Miracle-dz/UniFAR-FTUs huggingface dataset:
FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells

Single-cell RNA sequencing (scRNA-seq) allows the identification, characterization, and quantification of cell types in a tissue. When focused on B and T cells of the adaptive immune system, scRNA-seq carries the potential to track the clonal lineage of each analyzed cell through the unique rearranged sequence of its antigen receptor (BCR or TCR, respectively), and link it to the functional state inferred from transcriptome analysis. Here we introduce FB5P-seq, a FACS-based 5’-end scRNA-seq method for cost-effective integrative analysis of transcriptome and paired BCR or TCR repertoire in phenotypically defined B and T cell subsets. We describe in details the experimental workflow and provide a robust bioinformatics pipeline for computing gene count matrices and reconstructing repertoire sequences from FB5P-seq data. We further present two applications of FB5P-seq for the analysis of human tonsil B cell subsets and peripheral blood antigen-specific CD4 T cells. We believe our novel integrative scRNA-seq method will be a valuable option to study rare adaptive immune cell subsets in immunology research.
Intercultural communicative competence: Are Greek EFL teachers ready?

Abstract Over the years and because of globalization, English has undoubtedly become an international language, a lingua franca. In this interconnected context, a new reality for the EFL educators has arisen: the need to prepare learners for intercultural encounters, that is being able to learn and use English, for effective and appropriate interaction with other native or non-native speakers of English worldwide. It is, thus, imperative that teachers become aware of the importance of this competence so they can adapt their teaching approaches and incorporate them in the EFL classroom. This exploratory study investigated the beliefs and attitudes of EFL teachers, with regards to incorporating intercultural communicative competence (ICC) in their classroom. The aim of this study was to gain more understanding of the current status of teaching English for Intercultural Communication in the Greek EFL state classroom in terms of teachers’ understandings and attitudes towards cultural teaching and ICC. To this end, an online questionnaire with closed questions was employed to collect data from sixty-two EFL teachers teaching at Greek state schools. Statistical analyses showed that EFL teachers have high appreciation of integrating ICC in English teaching. Moreover, they seem highly value the affective and behavioural components of this competence. These findings are hoped to contribute to a better understanding of intercultural teaching in ELT so that implications should be made to enhance the quality of ELT in Greece.
Comparative Genome Analysis of the Lignocellulose Degrading Bacteria Citrobacter freundii so4 and Sphingobacterium multivorum w15

Two bacterial strains, denoted so4 and w15, isolated from wheat straw (WS)-degrading microbial consortia, were found to grow synergistically in media containing WS as the single carbon and energy source. They were identified as Citrobacter freundii so4 and Sphingobacterium multivorum w15 based on 16S rRNA gene sequencing and comparison to the respective C. freundii and S. multivorum type strains. In order to identify the mechanisms driving the synergistic interactions, we analyzed the draft genomes of the two strains and further characterized their metabolic potential. The latter analyses revealed that the strains had largely complementary substrate utilization patterns, with only 22 out of 190 compounds shared. The analyses further indicated C. freundii so4 to primarily consume amino acids and simple sugars, with laminarin as a key exception. In contrast, S. multivorum w15 showed ample capacity to transform complex polysaccharides, including intermediates of starch degradation. Sequence analyses revealed C. freundii so4 to have a genome of 4,883,214 bp, with a G + C content of 52.5%, 4,554 protein-encoding genes and 86 RNA genes. S. multivorum w15 has a genome of 6,678,278 bp, with a G + C content of 39.7%, 5,999 protein-encoding genes and 76 RNA genes. Genes for motility apparatuses (flagella, chemotaxis) were present in the genome of C. freundii so4, but absent from that of S. multivorum w15. In the genome of S. multivorum w15, 348 genes had regions matching CAZy family enzymes and/or carbohydrate-binding modules (CBMs), with 193 glycosyl hydrolase (GH) and 50 CBM domains. Remarkably, 22 domains matched enzymes of glycoside hydrolase family GH43, suggesting a strong investment in the degradation of arabinoxylan. In contrast, 130 CAZy family genes were found in C. freundii so4, with 61 GH and 12 CBM domains identified. Collectively, our results, based on both metabolic potential and genome analyses, revealed the two strains to harbor complementary catabolic armories, with S. multivorum w15 primarily attacking the WS hemicellulose and C. freundii so4 the cellobiose derived from cellulose, next to emerging oligo- or monosaccharides. Finally, C. freundii so4 may secrete secondary metabolites that S. multivorum w15 can consume, and detoxify the system by reducing the levels of (toxic) by-products.
Platelets in Amyloidogenic Mice Are Activated and Invade the Brain

