Search results for: gene identification

Authors: Recep Kesli, Gulsah Asik, Cengiz Demir, Onur Turkyilmaz

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Objective: Stenotrophomonas maltophilia (S. maltophilia) has recently emerged as an important nosocomial microorganism. Treatment of invasive infections caused by this organism is problematic because this microorganism is usually resistant to a wide range of commonly used antimicrobials. We aimed to evaluate clinical isolates of S. maltophilia in respect to sampling sites and antimicrobial resistant. Method: During a two years period (October 2013 and September 2015) eighteen samples collected from the intensive care unit (ICU) patients hospitalized in Afyon Kocatepe University, ANS Practice and Research Hospital. Identification of the bacteria was determined by conventional methods and automated identification system-VITEK 2 (bio-Mérieux, Marcy l’toile, France). Antibacterial resistance tests were performed by Kirby Bauer disc (Oxoid, England) diffusion method following the recommendations of CLSI. Results: Eighteen S. maltophilia strains were identified as the causative agents of different infections. The main type of infection was lower respiratory tract infection (83,4 %); three patients (16,6 %) had bloodstream infection. While, none of the 18 S. maltophilia strains were found to be resistant against to trimethoprim sulfametaxasole (TMP-SXT) and levofloxacine, eight strains 66.6 % were found to be resistant against ceftazidim. Conclusion: The isolation of S.maltophilia starains resistant to TMP-SXT is vital. In order to prevent or minimize infections due to S. maltophilia such precuations should be utilized: Avoidance of inappropriate antibiotic use, prolonged implementation of foreign devices, reinforcement of hand hygiene practices and the application of appropriate infection control practices. Microbiology laboratories also may play important roles in controlling S. maltophilia infections by monitoring the prevalence, continuously, the provision of local antibiotic resistance paterns data and the performance of synergistic studies also may help to guide appropirate antimicrobial therapy choices.

Keywords: Stenotrophomonas maltophilia, trimethoprim-sulfamethoxazole, antimicrobial resistance, Stenotrophomonas spp.

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Authors: Shwadhin Sharma, Monica Perez, Vinita Patel, Tyler Kuwatani, Siobhan Scott

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The purpose of this research is to explain and analyze why the Internet of Things (IoT) is an emerging technology trend. The aspects of this research paper include an overview of IoT, what research has already been done, the benefits, implications, and our own perspectives on the trend in order to thoroughly analyze how the trend of IoT will make an impact on society. Through the identification of what makes IoT important, it is concluded that IoT will have a tremendous impact for the whole world. Technology is never going to go away, it is going to get smarter and have the potential to change the world.

Keywords: internet of things, enablers of IoT, cost of IoT, benefits of IoT

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Authors: Jyoti Bharti, Navneet Manjhi, M. K.Gupta, Bimi Jain

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A reliable gait features are required to extract the gait sequences from an images. In this paper suggested a simple method for gait identification which is based on moments. Moment values are extracted on different number of frames of gray scale and silhouette images of CASIA database. These moment values are considered as feature values. Fuzzy logic and nearest neighbour classifier are used for classification. Both achieved higher recognition.

Keywords: gait, fuzzy logic, nearest neighbour, recognition rate, moments

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Authors: Yili Liu, Honghao Ren, Mariko Kondo

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In the field of second language (L2) speech learning, it is well-known that that learner’s first language (L1) phonetic and phonological characteristics will be transferred into their L2 production and perception, which lead to foreign accent. For L1 Mandarin learners of Japanese, the confusion of /u/ and /o/ in /CjV/ sequences has been observed in their utterance frequently. L1 transfer is considered to be the cause of this issue, however, other factors which influence the identification of /Cju/ and /Cjo/ sequences still under investigation. This study investigates the perception of Japanese /Cju/ and /Cjo/ units by L1 Mandarin learners of Japanese. It further examined whether learners’ proficiency, syllable position, phonetic features of preceding consonants and background noise affect learners’ performance in perception. Fifty-two Mandarin-speaking learners of Japanese and nine native Japanese speakers were recruited to participate in an identification task. Learners were divided into beginner, intermediate and advanced level according to their Japanese proficiency. The average correct rate was used to evaluate learners’ perceptual performance. Furthermore, the comparison of the correct rate between learners’ groups and the control group was conducted as well to examine learners’ nativelikeness. Results showed that background noise tends to pose an adverse effect on distinguishing /u/ and /o/ in /CjV/ sequences. Secondly, Japanese proficiency has no influence on learners’ perceptual performance in the quiet and in background noise. Then all learners did not reach a native-like level without the distraction of noise. Beginner level learners performed less native-like, although higher level learners appeared to have achieved nativelikeness in the multi-talker babble noise. Finally, syllable position tends to affect distinguishing /Cju/ and /Cjo/ only under the noisy condition. Phonetic features of preceding consonants did not impact learners’ perception in any listening conditions. Findings in this study can give an insight into a further understanding of Japanese vowel acquisition by L1 Mandarin learners of Japanese. In addition, this study indicates that L1 transfer is not the only explanation for the confusion of /u/ and /o/ in /CjV/ sequences, factors such as listening condition and syllable position are also needed to take into consideration in future research. It also suggests the importance of perceiving speech in a noisy environment, which is close to the actual conversation required more attention to pedagogy.

Keywords: background noise, Chinese learners of Japanese, /Cju/ and /Cjo/ sequences, second language perception

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Authors: Fengmei Li, Li Xu, Guoliang Xia

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Lysozyme is a catalytic enzyme that performs bacterial cell lysis by cleaving the β-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine of peptidoglycan in cell walls. In the present study, an invertebrate-type (i-type) lysozyme gene was cloned from Chinese mitten crab Eriocheir sinensis (designated as EsLysozyme) based on PCR-based rapid amplification of cDNA ends (RACE) technology. The full-length cDNA of EsLysozyme was of 831 bp. SMART and SIGNALP 3.0 program analysis revealed that EsLysozyme contained a signal peptide and a destabilase domain. The five amino acid residues (Tyr63, Trp64, Tyr91, His110, Pro114) and the conserved motif GSLSCG(P/Y)FQI and CL(E/L/R/H)C(I/M)C in i-type lysozymes were also found in EsLysozyme. The high similarity of EsLysozyme with L. vannamei lysozymes and phylogenetic analysis suggested that EsLysozyme should be a new member of i-type lysozyme family.

