Search results for: clinical samples

Authors: Fahimeh Palizban, Farshad Noravesh, Amir Hossein Saeidian, Mahya Mehrmohamadi

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In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the blood and contribute to a pool of circulating fragments called cell-free DNA. Accordingly, identifying the tissue origin of these DNA fragments from the plasma can result in more accurate and fast disease diagnosis and precise treatment protocols. Open chromatin regions are important epigenetic features of DNA that reflect cell types of origin. Profiling these features by DNase-seq, ATAC-seq, and histone ChIP-seq provides insights into tissue-specific and disease-specific regulatory mechanisms. There have been several studies in the area of cancer liquid biopsy that integrate distinct genomic and epigenomic features for early cancer detection along with tissue of origin detection. However, multimodal analysis requires several types of experiments to cover the genomic and epigenomic aspects of a single sample, which will lead to a huge amount of cost and time. To overcome these limitations, the idea of predicting OCRs from WGS is of particular importance. In this regard, we proposed a computational approach to target the prediction of open chromatin regions as an important epigenetic feature from cell-free DNA whole genome sequence data. To fulfill this objective, local sequencing depth will be fed to our proposed algorithm and the prediction of the most probable open chromatin regions from whole genome sequencing data can be carried out. Our method integrates the signal processing method with sequencing depth data and includes count normalization, Discrete Fourie Transform conversion, graph construction, graph cut optimization by linear programming, and clustering. To validate the proposed method, we compared the output of the clustering (open chromatin region+, open chromatin region-) with previously validated open chromatin regions related to human blood samples of the ATAC-DB database. The percentage of overlap between predicted open chromatin regions and the experimentally validated regions obtained by ATAC-seq in ATAC-DB is greater than 67%, which indicates meaningful prediction. As it is evident, OCRs are mostly located in the transcription start sites (TSS) of the genes. In this regard, we compared the concordance between the predicted OCRs and the human genes TSS regions obtained from refTSS and it showed proper accordance around 52.04% and ~78% with all and the housekeeping genes, respectively. Accurately detecting open chromatin regions from plasma cell-free DNA-seq data is a very challenging computational problem due to the existence of several confounding factors, such as technical and biological variations. Although this approach is in its infancy, there has already been an attempt to apply it, which leads to a tool named OCRDetector with some restrictions like the need for highly depth cfDNA WGS data, prior information about OCRs distribution, and considering multiple features. However, we implemented a graph signal clustering based on a single depth feature in an unsupervised learning manner that resulted in faster performance and decent accuracy. Overall, we tried to investigate the epigenomic pattern of a cell-free DNA sample from a new computational perspective that can be used along with other tools to investigate genetic and epigenetic aspects of a single whole genome sequencing data for efficient liquid biopsy-related analysis.

Keywords: open chromatin regions, cancer, cell-free DNA, epigenomics, graph signal processing, correlation clustering

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Authors: Sherif Keddis, Rafik Mitry, Norbert Schwesinger

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Intelligent networking of devices has rapidly been gaining importance over the past years and with recent advances in the fields of microcontrollers, integrated circuits and wireless communication, low power applications have emerged, enabling this trend even more. Connected devices provide a much larger database thus enabling highly intelligent and accurate systems. Ensuring safe drinking water is one of the fields that require constant monitoring and can benefit from an increased accuracy. Monitoring is mainly achieved either through complex measures, such as collecting samples from the points of use, or through metering systems typically distant to the points of use which deliver less accurate assessments of the quality of water. Constant metering near the points of use is complicated due to their inaccessibility; e.g. buried water pipes, locked spaces, which makes system maintenance extremely difficult and often unviable. The research presented here attempts to overcome this challenge by providing these systems with enough energy through a flow harvester inside the pipe thus eliminating the maintenance requirements in terms of battery replacements or containment of leakage resulting from wiring such systems. The proposed flow harvester exploits the piezoelectric properties of polyvinylidene difluoride (PVDF) films to convert turbulence induced oscillations into electrical energy. It is intended to be used in standard water pipes with diameters between 0.5 and 1 inch. The working principle of the harvester uses a ring shaped bluff body inside the pipe to induce pressure fluctuations. Additionally the bluff body houses electronic components such as storage, circuitry and RF-unit. Placing the piezoelectric films downstream of that bluff body causes their oscillation which generates electrical charge. The PVDF-film is placed as a multilayered wrap fixed to the pipe wall leaving the top part to oscillate freely inside the flow. The warp, which allows for a larger active, consists of two layers of 30µm thick and 12mm wide PVDF layered alternately with two centered 6µm thick and 8mm wide aluminum foil electrodes. The length of the layers depends on the number of windings and is part of the investigation. Sealing the harvester against liquid penetration is achieved by wrapping it in a ring-shaped LDPE-film and welding the open ends. The fabrication of the PVDF-wraps is done by hand. After validating the working principle using a wind tunnel, experiments have been conducted in water, placing the harvester inside a 1 inch pipe at water velocities of 0.74m/s. To find a suitable placement of the wrap inside the pipe, two forms of fixation were compared regarding their power output. Further investigations regarding the number of windings required for efficient transduction were made. Best results were achieved using a wrap with 3 windings of the active layers which delivers a constant power output of 0.53µW at a 2.3MΩ load and an effective voltage of 1.1V. Considering the extremely low power requirements of sensor applications, these initial results are promising. For further investigations and optimization, machine designs are currently being developed to automate the fabrication and decrease tolerance of the prototypes.

