Miracle-dz/UniFAR-FTUs huggingface dataset:
Viruses of Yams (Dioscorea spp.): Current Gaps in Knowledge and Future Research Directions to Improve Disease Management

Viruses are a major constraint for yam production worldwide. They hamper the conservation, movement, and exchange of yam germplasm and are a threat to food security in tropical and subtropical areas of Africa and the Pacific where yam is a staple food and a source of income. However, the biology and impact of yam viruses remains largely unknown. This review summarizes current knowledge on yam viruses and emphasizes gaps that exist in the knowledge of the biology of these viruses, their diagnosis, and their impact on production. It provides essential information to inform the implementation of more effective virus control strategies.
Identification of Adipocytokine Pathway-Related Genes in Epilepsy and Its Effect on the Peripheral Immune Landscape

Epilepsy is a multifactorial neurological disorder with recurrent epileptic seizures. Current research stresses both inflammatory and autoimmune conditions as enablers in the pathophysiological process of epilepsy. In view of the growing concern about the role of adipocytokines in antiepileptic and modulating immune responses, we aimed to investigate the relevance of the adipocytokine signaling pathway in the pathological process of epilepsy and its impacts on peripheral immune characteristics. In this study, expression profiles of 142 peripheral blood samples were downloaded from the Gene Expression Omnibus (GEO) database. Adipocytokine pathway-related genes were screened out by feature selection using machine-learning algorithms. A nomogram was then constructed and estimated for the efficacy of diagnosis. Cluster analysis was employed for the recognization of two distinct epilepsy subtypes, followed by an estimation of the immune cell infiltration levels using single-sample gene-set enrichment analysis (ssGSEA). The biological characteristics were analyzed by functional enrichment analysis. The aberrant regulation of adipocytokine signaling pathway was found in the peripheral blood of patients with epilepsy. Twenty-one differently expressed adipocytokine pathway-related genes were identified and five (RELA, PRKAB1, TNFRSF1A, CAMKK2, and CPT1B) were selected to construct a nomogram. Subsequent validations of its forecasting ability revealed that this model has satisfactory predictive value. The immune cell infiltration degrees, such as those of innate immune cells and lymphocytes, were found to significantly correlate to the levels of adipocytokine pathway-related genes. Additionally, 239 differentially expressed genes (DEGs) were identified and their biological functions were mainly enriched in the regulation of the immune response. In conclusion, our results confirmed the predictive value of adipocytokine pathway-related genes for epilepsy and explored their effects on immune infiltration, thereby improving our understanding of the pathogenesis of epilepsy and providing assistance in the diagnosis and treatment of epilepsy.
Joint design of the transmit and receive weights for coherent FDA radar

Frequency diverse array (FDA) differs from conventional array techniques in that it imposes an additional frequency offset (FO) across the array elements. The use of FO provides the FDA with the controllable degree of freedom in range dimension, offering preferable performance in joint angle and range localization, range-ambiguous clutter suppression, and low probability of intercept, as compared to its phased-array or multiple-input multiple-output (MIMO) counterparts. In particular, the FO of the coherent FDA is much smaller than the bandwidth of the baseband waveform, capable of obtaining higher transmit gain and output signal-to-interference-plus-noise ratio (SINR). In this paper, we investigate the problem of joint design of the transmit and receive weights for coherent FDA radar systems. The design problem is formulated as the maximization of the ratio of the power in the desired two-dimensional range-angle space to the power in the entire area, subject to an energy constraint that limits the emitted energy of each transmit antenna and a similarity constraint such that a good transmit beampattern can be guaranteed. Due to the resultant problem is NP-hard, therefore, a sequential optimization method based on semidefinite relaxation (SDR) technique is developed. Numerical simulations are provided to demonstrate the effectiveness of the proposed scheme.
Oscillating Water Column (OWC) Wave Energy Converter Part 1: Fixed OWC

