Search results for: sequence alignment

Authors: Iwuchukwu J. C., Mbah C.

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There seems to be dearth on information on how oil bean is being exploited, processed and conserved locally. This gap stifles initiatives on the evaluation of the suitability of the methods used and the invention of new and better methods. The study; therefore, assesses activities of processors in domestication/conservation and processing of oil bean (Pentaclethra macrophylla) Enugu State, South East Nigeria. Three agricultural zones, three blocks, nine circles and seventy-two respondents that were purposively selected made up the sample for the study. Data were presented in percentage, chart and mean score. The result shows that processors of oil bean in the area were middle-aged, married with relatively large household size and long years of experience in processing. They sourced oil bean they processed from people’s farmland and sourced information on processing of oil bean from friends and relatives. Activities involved in processing of oil bean were boiling, dehulling, washing, sieving, slicing, wrapping. However, the sequence of these activities varies among these processors. Little or nothing was done by the processors towards the conservation of the crop while poor storage and processing facilities and lack of knowledge on modern preservation technique were major constraints to processing of oil bean in the area. The study concluded that efforts should be made by governments and processors through cooperative group in provision of processing and storage facility for oil bean while research institute should conserve and generate improved specie of the crop to arouse interest of the farmers and processors on the crop which will invariably increase productivity.

Keywords: conservation, domestication, oil bean, processing

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Authors: Jingjie Li, Wenjie Hu

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Phraseological units in academic English texts have been a central focus in recent corpus linguistic research. A wide variety of phraseological units have been explored, including collocations, chunks, lexical bundles, patterns, semantic sequences, etc. This paper describes a special category of clause-level phraseological units, namely, Characteristic Sentence Stems (CSSs), with a view to describing their defining criteria and extraction method. CSSs are contiguous lexico-grammatical sequences which contain a subject-predicate structure and which are frame expressions characteristic of academic writing. The extraction of CSSs consists of six steps: Part-of-speech tagging, n-gram segmentation, structure identification, significance of occurrence calculation, text range calculation, and overlapping sequence reduction. Significance of occurrence calculation is the crux of this study. It includes the computing of both the internal association and the boundary independence of a CSS and tests the occurring significance of the CSS from both inside and outside perspectives. A new normalization algorithm is also introduced into the calculation of LocalMaxs for reducing overlapping sequences. It is argued that many sentence stems are so recurrent in academic texts that the most typical of them have become the habitual ways of making meaning in academic writing. Therefore, studies of CSSs could have potential implications and reference value for academic discourse analysis, English for Academic Purposes (EAP) teaching and writing.

Keywords: characteristic sentence stem, extraction method, phraseological unit, the statistical measure

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Authors: Nazira Kakulia

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The analysis of transformation of institutional changes outlines two important characteristics. These are: the speed of the changes and their sequence. Successful transformation must be carried out in three different stages; On the first stage, macroeconomic stabilization must be achieved with the help of fiscal and monetary tools. Two-tier banking system should be established and the active functions of central bank should be replaced by the passive ones (reserve requirements and refinancing rate), together with the involvement growth of private sector. Fiscal policy by itself here means the creation of tax system which must replace previously existing direct state revenues; the share of subsidies in the state expenses must be reduced also. The second stage begins after reaching the macroeconomic stabilization at a time of change of formal institutes which must stimulate the private business. Corporate legislation creates a competitive environment at the market and the privatization of state companies takes place. Bankruptcy and contract law is created. he third stage is the most extended one, which means the formation of all state structures that is necessary for the further proper functioning of a market economy. These three stages about the cycle period of political and social transformation and the hierarchy of changes can also be grouped by the different methodology: on the first and the most short-term stage the transfer of power takes place. On the second stage institutions corresponding to new goal are created. The last phase of transformation is extended in time and it includes the infrastructural, socio-cultural and socio-structural changes. The main goal of this research is to explore and identify the features of such kind of models.

Keywords: competitive environment, fiscal policy, macroeconomic stabilization, tax system

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Authors: Phornchanok Motantasut, Torkamol Hunsawong, Lugkana Mato, Wanida Donpunha

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Identifying abnormal foot posture is important for prescribing appropriate management in patients with lower limb disorders and chronic non-specific low back pain. The normalized navicular height truncated (NNHt) and the foot posture index-6 (FPI-6) have been recommended as the common, simple, valid, and reliable static measures for clinical application. The NNHt is a single plane measure while the FPI-6 is a triple plane measure. At present, there is inadequate information about the correlation between the NNHt and the FPI-6 for categorizing foot posture that leads to a difficulty of choosing the appropriate assessment. Therefore, the present study aimed to determine the correlation between the NNHt and the FPI-6 measures in adult participants with asymptomatic feet. Methods: A cross-sectional descriptive study was conducted in 47 asymptomatic individuals (23 males and 24 females) aged 28.89 ± 7.67 years with body mass index 21.73 ± 1.76 kg/m². The right foot was measured twice by the experienced rater using the NNHt and the FPI-6. A sequence of the measures was randomly arranged for each participant with a 10-minute rest between the tests. The Pearson’s correlation coefficient (r) was used to determine the relationship between the measures. Results: The mean NNHt score was 0.23 ± 0.04 (ranged from 0.15 to 0.36) and the mean FPI-6 score was 4.42 ± 4.36 (ranged from -6 to +11). The Pearson’s correlation coefficient among the NNHt score and the FPI-6 score was -0.872 (p < 0.01). Conclusion: The present finding demonstrates the strong correlation between the NNHt and FPI-6 in adult feet and implies that both measures could be substituted for each other in identifying foot posture.