Keywords: maintenance-free sensors, measurements at point of use, piezoelectric flow harvesting, universal micro generator, wireless metering systems

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Authors: Simon J. Wilde, David M. Herold, Michael J. Bryant

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Social media networks have become the hotbed for advertising activities, due mainly to their increasing consumer/user base, and secondly, owing to the ability of marketers to accurately measure ad exposure and consumer-based insights on such networks. More than half of the world’s population (4.8 billion) now uses social media (60%), with 150 million new users having come online within the last 12 months (to June 2022). As the use of social media networks by users grows, key business strategies used for interacting with these potential customers have matured, especially social media advertising. Unlike other traditional media outlets, social media advertising is highly interactive and digital channel-specific. Social media advertisements are clearly targetable, providing marketers with an extremely powerful marketing tool. Yet despite the measurable benefits afforded to businesses engaged in social media advertising, recent controversies (such as the relationship between Facebook and Cambridge Analytica in 2018) have only heightened the role trust and privacy play within these social media networks. The purpose of this exploratory paper is to investigate the extent to which social media users trust social media advertising. Understanding this relationship will fundamentally assist marketers in better understanding social media interactions and their implications for society. Using a web-based quantitative survey instrument, survey participants were recruited via a reputable online panel survey site. Respondents to the survey represented social media users from all states and territories within Australia. Completed responses were received from a total of 258 social media users. Survey respondents represented all core age demographic groupings, including Gen Z/Millennials (18-45 years = 60.5% of respondents) and Gen X/Boomers (46-66+ years = 39.5% of respondents). An adapted ADTRUST scale, using a 20 item 7-point Likert scale, measured trust in social media advertising. The ADTRUST scale has been shown to be a valid measure of trust in advertising within traditional different media, such as broadcast media and print media, and more recently, the Internet (as a broader platform). The adapted scale was validated through exploratory factor analysis (EFA), resulting in a three-factor solution. These three factors were named reliability, usefulness and affect, and the willingness to rely on. Factor scores (weighted measures) were then calculated for these factors. Factor scores are estimates of the scores survey participants would have received on each of the factors had they been measured directly, with the following results recorded (Reliability = 4.68/7; Usefulness and Affect = 4.53/7; and Willingness to Rely On = 3.94/7). Further statistical analysis (independent samples t-test) determined the difference in factor scores between the factors when age (Gen Z/Millennials vs. Gen X/Boomers) was utilised as the independent, categorical variable. The results showed the difference in mean scores across all three factors to be statistically significant (p<0.05) for these two core age groupings: Gen Z/Millennials Reliability = 4.90/7 vs Gen X/Boomers Reliability = 4.34/7; Gen Z/Millennials Usefulness and Affect = 4.85/7 vs Gen X/Boomers Usefulness and Affect = 4.05/7; and Gen Z/Millennials Willingness to Rely On = 4.53/7 vs Gen X/Boomers Willingness to Rely On = 3.03/7. The results clearly indicate that older social media users lack trust in the quality of information conveyed in social media ads, when compared to younger, more social media-savvy consumers. This is especially evident with respect to Factor 3 (Willingness to Rely On), whose underlying variables reflect one’s behavioural intent to act based on the information conveyed in advertising. These findings can be useful to marketers, advertisers, and brand managers in that the results highlight a critical need to design ‘authentic’ advertisements on social media sites to better connect with these older users, in an attempt to foster positive behavioural responses from within this large demographic group – whose engagement with social media sites continues to increase year on year.

Keywords: social media advertising, trust, older consumers, online

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Authors: E. O. Aluta, C. A. Booth, D. G. Proverbs, T. Appleby