Alzheimer’s disease (AD) is a neurodegenerative disease with a complex and not fully understood pathogenesis. Besides brain-intrinsic hallmarks such as abnormal deposition of harmful proteins, i.e., amyloid beta in plaques and hyperphosphorylated Tau in neurofibrillary tangles, blood-derived elements, in particular, platelets have been discussed to be involved in AD pathogenesis. The underlying mechanisms, however, are rather unexplored. Here, we investigate a potential role of platelets in an AD transgenic animal model with severe amyloid plaque formation, the APP-PS1 transgenic mice, and analyzed the presence, spatial location and activation status of platelets within the brain. In APP-PS1 mice, a higher number of platelets were located within the brain parenchyma, i.e., outside the cerebral blood vessels compared to WT controls. Such platelets were activated according to the expression of the platelet activation marker CD62P and to morphological hallmarks such as membrane protrusions. In the brain, platelets were in close contact exclusively with astrocytes suggesting an interaction between these two cell types. In the bloodstream, although the percentage of activated platelets did not differ between transgenic and age-matched control animals, APP-PS1 blood-derived platelets showed remarkable ultrastructural peculiarities in platelet-specific organelles such as the open canalicular system (OCS). This work urges for further investigations on platelets and their yet unknown functional roles in the brain, which might go beyond AD pathogenesis and be relevant for various age-related neurodegenerative diseases.
Procoagulant Phosphatidylserine-Exposing Platelets in vitro and in vivo

The physiological heterogeneity of platelets leads to diverse responses and the formation of discrete subpopulations upon platelet stimulation. Procoagulant platelets are an example of such subpopulations, a key characteristic of which is exposure either of the anionic aminophospholipid phosphatidylserine (PS) or of tissue factor on the activated platelet surface. This review focuses on the former, in which PS exposure on a subpopulation of platelets facilitates assembly of the intrinsic tenase and prothrombinase complexes, thereby accelerating thrombin generation on the activated platelet surface, contributing importantly to the hemostatic process. Mechanisms involved in platelet PS exposure, and accompanying events, induced by physiologically relevant agonists are considered then contrasted with PS exposure resulting from intrinsic pathway-mediated apoptosis in platelets. Pathologies of PS exposure, both inherited and acquired, are described. A consideration of platelet PS exposure as an antithrombotic target concludes the review.
Therapeutic Use of Vitamin C in Cancer: Physiological Considerations

Since the early studies of William J. McCormick in the 1950s, vitamin C has been proposed as a candidate for the treatment of cancer. A number of reports have shown that pharmacological concentrations of vitamin C selectively kill cancer cells in vitro and decrease the growth rates of a number of human tumor xenografts in immunodeficient mice. However, up to the date there is still doubt regarding this possible therapeutic role of vitamin C in cancer, mainly because high dose administration in cancer patients has not showed a clear antitumor activity. These apparent controversial findings highlight the fact that we lack information on the interactions that occurs between cancer cells and vitamin C, and if these transformed cells can uptake, metabolize and compartmentalize vitamin C like normal human cells do. The role of SVCTs and GLUTs transporters, which uptake the reduced form and the oxidized form of vitamin C, respectively, has been recently highlighted in the context of cancer showing that the relationship between vitamin C and cancer might be more complex than previously thought. In this review, we analyze the state of art of the effect of vitamin C on cancer cells in vitro and in vivo, and relate it to the capacity of cancer cells in acquiring, metabolize and compartmentalize this nutrient, with its implications on the potential therapeutic role of vitamin C in cancer.
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