Keywords: foot posture index, foot type, measurement of foot posture, navicular height

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Authors: Tarsem Singh

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The aim of the present study was to investigate the effect of yoga training on muscular strength, muscular endurance, flexibility and agility of female hockey players. For this purpose, a sample of forty (N=40) female hockey players of age ranging from 18 to 25 years were selected from different colleges affiliated to Guru Nanak Dev University Amritsar. Further, the subjects were purposively divided in two groups. First group, designated as experimental group (N1=20) and the second one as control group (N2=20). All the participants were informed about the objectives and methodology of this study and they volunteered to participate in this experimental study. The study was restricted to the variables: muscular strength, muscular endurance, flexibility and agility. The same were measured by using Flexed Arms Hang Test, Sit-Ups Test, Sit and Reach Test and Shuttle Run Test respectively. Experimental group have undergone yoga training for 8-week by following a sequence of selected yogic asanas i.e. Sarvangasana, Chakra-asana, Utthita Parsvakonasana, Parivrtta Trikonasana, Halasana, Bhujangasana, Dhanurasana, Ustrasana, Gomukasana, Paschimotansana, Ardha-Matsyendrasana and Hanumanasan. Paired sample t-test was applied to study the effects of yoga training on female hockey players. The level of significance was set at 0.05. Results revealed significant differences between pre and post-tests of experimental group in respect to Muscular strength (t-6.946*), Muscular endurance (t-9.863*), Flexibility (t-11.052*) and Agility (t-14.068*). However, insignificant differences were observed between pre and post-tests of control group.

Keywords: yoga, muscular strength, muscular endurance, flexibility, agility

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Authors: S. J. M. Mohd Saleh, S. Guo

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Composite materials have become an important option for the primary structure of aircraft due to their design flexibility and ability to improve the overall performance. At present, the option for composite usage in aircraft component is largely based on experience, knowledge, benchmarking and partly market driven. An inevitable iterative design during the design stage and validation process will increase the development time and cost. This paper aims at presenting the correlation between laminate and composite thin-wall beam structure, which contains the theoretical and numerical investigations on stiffness estimation of composite aerostructures with applications to aircraft wings. Classical laminate theory and thin-walled beam theory were applied to define the correlation between 1-dimensional composite laminate and 2-dimensional composite beam structure, respectively. Then FE model was created to represent the 3-dimensional structure. A detailed study on stiffness matrix of composite laminates has been carried out to understand the effects of stacking sequence on the coupling between extension, shear, bending and torsional deformation of wing box structures for 1-dimensional, 2-dimensional and 3-dimensional structures. Relationships amongst composite laminates and composite wing box structures of the same material have been developed in this study. These correlations will be guidelines for the design engineers to predict the stiffness of the wing box structure during the material selection process and laminate design stage.

Keywords: aircraft design, aircraft structures, classical lamination theory, composite structures, laminate theory, structural design, thin-walled beam theory, wing box design

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Authors: Ali Ben Abbes, ImedRiadh Farah, Vincent Barra

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Remotely sensed data are a significant source for monitoring and updating databases for land use/cover. Nowadays, changes detection of urban area has been a subject of intensive researches. Timely and accurate data on spatio-temporal changes of urban areas are therefore required. The data extracted from multi-temporal satellite images are usually non-stationary. In fact, the changes evolve in time and space. This paper is an attempt to propose a methodology for changes detection in urban area by combining a non-stationary decomposition method and stochastic modeling. We consider as input of our methodology a sequence of satellite images I₁, I₂, … I_n at different periods (t = 1, 2, ..., n). Firstly, a preprocessing of multi-temporal satellite images is applied. (e.g. radiometric, atmospheric and geometric). The systematic study of global urban expansion in our methodology can be approached in two ways: The first considers the urban area as one same object as opposed to non-urban areas (e.g. vegetation, bare soil and water). The objective is to extract the urban mask. The second one aims to obtain a more knowledge of urban area, distinguishing different types of tissue within the urban area. In order to validate our approach, we used a database of Tres Cantos-Madrid in Spain, which is derived from Landsat for a period (from January 2004 to July 2013) by collecting two frames per year at a spatial resolution of 25 meters. The obtained results show the effectiveness of our method.

Keywords: multi-temporal satellite image, urban growth, non-stationary, stochastic model

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Authors: Mohammad Borhani, Ahmad Jamshidzaei, Mehdi Koohsari

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The study of climate has captivated human interest throughout history. In response to this fascination, individuals historically organized their daily activities in alignment with prevailing climatic conditions and seasonal variations. Understanding the elements and specific climatic parameters of each region, such as precipitation, which directly impacts human life, is essential because, in recent years, there has been a significant increase in heavy rainfall in various parts of the world attributed to the effects of climate change. Climate prediction models suggest a future scenario characterized by an increase in severe precipitation events and related floods on a global scale. This is a result of human-induced greenhouse gas emissions causing changes in the natural precipitation patterns. The Intergovernmental Panel on Climate Change reported global warming in 2001. The average global temperature has shown an increasing trend since 1861. In the 20th century, this increase has been between (0/2 ± 0/6) °C. The present study focused on examining the trend of monthly, seasonal, and annual precipitation in Sistan and Baluchestan provinces. The study employed data obtained from 13 precipitation measurement stations managed by the Iran Water Resources Management Company, encompassing daily precipitation records spanning the period from 1997 to 2016. The results indicated that the total monthly precipitation at the studied stations in Sistan and Baluchestan province follows a sinusoidal trend. The highest intense precipitation was observed in January, February, and March, while the lowest occurred in September, October, and then November. The investigation of the trend of seasonal precipitation in this province showed that precipitation follows an upward trend in the autumn season, reaching its peak in winter, and then shows a decreasing trend in spring and summer. Also, the examination of average precipitation indicated that the highest yearly precipitation occurred in 1997 and then in 2004, while the lowest annual precipitation took place between 1999 and 2001. The analysis of the annual precipitation trend demonstrates a decrease in precipitation from 1997 to 2016 in Sistan and Baluchestan province.

