Search results for: alignments

Authors: Nancy Retzlaff, Sarah J. Berkemer, Trudie Strauss

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In the last couple of decades, the advent of digitalization of any kind of data was probably one of the major advances in all fields of study. This paves the way for also analysing these data even though they might come from disciplines where there was no initial computational necessity to do so. Especially in linguistics, one can find a rather manual tradition. Still when considering studies that involve the history of language families it is hard to overlook the striking similarities to bioinformatics (phylogenetic) approaches. Alignments of words are such a fairly well studied example of an application of bioinformatics methods to historical linguistics. In this paper we will not only consider alignments of strings, i.e., words in this case, but also alignments of syntax trees of selected Indo-European languages. Based on initial, crude alignments, a sophisticated scoring model is trained on both letters and syntactic features. The aim is to gain a better understanding on which features in two languages are related, i.e., most likely to have the same root. Initially, all words in two languages are pre-aligned with a basic scoring model that primarily selects consonants and adjusts them before fitting in the vowels. Mixture models are subsequently used to filter ‘good’ alignments depending on the alignment length and the number of inserted gaps. Using these selected word alignments it is possible to perform tree alignments of the given syntax trees and consequently find sentences that correspond rather well to each other across languages. The syntax alignments are then filtered for meaningful scores—’good’ scores contain evolutionary information and are therefore used to train the sophisticated scoring model. Further iterations of alignments and training steps are performed until the scoring model saturates, i.e., barely changes anymore. A better evaluation of the trained scoring model and its function in containing evolutionary meaningful information will be given. An assessment of sentence alignment compared to possible phrase structure will also be provided. The method described here may have its flaws because of limited prior information. This, however, may offer a good starting point to study languages where only little prior knowledge is available and a detailed, unbiased study is needed.

Keywords: alignments, bioinformatics, comparative linguistics, historical linguistics, statistical methods

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Authors: Yassir Abdelrazig, Ren Moses

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Roadway planning and design is a very complex process involving five key phases before a project is completed; planning, project development, final design, right-of-way, and construction. The planning phase for a new roadway transportation project is a very critical phase as it greatly affects all latter phases of the project. A location study is usually performed during the preliminary planning phase in a new roadway project. The objective of the location study is to develop alignment alternatives that are cost efficient considering land acquisition and construction costs. This paper describes a methodology to develop optimal preliminary roadway alignments utilizing spatial-data. Four optimization criteria are taken into consideration; roadway length, land cost, land slope, and environmental impacts. The basic concept of the methodology is to convert the proposed project area into a grid, which represents the search space for an optimal alignment. The aforementioned optimization criteria are represented in each of the grid’s cells. A spatial-data optimization technique is utilized to find the optimal alignment in the search space based on the four optimization criteria. Two case studies for new roadway projects in Duval County in the State of Florida are presented to illustrate the methodology. The optimization output alignments are compared to the proposed Florida Department of Transportation (FDOT) alignments. The comparison is based on right-of-way costs for the alignments. For both case studies, the right-of-way costs for the developed optimal alignments were found to be significantly lower than the FDOT alignments.

Keywords: gemoetric design, optimization, planning, roadway planning, roadway design

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Authors: Busra Nur Ozguler Aktel

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This research aims to understand the factors that affect the ways in which tribes perceive and respond to violent conflicts in fragile states, given that tribes are essential stakeholders in many conflict-ridden fragile states, whether Afghanistan, Iraq, Syria, Libya, Somalia, Nigeria, or Yemen. It explores the primary questions of why some tribes align with extremist groups while others align with states during civil wars and why some tribes switch alignments. It argues that tribes form and switch alignments based on their perception of threats to their traditional tribal structure (internal dynamics) and clientelist relationships (external dynamics). Put differently; threat perceptions lead them to choose either the state or extremist groups that will more likely secure their traditional structure and patronage networks. This study focuses on Iraqi tribes as a case study. It builds a theory of tribal alignment formation based on ethnographic fieldwork in the Middle East, with a particular focus on Iraqi Sunni tribes living in the Kurdish region of Iraq and Jordan. As a result of the interviews with tribal leaders and members, local journalists, researchers, and politicians, it concludes that complex (re)alignments of tribes can determine the course and outcome of the conflicts, either mitigating or escalating violence. This study contributes to the larger body of conflict management and peacebuilding literature by introducing tribes as non-state actors and exploring their interactions with other actors in civil wars.

Keywords: civil wars, tribes, alignment formation, side-switching, Iraq

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Authors: Victor Prevost, Solene Landerneau, Michel Duhamel, Joel Sternheimer, Olivier Gallet, Pedro Ferrandiz, Marwa Mokni

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The search for homologous proteins is one of the ongoing challenges in biology and bioinformatics. Traditionally, a pair of proteins is thought to be homologous when they originate from the same ancestral protein. In such a case, their sequences share similarities, and advanced scientific research effort is spent to investigate this question. On this basis, we propose the Protein-Wave Alignment Tool (”P-WAT”) developed within the framework of the France Relance 2030 plan. Our work takes into consideration the mass-related wave aspect of protein biosynthesis, by associating specific frequencies to each amino acid according to its mass. Amino acids are then regrouped within their mass category. This way, our algorithm produces specific alignments in addition to those obtained with a common amino acid coding system. For this purpose, we develop the ”P-WAT” original algorithm, able to address large protein databases, with different attributes such as species, protein names, etc. that allow us to align user’s requests with a set of specific protein sequences. The primary intent of this algorithm is to achieve efficient alignments, in this specific conceptual frame, by minimizing execution costs and information loss. Our algorithm identifies sequence similarities by searching for matches of sub-sequences of different sizes, referred to as primers. Our algorithm relies on Boolean operations upon a dot plot matrix to identify primer amino acids common to both proteins which are likely to be part of a significant alignment of peptides. From those primers, dynamic programming-like traceback operations generate alignments and alignment scores based on an adjusted PAM250 matrix.

