Miracle-dz/UniFAR-FTUs huggingface dataset:
Response to Cold: A Comparative Transcriptomic Analysis in Eight Cold-Adapted Yeasts

Microorganisms have evolved to colonize all biospheres, including extremely cold environments, facing several stressor conditions, mainly low/freezing temperatures. In general, terms, the strategies developed by cold-adapted microorganisms include the synthesis of cryoprotectant and stress-protectant molecules, cold-active proteins, especially enzymes, and membrane fluidity regulation. The strategy could differ among microorganisms and concerns the characteristics of the cold environment of the microorganism, such as seasonal temperature changes. Microorganisms can develop strategies to grow efficiently at low temperatures or tolerate them and grow under favorable conditions. These differences can be found among the same kind of microorganisms and from the same cold habitat. In this work, eight cold-adapted yeasts isolated from King George Island, subAntarctic region, which differ in their growth properties, were studied about their response to low temperatures at the transcriptomic level. Sixteen ORFeomes were assembled and used for gene prediction and functional annotation, determination of gene expression changes, protein flexibilities of translated genes, and codon usage bias. Putative genes related to the response to all main kinds of stress were found. The total number of differentially expressed genes was related to the temperature variation that each yeast faced. The findings from multiple comparative analyses among yeasts based on gene expression changes and protein flexibility by cellular functions and codon usage bias raise significant differences in response to cold among the studied Antarctic yeasts. The way a yeast responds to temperature change appears to be more related to its optimal temperature for growth (OTG) than growth velocity. Yeasts with higher OTG prepare to downregulate their metabolism to enter the dormancy stage. In comparison, yeasts with lower OTG perform minor adjustments to make their metabolism adequate and maintain their growth at lower temperatures.
Post-transplant Lymphoproliferative Disorder Following Cardiac Transplantation

Post-transplant lymphoproliferative disorder (PTLD) is a spectrum of lymphoid conditions frequently associated with the Epstein Barr Virus (EBV) and the use of potent immunosuppressive drugs after solid organ transplantation. PTLD remains a major cause of long-term morbidity and mortality following heart transplantation (HT). Epstein-Barr virus (EBV) is a key pathogenic driver in many PTLD cases. In the majority of PTLD cases, the proliferating immune cell is the B-cell, and the impaired T-cell immune surveillance against infected B cells in immunosuppressed transplant patients plays a key role in the pathogenesis of EBV-positive PTLD. Preventive screening strategies have been attempted for PTLD including limiting patient exposure to aggressive immunosuppressive regimens by tailoring or minimizing immunosuppression while preserving graft function, anti-viral prophylaxis, routine EBV monitoring, and avoidance of EBV seromismatch. Our group has also demonstrated that conversion from calcineurin inhibitor to the mammalian target of rapamycin (mTOR) inhibitor, sirolimus, as a primary immunosuppression was associated with a decreased risk of PTLD following HT. The main therapeutic measures consist of immunosuppression reduction, treatment with rituximab and use of immunochemotherapy regimens. The purpose of this article is to review the potential mechanisms underlying PTLD pathogenesis, discuss recent advances, and review potential therapeutic targets to decrease the burden of PTLD after HT.
A Ribosomal Perspective on Neuronal Local Protein Synthesis

Continued mRNA translation and protein production are critical for various neuronal functions. In addition to the precise sorting of proteins from cell soma to distant locations, protein synthesis allows a dynamic remodeling of the local proteome in a spatially variable manner. This spatial heterogeneity of protein synthesis is shaped by several factors such as injury, guidance cues, developmental cues, neuromodulators, and synaptic activity. In matured neurons, thousands of synapses are non-uniformly distributed throughout the dendritic arbor. At any given moment, the activity of individual synapses varies over a wide range, giving rise to the variability in protein synthesis. While past studies have primarily focused on the translation factors or the identity of translated mRNAs to explain the source of this variation, the role of ribosomes in this regard continues to remain unclear. Here, we discuss how several stochastic mechanisms modulate ribosomal functions, contributing to the variability in neuronal protein expression. Also, we point out several underexplored factors such as local ion concentration, availability of tRNA or ATP during translation, and molecular composition and organization of a compartment that can influence protein synthesis and its variability in neurons.
To Calculate Band Gap in Photonic Crystal in 2D using Finite Difference Time Domain Method