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Challenges in the effective management of potable water have attracted global attention in recent years and remain many world regions’ major priorities. Scarcity and unavailability of potable water may potentially escalate poverty, obviate democratic expression of views and militate against inter-sectoral development. These challenges contra-indicate the inherent potentials of the resource. Thus, while creation of poverty may be regarded as a broad-based problem, it is capable of reflecting life-span reduction diseases, the friction of interests manifesting in threats and warfare, the relegation of democratic principles for authoritarian definitions and Human Rights abuse. The challenges may be identified as manifestations of ineffective management of potable water resource and therefore, regarded as major problems in environmental protection. In reaction, some nations have re-examined their laws and policies, while others have developed innovative projects, which seek to ameliorate difficulties of providing sustainable potable water. The problems resonate in Nigeria, where the legal framework supporting the supply and management of potable water has been criticized as ineffective. This has impacted more on rural community members, often regarded as ‘voiceless’. At that level, the participation of non-state actors has been identified as an effective strategy, which can improve water supply. However, there are indications that there is no pragmatic application of this, resulting in over-centralization and top-down management. Thus, this study focuses on how the participatory process may enable the development of participatory water governance framework, for use in Nigeria rural communities. The Rural Advisory Board (RAB) is proposed as a governing body to promote proximal relationships, institute democratisation borne out of participation, while enabling effective accountability and information. The RAB establishes mechanisms for effectiveness, taking into consideration Transparency, Accountability and Participation (TAP), advocated as guiding principles of decision-makers. Other tools, which may be explored in achieving these are, Laws and Policies supporting the water sector, under the direction of the Ministries and Law Courts, which ensure non-violation of laws. Community norms and values, consisting of Nigerian traditional belief system, perceptions, attitude and reality (often undermined in favour of legislations), are relied on to pave the way for enforcement. While the Task Forces consist of community members with specific designation of duties, which ensure compliance and enforceability, a cross-section of community members are assigned duties. Thus, the principle of participation is pragmatically reflected. A review of the literature provided information on the potentials of the participatory process, in potable water governance. Qualitative methodology was explored by using the semi-structured interview as strategy for inquiry. The purposive sampling strategy, consisting of homogeneous, heterogeneous and criterion techniques was applied to enable sampling. The samples, sourced from diverse positions of life, were from the study area of Delta State of Nigeria, involving three local governments of Oshimili South, Uvwie and Warri South. From the findings, there are indications that the application of the participatory process is inhered with empowerment of the rural community members to make legitimate demands for TAP. This includes the obviation of mono-decision making for the supply and management of potable water. This is capable of restructuring the top-down management to a top-down/bottom-up system.

Keywords: participation, participatory process, participatory water governance, rural advisory board

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Authors: Rebeca V. Tholen, Elaine Bundy

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Background: Liver transplantation (LT) is considered the only curative treatment for end-stage liver disease Background: Liver transplantation (LT) is considered the only curative treatment for end-stage liver disease (ESLD). The effects of alcoholism can cause irreversible liver damage, cirrhosis and subsequent liver failure. Alcohol relapse after transplant occurs in 20-50% of patients and increases the risk for recurrent cirrhosis, organ rejection, and graft failure. Alcohol relapse after transplant has been identified as a problem among liver transplant recipients at a large urban academic transplant center in the United States. Transplantation will reverse the complications of ESLD, but it does not treat underlying alcoholism or reduce the risk of relapse after transplant. The purpose of this quality improvement project is to implement and evaluate the effectiveness of a High-Risk Alcoholism Relapse (HRAR) Scale to screen and identify patients at high-risk for alcohol relapse after receiving an LT. Methods: The HRAR Scale is a predictive tool designed to determine the severity of alcoholism and risk of relapse after transplant. The scale consists of three variables identified as having the highest predictive power for early relapse including, daily number of drinks, history of previous inpatient treatment for alcoholism, and the number of years of heavy drinking. All adult liver transplant recipients at a large urban transplant center were screened with the HRAR Scale prior to hospital discharge. A zero to two ordinal score is ranked for each variable, and the total score ranges from zero to six. High-risk scores are between three to six. Results: Descriptive statistics revealed 25 patients were newly transplanted and discharged from the hospital during an 8-week period. 40% of patients (n=10) were identified as being high-risk for relapse and 60% low-risk (n=15). The daily number of drinks were determined by alcohol content (1 drink = 15g of ethanol) and number of drinks per day. 60% of patients reported drinking 9-17 drinks per day, and 40% reported ≤ 9 drinks. 50% of high-risk patients reported drinking ≥ 25 years, 40% for 11-25 years, and 10% ≤ 11 years. For number of inpatient treatments for alcoholism, 50% received inpatient treatment one time, 20% ≥ 1, and 30% reported never receiving inpatient treatment. Findings reveal the importance and value of a validated screening tool as a more efficient method than other screening methods alone. Integration of a structured clinical tool will help guide the drinking history portion of the psychosocial assessment. Targeted interventions can be implemented for all high-risk patients. Conclusions: Our findings validate the effectiveness of utilizing the HRAR scale to screen and identify patients who are a high-risk for alcohol relapse post-LT. Recommendations to help maintain post-transplant sobriety include starting a transplant support group within the organization for all high-risk patients. (ESLD). The effects of alcoholism can cause irreversible liver damage, cirrhosis and subsequent liver failure. Alcohol relapse after transplant occurs in 20-50% of patients, and increases the risk for recurrent cirrhosis, organ rejection, and graft failure. Alcohol relapse after transplant has been identified as a problem among liver transplant recipients at a large urban academic transplant center in the United States. Transplantation will reverse the complications of ESLD, but it does not treat underlying alcoholism or reduce the risk of relapse after transplant. The purpose of this quality improvement project is to implement and evaluate the effectiveness of a High-Risk Alcoholism Relapse (HRAR) Scale to screen and identify patients at high-risk for alcohol relapse after receiving a LT. Methods: The HRAR Scale is a predictive tool designed to determine severity of alcoholism and risk of relapse after transplant. The scale consists of three variables identified as having the highest predictive power for early relapse including, daily number of drinks, history of previous inpatient treatment for alcoholism, and the number of years of heavy drinking. All adult liver transplant recipients at a large urban transplant center were screened with the HRAR Scale prior to hospital discharge. A zero to two ordinal score is ranked for each variable, and the total score ranges from zero to six. High-risk scores are between three to six. Results: Descriptive statistics revealed 25 patients were newly transplanted and discharged from the hospital during an 8-week period. 40% of patients (n=10) were identified as being high-risk for relapse and 60% low-risk (n=15). The daily number of drinks were determined by alcohol content (1 drink = 15g of ethanol) and number of drinks per day. 60% of patients reported drinking 9-17 drinks per day, and 40% reported ≤ 9 drinks. 50% of high-risk patients reported drinking ≥ 25 years, 40% for 11-25 years, and 10% ≤ 11 years. For number of inpatient treatments for alcoholism, 50% received inpatient treatment one time, 20% ≥ 1, and 30% reported never receiving inpatient treatment. Findings reveal the importance and value of a validated screening tool as a more efficient method than other screening methods alone. Integration of a structured clinical tool will help guide the drinking history portion of the psychosocial assessment. Targeted interventions can be implemented for all high-risk patients. Conclusions: Our findings validate the effectiveness of utilizing the HRAR scale to screen and identify patients who are a high-risk for alcohol relapse post-LT. Recommendations to help maintain post-transplant sobriety include starting a transplant support group within the organization for all high-risk patients.

