Search results for: proteomic variations

Authors: Jianhua Zhang, Weiping Chen, Guanjie Chen, Jason Flannick, Emma Fikse, Glenda Smerin, Yanqin Yang, Yulong Li, John A. Hanover, William F. Simonds

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Ethnic disparities in many diseases are well recognized and reflect the consequences of genetic, behavior, and environmental factors. However, direct scientific evidence connecting the ethnic genetic variations and the disease disparities has been elusive, which may have led to the ethnic inequalities in large scale genetic studies. Through the genome-wide analysis of data representing 185,934 subjects, including 14,955 from our own studies of the African America Diabetes Mellitus, we discovered sets of genetic variants either unique to or conserved in all ethnicities. We further developed a quantitative gene function-based high-risk variant index (hrVI) of 20,428 genes to establish profiles that strongly correlate with the subjects' self-identified ethnicities. With respect to the ability to detect human essential and pathogenic genes, the hrVI analysis method is both comparable with and complementary to the well-known genetic analysis methods, pLI and VIRlof. Application of the ethnicity-specific hrVI analysis to the type 2 diabetes mellitus (T2DM) national repository, containing 20,791 cases and 24,440 controls, identified 114 candidate T2DM-associated genes, 8.8-fold greater than that of ethnicity-blind analysis. All the genes identified are defined as either pathogenic or likely-pathogenic in ClinVar database, with 33.3% diabetes-associated and 54.4% obesity-associated genes. These results demonstrate the utility of hrVI analysis and provide the first genetic evidence by clustering patterns of how genetic variations among ethnicities may impede the discovery of diabetes and foreseeably other disease-associated genes.

Keywords: diabetes-associated genes, ethnic health disparities, high-risk variant index, hrVI, T2DM

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Authors: Masoud Irannezhad, Sirpa Rasmus, Saghar Ahmadian, Deliang Chen, Bjorn Klove

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Variability and changes in thermal conditions play a crucial role in functioning of human society, particularly over cold climate regions like Finland. Accordingly, the frost-free season (FFS) parameters in terms of start (FFSS), end (FFSE) and length (FFSL) have substantial effects not only on natural environment (e.g. flora and fauna), but also on human requirements (e.g. agriculture, forestry and energy generation). Applying the 0°C threshold of minimum temperature (Tmin), the FFS was defined as the period between the last spring frost as FFSS and the first fall frost as FFSE. For this study, gridded (10 x 10 km2) daily minimum temperature datasets throughout Finland during 1961-2011 was used to investigate recent spatio-temporal variations and trends in frost-free season (FFS) parameters and their relationships with the well-known large-scale climate teleconnections (CTs). The FFS in Finland naturally increases from north (~60 days) to south (~190 days), in association with earlier FFSS (~24 April) and later FFSE (~30 October). Statistically significant (p<0.05) trends in FFSL were all positive (increasing) ranged between 0 and 13.5 (days/decade) and mainly observed in the east, upper west, centre and upper north of Finland. Such lengthening trends in FFS were attributable to both earlier FFSS and later FFSE mostly over central and upper northern Finland, while only to later FFSE in eastern and upper western parts. Variations in both FFSL and FFSS were significantly associated with the Polar (POL) pattern over northern Finland, while with the East Atlantic (EA) pattern over eastern and upper western areas. However, the POL and Scandinavia (SCA) patterns were most influential CTs for FFSE variability over northern Finland.

Keywords: climate teleconnections, Finland, frost-free season, trend analysis

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Authors: Kamyar Maleki Bagherabadi, Torstein Aarseth Bø, Truls Flatberg, Olve Mo

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Hydrogen fuel cells and batteries are one of the promising solutions aligned with carbon emission reduction goals for the marine sector. However, the higher installation and operation costs of hydrogen-based systems compared to conventional diesel gensets raise questions about the appropriate hydrogen tank size, energy, and fuel consumption estimations. Ship designers need methodologies and tools to calculate energy and fuel consumption for different component sizes to facilitate decision-making regarding feasibility and performance for retrofits and design cases. The aim of this work is to compare three alternative modeling approaches for the estimation of energy and fuel consumption with various hydrogen tank sizes, battery capacities, and load-sharing strategies. A fishery vessel is selected as an example, using logged load demand data over a year of operations. The modeled power system consists of a PEM fuel cell, a diesel genset, and a battery. The methodologies used are: first, an energy-based model; second, considering load variations during the time domain with a rule-based Power Management System (PMS); and third, a load variations model and dynamic PMS strategy based on optimization with perfect foresight. The errors and potentials of the methods are discussed, and design sensitivity studies for this case are conducted. The results show that the energy-based method can estimate fuel and energy consumption with acceptable accuracy. However, models that consider time variation of the load provide more realistic estimations of energy and fuel consumption regarding hydrogen tank and battery size, still within low computational time.

Keywords: fuel cell, battery, hydrogen, hybrid power system, power management system

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Authors: Khenenou Tarek, Mohamed Amine Fares, Djallal Eddine Rahmoun

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The study intends to evaluate the morphological changes in the mesenteric lymph nodes of dromedaries in different rearing systems. we aimed to evaluate the adaptative behavior of the animal’s immune system with environmental variations, and to conduct a comparative analysis on the morphological features of the mesenteric lymph node of the one-humped camel (Camelus dromedarius) in the region of El Oued, with two different rearing systems, with different practices and different purposes. The study was conducted using histo-morphometric techniques to analyze the morphological features of the mesenteric lymph node of the one-humped camel (Camelus dromedarius) in the region of El Oued. Two groups of dromedaries were used in the study, one group raised in a free-roaming housing system and another group raised in a restricted-roaming housing system. The results revealed that there were significant differences between the two groups in terms of active follicle ratio and size and also the cellular population of functional zones. Animals living and roaming outside the farm barriers were more exposed to pathogens, which leads to the installation of an adaptative process, whereas the animals living under restricted-roaming housing system were not exposed to pathogens. This study indicated that the adaptative behavior of the animal’s immune system with environmental variations is the functional translation of morphological changes. The obtained findings revealed that the morphological features of the mesenteric lymph node of the one-humped camel (Camelus dromedarius) in the region of El Oued are directly linked to the rearing system practices

Keywords: adaptative behavior, dromedary, lymph node, morphology, rearing systems