The band gap for 2D PhC with different modes and different lattice structures using FDTD have been computed. Three PBGs between the first and the second bands, between the second and the third bands and between the fourth and fifth bands are concluded. Simulation results shows that for band structure computation is of 1D PhC using FDTD, it is found that some additional solutions appear, which are drop out from the general set. They are called spurious solutions. Such solutions appear due to space discretization and because of finite solution time interval and these could be eliminated manually.
Case Report: Atypical HUS Presenting With Acute Rhabdomyolysis Highlights the Need for Individualized Eculizumab Dosing

Background Atypical hemolytic uremic syndrome (aHUS) is an ultra-rare orphan disease caused by dysregulated complement activation resulting in thrombotic microangiopathy. Although complement-mediated endothelial injury predominantly affects the renal microvasculature, extra-renal manifestations are present in a significant proportion of patients. While eculizumab has significantly improved the morbidity and mortality of this rare disease, optimizing therapeutic regimens of this highly expensive drug remains an active area of research in the treatment of aHUS. Case Presentation This report describes the case of a previously healthy 4 year-old male who presented with rhabdomyolysis preceding the development of aHUS with anuric kidney injury requiring dialysis. Clinical stabilization required increased and more frequent eculizumab doses compared with the standardized weight-based guidelines. In the maintenance phase of his disease, pharmacokinetic analysis indicated adequate eculizumab levels could be maintained with an individualized dosing regimen every 3 weeks, as opposed to standard 2 week dosing, confirmed in this patient over a 4 year follow up period. Cost analyses show that weight-based maintenance dosing costs $312,000 per year, while extending the dosing interval to every 3 weeks would cost $208,000, a savings of $104,000 per year, relative to the cost of $72,000 from more frequent eculizumab dosing during his initial hospitalization to suppress his acute disease. Conclusion This case exemplifies the potential of severe, multisystem involvement of aHUS presenting with extra-renal manifestations, including rhabdomyolysis as in this case, and highlights the possibility for improved clinical outcomes and higher value care with individualized eculizumab dosing in patients over the course of their disease.
Molecular Characteristics and Distribution of Adult Human Corneal Immune Cell Types

Background The limbus is located at a 2-mm-wide area between the bulbar conjunctiva and the cornea and has been suggested to be the niche of corneal epithelial stem cells and immune cells. Like the skin and intestines, the cornea is also an important mucosal surface, and immune cells on the cornea play critical roles in immune surveillance to ensure barrier surface homeostasis and protection from various environmental damage and infections. Single-cell RNA sequencing (scRNA-seq) analysis of protein tyrosine phosphatase receptor type C positive (PTPRC+) hematopoietic cells from the corneal limbus could provide a single cell atlas of all the immune cell subsets. Methods We performed single-cell RNA sequencing to generate transcriptomic profile for 804 sort-purified hematopoietic cells from the corneal limbus of three healthy donors. Results Our analysis identified a primary transcriptomic pattern for multiple immune cell subtypes, including naive T cells, antiviral effector CD8+ T cells, and innate immune cells such as IDO1+ mature regulatory dendritic cells (mregDCs), macrophages, monocytes, and basophils in the human corneal limbus. Conclusion Overall, single-cell transcriptomic analysis of limbal immune cells suggested the possible contribution of these cells on the adaptive and innate immune response of the human cornea.
The Effect of Orlistat on Sterol Metabolism in Obese Patients