Keywords: i-type lysozyme, Eriocheir sinensis, cloning, characterization

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Authors: A. Berraf-Tebbal, Z. Bouznad, , A.J.L. Phillips

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Phaeomoniella is a fungus genus in the mitosporic ascomycota which includes Phaeomoniella chlamydospora specie associated with two declining diseases on grapevine (Vitis vinifera) namely Petri disease and esca. Recent studies have shown that several Phaeomoniella species also cause disease on many other woody crops, such as forest trees and woody ornamentals. Two new species, Phaeomoniella zymoides and Phaeomoniella pinifoliorum H.B. Lee, J.Y. Park, R.C. Summerbell et H.S. Jung, were isolated from the needle surface of Pinus densiflora Sieb. et Zucc. in Korea. The identification of species in Phaeomoniella genus can be a difficult task if based solely on morphological and cultural characters. In this respect, the application of molecular methods, particularly PCR-based techniques, may provide an important contribution. MSP-PCR (microsatellite primed-PCR) fingerprinting has proven useful in the molecular typing of fungal strains. The high discriminatory potential of this method is particularly useful when dealing with closely related or cryptic species. In the present study, the application of PCR fingerprinting was performed using the micro satellite primer M13 for the purpose of species identification and strain typing of 84 Phaeomoniella -like isolates collected from grapevines with typical symptoms of dieback. The bands produced by MSP-PCR profiles divided the strains into 3 clusters and 5 singletons with a reproducibility level of 80%. Representative isolates from each group and, when possible, isolates from Eutypa dieback and esca symptoms were selected for sequencing of the ITS region. The ITS sequences for the 16 isolates selected from the MSP-PCR profiles were combined and aligned with sequences of 18 isolates retrieved from GenBank, representing a selection of all known Phaeomoniella species. DNA sequences were compared with those available in GenBank using Neighbor-joining (NJ) and Maximum-parsimony (MP) analyses. The phylogenetic trees of the ITS region revealed that the Phaeomoniella isolates clustered with Phaeomoniella chlamydospora reference sequences with a bootstrap support of 100 %. The complexity of the pathosystems vine-trunk diseases shows clearly the need to identify unambiguously the fungal component in order to allow a better understanding of the etiology of these diseases and justify the establishment of control strategies against these fungal agents.

Keywords: Genotyping, MSP-PCR, ITS, phylogeny, trunk diseases

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Authors: Djebbar Atmani, Aghiles Karim Aissat, Nadjet Debbache-Benaida, Nassima Chaher-Bazizi, Dina Atmani-Kilani, Meriem Rahmani-Berboucha, Naima Saidene, Malika Benloukil, Lila Azib

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Medicinal plants are believed to be an important source for the discovery of potential antioxidant, anti-inflammatory and anti-diabetic substances. The present study was designed to investigate the neuroprotective, anti-inflammatory, anti-diabetic and anti-hyperuricemic potential of Pistacia lentiscus, as well as the identification of active compounds. The antioxidant potential of plant extracts against known radicals was measured using various standard in vitro methods. Anti-inflammatory activity was determined using the paw edema model in mice and by measuring the secretion of the pro-inflammatory cytokine, whereas the anti-diabetic effect was assessed in vivo on streptozotocin-induced diabetic rats and in vitro by inhibition of alpha-amylase. The anti-hyperuricemic activity was evaluated using the xanthine oxidase assay, whereas neuroprotective activity was investigated using an Aluminum-induced toxicity test. Pistacia lentiscus extracts and fractions exhibited high scavenging capacity against DPPH, NO. and ABTS+ radicals in a dose-dependent manner and restored blood glucose levels, in vivo, to normal values, in agreement with the in vitro anti-diabetic effect. Oral administration of plant extracts significantly decreased carrageenan-induced mice paw oedema, similar to the standard drug, diclofenac, was effective in reducing IL-1β levels in cell culture and induced a significant increase in urinary volume in mice, associated to a promising anti-hyperuricemic activity. Plant extracts showed good neuroprotection and restoration of cognitive functions in mice. HPLC-MS and NMR analyses allowed the identification of known and new phenolic compounds that could be responsible for the observed activities. Therefore, Pistacia lentiscus could be beneficial in the treatment of inflammatory conditions and diabetes complications and the enhancement of cognitive functions.

Keywords: Pistacia lentiscus, anti-inflammatory, antidiabetic, flavanols, neuroprotective

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Authors: Yousuf M. Al Suleimani, Robin Hiley

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The endogenous phospholipid lysophosphatidylinositol (LPI) was recently identified as a novel ligand for the G protein-coupled receptor 55 (GPR55) and an inducer of intracellular Ca2+ [Ca2+]i release. This study attempts to characterize Ca2+ signals provoked by LPI in HEK293 cells engineered to stably express human GPR55 and to test cannabinoid ligand activity at GPR55. The study shows that treatment with LPI stimulates a sustained, oscillatory Ca2+ release. The response is characterized by an initial rapid rise, which is mediated by the Gαq-PLC-IP3 pathway, and this is followed by prolonged oscillations that require RhoA activation. Ca2+ oscillations are initiated by intracellular mechanisms and extracellular Ca2+ is only required to replenish Ca2+ lost from the cytoplasm. Analysis of cannabinoid ligand activity at GPR55 revealed no clear effect of the endocannabinoid anandamide, however, rimonabant and the CB1 receptor antagonist AM251 evoked GPR55-mediated [Ca2+]i. Thus, LPI is likely to be a key plasma membrane mediator of signaling events and changes in gene expression through GPR55 activation.