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Authors: Revaz Chigladze

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The purpose of the research is to investigate the surfaces of Jupiter's Galilean moons, namely which moon has the most uniform surface among them, what is the difference between the front (in the direction of motion) and the back sides of each moon's surface, as well as the temporal variations of the moons. Since 1981, the E. Kharadze National Astrophysical Observatory of Georgia has been conducting polarimetric (P) and photometric (M) observations of Jupiter's Galilean moons with telescopes of different diameters (40 cm and 125 cm) and the polarimeter ASEP-78 in combination with them and the latest generation photometer with a polarimeter and modern light receiver SBIG. As it turns out from the analysis of the observed material, the parameters P and M depend on α-the phase angle of the moon (satellite), L- the orbital latitude of the moon (satellite), λ- the wavelength, and t - the period of observation, i.e., P = P (α, L, λ , t), and similarly M = M (α, L, λ. , t). Based on the analysis of the observed material, the following was studied: Jupiter's Galilean moons: dependence of the magnitude and phase angle of the degree of linear polarization for different wavelengths; Dependence of the degree of polarization and the orbital longitude; dependence between the magnitude of the degree of polarization and the wavelength; time dependence of the degree of polarization and the dependence between photometric and polarimetric characteristics (including establishing correlation). From the analysis of the obtained results, we get: The magnitude of the degree of polarization of Jupiter's Galilean moons near the opposition significantly differs from zero. Europa appears to have the most uniform surface, and Callisto the least uniform. Time variations are most characteristic of Io, which confirms the presence of volcanic activity on its surface. Based on the observed material, it can be seen that the intensity of light reflected from the front hemisphere of the first three moons: Io, Europa, and Ganymede, is less than the intensity of light reflected from the rear hemisphere, and in the case of the Callisto it is the opposite. The paper provides a convincing (natural, real) explanation of this fact.

Keywords: Galilean moons, polarization, degree of polarization, photometry, front and rear hemispheres

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Authors: Jung Ae Park, Jooyong Park

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Writing is an important learning activity that cultivates higher level thinking. Effective and immediate feedback is necessary to help improve students' writing skills. Peer assessment can be an effective method in writing tasks because it makes it possible for students not only to receive quick feedback on their writing but also to get a chance to examine different perspectives on the same topic. Peer assessment can be practiced frequently and has the advantage of immediate feedback. However, there is controversy about the accuracy of peer assessment. In this study, we tried to demonstrate experimentally how the accuracy of peer assessment could be improved. Participants (n=76) were randomly assigned to groups of 4 members. All the participant graded two sets of 4 essays on the same topic. They graded the first set twice, and the second set or the posttest once. After the first grading of the first set, each group in the experimental condition 1 (discussion group), were asked to discuss the results of the peer assessment and then to grade the essays again. Each group in the experimental condition 2 (reading group), were asked to read the assessment on each essay by an expert and then to grade the essays again. In the control group, the participants were asked to grade the 4 essays twice in different orders. Afterwards, all the participants graded the second set of 4 essays. The mean score from 4 participants was calculated for each essay. The accuracy of the peer assessment was measured by Pearson correlation with the scores of the expert. The results were analyzed by two-way repeated measure ANOVA. The main effect of grading was observed: Grading accuracy got better as the number of grading experience increased. Analysis of posttest accuracy revealed that the score variations within a group of 4 participants decreased in both discussion and reading conditions but not in the control condition. These results suggest that having students discuss their grading together can be an efficient means to improve peer assessment accuracy. By discussing, students can learn from others about what to consider in grading and whether their grading is too strict or lenient. Further research is needed to examine the exact cause of the grading accuracy.

Keywords: peer assessment, evaluation accuracy, discussion, score variations

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Authors: Tahsin A. H. Nishat, Raquib Ahsan

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Sensitivity analysis of design parameters of the optimization procedure can become a significant factor while designing any structural system. The objectives of the study are to analyze the sensitivity of deck slab thickness parameter obtained from both the conventional and optimum design methodology of pre-stressed post-tensioned I-girder and deck system and to compare the relative significance of slab thickness. For analysis on conventional method, the values of 14 design parameters obtained by the conventional iterative method of design of a real-life I-girder bridge project have been considered. On the other side for analysis on optimization method, cost optimization of this system has been done using global optimization methodology 'Evolutionary Operation (EVOP)'. The problem, by which optimum values of 14 design parameters have been obtained, contains 14 explicit constraints and 46 implicit constraints. For both types of design parameters, sensitivity analysis has been conducted on deck slab thickness parameter which can become too sensitive for the obtained optimum solution. Deviations of slab thickness on both the upper and lower side of its optimum value have been considered reflecting its realistic possible ranges of variations during construction. In this procedure, the remaining parameters have been kept unchanged. For small deviations from the optimum value, compliance with the explicit and implicit constraints has been examined. Variations in the cost have also been estimated. It is obtained that without violating any constraint deck slab thickness obtained by the conventional method can be increased up to 25 mm whereas slab thickness obtained by cost optimization can be increased only up to 0.3 mm. The obtained result suggests that slab thickness becomes less sensitive in case of conventional method of design. Therefore, for realistic design purpose sensitivity should be conducted for any of the design procedure of girder and deck system.

Keywords: sensitivity analysis, optimum design, evolutionary operations, PC I-girder, deck system

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Authors: Rinat Arbel-Goren, Joel Stavans

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Cell-to-cell variations in transcript or protein abundance, called noise, may give rise to phenotypic variability between isogenic cells, enhancing the probability of survival under stress conditions. These variations may be introduced by post-transcriptional regulatory processes such as non-coding, small RNAs stoichiometric degradation of target transcripts in bacteria. We study the iron homeostasis network in Escherichia coli, in which the RyhB small RNA regulates the expression of various targets as a model system. Using fluorescence reporter genes to detect protein levels and single-molecule fluorescence in situ hybridization to monitor transcripts levels in individual cells, allows us to compare noise at both transcript and protein levels. The experimental results and computer simulations show that extrinsic noise buffers through a feed-forward loop configuration the increase in variability introduced at the transcript level by iron deprivation, illuminating the important role that extrinsic noise plays during stress. Surprisingly, extrinsic noise also decouples of fluctuations of two different targets, in spite of RyhB being a common upstream factor degrading both. Thus, phenotypic variability increases under stress conditions by the decoupling of target fluctuations in the same cell rather than by increasing the noise of each. We also present preliminary results on the adaptation of cells to prolonged iron deprivation in order to shed light on the evolutionary role of post-transcriptional downregulation by small RNAs.

