposed method uses the Ichino-Yaguchi dissimilarity measure for mixed feature-type data analysis as a base and develops a dissimilarity measure specifically for histogram data, which allows to compare histograms with different number of bins and bin widths (so called general histogram). Proposed dissimilarity measure is then used as a measure for clustering. Furthermore, linkage method based on weighted averages is proposed with the concept of cluster compactness to measure the quality of clustering. The method is then validated with application on real datasets. As a result, the proposed dissimilarity measure is found producing adequate and comparable results with general histograms without the loss of detail or need to transform the data.

Keywords: dissimilarity measure, hierarchical clustering, histograms, symbolic data analysis

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Authors: Amirmohsen Behjat, Aleck Ostry, Christina Miewald, Bernie Pauly

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Substantial research has indicated that socioeconomic and demographic characteristics’ of neighborhoods are strong determinants of food security. The aim of this study was to develop a Food Insecurity Neighborhood Index (FINI) based on the associated socioeconomic and demographic variables to identify the areas at potential risk of food insecurity in rural British Columbia (BC). Principle Component Analysis (PCA) technique was used to calculate the FINI for each rural Dissemination Area (DA) using the food security determinant variables from Canadian Census data. Using ArcGIS, the neighborhoods with the top quartile FINI values were classified as food insecure. The results of this study indicated that the most food insecure neighborhood with the highest FINI value of 99.1 was in the Bulkley-Nechako (central BC) area whereas the lowest FINI with the value of 2.97 was for a rural neighborhood in the Cowichan Valley area. In total, 98.049 (19%) of the rural population of British Columbians reside in high food insecure areas. Moreover, the distribution of food insecure neighborhoods was found to be strongly dependent on the degree of rurality in BC. In conclusion, the cluster of food insecure neighbourhoods was more pronounced in Central Coast, Mount Wadington, Peace River, Kootenay Boundary, and the Alberni-Clayoqout Regional Districts.

Keywords: neighborhood food insecurity index, socioeconomic and demographic determinants, principal component analysis, Canada census, ArcGIS

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Authors: Sudipto Shanker Dasgupta

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One of the largest mining companies wanted to look at health analytics for their driverless trucks. These trucks were the key to their supply chain logistics. The automated trucks had multi-level sub-assemblies which would send out sensor information. The use case that was worked on was to capture the sensor signal from the truck subcomponents and analyze the health of the trucks from repair and replacement purview. Open source software was used to stream the data into a clustered Hadoop setup in Amazon Web Services cloud and Apache Spark SQL was used to analyze the data. All of this was achieved through a 10 node amazon 32 core, 64 GB RAM setup real-time analytics was achieved on ‘300 million records’. To check the scalability of the system, the cluster was increased to 100 node setup. This talk will highlight how Open Source software was used to achieve the above use case and the insights on the high data throughput on a cloud set up.

Keywords: streaming analytics, data science, big data, Hadoop, high throughput, sensor data

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Authors: Marijana M. Ačanski, Kristian A. Pastor, Djura N. Vujić

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The identification of lipid and soluble sugar components in flour samples of different cultivars belonging to common oat species (Avena sativa L.) was performed: spring oat, winter oat and hulless oat. Fatty acids were extracted from flour samples with n-hexane, and derivatized into volatile methyl esters, using TMSH (trimethylsulfonium hydroxide in methanol). Soluble sugars were then extracted from defatted and dried samples of oat flour with 96% ethanol, and further derivatized into corresponding TMS-oximes, using hydroxylamine hydrochloride solution and BSTFA (N,O-bis-(trimethylsilyl)-trifluoroacetamide). The hexane and ethanol extracts of each oat cultivar were analyzed using GC-MS system. Lipid and simple sugar compositions are very similar in all samples of investigated cultivars. Chemometric tool was applied to numeric values of automatically integrated surface areas of detected lipid and simple sugar components in their corresponding derivatized forms. Hierarchical cluster analysis shows a very high similarity between the investigated flour samples of oat cultivars, according to the fatty acid content (0.9955). Moderate similarity was observed according to the content of soluble sugars (0.50). These preliminary results support the idea of establishing methods for oat flour authentication, and provide the means for distinguishing oat flour samples, regardless of the variety, from flour samples made of other cereal species, just by lipid and simple sugar profile analysis.