The mitis group of streptococci (MGS) is a member of the healthy human microbiome in the oral cavity and upper respiratory tract. Troublingly, some MGS are able to escape this niche and cause infective endocarditis, a severe and devastating disease. Genome-scale models have been shown to be valuable in investigating metabolism of bacteria. Here we present the first genome-scale model, iCJ415, for Streptococcus oralis SK141. We validated the model using gene essentiality and amino acid auxotrophy data from closely related species. iCJ415 has 71-76% accuracy in predicting gene essentiality and 85% accuracy in predicting amino acid auxotrophy. Further, the phenotype of S. oralis was tested using the Biolog Phenotype microarrays, giving iCJ415 a 82% accuracy in predicting carbon sources. iCJ415 can be used to explore the metabolic differences within the MGS, and to explore the complicated metabolic interactions between different species in the human oral cavity.
The IGF/Insulin-IGFBP Axis in Corneal Development, Wound Healing, and Disease

The insulin-like growth factor (IGF) family plays key roles in growth and development. In the cornea, IGF family members have been implicated in proliferation, differentiation, and migration, critical events that maintain a smooth refracting surface that is essential for vision. The IGF family is composed of multiple ligands, receptors, and ligand binding proteins. Expression of IGF type 1 receptor (IGF-1R), IGF type 2 receptor (IGF-2R), and insulin receptor (INSR) in the cornea has been well characterized, including the presence of the IGF-1R and INSR hybrid (Hybrid-R) in the corneal epithelium. Recent data also indicates that each of these receptors display unique intracellular localization. Thus, in addition to canonical ligand binding at the plasma membrane and the initiation of downstream signaling cascades, IGF-1R, INSR, and Hybrid-R also function to regulate mitochondrial stability and nuclear gene expression. IGF-1 and IGF-2, two of three principal ligands, are polypeptide growth factors that function in all cellular layers of the cornea. Unlike IGF-1 and IGF-2, the hormone insulin plays a unique role in the cornea, different from many other tissues in the body. In the corneal epithelium, insulin is not required for glucose uptake, due to constitutive activation of the glucose transporter, GLUT1. However, insulin is needed for the regulation of metabolism, circadian rhythm, autophagy, proliferation, and migration after wounding. There is conflicting evidence regarding expression of the six IGF-binding proteins (IGFBPs), which function primarily to sequester IGF ligands. Within the cornea, IGFBP-2 and IGFBP-3 have identified roles in tissue homeostasis. While IGFBP-3 regulates growth control and intracellular receptor localization in the corneal epithelium, both IGFBP-2 and IGFBP-3 function in corneal fibroblast differentiation and myofibroblast proliferation, key events in stromal wound healing. IGFBP-2 has also been linked to cellular overgrowth in pterygium. There is a clear role for IGF family members in regulating tissue homeostasis in the cornea. This review summarizes what is known regarding the function of IGF and related proteins in corneal development, during wound healing, and in the pathophysiology of disease. Finally, we highlight key areas of research that are in need of future study.
Eye Movements During RAN as an Operationalization of the RAN-Reading “Microcosm”

Rapid Automatized Naming (RAN) is a strong predictor of reading aloud, though there is little agreement on what underpins RAN or how it relates to reading. Some theorize phonological skills, while others suggest that RAN reflects the “microcosm” of cognitive and attentional processes also required for reading, with more recent research using eye movements in an attempt to study this relationship. In the current study, we aimed to extend previous investigations to identify whether the temporal patterns of eye movements predict RAN and can, therefore, be established as a method to study the cognitive processes underlying RAN that could then be utilized to elucidate the relationship of RAN to reading. A Gazepoint eye tracker was used to record the eye movements of 93 learner readers aged 5–8 years (M age = 7.00) while performing a custom computerized alphabetic RAN task. Text reading accuracy, comprehension and rate; nonverbal intelligence; and phonological awareness abilities were also assessed. Regression analyses showed that, independently of phonological awareness, eye movements [Fixation Count (FC) and Fixation Duration (FD)] measured during RAN tasks were highly reflective of children’s rapid naming performance (92.8%). Both mean FC and mean FD during RAN tasks also predicted text reading accuracy (36.3%), comprehension (31.6%), and rate (36.2%) scores, and in predicting these text reading skills there was a high level of shared variance with RAN performance. In a sub-sample of participants, longer average FDs and counts independently discriminated children with reading difficulties (n = 18; aged 7–9) from neurotypical children matched for age (n = 18), but not from younger neurotypical children matched for reading level (n = 18; aged 5–6). Together, these results suggest that the analysis of eye movements recorded during RAN allows for the operationalization of many of the spatially and temporally-bound cognitive and attentional processes that underpin the RAN, and a step towards elucidating its relationship to reading.
Helicobacter pylori Is Associated With Precancerous and Cancerous Lesions of the Gastric Cardia Mucosa: Results of a Large Population-Based Study in China