Keywords: protein, alignment, homologous, Genodic

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Authors: Naveed Chughtai, Salman Atif, Azhar Ali Taj, Murtaza Asghar Bukhari

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Accessible transport systems play a crucial role in infrastructure management and ease of access to destinations. Thus, the necessity of knowledge of service coverage and service deprived areas is a prerequisite for devising policies. Integration of PTALs model with GIS network analysis models (Service Area Analysis, Closest Facility Analysis) facilitates the analysis of deprived areas. In this research, models presented determine the accessibility. The empirical evidence suggests that current bus network system caters only 18.5% of whole population. Using network analysis results as inputs for PTALs, it is seen that excellent accessibility indexed bands cover a limited areas, while 78.8% of area is totally deprived of any service. To cater the unserved catchment, new route alignments are proposed while keeping in focus the Socio-economic characteristics, land-use type and net population density of the deprived area. Change in accessibility with proposed routes show a 10% increment in service delivery and enhancement in terms of served population is up to 20.4%. PTALs result shows a decrement of 60 Km2 in unserved band. The result of this study can be used for planning, transport infrastructure management, allocation of new route alignments in combination with future land-use development and for adequate spatial distribution of service access points.

Keywords: GIS, public transport accessibility, PTALs, accessibility index, service area analysis, closest facility analysis

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Authors: Lien Gysens, Bert Vanmechelen, Maarten Haspeslagh, Piet Maes, Ann Martens

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Bovine papillomavirus (BPV) types 1 and 2 play a central role in the etiology of the most common neoplasm in horses, the equine sarcoid. The unknown mechanism behind the unique variety in a clinical presentation on the one hand and the host-dependent clinical outcome of BPV-1 infection, on the other hand, indicate the involvement of additional factors. Earlier studies have reported the potential functional significance of intratypic sequence variants, along with the existence of sarcoid-sourced BPV variants. Therefore, intratypic sequence variation seems to be an important emerging viral factor. This study aimed to give a broad insight in sarcoid-sourced BPV variation and explore its potential association with disease presentation. In order to do this, a nanopore sequencing approach was successfully optimized for screening a wide spectrum of clinical samples. Specimens of each tumour were initially screened for BPV-1/-2 by quantitative real-time PCR. A custom-designed primer set was used on BPV-positive samples to amplify the complete viral genome in two multiplex PCR reactions, resulting in a set of overlapping amplicons. For phylogenetic analysis, separate alignments were made of all available complete genome sequences for BPV-1/-2. The resulting alignments were used to infer Bayesian phylogenetic trees. We found substantial genetic variation among sarcoid-derived BPV-1, although this variation could not be linked to disease severity. Several of the BPV-1 genomes had multiple major deletions. Remarkably, the majority of the cluster within the region coding for late viral genes. Together with the extensiveness (up to 603 nucleotides) of the described deletions, this suggests an altered function of L1/L2 in disease pathogenesis. By generating a significant amount of complete-length BPV genomes, we succeeded in introducing next-generation sequencing into veterinary research focusing on the equine sarcoid, thus facilitating the first report of both nanopore-based sequencing of complete sarcoid-sourced BPV-1/-2 and the simultaneous nanopore sequencing of multiple complete genomes originating from a single clinical sample.

Keywords: Bovine papillomavirus, equine sarcoid, horse, nanopore sequencing, phylogenetic analysis

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Authors: E. Al Daoud

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The purpose of computing the similarity and the diversity in the species is to trace the process of evolution and to find the relationship between the species and discover the unique, the special, the common and the universal proteins. The proteins of the whole genome of 40 species are compared with the cronobacter genome which is used as reference genome. More than 3 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 172 proteins in cronobacter genome which have insignificant hits in other species, 116 significant proteins in the all tested species with very high score value and 129 common proteins in the plants but have insignificant hits in mammals, birds, fishes, and insects.

Keywords: genome, species, blastp, conserved genes, Cronobacter

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Authors: Gaylord K. Booto, Marinelli Giuseppe, Helge Brattebø, Rolf A. Bohne

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Emissions reduction has emerged among the principal targets in the process of planning and designing road alignments today. Intelligent road design methods that can result in optimized alignment constitute concrete and innovative responses towards better alternatives and more sustainable road infrastructures. As the largest amount of emissions of road infrastructures occur in the operation stage, it becomes very important to consider traffic weight and distribution in alignment design process. This study analyzes the effects of four traffic factors (i.e. operating speed, vehicle category, technology and fuel type) on adjusting the vertical alignment of a given road, using optimization techniques. Further, factors’ effects are assessed qualitatively and quantitatively, and the emission profiles of resulting alignment alternatives are compared.

Keywords: alignment adjustment, emissions reduction, optimization, traffic-oriented

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Authors: Michiko Miyamoto

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This paper empirically investigates whether information technology (IT) strategies, business strategies, and divisions are aligned to meet overall business goals for Korean Small and medium-sized enterprises (SMEs), based on structure based Strategic Alignment Model, and make comparison with those of Japanese SMEs. Using 2,869 valid responses of Korean Human Capital Corporate Panel survey, a result of this study suggests that Korean human resources (HR) departments have a major influence over IT strategy, which is the same as Japanese SMEs, even though their management styles are quite different. As for IT strategy, it is not related to other departments at all for Korean SMEs. The Korean management seems to possess a great power over each division, such as Sales/Service, Research and Development/Technical Experts, HR, and Production.