Keywords: oat cultivars, lipid composition, soluble sugar composition, GC-MS, chemometrics, authentication

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Authors: Hadi Molaei, Yasavoli Davoud, Keshavarz, Mozhde Poordana

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The present study aimed was to prediction the academic performance based on academic motivation, self-efficacy and Resiliency in the students. The present study was descriptive and correlational. Population of the study consisted of all students in Arak schools in year 1393-94. For this purpose, the number of 304 schools students in Arak was selected using multi-stage cluster sampling. They all questionnaires, self-efficacy, Resiliency and academic motivation Questionnaire completed. Data were analyzed using Pearson correlation and multiple regressions. Pearson correlation showed academic motivation, self-efficacy, and Resiliency with academic performance had a positive and significant relationship. In addition, multiple regression analysis showed that the academic motivation, self-efficacy and Resiliency were predicted academic performance. Based on the findings could be conclude that in order to increase the academic performance and further progress of students must provide the ground to strengthen academic motivation, self-efficacy and Resiliency act on them.

Keywords: academic motivation, self-efficacy, resiliency, academic performance

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Authors: Isari Pairoa, Proud Arunrangsiwed

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Brand mascots are the cartoon characters, which are mainly designed for advertising or other related marketing purposes. Many brand mascots are extremely popular, since they were presented in commercial advertisements and Line Stickers. Brand Line Stickers could lead the users to identify with the brand and brand mascots, where might influence users to become loyal customers, and share the identity with the brand. The objective of the current study is to examine the effect of brand mascots on consumers’ decision and consumers’ intention to purchase the product. This study involved 400 participants, using cluster sampling from 50 districts in Bangkok metropolitan area. The descriptive analysis shows that using brand mascot causes consumers' positive attitude toward the products, and also heightens the possibility to purchasing the products. The current study suggests the new type of marketing strategy, which is brand fandom. This study has also contributed the knowledge to the area of integrated marketing communication and identification theory.

Keywords: brand mascot, consumers’ behavior, marketing communication, purchasing

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Authors: Danyi Wang, Andrew Schriefer, Dennis O'Rourke, Brajendra Kumar, Yang Liu, Fei Zhong, Juergen Scheuenpflug, Zheng Feng

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Purpose: It has been recognized that the microbiome plays critical roles in disease pathogenesis, including cancer, autoimmune disease, and multiple sclerosis. To develop a clinical-grade assay for exploring microbiome-derived clinical biomarkers across disease areas, a two-phase approach is implemented. 1) Identification of the optimal sample preparation reagents using pre-mixed bacteria and healthy donor stool samples coupled with proprietary Sigma-Aldrich® bioinformatics solution. 2) Exploratory analysis of patient samples for enabling precision medicine. Study Procedure: In phase 1 study, we first compared the 16S sequencing results of two ATCC® microbiome standards (MSA 2002 and MSA 2003) across five different extraction kits (Kit A, B, C, D & E). Both microbiome standards samples were extracted in triplicate across all extraction kits. Following isolation, DNA quantity was determined by Qubit assay. DNA quality was assessed to determine purity and to confirm extracted DNA is of high molecular weight. Bacterial 16S ribosomal ribonucleic acid (rRNA) amplicons were generated via amplification of the V3/V4 hypervariable region of the 16S rRNA. Sequencing was performed using a 2x300 bp paired-end configuration on the Illumina MiSeq. Fastq files were analyzed using the Sigma-Aldrich® Microbiome Platform. The Microbiome Platform is a cloud-based service that offers best-in-class 16S-seq and WGS analysis pipelines and databases. The Platform and its methods have been extensively benchmarked using microbiome standards generated internally by MilliporeSigma and other external providers. Data Summary: The DNA yield using the extraction kit D and E is below the limit of detection (100 pg/µl) of Qubit assay as both extraction kits are intended for samples with low bacterial counts. The pre-mixed bacterial pellets at high concentrations with an input of 2 x106 cells for MSA-2002 and 1 x106 cells from MSA-2003 were not compatible with the kits. Among the remaining 3 extraction kits, kit A produced the greatest yield whereas kit B provided the least yield (Kit-A/MSA-2002: 174.25 ± 34.98; Kit-A/MSA-2003: 179.89 ± 30.18; Kit-B/MSA-2002: 27.86 ± 9.35; Kit-B/MSA-2003: 23.14 ± 6.39; Kit-C/MSA-2002: 55.19 ± 10.18; Kit-C/MSA-2003: 35.80 ± 11.41 (Mean ± SD)). Also, kit A produced the greatest yield, whereas kit B provided the least yield. The PCoA 3D visualization of the Weighted Unifrac beta diversity shows that kits A and C cluster closely together while kit B appears as an outlier. The kit A sequencing samples cluster more closely together than both the other kits. The taxonomic profiles of kit B have lower recall when compared to the known mixture profiles indicating that kit B was inefficient at detecting some of the bacteria. Conclusion: Our data demonstrated that the DNA extraction method impacts DNA concentration, purity, and microbial communities detected by next-generation sequencing analysis. Further microbiome analysis performance comparison of using healthy stool samples is underway; also, colorectal cancer patients' samples will be acquired for further explore the clinical utilities. Collectively, our comprehensive qualification approach, including the evaluation of optimal DNA extraction conditions, the inclusion of positive controls, and the implementation of a robust qualified bioinformatics pipeline, assures accurate characterization of the microbiota in a complex matrix for deciphering the deep biology and enabling precision medicine.