Keywords: cell-to-cell variability, Escherichia coli, noise, single-molecule fluorescence in situ hybridization (smFISH), transcript

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Authors: Anida Causevic-Ramosevac, Sabina Semiz

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The aim of this study was to investigate the association of four single nucleotide polymorphisms (SNPs) - rs673548, rs693 in ApoB gene, rs1800775 in CETP gene and rs4846914 in GALNT2 gene with parameters of type 2 diabetes (T2D) and diabetic dyslipidemia in the population of Bosnia and Herzegovina (BH). Materials and methods: Our study involved 352 patients with T2D and 156 healthy subjects. Biochemical and anthropometric parameters were measured in all participants. DNA was extracted from the peripheral blood for the purpose of genetic testing. Polymorphisms in ApoB (rs673548, rs693), CETP (rs1800775) and GALNT2 (rs4846914) genes were analyzed by using Sequenom IPLEX platform. Results: Our results demonstrated significant associations for rs180075 polymorphism in CETP gene with levels of fasting insulin (p = 0.020; p = 0.027; p = 0.044), triglycerides (p = 0.046) and ALT (p = 0.031) activity in control group. In group of diabetic patients, results showed a significant association of rs673548 in ApoB gene with levels of fasting insulin (p = 0.008), HOMA-IR (p = 0.013), VLDL-C (p = 0.037) and CRP (p = 0.029) and rs693 in ApoB gene with BMI (p = 0.025), systolic blood pressure (p = 0.027), fasting insulin (p = 0.037) and HOMA-IR (p = 0.023) levels. Significant associations were also observed for rs1800775 in CETP gene with triglyceride (p = 0.023) levels and rs4846914 in GALNT2 gene with HbA1C (p = 0.013) and triglyceride (p = 0.043) levels. Conclusion: In conclusion, this is the first study that examined the impact of variations of candidate genes on a wide range of metabolic parameters in BH population. Our results suggest an association of variations of ApoB, CETP and GALNT2 genes with specific markers of T2D and dyslipidemia. Further studies would be needed in order to confirm these genetic effects in other ethnic groups as well.

Keywords: ApoB, CETP, dyslipidemia, GALNT2, type 2 diabetes

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Authors: Yushinta Fujaya, Andi Ivo Asphama, Andi Parenrengi, Andi Tenriulo

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Blue Swimming crab (Portunus pelagicus) is an important commercial species throughout the subtropical waters and as such constitutes part of the fisheries resources. Data are lacking on the morphological variations of selected fast-growing crabs reared in a pond. This study aimed to analyze the morphological and molecular character of a selected fast-growing crab reared in ponds in South of Sulawesi. The crab seeds were obtained from local fish-trap and hatchery. A study on the growth was carried out in the population of crabs. The dimensions analyzed were carapace width (CW) measured after 3 months of grow out. Morphological character states were examined based on the pattern of spots on the carapace. Molecular analysis was performed using RAPD (Random Amplified Polymorphic DNA). Genetic distance was analysed using TFPGA (Tools for Population Genetic Analyses) version 1.3. The results showed that there were variations in the growth of crabs. These crabs clustered morphologically into three quite distinct groups. The crab with white spots irregularly spread over its carapace was the largest size while the crab with large white spots scattered over the carapace was the smaller size (3%). The crab with small white spots scattered over the carapace was the smallest size found in this study. Molecular analysis showed that there are morphologically and genetically different between groups of crabs. Genetic distances among crabs ranged from 0.1527 to 0.5856. Thus, this study provides information the use of white spots pattern over carapace as indicators to identify the type of blue swimming crabs.

Keywords: crab, portunus pelagicus, morphology, RAPD, Carapace

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Authors: Y. Hamaizi, H. Triki, A. El-Akrmi

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In this paper, the reflection spectra, group delay and dispersion of a uniform fiber Bragg grating (FBG) are obtained. FBGs with two types of apodized variations of the refractive index were modeled to show how the side-lobes can be suppressed. Apodization techniques are used to get optimized reflection spectra. The simulation is based on solving coupled mode equations together with the transfer matrix method.

Keywords: fiber bragg gratings, coupled-mode theory, reflectivity, apodization

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Authors: Mohit Wadhawan, Sushma Rathaur

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Lymphatic filariasis, also called elephantiasis is a tropical disease afflicting over 120 million people in 81 countries worldwide. Existing anti filarial drugs are effective against the larval stages of filarial parasites which call for an urgent need of drugs which are macrofilaricidal. Identification of molecular targets crucial for survival of filarial parasites is a prerequisite for drug designing. Prolyl oligopeptidase (POP) is one such crucial enzyme involved in the maturation and degradation of neuropeptides and peptide hormones. We have identified this peptidase in the bovine filarial parasite, Setaria cervi. Effect of inhibition of POP on the proteome profile of filarial parasite has been discussed in this study. Filarial parasites were exposed to Z-pro-prolinal (ZPP), a specific POP inhibitor for 8 h and the motility and viability of the parasites was observed. It significantly reduced the motility and viability of the parasites. To study the proteome profile, the cytosolic, endoplasmic reticulum (ER) and mitochondrial extracts of the adult female parasites were subjected to 2-dimensional electrophoresis. As analyzed by the PD-Quest software, the ZPP caused the alteration in the different subcellular proteins, and the significantly altered proteins were identified using MALDI-MS/MS spectrometry. The major proteins identified were found to play important role in diverse biological functions like signaling, redox regulation, energy metabolism, stress response, and cytoskeleton formation. Moreover, we found upregulation in the calcium binding proteins such as calreticulin, calponin, and calpain-6 suggesting that POP inhibition regulates calcium release. This relates to earlier reports that POP plays non-catalytic role in inositol 1,4,5-trisphosphate (IP3) signaling inducing release of calcium from ER. Taken together, the data demonstrated that inhibition of prolyl oligopeptidase alter the overall proteome signifying its role in survival of the filarial parasites. Thus this study provides a basis for the use of POP as a chemotherapeutic target for the treatment of lymphatic filariasis.