This study reviews the recent development and research results of a fixed oscillating water column (OWC) wave energy converter (WEC). The OWC WEC can be divided into fixed and floating types based on the installation location and movement of the structure. In this article, the study on a stationary OWC WEC, which is close to commercialization through the accumulation of long-term research achievements, is divided into five research categories with a focus on primary energy conversion research. These research categories include potential-flow-based numerical analysis, wave tank experiments, computational fluid dynamics analyses toward investigation of fluid viscous effects, U-shaped OWC studies that can amplify water surface displacement in the OWC chamber, and studies on OWC prototypes that have been installed and operated in real sea environments. This review will provide an overview of recent research on the stationary OWC WEC and basic information for further detailed studies on the OWC.
Measurement of Serum Levels of 5 Amino Acids and Dimethylamine Using Liquid Chromatography-Tandem Mass Spectrometry in Patients without Septic Associated Acute Kidney Injury and with Septic Associated Acute Kidney Injury Requiring Continuous Renal Replacement Therapy

Background Acute kidney injury (AKI) is one of the most common organ failures. An early diagnosis of AKI using specific biomarkers is essential for effective treatment. This study determined the serum concentrations of selected amino acids and amines using targeted liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) in patients with AKI during sepsis and septic shock treated in the Intensive Care Unit (ICU). Material/Methods A sample of 41 patients was divided into 2 groups: (1) patients with sepsis and septic shock along required continuous renal replacement therapy (CRRT) due to AKI (n=13), and (2) patients with sepsis and septic shock but without AKI (n=28). LC-MS/MS was used to measure a serum concentration of 6 amino acids and amines: arginine, ornithine, asymmetric dimethylarginine (ADMA), symmetric dimethylarginine (SDMA), dimethylamine (DMA), and citrulline. Results There was a statistically significantly higher median DMA level in AKI patients compared to those without AKI (8.1 vs 5.2 umol/L; P=0.022). The results for the remaining molecules showed no significant differences (P>0.05). Patients with DMA ≥14.95 umol/L (n=5; 100%) and treated with CRRT presented DMA level below the cut-off point (n=7; 20%). Subjects with creatinine levels ≥1.19 mg/dL (n=11; 28%) and treated with CRRT presented creatinine levels below the cut-off point (n=1; 3%). Conclusions In patients with sepsis, increased serum levels of DMA were significantly associated with AKI requiring CRRT. It remains unclear whether increased DMA concentrations are secondary to sepsis-induced AKI or are a cause.
Adaptation of a Potyvirus Chimera Increases Its Virulence in a Compatible Host through Changes in HCPro

A viral chimera in which the P1-HCPro bi-cistron of a plum pox virus construct (PPV-GFP) was replaced by that of potato virus Y (PVY) spread slowly systemically in Nicotiana benthamiana plants and accumulated to levels that were 5−10% those of parental PPV-GFP. We tested whether consecutive mechanical passages could increase its virulence, and found that after several passages, chimera titers rose and symptoms increased. We sequenced over half the genome of passaged chimera lineages infecting two plants. The regions sequenced were 5′NCR-P1-HCPro-P3; Vpg/NIa; GFP-CP, because of being potential sites for mutations/deletions leading to adaptation. We found few substitutions, all non-synonymous: two in one chimera (nt 2053 HCPro, and 5733 Vpg/NIa), and three in the other (2359 HCPro, 5729 Vpg/NIa, 9466 CP). HCPro substitutions 2053 AUU(Ile)→ACU(Thr), and 2359 CUG(Leu)→CGG(Arg) occurred at positions where single nucleotide polymorphisms were observed in NGS libraries of sRNA reads from agroinfiltrated plants (generation 1). Remarkably, position 2053 was the only one in the sequenced protein-encoding genome in which polymorphisms were common to the four libraries, suggesting that selective pressure existed to alter that specific nucleotide, previous to any passage. Mutations 5729 and 5733 in the Vpg by contrast did not correlate with polymorphisms in generation 1 libraries. Reverse genetics showed that substitution 2053 alone increased several-fold viral local accumulation, speed of systemic spread, and systemic titers.
Extending SysML to Integrate Cost Analysis Into Model-Based Systems Engineering

