Miracle-dz/UniFAR-FTUs huggingface dataset:
Differences in the Fatty Acid Profile, Morphology, and Tetraacetylphytosphingosine-Forming Capability Between Wild-Type and Mutant Wickerhamomyces ciferrii

One tetraacetylphytosphingosine (TAPS)-producing Wickerhamomyces ciferrii mutant was obtained by exposing wild-type W. ciferrii to γ-ray irradiation. The mutant named 736 produced up to 9.1 g/L of TAPS (218.7 mg-TAPS/g-DCW) during batch fermentation in comparison with 1.7 g/L of TAPS (52.2 mg-TAPS/g-DCW) for the wild type. The highest production, 17.7 g/L of TAPS (259.6 mg-TAPS/g-DCW), was obtained during fed-batch fermentation by mutant 736. Fatty acid (FA) analysis revealed an altered cellular FA profile of mutant 736: decrease in C16:0 and C16:1 FA levels, and increase in C18:1 and C18:2 FA levels. Although a significant change in the cellular FA profile was observed, scanning electron micrographs showed that morphology of wild-type and mutant 736 cells was similar. Genetic alteration analysis of eight TAPS biosynthesis-related genes revealed that there are no mutations in these genes in mutant 736; however, mRNA expression analysis indicated 30% higher mRNA expression of TCS10 among the eight genes in mutant 736 than that in the wild-type. Collectively, these results imply that the enhancement of TAPS biosynthesis in mutant 736 may be a consequence of system-level genetic and physiological alterations of a complicated metabolic network. Reverse metabolic engineering based on system-level omics analysis of mutant 736 can make the mutant more suitable for commercial production of TAPS.
Leber's Hereditary Optic Neuropathy: A Report on Novel mtDNA Pathogenic Variants

Leber's hereditary optic neuropathy (LHON) is due to missense point mutations affecting mitochondrial DNA (mtDNA); 90% of cases harbor the m.3460G>A, m.11778G>A, and m.14484T>C primary mutations. Here, we report and discuss five families with patients affected by symptomatic LHON, in which we found five novel mtDNA variants. Remarkably, these mtDNA variants are located in complex I genes, though without strong deleterious effect on respiration in cellular models: this finding is likely linked to the tissue specificity of LHON. This study observes that in the case of a strong clinical suspicion of LHON, it is recommended to analyze the whole mtDNA sequence, since new rare mtDNA pathogenic variants causing LHON are increasingly identified.
Dominant Optic Atrophy (DOA): Modeling the Kaleidoscopic Roles of OPA1 in Mitochondrial Homeostasis

In the year 2000, the discovery of OPA1 mutations as causative for dominant optic atrophy (DOA) was pivotal to rapidly expand the field of mitochondrial dynamics and describe the complex machinery governing this pathway, with a multitude of other genes and encoded proteins involved in neurodegenerative disorders of the optic nerve. OPA1 turned out to be a much more complex protein than initially envisaged, connecting multiple pathways beyond its strict role in mitochondrial fusion, such as sensing of OXPHOS needs and mitochondrial DNA maintenance. As a consequence, an increasing need to investigate OPA1 functions at multiple levels has imposed the development of multiple tools and models that are here reviewed. Translational mitochondrial medicine, with the ultimate objective of translating basic science necessary to understand pathogenic mechanisms into therapeutic strategies, requires disease modeling at multiple levels: from the simplest, like in yeast, to cell models, including the increasing use of reprogrammed stem cells (iPSCs) from patients, to animal models. In the present review, we thoroughly examine and provide the state of the art of all these approaches.
The Spatial Distribution of Relative Corneal Refractive Power Shift and Axial Growth in Myopic Children: Orthokeratology Versus Multifocal Contact Lens