Keywords: lymphatic filariasis, setaria cervi, prolyl oligopeptidase, proteomics

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Authors: Denise Schrama, Claudia Raposo, Pedro Rodrigues

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Background: Food allergies are conducted by a hypersensitive response of the immune system. These allergies are a global concern for the public health. Consumption of fish is increasing worldwide as it is a healthy meat with high nutritional value. Unfortunately, fish can cause adverse immune-mediate reactions, affecting part of the population with higher incidence in children. β-parvalbumin, a small, highly conserved stable, calcium or magnesium binding muscle protein is the main fish allergen. In fish-allergic patients, cross-reactivity between different fish species exist due to recognition of highly identical protein regions. Enolases, aldolases, or fish gelatin are other identified fish allergens in some fish species. With no available cure for fish allergies, clinical management is only based on an avoidance diet aiming at the total exclusion of offending food. Methods: Mediterranean fish (S. aurata and D. labrax) were fed specifically designed diets, enriched in components that target the expression or inactivation of parvalbumin (creatine and EDTA, respectively). After 90 days fish were sampled and biological tissues were excised. Proteomics was used to access fish allergens characterization and expression in muscle while IgE assays to confirm the lower allergenic potential are conducted in patients with history of fish allergies. Fish welfare and quality of flesh were established with biochemical, texture and sensorial analysis. Results: Fish welfare shows no major impact between diets. In case of creatine supplementation in D. labrax proteomic analysis show a slight decrease in parvalbumin expression. No accumulation of this compound was found in muscle. For EDTA supplementation in S. aurata IgE assay show a slight decrease in allergenicity when using sera of fish allergic patients. Conclusion: Supplementation with these two compounds seems to change slightly the allergenicity of the two mean Mediterranean species.

Keywords: fish allergies, fish nutrition, proteomics, aquaculture

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Authors: Ahmed Hamid Nassr

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The significant of the old stone ages in the Sudan, seems from the longest times and the large differentiation in antiquities, so many Neolithic cemeteries have been discovered in the Sudan, which the studies revealed costumes’ funerary from the Form of grave and the contents has been contrasted in some elements and constant in the others. Many interpretations of the late Neolithic cemeteries tradition written from the earlier studies, most of them focus of the development and change in the burial from society’s development and ideas of afterlife beginnings. Another emphasis undertaken is the relationship between societies cultural aspects and the environmental conditions of the period; it has been considered that it hyper-affected the development of farming in one way or another. The site of Qalaat Shanan noted in earlier 1990 and excavated by the Author from 2011-2013, the site located north of Khartoum about 170 km in Shendi town. Site setting lies amongst a group of Neolithic sites in the Shendi area, it reflected a succession of various Neolithic activities from the early to the late horizons. Excavation revealed many late Neolithic graves, the adult and child graves show large funerary content, different in quality and quantity, which indicates of societies development and related to religion and ideas about the afterlife. This presentation discusses the variations of the Late Neolithic cemeteries in Galaat Shanan site from the grave form, content and differentiation of the sex and age and compared with other late Neolithic discoveries in Sudan and the Nile valley. The study shows many changes in the graves related to the societies changes in late Neolithic in Sudan, climate and economic subsistence's are well reasons, but also the idea change is the main reason for the changes. That is clear from the variations of grave shape and content in age and sex and might be society’s status and levels.

Keywords: Sudan, Shendi town, Qalaat Shanan, late neolithic, cemeteries, funerary, tradition

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Authors: Abdullah Alnutayfat, Alexander Sutin

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One of the most important types of renewable energy resources is wind energy which can be produced by wind turbines. The blades of the wind turbine are exposed to the pressure of the harsh environment, which causes a significant issue for the wind power industry in terms of the maintenance cost and failure of blades. One of the reliable methods for blade inspection is the vibroacoustic structural health monitoring (SHM) method which examines information obtained from the structural vibrations of the blade. However, all vibroacoustic SHM techniques are based on comparing the structural vibration of intact and damaged structures, which places a practical limit on their use. Methods for nonlinear vibroacoustic SHM are more sensitive to damage and cracking and do not need to be compared to data from the intact structure. This paper presents the Vibro-Acoustic Modulation (VAM) method based on the modulation of high-frequency (probe wave) by low-frequency loads (pump wave) produced by the blade rotation. The blade rotation alternates bending stress due to gravity, leading to crack size variations and variations in the blade resonance frequency. This method can be used with the classical SHM vibration method in which the blade is excited by piezoceramic actuator patches bonded to the blade and receives the vibration response from another piezoceramic sensor. The VAM modification of this method analyzes the spectra of the detected signal and their sideband components. We suggest the VAM model as the simple mechanical oscillator, where the parameters of the oscillator (resonance frequency and damping) are varied due to low-frequency blade rotation. This model uses the blade vibration parameters and crack influence on the blade resonance properties from previous research papers to predict the modulation index (MI).

Keywords: wind turbine blades, damaged detection, vibro-acoustic structural health monitoring, vibro-acoustic modulation

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Authors: Sarah Nasser, Anne Moreau, Alain Hedoux, Romain Jeantet, Guillaume Delaplace

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Background: Spray dryed powders containing some caseins are commonly produced in dairy industry. It is widely admitted that the structure of casein evolves during powder storage, inducing a loss of solubility. However few studies evaluate accurately the destabilization mechanisms at molecular and mesoscopic level, in particular for Native Phospho Casein powder (NPC). Consequently, at the state of the art, it is very difficult to assess which secondary structure change or crosslinks initiate insolubility during storage. To address this issue, controlled ageing conditions have been applied to a NPC powder (which was obtained by spray drying a concentrate containing a higher content of casein (90%), whey protein (8%) and lactose (few %)). Evolution of structure and loss of solubility, with the effects of temperature and time of storage were systematically reported. Methods: FTIR spectroscopy, Raman and Circular Dichroism were used to monitor changes of secondary structure in dry powder and in solution after rehydration. Besides, proteomic tools and electrophoresis have been performed after varying storage conditions for evaluating aggregation and post translational modifications, like lactosylation or phosphorylation. Finally, Tof Sims and MEB were used to follow in parallel evolution of structure in surface and skin formation due to storage. Results + conclusion: These results highlight the important role of storage temperature in the stability of NPC. It is shown that this is not lactosylation at the heart of formation of aggregates, as advanced in others publications This is almost the rise of multitude post translational modifications (chemical cross link), added to disulphide bridges (physical cross link) wich contribute to the destabilisation of structure and aggregation of casein. A relative quantification of each kind of cross link, source of aggregates, is proposed. In addition, it has been proved that migration of lipids and formation of skin in surface during the ageing also explains the evolution of structure casein and thus the alterations of functional properties of NPC powder.