Keywords: IT-business alignment, structured based strategic alignment model, structural equation model, human resources department

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Authors: Hyuk Sang Yoo, Young Ju Son, Wei Mao, Myung Gu Kang, Sol Lee

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Biomedical applications of electrospun nanofibrous meshes have been received tremendous attentions because of their unique structures and versatilities as biomaterials. Incorporation of growth factors in fibrous meshes can be performed by surface-modification and encapsulation. Those growth factors stimulate differentiation and proliferation of specific types of cells and thus lead tissue regenerations of specific cell types. Topographical cues of electrospun nanofibrous meshes also increase differentiation of specific cell types according to alignments of fibrous structures. Wound healing treatments of diabetic ulcers were performed using nanofibrous meshes encapsulating multiple growth factors. Aligned nanofibrous meshes and those with random configuration were compared for differentiating mesenchymal stem cells into neuronal cells. Thus, nanofibrous meshes can be applied to drug delivery carriers and matrix for promoting cellular proliferation.

Keywords: nanofiber, tissue, mesh, drug

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Authors: Hung Nguyen, Norma Harrison

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This paper examines the role supply chain dependence as contingency factors which affect the effectiveness of different critical factors (in terms trust, information exchange and shared culture) in delivering supply chain satisfaction and financial performance. Using the data of 468 manufacturing firms in the Global Manufacturing Research Group, this study shows that supply chain dependence strengthens the positive relationship between shared culture & vision and supply chain satisfaction while dampens the relationship between trust and satisfaction. The study also demonstrates the direct positive effect of satisfaction on financial performance. Supply chain managers were advised to emphasize on the alignments of common understanding, codes, languages, common shared vision and similar cultures.

Keywords: information exchange, shared culture, satisfaction, supply chain dependence

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Authors: Sawsan Eissa, Omnia Kabbany

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The coastline of Togo has been historically suffering from erosion for decades, which requires a solution to help control and reduce the erosion to allow for the development of the coastal area. A morpho-dynamic model using X-beach software was developed for the Western 14 Km of the Togolese coast. The model was coupled with the hydrodynamic module of DELFT 3D, flow, and the Wave module, SWAN. The data used as input included a recent bathymetric survey, a recent shoreline topographic survey, aerial photographs, ERA 5 water level and wave data, and recent test results of seabed samples. A number of scenarios were modeled: do nothing scenario, groynes, detached breakwaters system with different crest levels and alignments. The findings showed that groynes is not expected to be effective for protection against erosion, and that the best option is a system of detached breakwater, partially emerged-partially submerged couples with periodical maintenance.

Keywords: hydrodynamics, morphology, Togo, Delft3D, SWAN, XBeach, coastal erosion, detached breakwaters

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Authors: David Tresner-Kirsch

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Reconciling patient medication lists from multiple sources is a critical task supporting the safe delivery of patient care. Manual reconciliation is a time-consuming and error-prone process, and recently attempts have been made to develop efficiency- and safety-oriented automated support for professionals performing the task. An important capability of any such support system is automated alignment – finding which medications from a list correspond to which medications from a different source, regardless of misspellings, naming differences (e.g. brand name vs. generic), or changes in treatment (e.g. switching a patient from one antidepressant class to another). This work describes a new algorithmic solution to this alignment task, using a greedy matching approach based on string similarity, edit distances, concept extraction and normalization, and synonym search derived from the RxNorm nomenclature. The accuracy of this algorithm was evaluated against a gold-standard corpus of 681 medication records; this evaluation found that the algorithm predicted alignments with 99% precision and 91% recall. This performance is sufficient to support decision support applications for medication reconciliation.

Keywords: clinical decision support, medication reconciliation, natural language processing, RxNorm

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Authors: Alice Petzold, Alexandre Hassanin

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The number of giraffe species has been in focus of interest since the exploration of sub-Saharan Africa by European naturalists during the 18th and 19th centuries, as previous taxonomists, like Geoffroy Saint-Hilaire, Richard Owen or William Edward de Winton, recognized two or three species of Giraffa. For the last decades, giraffes were commonly considered as a single species subdivided into nine subspecies. In this study, we have re-examined available nuclear and mitochondrial data. Our genetic admixture analyses of seven introns support three species: G. camelopardalis (i.e., northern giraffes including reticulated giraffes), G. giraffa (southern giraffe) and G. tippelskirchi (Masai giraffe). However, the nuclear alignments show small variation and our phylogenetic analyses provide high support only for the monophyly of G. camelopardalis. Comparisons with the mitochondrial tree revealed a robust conflict for the position and monophyly of G. giraffa and G. tippelskirchi, which is explained firstly by a mitochondrial introgression from Masai giraffe to southeastern giraffe, and secondly, by gene flow mediated by male dispersal between southern populations (subspecies angolensis and giraffa). We conclude that current data gives only moderate support for three giraffe species and point out that additional nuclear data need to be studied to revise giraffe taxonomy.

Keywords: autosomal markers, Giraffidae, mitochondrial introgression, taxonomy

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Authors: Mehrnoosh Askarizadeh

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People, process and IT are the most important assets of any organization. Optimal utilization of these resources has been the question of research in business for many decades. The business world have responded by inventing various methodologies that can be used for addressing problems of quality improvement, efficiency of processes, continuous improvement, reduction of waste, automation, strategy alignments etc. Some of these methodologies can be commonly called as Business Process Quality Management methodologies (BPQM). In essence, the first references to the process management can be traced back to Frederick Taylor and scientific management. Time and motion study was addressed to improvement of manufacturing process efficiency. The ideas of scientific management were in use for quite a long period until more advanced quality management techniques were developed in Japan and USA. One of the first prominent methods had been Total Quality Management (TQM) which evolved during 1980’s. About the same time, Six Sigma (SS) originated at Motorola as a separate method. SS spread and evolved; and later joined with ideas of Lean manufacturing to form Lean Six Sigma. In 1990’s due to emerging IT technologies, beginning of globalization, and strengthening of competition, companies recognized the need for better process and quality management. Business Process Management (BPM) emerged as a novel methodology that has taken all this into account and helped to align IT technologies with business processes and quality management. In this article we will study various aspects of above mentioned methods and identified their relations.