Purpose To determine if the spatial distribution of the relative corneal refractive power shift (RCRPS) explains the retardation of axial length (AL) elongation after treatment by either orthokeratology (OK) or multifocal soft contact lenses (MFCLs). Methods Children (8–14 years) were enrolled in the OK (n = 35) or MFCL (n = 36) groups. RCRPS maps were derived by computing the difference between baseline and 12-month corneal topography maps and then subtracting the apex values. Values at the same radius were averaged to obtain the RCRPS profile, from which four parameters were extracted: (1) Half_x and (2) Half_y, i.e., the x- and y-coordinates where each profile first reached the half peak; (3) Sum4 and (4) Sum7, i.e., the summation of powers within a corneal area of 4- and 7-mm diameters. Correlations between AL elongation and these parameters were analyzed by multiple linear regression. Results AL elongation in the OK group was significantly smaller than that in the MFCL group (p = 0.040). Half_x and Half_y were also smaller in the OK group than the MFCL group (p < 0.001 each). Half_x was correlated with AL elongation in the OK group (p = 0.005), but not in the MFCL group (p = 0.600). In an analysis that combined eyes of both groups, Half_x was correlated with AL elongation (β = 0.161, p < 0.001). Conclusions The OK-induced AL elongation and associated RCRPS Half_x were smaller than for the MFCL. Contact lenses that induce RCRPS closer to the corneal center may exert better myopia control.
Abnormal Liver Function Tests Were Associated With Adverse Clinical Outcomes: An Observational Cohort Study of 2,912 Patients With COVID-19

Background and Aim: The impact of liver function test (LFTs) abnormality on adverse clinical outcomes in coronavirus disease 2019 (COVID-19) patients remains controversial. The aim of this study was to assess the impact of abnormal LFTs on clinical outcomes in a large cohort of hospitalized patients with COVID-19. Methods: We retrospectively collected data on 2,912 consecutive patients with COVID-19 who were admitted to a makeshift hospital in China between 5 February and 23 March 2020. The association between LFTs abnormalities (baseline and peak values) and clinical outcomes was measured by using Cox regression models. Results: On admission 1,414 patients (48.6%) had abnormal LFTs, with alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL), alkaline phosphatase (ALP), and gamma-glutamyltransferase (GGT) elevation in 662 (22.7%), 221 (7.6%), 52 (1.8%), 135 (4.6%), and 536 (18.5%) patients, respectively, and hypoalbuminemia in 737 (25.3%) patients. During a median 13 (IQR: 8–19) days of hospitalization, 61 patients (2.1%) died, 106 patients (3.6%) admitted to intensive care unit (ICU), and 75 patients (2.6%) required mechanical ventilation. After adjustment for confounders, baseline abnormal LFTs were independently associated with increased risks of mortality (adjusted HR 3.66, 95%CI 1.64–8.19, p = 0.002), ICU admission (adjusted HR 3.12 95%CI 1.86–5.23, p < 0.001), and mechanical ventilation (adjusted HR 3.00, 95%CI 1.63–5.52, p < 0.001), which was homogeneous across the severity of COVID-19 infection. Among the parameters of LTFs, the associations with the outcomes were more pronounced for AST and albumin abnormality. In contrast, ALT elevation was not significantly associated with those outcomes. Similar results were observed for peak values of LFTs during hospitalization. Conclusions: Abnormality of AST, albumin, TBIL, ALP, and GGT but not ALT were independently associated with adverse outcomes.
What Is an L-Cell and How Do We Study the Secretory Mechanisms of the L-Cell?

Synthetic glucagon-like peptide-1 (GLP-1) analogues are effective anti-obesity and anti-diabetes drugs. The beneficial actions of GLP-1 go far beyond insulin secretion and appetite, and include cardiovascular benefits and possibly also beneficial effects in neurodegenerative diseases. Considerable reserves of GLP-1 are stored in intestinal endocrine cells that potentially might be mobilized by pharmacological means to improve the body’s metabolic state. In recognition of this, the interest in understanding basic L-cell physiology and the mechanisms controlling GLP-1 secretion, has increased considerably. With a view to home in on what an L-cell is, we here present an overview of available data on L-cell development, L-cell peptide expression profiles, peptide production and secretory patterns of L-cells from different parts of the gut. We conclude that L-cells differ markedly depending on their anatomical location, and that the traditional definition of L-cells as a homogeneous population of cells that only produce GLP-1, GLP-2, glicentin and oxyntomodulin is no longer tenable. We suggest to sub-classify L-cells based on their differential peptide contents as well as their differential expression of nutrient sensors, which ultimately determine the secretory responses to different stimuli. A second purpose of this review is to describe and discuss the most frequently used experimental models for functional L-cell studies, highlighting their benefits and limitations. We conclude that no experimental model is perfect and that a comprehensive understanding must be built on results from a combination of models.
Neurofeedback and the Aging Brain: A Systematic Review of Training Protocols for Dementia and Mild Cognitive Impairment