Model-based systems design (MBSD), a current trend adopted by INCOSE, employs the systems modeling language (SysML), a standard introduced by OMG and INCOSE. Though there are numerous works on integrating performance exploitation in SysML, cost is not sufficiently explored as a driving design parameter. By integrating cost analysis in a popular modeling language like SysML, the proposed approach may be applied to any system designed using standardized languages and tools. In this work, we integrate cost analysis within SysML models at a generic level to explore design alternatives under specific cost and performance restrictions and perform tradeoff analysis. The proposed SysML extensions provide: 1) cost-related entities to encode cost aspects, such as capital and operating expenses, and 2) functions that enable the automatic computation of costs; these extensions are contained in a custom SysML cost profile. The feasibility and benefits of the approach are explored in two distinct real-world case studies with different purpose and characteristics. 1) Configuring a remote elderly monitoring system, taking into consideration patients' budgetary and operational concerns regarding the equipment installed in their homes. In this case, patients had the opportunity to evaluate and prioritize their concerns prior to using the system. 2) Exploring the improvement of the passengers' comfort as a level of service indicator in the Athens Metro railway system, taking into account operational cost constraints. In this case, the operator obtained forecasts of performance and cost of the metro system operation in order to choose between different operational policies.
Investigating the impact of COVID-19 pandemic on volatility patterns
and its global implication for textile industry: An empirical case study
for Shanghai Stock Exchange of China

This research paper aims to examine the impact of the COVID-19 pandemic on volatility patterns and its global implication for the textile industry in China. The COVID-19 pandemic has generated a global health crisis with profound economic, social and financial implications, but also has triggered a ruthless global recession. The global economic recovery as a result of the COVID-19 pandemic can also generate significant investment opportunities for the textile industry in China. In this paper, the application of empirical methods could explain historical prices, the movement dynamics of financial assets, and investigate various important characteristics of asset pricing that explore details of the Chinese stock market. The econometric framework includes the following: symmetric Generalize Autoregressive Conditional Heteroscedastic GARCH (1, 1) model, asymmetric GARCH models such as EGARCH and GJR models. The main aim is to identify the asymmetric volatility effect, and impact of news on the SSE Composite Index and investigate long memory properties in volatility using daily data for the sample period from 19th December 1990 to 31st December 2020. This empirical study contributes to the existing literature on the impact of the COVID-19 pandemic on international stock markets, by investigating symmetric and asymmetric volatility patterns in the case of the Shanghai Stock Exchange from China
Nanofabrication of III–V semiconductors employing diblock copolymer lithography

To fully exploit the potential advantages of ideal quantum dots (QDs) (i.e. full 3D carrier confinement), elimination of the wetting layer and a uniform monomodal QD size distribution is needed. Nanopatterning with selective metalorganic chemical vapour deposition (MOCVD) QD growth has potential for achieving a higher degree of control over the QD formation, compared with the conventional Stranski–Krastanov (SK) self-assembly growth process. QD formation employing large surface area patterning prepared by dense nano-scale (20–30 nm diameter) diblock copolymer lithography is described. The resulting pattern consists of perpendicularly ordered cylindrical domain formed as part of a self-organizing diblock copolymer, such as polystyrene-block-poly(methylmethacrylate) (PS-b-PMMA). This pattern can be transferred to an underlying substrate or dielectric layer. Selective MOCVD growth of the QDs is achieved by employing the nanopatterned template mask. The resulting QD densities of 5 × 1010 cm−2 are comparable to densities achieved using the SK self-assembly growth mode. Nanopatterned growth yields a nearly monomodal QD size distribution. Variable temperature photoluminescence has been used to characterize the optical properties of capped InGaAs QDs on GaAs (λ ∼ 1.1 µm) and InP (λ ∼ 1.5 µm) substrates and preliminary results on the incorporation of such materials into diode laser structures are discussed. The extension of nanopatterned growth, beyond the pseudomorphic limit in the case of growth of strained-layer epitaxy, can lead to defect reduction and an improved morphology when compared with non-patterned growth.
Correlation of oocyte number with serum anti-Müllerian hormone levels measured by either Access or Elecsys in fresh in vitro fertilization cycles

