Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Multi-epitope Vaccine Against SARS-CoV-2 Variants of Concern Strains Applying Immunoinformatics Approaches

Background: The newly emerged coronavirus, SARS-CoV-2, the causative agent of the COVID-19 disease, appeared in Wuhan, China in December 2019 and led to the death of millions of people. The pandemic has increased the demand for effective vaccines and treatments worldwide. Due to the changes in the virus genome caused by mutation, variants with higher transmission ability and pathogenicity have emerged and raised excessive concerns about the efficiency of the developed vaccines. This study aimed to design a multi-epitope vaccine that targets the primary SARS-CoV-2 strain and its five variants of concern using immunoinformatics approaches. Methods: B-cell, cytotoxic T lymphocytes (CTLs) and helper T lymphocytes epitopes of the conserved and mutated SARS-CoV-2 surface glycoproteins were predicted using immunoinformatics approaches. These epitopes were attached utilizing appropriate linkers, and to provoke the immune response efficiently, the cholera toxin B subunit was added as an adjuvant. Results: Analyses by different bioinformatics softwares revealed that the designed vaccine’s high safety, stability, and efficacy. Conclusion: In this study, the vaccine designed by immunoinformatics tools showed specific reactivity to Toll-like receptor 4. Given the validation of other epitope-based vaccines, our vaccine might be capable of providing strong immunity in a wide range of populations.
The Feni-river closure dam reviewed

The subject of this study is the Feni River Closure Dam in Bangladesh, which was designed in 1983 and subsequently built in 1985. In this final report the influence is analyzed of advanced design methods, which have become available since 1983, on the geometric dam profile and sea side slope protection. For this purpose the Feni dam was redesigned using these advanced design techniques. First the methods used for the original design were analyzed, with regard to the geometric profile and sea side slope protection. Subsequently the Feni dam was redesigned, using advanced design methods and considering the afore mentioned items. Contrary to the original design, the distinction between monsoon and cyclone conditions was made, because of the different character of both hydraulic situations. As a result of the closure of the Feni river by means of the Feni dam, a huge area downstream of the dam has accreted. The geometric redesign and structural redesign of the slope protection was carried out twice: With and without accretion influence. In this way, the influence of a hypothetical method to predict the morphological process, which was not available at the time the original design was originally made, is demonstrated. In order to derive the hydraulic loading conditions first the water levels were analyzed. The influence of the accretion process on the water levels near the dam was assumed to be zero. By analyzing gauge readings near the dam site, a probability distribution for water levels during monsoon conditions was derived. The probability distribution of water levels for cyclone conditions was obtained by means of a numerical storm surge model. After calibrating this model, 40 synthetic situations were derived, of which the probability of occurrence could be derived from the meteorological cyclone record since 1900. By computing the maximum water levels for these 40 situations and by means of relations between gauge stations the probability distribution for cyclone conditions near the Feni dam could be obtained. For the wave climate the influence of the accretion process is not negligible. As no wave observations have been carried out in the neighbourhood of the Feni dam, again a numerical model was used. By means of a wave hindcast model, the wave climate could be estimated during cyclones and monsoon winds and for the two cases: with or without accretion influence. It was found out that the wave height 3 years after closure was about 10 to 20% lower than at the time of closure for the same probability of exceedance. This effect is caused by the accretion of the fore shore.
Preclinical proof of concept of a tetravalent lentiviral T-cell vaccine against dengue viruses

