Rapid Isothermal Amplification and Portable Detection System for SARS-CoV-2

The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay details and primer sequences become widely known, many laboratories could perform diagnostic tests using methods such as RT-PCR or isothermal RT-LAMP amplification. A key advantage of RT-LAMP based approaches compared to RT-PCR is that RT-LAMP is known to be robust in detecting targets from unprocessed samples. In addition, RT-LAMP assays are performed at a constant temperature enabling speed, simplicity, and point-of-use testing. Here, we provide the details of an RT-LAMP isothermal assay for the detection of SARS-CoV-2 virus with performance comparable to currently approved tests using RT-PCR. We characterize the assay by introducing swabs in virus spiked synthetic nasal fluids, moving the swab to viral transport medium (VTM), and using a volume of that VTM for performing the amplification without an RNA extraction kit. The assay has a Limit-of-Detection (LOD) of 50 RNA copies/μL in the VTM solution within 20 minutes, and LOD of 5000 RNA copies/μL in the nasal solution. Additionally, we show the utility of this assay for real-time point-of-use testing by demonstrating detection of SARS-CoV-2 virus in less than 40 minutes using an additively manufactured cartridge and a smartphone-based reader. Finally, we explore the speed and cost advantages by comparing the required resources and workflows with RT-PCR. This work could accelerate the development and availability of SARS-CoV-2 diagnostics by proving alternatives to conventional laboratory benchtop tests.

Enhanced Anaerobic Digestion of Long Chain Fatty Acid by Adding Magnetite and Carbon Nanotubes

This study investigated the impact of stimulating direct interspecies electron transfer (DIET), by supplementing nano-sized magnetite (nFe3O4, 0.5 g Fe/g VSS) and carbon nanotubes (CNT, 1 g/L), in anaerobic digestion of oleic acid (OA) at various concentrations (0.10 - 4.00 g chemical oxygen demand(COD)/L). Both supplementations could enhance CH4 production, and its beneficial impact increased with increased OA concentration. The biggest improvements of 114% and 165% compared to the control were achieved by nFe3O4 and CNT, respectively, at OA of 4 g COD/L. The enhancement can be attributed to the increased sludge conductivity: 7.1 ± 0.5 (control), 12.5 ± 0.8 (nFe3O4-added), and 15.7 ± 1.1 µS/cm (CNT-supplemented). Dissolved iron concentration, released from nFe3O4, seemed to have a negligible role in improving CH4 production. The excretion of electron shuttles, i.e., humic-like substances and protein-like substances, were found to be stimulated by supplementing nFe3O4 and CNT. Microbial diversity was found to be simplified under DIET-stimulating conditions, whereby five genera accounted for 88% of the total sequences in the control, while more than 82% were represented by only two genera (Methanotrix concilli and Methanosarcina flavescens) by supplementing nFe3O4 and CNT. In addition, the abudance of electro-active bacteria such as Syntrophomonas zehnderi was significantly increased from 17% to around 45%.

Nutrients balance for hydrogen potential upgrading from fruit and vegetable peels via fermentation process

The sole, dual and multi-fermentations of fruit and vegetable peels (FVPs) were investigated in order to balance nutrition hierarchy for maximizing hydrogen potential via Batch experiments. The highest volumetric hydrogen production of 2.55 ± 0.07 L/L and hydrogen content of 64.7 ± 3.7% were registered for multi-fermentation of M-PTBO (25% pea +25% tomato + 25% banana +25% orange). These values outperformed sole and dual fermentation. The multi-fermentation of FVPs provided sufficient nutrients and trace elements for anaerobes, where C/N and C/P ratios were at levels of 24.7 ± 0.2 and 113.2 ± 9.4, respectively. In specific, harmonizing of macro and micro-nutrients remarkably maximized activities of amylase, protease and lipase to 4.23 ± 0.42, 0.035 ± 0.002 and 0.31 ± 0.02 U/mL, respectively, as well as, substantially incremented counts of Clostridium and Enterobacter sp. up to 5.81 ± 0.23 × 10⁵ and 2.17 ± 0.09 × 10⁶ cfu/mL, respectively. Furthermore, multi-fermentation of M-PTBO achieved the maximum net energy gain and profit of 1.82 kJ/g_feedstock and 4.11 $/kg_feedstock, respectively. Nutrients balance significantly develops bacterial activity in terms of hydrogen productivity, anaerobes reproduction, enzyme activities and soluble metabolites. As a result, overall fermentation bioprocess performance was improved.

