Miracle-dz/UniFAR-FTUs huggingface dataset:
Ocean acidification reduces hardness and stiffness of the Portuguese oyster shell with impaired microstructure: a hierarchical analysis

Abstract. The rapidly intensifying process of ocean acidification (OA) due to anthropogenic CO2 is not only depleting carbonate ions necessary for calcification but also causing acidosis and disrupting internal pH homeostasis in several marine organisms. These negative consequences of OA on marine calcifiers, i.e. oyster species, have been very well documented in recent studies; however, the consequences of reduced or impaired calcification on the end-product, shells or skeletons, still remain one of the major research gaps. Shells produced by marine organisms under OA are expected to show signs of dissolution, disorganized microstructure and reduced mechanical properties. To bridge this knowledge gap and to test the above hypothesis, we investigated the effect of OA on juvenile shells of the commercially important oyster species, Magallana angulata, at ecologically and climatically relevant OA levels (using pH 8.1, 7.8, 7.5, 7.2). In lower pH conditions, a drop of shell hardness and stiffness was revealed by nanoindentation tests, while an evident porous internal microstructure was detected by scanning electron microscopy. Crystallographic orientation, on the other hand, showed no significant difference with decreasing pH using electron back-scattered diffraction (EBSD). These results indicate the porous internal microstructure may be the cause of the reduction in shell hardness and stiffness. The overall decrease of shell density observed from micro-computed tomography analysis indicates the porous internal microstructure may run through the shell, thus inevitably limiting the effectiveness of the shell's defensive function. This study shows the potential deterioration of oyster shells induced by OA, especially in their early life stage. This knowledge is critical to estimate the survival and production of edible oysters in the future ocean.
Ecological niche modelling for predicting the risk of cutaneous leishmaniasis in the Neotropical moist forest biome

A major challenge of eco-epidemiology is to determine which factors promote the transmission of infectious diseases and to establish risk maps that can be used by public health authorities. The geographic predictions resulting from ecological niche modelling have been widely used for modelling the future dispersion of vectors based on the occurrence records and the potential prevalence of the disease. The establishment of risk maps for disease systems with complex cycles such as cutaneous leishmaniasis (CL) can be very challenging due to the many inference networks between large sets of host and vector species, with considerable heterogeneity in disease patterns in space and time. One novelty in the present study is the use of human CL cases to predict the risk of leishmaniasis occurrence in response to anthropogenic, climatic and environmental factors at two different scales, in the Neotropical moist forest biome (Amazonian basin and surrounding forest ecosystems) and in the surrounding region of French Guiana. With a consistent data set never used before and a conceptual and methodological framework for interpreting data cases, we obtained risk maps with high statistical support. The predominantly identified human CL risk areas are those where the human impact on the environment is significant, associated with less contributory climatic and ecological factors. For both models this study highlights the importance of considering the anthropogenic drivers for disease risk assessment in human, although CL is mainly linked to the sylvatic and peri-urban cycle in Meso and South America.
Fluorescence in Situ Hybridization (FISH) for Detecting Anaplastic Lymphoma Kinase (ALK) Rearrangement in Lung Cancer: Clinically Relevant Technical Aspects

In 2011, the Vysis Break Apart ALK fluorescence in situ hybridization (FISH) assay was approved by the United States Food and Drug Administration as a companion diagnostic for detecting ALK rearrangement in lung cancer patients who may benefit from treatment of tyrosine kinase inhibitor therapy. This assay is the current “gold standard”. According to updated ALK testing guidelines from the College of American Pathologists, the International Association for the Study of Lung Cancer and the Association for Molecular Pathology published in 2018, ALK immunohistochemistry is formally an alternative to ALK FISH, and simultaneous detection of multiple hot spots, including, at least, ALK, ROS1, RET, MET, ERBB2, BRAF and KRAS genes is also recommended while performing next generation sequencing (NGS)-based testing. Therefore, ALK status in a specimen can be tested by different methods and platforms, even in the same institution or laboratory. In this review, we discuss several clinically relevant technical aspects of ALK FISH, including pros and cons of the unique two-step (50- to 100-cell) analysis approach employed in the Vysis Break Apart ALK FISH assay, including: the preset cutoff value of ≥15% for a positive result; technical aspects and biology of discordant results obtained by different methods; and incidental findings, such as ALK copy number gain or amplification and co-existent driver mutations. These issues have practical implications for ALK testing in the clinical laboratory following the updated guidelines.
Characterization of a novel separase-interacting protein and candidate new securin, Eip1p, in the fungal pathogen Candida albicans