Keywords: lysophosphatidylinositol, calcium, GPR55, cannabinoid

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Authors: Anuj Tyagi, Balwinder Singh, Naveen Kumar B. T., Niraj K. Singh

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Characterization of diverse microbial communities in specific environment plays a crucial role in the better understanding of their functional relationship with the ecosystem. It is now well established that gut microbiome of fish is not the simple replication of microbiota of surrounding local habitat, and extensive species, dietary, physiological and metabolic variations in fishes may have a significant impact on its composition. Moreover, overuse of antibiotics in human, veterinary and aquaculture medicine has led to rapid emergence and propagation of antibiotic resistance genes (ARGs) in the aquatic environment. Microbial communities harboring specific ARGs not only get a preferential edge during selective antibiotic exposure but also possess the significant risk of ARGs transfer to other non-resistance bacteria within the confined environments. This phenomenon may lead to the emergence of habitat-specific microbial resistomes and subsequent emergence of virulent antibiotic-resistant pathogens with severe fish and consumer health consequences. In this study, gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. Metagenomic DNA, extracted from the fish gut, was subjected to sequencing on Illumina NextSeq to generate paired-end (PE) 2 x 150 bp sequencing reads. After the QC of raw sequencing data by Trimmomatic, taxonomic analysis by Kraken2 taxonomic sequence classification system revealed the presence of 36 phyla, 326 families and 985 genera in the fish gut microbiome. At phylum level, Proteobacteria accounted for more than three-fourths of total bacterial populations followed by Actinobacteria (14%) and Cyanobacteria (3%). Commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) were found to be very less prevalent in fish gut. After sequencing data assembly by MEGAHIT v1.1.2 assembler and PROKKA automated analysis pipeline, pathway analysis revealed the presence of 1,608 Metacyc pathways in the fish gut microbiome. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy-metabolism (4%) and fermentation (2%). Almost one-third (33%) of biosynthesis pathways were involved in the synthesis of secondary metabolites. Metabolic pathways for the biosynthesis of 35 antibiotic types were also present, and these accounted for 5% of overall metabolic pathways in the fish gut microbiome. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. More than 90% ARGs in fish gut microbiome were against beta-lactams (penicillins, cephalosporins, penems, and monobactams). Resistance against tetracycline, macrolides, fluoroquinolones, and phenicols ranged from 0.7% to 1.3%. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment.

Keywords: antibiotic resistance, fish gut, metabolic pathways, microbial diversity

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Authors: Hyppolite Aignon, Souleymane Yorou, Martin Ryberg, Anneli Svanholm

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Climate change and human actions cause the extinction of wild mushrooms. In Benin, the diversity of fungi is large and may still contain species new to science but the inventory effort remains low and focuses on particularly edible species (Russula, Lactarius, Lactifluus, and also Amanita). In addition, inventories have started recently and some groups of fungi are not sufficiently sampled, however, the degradation of fungal habitat continues to increase and some species are already disappearing. (Yorou and De Kesel, 2011), however, the degradation of fungi habitat continues to increase and some species may disappear without being known. This genus (Inocybe) overlooked has a worldwide distribution and includes more than 700 species with many undiscovered or poorly known species worldwide and particularly in tropical Africa. It is therefore important to orient the inventory to other genera or important families such as Inocybe (Fungi, Agaricales) in order to highlight their diversity and also to know their phylogenetic positions with a combined approach of gene regions. This study aims to evaluate the species richness and phylogenetic position of Inocybe species and affiliated taxa in West Africa. Thus, in North Benin, we visited the Forest Reserve of Ouémé Supérieur, the Okpara forest and the Alibori Supérieur Forest Reserve. In the center, we targeted the Forest Reserve of Toui-Kilibo. The surveys have been carried during the raining season in the study area meaning from June to October. A total of 24 taxa were collected, photographed and described. The DNA was extracted, the Polymerase Chain Reaction was carried out using primers (ITS1-F, ITS4-B) for Internal transcribed spacer (ITS), (LROR, LWRB, LR7, LR5) for nuclear ribosomal (LSU), (RPB2-f5F, RPB2-b6F, RPB2- b6R2, RPB2-b7R) for RNA polymerase II gene (RPB2) and sequenced. The ITS sequences of the 24 collections of Inocybaceae were edited in Staden and all the sequences were aligned and edited with Aliview v1.17. The sequences were examined by eye for sufficient similarity to be considered the same species. 13 different species were present in the collections. In addition, sequences similar to the ITS sequences of the thirteen final species were searched using BLAST. The nLSU and RPB2 markers for these species have been inserted in a complete alignment, where species from all major Inocybaceae clades as well as from all continents except Antarctica are present. Our new sequences for nLSU and RPB2 have been manually aligned in this dataset. Phylogenetic analysis was performed using the RAxML v7.2.6 maximum likelihood software. Bootstrap replications have been set to 100 and no partitioning of the dataset has been performed. The resulting tree was viewed and edited with FigTree v1.4.3. The preliminary tree resulting from the analysis of maximum likelihood shows us that these species coming from Benin are much diversified and are distributed in four different clades (Inosperma, Inocybe, Mallocybe and Pseudosperma) on the seven clades of Inocybaceae but the phylogeny position of 7 is currently known. This study marks the diversity of Inocybe in Benin and the investigations will continue and a protection plan will be developed in the coming years.

Keywords: Benin, diversity, Inocybe, phylogeny placement

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Authors: Won Il Jung, Gene Lee, Luis Rabelo

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Since many weapon systems are getting more complex and diverse, various problems occur in terms of the acquisition cost, time, and performance limitation. As a matter of fact, the experiment execution in real world is costly, dangerous, and time-consuming to obtain Required Operational Characteristics (ROC) for a new weapon acquisition although enhancing the fidelity of experiment results. Also, until presently most of the research contained a large amount of assumptions so therefore a bias is present in the experiment results. At this moment, the new methodology is proposed to solve these problems without a variety of assumptions. ROC of the new weapon system is developed through the new methodology, which is a way to analyze big data generated by simulating various scenarios based on virtual and constructive models which are involving 6 Degrees of Freedom (6DoF). The new methodology enables us to identify unbiased ROC on new weapons by reducing assumptions and provide support in terms of the optimal weapon systems acquisition.