Keywords: 16S rRNA sequencing, analytical validation, bioinformatics pipeline, metagenomics

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Authors: Yahaya Abdullahi, Ben Coetzee, Linda Van Den Berg

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The study aimed at establishing the global positioning system (GPS) determined singles match characteristics that act as predictors of successful and less-successful male singles badminton players’ group classification. Twenty-two (22) male single players (aged: 23.39 ± 3.92 years; body stature: 177.11 ± 3.06cm; body mass: 83.46 ± 14.59kg) who represented 10 African countries participated in the study. Players were categorised as successful and less-successful players according to the results of five championships’ of the 2014/2015 season. GPS units (MinimaxX V4.0), Polar Heart Rate Transmitter Belts and digital video cameras were used to collect match data. GPS-related variables were corrected for match duration and independent t-tests, a cluster analysis and a binary forward stepwise logistic regression were calculated. A Receiver Operating Characteristic Curve (ROC) was used to determine the validity of the group classification model. High-intensity accelerations per second were identified as the only GPS-determined variable that showed a significant difference between groups. Furthermore, only high-intensity accelerations per second (p=0.03) and low-intensity efforts per second (p=0.04) were identified as significant predictors of group classification with 76.88% of players that could be classified back into their original groups by making use of the GPS-based logistic regression formula. The ROC showed a value of 0.87. The identification of the last-mentioned GPS-related variables for the attainment of badminton performances, emphasizes the importance of using badminton drills and conditioning techniques to not only improve players’ physical fitness levels but also their abilities to accelerate at high intensities.

Keywords: badminton, global positioning system, match analysis, inertial movement analysis, intensity, effort

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Authors: An Chengrui, Yin Zi, Wu Bingbing, Ma Yuanzhu, Jin Kaixiu, Chen Xiao, Ouyang Hongwei

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Single cell RNA sequence (scRNA-seq) is one of the effective tools to study transcriptomics of biological processes. Recently, similarity measurement of cells is Euclidian distance or its derivatives. However, the process of scRNA-seq is a multi-variate Bernoulli event model, thus we hypothesize that it would be more efficient when the divergence between cells is valued with relative entropy than Euclidian distance. In this study, we compared the performances of Euclidian distance, Spearman correlation distance and Relative Entropy using scRNA-seq data of the early, medial and late stage of limb development generated in our lab. Relative Entropy is better than other methods according to cluster potential test. Furthermore, we developed KL-SNE, an algorithm modifying t-SNE whose definition of divergence between cells Euclidian distance to Kullback–Leibler divergence. Results showed that KL-SNE was more effective to dissect cell heterogeneity than t-SNE, indicating the better performance of relative entropy than Euclidian distance. Specifically, the chondrocyte expressing Comp was clustered together with KL-SNE but not with t-SNE. Surprisingly, cells in early stage were surrounded by cells in medial stage in the processing of KL-SNE while medial cells neighbored to late stage with the process of t-SNE. This results parallel to Heatmap which showed cells in medial stage were more heterogenic than cells in other stages. In addition, we also found that results of KL-SNE tend to follow Gaussian distribution compared with those of the t-SNE, which could also be verified with the analysis of scRNA-seq data from another study on human embryo development. Therefore, it is also an effective way to convert non-Gaussian distribution to Gaussian distribution and facilitate the subsequent statistic possesses. Thus, relative entropy is potentially a better way to determine the divergence of cells in scRNA-seq data analysis.