Keywords: e-process, quality, TQM, BPM, lean, six sigma, CPI, information technology, management

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Authors: Osa D Egonwa

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In the 21^st century, the disciplinary boundaries of past centuries that we often create through mainstream art historical classification, techniques and sources may have been eroded by visual culture, which seems to provide a more inclusive umbrella for the new ways artists go about the creative process and its resultant commodities. Over the past four decades, artists in Africa have resorted to new materials, techniques and themes which have affected our ways of research on these artists and their art. Frontline artists such as El Anatsui, Yinka Shonibare, Erasmus Onyishi are demonstrating that any material is just suitable for artistic expression. Most of times, these materials come with their own techniques/effects and visual syntax: a combination of materials compounds techniques, formal aesthetic indexes, halo effects, and iconography. This tends to challenge the categories and we lean on to view, think and talk about them. This renders our main stream art historical research methods inadequate, thus suggesting new discursive concepts, terms and theories. This paper proposed the Africanist eclectic methods derived from the dual framework of Masquerade Theory and What Comes Behind Six is More Than Seven. This paper shares thoughts/research on art historical methods, terminological re-alignments on classification/source data, presentational format and interpretation arising from the emergent trends in our subject. The outcome provides useful tools to mediate new thoughts and experiences in recent African art and visual culture.

Keywords: art historical methods, classifications, concepts, re-alignment

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Authors: Anjana Goel, Ashok Kumar Bhatia

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Ocimum sanctum, a well known medicinal plant is used for various alignments in Ayurvedic medicines. It was found to be effective in treating the humans suffering from different viral infections like chicken pox, small pox, measles and influenza. In addition, curative effect of the plant in malignant patients was also reported. In the present study, leaves of this plant were screened against animal viruses i.e. Bovine Herpes Virus-type-1 (BHV-1), Foot and Mouth disease virus (FMDV) and Newcastle Disease Virus (NDV). BHV-1 and FMDV were screened in MDBK and BHK cell lines respectively using cytopathic inhibition test. While NDV was propagated in chick embryo fibroblast culture and tested by haemagglutination inhibition test. Maximum non toxic dose of aqueous extract of Ocimum sanctum leaves was calculated by MTT assay in all the cell cultures and nontoxic doses were used for antiviral activity against viruses. 98.4% and 85.3% protection were recorded against NDV and BHV-1 respectively. However, Ocimum sanctum extract failed to show any inhibitory effect on the cytopathic effect caused by FMD virus. It can be concluded that Ocimum sanctum is a very effective remedy for curing viral infections in animals also.

Keywords: bovine herpes virus-type-1, foot and mouth disease virus, newcastle disease virus, Ocimum sanctum

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Authors: Ashish Kumar, Munesh Raghuraj Varma, Nisarg Joshi, Gujjula Vishwa Teja, Srikanth Sambi, Arpit Awasthi

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Autonomous driving vehicles are revolutionizing the transportation system of the 21st century. This has been possible due to intensive research put into making a robust, reliable, and intelligent program that can perceive and understand its environment and make decisions based on the understanding. It is a very data-intensive task with data coming from multiple sensors and the amount of data directly reflects on the performance of the system. Researchers have to design the preprocessing pipeline for different datasets with different sensor orientations and alignments before the dataset can be fed to the model. This paper proposes a solution that provides a method to unify all the data from different sources into a uniform format using the intrinsic and extrinsic parameters of the sensor used to capture the data allowing the same pipeline to use data from multiple sources at a time. This also means easy adoption of new datasets or In-house generated datasets. The solution also automates the complete deep learning pipeline from preprocessing to post-processing for various tasks allowing researchers to design multiple custom end-to-end pipelines. Thus, the solution takes care of the input and output data handling, saving the time and effort spent on it and allowing more time for model improvement.

Keywords: augmentation, autonomous driving, camera, custom end-to-end pipeline, data unification, lidar, post-processing, preprocessing

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Authors: A. Elsayed, M. H. Dewaidar, M. Ghali

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We report on deposition of smooth, pinhole-free, low-surface roughness ( < 4nm) and high optical quality cadmium sulfide (CdS) thin films on glass substrates using our new method based on chemical surface deposition principle. In this method, cadmium acetate and thiourea are used as reactants under special growth conditions for deposition of CdS films. X-ray diffraction (XRD) measurements were used to examine the crystal structure properties of the deposited CdS films. In addition, UV-vis transmittance and low-temperature (4K) photoluminescence (PL) measurements were performed for quantifying optical properties of the deposited films. Interestingly, we found that XRD pattern of the deposited films has dramatically changed when the growth temperature was raised during the reaction. Namely, the XRD measurements reveal a structural change of CdS film from Cubic to Hexagonal phase upon increase in the growth temperature from 75 °C to 200 °C. Furthermore, the deposited films show high optical quality as confirmed from observation of both sharp edge in the transmittance spectra and strong PL intensity at room temperature. Also, we found a strong effect of the growth conditions on the optical band gap of the deposited films; where remarkable red-shift in the absorption edge with temperature is clearly seen in both transmission and PL spectra. Such tuning of both optical band gap and crystal structure of the deposited CdS films; can be utilized for tuning the electronic bands alignments between CdS and other light harvesting materials, like CuInGaSe or CdTe, for potential improvement in the efficiency of all-solution processed solar cells devices based on these heterostructures.