Dengue virus (DENV) is responsible for approximately 100 million cases of dengue fever annually, including severe forms such as hemorrhagic dengue and dengue shock syndrome. Despite intensive vaccine research and development spanning several decades, a universally accepted and approved vaccine against dengue fever has not yet been developed. The major challenge associated with the development of such a vaccine is that it should induce simultaneous and equal protection against the four DENV serotypes, because past infection with one serotype may greatly increase the severity of secondary infection with a distinct serotype, a phenomenon known as antibody-dependent enhancement (ADE). Using a lentiviral vector platform that is particularly suitable for the induction of cellular immune responses, we designed a tetravalent T-cell vaccine candidate against DENV (“LV-DEN”). This vaccine candidate has a strong CD8+ T-cell immunogenicity against the targeted non-structural DENV proteins, without inducing antibody response against surface antigens. Evaluation of its protective potential in the preclinical flavivirus infection model, i.e., mice knockout for the receptor to the type I IFN, demonstrated its significant protective effect against four distinct DENV serotypes, based on reduced weight loss, viremia, and viral loads in peripheral organs of the challenged mice. These results provide proof of concept for the use of lentiviral vectors for the development of efficient polyvalent T-cell vaccine candidates against all DENV serotypes.
Applications of Deep Learning Algorithms to Ultrasound Imaging Analysis in Preclinical Studies on In Vivo Animals

Background and Aim: Ultrasound (US) imaging is increasingly preferred over other more invasive modalities in preclinical studies using animal models. However, this technique has some limitations, mainly related to operator dependence. To overcome some of the current drawbacks, sophisticated data processing models are proposed, in particular artificial intelligence models based on deep learning (DL) networks. This systematic review aims to overview the application of DL algorithms in assisting US analysis of images acquired in in vivo preclinical studies on animal models. Methods: A literature search was conducted using the Scopus and PubMed databases. Studies published from January 2012 to November 2022 that developed DL models on US images acquired in preclinical/animal experimental scenarios were eligible for inclusion. This review was conducted according to PRISMA guidelines. Results: Fifty-six studies were enrolled and classified into five groups based on the anatomical district in which the DL models were used. Sixteen studies focused on the cardiovascular system and fourteen on the abdominal organs. Five studies applied DL networks to images of the musculoskeletal system and eight investigations involved the brain. Thirteen papers, grouped under a miscellaneous category, proposed heterogeneous applications adopting DL systems. Our analysis also highlighted that murine models were the most common animals used in in vivo studies applying DL to US imaging. Conclusion: DL techniques show great potential in terms of US images acquired in preclinical studies using animal models. However, in this scenario, these techniques are still in their early stages, and there is room for improvement, such as sample sizes, data preprocessing, and model interpretability.
Characterization of a Small Crater-like Structure in SE Bavaria, Germany

STRUCTURE IN SE BAVARIA, GERMANY V. Hoffmann, W. Rösler, A. Patzelt, B. Raeymaekers, P. Van Espen Institute for Geosciences, University of Tübingen, Sigwartstr. 10, D-72076 Tübingen, Germany. wolfgang.roesler @uni-tuebingen.de. Terrana Geophysik, Zeppelinstr. 15 D-72116 Mössingen, Germany. Infraserv Gendorf, D-84504 Burgkirchen, Germany. Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
Combined Incisional Negative Pressure Wound Therapy and Subfascial Suction Drainage: The Suction Taco Approach

An 18-year-old male with T4-L3 adult idiopathic scoliosis was treated with posterior spinal fusion followed by the application of a combined incisional negative pressure wound therapy (NPWT) and subfascial suction drainage system. In this report, we describe a novel technique that incorporates subfascial drains into an NPWT incisional vacuum system leading to a single exiting suction line. This effectively mitigates drain burden, maintains a sterile environment during the in-hospital postoperative period, provides NPWT to the drain exiting and incisional sites, and provides negative pressure-assisted deep space closure.
Bioinformatic analysis of highly consumed phytochemicals as P-gp binders to overcome drug-resistance