Keywords: alcoholism, liver transplant, quality improvement, substance abuse

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Authors: Yogesh Dalvi, Ruby Varghese, Nibu Varghese, C. K. Krishnan Nair

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Introduction: The Genus Phellinus, locally known as Phansomba is a well-known traditional folk medicine. Especially, in Western Ghats of India, many tribes use several species of Phellinus for various ailments related to teeth, throat, tongue, stomach and even wound healing. It is one of the few mushrooms which play a pivotal role in Ayurvedic Dravyaguna. Aim: The present study focuses on to investigate phytochemical analysis, antioxidant, and antitumor (in vitro and in vivo) potential of Phellinus robinae from South India, Kerala Material and Methods: The present study explores the following: 1. Phellinus samples were collected from Ranni, Pathanamthitta district of Kerala state, India from Artocarpus heterophyllus Lam. and species were identified using rDNA region. 2. The fruiting body was shadow dried, powdered and extracted with 50% alcohol using water bath at 60°C which was further condensed by rotary evaporator and lyophilized at minus 40°C temperature. 3. Secondary metabolites were analyzed by using various phytochemical screening assay (Hager’s Test, Wagner’s Test, Sodium hydroxide Test, Lead acetate Test, Ferric chloride Test, Folin-ciocalteu Test, Foaming Test, Benedict’s test, Fehling’s Test and Lowry’s Test). 4. Antioxidant and free radical scavenging activity were analyzed by DPPH, FRAP and Iron chelating assay. 5. The antitumor potential of Water alcohol extract of Phellinus (PAWE) is evaluated through In vitro condition by Trypan blue dye exclusion method in DLA cell line and In vivo by murine model. Result and Discussion: Preliminary phytochemical screening by various biochemical tests revealed presence of a variety of active secondary molecules like alkaloids, flavanoids, saponins, carbohydrate, protein and phenol. In DPPH and FRAP assay PAWE showed significantly higher antioxidant activity as compared to standard Ascorbic acid. While, in Iron chelating assay, PAWE exhibits similar antioxidant activity that of Butylated Hydroxytoluene (BHT) as standard. Further, in the in vitro study, PAWE showed significant inhibition on DLA cell proliferation in dose dependent manner and showed no toxicity on mice splenocytes, when compared to standard chemotherapy drug doxorubicin. In vivo study, oral administration of PAWE showed dose dependent tumor regression in mice and also raised the immunogenicity by restoring levels of antioxidant enzymes in liver and kidney tissue. In both in vitro and in vivo gene expression studies PAWE up-regulates pro-apoptotic genes (Bax, Caspases 3, 8 and 9) and down- regulates anti-apoptotic genes (Bcl2). PAWE also down regulates inflammatory gene (Cox-2) and angiogenic gene (VEGF). Conclusion: Preliminary phytochemical screening revealed that PAWE contains various secondary metabolites which contribute to its antioxidant and free radical scavenging property as evaluated by DPPH, FRAP and Iron chelating assay. PAWE exhibits anti-proliferative activity by the induction of apoptosis through a signaling cascade of death receptor-mediated extrinsic (Caspase8 and Tnf-α), as well as mitochondria-mediated intrinsic (caspase9) and caspase pathways (Caspase3, 8 and 9) and also by regressing angiogenic factor (VEGF) without any inflammation or adverse side effects. Hence, PAWE serve as a potential antioxidant and antitumor agent.