Keywords: Single cell RNA sequence, Similarity measurement, Relative Entropy, KL-SNE, t-SNE

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Authors: Rama Krishna Supramanian, Marzuki Isahak, Noran Naqiah Hairi

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Noise-induced hearing loss (NIHL) is one of the highest recorded occupational diseases, despite being preventable. Hearing Conservation Program (HCP) is designed to protect workers hearing and prevent them from developing hearing impairment due to occupational noise exposures. However, there is still a lack of evidence regarding the effectiveness of this program. The purpose of this study was to determine the effectiveness of a Hearing Conservation Program (HCP) in preventing or reducing audiometric threshold changes among vector control workers. This study adopts a cluster randomized controlled trial study design, with district health offices as the unit of randomization. Nine district health offices were randomly selected and 183 vector control workers were randomized to intervention or control group. The intervention included a safety and health policy, noise exposure assessment, noise control, distribution of appropriate hearing protection devices, training and education program and audiometric testing. The control group only underwent audiometric testing. Audiometric threshold changes observed in the intervention group showed improvement in the hearing threshold level for all frequencies except 500 Hz and 8000 Hz for the left ear. The hearing threshold changes range from 1.4 dB to 5.2 dB with largest improvement at higher frequencies mainly 4000 Hz and 6000 Hz. Meanwhile for the right ear, the mean hearing threshold level remained similar at 4000 Hz and 6000 Hz after 3 months of intervention. The Hearing Conservation Program (HCP) is effective in preserving the hearing of vector control workers involved in fogging activity as well as increasing their knowledge, attitude and practice towards noise-induced hearing loss (NIHL).

Keywords: adult, hearing conservation program, noise-induced hearing loss, vector control worker

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Authors: Deepak Kumar, Debasish Deb, Reena Mamgain

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Radar signal processing requires high number crunching capability. Most often this is achieved using multiprocessor platform. Though multiprocessor platform provides the capability of meeting the real time computational challenges, the architecture of the same along with mapping of the algorithm on the architecture plays a vital role in efficiently using the platform. Towards this, along with standard performance metrics, few additional metrics are defined which helps in evaluating the multiprocessor platform along with the algorithm mapping. A generic multiprocessor architecture can not suit all the processing requirements. Depending on the system requirement and type of algorithms used, the most suitable architecture for the given problem is decided. In the paper, we study different architectures and quantify the different performance metrics which enables comparison of different architectures for their merit. We also carried out case study of different architectures and their efficiency depending on parallelism exploited on algorithm or data or both.

Keywords: radar signal processing, multiprocessor architecture, efficiency, load imbalance, buffer requirement, pipeline, parallel, hybrid, cluster of processors (COPs)

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Authors: Somayeh Akrami, Habib Onsori, Elham Tahmassebian

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Species of Anemone narcissiflora is belonged to Anemone genus of Ranunculaceae family. This species has two subspecies named narcissiflora and willdenowii which the latest is recorded in Iran in 2010. Some samples of A. narcissiflora is gathered from kuhkamar-zonouz region of East -Azerbaijan province, Iran to study the genetic diversity of the species by using RAPD molecular markers, and estimation of genetic diversity were evaluated with the using 10mer RAPD primers by PCR-RAPD method. 39 polymorphic bands were produced from the six primers used in this technique that the maximum band is related to the RP1 primer, the lowest band is related to the RP7 and the average band for all primers were 6.5 polymorphic bands. Cluster analysis of samples in done by UPGMA method in NTSYSpc 2.02 software. Dendrogram resulting from migrating bands showed that the studied samples can be divided into two groups. The first group includes samples with 1-2 flowers and the second group consists of two sub-groups which the first subgroup consists of samples with 3-5 flowers, and the second subgroup consists of samples with 6-7 flowers. The results of the comparison and analysis of the data obtained from RAPD technique and similarity matrix represents the genetic variation between collected samples. This study shows that RAPD markers can determine the polymorphisms between different genotypes of A. narcissiflora and their hybrids. So RAPD technique can serve as a suitable molecular method to determine the genetic diversity of samples.