Background and purpose: P-glycoprotein (P-gp) is an adenosine triphosphate (ATP)-dependent membrane efflux pump for protecting cells against xenobiotic compounds. Unfortunately, overexpressed P-gp in neoplastic cells prevents cell entry of numerous chemotherapeutic agents leading to multidrug resistance (MDR). MDR cells may be re-sensitized to chemotherapeutic drugs via P-gp inhibition/modulation. Side effects of synthetic P-gp inhibitors encouraged the development of natural products. Experimental approach: Molecular docking and density functional theory (DFT) calculations were used as fast and accurate computational methods to explore a structure binding relationship of some dietary phytochemicals inside distinctive P-gp binding sites (modulatory/inhibitory). For this purpose, top-scored docked conformations were subjected to per-residue energy decomposition analysis in the B3LYP level of theory with a 6-31g (d, p) basis set by Gaussian98 package. Findings/Results: Consecutive application of computational techniques revealed binding modes/affinities of nutritive phytochemicals within dominant binding sites of P-gp. Blind docking scores for best-ranked compounds were superior to verapamil and rhodamine-123. Pairwise amino acid decomposition of superior docked conformations revealed Tyr303 as an important P-gp binding residue. DFT-based induced polarization analysis revealed major electrostatic fluctuations at the atomistic level and confirmed larger effects for amino acids with energy-favored binding interactions. Conformational analysis exhibited that auraptene and 7,4′,7″,4‴-tetra-O-methylamentoflavone might not necessarily interact to P-gp binding sites through minimum energy conformations. Conclusion and implications: Although there are still many hurdles to overcome, obtained results may propose a few nutritive phytochemicals as potential P-gp binding agents. Moreover; top-scored derivatives may have the chance to exhibit tumor chemo-sensitizing effects.
Forest Height Estimation by means of Pol-InSAR Limitations posed by Temporal Decorrelation

Polarimetric Synthetic Aperture Radar (SAR) Interferometry (Pol-InSAR) is a radar remote sensing technique, based on the coherent combination of radar polarimetry (Pol-SAR) and SAR interferometry (InSAR) which is substantially more sensitive to structural parameters of forest volume scatterers (e.g. forest) than conventional interferometry or polarimetry alone. However, temporal decorrelation is probably the most critical factor towards a successful implementation of Pol-InSAR parameter inversion techniques in terms of repeat-pass InSAR scenarios. This report focuses on the quantification of the effect of temporal decorrelation at L-band as a function of temporal baseline based on multi-temporal airborne experimental data acquired in the frame of dedicated air-borne experiments. Conclusions on the suitability of ALOS/PalSAR for Pol-InSAR applications are drawn and recommendations for mission characteristics of a potential follow on mission are addressed.
Secure Cloud-Assisted Data Pub/Sub Service With Fine-Grained Bilateral Access Control

Secure cloud-assisted data publish/subscribe (Pub/Sub) service provides an asynchronous method for publishers and subscribers to non-interactively exchange encrypted messages. Besides performing conjunctive subscription policy, numerous data Pub/Sub systems have recently been proposed to provide dynamic access control enforced from the publisher side to the subscriber side. However, these solutions fail to consider the following properties: (i) bilateral access control for both publishers and subscribers; (ii) the anonymity of the publisher; (iii) high matching time cost between publication and subscription. Therefore, we present P/S-BiAC, a secure and boolean cloud-assisted data Pub/Sub system with attribute-based bilateral access control that achieves authenticity and anonymity of publishers. In particular, P/S-BiAC enables cloud-based brokers to use the subscriber’s trapdoor to match published data with sub-linear time complexity. Technically, we introduce a “BiAC-and-Hidden” technique to refine publication tuples and trapdoor in classic searchable symmetric encryption solutions. Moreover, we implement P/S-BiAC and evaluate its practical performance based on Enron dataset in real cloud environment. To deal with a conjunctive subscription policy, P/S-BiAC runs $27.8\times $ faster for matching time cost (with $s$ -term=10) compared to state-of-the-art solutions, which demonstrates its feasibility in practical data Pub/Sub services with strong security properties.
Impacts of non-native rainbow trout on stream food webs in the Cape Floristic Region, South Africa integrating evidence from surveys and experiments

iv Chapter 1 General introduction 1 Chapter 2 Predatory impact of non-native rainbow trout on native fish 20 populations in headwater streams of the upper Breede River catchment, South Africa Chapter 3 Influence of non-native rainbow trout on benthic community 67 structure in headwater streams of the upper Breede River catchment, South Africa Chapter 4 Characterising and contrasting the trophic niches of native Breede 120 River redfin and non-native rainbow trout in headwater streams of the upper Breede River catchment, South Africa Chapter 5 Relative top-down effect of native benthic-feeding redfin vs. 181 non-native drift-feeding trout on benthic community structure in a Cape Floristic Region headwater stream Chapter 6 General discussion 240
A modified least squares-based tomography with density matrix perturbation and linear entropy consideration along with performance analysis