Keywords: casein, cross link, powder, storage

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Authors: Abanoub Mikhael, Darryl Hardie, Derek Smith, Helena Petrosova, Robert Ernst, David Goodlett

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Lipopolysaccharide (LPS) is a hallmark virulence factor of Gram-negative bacteria. It is a complex, structurally het- erogeneous mixture due to variations in number, type, and position of its simplest units: fatty acids and monosaccharides. Thus, LPS structural characterization by traditional mass spectrometry (MS) methods is challenging. Here, we describe the benefits of field asymmetric ion mobility spectrometry (FAIMS) for analysis of intact R-type lipopolysaccharide complex mixture (lipooligo- saccharide; LOS). Structural characterization was performed using Escherichia coli J5 (Rc mutant) LOS, a TLR4 agonist widely used in glycoconjugate vaccine research. FAIMS gas phase fractionation improved the (S/N) ratio and number of detected LOS species. Additionally, FAIMS allowed the separation of overlapping isobars facilitating their tandem MS characterization and un- equivocal structural assignments. In addition to FAIMS gas phase fractionation benefits, extra sorting of the structurally related LOS molecules was further accomplished using Kendrick mass defect (KMD) plots. Notably, a custom KMD base unit of [Na-H] created a highly organized KMD plot that allowed identification of interesting and novel structural differences across the different LOS ion families, i.e., ions with different acylation degrees, oligosaccharides composition, and chemical modifications. Defining the composition of a single LOS ion by tandem MS along with the organized KMD plot structural network was sufficient to deduce the composition of 181 LOS species out of 321 species present in the mixture. The combination of FAIMS and KMD plots allowed in-depth characterization of the complex LOS mixture and uncovered a wealth of novel information about its structural variations.

Keywords: lipopolysaccharide, ion mobility MS, Kendrick mass defect, Tandem mass spectrometry

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Authors: Syed Towseef Ahmad, Fatima Amin, Pritha Acharya, Anil K. Gupta, Pervez Ahmad

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Glaciers being the sentinels of climate change, are the most visible evidence of global warming. Given the unavailability of observed field-based data, this study has focussed on the use of geospatial techniques to obtain information about the glaciers of Pir-Panjal (PPJ) and the Great Himalayan Regions of Jhelum Basin (GHR). These glaciers need to be monitored in line with the variations in climatic conditions because they significantly contribute to various sectors in the region. The main aim of this study is to map the glaciers in the two adjacent regions (PPJ and GHR) in the north-western Himalayas with different topographies and compare the changes in various glacial attributes during two different time periods (1990-2020). During the last three decades, both PPJ as well as GHR regions have observed deglaciation of around 36 and 26 percent, respectively. The mean elevation of GHR glaciers has increased from 4312 to 4390 masl, while the same for PPJ glaciers has increased from 4085 to 4124 masl during the observation period. Using accumulation area ratio (AAR) method, mean mass balance of -34.52 and -37.6 cm.w.e was recorded for the glaciers of GHR and PPJ, respectively. The difference in areal and mass loss of glaciers in these regions may be due to (i) the smaller size of PPJ glaciers which are all smaller than 1 km² and are thus more responsive to climate change (ii) Higher mean elevation of GHR glaciers (iii) local variations in climatic variables in these glaciated regions. Time series analysis of climate variables indicates that both the mean maximum and minimum temperatures of Qazigund station (Tmax= 19.2, Tmin= 6.4) are comparatively higher than the Pahalgam station (Tmax= 18.8, Tmin= 3.2). Except for precipitation in Qazigund (Slope= - 0.3 mm a⁻¹), each climatic parameter has shown an increasing trend during these three decades, and with the slope of 0.04 and 0.03°c a⁻¹, the positive trend in Tmin (pahalgam) and Tmax (qazigund) are observed to be statistically significant (p≤0.05).

Keywords: glaciers, climate change, Pir-Panjal, greater Himalayas, mass balance

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Authors: Chloé Kernaléguen, Laura Kundun, Tessie Lery, Ryan Laleg, Zhangyun Tan

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This study explores global disparities in respiratory syncytial virus (RSV) bronchiolitis incidence among children aged 0-2 years, focusing on the human development index (HDI) as a key determinant. RSV bronchiolitis poses a significant health risk to young children, influenced by factors, including socio-economic conditions captured by the HDI. Through a comprehensive systematic review and dataset selection (Switzerland, Brazil, United States of America), we formulated an HDI-SEIRS numerical model within the SEIRS framework. Results show variations in RSV bronchiolitis dynamics across countries, emphasizing the influence of HDI. Modelling reveals a correlation between higher HDI and increased bronchiolitis spread, notably in the USA and Switzerland. The ratios HDIcountry over HDImax strengthen this association, while climate disparities contribute to variations, especially in colder climates like the USA and Switzerland. The study raises the hypothesis of an indirect link between higher HDI and more frequent bronchiolitis, underlining the need for nuanced understanding. Factors like improved healthcare access, population density, mobility, and social behaviors in higher HDI countries might contribute to unexpected trends. Limitations include dataset quality and restricted RSV bronchiolitis data. Future research should encompass diverse HDI datasets to refine HDI's role in bronchiolitis dynamics. In conclusion, HDI-SEIRS models offer insights into factors influencing RSV bronchiolitis spread. While HDI is a significant indicator, its impact is indirect, necessitating a holistic approach to effective public health policies. This analysis sets the stage for further investigations into multifaceted interactions shaping bronchiolitis dynamics in diverse socio-economic contexts.