Dementia describes a set of symptoms that occur in neurodegenerative disorders and that is characterized by gradual loss of cognitive and behavioral functions. Recently, non-invasive neurofeedback training has been explored as a potential complementary treatment for patients suffering from dementia or mild cognitive impairment. Here we systematically reviewed studies that explored neurofeedback training protocols based on electroencephalography or functional magnetic resonance imaging for these groups of patients. From a total of 1,912 screened studies, 10 were included in our final sample (N = 208 independent participants in experimental and N = 81 in the control groups completing the primary endpoint). We compared the clinical efficacy across studies, and evaluated their experimental designs and reporting quality. In most studies, patients showed improved scores in different cognitive tests. However, data from randomized controlled trials remains scarce, and clinical evidence based on standardized metrics is still inconclusive. In light of recent meta-research developments in the neurofeedback field and beyond, quality and reporting practices of individual studies are reviewed. We conclude with recommendations on best practices for future studies that investigate the effects of neurofeedback training in dementia and cognitive impairment.
The Role and Meaning of the Digital Transformation As a Disruptive Innovation on Small and Medium Manufacturing Enterprises

The research reported in this paper explores the impact of digital transformation as a disruptive innovation on manufacturing SMEs. The research is based on a qualitative Delphi study encompassing 49 experts from eleven EU countries. The paper aims to demonstrate how disruptive innovations affect organizational changes and determine critical factors in organizations that impact the initiating and promoting R&D of disruptive innovation. We discovered that disruptive innovations impact product/process development methods, new production concepts, new materials for products, and new organization plans. Additionally, we identified organizational changes related to the development and use of disruptive innovations in the future. We also indicate how disruptive innovations influence social and technological changes in the organizational environment. The analysis also disclosed three main groups of disruptive innovations and their impact on future smart factory development, namely the following: technological changes, the emergence of innovative products, business models and solutions and organizational culture as one of the crucial key success factors. The analysis also examined the enablers of the successful development/introduction of disruptive innovations, wherein internal and external factors were determined. Additionally, we presented obstacles and the approaches necessary to mitigate them. We can conclude from the findings that in the timeframe of 5–10 years, only the SME that uses/develops disruptive innovations will survive in the market. However, the companies do not always have a clear idea of the meaning of disruptive innovations. Therefore, it is important to set clear goals regarding the achievement of disruptive innovations in companies. It is also necessary to creatively apply presented instruments enabling improvement of organizational changes and apply some additional concepts, which we have suggested.
Multi-Platform Metabolomics Analyses Revealed the Complexity of Serum Metabolites in LPS-Induced Neuroinflammed Rats Treated with Clinacanthus nutans Aqueous Extract

The use of metabolomics as a comprehensive tool in the analysis of metabolic profiles in disease progression and therapeutic intervention is rapidly advancing. Yet, a single analytical platform could not be applied to cover the entire spectrum of a biological sample’s metabolome. In the present paper, multi-platform metabolomics approaches were explored to determine the diverse rat sera metabolites extracted from intracerebroventricular lipopolysaccharides (LPS)-induced neuroinflammed rats treated with oral therapeutic interventions of positive drug (dextromethorphan, 5 mg/kg BW); with Clinacanthus nutans (CN) aqueous extract (CNE, 500 mg/kg BW); and with phosphate buffer saline (PBS) as the control group for 14 days. Analyzed by nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC-MS) techniques, this study depicted the potential of metabolites associated with neuroinflammation and verified by MetDisease. The key observations in the perturbed metabolic pathways that showed ameliorative effects were linked to the class of amino acid and peptide metabolism involving valine, leucine, and isoleucine biosynthesis; phenylalanine, tyrosine, and tryptophan biosynthesis; and phenylalanine metabolism. Lipid metabolism of arachidonic acid metabolism, glycerophospholipid metabolism, terpenoid backbone biosynthesis, and glycosphingolipid metabolism were also affected. Current findings suggested that the putative biomarkers, especially lysophosphatidic acid (LPA) and 5-diphosphomevalonic acid from glycerophospholipid and squalene/terpenoid and cholesterol biosynthesis, respectively, showed the ameliorative effects of the drug and CN treatments by controlling cell differentiation and proliferation. Our study proved that the complex and dynamic sera profiling affected during the CN treatment was greatly influenced by the analytical platform selection as integration between the two data yielded a more holistic summary of the metabolite pattern changes. Hence, an evidence-based herb, such as CN, can be used for novel diagnostic tools in the quest for ethnopharmacological studies.
Technology Transfer Opportunities: Automated Ground-Water Monitoring, A Proven Technology