Keywords: big data, required operational characteristics (ROC), virtual and constructive models, weapon acquisition

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Authors: K. Frahtia, I. Mihoubi, S. Picot

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Leishmaniasis is a group of parasitic disease with a varied clinical expression caused by flagellate protozoa of the Leishmania genus. These diseases are transmitted to humans and animals by the sting of a vector insect, the female sandfly. Among the groups of dipteral disease vectors, Phlebotominae occupy a prime position and play a significant role in human pathology, such as leishmaniasis that affects nearly 350 million people worldwide. The vector control operation launched by health services throughout the country proves to be effective since despite the prevalence of the disease remains high especially in rural areas, leishmaniasis appears to be declining in Algeria. In this context, this study mainly concerns molecular detection of Leishmania from the vector. Furthermore, a molecular diagnosis has also been made on skin samples taken from patients in the region of Constantine, located in the North-East of Algeria. Concerning the vector, 5858 sandflies were captured, including 4360 males and 1498 females. Male specimens were identified based on their morphological. The morphological identification highlighted the presence of the Phlebotomus genus with a prevalence of 93% against 7% represented by the Sergentomyia genus. About the identified species, P. perniciosus is the most abundant with 59.4% of the male identified population followed by P. longicuspis with 24.7% of the workforce. P. perfiliewi is poorly represented by 6.7% of specimens followed by P. papatasi with 2.2% and 1.5% S. dreyfussi. Concerning skin samples, 45/79 (56.96%) collected samples were found positive by real-time PCR. This rate appears to be in sharp decline compared to previous years (alert peak of 30,227 cases in 2005). Concerning the detection of Leishmania from sandflies by RT-PCR, the results show that 3/60 PCR performed genus are positive with melting temperatures corresponding to that of the reference strain (84.1 +/- 0.4 ° C for L. infantum). This proves that the vectors were parasitized. On the other side, identification by RT-PCR species did not give any results. This could be explained by the presence of an insufficient amount of leishmanian DNA in the vector, and therefore support the hypothesis of the regression of leishmaniasis in Constantine.

Keywords: Algeria, molecular diagnostic, phlebotomus, real time PCR

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Authors: Jamie Lee Harder

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In the context of rapidly changing social and economic circumstances in the developing world, this paper analyses access to public healthcare for poor people with disabilities in Cambodia. Like other countries of South East Asia, Cambodia is developing at rapid pace. The historical past of Cambodia, however, has set former social policy structures to zero. This past forces Cambodia and its citizens to implement new public health policies to align with the needs of social care, healthcare, and urban planning. In this context, the role of people with disabilities (PwDs) is crucial as new developments should and can take into consideration their specific needs from the beginning onwards. This paper is based on qualitative research with expert interviews and focus group discussions in Cambodia. During the field work it became clear that the identification tool for the poorest households (HHs) does not count disability as a financial risk to fall into poverty neither when becoming sick nor because of higher health expenditures and/or lower income because of the disability. The social risk group of poor PwDs faces several barriers in accessing public healthcare. The urbanization, the socio-economic health status, and opportunities for education; all influence social status and have an impact on the health situation of these individuals. Cambodia has various difficulties with providing access to people with disabilities, mostly due to barriers regarding finances, geography, quality of care, poor knowledge about their rights and negative social and cultural beliefs. Shortened budgets and the lack of prioritizations lead to the need for reorientation of local communities, international and national non-governmental organizations and social policy. The poorest HHs are identified with a questionnaire, the IDPoor program, for which the Ministry of Planning is responsible. The identified HHs receive an ‘Equity Card’ which provides access free of charge to public healthcare centers and hospitals among other benefits. The dataset usually does not include information about the disability status. Four focus group discussions (FGD) with 28 participants showed various barriers in accessing public healthcare. These barriers go far beyond a missing ramp to access the healthcare center. The contents of the FGDs were ratified and repeated during the expert interviews with the local Ministries, NGOs, international organizations and private persons working in the field. The participants of the FGDs faced and continue to face high discrimination, low capacity to work and earn an own income, dependency on others and less social competence in their lives. When discussing their health situation, we identified, a huge difference between those who are identified and hold an Equity Card and those who do not. Participants reported high costs without IDPoor identification, positive experiences when going to the health center in terms of attitude and treatment, low satisfaction with specific capacities for treatments, negative rumors, and discrimination with the consequence of fear to seek treatment in many cases. The problem of accessing public healthcare by risk groups can be adapted to situations in other countries.

Keywords: access, disability, health, inequality, Cambodia

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Authors: Shashank Tiwari

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The most common method of drug delivery is the oral solid dosage form, of which tablets and capsules are predominant. The tablet is more widely accepted and used compared to capsules for a number of reasons, such as cost/price, tamper resistance, ease of handling and packaging, ease of identification, and manufacturing efficiency. Over the past several years, the issue of tamper resistance has resulted in the conversion of most over-the-counter (OTC) drugs from capsules to predominantly all tablets.

Keywords: capsule, drug delivery, dosages, solid, tablet

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Authors: Shuyi Wu, Chuang Li, Quanshui Zheng, Luping Xu

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Stretching and snipping DNA molecule by microfluidic has important application value in gene analysis by lab on a chip. Movement, deformation and fragmenting of DNA in microfluidic are typical fluid-solid coupling problems. An efficient and common simulation system for researching the movement, deformation and fragmenting of DNA by microfluidic has not been well developed. In our study, Brownian dynamics-finite element method (BD-FEM) is used to simulate the dynamic process of stretching and fragmenting DNA by contraction flow. The shape and parameters of micro-channels are changed to optimize the stretching and fragmenting properties of DNA. Our results indicate that strain rate, resulting from contraction microchannel, is the main control parameter for stretching and fragmenting DNA. There is good consistency between the simulation data and previous experimental result about the single DNA molecule behavior and averaged fragmenting properties in this study. BD-FEM method is an efficient calculating tool to research stretching and fragmenting behavior of single DNA molecule and optimize microfluidic devices for manipulating, stretching and fragmenting DNA.

Keywords: fragmenting, DNA, microfluidic, optimize.