Harvesting zero waste from co-digested fruit and vegetable peels via integrated fermentation and pyrolysis processes

The aim of this study is to assess an innovative economic approach for the production of both fermentative hydrogen and biochar from fruit and vegetable peels (FVPs) via fermentation/pyrolysis process. Firstly, in fermentation batches, multi-fermentation of FVPs positively affected the harvested hydrogen yield and COD reduction efficiency, which reached their maximal values of 3.9 ± 0.6 mmol/g_COD and 56.2 ± 4.6% at batch of 25% pea + 25% tomato + 25% banana + 25% orange (M4). Secondly, digestates produced from all batches were pyrolyzed at 500 °C for investigating the potential for biochar production. Based on the characteristics of the pyrolyzed digestate, biochar produced from S1 (spinach) exhibited the highest specific surface area, density, pore volume, biochar production yield, and pyrolysis profit of 28.43 ± 3.95 m²/g, 1.93 ± 0.18 g/cm³, 0.59 ± 0.08 cm³/g, 59.04 ± 2.36%, and 3.66 $/kg_feedstock, respectively. However, the maximum overall profit from both fermentation and pyrolysis processes was 5.21 $/kg_feedstock and was denoted for M4.

Effects of pig slurry acidification on methane emissions during storage and subsequent biogas production

In addition to undesirable odorous gases, substantial amounts of greenhouse gases (GHG), particularly methane (CH₄), are generated during the storage of livestock manure. To reduce the CH₄ emissions, first, pig slurry (PS) was stored for 40 d at 30 °C after adjusting the pH at 5.0-7.0 using H₂SO₄ solution. In the control (non-acidified PS), 3.7 kg CO₂ eq./ton PS of CH₄ emissions was detected, which was reduced to 1.8, 0.9, 0.4, 0.2, and 0.1 kg CO₂ eq./ton PS at pH 7.0, 6.5, 6.0, 5.5, and 5.0, respectively. Methanosarcina was found to be the dominant genus (67% of the total archaeal sequence) in the control, whose dominance was reduced as storage pH decreased. The results of ribonucleic acid analysis and specific methanogenic activity test further confirmed the inhibition of indigenous methanogens by acidification. Later, the biochemical CH₄ potential of stored PS was tested. Compared to the control (10.6 L CH₄/L PS), the acidified PS showed higher CH₄ yields of 12.7-14.6 L CH₄/L PS, presumably by keeping degradable organic matters in PS under acidic condition. Among different acidification pHs tested, the maximum amount of GHG reduction was achieved at pH 6.0 by reducing CH₄ emission to +0.4 kg CO₂ eq./ton PS during storage while increasing biogas production potential equivalent to 48.3 kWh/ton PS (-22.5 kg CO₂ eq./ton PS), resulting in a further reduction of (-)9.6 kg CO₂ eq./ton PS compared to the control.

Clinicopathological Criteria and Prognostic Factors in Gastric Adenocarcinoma in Kuwait