Background Orlistat, a reversible inhibitor of pancreatic and gastric lipase, is known to have anti-obesity and antioxidant properties. Cholesterol intermediates and metabolites have diverse and important functions in cardiovascular disease. Therefore, we aimed to evaluate the effect of orlistat on sterol metabolism in overweight and obese adults after weight loss during the intervention or weight loss at 12 weeks. Methods A total of 51 (27 in the control group and 24 in the experimental group), patients with a BMI of 27 or greater were randomly assigned in a 1:1 ratio to receive either orlistat (120 mg) three times a day plus phentermine hydrochloride (37.5 mg) once daily or a placebo three times a day plus phentermine hydrochloride (37.5 mg) once daily. The primary study outcome was sterol metabolism. Results The experimental group exhibited significantly decreased metabolic signatures of serum sterols, free cholesterol, sitosterol, 7α-hydroxycholesterol (7α-OHC), and 7β-OHC at 12 weeks. The experimental group also exhibited significantly decreased metabolic ratios of sitosterol and 7α-OHC to cholesterol at 12 weeks. Regarding changes in sterol signatures from baseline to 6-month follow-up, free cholesterol, plant sterols, and cholesterol precursors tended to decrease with weight loss during the intervention and increase again as the weight was regained in both groups. Conclusion Orlistat treatment improves oxysterol metabolism in overweight and obese adults. Our findings support that orlistat plays a crucial role in the process of endothelial dysfunction and atherosclerosis via oxysterol modulation.
A generic lightwave integrated chip (GLIC) for fast high-resolution wavelength monitoring

Optical transmission technologies such as Dense-Wavelength Division Multiplexing (DWDM) have emerged in recent years to meet the demand for higher bandwidths and data rates. In order to implement such technologies, accurate determination of channel wavelengths is required. The Fabry-Perot Interferometer (FPI) offers the ability to resolve wavelengths with a 2-5 pm precision in resolution. We present here a novel Generic Lightwave Integrated Chip (GLIC) founded on the FPI. The device has been realised on a Planar Lightwave Circuit (PLC) in SiO2 on Silicon as a means to achieve the desired rapid wavelength monitoring with high resolution. In this paper, the simulation and characterisation of the device is reported and the advantages of this technology are revealed. The theory is founded on employing the concept of quadrature between 2 phase-shifted signals provided by 2 similar Fabry-Perot cavities to determine the wavelength in question with a sub-microsecond response time. The compact features of the device make it an ideal candidate for application in future silica based PLC DWDM networks. By its generic nature, the device is also an attractive choice for applications in optical sensing and biophotonics.
Insecticide selectivity to the predator Podisus nigrispinus (Heteroptera: Pentatomidae) used in eucalyptus culture

The control of defoliating caterpillars in forestry includes chemical and biological insect management. The predatory stink bug Podisus nigrispinus Dallas (Heteroptera: Pentatomidae) is a biological control agent, but some insecticides can affect this natural enemy, which needs risk assessment. Therefore, the selectivity of insecticides for use with non-target organisms in agricultural and forestry areas is essential for integrated pest management. The present work aimed to fill gaps about the effects of insecticides when used together with the predator P. nigrispinus. In chapter 1, the objective was to evaluate the side effects on survival, respiration, behavioral response, preference and consumption in third instar nymphs of P. nigrispinus when exposed to Bacillus thuringiensis (Bt), permethrin, tebufenozide and thiamethoxam in the laboratory. The insecticides permethrin and thiamethoxam were the most toxic to P. nigrispinus nymphs. The survival of nymphs of this predator was 93.3%, 66.7%, 56.6%, 0% and 0% in the control, treatments with tebufenozide, Bt, permethrin and thiamethoxam, respectively. Bt and the insecticides tebufenozide, permethrin and thiamethoxam reduced the respiratory rate of P. nigrispinus. Permethrin, tebufenozide and thiamethoxam affected the locomotion of this insect's nymphs. Prey treated with Bt, permethrin and thiamethoxam were less preferred by P. nigrispinus. Furthermore, the reduction in the consumption of prey, treated with neurotoxic insecticides, reduced the predatory potential of this natural enemy. Bt and tefubenozide had low toxicity for P. nigrispinus, but neurotoxic products had low compatibility with this natural enemy and, therefore, they are not recommended, with this predator, in the management of forest pests. In chapter 2 we investigated the survival, preference and consumption of prey and the histopathology of the midgut of adults of P. nigrispinus fed on prey treated with the lethal concentration (LC 50 ) of Bacillus thuringiensis (Bt), permethrin, tebufenozide and thiamethoxam. The insecticides Bt, permethrin and thiamethoxam reduced survival and prey consumption in P. nigrispinus fed on prey contaminated with these insecticides.However, the four insecticides tested, including tebufenozide, caused histological changes, such as irregular epithelial architecture, cytoplasmic vacuolization and release of cell fragments in the lumen of the midgut of P. nigrispinus. The sublethal effects of Bt, permethrin, tebufenozide and thiamethoxam on the natural enemy suggest that they should be better evaluated to be used in conjunction with P. nigrispinus for integrated pest management in forestry. Keywords: Biological control. Compatibility. Non target organism. Pesticides.
Nonlinear interfacial wave phenomena from the micro- to the macro-scale geometry-induced oscillations of finite bubbles in microchannels