Objective The aim of this study was to assess the correlation of oocyte number with serum anti-Müllerian hormone (AMH) levels measured by two automated methods (Access or Elecsys) in fresh stimulated in vitro fertilization (IVF) cycles. Methods In this retrospective study at a university hospital, data were collected from 243 fresh stimulated IVF cycles performed from August 2016 to December 2020. The serum AMH level was measured by Access in 120 cycles and by Elecsys in 123 cycles. The cut-off of serum AMH for prediction of poor responders (three or fewer oocytes) or high responders (15 or more oocytes) was calculated by the receiver operating characteristic curve analysis. Results For the two automated methods, the following equations were derived: total oocyte number=2.378+1.418×(Access-AMH) (r=0.645, p<0.001) and total oocyte number=2.417+2.163×(Elecsys-AMH) (r=0.686, p<0.001). The following combined equation could be derived: (Access-AMH)=0.028+1.525×(Elecsys-AMH). To predict poor responders, the cut-off of Access-AMH was 1.215 ng/mL (area under the curve [AUC], 0.807; 95% confidence interval [CI], 0.730–0.884; p<0.001), and the cut-off of Elecsys-AMH was 1.095 ng/mL (AUC, 0.848; 95% CI, 0.773–0.923; p<0.001). To predict high responders, the cut-off of Access-AMH was 3.450 ng/mL (AUC, 0.922; 95% CI, 0.862–0.981; p<0.001), and the cut-off of Elecsys-AMH was 2.500 ng/mL (AUC, 0.884; 95% CI, 0.778–0.991; p<0.001). Conclusion Both automated methods for serum AMH measurement showed a good correlation with oocyte number and good performance for predicting poor and high responders in fresh stimulated IVF cycles. The Access method usually yielded higher measured serum AMH levels than the Elecsys method.
Corrosion properties of tempered medium carbon steel in 1.0 M HCl and homemade vinegar

ABSTRACT. The consumable palm wine has never been used in heat treatment process of steels. This research therefore focuses on the utilization of the consumable palm wine and other palm tree products as quenchants. The mechanical and physical properties of the samples were also evaluated to determine which of the quenchants that influences the hardness and corrosion rate values of medium carbon steel the most. The corrosion test was performed in 1.0 M of HCl solution and homemade vinegar using potentiodynamic polarization method. The results revealed a hardness value of 431, 351, 359 and 265 HB for the samples quenched in palm wine, palm kernel oil, palm oil and as-received, respectively. The corrosion rates of palm oil tempered samples showed more susceptibity to corrosion in HCl solution with a value of 2.261e+003 mil/year. Vinegar offers the highest corrosion rate with a value of 4.017e+002 mil/year for palm wine tempered. The corrosion rate of the as-received samples pulled the lowest values while on the treated samples, palm kernel oil showed the least corrosion rate values. KEY WORDS: Consumable palm wine, Palm oil, Hardness, Corrosion rate, Austenitization, Quenching Bull. Chem. Soc. Ethiop. 2022, 36(4), 893-901. DOI: https://dx.doi. org/10.4314/bcse.v36i4. 14
Organizational innovation and ports logistiques: The case of Agadir port

The aim of this work is to study the contribution of organizational innovation to the achievement of the logistical performance of the port of Agadir. The results of this research highlight three areas of innovative organizational practices: structure, IS, and Human Resources. The port of Agadir has an interest in adopting management practices. This fact is observed in our qualitative study where the significant impact of organizational innovation on the logistics performance of the port is positive. The mobilization of Network theory recognizes that the managerial approach is a strategic tool for the adoption of innovative organizational practices and not as a source of costs (Michel Callon and Bruno Latour (2016).
The non-coding RNA (ncRNA)-mediated high expression of polycomb group factor 1 (PCGF1) is a prognostic biomarker and is correlated with tumor immunity infiltration in liver hepatocellular carcinoma