Keywords: climate change, extreme precipitation, greenhouse gas, trend analysis

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Authors: Oljana Hoxhaj

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The integration process of Albania into the European family carries many difficulties. In this context, the Albanian legislator is inclined to implement in the domestic legal framework models which have been successful in other countries. Our paper aims to present an analytical and comparative approach to the health system in Albania and France, mainly focusing on citizen’s access to these services. Different standards and cultures between states, in the context of an approximate model, will be the first challenge of our paper. Over the last few years, the Albanian government has undertaken concrete reforms in this sector, aiming to transform the vision on which the previous health system was structured. In this perspective, the state fulfills not only an obligation to its citizens, but also consolidates progressive steps toward alignment with European Union standards. The necessity to undertake a genuine reform in this area has come as an exigency of society, which has permanently identified problems within this sector, considering it ineffective, out of standards, and corrupt. The inclusion of health services on the Albanian government agenda reflects its will in the function of good governance, transparency, and broadening access to the provision of quality health services in the public and private sectors. The success of any initiative in the health system consists of giving priority to patient needs. Another objective that should be in the state's consideration is to create the premise to provide a comprehensive process on whose foundations partnership and broader co-operation with beneficiary entities are established in any decision-making that is directly related to their interests. Some other important and widespread impacts on the effective realization of citizens' access to the healthcare system coincide with the construction of appropriate infrastructure, increasing the professionalism and qualification of medical staff, and the allocation of a higher budget. France has one of the most effective healthcare models in Europe. That is why we have chosen to analyze this country, aiming to highlight the advantages of this system, as well as the commitment of the French state to drafting effective health policies. In the framework of the process of harmonization of the Albanian legislation with that of the European Union, through our work, we aim to identify the space to implement the whole of these legislative innovations in the Albanian legislation.

Keywords: effective service, harmonization level, innovation, reform

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Authors: Satpal Yadav, Biswajit Basumatary, Arvind S. Sajwan, Ranjan Chakravarty

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The purpose of the study was to assess the effect of 2D kinematical selected variables on sprint start with sprinting performance of novice athletes. Six (3 National and 3 State level) athletes of sports authority of India, Guwahati has been selected for this study. The mean (M) and standard deviation (SD) of sprinters were age (17.44, 1.55), height (1.74m, .84m), weight (62.25 kg, 4.55), arm length (65.00 cm, 3.72) and leg length (96.35 cm, 2.71). Biokin-2D motion analysis system V4.5 can be used for acquiring two-dimensional kinematical data/variables on sprint start with Sprinting Performance. For the purpose of kinematic analysis a standard motion driven camera which frequency of the camera was 60 frame/ second i.e. handy camera of Sony Company were used. The sequence of photographic was taken under controlled condition. The distance of the camera from the athletes was 12 mts away and was fixed at 1.2-meter height. The result was found that National and State level athletes significant difference in there, trajectory knee, trajectory ankle, displacement knee, displacement ankle, linear velocity knee, linear velocity ankle, and linear acceleration ankle whereas insignificant difference was found between National and State level athletes in their linear acceleration knee joint on sprint start with sprinting performance. For all the Statistical test the level of significance was set at p<0.05.

Keywords: 2D kinematic analysis, sprinting performance, novice athletes, sprint start

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Authors: Arabi Abderrazak, Bourouba Nacerdine, Ayad Mouloud, Belaout Abdeslam

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In this paper, a new test technique of analog circuits using time mode simulation is proposed for the single catastrophic faults detection in analog circuits. This test process is performed to overcome the problem of catastrophic faults being escaped in a DC mode test applied to the inverter amplifier in previous research works. The circuit under test is a second-order low pass filter constructed around this type of amplifier but performing a function that differs from that of the previous test. The test approach performed in this work is based on two key- elements where the first one concerns the unique square pulse signal selected as an input vector test signal to stimulate the fault effect at the circuit output response. The second element is the filter response conversion to a square pulses sequence obtained from an analog comparator. This signal conversion is achieved through a fixed reference threshold voltage of this comparison circuit. The measurement of the three first response signal pulses durations is regarded as fault effect detection parameter on one hand, and as a fault signature helping to hence fully establish an analog circuit fault diagnosis on another hand. The results obtained so far are very promising since the approach has lifted up the fault coverage ratio in both modes to over 90% and has revealed the harmful side of faults that has been masked in a DC mode test.

Keywords: analog circuits, analog faults diagnosis, catastrophic faults, fault detection

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Authors: Mohammad Salem Abdullah Al-Hwaiti

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The stratiform copper mineralization of the Burj-Dolomite shale (BDS) formations of deposits shows that the copper mineralization within the BDS occurs as hydrated copper chlorides and carbonates (mainly paratacamite and malachite, respectively), while copper silicates (mainly chrysocolla and planchette) are the major ore minerals in the BDS. Thus, on the basis of the petrographic and field occurrence, three main stages operated during the development of the copper ore in the sandy and shaly lithofacies. During the first stage, amorphous chrysocolla replaced clays, feldspars, and quartz. This stage was followed by the transition from an amorphous phase to a better-crystallized phase, i.e., the formation of planchette and veins from chrysocolla. The third stage was the formation of chrysocolla along fracture planes. Other secondary minerals are pseudomalachite, dioptase, neoticite together with authigenic fluorapatite. Paratacamite and malachite, which are common in the dolomitic lithofacies, are relatively rare in the sandy and silty lithofacies. The Rare Earth Elements (REEs) patterns for the BDS showed three stages in the evolution of the Precambrian–Cambrian copper mineralization system, involving the following: (A) Epigenetic mobilization of Cu-bearing solution with formation Cu-carbonate in dolomite and limestone mineralization and Cu-silicate mineralization in sandstone; (B) Transgression of Cambrian Sea and SSC deposition of Cu-sulphides during dolomite diagenesis in the BDS Formation; continued diagenesis and oxidation leads to the formation of Cu(II) minerals; (C) Erosion and supergene enrichment of Cu in basement rocks. Detrital copper-bearing sediments accumulate in the lower Cambrian clastic sequence.