Keywords: thin film, CdS, new method, optical properties

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Authors: Sumeeta Khurana, Kirti Megha, Amit Gupta, Rakesh Sehgal

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Background: Amoebic keratitis is a painful vision threatening infection caused by a free living pathogenic amoeba Acanthamoeba. It can be misdiagnosed and very difficult to treat if not suspected early. The epidemiology of Acanthamoeba genotypes causing infection in our geographical area is not yet known to the best of our knowledge. Objective: To characterize Acanthamoeba isolates from amoebic keratitis patients. Methods: A total of 19 isolates obtained from patients with amoebic keratitis presenting to the Advanced Eye Centre at Postgraduate Institute of Medical Education and Research, a tertiary care centre of North India over a period of last 10 years were included. Their corneal scrapings, lens solution and lens case (in case of lens wearer) were collected for microscopic examination, culture and molecular diagnosis. All the isolates were maintained in the Non Nutrient agar culture medium overlaid with E.coli and 13 strains were axenised and maintained in modified Peptone Yeast Dextrose Agar. Identification of Acanthamoeba genotypes was based on amplification of diagnostic fragment 3 (DF3) region of the 18srRNA gene followed by sequencing. Nucleotide similarity search was performed by BLAST search of sequenced amplicons in GenBank database (http//www.ncbi.nlm.nih.gov/blast). Multiple Sequence alignments were determined by using CLUSTAL X. Results: Nine out of 19 Acanthamoeba isolates were found to belong to Genotype T4 followed by 6 isolates of genotype T11, 3 T5 and 1 T3 genotype. Conclusion: T4 is the predominant Acanthamoeba genotype in our geographical area. Further studies should focus on differences in pathogenicity of these genotypes and their clinical significance.

Keywords: Acanthamoeba, free living amoeba, keratitis, genotype, ocular

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Authors: M. Irfan Fareed, Muhammad Tahir, Alvina Gul Kazi

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Castor bean (Ricinus communis; family Euphorbiaceae) is cultivated for the production of oil and as an ornamental plant throughout tropical regions. Leaf samples from castor bean plants with leaf curl and vein thickening were collected from areas around Okara (Pakistan) in 2011. PCR amplification using diagnostic primers showed the presence of a begomovirus and subsequently the specific pair (BurNF 5’- CCATGGTTGTGGCAGTTGATTGACAGATAC-3’, BurNR 5’- CCATGGATTCACGCACAGGGGAACCC-3’) was used to amplify and clone the whole genome of the virus. The complete nucleotide sequence was determined to be 2,759 nt (accession No. HE985227). Alignments showed the highest levels of nucleotide sequence identity (98.8%) with Cotton leaf curl Burewala virus (CLCuBuV; accession No. JF416947) No. JF416947). The virus in castor beans lacks on intact C2 gene, as is typical of CLCuBuV in cotton. An amplification product of ca. 1.4 kb was obtained in PCR with primers for betasatellites and the complete nucleotide sequence of a clone was determined to be 1373 nt (HE985228). The sequence showed 96.3% nucleotide sequence identity to the recombinant Cotton leaf curl Multan betasatellite (CLCuMB; JF502389). This is the first report of CLCuBuV and its betasatellite infecting castor bean, showing this plant species as an alternate host of the virus. Already many alternate host have been reported from different alternate host like tobacco, tomato, hibiscus, okra, ageratum, Digera arvensis, habiscus, Papaya and now in Ricinus communis. So, it is suggested that these alternate hosts should be avoided to grow near cotton growing regions.

Keywords: Ricinus communis, begomovirus, betasatellite, agriculture

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Authors: D. Manai, J. Alvarez-Marron, M. Inoubli

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The southern Tunisian Atlas is a part of the wide Cenozoic intracontinental deformation that affected North Africa as a result of convergence between African and Eurasian plates. The Southern Tunisian Atlas Front (STAF) corresponds to the chotts area that covers several hundreds of Km² and represents a 60 km wide transition between the deformed Tunisian Atlas to the North and the undeformed Saharan platform to the South. It includes three morphostructural alignments, a fold and thrust range in the North, a wide depression in the middle and a monocline to horizontal zone to the south. Four cross-sections have been constructed across the chotts area to illustrate the structure of the Southern Tunisian Atlas Front based on integrated geological and geophysical data including geological maps, petroleum wells, and seismic data. The fold and thrust zone of the northern chotts is interpreted as related to a detachment level near the Triassic-Jurassic contact. The displacement of the basal thrust seems to die out progressively under the Fejej antiform and it is responsible to the south dipping of the southern chotts range. The restoration of the cross-sections indicates that the Southern Tunisian Atlas front is a weakly deformed wide zone developed during the Cenozoic inversion with a maximum calculated shortening in the order of 1000 m. The wide structure of this STAF has been influenced by a pre-existing large thickness of upper Jurassic-Aptian sediments related to the rifting episodes associated to the evolution of Tethys in the Maghreb. During Jurassic to Aptian period, the chotts area corresponded to a highly subsiding basin.

Keywords: Southern Tunisian Atlas Front, subsident sub- basin, wide deformation, balanced cross-sections.