Keywords: antioxidant, antitumor, Dalton lymphoma ascites (DLA), fungi, Phellinus robinae

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Authors: Doriane Delafosse, Dominique Fontvieille

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Background: Wastewater treatment plants (WWTPs) generally display significant efficacy in virus retention yet, are sometimes highly variable, partly in relation to large fluctuating loads at the head of the plant and partly because of episodic dysfunctions in some treatment processes. The problem is especially sensitive when human enteric viruses, such as human Noroviruses Genogroup I or Adenoviruses, are in concern: their release downstream WWTP, in environments often interconnected to recreational areas, may be very harmful to human communities even at low concentrations. It points out the importance of WWTP permanent monitoring from which their internal treatment processes could be adjusted. One way to adjust primary treatments is to add coagulants and flocculants to sewage ahead settling tanks to improve decantation. In this work, sludge produced by three coagulants (two organics, one mineral), four flocculants (three cationic, one anionic), and their combinations were studied for their efficacy in human enteric virus retention. Sewage samples were coming from a WWTP in the vicinity of the laboratory. All experiments were performed three times and in triplicates in laboratory pilots, using Murine Norovirus (MNV-1), a surrogate of human Norovirus, as an internal control (spiking). Viruses were quantified by (RT-)qPCR after nucleic acid extraction from both treated water and sediment. Results: Low values of sludge virus retention (from 4 to 8% of the initial sewage concentration) were observed with each cationic organic flocculant added to wastewater and no coagulant. The largest part of the virus load was detected in the treated water (48 to 90%). However, it was not counterbalancing the amount of the introduced virus (MNV-1). The results pertained to two types of cationic flocculants, branched and linear, and in the last case, to two percentages of cations. Results were quite similar to the association of a linear cationic organic coagulant and an anionic flocculant, though suggesting that differences between water and sludges would sometimes be related to virus size or virus origins (autochthonous/allochthonous). FeCl₃, as a mineral coagulant associated with an anionic flocculant, significantly increased both auto- and allochthonous virus retention in the sediments (15 to 34%). Accordingly, virus load in treated water was lower (14 to 48%) but with a total that still does not reach the amount of the introduced virus (MNV-1). It also appeared that the virus retrieval in a bare 0.1M NaCl suspension varied rather strongly according to the FeCl₃ concentration, suggesting an inhibiting effect on the molecular analysis used to detect the virus. Finally, no viruses were detected in both phases (sediment and water) with the combination branched cationic coagulant-linear anionic flocculant, which was later demonstrated as an effect, here also, of polymers on the virus detection-molecular analysis. Conclusions: The combination of FeCl₃-anionic flocculant gave its highest performance to the decantation-based virus removal process. However, large unbalanced values in spiking experiments were observed, suggesting that polymers cast additional obstacles to both elution buffer and lysis buffer on their way to reach the virus. The situation was probably even worse with autochthonous viruses already embedded into sewage's particulate matter. Polymers and FeCl₃ also appeared to interfere in some steps of molecular analyses. More attention should be paid to such impediments wherever chemical additives are considered to be used to enhance WWTP processes. Acknowledgments: This research was supported by the ABIOLAB laboratory (Montbonnot Saint-Martin, France) and by the ASPOSAN association. Field experiments were possible thanks to the Grand Chambéry WWTP authorities (Chambéry, France).

Keywords: flocculants-coagulants, polymers, enteric viruses, wastewater sedimentation treatment plant

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Authors: M. M. Hassani, S. Ammann, F. K. Wittel, P. Niemz, H. J. Herrmann

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Application of engineered wood, especially in the form of glued-laminated timbers has increased significantly. Recent progress in plywood made of high strength and high stiffness hardwoods, like European beech, gives designers in general more freedom by increased dimensional stability and load-bearing capacity. However, the strong hygric dependence of basically all mechanical properties renders many innovative ideas futile. The tendency of hardwood for higher moisture sorption and swelling coefficients lead to significant residual stresses in glued-laminated configurations, cross-laminated patterns in particular. These stress fields cause initiation and evolution of cracks in the bond-lines resulting in: interfacial de-bonding, loss of structural integrity, and reduction of load-carrying capacity. Subsequently, delamination of glued-laminated timbers made of hardwood elements can be considered as the dominant failure mechanism in such composite elements. In addition, long-term creep and mechano-sorption under changing environmental conditions lead to loss of stiffness and can amplify delamination growth over the lifetime of a structure even after decades. In this study we investigate the delamination process of adhesively bonded hardwood (European beech) elements subjected to changing climatic conditions. To gain further insight into the long-term performance of adhesively bonded elements during the design phase of new products, the development and verification of an authentic moisture-dependent constitutive model for various species is of great significance. Since up to now, a comprehensive moisture-dependent rheological model comprising all possibly emerging deformation mechanisms was missing, a 3D orthotropic elasto-plastic, visco-elastic, mechano-sorptive material model for wood, with all material constants being defined as a function of moisture content, was developed. Apart from the solid wood adherends, adhesive layer also plays a crucial role in the generation and distribution of the interfacial stresses. Adhesive substance can be treated as a continuum layer constructed from finite elements, represented as a homogeneous and isotropic material. To obtain a realistic assessment on the mechanical performance of the adhesive layer and a detailed look at the interfacial stress distributions, a generic constitutive model including all potentially activated deformation modes, namely elastic, plastic, and visco-elastic creep was developed. We focused our studies on the three most common adhesive systems for structural timber engineering: one-component polyurethane adhesive (PUR), melamine-urea-formaldehyde (MUF), and phenol-resorcinol-formaldehyde (PRF). The corresponding numerical integration approaches, with additive decomposition of the total strain are implemented within the ABAQUS FEM environment by means of user subroutine UMAT. To predict the true stress state, we perform a history dependent sequential moisture-stress analysis using the developed material models for both wood substrate and adhesive layer. Prediction of the delamination process is founded on the fracture mechanical properties of the adhesive bond-line, measured under different levels of moisture content and application of the cohesive interface elements. Finally, we compare the numerical predictions with the experimental observations of de-bonding in glued-laminated samples under changing environmental conditions.