Keywords: dolomite shale, copper mineralization, REE, Jordan

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Authors: Niloofar Fariborzi, Hamzeh Alipour, Kourosh Azizi, Neda Eskandarzade, Abozar Ghorbani

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The family Parvoviridae consists of a large diversity of single-stranded DNA viruses, which cause mild to severe diseases in both vertebrates and invertebrates. The Parvoviridae are classified into three subfamilies: Parvovirinae infect vertebrates, Densovirinae infects invertebrates, while Hamaparovirinae infects both vertebrates and invertebrates. Except for the NS1 region, which is the prime criterion for phylogeny analysis, other parts of the parvoviruses genome, such as UTRs, are diverse even among closely related viruses or within the same genus. It is believed that host switching in parvoviruses may be related to genetic changes in regions other than NS1; therefore, whole-genome screening is valuable for studying parvoviruses' host-virus interactions. The aim of this study was to analyze genome organization and phylogeny of the complete genome sequence of the 132 Paroviridae family members, focusing on viruses that infect invertebrates. The maximum and minimum divergence within each subfamily belonged to Densovirinae and Parvovirinae, respectively. The greatest evolutionary divergence was between Hamaparovirinae and Parvovirinae. Unclassified viruses were mostly from Parovirinae and had the highest divergence to densoviruses and the lowest divergence to Parovirinae viruses. In a phylogenetic tree, all hamparoviruses were found in the center of densoviruses, with the exception of Syngnathid Ichthamaparvovirus 1 (NC_055527), which was positioned between two Parvovirinae members (NC _022089 and NC_038544). The proximity of hamparoviruses members to some densoviruses strengthens the possibility that densoviruses may be the ancestors of hamaparoviruses or vice versa. Therefore, examination and phylogeny analysis of the whole genome is necessary to understand Parvoviridae family host selection.

Keywords: densoviruses, parvoviridae, bioinformatics, phylogeny

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Authors: Feng Ji Mervin Goh, Edmund Chee Jian Pua, Stuart Alexander Cook

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Dilated cardiomyopathy (DCM) is a common cause of heart failure. Genetic mutations account for 50% of DCM cases with TTN mutations being the most common, accounting for up to 25% of DCM cases. However, the genetic architecture underlying Asian DCM patients is unknown. We evaluated 68 patients (female= 17) with DCM who underwent follow-up at the National Heart Centre, Singapore from 2013 through 2014. Clinical data were obtained and analyzed retrospectively. Genomic DNA was subjected to next-generation targeted sequencing. Nextera Rapid Capture Enrichment was used to capture the exons of a panel of 169 cardiac genes. DNA libraries were sequenced as paired-end 150-bp reads on Illumina MiSeq. Raw sequence reads were processed and analysed using standard bioinformatics techniques. The average age of onset of DCM was 46.1±10.21 years old. The average left ventricular ejection fraction (LVEF), left ventricular diastolic internal diameter (LVIDd), left ventricular systolic internal diameter (LVIDs) were 26.1±11.2%, 6.20±0.83cm, and 5.23±0.92cm respectively. The frequencies of mutations in major DCM-associated genes were as follows TTN (5.88% vs published frequency of 20%), LMNA (4.41% vs 6%), MYH7 (5.88% vs 4%), MYH6 (5.88% vs 4%), and SCN5a (4.41% vs 3%). The average callability at 10 times coverage of each major gene were: TTN (99.7%), LMNA (87.1%), MYH7 (94.8%), MYH6 (95.5%), and SCN5a (94.3%). In conclusion, TTN mutations are not common in Singaporean DCM patients. The frequencies of other major DCM-associated genes are comparable to frequencies published in the current literature.

Keywords: heart failure, dilated cardiomyopathy, genetics, next-generation sequencing

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Authors: Asma Karim

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Fish taxonomy plays a fundamental role in the study of biodiversity. However, traditional methods of fish taxonomy rely on morphological features, which can lead to confusion due to great similarities between closely related species. To overcome this limitation, modern taxonomy employs DNA barcoding as a species identification method. This involves using a short standardized mitochondrial DNA region as a barcode, specifically a 658 base pair fragment near the 5′ ends of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene, to exploit the diversity in this region for identification of species. To test the effectiveness and reliability of DNA barcoding, 25 fish specimens from nine different fish species found in various rivers of Pakistan were identified morphologically using a dichotomous key at the start of the study. Comprising nine freshwater fish species, including Mystus cavasius, Mystus bleekeri, Osteobrama cotio, Labeo rohita, Labeo culbasu, Labeo gonius, Cyprinus carpio, Catla catla and Cirrhinus mrigala from different rivers of Pakistan were used in the present study. DNA was extracted from one of the pectoral fins and a partial sequence of CO1 gene was amplified using the conventional PCR method. Analysis of the barcodes confirmed that genetically identified fishes were the same as those identified morphologically at the beginning of the study. The sequences were also analyzed for biodiversity and phylogenetic studies. Based on the results of the study, it can be concluded that DNA barcoding is an effective and reliable method for studying biodiversity and conducting phylogenetic analysis of different fish species in Pakistan.