Keywords: Anemone narcissiflora, genetic diversity, RAPD-PCR

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Authors: Vithya Veeramani, Karunanidhi Subbaiah

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Emotional problems were found to be the predominant cause of suicide and second leading cause of death among adolescents in India. Emotional problems seem to be the underlying cause for various other severe psycho-social problems experienced in adolescence and also in later years of life. The Corporation schools in Chennai city are named as Chennai High School or Chennai Higher Secondary School run by the Corporation of Chennai. These schools fulfill the educational needs of students who hail from lower socio-economic status living in slums of the Chennai city. Adolescent students of Chennai schools tend to lack basic needs like food, clothes, shelter, etc. Some of the other significant problems faced by them are broken family, lack of parental support, frequent quarrel between parents, alcoholic parents, drug abuse and substance abuse among parents and neighbors, extended family, illiterate parents, deprivation of love and care, and lack of sense of belongingness. This prevailing condition may affect them emotionally and could lead to maladaptive behaviour, aggressiveness, poor interpersonal relationship with others, school refusal behaviour, school drop-out, suicide, etc. Therefore, it is very important to investigate the emotional problems faced by the adolescent students studying in Chennai schools, Chennai. A cross-sectional survey design was used to find the prevalence of emotional problems among adolescent students. Cluster sampling technique was used to select the schools for the present study considering the school as a cluster. In total, there are 15 zones, under the control of Chennai Corporation, of which only 7 zones have Corporation Schools in Chennai city, comprising of 32 Chennai Higher Secondary Schools and 38 Chennai High Schools. Out of these 70 schools, 29 schools comprising of 17 high schools and 12 higher secondary schools were selected randomly using lottery method. A sample of 2594 adolescent students from 9th standard and 11th standard was chosen for the study. Percentage analysis was done to find out the prevalence rate of emotional problems among adolescents students studying in Chennai Schools. Results of the study revealed that, out of 2594 students surveyed, 21.04% adolescent students were found to have academic problems (n = 546), 15.99% adolescent students had social problems (n = 415), behaviour problems was found to be prevalent among 12.87% adolescent students (n = 334), depression was prevalent among 15.88% adolescent students (n = 412) and anxiety was prevalent among 14.42% adolescent students (n = 374). Prevalence of emotional problems among male and female revealed that academic problems were more prevalent compared to other problems. Behaviour problems were least prevalent among boys and anxiety was least prevalent among girls than other problems. The overall prevalence rate of emotional problems was found to be on an increasing trend among adolescent students of low socio-economic status in Chennai city. The findings indicated the need for intervention to prevent and rehabilitate these adolescent students.

Keywords: adolescents, corporation schools, emotional problems, prevalence

Procedia PDF Downloads 195

Authors: Choukri Lekbir, Mira Mokhtari

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Hydrogen-Materials interaction and mechanisms can be modeled at nano scale by quantum methods. In this work, the effect of hydrogen on the electronic properties of a cluster material model «nickel» has been studied by using of density functional theoretical (DFT) method. Two types of clusters are optimized: Nickel and hydrogen-nickel system. In the case of nickel clusters (n = 1-6) without presence of hydrogen, three types of electronic structures (neutral, cationic and anionic), have been optimized according to three basis sets calculations (B3LYP/LANL2DZ, PW91PW91/DGDZVP2, PBE/DGDZVP2). The comparison of binding energies and bond lengths of the three structures of nickel clusters (neutral, cationic and anionic) obtained by those basis sets, shows that the results of neutral and anionic nickel clusters are in good agreement with the experimental results. In the case of neutral and anionic nickel clusters, comparing energies and bond lengths obtained by the three bases, shows that the basis set PBE/DGDZVP2 is most suitable to experimental results. In the case of anionic nickel clusters (n = 1-6) with presence of hydrogen, the optimization of the hydrogen-nickel (anionic) structures by using of the basis set PBE/DGDZVP2, shows that the binding energies and bond lengths increase compared to those obtained in the case of anionic nickel clusters without the presence of hydrogen, that reveals the armor effect exerted by hydrogen on the electronic structure of nickel, which due to the storing of hydrogen energy within nickel clusters structures. The comparison between the bond lengths for both clusters shows the expansion effect of clusters geometry which due to hydrogen presence.