Keywords: bronchiolitis propagation, HDI influence, respiratory syncytial virus, SEIRS model

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Authors: Zainab Abbas Soharwardi, Chunli Su, Harold Wilson Tumwitike Mapoma, Syed Zahid Aziz, Mahmut Ince

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This study investigated the spatial variations of groundwater chemistry used by communities in Lahore city with emphasis on arsenic (As) and fluoride (F) levels. A total of 472 tubewell samples were collected from 7 towns and analyzed for physical and chemical parameters, including pH, turbidity, electrical conductivity (EC), total dissolved solids (TDS), total hardness, HCO3, Ca2+, Mg2+, Na+, K+, SO42-, Cl-, NO3-, NO2-, F- and As. There were significant spatial variations observed for total hardness, TDS, HCO3, NO3 and As. In general, the south-east of the city displayed higher TH and HCO3 while the north-east showed significantly higher As concentrations attributed to the heterogeneity of the aquifer and industrial activities. In most cases, As was higher than WHO limit value. Indiscriminate disposal of domestic and commercial wastewater into River Ravi is the cause of elevated NO3 observed in the north-west compared to other places in the area. Investigation of the groundwater type revealed facies in the order: Ca-Mg-HCO3-SO4 > Mg-Ca-HCO3-SO4 > Ca-Mg-HCO3-SO4-Cl > Mg-Ca-HCO3-SO4 > Ca-HCO3-SO4 > Ca-Mg-SO4-HCO3. The plausible mineralization control mechanism seems to be that of carbonate weathering, although silicate weathering is probable. Moreover, PHREEQC model results showed that the groundwater was under saturated with respect to evaporites (anhydrite, fluorite, gypsum and halite) while generally equilibrium to saturated with respect to aragonite, calcite and dolomite. The Hierarchical Cluster Analysis (HCA) showed that pH significantly affected As, F, NO3 and NO2 while HCO3 contributing most to the observed TDS values in Lahore. It is concluded that inherent mineral dissolution/ precipitation, pH, oxic conditions, anthropogenic activities, atmospheric transport/ wet deposition, microbial activities and surface soil characteristics play their significant roles in elevating both As and F in the city's groundwater.

Keywords: Lahore, arsenic, fluoride, groundwater

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Authors: Ibrahim M. Mehedi, Uzair Ansari, Ubaid M. Al-Saggaf, Abdulrahman H. Bajodah

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This paper presents a methodology for balancing a rotary inverted pendulum system using Robust Generalized Dynamic Inversion (RGDI) under influence of parametric variations and external disturbances. In GDI control, dynamic constraints are formulated in the form of asymptotically stable differential equation which encapsulates the control objectives. The constraint differential equations are based on the deviation function of the angular position and its rates from their reference values. The constraint dynamics are inverted using Moore-Penrose Generalized Inverse (MPGI) to realize the control expression. The GDI singularity problem is addressed by augmenting a dynamic scale factor in the interpretation of MPGI which guarantee asymptotically stable position tracking. An additional term based on Sliding Mode Control is appended within GDI control to make it robust against parametric variations, disturbances and tracking performance deterioration due to generalized inversion scaling. The stability of the closed loop system is ensured by using positive definite Lyapunov energy function that guarantees semi-global practically stable position tracking. Numerical simulations are conducted on the dynamic model of rotary inverted pendulum system to analyze the efficiency of proposed RGDI control law. The comparative study is also presented, in which the performance of RGDI control is compared with Linear Quadratic Regulator (LQR) and is verified through experiments. Numerical simulations and real-time experiments demonstrate better tracking performance abilities and robustness features of RGDI control in the presence of parametric uncertainties and disturbances.

Keywords: generalized dynamic inversion, lyapunov stability, rotary inverted pendulum system, sliding mode control

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Authors: Belinda Vega, Claudio Alvarez, Héctor Flores, Marcia Oliva, Katherine Alveal, Teresa Toro, María José Tapia, Fanny Guzmán

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With the increase in global temperatures and the decrease of oxygen (O2) concentration in the oceans, fish cultures are exposed to frequent fluctuations in dissolved O2 (DO) concentration that can cause chronic stress in the animals, altering the normal functioning of their immune system and making them vulnerable to infections, consequently increasing morbidity and mortality in the farms with economic losses. The mucosal organs (skin -and mucus-, gills, gut, and nasal mucosa) are the first line of defense of the fish against pathogens. Therefore, the objective of this study is to evaluate the effect of hypoxia on the antimicrobial activity of epidermal mucus from corvina drum (Cilus Gilberti), a native marine species with the potential for the diversification of aquaculture in Chile. To achieve this, the epidermal mucus of juveniles (~220g) kept under normoxia (7 mg/L DO) and hypoxia (2 mg/L DO) environmental conditions was collected after 6 weeks, as well as after 6 days of intraperitoneal inoculation with lipopolysaccharide from Vibrio anguillarum to induce an immune response in the fish. Total protein extracts of the mucus were used for bactericidal activity and lysozyme and peroxidase activity assays. Although the mucus from both experimental groups showed inhibitory effects on the bacterial growth of Vibrio anguillarum and Vibrio ordalli, this effect was more long-lasting in the normoxia group. We also observed a notable reduction in the presence of lysozyme in the mucus from fish exposed to hypoxia, with no differences in peroxidase content. Future proteomic studies of corvina mucus associated with the environmental conditions studied in this work will allow the isolation and identification of peptides with antimicrobial activity, those responsible for the results obtained. This will help establish strategies aimed at minimizing the impacts of hypoxia on the defense responses of corvina drum against potential pathogens. Funding: FONDECYT 3200440 and FONDECYT 1210056

Keywords: Cilus gilberti, mucus, antimicrobial activity, HYPOXIA

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Authors: Novee Lor C. Leyso, Maylin C. Palatino

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Under-five malnutrition continues to persist in the Philippines, particularly in the island Province of Marinduque, with prevalence of some forms of malnutrition even worsening in recent years. Local spatial cluster detection provides a spatial perspective in understanding this phenomenon as key in analyzing patterns of geographic variation, identification of community-appropriate programs and interventions, and focused targeting on high-risk areas. Using data from a province-wide household-based census conducted in 2014–2016, this study aimed to determine and evaluate spatial clusters of under-five malnutrition, across the province and within each municipality at the individual level using household location. Malnutrition was defined as weight-for-age z-score that fall outside the 2 standard deviations from the median of the WHO reference population. The Kulldorff’s elliptical spatial scan statistic in binomial model was used to locate clusters with high-risk of malnutrition, while adjusting for age and membership to government conditional cash transfer program as proxy for socio-economic status. One large significant cluster of under-five malnutrition was found southwest of the province, in which living in these areas at least doubles the risk of malnutrition. Additionally, at least one significant cluster were identified within each municipality—mostly located along the coastal areas. All these indicate apparent geographical variations across and within municipalities in the province. There were also similarities and disparities in the patterns of risk of malnutrition in each cluster across municipalities, and even within municipality, suggesting underlying causes at work that warrants further investigation. Therefore, community-appropriate programs and interventions should be identified and should be focused on high-risk areas to maximize limited government resources. Further studies are also recommended to determine factors affecting variations in childhood malnutrition considering the evidence of spatial clustering found in this study.