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Authors: Shashank. S. Bagane, H. N. Rajendra Prasad

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Building Information Modeling (BIM) has currently developed into a potent solution. The consistent development of BIM technology in the sphere of Architecture, Engineering, and Construction (AEC) industry has enhanced the effectiveness of construction and decision making. However, aggrandized global warming and energy crisis has impacted on building energy analysis. It is now becoming an important factor to be considered in the AEC industry. Amalgamating energy analysis in the planning and design phase of a structure has become a necessity. In the current construction industry, estimating energy usage and reducing its footprint is of high priority. The construction industry is giving more prominence to sustainability alongside energy efficiency. This demand is compelling the designers, planners, and engineers to inspect the sustainable performance throughout the building's life cycle. The current study primarily focuses on energy consumption, space arrangement, and spatial geometry of a residential building. Most commonly residential structures in India are constructed considering Vastu Shastra. Vastu designs are intended to integrate architecture with nature and utilizing geometric patterns, symmetry, and directional alignments. In the current study, a residential brick masonry structure is considered for BIM analysis, Architectural model of the structure will be created using Revit software, later the orientation and spatial arrangement will be finalized based on Vastu principles. Furthermore, the structure will be investigated for the impact of building orientation and spatial arrangements on energy using Green Building Studio software. Based on the BIM analysis of the structure, energy consumption of subsequent building orientations will be understood. A well-orientated building having good spatial arrangement can save a considerable amount of energy throughout its life cycle and reduces the need for heating and lighting which will prove to diminish energy usage and improve the energy efficiency of the residential building.

Keywords: building information modeling, energy impact, spatial geometry, vastu

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Authors: Anahita Dalmia

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There has been a recent rise in ‘audience-centric’ and immersive storytelling. This indicates audiences are gaining interest in experiencing real adventure with everything that encompasses the struggle, the new friendships, skill development, and growth. This paper examines two themed alternate reality games created by a group of students at the University of Southern California as an experiment in how to design an adventure and to evaluate its impact on participants. The experiences combined immersive improvisational theatre and live-action roleplaying to create socially aware experiences within the timespan of four hours, using Harry Potter and mythology as themes. In each experiment, over 500 players simultaneously embarked on quests -a series of challenges including puzzle-solving, scavenger-hunting, and character interactions- to join a narrative faction. While playing, the participants were asked to choose faction alignments based on the characters they interacted with, as well as their own backgrounds and moral values. During the narrative finale, the impact of their individual choices on the larger story and game were revealed. After the conclusion of each experience, participants filled out questionnaires and were interviewed. Through this, it was discovered that participants developed transferable problem-solving, team-work, and persuasion skills. They also learned about the theme of the experience and reflected on their own moral values and judgment-making abilities after they realized the consequences of their actions in the game-world, inspiring some participants to make changes outside of it. This reveals that alternative reality games can lead to socialization, educational development, and real-world change in a variety of contexts when implemented correctly. This experiment has begun to discover the value of alternate reality games in a real-world context and to develop a reproducible format to continue to create such an impact.

Keywords: adventure, alternate reality games, education, immersive entertainment, interactive entertainment

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Authors: A. Elsayed, M. H. Dewaidar, M. Ghali, M. Elkemary

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The high production cost of the conventional solar cells requires the search for economic methods suitable for solar energy conversion. Cadmium Sulfide (CdS) is one of the most important semiconductors used in photovoltaics, especially in large area solar cells; and can be prepared in a thin film form by a wide variety of deposition techniques. The preparation techniques include vacuum evaporation, sputtering and molecular beam epitaxy. Other techniques, based on chemical solutions, are also used for depositing CdS films with dramatically low-cost compared to other vacuum-based methods. Although this technique is widely used during the last decades, due to simplicity and low-deposition temperature (~100°C), there is still a strong need for more information on the growth process and its relation with the quality of the deposited films. Here, we report on deposition of high-quality CdS thin films; with low-surface roughness ( < 3.0 nm) and sharp optical absorption edge; on low-temperature glass substrates (70°C) using a new method based on the room-temperature chemical solution. In this method, a mixture solution of cadmium acetate and thiourea at room temperature was used under special growth conditions for deposition of CdS films. X-ray diffraction (XRD) measurements were used to examine the crystal structure properties of the deposited CdS films. In addition, UV-VIS transmittance and low-temperature (4K) photoluminescence (PL) measurements were performed for quantifying optical properties of the deposited films. The deposited films show high optical quality as confirmed by observation of both, sharp edge in the transmittance spectra and strong PL intensity at room temperature. Furthermore, we found a strong effect of the growth conditions on the optical band gap of the deposited films; where remarkable red-shift in the absorption edge with temperature is clearly seen in both transmission and PL spectra. Such tuning of both optical band gap of the deposited CdS films can be utilized for tuning the electronic bands' alignments between CdS and other light-harvesting materials, like CuInGaSe or CdTe, for potential improvement in the efficiency of solar cells devices based on these heterostructures.

Keywords: chemical deposition, CdS, optical properties, surface, thin film

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Authors: Amrita Sen

Abstract:

In the face of a growing insurgent movement and the perceived failure of the state and the market towards sustainable resource management, a range of decentralized forest management policies was formulated in the last two decades, which recognized the need for community representations within the statutory methods of forest management. The recognition conceded on the virtues of ecological sustainability and traditional environmental knowledge, which were considered to be the principal repositories of the forest dependent communities. The present study, in the light of empirical insights, reflects on the contemporary disjunctions between the preconceived communitarian ethic in environmentalism and the lived reality of forest based life-worlds. Many of the popular as well as dominant ideologies, which have historically shaped the conceptual and theoretical understanding of sociology, needs further perusal in the context of the emerging contours of empirical knowledge, which lends opportunities for substantive reworking and analysis. The image of the community appears to be one of those concepts, an identity which has for long defined perspectives and processes associated with people living together harmoniously in small physical spaces. Through an ethnographic account of the implementation of Joint Forest Management (JFM) in a forest fringe village in Sundarban, the study explores the ways in which the idea of ‘community’ gets transformed through the process of state-making, rendering the necessity of its departure from the standard, conventional definition of homogeneity and internal equity. The study necessitates an attention towards the anthropology of micro-politics, disaggregating an essentially constructivist anthropology of ‘collective identities’, which can render the visibility of political mobilizations plausible within the seemingly culturalist production of communities. The two critical questions that the paper seeks to ask in this context are: how the ‘local’ is constituted within community based conservation practices? Within the efforts of collaborative forest management, how accurately does the depiction of ‘indigenous environmental knowledge’, subscribe to its role of sustainable conservation practices? Reflecting on the execution of JFM in Sundarban, the study critically explores the ways in which the state ceases to be ‘trans-national’ and interacts with the rural life-worlds through its local factions. Simultaneously, the study attempts to articulate the scope of constructing a competing representation of community, shaped by increasing political negotiations and bureaucratic alignments which strains against the usual preoccupations with tradition primordiality and non material culture as well as the amorous construction of indigeneity.

Keywords: community, environmentalism, JFM, state-making, identities, indigenous

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Authors: Leonard Lipovich, Pattaraporn Thepsuwan, Anton-Scott Goustin, Juan Cai, Donghong Ju, James B. Brown

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Two-thirds of human genes do not encode any known proteins. Aside from long non-coding RNA (lncRNA) genes with recently-discovered functions, the ~40,000 non-protein-coding human genes remain poorly understood, and a role for their transcripts as de-facto unconventional messenger RNAs has not been formally excluded. Ribosome profiling (Riboseq) predicts translational potential, but without independent evidence of proteins from lncRNA open reading frames (ORFs), ribosome binding of lncRNAs does not prove translation. Previously, we mass-spectrometrically documented translation of specific lncRNAs in human K562 and GM12878 cells. We now examined lncRNA translation in human MCF7 cells, integrating strand-specific Illumina RNAseq, Riboseq, and deep mass spectrometry in biological quadruplicates performed at two core facilities (BGI, China; City of Hope, USA). We excluded known-protein matches. UCSC Genome Browser-assisted manual annotation of imperfect (tryptic-digest-peptides)-to-(lncRNA-three-frame-translations) alignments revealed three peptides hypothetically explicable by 'stop-to-nonstop' in-frame replacement of stop codons by amino acids in two ORFs of the lncRNA MMP24-AS1. To search for this phenomenon genomewide, we designed and implemented a novel pipeline, matching tryptic-digest spectra to wildcard-instead-of-stop versions of repeat-masked, six-frame, whole-genome translations. Along with singleton putative stop-to-nonstop events affecting four other lncRNAs, we identified 24 additional peptides with stop-to-nonstop in-frame substitutions from multiple positive-strand MMP24-AS1 ORFs. Only UAG and UGA, never UAA, stop codons were impacted. All MMP24-AS1-matching spectra met the same significance thresholds as high-confidence known-protein signatures. Targeted resequencing of MMP24-AS1 genomic DNA and cDNA from the same samples did not reveal any mutations, polymorphisms, or sequencing-detectable RNA editing. This unprecedented apparent gene-specific violation of the genetic code highlights the importance of matching peptides to whole-genome, not known-genes-only, ORFs in mass-spectrometry workflows, and suggests a new mechanism enhancing the combinatorial complexity of the proteome. Funding: NIH Director’s New Innovator Award 1DP2-CA196375 to LL.

Keywords: genetic code, lncRNA, long non-coding RNA, mass spectrometry, proteogenomics, ribo-seq, ribosome, RNAseq

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Authors: N. Manjunatha, K. T. Rangswamy, N. Nagaraju, H. A. Prameela, P. Rudraswamy, M. Krishnareddy

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The identification of virus in cowpea especially potyviruses is confusing. Even though there are several studies on viruses causing diseases in cowpea, difficult to distinguish based on symptoms and serological detection. The differentiation of potyviruses considering as a constraint, the present study is initiated for molecular characterization, host plant resistance and epidemiology of the BCMV infecting cowpea. The etiological agent causing cowpea mosaic was identified as Bean Common Mosaic Virus (BCMV) on the basis of RT-PCR and electron microscopy. An approximately 750bp PCR product corresponding to coat protein (CP) region of the virus and the presence of long flexuous filamentous particles measuring about 952 nm in size typical to genus potyvirus were observed under electron microscope. The characterized virus isolate genome had 10054 nucleotides, excluding the 3’ terminal poly (A) tail. Comparison of polyprotein of the virus with other potyviruses showed similar genome organization with 9 cleavage sites resulted in 10 functional proteins. The pairwise sequence comparison of individual genes, P1 showed most divergent, but CP gene was less divergent at nucleotide and amino acid level. A phylogenetic tree constructed based on multiple sequence alignments of the polyprotein nucleotide and amino acid sequences of cowpea BCMV and potyviruses showed virus is closely related to BCMV-HB. Whereas, Soybean variant of china (KJ807806) and NL1 isolate (AY112735) showed 93.8 % (5’UTR) and 94.9 % (3’UTR) homology respectively with other BCMV isolates. This virus transmitted to different leguminous plant species and produced systemic symptoms under greenhouse conditions. Out of 100 cowpea genotypes screened, three genotypes viz., IC 8966, V 5 and IC 202806 showed immune reaction in both field and greenhouse conditions. Single marker analysis (SMA) was revealed out of 4 SSR markers linked to BCMV resistance, M135 marker explains 28.2 % of phenotypic variation (R2) and Polymorphic information content (PIC) value of these markers was ranged from 0.23 to 0.37. The correlation and regression analysis showed rainfall, and minimum temperature had significant negative impact and strong relationship with aphid population, whereas weak correlation was observed with disease incidence. Path coefficient analysis revealed most of the weather parameters exerted their indirect contributions to the aphid population and disease incidence except minimum temperature. This study helps to identify specific gaps in knowledge for researchers who may wish to further analyse the science behind complex interactions between vector-virus and host in relation to the environment. The resistant genotypes identified are could be effectively used in resistance breeding programme.