Background: Gastric cancer is the 5th most common cancer in the world and 2nd leading cause of cancer deaths. It has marked geographic incidence variation. Most common in Japan, China, other East Asian countries, Eastern Europe and South America. There is sharp decrease in incidence in western countries over the past 60 years but incidence of GE junction and proximal gastric tumors is increasing. In state of Kuwait in 2012 ASR was 2.6/100,000 population (similar to other Gulf countries; apart from Oman). There are many known risk factors including eating smoked and salted food and H. pylori infection. Aim: The aim of this study is to analyze gastric cancer diagnosed cases from 2009 to 2015 in Kuwait and to analyze clinicopathological criteria and prognostic factors. Methods: A total of 145 adult patients with newly diagnosed gastric cancers were treated and followed-up at Kuwait Cancer Control Center (KCCC) between 2009-2015. Patients' data were examined retrospectively. In all cases: age, performance status, sex, ethnicity, smoking and dietary habit, tumor site, pathology, staging and type of treatment were identified. Survival analysis was done using Kaplan-Meier, and comparison was done using long-rank test. Results: The median age at diagnosis was 54 (29-94). Men represented 63.5%. 75.2% had adenocarcinoma, 14.5% gastric lymphoma, 6.2% GIST, 3.4% carcinoid and 1 case squamous cell carcinoma. For gastric adenocarcinoma, 22 were metastatic (20.2%). In spite of composing almost 25% of country population and expected high incidence in their home countries, only 19.5% of patients were Asian with known habit of spicy food intake. 31% of patients were smokers. Performance at diagnosis was ECOG 0-1 in majority. Median follow-up was 45 months (1-89) and median overall survival was 34 months (0.5-89). Almost half of tumors were poorly differentiated with signet-ring feature in 36.8%. 12.6% presented with clinically advanced tumor but after surgery the number upstaged to be 25.9% (Stage III). Tumor epicenter localization was almost equivalent with 43 (49.4%) localized proximally and 44 (50.6%) distally. Surgery was the main treatment in majority (85.1%) while radiation was used in 58.6% and chemotherapy in 74.4% (adjuvant, neoadjuvant or concomitant). 22 patients failed; 7 locoregionally, 15 had distant metastasis while 2 patients failed both locally and distantly. Close surgical margins, and proximal localization were poor prognostic factors. Age and ethnicity had no impact on outcomes in our cohort. Conclusion: Gastric adenocarcinoma in Kuwait has similar profile to that documented worldwide and regionally (apart from Oman). Proximal tumors represent a challenge and has poorer prognosis that may need more intensification of treatment. Current (neo)adjuvant treatment seem to be effective in our population. Molecular profiling and studies are needed for further understanding of this potentially curable disease.

Influence of Melt Compounding on Blast Furnace Slag Filled PP Compounds: A Comparative Study

In the current study, an assessment of the melt-compounding approach upon the behavior of blast furnace slag (BFS) filled polypropylene (PP) is reported. Two melt-compounding technologies are compared in terms of thermodynamic considerations as well as final behavior of the produced compounds. For this comparison, three PP-BFS formulations are introduced, where non-treated BFS is melt-mixed with PP via (1) internal lab mixer (IM) and (2) co-rotating twin-screw compounder (TSC). PP-BFS compounds from both processes are formed into plates via compression molding, characterized and tested for rheological, thermal and mechanical behavior. Processing parameters were evaluated for both processes such as specific shear work, residence time and shear rates. In addition, the rheological, thermal and mechanical behavior of comparable compounds are evaluated. The calculated specific shear work values for IM and TSC are 0.15 and 0.1 kW · h · kg−1. Calculated residence time for TSC is 55 s. Regarding the rheological behavior, it was found that melt mixing via both technologies did not show major differences in complex viscosity or storage- and loss moduli values. DSC findings show that crystallization and melting temperatures of IM- and TSC formulations are comparable. Decreased strain values are noticed for TSC compounds, while tensile modulus is found to be independent of process variation.

Biological H2 potential harvested from complex gelatinaceous wastewater via attached versus suspended growth culture anaerobes

The effect of cultural growth treating gelatinaceous wastewater on hydrogen fermentative was assessed using up-flow multi-stage anaerobic sponge reactor (UMASR) and anaerobic sequencing batch reactor (AnSBR). Both reactors were operated at five hydraulic retention times (HRTs). UMASR achieved the maximum COD removal efficiency of 60.2±4.4% at HRT of 48h. Moreover, UMASR exhibited superiority in the course of carbohydrates and proteins removal efficiencies' of 100 and 52.5±2.4% due to high amylase and protease activities' of 4.1±0.3 and 0.032±0.002U, respectively. Contrariwise, AnSBR assigned for the peak hydrogen production rate of 1.17±0.14L/L/day at HRT of 24-h. Lipase activity was quite high (0.307±0.023U) in AnSBR resulting in removal efficiency of 35.2±2.1% for lipids. Stover-Kincannon model emphasized that UMASR required lesser volume than AnSBR to sustain the same substrate degradation efficacy. Nevertheless, the net gain energy harvested from AnSBR surpassed UMASR by 4.0-folds at HRT of 24-h.