Keywords: DNA barcoding, fresh water fishes, taxonomy, biodiversity, Pakistan

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Authors: Atif Zafar, Fan Haijun

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A sequence of different Reservoir Engineering methods and tools in reservoir characterization and field development are presented in this paper. The real data of Jin Gas Field of L-Basin of Pakistan is used. The basic concept behind this work is to enlighten the importance of well test analysis in a broader way (i.e. reservoir characterization and field development) unlike to just determine the permeability and skin parameters. Normally in the case of reservoir characterization we rely on well test analysis to some extent but for field development plan, the well test analysis has become a forgotten tool specifically for locations of new development wells. This paper describes the successful implementation of well test analysis in Jin Gas Field where the main uncertainties are identified during initial stage of field development when location of new development well was marked only on the basis of G&G (Geologic and Geophysical) data. The seismic interpretation could not encounter one of the boundary (fault, sub-seismic fault, heterogeneity) near the main and only producing well of Jin Gas Field whereas the results of the model from the well test analysis played a very crucial rule in order to propose the location of second well of the newly discovered field. The results from different methods of well test analysis of Jin Gas Field are also integrated with and supported by other tools of Reservoir Engineering i.e. Material Balance Method and Volumetric Method. In this way, a comprehensive way out and algorithm is obtained in order to integrate the well test analyses with Geological and Geophysical analyses for reservoir characterization and field development. On the strong basis of this working and algorithm, it was successfully evaluated that the proposed location of new development well was not justified and it must be somewhere else except South direction.

Keywords: field development plan, reservoir characterization, reservoir engineering, well test analysis

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Authors: Sina Keyhanian, Abbas Ahmadi, Behrooz Karimi

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We present a multi-objective binary programming model which considers surgical cases are scheduling among operating rooms and the configuration of surgical instruments in limited capacity hospital trays, simultaneously. Many mathematical models have been developed previously in the literature addressing different challenges in health-care logistics such as assigning operating rooms, leveling beds, etc. But what happens inside the operating rooms along with the inventory management of required instruments for various operations, and also their integration with surgical scheduling have been poorly discussed. Our model considers the minimization of movements between trays during a surgery which recalls the famous cell formation problem in group technology. This assumption can also provide a major potential contribution to robotic surgeries. The tray configuration problem which consumes surgical instruments requirement plan (SIRP) and sequence of surgical procedures based on required instruments (SIRO) is nested inside the bin packing problem. This modeling approach helps us understand that most of the same-output solutions will not be necessarily identical when it comes to the rearrangement of surgeries among rooms. A numerical example has been dealt with via a proposed nested simulated annealing (SA) optimization approach which provides insights about how various configurations inside a solution can alter the optimal condition.

Keywords: health-care logistics, hospital tray configuration, off-line bin packing, simulated annealing optimization, surgical case scheduling

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Authors: Juan Antonio Mondragon Sanchez, Ruben Santamaria

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The DNA G-quadruplex is a four-stranded DNA structure conformed by stacked planes of four base paired guanines (G-quartet). The guanine rich DNA sequences are present in many sites of genomic DNA and can potentially lead to the formation of G-quadruplexes, especially at the 3'-terminus of the human telomeric DNA with many TTAGGG repeats. The formation and stabilization of a G-quadruplex by small ligands at the telomeric region can inhibit the telomerase activity. In turn, the ligands can be used to regulate oncogene expression making the G-quadruplex an attractive target for anticancer therapy. Clearly, the G-quadruplex structured in the telomeric DNA is of fundamental importance for rational drug design. In this context, we investigate two G-quadruplex structures, the first follows from the sequence TTAGGG(TTAGGG)3TT (HUT1), and the second from AAAGGG(TTAGGG)3AA (HUT2), both in a K+ solution. We determine the free energy surfaces of the HUT1 and HUT2 structures and investigate their conformations using replica-exchange metadynamics simulations. The carbonyl-carbonyl distances belonging to different guanines residues are selected as the main collective variables to determine the free energy surfaces. The surfaces exhibit two main local minima, compatible with experiments on the conformational transformations of HUT1 and HUT2 under substitution of the K+ ions by the Na+ ions. The conformational transitions are not observed in short MD simulations without the use of the metadynamics approach. The results of this work should be of help to understand the formation and stability of human telomeric G-quadruplex in environments including the presence of K+ and Na+ ions.

Keywords: g-quadruplex, metadynamics, molecular dynamics, replica-exchange

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Authors: Zeeshan Khan, Faisal Nouroz, Shumaila Noureen

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European or common rabbit (Oryctolagus cuniculus) belongs to class Mammalia, order Lagomorpha of family Leporidae. They are distributed worldwide and are native to Europe (France, Spain and Portugal) and Africa (Morocco and Algeria). LTR retrotransposons are major Class I mobile genetic elements of eukaryotic genomes and play a crucial role in genome expansion, evolution and diversification. They were mostly annotated in various genomes by conventional approaches of homology searches, which restricted the annotation of novel elements. Present work involved de novo identification of LTR retrotransposons by LTR_FINDER in haploid genome of rabbit (2247.74 Mb) distributed in 22 chromosomes, of which 7,933 putative full-length or partial copies were identified containing 69.38 Mb of elements, accounting 3.08% of the genome. Highest copy numbers (731) were found on chromosome 7, followed by chromosome 12 (705), while the lowest copy numbers (27) were detected in chromosome 19 with no elements identified from chromosome 21 due to partially sequenced chromosome, unidentified nucleotides (N) and repeated simple sequence repeats (SSRs). The identified elements ranged in sizes from 1.2 - 25.8 Kb with average sizes between 2-10 Kb. Highest percentage (4.77%) of elements was found in chromosome 15, while lowest (0.55%) in chromosome 19. The most frequent tRNA type was Arginine present in majority of the elements. Based on gained results, it was estimated that rabbit exhibits 15,866 copies having 137.73 Mb of elements accounting 6.16% of diploid genome (44 chromosomes). Further molecular analyses will be helpful in chromosomal localization and distribution of these elements on chromosomes.