Keywords: cowpea, epidemiology, genotypes, virus

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Authors: Jonas De Kerf, Rein De Cooman, Sara De Gieter

Abstract:

For many decades, scholars have aimed to understand how work can become more meaningful by maximizing both potential and enhancing feelings of satisfaction. One of the largest contributions towards such positive psychology was made with the introduction of the concept of ‘flow,’ which refers to a condition in which people feel intense engagement and effortless action. Since then, valuable research on work-related flow has indicated that this state of mind is related to positive outcomes for both organizations (e.g., social, supportive climates) and workers (e.g., job satisfaction). Yet, scholars still do not fully comprehend how such deep involvement at work is obtained, given the notion that flow is considered a short-term, complex, and dynamic experience. Most research neglects that people who experience flow ought to be optimally challenged so that intense concentration is required. Because attention is at the core of this enjoyable state of mind, this study aims to comprehend how elements that affect workers’ cognitive functioning impact flow at work. Research on cognitive performance suggests that working on mentally demanding tasks (e.g., information processing tasks) requires workers to concentrate deeply, as a result leading to flow experiences. Based on social facilitation theory, working on such tasks in an isolated environment eases concentration. Prior research has indicated that working at home (instead of working at the office) or in a closed office (rather than in an open-plan office) impacts employees’ overall functioning in terms of concentration and productivity. Consequently, we advance such knowledge and propose an interaction by combining cognitive task characteristics and work environments among part-time teleworkers. Hence, we not only aim to shed light on the relation between cognitive tasks and flow but also provide empirical evidence that workers performing such tasks achieve the highest states of flow while working either at home or in closed offices. In July 2022, an experience-sampling study will be conducted that uses a semi-random signal schedule to understand how task and environment predictors together impact part-time teleworkers’ flow. More precisely, about 150 knowledge workers will fill in multiple surveys a day for two consecutive workweeks to report their flow experiences, cognitive tasks, and work environments. Preliminary results from a pilot study indicate that on a between level, tasks high in information processing go along with high self-reported fluent productivity (i.e., making progress). As expected, evidence was found for higher fluency in productivity for workers performing information processing tasks both at home and in a closed office, compared to those performing the same tasks at the office or in open-plan offices. This study expands the current knowledge on work-related flow by looking at a task and environmental predictors that enable workers to obtain such a peak state. While doing so, our findings suggest that practitioners should strive for ideal alignments between tasks and work locations to work with both deep involvement and gratification.

Keywords: cognitive work, office lay-out, work location, work-related flow

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Authors: Chunyang Miao, Bingxin Li, Shanglong Ning, Christopher J. B. Ford

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While it is challenging to fabricate electronic devices close to atomic dimensions in conventional top-down lithography, molecular electronics is promising to help maintain the exponential increase in component densities via using molecular building blocks to fabricate electronic components from the bottom up. It offers smaller, faster, and more energy-efficient electronic and photonic systems. A self-assembled monolayer (SAM) of molecules is a layer of molecules that self-assembles on a substrate. They are mechanically flexible, optically transparent, low-cost, and easy to fabricate. A large-area multi-layer structure has been designed and investigated by the team, where a SAM of designed molecules is sandwiched between graphene and gold electrodes. Each molecule can act as a quantum dot, with all molecules conducting in parallel. When a source-drain bias is applied, significant current flows only if a molecular orbital (HOMO or LUMO) lies within the source-drain energy window. If electrons tunnel sequentially on and off the molecule, the charge on the molecule is well-defined and the finite charging energy causes Coulomb blockade of transport until the molecular orbital comes within the energy window. This produces ‘Coulomb diamonds’ in the conductance vs source-drain and gate voltages. For different tunnel barriers at either end of the molecule, it is harder for electrons to tunnel out of the dot than in (or vice versa), resulting in the accumulation of two or more charges and a ‘Coulomb staircase’ in the current vs voltage. This nanostructure exhibits highly reproducible Coulomb-staircase patterns, together with additional oscillations, which are believed to be attributed to molecular vibrations. Molecules are more isolated than semiconductor dots, and so have a discrete phonon spectrum. When tunnelling into or out of a molecule, one or more vibronic states can be excited in the molecule, providing additional transport channels and resulting in additional peaks in the conductance. For useful molecular electronic devices, achieving the optimum orbital alignment of molecules to the Fermi energy in the leads is essential. To explore it, a drop of ionic liquid is employed on top of the graphene to establish an electric field at the graphene, which screens poorly, gating the molecules underneath. Results for various molecules with different alignments of Fermi energy to HOMO have shown highly reproducible Coulomb-diamond patterns, which agree reasonably with DFT calculations. In summary, this large-area SAM molecular junction is a promising candidate for future electronic circuits. (1) The small size (1-10nm) of the molecules and good flexibility of the SAM lead to the scalable assembly of ultra-high densities of functional molecules, with advantages in cost, efficiency, and power dissipation. (2) The contacting technique using graphene enables mass fabrication. (3) Its well-observed Coulomb blockade behaviour, narrow molecular resonances, and well-resolved vibronic states offer good tuneability for various functionalities, such as switches, thermoelectric generators, and memristors, etc.

Keywords: molecular electronics, Coulomb blokade, electron-phonon coupling, self-assembled monolayer

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