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Authors: Mohammad A. U. Khan, Tariq M. Khan, Yinan Kong

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Fingerprint image enhancement is one of the most important step in an automatic fingerprint identification recognition (AFIS) system which directly affects the overall efficiency of AFIS. The conventional fingerprint enhancement like Gabor and Anisotropic filters do fill the gaps in ridge lines but they fail to tackle scar lines. To deal with this problem we are proposing a method for enhancing the ridges and valleys with scar so that true minutia points can be extracted with accuracy. Our results have shown an improved performance in terms of enhancement.

Keywords: fingerprint image enhancement, removing noise, coherence, enhanced diffusion

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Authors: Yasir E. Mohieldeen

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Qatar is one of the most water scarce countries in the World. In 2014, the average per capita rainfall was less than 29 m3/y/ca, while the global average is 6,000 m3/y/ca. However, the per capita water consumption in Qatar is among the highest in the World: more than 500 liters per person per day, whereas the global average is 160 liters per person per day. Since the early 2000s, Qatar has been relying heavily on desalinated water from the Arabian Gulf as the main source of fresh water. In 2009, about 99.9% of the total potable water produced was desalinated. Reliance on desalinated water makes Qatar very vulnerable to water related natural disasters, such as the red-tide phenomenon. Qatar’s strategic water reserve lasts for only 7 days. In case of red-tide outbreak, the country would not be able to desalinate water for days, let alone the months that this disaster would bring about (as it clogs the desalination equipment). The 2008-09 red-tide outbreak, for instance, lasted for more than eight months and forced the closure of desalination plants in the region for weeks. This study aims at identifying favorite conditions for red-tide outbreaks, using satellite data along with in-situ measurements. This identification would allow the prediction of these outbreaks and their hotspots. Prediction and monitoring of outbreaks are crucial to water security in the country, as different measures could be put in place in advance to prevent an outbreak and mitigate its impact if it happened. Red-tide outbreaks are detected using different algorithms for chlorophyll concentration in the Gulf waters. Vegetation indices, such as Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI) were used along with Surface Algae Bloom Index (SABI) to detect known outbreaks. MODIS (or Moderate Resolution Imaging Spectroradiometer) bands are used to calculate these indices. A red-tide outbreaks atlas in the Arabian Gulf is being produced. Prediction of red-tide outbreaks ahead of their occurrences would give critical information on possible water-shortage in the country. Detecting known outbreaks in the past few decades and related parameters (e.g. water salinity, water surface temperature, nutrition, sandstorms, … etc) enables the identification of favorite conditions of red-tide outbreak that are key to the prediction of these outbreaks.

Keywords: Arabian Gulf, MODIS, red-tide detection, strategic water reserve, water desalination

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Authors: Zahid Ullah, Atlas Khan

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This abstract focuses on the advancements in mathematical modeling and optimization techniques that play a crucial role in enhancing the efficiency, reliability, and performance of these systems. In this era of rapidly evolving technology, mathematical modeling and optimization offer powerful tools to tackle the complex challenges faced by control, signal processing, and energy systems. This abstract presents the latest research and developments in mathematical methodologies, encompassing areas such as control theory, system identification, signal processing algorithms, and energy optimization. The abstract highlights the interdisciplinary nature of mathematical modeling and optimization, showcasing their applications in a wide range of domains, including power systems, communication networks, industrial automation, and renewable energy. It explores key mathematical techniques, such as linear and nonlinear programming, convex optimization, stochastic modeling, and numerical algorithms, that enable the design, analysis, and optimization of complex control and signal processing systems. Furthermore, the abstract emphasizes the importance of addressing real-world challenges in control, signal processing, and energy systems through innovative mathematical approaches. It discusses the integration of mathematical models with data-driven approaches, machine learning, and artificial intelligence to enhance system performance, adaptability, and decision-making capabilities. The abstract also underscores the significance of bridging the gap between theoretical advancements and practical applications. It recognizes the need for practical implementation of mathematical models and optimization algorithms in real-world systems, considering factors such as scalability, computational efficiency, and robustness. In summary, this abstract showcases the advancements in mathematical modeling and optimization techniques for control, signal processing, and energy systems. It highlights the interdisciplinary nature of these techniques, their applications across various domains, and their potential to address real-world challenges. The abstract emphasizes the importance of practical implementation and integration with emerging technologies to drive innovation and improve the performance of control, signal processing, and energy.

Keywords: mathematical modeling, optimization, control systems, signal processing, energy systems, interdisciplinary applications, system identification, numerical algorithms

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Authors: Farzad Alaeimoghadam, Farnaz Alaeimoghadam

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Plants are always being threatened by biotic and abiotic elements in their abode. Although they have inherited mechanisms to defend themselves, sometimes due to overpowering of their enemies or weakening of themselves, they just suffer from those elements. Human, as to help plants defend themselves, have developed several methods among which application of terpenes via plant biotechnology is promising. Terpenes are the most frequent and diverse secondary metabolites in plants. In these plants, terpenes are involved in different protective aspects. In this field, by utilizing biotechnological approaches on them, a delicate, precise, and an economic intervention will be achieved. In this review, first, the importance of terpenes as guardians in plants, which include their allelopathy effect, a call for alliances, and a mitigation impact on abiotic stresses will be pointed out. Second, problems concerning terpenes application in plant biotechnology comprising: damage to cell, undesirable terpene production and undesirable concentration and proportion of terpenes will be discussed. At the end, the approaches in plant biotechnology of terpenes including tampering with terpene gene sequences, compartmentalization, and localization and utilization of membrane transporters will be expressed. It is concluded with some useful notions concerning the topic.

Keywords: plant biotechnology, plant protection, terpenes, terpenoids

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Authors: D. Estrella, A. Silva, R. Zapata, H. Rubio

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A total of 100 primary caregivers (mothers, fathers, grandparents) with at least one child or grandchild with a diagnosis of congenital bilateral profound deafness were assessed in order to evaluate the functionality of families with a deaf member, who was evaluated by specialists in audiology, molecular biology, genetics and psychology. After confirmation of the clinical diagnosis, DNA from the patients and parents were analyzed in search of the 35delG deletion of the GJB2 gene to determine who possessed the mutation. All primary caregivers were provided psychological support, regardless of whether or not they had the mutation, and prior and subsequent, the family APGAR test was applied. All parents, grandparents were informed of the results of the genetic analysis during the psychological intervention. The family APGAR, after psychological and genetic counseling, showed that 14% perceived their families as functional, 62% moderately functional and 24% dysfunctional. This shows the importance of psychological support in family functionality that has a direct impact on the quality of life of these families.