Magnetite/graphene oxide nano-composite for enhancement of hydrogen production from gelatinaceous wastewater

The effect of substrate to inoculum (So/Xo) ratio and supplementation of magnetite/graphene oxide (MGO) nano-composite material on hydrogen production from gelatinaceous wastewater via dark fermentation process was investigated. Results demonstrated that optimum So/Xo ratio of 1.0gCOD/gVSS achieved maximal hydrogen yield (HY) of 79.2±11.9mL H2/gCOD removed. Supplementation of anaerobes with 100mg/L MGO promoted HY up to 112.4±10.5mL H2/gCOD removed. Moreover, the degradation efficiency of carbohydrates, proteins and lipids was improved to 80.8±7.6, 34.4±2.3 and 31.4±2.2%, respectively. Acetate (HAc) and butyrate (HBu) concentrations increased from 102±6.8 to 125.3±6.3 and from 31.1±1.5 to 48.8±3.5mg/gVSS, respectively. However, propionate (HPr) concentration dropped from 35.9±2.7 to 15±1.3mg/gVSS. Hydrogenase enzyme activity increased 9-folds and the anaerobes elongated from ca. 1.8-2.9 to ca. 2.5-5.1μm with MGO addition. Moreover, Proteobacteria, Firmicutes, Clostridia and Bacilli were detected with the batches supplemented with MGO.

Introduction and enzootic of A/H5N1 in Egypt: Virus evolution, pathogenicity and vaccine efficacy ten years on

It is almost a decade since the highly pathogenic H5N1 avian influenza virus (A/H5N1) of clade 2.2.1 was introduced to Egypt in 2005, most likely, via wild birds; marking the longest endemic status of influenza viruses in poultry outside Asia. The endemic A/H5N1 in Egypt still compromises the poultry industry, poses serious hazards to public health and threatens to become potentially pandemic. The control strategies adopted for A/H5N1 in Egyptian poultry using diverse vaccines in commercialized poultry neither eliminated the virus nor did they decrease its evolutionary rate. Several virus clades have evolved, a few of them disappeared and others prevailed. Disparate evolutionary traits in both birds and humans were manifested by accumulation of clade-specific mutations across viral genomes driven by a variety of selection pressures. Viruses in vaccinated poultry populations displayed higher mutation rates at the immunogenic epitopes, promoting viral escape and reducing vaccine efficiency. On the other hand, viruses isolated from humans displayed changes in the receptor binding domain, which increased the viral affinity to bind to human-type glycan receptors. Moreover, viral pathogenicity exhibited several patterns in different hosts. This review aims to provide an overview of the viral evolution, pathogenicity and vaccine efficacy of A/H5N1 in Egypt during the last ten years.

A texture classification method for diffused liver diseases using Gabor wavelets

We proposed an efficient method for classification of diffused liver diseases based on Gabor wavelet. It is well known that Gabor wavelets attain maximum joint space-frequency resolution which is highly significant in the process of texture extraction and presentation. This property has been explored here as the proposed method outperforms the classification rate obtained by using dyadic wavelets and methods based on statistical properties of textures. The feature vector is relatively small compared to other methods. This has a significant impact on the speed of retrieval process. In addition, the proposed algorithm is not sensitive to shift of the image contents. Since shifting the contents of an image will cause a circular shift of the Gabor filter coefficients in each sub-band. The proposed algorithm applied to discriminate ultrasonic liver images into three disease states that are normal liver, liver hepatitis and cirrhosis. In our experiment 45 liver sample images from each three disease states which already proven by needle biopsy were used. We achieved the sensitivity 85% in the distinction between normal and hepatitis liver images and 86% in the distinction between normal and cirrhosis liver images. Based on our experiments, the Gabor wavelet is more appropriate than dyadic wavelets and statistical based methods for texture classification as it leads to higher classification accuracy.