Introduction The U.S. Geological Survey (USGS) has developed and tested an automated ground-water monitoring system that measures and records values of selected water-quality properties and constituents using protocols approved for manual sampling. Prototypes using the automated process have demonstrated the ability to increase the quantity and quality of data collected and have shown the potential for reducing labor and material costs for ground-water quality data collection. Automated ground-water monitoring systems can be used to monitor known or potential contaminant sites, such as near landfills, underground storage tanks, or other facilities where potential contaminants are stored, to serve as early warning systems monitoring ground-water quality near public water-supply wells, and for ground-water quality research.
Improving Time Efficiency of TF-IDF Algorithm for Dynamic Data Streams

Different applications including search engines, plagiarism detection systems and recommender systems need to crunch the data frequently after a specific period of time. The data indexing and retrieval for such applications is becoming popular research area due to availability of huge electronic content through Internet, which is growing rapidly on daily basis. TF-IDF based term weighting scheme is commonly used to extract features of a document which are used for relevant document searching. In this paper, TF-IDF algorithm is analyzed and an efficient implementation of TF-IDF algorithm is proposed to handle such dynamic text data. Two major improvements of the traditional TF-IDF algorithm are proposed; (1) Algorithm-1: Expansion of IDF using logarithm properties and (2) Algorithm-2: Store lookup of term frequency, document frequency and IDF for reuse in next batch and efficiently update IDF of terms. The systems are evaluated on dataset of 100,000 Urdu documents. Traditional TF-IDF algorithm takes 2676520 ms (10256 ms for IDF calculation) to process complete dataset. Algorithm-1 takes 2676272 ms (10008 ms for IDF calculation), showing time efficiency in IDF calculation. Algorithm-2 is specifically designed to handle the dynamic growth of the data, which calculates the new IDF of a term using the previously computed IDF. This algorithm takes 707823 ms to process 100,000 documents. Another contribution of this study involves reduced memory consumption for TF-IDF vectors using the sparse representation of vectors. This reduces 8,945,445 MB to 353 MB to store TF-IDF of 11,724,976 terms computed from 100,000 Urdu documents.
Practical Synthesis of OpticallyPure Menthylamines Starting from Racemic Neomenthol

A reliable and scalable route to racemic and highly enantiomerically enriched menthylamines exploits the technical product rac neomenthol as the starting material. The elaborated protocol is based on nucleophilic substitution of the hydroxy moiety by azide. Subsequent reduction and resolution with tartaric acid provides the desired optically enriched menthylamines.
Do U.S. firms fly higher when bypassing the U.S. capital markets? An investigation of the short-term performance of foreign IPOs

This paper investigates the performance of U.S. firms that partake in a foreign IPO – bypassing their domestic exchanges and raising their equity in a foreign market. The globalization of equity markets along with the increased regulations to financial markets in the U.S. has potentially led to the U.S. losing its title as the premier listing market. Using a sample of 77 U.S. based firms that totally bypassed the U.S. equity markets in their capital(equity) raising activities we are able to investigate the performance of this unique sample of firms. This investigation contributes to the literature by finding that U.S. firms which bypassed the U.S. market experienced less underpricing compared with U.S. only IPOs. We alsotest the window of opportunity and prestigious underwriter IPO hypotheses on our unique data set and find statistical evidence supporting the former hypothesis yet no statistical evidence confirming the latter hypothesis.
Optimization Techniques for Lung Cancer Analysis-A Survey