Keywords: Binomial model, Kulldorff’s elliptical spatial scan statistic, Philippines, under-five malnutrition

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Authors: Sanskriti Singh, Ankit Tomar

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Banks are the instrument of growth of a country. Banks mobilize the savings of the public in the form of deposits and channelize it as advances for various activities required for the development of society at large. The advance which becomes unpaid for a certain period is called Non Performing Asset of the bank. The study makes an attempt to bring out the magnitude of NPA and its impact on profit, advances. An attempt is also made to bring out the challenges NPA poses to the banks and suggestions to overcome and to manage NPA effectively.

Keywords: India, NPAs, private banks, public banks

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Authors: Farzam Fatolazadeh, Kalifa Goita, Mehdi Eshagh, Shusen Wang

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The Gravity Recovery and Climate Experiment (GRACE) is a satellite mission with twin satellites for the precise determination of spatial and temporal variations in the Earth’s gravity field. The products of this mission are monthly global gravity models containing the spherical harmonic coefficients and their errors. These GRACE models can be used for estimating terrestrial water storage (TWS) variations across the globe at large scales, thereby offering an opportunity for surface and groundwater storage (GWS) assessments. Yet, the ability of GRACE to monitor changes at smaller scales is too limited for local water management authorities. This is largely due to the low spatial and temporal resolutions of its models (~200,000 km2 and one month, respectively). High-resolution GRACE data products would substantially enrich the information that is needed by local-scale decision-makers while offering the data for the regions that lack adequate in situ monitoring networks, including northern parts of Canada. Such products could eventually be obtained through downscaling. In this study, we extended the spectral combination theory to simultaneously downscale spatiotemporally the 3o spatial coarse resolution of GRACE to 0.25o degrees resolution and monthly coarse resolution to daily resolution. This method combines the monthly gravity field solution of GRACE and daily hydrological model products in the form of both low and high-frequency signals to produce high spatiotemporal resolution TWSA and GWSA products. The main contribution and originality of this study are to comprehensively and simultaneously consider GRACE and hydrological variables and their uncertainties to form the estimator in the spectral domain. Therefore, it is predicted that we reach downscale products with an acceptable accuracy.

Keywords: GRACE satellite, groundwater storage, spectral combination, terrestrial water storage

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Authors: Shanlong Lu, Jiming Jin, Xiaochun Wang

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The Tibetan Plateau has the largest number of inland lakes with the highest elevation on the planet. These massive and large lakes are mostly in natural state and are less affected by human activities. Their shrinking or expansion can truly reflect regional climate and environmental changes and are sensitive indicators of global climate change. However, due to the sparsely populated nature of the plateau and the poor natural conditions, it is difficult to effectively obtain the change data of the lake, which has affected people's understanding of the temporal and spatial processes of lake water changes and their influencing factors. By using the MODIS (Moderate Resolution Imaging Spectroradiometer) MOD09Q1 surface reflectance images as basic data, this study produced the 8-day lake water surface data set of the Tibetan Plateau from 2000 to 2012 at 250 m spatial resolution, with a lake water surface extraction method of combined with lake water surface boundary buffer analyzing and lake by lake segmentation threshold determining. Then based on the dataset, the lake water surface variations and their influencing factors were analyzed, by using 4 typical natural geographical zones of Eastern Qinghai and Qilian, Southern Qinghai, Qiangtang, and Southern Tibet, and the watersheds of the top 10 lakes of Qinghai, Siling Co, Namco, Zhari NamCo, Tangra Yumco, Ngoring, UlanUla, Yamdrok Tso, Har and Gyaring as the analysis units. The accuracy analysis indicate that compared with water surface data of the 134 sample lakes extracted from the 30 m Landsat TM (Thematic Mapper ) images, the average overall accuracy of the lake water surface data set is 91.81% with average commission and omission error of 3.26% and 5.38%; the results also show strong linear (R2=0.9991) correlation with the global MODIS water mask dataset with overall accuracy of 86.30%; and the lake area difference between the Second National Lake Survey and this study is only 4.74%, respectively. This study provides reliable dataset for the lake change research of the plateau in the recent decade. The change trends and influencing factors analysis indicate that the total water surface area of lakes in the plateau showed overall increases, but only lakes with areas larger than 10 km2 had statistically significant increases. Furthermore, lakes with area larger than 100 km2 experienced an abrupt change in 2005. In addition, the annual average precipitation of Southern Tibet and Southern Qinghai experienced significant increasing and decreasing trends, and corresponding abrupt changes in 2004 and 2006, respectively. The annual average temperature of Southern Tibet and Qiangtang showed a significant increasing trend with an abrupt change in 2004. The major reason for the lake water surface variation in Eastern Qinghai and Qilian, Southern Qinghai and Southern Tibet is the changes of precipitation, and that for Qiangtang is the temperature variations.