Proper chromosome segregation is crucial for maintaining genomic stability and dependent on separase, a conserved and essential cohesin protease. Securins are key regulators of separases, but remain elusive in many organisms due to sequence divergence. Here, we demonstrate that the separase homologue Esp1p in the ascomycete Candida albicans, an important pathogen of humans, is essential for chromosome segregation. However, C. albicans lacks a sequence homologue of securins found in model ascomycetes. We sought a functional homologue through identifying Esp1p interacting factors. Affinity purification of Esp1p and mass spectrometry revealed Esp1p-Interacting Protein1 (Eip1p)/Orf19.955p, an uncharacterized protein specific to Candida species. Functional analyses demonstrated that Eip1p is important for chromosome segregation but not essential, and modulated in an APCCdc20-dependent manner, similar to securins. Eip1p is strongly enriched in response to methyl methanesulfate (MMS) or hydroxyurea (HU) treatment, and its depletion partially suppresses an MMS or HU-induced metaphase block. Further, Eip1p depletion reduces Mcd1p/Scc1p, a cohesin subunit and separase target. Thus, Eip1p may function as a securin. However, other defects in Eip1p-depleted cells suggest additional roles. Overall, the results introduce a candidate new securin, provide an approach for identifying these divergent proteins, reveal a putative anti-fungal therapeutic target, and highlight variations in mitotic regulation in eukaryotes.
Characterization of Cell Glycocalyx with Mass Spectrometry Methods

The cell membrane plays an important role in protecting the cell from its extracellular environment. As such, extensive work has been devoted to studying its structure and function. Crucial intercellular processes, such as signal transduction and immune protection, are mediated by cell surface glycosylation, which is comprised of large biomolecules, including glycoproteins and glycosphingolipids. Because perturbations in glycosylation could result in dysfunction of cells and are related to diseases, the analysis of surface glycosylation is critical for understanding pathogenic mechanisms and can further lead to biomarker discovery. Different mass spectrometry-based techniques have been developed for glycan analysis, ranging from highly specific, targeted approaches to more comprehensive profiling studies. In this review, we summarized the work conducted for extensive analysis of cell membrane glycosylation, particularly those employing liquid chromatography with mass spectrometry (LC-MS) in combination with various sample preparation techniques.
Utilization of Percutaneous Mechanical Circulatory Support Devices in Cardiogenic Shock Complicating Acute Myocardial Infarction and High-Risk Percutaneous Coronary Interventions

Given the tremendous progress in interventional cardiology over the last decade, a growing number of older patients, who have more comorbidities and more complex coronary artery disease, are being considered for technically challenging and high-risk percutaneous coronary interventions (PCI). The success of performing such complex PCI is increasingly dependent on the availability and improvement of mechanical circulatory support (MCS) devices, which aim to provide hemodynamic support and left ventricular (LV) unloading to enable safe and successful coronary revascularization. MCS as an adjunct to high-risk PCI may, therefore, be an important component for improvement in clinical outcomes. MCS devices in this setting can be used for two main clinical conditions: patients who present with cardiogenic shock complicating acute myocardial infarction (AMI) and those undergoing technically complex and high-risk PCI without having overt cardiogenic shock. The current article reviews the advancement in the use of various devices in both AMI complicated by cardiogenic shock and complex high-risk PCI, highlights the available hemodynamic and clinical data associated with the use of MCS devices, and presents suggestive management strategies focusing on appropriate patient selection and optimal timing and support to potentially increase the clinical benefit from utilizing these devices during PCI in this high-risk group of patients.
THEORETICAL AND EXPERIMENTAL RESEARCH OF STRENGTH PROPERTIES OF SPINE BEAM OF FREIGHT CARS

Purpose . The purpose of this paper is to analyze the results of theoretical and experimental studies of the strength properties of rolling stock; search for design tools, modeling, selection, justification of the service life extension of freight cars and their elements. Methodology . The article is based on the finite element method (FEM). It makes possible to completely automate the calculation of mechanical systems, although, as a rule, it requires a much larger number of computational operations than the classical methods of mechanics. The modern level of development of computer technology opens wide opportunities for the introduction of FEM into engineering practice. FEM is implemented in many well-known and widely distributed software products that provide strength analysis of models of machines, mechanisms, structures, including the rolling stock of railways. Findings . The article presents an analysis of the theoretical and experimental studies of the strength properties of rolling stock elements on the example of the spine beam of freight cars; calculations were performed using a modern application program package. The presented example of use of the offered approach has shown its operation capacity and efficiency, as well as correctness of the research direction. The offered approach can be used when solving similar optimization tasks in research and developmental practice of transport mechanical engineering. Originality . The authors proposed me-thod of determining the reliability indicators and solving scientific and applied problem of calculating the elements of freight cars, taking into account the operation features and the loading mode impact. This allows determining their durability at the design stage. There were developed and investigated the models of the spine beam of a freight car, on the basis of which the dependences characterizing the stress-strain state of its elements were obtained. Scientifically substantiated results of the evaluation of strength properties of spine beams of freight cars were obtained depending on their design. The aspects related to the current state and development prospects of railway transport, the use of the software complex in the design and calculation of rolling stock in the railway industry are considered. Practical value . The theoretical and experimental studies of the strength properties of rolling stock elements were considered on the example of a spine beam in a freight car. Calculations were performed using a modern software package. The application of these results will contribute to increase the safety of freight cars and improve the technical and economic performance of railway transport.
Polyphenols and Metabolites Enhance Survival in Rodents and Nematodes—Impact of Mitochondria