Keywords: deafness, psychological support, family, adaptation to disability

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Authors: Binder Hans

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Cancer is no longer seen as solely a genetic disease where genetic defects such as mutations and copy number variations affect gene regulation and eventually lead to aberrant cell functioning which can be monitored by transcriptome analysis. It has become obvious that epigenetic alterations represent a further important layer of (de-)regulation of gene activity. For example, aberrant DNA methylation is a hallmark of many cancer types, and methylation patterns were successfully used to subtype cancer heterogeneity. Hence, unraveling the interplay between different omics levels such as genome, transcriptome and epigenome is inevitable for a mechanistic understanding of molecular deregulation causing complex diseases such as cancer. This objective requires powerful downstream integrative bioinformatics methods as an essential prerequisite to discover the whole genome mutational, transcriptome and epigenome landscapes of cancer specimen and to discover cancer genesis, progression and heterogeneity. Basic challenges and tasks arise ‘beyond sequencing’ because of the big size of the data, their complexity, the need to search for hidden structures in the data, for knowledge mining to discover biological function and also systems biology conceptual models to deduce developmental interrelations between different cancer states. These tasks are tightly related to cancer biology as an (epi-)genetic disease giving rise to aberrant genomic regulation under micro-environmental control and clonal evolution which leads to heterogeneous cellular states. Machine learning algorithms such as self organizing maps (SOM) represent one interesting option to tackle these bioinformatics tasks. The SOMmethod enables recognizing complex patterns in large-scale data generated by highthroughput omics technologies. It portrays molecular phenotypes by generating individualized, easy to interpret images of the data landscape in combination with comprehensive analysis options. Our image-based, reductionist machine learning methods provide one interesting perspective how to deal with massive data in the discovery of complex diseases, gliomas, melanomas and colon cancer on molecular level. As an important new challenge, we address the combined portrayal of different omics data such as genome-wide genomic, transcriptomic and methylomic ones. The integrative-omics portrayal approach is based on the joint training of the data and it provides separate personalized data portraits for each patient and data type which can be analyzed by visual inspection as one option. The new method enables an integrative genome-wide view on the omics data types and the underlying regulatory modes. It is applied to high and low-grade gliomas and to melanomas where it disentangles transversal and longitudinal molecular heterogeneity in terms of distinct molecular subtypes and progression paths with prognostic impact.

Keywords: integrative bioinformatics, machine learning, molecular mechanisms of cancer, gliomas and melanomas

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Authors: Rogerio Vieira Dos Reis

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Countries like Brazil that despite fighting hard against corruption are not improving their corruption perception, especially due to systemic political corruption, should review their corruption prevention strategies. This thesis brings a case study based on an alternative way of preventing corruption: addressing the corruption drivers in public policies that lead to poor economic performance. After discussing the Brazilian industrial policies adopted recently, especially the measures towards the automotive sector, two corruption issues in this sector are analyzed: facilitating payment for fiscal benefits and buying the extension of fiscal benefits. In-depth interviews conducted with a policymaker and an executive of the automobile sector provide insights for identifying three main corruption drivers: excessive and unnecessary bureaucracy, a complex tax system and the existence of a closed market without setting performance requirements to be achieved by the benefited firms. Both the identification of the drivers of successful industrial policies and the proposal of anti-corruption strategies to ensure developmental outcomes are based on the economic perspective of industrial policy advocated by developmental authors and on the successful South Korean economic development experience. Structural anti-corruption measures include tax reform, the regulation of lobbying and legislation to allow corporate political contribution. Besides improving policymakers’ technical capabilities, measures at the ministry level include redesigning the automotive regimes as long-term policies focused on national investment with simple and clear rules and making fiscal benefits conditional upon performance targets focused on suppliers. This case study is of broader interest because it recommends the importance of adapting performance audits conducted by anti-corruption agencies, to focus not only on the delivery of public services, but also on the identification of potentially highly damaging corruption drivers in public policies that grant fiscal benefits to achieve developmental outcomes.

Keywords: Brazilian automotive sector, corruption, economic development, industrial policy, Inovar-Auto

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Authors: Eugene Stepanov, Arcady Ponosov

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To model gene regulatory networks one uses ordinary differential equations with switching nonlinearities, where the initial value problem is known to be well-posed if the trajectories cross the discontinuities transversally. Otherwise, the initial value problem is usually ill-posed, which lead to theoretical and numerical complications. In the presentation, it is proposed to apply the theory of hybrid dynamical systems, rather than switched ones, to regularize the problem. 'Hybridization' of the switched system means that one attaches a dynamic discrete component ('automaton'), which follows the trajectories of the original system and governs its dynamics at the points of ill-posedness of the initial value problem making it well-posed. The construction of the automaton is based on the classification of the attractors of the specially designed adjoint dynamical system. Several examples are provided in the presentation, which support the suggested analysis. The method can also be of interest in other applied fields, where differential equations contain switchings, e.g. in neural field models.

Keywords: hybrid dynamical systems, ill-posed problems, singular perturbation analysis, switching nonlinearities

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Authors: Rohita Gupta, G. S. Brah, R. Verma, C. S. Mukhopadhayay

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Although chicken strains show differences in susceptibility to a number of diseases, the underlying immunological basis is yet to be elucidated. In the present study, heterophils were subjected to LPS stimulation and total RNA extraction, further differential gene expression was studied in broiler, layer and indigenous Aseel strain by Real Time RT-PCR at different time periods before and after induction. The expression of the 14 AvBDs and chTLR 1, 2, 3, 4, 5, 7, 15 and 21 was detectable in heterophils. The expression level of most of the AvBDs significantly increased (P<0.05) 3 hours post in vitro lipopolysaccharide challenge. Higher expression level and stronger activation of most AvBDs, NFkB-1 and IRF-3 in heterophils was observed with the stimulation of LPS in layer compared to broiler, and in Aseel compared to both layer and broiler. This investigation will allow more refined interpretation of immuno-genetic basis of the variable disease resistance/susceptibility in divergent stock of chicken including indigenous breed. Moreover, this study will be helpful in formulation of strategy for isolation of antimicrobial peptides from heterophils.