Keywords: engineered wood, adhesive, material model, FEM analysis, fracture mechanics, delamination

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Authors: L. Malic, X. Zhang, D. Brassard, L. Clime, J. Daoud, C. Luebbert, V. Barrere, A. Boutin, S. Bidawid, N. Corneau, J. Farber, T. Veres

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The incidence of infections caused by foodborne pathogens such as Listeria monocytogenes (L. monocytogenes) poses a great potential threat to public health and safety. These issues are further exacerbated by legal repercussions due to “zero tolerance” food safety standards adopted in developed countries. Unfortunately, a large number of related disease outbreaks are caused by pathogens present in extremely low counts currently undetectable by available techniques. The development of highly sensitive and rapid detection of foodborne pathogens is therefore crucial, and requires robust and efficient pre-analytical sample preparation. Immunomagnetic separation is a popular approach to sample preparation. Microfluidic chips combined with external magnets have emerged as viable high throughput methods. However, external magnets alone are not suitable for the capture of nanoparticles, as very strong magnetic fields are required. Devices that incorporate externally applied magnetic field and microstructures of a soft magnetic material have thus been used for local field amplification. Unfortunately, very complex and costly fabrication processes used for integration of soft magnetic materials in the reported proof-of-concept devices would prohibit their use as disposable tools for food and water safety or diagnostic applications. We present a sample preparation magnetic microfluidic device implemented in low-cost thermoplastic polymers using fabrication techniques suitable for mass-production. The developed magnetic capture chip (M-chip) was employed for rapid capture and release of L. monocytogenes conjugated to immunomagnetic nanoparticles (IMNs) in buffer and beef filtrate. The M-chip relies on a dense array of Nickel-coated high-aspect ratio pillars for capture with controlled magnetic field distribution and a microfluidic channel network for sample delivery, waste, wash and recovery. The developed Nickel-coating process and passivation allows generation of switchable local perturbations within the uniform magnetic field generated with a pair of permanent magnets placed at the opposite edges of the chip. This leads to strong and reversible trapping force, wherein high local magnetic field gradients allow efficient capture of IMNs conjugated to L. monocytogenes flowing through the microfluidic chamber. The experimental optimization of the M-chip was performed using commercially available magnetic microparticles and fabricated silica-coated iron-oxide nanoparticles. The fabricated nanoparticles were optimized to achieve the desired magnetic moment and surface functionalization was tailored to allow efficient capture antibody immobilization. The integration, validation and further optimization of the capture and release protocol is demonstrated using both, dead and live L. monocytogenes through fluorescence microscopy and plate- culture method. The capture efficiency of the chip was found to vary as function of listeria to nanoparticle concentration ratio. The maximum capture efficiency of 30% was obtained and the 24-hour plate-culture method allowed the detection of initial sample concentration of only 16 cfu/ml. The device was also very efficient in concentrating the sample from a 10 ml initial volume. Specifically, 280% concentration efficiency was achieved in 17 minutes only, demonstrating the suitability of the system for food safety applications. In addition, flexible design and low-cost fabrication process will allow rapid sample preparation for applications beyond food and water safety, including point-of-care diagnosis.