Keywords: lake water surface variation, MODIS MOD09Q1, remote sensing, Tibetan Plateau

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Authors: Preethy Mary Donald, Renjith George

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Oral tori are localized non-neoplastic protuberances of maxilla and mandible. Torus palatinus (TP) is found on the midline of the roof of mouth existing as single growth or in clusters. Torus mandibularis(TM) is located on the lingual aspect of the mandible commonly between canine and premolar region. Etiology of their presence was not clear and was found to be multifactorial. Their variations in relation to age, gender, ethnicity and also the characteristics of TP and TM have become the interest of multiple studies. The objectives of this study were to determine the prevalence of torus palatinus (TP) and torus mandibularis (TM) among patients who have visited outpatient department, Faculty of Dentistry, Melaka Manipal Medical College. 108 patients were examined for the presence of oral tori at the outpatient department, Faculty of Dentistry, Melaka-Manipal Medical College. Factors such as age, gender, ethnicity of the patients and size, shape, location of the oral tori were studied. For TP, Malays (62.96%) have been found to have the highest prevalence than Chinese (43.3%) and Indians (35.71%). For TM, Chinese (7.46%) had predominated compared to Malays (7.41%) and Indians (0%). There is no significant association between occurrence of TP and TM with age, gender and ethnicity. For Torus palatinus, the most common size was Grade 1(1-3mm), most common location was molar region, and the most common shape was spindle. For Torus mandibularis, the most frequent location was canine premolar region and exists in unilateral single or bilateral single fashion. The overall prevalence rates were 47.2% for TP and 6.48% for TM. However, there is no significant association between occurrence of TP and TM with age, gender and ethnicity. The results showed variations in clinical characteristics and support the findings that occurrence of tori is a dynamic phenomenon which is multifactorial owing to the environmental factors such as stress from occlusion and dietary habits. It could be due to the genetic make-up of the individual.

Keywords: torus palatinus, torus mandibularis, age, gender

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Authors: Eirini Konstanta, Cedric Gouedard, Aggeliki Delimitsou, Stefania Patera, Samuel Murray

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Introduction: Quality reference DNA standards (QRS) for molecular testing by next-generation sequencing (NGS) are essential for accurate quantitation of copy number variations (CNV) for germline and variant allelic frequencies (VAF) for somatic analyses. Objectives: Presently, several molecular analytics for oncology patients are reliant upon quantitative metrics. Test validation and standardisation are also reliant upon the availability of surrogate control materials allowing for understanding test LOD (limit of detection), sensitivity, specificity. We have developed a dual calibration platform allowing for QRS pairs to be included in analysed DNA samples, allowing for accurate quantitation of CNV and VAF metrics within and between patient samples. Methods: QRS™ blocks up to 500nt were designed for common NGS panel targets incorporating ≥ 2 identification tags (IDTDNA.com). These were analysed upon spiking into gDNA, somatic, and ctDNA using a proprietary CalSuite™ platform adaptable to common LIMS. Results: We demonstrate QRS™ calibration reproducibility spiked to 5–25% at ± 2.5% in gDNA and ctDNA. Furthermore, we demonstrate CNV and VAF within and between samples (gDNA and ctDNA) with the same reproducibility (± 2.5%) in a clinical sample of lung cancer and HBOC (EGFR and BRCA1, respectively). CNV analytics was performed with similar accuracy using a single pair of QRS calibrators when using multiple single targeted sequencing controls. Conclusion: Dual paired QRS™ calibrators allow for accurate and reproducible quantitative analyses of CNV, VAF, intrinsic sample allele measurement, inter and intra-sample measure not only simplifying NGS analytics but allowing for monitoring clinically relevant biomarker VAF across patient ctDNA samples with improved accuracy.

Keywords: calibrator, CNV, gene copy number, VAF

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Authors: Vito Telesca, Giuseppina A. Giorgio

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The earth system is subject to a wide range of human activities that have changed the ecosystem more rapidly and extensively in the last five decades. These global changes have a large impact on human health. The relationship between extreme weather events and mortality are widely documented in different studies. In particular, a number of studies have investigated the relationship between climatological variations and the cardiovascular and respiratory system. The researchers have become interested in the evaluation of the effect of environmental variations on the occurrence of different diseases (such as infarction, ischemic heart disease, asthma, respiratory problems, etc.) and mortality. Among changes in weather conditions, the heat waves have been used for investigating the association between weather conditions and cardiovascular events and cerebrovascular, using thermal indices, which combine air temperature, relative humidity, and wind speed. The effects of heat waves on human health are mainly found in the urban areas and they are aggravated by the presence of atmospheric pollution. The consequences of these changes for human health are of growing concern. In particular, meteorological conditions are one of the environmental aspects because cardiovascular diseases are more common among the elderly population, and such people are more sensitive to weather changes. In addition, heat waves, or extreme heat events, are predicted to increase in frequency, intensity, and duration with climate change. In this context, are very important public health and climate change connections increasingly being recognized by the medical research, because these might help in informing the public at large. Policy experts claim that a growing awareness of the relationships of public health and climate change could be a key in breaking through political logjams impeding action on mitigation and adaptation. The aims of this study are to investigate about the importance of interactions between weather variables and your effects on human health, focusing on Italy. Also highlighting the need to define strategies and practical actions of monitoring, adaptation and mitigation of the phenomenon.

Keywords: climate change, illness, Italy, temperature, weather

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Authors: Priyanka Dargode, Suhas Gore, Manju Sharma, Arvind Lali

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Anaerobic digestion has been widely used for production of methane from different biowastes. However, the complexity of microbial communities involved in the process is poorly understood. The performance of biogas production process concerning the process productivity is closely coupled to its microbial community structure and syntrophic interactions amongst the community members. The present study aims at understanding taxonomic variations occurring in any starter inoculum when acclimatised to different lignocellulosic biomass (LBM) feedstocks relating to time of digestion. The work underlines use of high throughput Next Generation Sequencing (NGS) for validating the changes in taxonomic patterns of microbial communities. Biomethane Potential (BMP) batches were set up with different pretreated and non-pretreated LBM residues using the same microbial consortium and samples were withdrawn for studying the changes in microbial community in terms of its structure and predominance with respect to changes in metabolic profile of the process. DNA of samples withdrawn at different time intervals with reference to performance changes of the digestion process, was extracted followed by its 16S rRNA amplicon sequencing analysis using Illumina Platform. Biomethane potential and substrate consumption was monitored using Gas Chromatography(GC) and reduction in COD (Chemical Oxygen Demand) respectively. Taxonomic analysis by QIIME server data revealed that microbial community structure changes with different substrates as well as at different time intervals. It was observed that biomethane potential of each substrate was relatively similar but, the time required for substrate utilization and its conversion to biomethane was different for different substrates. This could be attributed to the nature of substrate and consequently the discrepancy between the dominance of microbial communities with regards to different substrate and at different phases of anaerobic digestion process. Knowledge of microbial communities involved would allow a rational substrate specific consortium design which will help to reduce consortium adaptation period and enhance the substrate utilisation resulting in improved efficacy of biogas process.

Keywords: amplicon sequencing, biomethane potential, community predominance, taxonomic analysis

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