Quantum state tomography identifies target quantum states by performing repetitive measurements on identical copies. In this paper, we have two key contributions aimed at improving traditional post-processing computational complexity and sample complexity of quantum tomography protocols. In the first case, we propose a new low-cost positivity constraint method based on density matrix perturbation after the least squares (LS) estimation of the density matrix. In the second case, we propose a new cost function with the maximum linear entropy and LS method to improve the sample average trace distance with reasonably low sample complexity. We call it the LS with the maximum entropy (LSME) method. Our proposed algorithm does not follow the iterative optimization technique, which is true for existing maximum likelihood and entropy-based ones. Performance analysis is conducted for our proposed methods by studying how they compare to the existing techniques for different sample complexities and dimensionalities. Extensive numerical simulations have been conducted to demonstrate the advantages of the proposed tomography algorithms.
Protective effects of limb remote ischemic per-conditioning on the heart injury induced by renal ischemic-reperfusion through the interaction of the apelin with the RAS/iNOS pathway

Introduction: Remote ischemic conditioning upregulates endogenous protective pathways in response to ischemia-reperfusion injury. This study tested the hypothesis that limb remote ischemic per- conditioning (RIPerC) exerts cardioprotective effects via the renin-angiotensin system (RAS)/inducible nitric oxide synthase (iNOS)/apelin pathway. Methods: Renal ischemia-reperfusion injury (I/R) was induced by bilateral occlusion of the renal pedicles for 60 minutes, followed by 24 hours of reperfusion; sham-operated rats served as controls. RIPerC was induced by four cycles (5 minutes) of limb ischemia-reperfusion along with bilateral renal ischemia. The functional disturbance was evaluated by renal (BUN and creatinine) and cardiac (troponin I and lactate dehydrogenase) injury biomarkers. Results: Renal I/R injury increased renal and cardiac injury biomarkers that were reduced in the RIPerC group. Histopathological findings of the kidney and heart were also suggestive of amelioration injury-induced changes in the RIPerC group. Assessment of cardiac electrophysiology revealed that RIPerC ameliorated the decline in P wave duration without significantly affecting other cardiac electrophysiological changes. Further, renal I/R injury increased the plasma (322.40±34.01 IU/L), renal (8.27±1.10 mIU/mg of Protein), and cardiac (68.28±10.28 mIU/mg of protein) angiotensin-converting enzyme (ACE) activities in association with elevations in the plasma and urine nitrite (25.47±2.01 & 16.62±3.05 μmol/L) and nitrate (15.47±1.33 & 5.01±0.96 μmol/L) levels; these changes were reversed by RIPerC. Further, renal ischemia-reperfusion injury significantly (P=0.047) decreased the renal (but not cardiac) apelin mRNA expression, while renal and cardiac ACE2 (P<0.05) and iNOS (P=0.043) mRNA expressions were significantly increased compared to the sham group; these effects were largely reversed by RIPerC. Conclusion: Our results indicated that RIPerC protects the heart against renal ischemia- reperfusion injury, likely via interaction of the apelin with the RAS/iNOS pathway.
A little-known scientific club in Hobart, Tasmania - its early years

A history of the early years (1935-1939) of the Biological Club in Hobart, Tasmania, is presented, describing briefly the titles and content of some of the talks given in those formative years. The genesis of the Club is put into the broader context of the development of science in Tasmania during that period. The question of why women were not included in the membership in the Club at that time is explored.
Impact of high atmospheric carbon dioxide on the biotic stress response of the model cereal species Brachypodium distachyon