(1) Background: Polyphenols (PP) play an important role in the prevention of non-communicable diseases and may contribute to healthy aging. To investigate the molecular and cellular aspects of PP metabolites on longevity with a focus on mitochondrial function, we applied a pre-fermented mixture of polyphenols (Rechtsregulat®, RR) to rodents and nematodes. (2) Methods: The lifespans of Navar Medical Research Institute (NMRI) mice and C. elegans were recorded. The heat-stress resistance (37 °C) of C. elegans N2 was measured using nucleic staining. Respiration and membrane potential (ΔΨm) were measured in isolated mitochondria. The energetic metabolites adenosine triphosphate (ATP), lactate, and pyruvate were determined in lysates. Expression levels of longevity related genes were determined using quantitative real time polymerase chain reaction (qRT-PCR). Phenolic compounds were identified using ultra high performance liquid chromatography-diode array detection-Iontrap-multiple stage mass spectrometry (UHPLC-DAD-Iontrap-MSn). (3) Results: Several phenolic metabolites including protocatechuic acid (PCA) were identified in RR. Feeding of mice with RR resulted in a significantly increased lifespan. Heat-stress resistance (RR *** p = 0.0006; PCA **** p < 0.0001), median lifespan (NMRI: RR ** p = 0.0035; C. elegans RR * p = 0.0279; PCA **** p < 0.0001), and activity of mitochondrial respiratory chain complexes (RR *−** p = 0.0237 − 0.0052; PCA * p = 0.019 − 0.0208) of C. elegans were significantly increased after incubation with RR (10%) or PCA (780 µM). PCA significantly improved nematodes ΔΨm (* p = 0.02058) and ATP levels (* p = 0.029). RR significantly up-regulated lactate levels, indicating enhanced glycolysis. The expression levels of longevity related genes daf-16, sir-2.1, and skn-1 were significantly upregulated after PCA, and partially after RR administration. (4) Conclusion: Phenolic metabolites such as PCA have the potential to enhance health and lifespan and mitochondrial function, and thus may contribute to healthy aging.
Role of a patatin-like phospholipase in Plasmodium falciparum gametogenesis and malaria transmission

Significance Malaria transmission involves a complex process that is initiated when Plasmodium gametocytes ingested during a blood meal are activated in the mosquito midgut and transform into gametes. The process of gametogenesis involves rounding up of activated gametocytes, exflagellation of male gametes, and gamete egress. Here, we have used a genetic approach to identify a patatin-like phospholipase, PfPATPL1, that mediates gametocyte rounding up, exflagellation, and secretion of a perforin-like protein, PfPLP2, which ruptures peripheral membranes to enable egress. We demonstrate that genetic depletion of PfPATPL1 reduces the transmission efficiency of malaria parasites in mosquitoes. Our study identifies PfPATPL1 as a player in the process of gametogenesis and suggests that phospholipases could be targeted to inhibit transmission and help eliminate malaria. Transmission of Plasmodium falciparum involves a complex process that starts with the ingestion of gametocytes by female Anopheles mosquitoes during a blood meal. Activation of gametocytes in the mosquito midgut triggers “rounding up” followed by egress of both male and female gametes. Egress requires secretion of a perforin-like protein, PfPLP2, from intracellular vesicles to the periphery, which leads to destabilization of peripheral membranes. Male gametes also develop flagella, which assist in binding female gametes for fertilization. This process of gametogenesis, which is key to malaria transmission, involves extensive membrane remodeling as well as vesicular discharge. Phospholipase A2 enzymes (PLA2) are known to mediate membrane remodeling and vesicle secretion in diverse organisms. Here, we show that a P. falciparum patatin-like phospholipase (PfPATPL1) with PLA2 activity plays a key role in gametogenesis. Conditional deletion of the gene encoding PfPATPL1 does not affect P. falciparum blood stage growth or gametocyte development but reduces efficiency of rounding up, egress, and exflagellation of gametocytes following activation. Interestingly, deletion of the PfPATPL1 gene inhibits secretion of PfPLP2, reducing the efficiency of gamete egress. Deletion of PfPATPL1 also reduces the efficiency of oocyst formation in mosquitoes. These studies demonstrate that PfPATPL1 plays a role in gametogenesis, thereby identifying PLA2 phospholipases such as PfPATPL1 as potential targets for the development of drugs to block malaria transmission.
Interleaved Transcranial Magnetic Stimulation and Functional Magnetic Resonance Imaging: A Translational Tool