Background: Helicobacter pylori (H. pylori) is widely accepted to be the most important cause of gastric non-cardia adenocarcinoma (GNCA), while its role in the development of gastric cardia adenocarcinoma (GCA) is not well-defined. We aimed to investigate current H. pylori infection in relation to the severity of both precancerous and cancerous lesions of the gastric cardia in an Asian population at high risk of GCA. Methods: A population-based cross-sectional study was conducted in Linzhou County, Henan Province, China. Two thousand three (2,003) randomly selected participants with data on current H. pylori infection, assayed by 13C-urea breath test (13C-UBT), and a sequence of histological diagnoses of the gastric cardia mucosa were analyzed. Results: Of 2,003 subjects, 828 (41.33%) were currently infected with H. pylori. The prevalence of current H. pylori infection increased with increasing severity of histological lesions, from 34.12% in subjects with normal gastric cardia mucosa to 52.17% in subjects with gastric cardia high-grade intraepithelial neoplasia (CHIN)/ gastric cardia adenocarcinoma (GCA) (P for trend <0.001). With H. pylori-negative subjects as the reference category, H. pylori-positive subjects had statistically significant elevated adjusted prevalence odds ratios (PORs) for each of the histological lesions. The PORs (95% CI) were 2.15 (1.74–2.64), 3.46 (2.08–5.75), 2.78 (1.90–4.07), and 3.05 (1.30–7.17) for subjects with carditis, cardia intestinal metaplasia (CIM), cardia low-grade intraepithelial neoplasia (CLIN), and CHIN/GCA), respectively. The associations remained when subjects with abnormal stomach non-cardia mucosa were excluded. Conclusions: This large epidemiologic study demonstrates a positive association between current H. pylori infection and the severity of both precancerous and cancerous lesions of the gastric cardia in an Asian population at high risk of GCA. These findings suggest that H. pylori infection may play a role throughout both early- and late-stage development of GCA.
Comparison on the Growth Variability of Vibrio parahaemolyticus Coupled With Strain Sources and Genotypes Analyses in Simulated Gastric Digestion Fluids

Vibrio parahaemolyticus is a food-borne pathogen that causes pathogenic symptoms such as diarrhea and abdominal pain. Currently no studies have shown that either pathogenic and non-pathogenic V. parahaemolyticus possess growth heterogeneity in a human environment, such as in gastric and intestinal fluids. The tlh gene is present in both pathogenic and non-pathogenic V. parahaemolyticus strains, while the tdh and trh genes are only present in pathogenic strains. This study firstly applied simulated human gastric fluids to explore growth variability of 50 strains of V. parahaemolyticus at 37°C. The bacterial growth curves were fitted by primary modified Gompertz model, and the maximum growth rate (μmax), lag time (LT), and their CV values were calculated to compare the stress response of pathogenic and non-pathogenic V. parahaemolyticus to simulated human gastric fluids. Results showed that the simulated human gastric fluids treatment significantly increased the μmax of pathogenic strains and shortened the lag time, while decreased the μmax of non-pathogenic strains and prolonged the lag time. Meanwhile, the CV values of genotypes (tlh+/tdh+/trh–) evidently increased, showing that the pathogenic genotype (tlh+/tdh+/trh–) strains had strong activity to simulated gastric fluids. All of the results indicated that the V. parahaemolyticus strains exhibited a great stress-resistant variability and growth heterogeneity to the simulated gastric fluids, which provides a novel insight to unlock the efficient control of pathogenic V. parahaemolyticus.
Integrating Social Media in Emergency Dispatch via Distributed Sensemaking