Keywords: array of pillars, bacteria isolation, immunomagnetic sample preparation, polymer microfluidic device

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Authors: Nanine Fouche

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The Cape Flats is a low-lying sand-covered expanse of approximately 460 square kilometres, situated to the southeast of the central business district of Cape Town in the Western Cape of South Africa. The aeolian sands masking this area are often loose and compressible in the upper 1m to 1.5m of the surface, and there is a general exceedance of the maximum allowable settlement in these sands. The settlement of shallow foundations on Cape Flats sands is commonly predicted using the results of in-situ tests such as the SPT or DPSH due to the difficulty of retrieving undisturbed samples for laboratory testing. Varying degrees of accuracy and reliability are associated with these methods. More recently, shear wave velocity (Vs) profiles obtained from seismic testing, such as continuous surface wave tests (CSW), are being used for settlement prediction. Such predictions have the advantage of considering non-linear stress-strain behaviour of soil and the degradation of stiffness with increasing strain. CSW tests are rarely executed in the Cape Flats, whereas SPT’s are commonly performed. For this reason, and to facilitate better settlement predictions in Cape Flats sand, equations representing shear wave velocity (Vs) as a function of SPT blow count (N60) and vertical effective stress (v’) were generated by statistical regression of site investigation data. To reveal the most appropriate method of overburden correction, analyses were performed with a separate overburden term (Pa/σ’v) as well as using stress corrected shear wave velocity and SPT blow counts (correcting Vs. and N60 to Vs1and (N1)60respectively). Shear wave velocity profiles and SPT blow count data from three sites masked by Cape Flats sands were utilised to generate 80 Vs-SPT N data pairs for analysis. Investigated terrains included sites in the suburbs of Athlone, Muizenburg, and Atlantis, all underlain by windblown deposits comprising fine and medium sand with varying fines contents. Elastic settlement analysis was also undertaken for the Cape Flats sands, using a non-linear stepwise method based on small-strain stiffness estimates, which was obtained from the best Vs-N60 model and compared to settlement estimates using the general elastic solution with stiffness profiles determined using Stroud’s (1989) and Webb’s (1969) SPT N60-E transformation models. Stroud’s method considers strain level indirectly whereasWebb’smethod does not take account of the variation in elastic modulus with strain. The expression of Vs. in terms of N60 and Pa/σv’ derived from the Atlantis data set revealed the best fit with R2 = 0.83 and a standard error of 83.5m/s. Less accurate Vs-SPT N relations associated with the combined data set is presumably the result of inversion routines used in the analysis of the CSW results showcasing significant variation in relative density and stiffness with depth. The regression analyses revealed that the inclusion of a separate overburden term in the regression of Vs and N60, produces improved fits, as opposed to the stress corrected equations in which the R2 of the regression is notably lower. It is the correction of Vs and N60 to Vs1 and (N1)60 with empirical constants ‘n’ and ‘m’ prior to regression, that introduces bias with respect to overburden pressure. When comparing settlement prediction methods, both Stroud’s method (considering strain level indirectly) and the small strain stiffness method predict higher stiffnesses for medium dense and dense profiles than Webb’s method, which takes no account of strain level in the determination of soil stiffness. Webb’s method appears to be suitable for loose sands only. The Versak software appears to underestimate differences in settlement between square and strip footings of similar width. In conclusion, settlement analysis using small-strain stiffness data from the proposed Vs-N60 model for Cape Flats sands provides a way to take account of the non-linear stress-strain behaviour of the sands when calculating settlement.

Keywords: sands, settlement prediction, continuous surface wave test, small-strain stiffness, shear wave velocity, penetration resistance

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Authors: Rowan Moore, Kai Scheffler, Eugen Damoc, Jennifer Sutton, Aaron Bailey, Stephane Houel, Simon Cubbon, Jonathan Josephs

Abstract:

Purpose: MS analysis of monoclonal antibodies (mAbs) at the protein and peptide levels is critical during development and production of biopharmaceuticals. The compositions of current generation therapeutic proteins are often complex due to various modifications which may affect efficacy. Intact proteins analyzed by MS are detected in higher charge states that also provide more complexity in mass spectra. Protein analysis in native or native-like conditions with zero or minimal organic solvent and neutral or weakly acidic pH decreases charge state value resulting in mAb detection at higher m/z ranges with more spatial resolution. Methods: Three commercially available mAbs were used for all experiments. Intact proteins were desalted online using size exclusion chromatography (SEC) or reversed phase chromatography coupled on-line with a mass spectrometer. For streamlined use of the LC- MS platform we used a single SEC column and alternately selected specific mobile phases to perform separations in either denaturing or native-like conditions: buffer A (20 % ACN, 0.1 % FA) with Buffer B (100 mM ammonium acetate). For peptide analysis mAbs were proteolytically digested with and without prior reduction and alkylation. The mass spectrometer used for all experiments was a commercially available Thermo Scientific™ hybrid Quadrupole-Orbitrap™ mass spectrometer, equipped with the new BioPharma option which includes a new High Mass Range (HMR) mode that allows for improved high mass transmission and mass detection up to 8000 m/z. Results: We have analyzed the profiles of three mAbs under reducing and native conditions by direct infusion with offline desalting and with on-line desalting via size exclusion and reversed phase type columns. The presence of high salt under denaturing conditions was found to influence the observed charge state envelope and impact mass accuracy after spectral deconvolution. The significantly lower charge states observed under native conditions improves the spatial resolution of protein signals and has significant benefits for the analysis of antibody mixtures, e.g. lysine variants, degradants or sequence variants. This type of analysis requires the detection of masses beyond the standard mass range ranging up to 6000 m/z requiring the extended capabilities available in the new HMR mode. We have compared each antibody sample that was analyzed individually with mixtures in various relative concentrations. For this type of analysis, we observed that apparent native structures persist and ESI is benefited by the addition of low amounts of acetonitrile and formic acid in combination with the ammonium acetate-buffered mobile phase. For analyses on the peptide level we analyzed reduced/alkylated, and non-reduced proteolytic digests of the individual antibodies separated via reversed phase chromatography aiming to retrieve as much information as possible regarding sequence coverage, disulfide bridges, post-translational modifications such as various glycans, sequence variants, and their relative quantification. All data acquired were submitted to a single software package for analysis aiming to obtain a complete picture of the molecules analyzed. Here we demonstrate the capabilities of the mass spectrometer to fully characterize homogeneous and heterogeneous therapeutic proteins on one single platform. Conclusion: Full characterization of heterogeneous intact protein mixtures by improved mass separation on a quadrupole-Orbitrap™ mass spectrometer with extended capabilities has been demonstrated.