Keywords: rabbit, LTR retrotransposons, genome, chromosome

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Authors: Esther Chiramal, Kelvin Soh Boon Kai

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Explainable AI is a strong strategy implemented to understand complex black-box model predictions in a human-interpretable language. It provides the evidence required to execute the use of trustworthy and reliable AI systems. On the other hand, however, it also opens the door to locating possible vulnerabilities in an AI model. Traditional adversarial text attack uses word substitution, data augmentation techniques, and gradient-based attacks on powerful pre-trained Bidirectional Encoder Representations from Transformers (BERT) variants to generate adversarial sentences. These attacks are generally white-box in nature and not practical as they can be easily detected by humans e.g., Changing the word from “Poor” to “Rich”. We proposed a simple yet effective Grey-box cum Black-box approach that does not require the knowledge of the model while using a set of surrogate Transformer/BERT models to perform the attack using Explainable AI techniques. As Transformers are the current state-of-the-art models for almost all Natural Language Processing (NLP) tasks, an attack generated from BERT1 is transferable to BERT2. This transferability is made possible due to the attention mechanism in the transformer that allows the model to capture long-range dependencies in a sequence. Using the power of BERT generalisation via attention, we attempt to exploit how transformers learn by attacking a few surrogate transformer variants which are all based on a different architecture. We demonstrate that this approach is highly effective to generate semantically good sentences by changing as little as one word that is not detectable by humans while still fooling other BERT models.

Keywords: BERT, explainable AI, Grey-box text attack, transformer

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Authors: Eileen K. Africa, Karel J. van Deventer

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Neuro-typical children develop the motor skills necessary to play, do schoolwork and interact with others. However, this is not observed in children who have learning or behavioural problems. Children with Autism Spectrum Disorder (ASD) are often referred to as clumsy because their body parts do not work well together in a sequence. Physical Activity (PA) has shown to be beneficial to the general population, therefore, providing children with ASD opportunities to take part in PA programmes, could prove to be beneficial in many ways and should be investigated. The purpose of this study was to design a specialised group intervention programme, to attempt to improve gross motor skills of selected children diagnosed with ASD between the ages of eight and 13 years. A government school for ASD learners was recruited to take part in this study, and a sample of convenience (N=7) was selected. Children in the experimental group (n=4) participated in a 12-week group intervention programme twice per week, while the control group continued with their normal daily routine. The Movement Assessment Battery for Children-Second Edition (MABC-2), was administered pre- and post-test to determine the children’s gross motor proficiency and to determine if the group intervention programme had an effect on the gross motor skills of the experimental group. Statistically significant improvements were observed in total motor skill proficiency (p < 0.05), of the experimental group. These results demonstrate the importance of gross motor skills interventions for children diagnosed with ASD. Future research should include more participants to ensure that the results can be generalised.

Keywords: autism spectrum disorder, children, gross motor skills, group intervention programme

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Authors: Naoum Abderrahmane, Boumehed Meriem, Alshaqaqi Belal

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Background subtraction algorithm is a larger used technique for detecting moving objects in video surveillance to extract the foreground objects from a reference background image. There are many challenges to test a good background subtraction algorithm, like changes in illumination, dynamic background such as swinging leaves, rain, snow, and the changes in the background, for example, moving and stopping of vehicles. In this paper, we propose an efficient and accurate background subtraction method for moving object detection in video surveillance. The main idea is to use a developed fast-independent component analysis (ICA) algorithm to separate background, noise, and foreground masks from an image sequence in practical environments. The fast-ICA algorithm is adapted and adjusted with a matrix calculation and searching for an optimum non-quadratic function to be faster and more robust. Moreover, in order to estimate the de-mixing matrix and the denoising de-mixing matrix parameters, we propose to convert all images to YCrCb color space, where the luma component Y (brightness of the color) gives suitable results. The proposed technique has been verified on the publicly available datasets CD net 2012 and CD net 2014, and experimental results show that our algorithm can detect competently and accurately moving objects in challenging conditions compared to other methods in the literature in terms of quantitative and qualitative evaluations with real-time frame rate.

Keywords: background subtraction, moving object detection, fast-ICA, de-mixing matrix

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Authors: Mojgan Rabiey, Shyamali Roy, Billy Quilty, Ryan Creeth, George Sundin, Robert W. Jackson

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Bacterial canker is a major disease of Prunus species such as cherry (Prunus avium). It is caused by Pseudomonas syringae species including P. syringae pv. syringae (Pss) and P. syringae pv. morsprunorum race 1 (Psm1) and race 2 (Psm2). Concerns over the environmental impact of, and developing resistance to, copper controls call for alternative approaches to disease management. One method of control could be achieved using naturally occurring bacteriophage (phage) infective to the bacterial pathogens. Phages were isolated from soil, leaf, and bark of cherry trees in five locations in the South East of England. The phages were assessed for their host range against strains of Pss, Psm1, and Psm2. The phages exhibited a differential ability to infect and lyse different Pss and Psm isolates as well as some other P. syringae pathovars. However, the phages were unable to infect beneficial bacteria such as Pseudomonas fluorescens. A subset of 18 of these phages were further characterised genetically (Random Amplification of Polymorphic DNA-PCR fingerprinting and sequencing) and using electron microscopy. The phages are tentatively identified as belonging to the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae, with genetic material being dsDNA. Future research will fully sequence the phage genomes. The efficacy of the phage, both individually and in cocktails, to reduce disease progression in vivo will be investigated to understand the potential for practical use of these phages as biocontrol agents.