Background Liver hepatocellular carcinoma (LIHC) has a poor prognosis worldwide. Polycomb group factor 1 (PCGF1) was recently reported to play a tumor suppressive role in cancers. However, the molecular mechanism and competitive endogenous ribonucleic acid (ceRNA) regulatory networks of PCGF1 in LIHC are still unclear. Methods We constructed a PCGF1 ceRNA regulatory network in LIHC and identified potential prognostic markers, especially for tumor immunity. We identified the gene expression profiles and conducted correlation and survival analyses of PCGF1 and the related RNAs. We also explored the clinicopathological features and diagnostic and prognostic values of PCGF1 and constructed a nomogram to predict 1-, 3-, and 5-year survival. Based on a variety of bioinformatics tools, we confirmed the PCGF1-related signaling pathways in LIHC. Finally, the role of PCGF1 in immune cell infiltration was also analyzed. Results We found that PCGF1 was overexpressed in LIHC (P<0.001) and was linked to a poor prognosis in terms of overall survival (OS, P=0.029), the progress-free interval (PFI, P=0.002), and disease-free survival (DFS, P=0.02). Hsa-miR-22-3p was highly negatively correlated with PCGF1. Further, 3 upstream long non-coding RNAs (lncRNAs) (i.e., AC016405.3, BX284668.6, and MIR4435-2HG) were confirmed to further research. PCGF1 was positively associated with pathologic tumor stages (P=0.001), histologic grade (P=0.030), alpha fetoprotein (AFP) level (P=0.030), and vascular invasion (P=0.022). The area under the curve of PCGF1 was 0.983 [confidence interval (CI): 0.972–0.994]. In the multivariate analyses, high PCGF1 expression remained an independent factor associated with OS [hazards ratio (HR): 1.696, P=0.027], DSS (HR: 2.139, P=0.024), and the PFI (HR: 1.512, P=0.034). We found that PCGF1 was involved in some malignancy-associated signaling pathways and plays a role in regulating the immune response. Conclusions We confirmed the upstream ceRNA regulatory network of PCGF1 in LIHC. PCGF1 has an oncogenic effect and correlates with tumor immunity.
Human Polymorphonuclear Neutrophil Phenotypes Generated in vitro

Background: There are a variety of polymorphonuclear neutrophil phenotypes described in different species and health or disease situations. Objective: Study human neutrophil phenotypes generated in vitro. Methods: Heparinized human blood samples were collected with ethical consent. Polymorphonuclear neutrophils purification and autologous cultures was performed. Neutrophil stimulation was performed with LPS, fMLP or OVA. Immunofluorescence was applied. Results: “Polymorphonuclear neutrophil-antigen presenting cell” profile was generated in vitro, expressing CD80, CD86 and HLA-DR molecules. Immunofluorescence analysis show: CD80 expression, significant differences between CTFT control and CTFT fMLP (p<0.05), CTFT control and CTFT OVA (p<0.0001). CD86 expression, significant differences between CTFT control and CTFT fMLP (p<0.05), CTFT control and CTFT LPS (p<0.05), CTFT control and CTFT OVA (p<0.0001). HLA-DR expression, significant differences between CTFT control and CTFT LPS (p<0.05). About “Polymorphonuclear neutrophil-CD4-CD45RO” profile, analysis show: CD4 expression, significant differences between CTFT control and CTFT fMLP (p<0.05). CD45RO expression, no significant differences. “Polymorphonuclear neutrophil-antigen presenting cell” phenotype, released NETs with CD80, CD86 at 30 minutes: paired control samples (7.4%), stimulated with LPS (12.69%), fMLP (16.67%) and OVA (18.47%). HLA-DR expression in NETs, at 30 minutes, in paired control samples (0%), stimulated with LPS (16.17%). At 17 hs, in paired control samples (0%), with OVA stimulation (4.54%). “Polymorphonuclear neutrophil-CD4-CD45RO” phenotype, released NETs expressing CD4 and C45RO molecules. At 30 minutes, in paired control samples (0%), stimulated with LPS (7.67%), fMLP (6.38%) and OVA (0%). Conclusions: Molecules expressed by phenotypes can play a relevant role by influencing cellular microenvironment and can be taken into account as possible therapeutic targets.
An Empirical Study of Near-synonym Choice: A Comparison of Advanced EFL Learners to L1 English Speakers

Near-synonyms are words which share certain semantic similarities, yet differ in their contextual usage (e.g. acquire vs obtain, evaluate vs judge). The current study compares lexical preferences and rationalizations for choosing near-synonyms of advanced C1 level non-native speakers of English (n = 45) to those given by native speakers of English (n = 58). The data has been collected using a forced-choice questionnaire which also included a justification section meant to explore respondents’ reasoning behind their lexical choices. The findings of the study suggest that EFL students may lack the depth of vocabulary knowledge necessary to choose the most suitable word from a pair of near-synonyms. Insufficient knowledge of target words resulted in EFL learners’ lexical choices and justifications being statistically different from those given by native speakers. Based on the findings of the study, it is recommended that EFL teachers increase students’ exposure to various contexts as well as focus on vocabulary depth.