The aim of this perspective is to introduce the reader to the concurrent use of transcranial magnetic stimulation and functional magnetic resonance imaging (TMSfMRI). Our aim is to provide a thorough perspective that encompasses aspects of technical development of the technique as well as the contributions that have emerged from its use to date in cognitive neurosciences and clinical research.
A Critical Review of Animal Models Used in Acute Myeloid Leukemia Pathophysiology

Acute myeloid leukemia (AML) is one of the most frequent, complex, and heterogeneous hematological malignancies. AML prognosis largely depends on acquired cytogenetic, epigenetic, and molecular abnormalities. Despite the improvement in understanding the biology of AML, survival rates remain quite low. Animal models offer a valuable tool to recapitulate different AML subtypes, and to assess the potential role of novel and known mutations in disease progression. This review provides a comprehensive and critical overview of select available AML animal models. These include the non-mammalian Zebrafish and Drosophila models as well as the mammalian rodent systems, comprising rats and mice. The suitability of each animal model, its contribution to the advancement of knowledge in AML pathophysiology and treatment, as well as its advantages and limitations are discussed. Despite some limitations, animal models represent a powerful approach to assess toxicity, and permit the design of new therapeutic strategies.
Improved Machine Learning Approach for Wavefront Sensing

In the adaptive optics (AO) system, to improve the effectiveness and accuracy of wavefront sensing-less technology, a phase-based sensing approach using machine learning is proposed. In contrast to the traditional gradient-based optimization methods, the model we designed is based on an improved convolutional neural network. Specifically, the deconvolution layer, which reconstructs unknown input by measuring output, is introduced to represent the phase maps of the point spread functions at the in focus and defocus planes. The improved convolutional neural network is utilized to establish the nonlinear mapping between the input point spread functions and the corresponding phase maps of the optical system. Once well trained, the model can directly output the aberration map of the optical system with good precision. Adequate simulations and experiments are introduced to demonstrate the accuracy and real-time performance of the proposed method. The simulations show that even when atmospheric conditions D/r0 = 20, the detection root-mean-square of wavefront error of the proposed method is 0.1307 λ, which has a better accuracy than existing neural networks. When D/r0 = 15 and 10, the root-mean-square error is respectively 0.0909 λ and 0.0718 λ. It has certain applicative value in the case of medium and weak turbulence. The root-mean-square error of experiment results with D/r0 = 20 is 0.1304 λ, proving the correctness of simulations. Moreover, this method only needs 12 ms to accomplish the calculation and it has broad prospects for real-time wavefront sensing.
Exploring North Carolina Family and Consumer Sciences Teachers’ Attitudes Towards Breastfeeding and Infant Feeding Education Practices

Background The World Health Organization (WHO) and the United Kingdom Committee for UNICEF recommend that secondary schools include infant feeding education in the curriculum. However, little attention has been given to the study of educators’ views and practices regarding infant feeding education. Aims The aims of this research were to (1) explore North Carolina Family and Consumer Sciences teachers’ attitudes towards infant feeding education in secondary schools and (2) describe North Carolina Family and Consumer Sciences teachers’ infant feeding education practices. Methods Researchers conducted interviews (N = 19) and a survey (N = 137) using a sequential mixed methods design. The constant comparative method was used to analyze interview transcripts. Subsequently, a 33-item survey was developed to assess teachers’ attitudes and practices, and this survey was tested for validity and reliability. Results The majority of participants supported including infant feeding (n = 119, 86.9%) and breastfeeding (n = 116, 84.7%) education in high school. Approximately half of the participants supported including infant feeding (n = 71, 51.9%) and breastfeeding (n = 64, 46.7%) education in middle school. Participants reported that they taught infant feeding at both levels; topics taught included complementary foods, patterns of infant feeding, and the safe preparation of infant formula. Breastfeeding content was covered primarily in the high school Parenting and Child Development course. Conclusions North Carolina Family and Consumer Sciences teachers have positive attitudes towards teaching about breastfeeding at the secondary school level. Content about infant nutrition and breastfeeding is currently included in courses that cover child development and human nutrition.