We characterise novel propagation modes that occur when semi-infinite air fingers and finite air bubbles displace viscous fluid from microchannels. The presence of an axially-uniform rectangular occlusion within a rectangular cross-section leads to a mul- tiplicity of modes, in contrast to the single symmetric mode present in unoccluded channels. For air fingers, the asymmetric 1, oscillatory 2 and localised modes 3 first identified in millimetric channels persist at the micron-scale, confirming that significant gravitational effects are not necessary to support these states. Sufficiently large finite bubbles exhibit analogous modes with quanti- tatively similar flow measures, indicating that the physical mechanisms supporting the propagation modes of finite bubbles are the same as those identified for the air fingers 4. In contrast to the air fingers, in which oscillations are always initiated near the finger tip and propagate backwards, oscillations in finite bubbles can arise from either end of the bubble.
Denisenko N.P.1, Abdullaev Sh.P.1, Akmalova K.A.1, Sozaeva Zh.A.1, Kachanova A.A.1, Sozaeva M.S-Kh.2, Bolieva L.Z.3, Grishina E.A.1, Sychev D.A.1

common group of medicines used for pain relief in various areas of clinical medicine, accounting for 5–10% of all drugs prescribed annually [1]. However, the reasons for the possible ineffectiveness of NSAIDs and a high frequency of adverse reactions during their use in certain groups of patients have not yet been studied. NSAIDs are metabolized by CYP450 family enzymes, mainly CYP2C8 and CYP2C9 [2, 3]. Some variants of CYP2C8 and CYP2C9 genes have been shown to significantly affect the cytochrome activity profile and pharmacokinetic parameters of NSAIDs [2]. CYP2C8 and CYP2C9 genes are highly polymorphic, with 18 polymorphisms and over 70 allelic variants for each gene described to date. The allelic variants of the genes affect the enzymatic activity of CYP450, and their combination determines four different metabolic phenotypes: ultrafast, extensive (normal), intermediate and poor metabolizers [2, 3]. The phenotypic manifestations of the combinations of CYP2C8 and CYP2C9 genes variants may be among the markers of variability in the therapeutic effect and safety of NSAIDs. The second component of this variability may be genetic variants of two enzymes – prostaglandin-endoperoxide synthetase 1 and 2 (PTGS1 and PTGS2), which determine their interaction with NSAIDs. Polymorphisms of PTGS1 and PTGS2 genes that modify their activity affect the pharmacodynamic effect of NSAIDs. Recommendations from the Clinical Pharmacogenetics Implementation Consortium (CPIC) include adjusting the regimen and dose of NSAIDs according to CYP2C9 genetic variants. The recommendations consider CYP2C8, PTGS1 and PTGS2 genes as potential markers. However, the need to expand their evidence base is emphasized [4]. Given a high genetic heterogeneity of Russia's multinational population [5], identifying the pattern of the carriage of pharmacogenetic markers in ethnic groups remains an important task, especially in the context of the transition to personalized medicine. CYP2C9 isoenzymes significantly affect the biotransformation rate of many NSAIDs. Carriage of CYP2C9*2 (rs1799853) and CYP2C9*3 (rs1057910) variants has been shown to slow down NSAID metabolism that leads to increased plasma drug concentrations and an increased risk of gastrointestinal bleeding (GIB) [2, 6]. The prevalence of CYP2C9*2 and CYP2C9*3 in some Russian ethnic groups has been studied previously [7, 8], but the distribution of CYP2C8 gene variants has not been characterized. O R I G I N A L I N V E S T I G A T I O N S
Relationships of Nest-Site Selection and Nest Success of Saltmarsh Sparrows ( Ammospiza caudacuta ) in Upper Narragansett Bay , Rhode Island