Keywords: disulfide bond analysis, intact analysis, native analysis, mass spectrometry, monoclonal antibodies, peptide mapping, post-translational modifications, sequence variants, size exclusion chromatography, therapeutic protein analysis, UHPLC

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Authors: M. Agostini, A. Sonato, G. Greco, M. Travagliati, G. Ruffato, E. Gazzola, D. Liuni, F. Romanato, M. Cecchini

Abstract:

Since their first demonstration in the early 1980s, surface plasmon resonance (SPR) sensors have been widely recognized as useful tools for detecting chemical and biological species, and the interest of the scientific community toward this technology has known a rapid growth in the past two decades owing to their high sensitivity, label-free operation and possibility of real-time detection. Recent works have suggested that a turning point in SPR sensor research would be the combination of SPR strategies with other technologies in order to reduce human handling of samples, improve integration and plasmonic sensitivity. In this light, microfluidics has been attracting growing interest. By properly designing microfluidic biochips it is possible to miniaturize the analyte-sensitive areas with an overall reduction of the chip dimension, reduce the liquid reagents and sample volume, improve automation, and increase the number of experiments in a single biochip by multiplexing approaches. However, as the fluidic channel dimensions approach the micron scale, laminar flows become dominant owing to the low Reynolds numbers that typically characterize microfluidics. In these environments mixing times are usually dominated by diffusion, which can be prohibitively long and lead to long-lasting biochemistry experiments. An elegant method to overcome these issues is to actively perturb the liquid laminar flow by exploiting surface acoustic waves (SAWs). With this work, we demonstrate a new approach for SPR biosensing based on the combination of microfluidics, SAW-induced mixing and the real-time phase-interrogation grating-coupling SPR technology. On a single lithium niobate (LN) substrate the nanostructured SPR sensing areas, interdigital transducer (IDT) for SAW generation and polydimethylsiloxane (PDMS) microfluidic chambers were fabricated. SAWs, impinging on the microfluidic chamber, generate acoustic streaming inside the fluid, leading to chaotic advection and thus improved fluid mixing, whilst analytes binding detection is made via SPR method based on SPP excitation via gold metallic grating upon azimuthal orientation and phase interrogation. Our device has been fully characterized in order to separate for the very first time the unwanted SAW heating effect with respect to the fluid stirring inside the microchamber that affect the molecules binding dynamics. Avidin/biotin assay and thiol-polyethylene glycol (bPEG-SH) were exploited as model biological interaction and non-fouling layer respectively. Biosensing kinetics time reduction with SAW-enhanced mixing resulted in a ≈ 82% improvement for bPEG-SH adsorption onto gold and ≈ 24% for avidin/biotin binding—≈ 50% and 18% respectively compared to the heating only condition. These results demonstrate that our biochip can significantly reduce the duration of bioreactions that usually require long times (e.g., PEG-based sensing layer, low concentration analyte detection). The sensing architecture here proposed represents a new promising technology satisfying the major biosensing requirements: scalability and high throughput capabilities. The detection system size and biochip dimension could be further reduced and integrated; in addition, the possibility of reducing biological experiment duration via SAW-driven active mixing and developing multiplexing platforms for parallel real-time sensing could be easily combined. In general, the technology reported in this study can be straightforwardly adapted to a great number of biological system and sensing geometry.

Keywords: biosensor, microfluidics, surface acoustic wave, surface plasmon resonance

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Authors: Zhi-Zhong Chen, Jun-Hao Lu, Jr., Shih-Ying Chueh

Abstract:

Based on Unified Theory of Acceptance and Use of Technology (UTAUT), the study investigates people’s intention on using smart phones. The study additionally incorporates two new variables: 'self-efficacy' and 'attitude toward using'. Samples are collected by questionnaire survey, in which 240 are valid. After Correlation Analysis, Reliability Test, ANOVA, t-test and Multiple Regression Analysis, the study finds that social impact and self-efficacy have positive effect on use intentions, and the use intentions also have positive effect on use behavior.

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