Losses due to disease and climate change are among the most important issues currently facing crop production. It is therefore important to establish the impact of climate change, and particularly of high carbon dioxide (hCO2), on plant immunity in cereals, which provide 60% of human calories. The aim of this study was to determine if hCO2 impacts Brachypodium distachyon immunity, a model plant for temperate cereals. Plants were grown in air (430 ppm CO2) and at two high CO2 conditions, one that is relevant to projections within the coming century (1000 ppm) and a concentration sufficient to saturate photosynthesis (3000 ppm). The following measurements were performed: phenotyping and growth, salicylic acid contents, pathogen resistance tests, and RNAseq analysis of the transcriptome. Improved shoot development was observed at both 1000 and 3000 ppm. A transcriptomic analysis pointed to an increase in primary metabolism capacity under hCO2. Alongside this effect, up-regulation of genes associated with secondary metabolism was also observed. This effect was especially evident for the terpenoid and phenylpropanoid pathways, and was accompanied by enhanced expression of immunity-related genes and accumulation of salicylic acid. Pathogen tests using the fungus Magnaporthe oryzae revealed that hCO2 had a complex effect, with enhanced susceptibility to infection but no increase in fungal development. The study reveals that immunity in B. distachyon is modulated by growth at hCO2 and allows identification of pathways that might play a role in this effect.
Kinetics of Formation of Butyric and Pyroglutamic Acid during the Shelf Life of Probiotic, Prebiotic and Synbiotic Yoghurt

Butyric acid (C4) and pyroglutamic acid (pGlu) exert significant beneficial effects on human health. In this study, the influence of probiotics (Lactobacillus acidophilus and Bifidobacteria) and/or prebiotics (1 and 3% inulin and fructo-oligosaccharides) on the content of C4 and pGlu in yoghurt during the shelf-life period was evaluated. The contents of C4 and pGlu were determined in probiotic, prebiotic and synbiotic yoghurts during 30 days of storage at 4 °C by solid-phase microextraction coupled with gas chromatography/mass spectrometry and HPLC analysis. Traditional yoghurt and uninoculated milk were used as control. Prebiotic yoghurt contained more C4 (2.2–2.4 mg/kg) than the uninoculated milk, and no increase was detected with respect to traditional yoghurt. However, probiotic yoghurt showed 10% more C4 than traditional yoghurt. Adding fibre to probiotics (synbiotic yoghurt) the C4 content increased by 30%. Regarding pGlu, probiotic yoghurt presented the highest content of approximately 130 mg/100 g. Fibre did not affect pGlu content. Finally, C4 and pGlu contents generally increased up to 20 days of storage and then decreased up to 30 days of storage. The results might be useful for the preparation of other functional foods rich in C4 and pGlu using lactic acid bacteria.
The Antecedents and Success of the Thai Spa Business

The objectives of this mixed method research combined both quantitative and qualitative methods were 1) to investigate the degree of predominance including service quality, 7Ps strategy, and administration critical to the success of the spa business in Thailand, 2) to study the impact of service quality, the 7Ps strategy, and administration on the performance of the Thai spa company, 3) to develop a model for the Thailand spa business’s success. The sample group consisted of 400 spa business entrepreneurs in Thailand researched with stratified random sampling and simple random sampling. The key informants were 18 spa business entrepreneurs in Thailand by purposive random sampling. The tool used in the data collection is a semi-structured interview. The quantitative data were analyzed by a structural equation model using the LISREL program and the content analysis was used in the qualitative data. The research results revealed that 1) service quality, 7Ps strategy, and administration is at the highest level, respectively, while the success of the spa business in Thailand is at a high level with an average of 4.19. 2) The service quality, the 7 Ps strategy, and administration all have a statistically significant impact on spa business success at the.05 levels. 3) The development of a spa business success model in Thailand is MQ2S Model. The qualitative research results promoted the importance of spa business management. The findings of this research can be used as the approach in formulating the policy in spa business operation to encourage entrepreneurs to operate a spa company in Thailand and be successful in long-term competition.