This report summarizes results after 4 years (2017‒2020) of a 5-year, comprehensive field study of Saltmarsh Sparrow breeding ecology and reproductive success in a 10-ha salt marsh in upper Narragansett Bay. We found 153 active nests and documented outcomes for 152: 55 (36%) failed due to flooding, and 42 (28%) failed due to predation. Nest success (as defined by at least one chick fledging from a nest) averaged 28% over four years, with a range of 24% (2020) to 38% (2017). We banded 316 Saltmarsh Sparrows, 48% of which were adults. As is typical for the species, most Saltmarsh Sparrows nested in marsh habitats dominated by grasses: 59% of nests were placed at sites dominated by stands or mixtures of the “salt meadow” grasses (Spartina patens, Distichlis spicata, Juncus gerardii), and 18% of nests were placed in salt meadow grasses mixed with Spartina alterniflora. Sparrows selected nest sites in S. patens more frequently than would be expected based on that species’ abundance on the marsh. Unlike findings from other published studies, Saltmarsh Sparrows at our study site nested regularly (24%) at the base of, or within 15 cm of, the erect, woody stems of Iva frutescens, and nest success in that microhabitat (38%) was significantly greater than at sites lacking I. frutescens plants (22%). Based on these findings, we suggest that on salt marshes targeted for management activities to combat the negative impacts of sea-level rise, sparrow biologists work in concert with marsh-restoration specialists to strategically place spoils from restoration operations so as to promote the growth of patches of I. frutescens for use by nesting sparrows.
A case study on service quality perceptions and member retention towards Taekwondo participants in North America

COVID-19 continues to represent the challenge to Taekwondo (TKD) schools. TKD schools have been closed and faced with decreasing participants due to the Pandemic. The purpose of this study is to examine the extent to which service quality factors predict member intention for renewal in TKD schools. The target population evaluated for this study consisted of individuals aged at least 18 years or older who had attended a TKD schools. This study conducted for TKD members in the U.S. A total of 159 participants were recruited via both in-person and online surveys. This study revealed that TKD members in U.S. of various demographic backgrounds had different perceptions of service quality factors that affected their attendance at TKD schools. The findings of this study will indicate the impact on the satisfaction of various TKD programs and maintenance of membership.
The Antecedent Factors Product Innovation, Process Innovation and Firm Performance of Listed Companies in the Stock Exchange of Thailand

The purpose of this research is to study the antecedent factors product innovation, process innovation and firm performance of Listed Companies in the Stock Exchange of Thailand. This study used structured questionnaire and analyzed data gathered from 251 employees of Listed Companies in the Stock Exchange of Thailand by using stratified sampling technique and hypotheses verified through Structural Equations Modelling (SEM). The findings indicate that both product and process innovation have a strong and positive association with firm performance. Furthermore, antecedents such as customer focus, organizational learning capability and creative capability have significant impact on product innovation and positive impact on product innovation and process innovation. The results of this study could be used by any managers of Listed Companies in the Stock Exchange of Thailand to improve successful innovation projects. The results also provide companies operating in Listed Companies in the Stock Exchange of Thailand with useful information on how their policies and actions might affect their firm innovation.
Medicarpin Increases Antioxidant Genes by Inducing NRF2 Transcriptional Level in HeLa Cells

The nuclear factor erythroid-derived 2-related factor 2 (NRF2) plays a pivotal role in the regulation of genes involved in oxidative stress and drug detoxification. Therefore, it is important to find NRF2 inducers to protect cells from excessive oxidative damage. Here, we investigated the effect of medicarpin isolated from the root of Robinia pseudoacacia L. on the activity of NRF2 in HeLa cells. Medicarpin significantly induced the antioxidant response elements (ARE)-luciferase activity in a concentration-dependent manner. Furthermore, medicarpin not only induced HO-1, GCLC, and NQO1 mRNA by translocating NRF2 to the nucleus but also induced the mRNA level of NRF2. To verify the NRF2 induction mechanism by medicarpin, ~2 kb of NRF2 promoter-luciferase assay was executed. As a result, medicarpin significantly induced NRF2-luciferase activity. Moreover, medicarpin strongly inhibited the ubiquitin-dependent proteasomal degradation of NRF2. Thus, medicarpin might protect cells by promoting the NRF2 transcriptional activity.