Keywords: differential expression, heterophils, cytokines, defensin, TLR

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Authors: A. Elain, M. Le Fellic, A. Le Pemp, N. Hachet

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Iodinated Compounds (IC) are widely detected contaminants in most aquatic environments including sewage treatment plant, surface water, ground water and even drinking water, up to the µg.L-1 range. As IC contribute in the adsorbable organic halides (AOX) level, their removal or dehalogenation is expected. We report here on the biodegradability of a mixture of IC from an industrial effluent using a microbial consortium adapted to grow on IC as well as the native microorganisms. Both aerobic and anaerobic treatments were studied during batch experiments in 500-mL flasks. The degree of mineralization and recovery of iodide were monitored by HPLC-UV, TOC analysis and potentiometric titration. Providing ethanol as an electron acceptor was found to stimulate anaerobic reductive deiodination of IC while sodium chloride even at high concentration (22 g.l-1) had no influence on the degradation rates nor on the microbial viability. Phylogenetic analysis of 16S RNA gene sequence (MicroSeq®) was applied to provide a better understanding of the degradative microbial community.

Keywords: iodinated compounds, biodegradability, deiodination, electron-accepting conditions, microbial consortium

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Authors: Altayeb Abdalla Ahmed

Abstract:

Skeletal phenotype is a product of a balanced interaction between genetics and environmental factors throughout different life stages. Therefore, interlimb proportions are variable between populations. Although interlimb proportion indices have been used in anthropology in assessing the influence of various environmental factors on limbs, an extensive literature review revealed that there is a paucity of published research assessing interlimb part correlations and possibility of reconstruction. Hence, this study aims to assess the relationships between upper and lower limb parts and develop regression formulae to reconstruct the parts from one another. The left upper arm length, ulnar length, wrist breadth, hand length, hand breadth, tibial length, bimalleolar breadth, foot length, and foot breadth of 376 right-handed subjects, comprising 187 males and 189 females (aged 25-35 years), were measured. Initially, the data were analyzed using basic univariate analysis and independent t-tests; then sex-specific simple and multiple linear regression models were used to estimate upper limb parts from lower limb parts and vice-versa. The results of this study indicated significant sexual dimorphism for all variables. The results indicated a significant correlation between the upper and lower limbs parts (p < 0.01). Linear and multiple (stepwise) regression equations were developed to reconstruct the limb parts in the presence of a single or multiple dimension(s) from the other limb. Multiple stepwise regression equations generated better reconstructions than simple equations. These results are significant in forensics as it can aid in identification of multiple isolated limb parts particularly during mass disasters and criminal dismemberment. Although a DNA analysis is the most reliable tool for identification, its usage has multiple limitations in undeveloped countries, e.g., cost, facility availability, and trained personnel. Furthermore, it has important implication in plastic and orthopedic reconstructive surgeries. This study is the only reported study assessing the correlation and prediction capabilities between many of the upper and lower dimensions. The present study demonstrates a significant correlation between the interlimb parts in both sexes, which indicates a possibility to reconstruction using regression equations.

Keywords: anthropometry, correlation, limb, Sudanese

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Authors: M. G. Gopisankar, A. Surendiran, M. Hemachandren

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The dose requirement of warfarin to achieve target INR range varies in patients with prosthetic heart valve. This variation in is affected by both genetic and non-genetic factors. Earlier studies have identified role of CYP2C9 and VKORC1 genetic polymorphisms on warfarin dose requirement. Warfarin being a substrate for drug transporter, P-glycoprotein coded by ABCB1 gene, may also be influenced by its genetic polymorphisms. This study was aimed to study the effect of single nucleotide polymorphism (SNP), ABCB1 2677G > T on warfarin maintenance dose requirement in patients with steady-state International Normalized Ratio (INR). The median dose requirement was significantly different between the genotype groups GG vs. GT (35 ± 20; 42.5 ± 18, p < 0.05), GG vs. TT (35 ± 20; 41.25 ± 25, p<0.05). There was no significant difference between GT vs. TT. In conclusion, patients with variant allele require a higher weekly maintenance dose of warfarin compared to patients without variant allele.

Keywords: warfarin pharamcogenetics, pharmacogenomics of warfarin, ABCB1 and warfarin, pglycoprotein and warfarin

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Authors: Rachel deCatanzaro, Madeline Austen, Ken Tuininga, Kathy St. Laurent, Christina Rohe

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In Canada, the federal Species at Risk Act (SARA) provides protection for wildlife species at risk and a national legislative framework for the conservation or recovery of species that are listed as endangered, threatened, or special concern under Schedule 1 of SARA. Key aspects of the federal species at risk program include the development of recovery documents (recovery strategies, action plans, and management plans) outlining threats, objectives, and broad strategies or measures for conservation or recovery of the species; the identification and protection of critical habitat for threatened and endangered species; and working with groups and organizations to implement on-the-ground recovery actions. Environment Canada’s progress on the development of recovery documents and on the identification and protection of critical habitat in Ontario will be presented, along with successes and challenges associated with on-the ground implementation of recovery actions. In Ontario, Environment Canada is currently involved in several recovery and monitoring programs for at-risk bird species such as the Loggerhead Shrike, Piping Plover, Golden-winged Warbler and Cerulean Warbler and has provided funding for a wide variety of recovery actions targeting priority species at risk and geographic areas each year through stewardship programs including the Habitat Stewardship Program, Aboriginal Fund for Species at Risk, and the Interdepartmental Recovery Fund. Key research needs relevant to the recovery of species at risk have been identified, and include: surveys and monitoring of population sizes and threats, population viability analyses, and addressing knowledge gaps identified for individual species (e.g., species biology and habitat needs). The engagement of all levels of government, the local and international conservation communities, and the scientific research community plays an important role in the conservation and recovery of species at risk in Ontario– through surveying and monitoring, filling knowledge gaps, conducting public outreach, and restoring, protecting, or managing habitat – and will be critical to the continued success of the federal species at risk program.