Prediction of cancer cells from lung image is such a difficult task for physicians and researchers. Direct observation from images may not give exact identification of nodules present in the lung image. Optimization technique may give a better solution for analyzing the variety of cells from the images and economically it is good way of approach. The MATLAB tool box is a sufficient tool for optimization. This paper gives a brief survey on performance of different classifiers for lung cancer analysis.
The Broad-band Impedance of the SPring-8 Storage Ring

The l ongi tudi na l and t ra nsve rs e broa d-ba nd i m pedanc e of t he vac uum cha m ber of t he S Pri ng8 storage ring is estimated by simulations assuming several m odel i m pedanc e and t he re l at i on bet we en l ongi tudi na l and t ra nsve rs e i m pedanc e. The se as s um pt i ons ar e confiremed by the simulation. 1 DIMENSION OF STRUCTURE OF BEAM PIPE F igur e 1 , F igur e 2, F igur e 3, Ta ble 1 and Ta ble 2 s how t he s hape of di s cont i nuit i es of t he i nner wa ll of t he beam pipe of the storage ring[1].
Experimental study of turbulent oscillatory boundary layers in an oscillating water tunnel

A high-quality experimental study including a large number of tests which correspond to full-scale coastal boundary layer flows is conducted using an oscillating water tunnel for flow generations and a Particle Image Velocimetry system for velocity measurements. Tests are performed for sinusoidal, Stokes and forward-leaning waves over three fixed bottom roughness configurations, i.e. smooth, “sandpaper” and ceramic-marble bottoms. The experimental results suggest that the logarithmic profile can accurately represent the boundary layer flows in the very near-bottom region, so the log-profile fitting analysis can give highly accurate determinations of the theoretical bottom location and the bottom roughness. The first-harmonic velocities of both sinusoidal and nonlinear waves, as well as the second-harmonic velocities of nonlinear waves, exhibit similar patterns of vertical variation. Two dimensionless characteristic boundary layer thicknesses, the elevation of 1% velocity deficit and the elevation of maximum amplitude, are found to have power-law dependencies on the relative roughness for rough bottom tests. A weak boundary layer streaming embedded in nonlinear waves and a small Preprint submitted to Coastal Engineering March 25, 2014 but meaningful third-harmonic velocity embedded in sinusoidal waves are observed. They can be only explained by the effect of a time-varying turbulent eddy viscosity. The measured period-averaged vertical velocities suggest the presence of Prandtl’s secondary flows of the second kind in the test channel. Among the three methods to infer bottom shear stress from velocity measurements, the Reynolds stress method underestimates shear stress due to missed turbulent eddies, and the momentum integral method also significantly underestimates bottom shear stress for rough bottom tests due to secondary flows, so only the log-profile fitting method is considered to yield the correct estimate. The obtained bottom shear stresses are analyzed to give the maximum and the first three harmonics, and the results are used to validate some existing theoretical models.
Immunoinformatics studies and design of breast cancer multiepitope peptide vaccines: Diversity analysis approach

Breast cancer is one of the most diagnosed cancers in women; the number of cases continues to rise. The high prevalence and increased incidence need more attention in developing effective therapy. Current passive therapy has several drawbacks that have not yet been resolved. Thus, an alternative and preventive therapy for cancer is needed by utilizing vaccines. Immunoinformatics approach is one of the promising methods predicting epitopes in vaccine research. This approach could accelerate the initial study process of vaccine development and reduce research costs. Epitope conservancy and vaccine coverage are important parameters in vaccine research due to addressing the variability and diversity of cancer genomics. This study will be carried out on the multiepitope characterization of potential T cells against the protein mechanism in breast cancer. Proteins used in this study are Mucin-4, Phosphatase And Tensin Homolog, and Receptor tyrosine-protein kinase erbB-2. CTL epitopes, antigenicity, immunogenicity, allergenicity, and toxicity were predicted for the peptide vaccine. Immunoinformatics analysis generates a multiepitope sequence consisting of seven epitopes: DPVALVAPF, SVAYRLGTL, SQINTLNTL, RFRELVSEF, VTSANIQEF, RPRFRELVS, and MYFEFPQPL by AAY linker. The docking and molecular dynamics analyses were conducted to confirm the interactions between the multiepitope vaccine molecule and TLR-4-MD. The multiepitope vaccine construct can be an appropriate choice for further experiments.