Keywords: binding energies, bond lengths, density functional theoretical, geometry optimization, hydrogen energy, nickel cluster

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Authors: Andrii Natochii

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The UA9 collaboration in the last two years has installed two different types of detectors to investigate the channeling effect in the bent silicon crystals with high-energy particles beam on the CERN accelerator facilities: Cherenkov detector CpFM and silicon pixel detector Timepix. In the current work, we describe the main performances of the Timepix detector operation at the SPS and H8 extracted beamline at CERN. We are presenting some detector calibration results and tuning. Our research topics also cover a cluster analysis algorithm for the particle hits reconstruction. We describe the optimal acquisition setup for the Timepix device and the edges of its functionality for the high energy and flux beam monitoring. The measurements of the crystal parameters are very important for the future bent crystal applications and needs a track reconstruction apparatus. Thus, it was decided to construct a short range (1.2 m long) particle telescope based on the Timepix sensors and test it at H8 SPS extraction beamline. The obtained results will be shown as well.

Keywords: beam monitoring, channeling, particle tracking, Timepix detector

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Authors: Jair Servín-Aguilar, Yu Tang

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We address the problem of robust attitude tracking for agile satellites under unknown bounded torque disturbances using a double-gimbal variable-speed control-moment gyro (DGVSCMG) driven by a cluster of three permanent magnet synchronous motors (PMSMs). Uniform practical asymptotic stability is achieved at the torque control level first. The desired speed of gimbals and the acceleration of the spin wheel to produce the required torque are then calculated by a velocity-based steering law and tracked at the PMSM speed-control level by designing a speed-tracking controller with compensation for the vibration caused by eccentricity and imbalance due to mechanical imperfection in the DGVSCMG. Uniform practical asymptotic stability of the overall system is ensured by loan relying on the analysis of the resulting cascaded system. Numerical simulations are included to show the performance improvement of the proposed controller.

Keywords: agile satellites, vibration compensation, internal model, stability

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Authors: Rita Riekstina-Dolge, Zanda Kruma, Daina Karklina, Fredijs Dimins

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Apple juice is the main raw material for cider production. In this study apple juices obtained from 14 dessert and crab variety apples grown in Latvia were investigated. For all samples soluble solids, titratable acidity, pH and sugar content were determined. Crab apples produce more dry matter, total sugar and acid content compared to the dessert apples but it depends on the apple variety. Total sugar content of crab apple juices was 1.3 to 1.8 times larger than in dessert apple juices. Titratable acidity of dessert apple juices is in the range of 4.1g L-1 to 10.83g L-1 and in crab apple juices titratable acidity is from 7.87g L-1 to 19.6g L-1. Fructose was detected as the main sugar whereas glucose level varied depending on the variety. The highest titratable acidity and content of sugars was detected in ‘Cornelia’ apples juice.

Keywords: apple juice, hierarchical cluster analysis, sugars, titratable acidity

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Authors: Raees Khan, Mir A. Khan, Sheikh Z. Ul Abidin, Abdul S. Mumtaz

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In the present study, phytogeography and conservation status of gymnosperms of Pakistan were investigated. 44 gymnosperms species of 18 genera and 9 families were collected from 66 districts of the country. Among the 44 species, 20 species were native (wild) and 24 species were exotic (cultivated). Ephedra sarocarpa of Ephedraceae was not collected in this study from its distribution area and most probably it may be Nationally Extinct now from this area. Previously in Gymnosperms Flora of Pakistan 34 species was reported. 12 new gymnosperms species were recorded for the first time. Pinus wallichiana (40 districts), Cedrus deodara (39 districts) Pinus roxburghii (36 districts), Picea smithiana (36 districts) and Abies pindrow (34 districts) have the maximum ecological amplitude. Juniperus communis (17districts) and Juniperus excelsa (14 districts) were the widely distributed among the junipers. Ephedra foliata (23 districts), Ephedra gerardiana (20 districts) and Ephedra intermedia (19 districts) has the widest distribution range. Taxus fuana was also wider distribution range and recorded in 19 districts but its population was not very stable. These species was recorded to support local flora and fuana, especially endemics. PCORD version 5 clustered all gymnosperms species into 4 communities and all localities into 5 groups through cluster analyses. The Two Way Cluster Analyses of 66 districts (localities) resulted 4 various plant communities. The Gymnosperms in Pakistan are distributed in 3 floristic regions i.e. Western plains of the country, Northern and Western mountainous regions and Western Himalayas. The assessment of the National conservation status of these species, 10 species were found to be threatened, 6 species were endangered, 4 species were critically endangered and 1 species have become extinct (Ephedra sarcocarpa). The population of some species i.e. Taxus fuana, Ephedra gerardiana, Ephedra monosperma, Picea smithiana and Abies spectabilis is decreasing at an alarming rate.

Keywords: conservation status, gymnosperms, phytogeography, Pakistan

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