Keywords: conservation biology, habitat protection, species at risk, wildlife recovery

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Authors: Vikas Kumar, Kailash Chandra, Kaomud Tyagi

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The insect order Thysanoptera includes small insects commonly called thrips. As insect vectors, only thrips are capable of Tospoviruses transmission (genus Tospovirus, family Bunyaviridae) affecting various crops. Currently, fifteen species of subfamily Thripinae (Thripidae) have been reported as vectors for tospoviruses. Frankliniella schultzei, which is reported as act as a vector for at least five tospovirses, have been suspected to be a species complex with more than one species. It is one of the historical unresolved issues where, two species namely, F. schultzei Trybom and F. sulphurea Schmutz were erected from South Africa and Srilanaka respectively. These two species were considered to be valid until 1968 when sulphurea was treated as colour morph (pale form) and synonymised under schultzei (dark form) However, these two have been considered as valid species by some of the thrips workers. Parallel studies have indicated that brown form of schultzei is a vector for tospoviruses while yellow form is a non-vector. However, recent studies have shown that yellow populations have also been documented as vectors. In view of all these facts, it is highly important to have a clear understanding whether these colour forms represent true species or merely different populations with different vector carrying capacities and whether there is some hidden diversity in 'Frankliniella schultzei species complex'. In this study, we aim to study the 'Frankliniella schultzei species complex' with molecular spectacles with DNA data from India and Australia and Africa. A total of fifty-five specimens was collected from diverse locations in India and Australia. We generated molecular data using partial fragments of mitochondrial cytochrome c oxidase I gene (mtCOI) and 28S rRNA gene. For COI dataset, there were seventy-four sequences, out of which data on fifty-five was generated in the current study and others were retrieved from NCBI. All the four different tree construction methods: neighbor-joining, maximum parsimony, maximum likelihood and Bayesian analysis, yielded the same tree topology and produced five cryptic species with high genetic divergence. For, rDNA, there were forty-five sequences, out of which data on thirty-nine was generated in the current study and others were retrieved from NCBI. The four tree building methods yielded four cryptic species with high bootstrap support value/posterior probability. Here we could not retrieve one cryptic species from South Africa as we could not generate data on rDNA from South Africa and sequence for rDNA from African region were not available in the database. The results of multiple species delimitation methods (barcode index numbers, automatic barcode gap discovery, general mixed Yule-coalescent, and Poisson-tree-processes) also supported the phylogenetic data and produced 5 and 4 Molecular Operational Taxonomic Units (MOTUs) for mtCOI and 28S dataset respectively. These results of our study indicate the likelihood that F. sulphurea may be a valid species, however, more morphological and molecular data is required on specimens from type localities of these two species and comparison with type specimens.

Keywords: DNA barcoding, species complex, thrips, species delimitation

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Authors: Yuli Hou, Jianping Sun, Mengdan Gao, Hui Liu, Ling Qin, Ang Li, Dongfu Li, Yonghong Zhang, Yan Zhao

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Background and Aims: Interferon-induced transmembrane protein 3 (IFITM3) is a component of ISG (Interferon-Stimulated Gene) family. IFITM3 has been recognized as a key signal molecule regulating cell growth in some tumors. However, the function of IFITM3 rs12252-CC genotype in the hepatocellular carcinoma (HCC) remains unknown to author’s best knowledge. A cohort study was employed to clarify the relationship between IFITM3 rs12252-CC genotype and HCC progression, and cellular experiments were used to investigate the correlation of function of IFITM3 and the progress of HCC. Methods: 336 candidates were enrolled in study, including 156 with HBV related HCC and 180 with chronic Hepatitis B infections or liver cirrhosis. Polymerase chain reaction (PCR) was employed to determine the gene polymorphism of IFITM3. The functions of IFITM3 were detected in PLC/PRF/5 cell with different treated:LV-IFITM3 transfected with lentivirus to knockdown the expression of IFITM3 and LV-NC transfected with empty lentivirus as negative control. The IFITM3 expression, proliferation and migration were detected by Quantitative reverse transcription polymerase chain reaction (qRT-PCR), QuantiGene Plex 2.0 assay, western blotting, immunohistochemistry, Cell Counting Kit(CCK)-8 and wound healing respectively. Six samples (three infected with empty lentiviral as control; three infected with LV-IFITM3 vector lentiviral as experimental group ) of PLC/PRF/5 were sequenced at BGI (Beijing Genomics Institute, Shenzhen,China) using RNA-seq technology to identify the IFITM3-related signaling pathways and chose PI3K/AKT pathway as related signaling to verify. Results: The patients with HCC had a significantly higher proportion of IFITM3 rs12252-CC compared with the patients with chronic HBV infection or liver cirrhosis. The distribution of CC genotype in HCC patients with low differentiation was significantly higher than that in those with high differentiation. Patients with CC genotype found with bigger tumor size, higher percentage of vascular thrombosis, higher distribution of low differentiation and higher 5-year relapse rate than those with CT/TT genotypes. The expression of IFITM3 was higher in HCC tissues than adjacent normal tissues, and the level of IFITM3 was higher in HCC tissues with low differentiation and metastatic than high/medium differentiation and without metastatic. Higher RNA level of IFITM3 was found in CC genotype than TT genotype. In PLC/PRF/5 cell with knockdown, the ability of cell proliferation and migration was inhibited. Analysis RNA sequencing and verification of RT-PCR found out the phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin(PI3K/AKT/mTOR) pathway was associated with knockdown IFITM3.With the inhibition of IFITM3, the expression of PI3K/AKT/mTOR signaling pathway was blocked and the expression of vimentin was decreased. Conclusions: IFITM3 rs12252-CC with the higher expression plays a vital role in the progress of HCC by regulating HCC cell proliferation and migration. These effects are associated with PI3K/AKT/mTOR signaling pathway.

Keywords: IFITM3, interferon-induced transmembrane protein 3, HCC, hepatocellular carcinoma, PI3K/ AKT/mTOR, phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin

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