Emergency dispatchers typically answer 911 calls and relay information to first responders; however, new workflows arise when social media analysts are included in emergency dispatch work. In this study we examine emergency dispatch workflows as distributed sensemaking processes performed among 911 call takers, dispatchers, and social media analysts during simulated emergency dispatch operations. In active shooter and water rescue scenarios, emergency dispatch teams including call takers, dispatchers, and social media analysts make sense of unfolding events by analyzing, aggregating, and synthesizing information provided by 911 callers and social media users during each scenario. Findings from the simulations inform design requirements for social media analysis tools that can help analysts detect, seek, and analyze information posted on social media during a crisis, and protocols for coordinating analysts’ sensemaking activities with those of 911 call takers and dispatchers in reconfigured emergency dispatch workflows.
Information Uses and Gratifications Related to Crisis: Student Perceptions since the Egyptian Uprising

People use diverse sources of information, e.g., newspapers, TV, Internet news, social media, and face-to-face conversations, to make sense of crises. We apply uses and gratifications theory (UGT) and structural equation modeling to illustrate how using internet-based information sources since the political uprisings in Egypt influence perceptions of information satisfaction. Consistent with expectations we find that content and process gratifications constructs combine to explain information satisfaction, while social gratifications do not significantly influence satisfaction in the context of a crisis. This suggests that UGT is useful for evaluating the use of information technology in a context where information is limited in quantity and reliability.
#CampFireMissing: An Analysis of Tweets About Missing and Found People From California Wildfires

Several research studies have shown the importance of social media data for humanitarian aid. Among others, the issue of missing and lost people during disasters and emergencies is crucial for disaster managers. This work analyzes Twitter data from a recent wildfire event to determine its usefulness for the mitigation of the missing and found people issue. Data analysis performed using various filtering techniques, and trend analysis revealed that Twitter contains important information potentially useful for emergency managers and volunteers to tackle this issue. Many tweets were found containing full names, partial names, location information, and other vital clues which could be useful for finding missing people.
Novel and Stable Modifications of Intelligent Cadmium Oxide (CdO)Nanoparticles as Anti-Cancer Drug in Formation of Nucleic AcidsComplexes for Human Cancer Cells Treatment

Copyright: © 2016 Heidari A. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Modern science is based on interaction among disciplines. Biochemistry and pharmaceutical chemistry have transformed the nano-materials of everyday life, but this is merely a quick look of the future of pharmaceutical nano-compounds such as intelligent nanoparticles that behave as a sensor, anti–cancer drugs, self– reproducing pharmaceutical nano-compounds, molecules that work nano–engineering and even molecules that think may transform our world in ways not yet imagined. These advancements and developments are the result of cooperation among biochemists, pharmaceutical chemists, medicinal chemists, computer experts, materials engineers, organic chemists, physicists, pharmacists and many other researchers and scientists in all over the world. The most dramatic advancements and developments at the beginning of the twenty–first century are novel methods and techniques in biochemistry and pharmacology from collaborations among biochemists and pharmaceutical chemists [1-21].
Prevenção de recidiva de úlcera varicosa: um estudo de coorte

Objetivo Determinar a taxa de recidiva de ulcera varicosa, e verificar a associacao entre recidiva e medidas de prevencao adotadas. Metodos Estudo de coorte com 50 pacientes maiores de 18 anos com ulcera varicosa pos-cicatrizacao acompanhados durante 10 anos. A recidiva foi avaliada por meio de inspecao direta durante a avaliacao clinica, e as medidas de prevencao usadas foram informadas pelo paciente. Utilizou-se o teste qui quadrado de Pearson, sendo significante p-value ≤0,05. Resultados A recidiva de ulcera varicosa foi de 62,2%, a maioria em mulheres, seguida por idosos, analfabetos e aposentados. Mostrou-se medida eficaz na prevencao de recidivas o seguinte conjunto: uso da meia de compressao, repouso e aplicar creme hidratante. Conclusao A taxa de recidiva de ulcera varicosa foi elevada e as principais medidas de prevencao aplicadas em conjunto foram usar meia de compressao, repousar e aplicar creme hidratante.