Keywords: bacteriophage, pseudomonas, bacterial cancker, biological control

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Authors: Muhammad SAFDAR, Mehmet Ozaslan, Musarrat Abbas Khan

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Babesiosis is a haemoparasitic disease due to the multiplication of protozoan’s parasite, Babesia ovis in the red blood cells of the host, and contributes numerous economical losses, including sheep and goat ruminants. The early identification and successful treatment of Babesia Ovis spp. belong to the key steps of control and health management of livestock resources. The objective of this study was to construct a polymerase chain reaction (PCR) based method for the detection of Babesia spp. in small ruminants and to determine the risk factors involved in the spreading of babesiosis infections. A total of 100 blood samples were collected from 50 sheep and 50 goats along with different areas of Muzaffargarh, Pakistan, from randomly selected herds. Data on the characteristics of sheep and goats were collected through questionnaires. Of 100 blood samples examined, 18 were positive for Babesia ovis upon microscopic studies, whereas 11 were positive for the presence of Babesia spp. by PCR assay. For the recognition of parasitic DNA, a set of 500bp oligonucleotide was designed by PCR amplification with sequence 18S rRNA gene for B. ovis. The prevalence of babesiosis in small ruminant’s sheep and goat detected by PCR was significantly higher in female animals (28%) than male herds (08%). PCR analysis of the reference samples showed that the detection limit of the PCR assay was 0.01%. Taken together, all data indicated that this PCR assay was a simple, fast, specific detection method for Babesia ovis species in small ruminants compared to other available methods.

Keywords: Babesia ovis, PCR amplification, 18S rRNA, sheep and goat

Procedia PDF Downloads 115

Authors: Amrit Ladhani

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The cyclic universe theory is a model of cosmic evolution according to which the universe undergoes endless cycles of expansion and cooling, each beginning with a “big bang” and ending in a “big crunch”. In this paper, we propose a unique property of Space-time. This particular and marvelous nature of space shows us that space can stretch, expand, and shrink. This property of space is caused by the size of the universe change over time: growing or shrinking. The observed accelerated expansion, which relates to the stretching of Shrunk space for the new theory, is derived. This theory is based on three underlying notions: First, the Big Bang is not the beginning of Space-time, but rather, at the very beginning fraction of a second, there was an infinite force of infinite Shrunk space in the cosmic singularity that force gave rise to the big bang and caused the rapidly growing of space, and all other forms of energy are transformed into new matter and radiation and a new period of expansion and cooling begins. Second, there was a previous phase leading up to it, with multiple cycles of contraction and expansion that repeat indefinitely. Third, the two principal long-range forces are the gravitational force and the repulsive force generated by shrink space. They are the two most fundamental quantities in the universe that govern cosmic evolution. They may provide the clockwork mechanism that operates our eternal cyclic universe. The universe will not continue to expand forever; no need, however, for dark energy and dark matter. This new model of Space-time and its unique properties enables us to describe a sequence of events from the Big Bang to the Big Crunch.

Keywords: dark matter, dark energy, cosmology, big bang and big crunch

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Authors: Savjot Kaur, Mridula Mahajan, AJS Bhanwer, Santokh Singh, Kawaljit Matharoo

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Background: Disorders of lipid metabolism and genetic predisposition are CAD risk factors. ApoA1 is the apolipoprotein component of anti-atherogenic high density lipoprotein (HDL) particles. The protective action of HDL and ApoA1 is attributed to their central role in reverse cholesterol transport (RCT). Aim: This study was aimed at identifying sequence variations in ApoA1 (-75G>A) and its association with serum ApoA1 levels. Methods: A total of 300 CAD patients and 300 Normal individuals (controls) were analyzed. PCR-RFLP method was used to determine the DNA polymorphism in the ApoA1 gene, PCR products digested with restriction enzyme MspI, followed by Agarose Gel Electrophoresis. Serum apolipoprotein A1 concentration was estimated with immunoturbidimetric method. Results: Deviation from Hardy- Weinberg Equilibrium (HWE) was observed for this gene variant. The A- allele frequency was higher among Coronary Artery disease patients (53.8) compared to controls (45.5), p= 0.004, O.R= 1.38(1.11-1.75). Under recessive model analysis (AA vs. GG+GA) AA genotype of ApoA1 G>A substitution conferred ~1 fold increased risk towards CAD susceptibility (p= 0.002, OR= 1.72(1.2-2.43). With serum ApoA1 levels < 107 A allele frequency was higher among CAD cases (50) as compared to controls (43.4) [p=0.23, OR= 1.2(0.84-2)] and there was zero % occurrence of A allele frequency in individuals with ApoA1 levels > 177. Conclusion: Serum ApoA1 levels were associated with ApoA1 promoter region variation and influence CAD risk. The individuals with the APOA1 -75 A allele confer excess hazard of developing CAD as a result of its effect on low serum concentrations of ApoA1.

Keywords: apolipoprotein A1 (G>A) gene polymorphism, coronary artery disease (CAD), reverse cholesterol transport (RCT)

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Authors: Jyh-Cherng Chen, Yi-Jie Lin

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This study tries to reuse the fly ash of municipal solid waste incinerator (MSWI) for the synthesis of zeolites. The fly ashes were treated with NaOH alkali fusion at different temperatures for 40 mins and then synthesized the zeolites with hydrothermal method at 105oC for different operation times. The effects of different operation conditions and the optimum synthesis parameters were explored. The specific surface area, surface morphology, species identification, adsorption capacity, and the reuse potentials of the synthesized zeolites were analyzed and evaluated. Experimental results showed that the optimum operation conditions for the synthesis of zeolite from the mixed fly ash were Si/Al=20, alkali/ash=1.5, alkali fusion reaction with NaOH at 800oC for 40 mins, hydrolysis with L/S=200 at 105oC for 24 hr, and hydrothermal synthesis at 105oC for 48 hr. The largest specific surface area of synthesized zeolite could be increased to 943.05m2/g. The influence of different operation parameters on the synthesis of zeolite from mixed fly ash followed the sequence of Si/Al > hydrolysis L/S> hydrothermal time > alkali fusion temperature > alkali/ash ratio. The XRD patterns of synthesized zeolites were identified to be similar with the ZSM-23 zeolite. The adsorption capacities of synthesized zeolite for pollutants were increased as rising the specific surface area of synthesized zeolite. In summary, MSWI fly ash can be treated and reused to synthesize the zeolite with high specific surface area by the alkali fusion and hydrothermal method. The zeolite can be reuse for the adsorption of various pollutants. They have great potential for development.

Keywords: alkali fusion, hydrothermal, fly ash, zeolite

Procedia PDF Downloads 153

Authors: Mahjabeen Akbar

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Dental aesthetics and its associated psychosocial influence have a significant impact on individuals. Correcting malocclusions is a key motivating factor for majority patients; however, psychosocial factors have been rarely incorporated in evaluating malocclusions. Therefore, it is necessary to study the psychosocial influence of malocclusion in patients. The study aimed to determine the psychosocial influence of dental aesthetics in dental students by the ‘Psychosocial Impact of Dental Aesthetics Questionnaire’ and self-rated Aesthetic Component of the Index of Orthodontic Treatment Need (IOTN). This was a quantitative study using a cross-sectional study design. One hundred twenty dental students (71 females and 49 males; mean age 24.5) were selected via purposive sampling from July to August 2019. Dental students with no former orthodontic treatment were requested to fill out the ‘Psychosocial Impact of Dental Aesthetics Questionnaire.’ Variables including; self-confidence/insecurity, social influence, psychological influence and self-perception of the need of an orthodontic treatment were evaluated by a sequence of statements, while dental aesthetics were evaluated by using the IOTN Aesthetic Component. To determine the significance, the Kruskal-Wallis test was utilized. The results show that all four variables measuring psychosocial impact indicated significant correlations with the perceived malocclusions with a p-value of less than 0.01. The results conclude there is a strong psychological and social influence of altered dental aesthetics on an individual. Moreover, the relationship between the IOTN-AC grading with the psychosocial wellbeing of an individual stands proven, indicating that the perception of altered dental aesthetics is as important as a factor in treatment need as the amount of malocclusion.

Keywords: dental aesthetics, malocclusion, psychosocial influence, dental students

Procedia PDF Downloads 135

Authors: William Li

Abstract:

Lane-change path planning is a crucial and yet complex task in autonomous driving. The traditional path planning approach based on a system of carefully-crafted rules to cover various driving scenarios becomes unwieldy as more and more rules are added to deal with exceptions and corner cases. This paper proposes to divide the entire path planning to two stages. In the first stage the ego vehicle travels longitudinally in the source lane to reach a safe state. In the second stage the ego vehicle makes lateral lane-change maneuver to the target lane. The paper derives the safe state conditions based on lateral lane-change maneuver calculation to ensure collision free in the second stage. To determine the acceleration sequence that minimizes the time to reach a safe state in the first stage, the paper proposes three schemes, namely, kinetic model based optimization, deep reinforcement learning, and 5G vehicle-to-vehicle (V2V) communications. The paper investigates these schemes via simulation. The model-based optimization is sensitive to the model assumptions. The deep reinforcement learning is more flexible in handling scenarios beyond the model assumed by the optimization. The 5G V2V eliminates uncertainty in predicting future behaviors of surrounding vehicles by sharing driving intents and enabling cooperative driving.

Keywords: lane change, path planning, autonomous driving, deep reinforcement learning, 5G, V2V communications, connected vehicles

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Authors: Rubina Jahan, Mohammad Zayeed Bin Alam, Sazzad Chowdhury, Sadia Chowdhury

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Access to mental health services in Bangladesh is a tale of urban privilege and rural struggle. Mental health services in the country are primarily centered in urban medical hospitals, with only 260 psychiatrists for a population of more than 162 million, while rural populations face far more severe and daunting challenges. In alignment with the World Health Organization's perspective on mental health as a basic human right and a crucial component for personal, community, and socioeconomic development; SAJIDA Foundation a value driven non-government organization in Bangladesh has introduced a Community Based Mental Health (CMHI) program to fill critical gaps in mental health care, providing accessible and affordable community-based services to protect and promote mental health, offering support for those grappling with mental health conditions. The CMHI programme is being implemented in 3 districts in Bangladesh, 2 of them are remote and most climate vulnerable areas targeting total 6,797 individual. The intervention plan involves a screening of all participants using a 10-point vulnerability assessment tool to identify vulnerable individuals. The assumption underlying this is that individuals assessed as vulnerable is primarily due to biological, psychological, social and economic factors and they are at an increased risk of developing common mental health issues. Those identified as vulnerable with high risk and emergency conditions will receive Mental Health First Aid (MHFA) and undergo further screening with GHQ-12 to be identified as cases and non-cases. The identified cases are then referred to community lay counsellors with basic training and knowledge in providing 4-6 sessions on problem solving or behavior activation. In situations where no improvement occurs post lay counselling or for individuals with severe mental health conditions, a referral process will be initiated, directing individuals to ensure appropriate mental health care. In our presentation, it will present the findings from 6-month pilot implementation focusing on the community-based screening versus outcome of the lay counseling session and barriers and facilitators of implementing community based mental health care in a resource constraint country like Bangladesh.

Keywords: community-based mental health, lay counseling, rural bangladesh, treatment gap

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