Miracle-dz/UniFAR-FTUs huggingface dataset:
Microalgae from aeroterrestrial environments: scenedesmus vacuolatus as a potential resource for mass cultivation

Microalgae are promising microorganisms deserving attention within the vast array of new biotechnologies. They are employed in many commercial applications: human and animal nutrition, pharmaceutical and cosmetical components, wastewater treatments. One of the critical factor for the industrial uses of microalgae is the production of biomass. So two types of cultivation system have been developed to increase the biomass production: liquid cultivations and immobilized cultivations. Moreover the biomass production depends on the type of organisms. Scenedesmus vacuolatus is known to have high biomass productivity among green algae, and has been frequently tested for biotechnological applications. Understanding the real potentiality of cultivation of this alga still needs new experimental evidences. In my dissertation, I focus the attention to the possible use of Scenedesmus vacuolatus as a model organism for massive cultivation and, consequently, to develop an industrial production, either in liquid- or immobilized-culture systems. To assess potential applications of Scenedesmus vacuolatus in the fields of biomass production, it is necessary to characterize its growth and photosynthetic activity. Different sets of experiments have been carried out in both type of cultivations liquid and immobilized. Firstly, I analyze several Scenedesmus vacuolatus strains and I prove the best candidate for my experiments is 053. Secondly, in liquid culture, thanks to the support of kinetic model I highlight the bottleneck of the photosynthesis process in photobioreactor in different operating conditions is photoinhibition. Moreover, in liquid culture, Scenedesmus vacuolatus shows a very good growth performances in enclosed photobioreactors achieving high biomass in presence of 2% CO2. Thirdly, in the study of immobilized cultivation, thanks to the combination of photograph imaging analysis and pulse amplitude modulation fluorimetry, I study the first steps of the adhesion process of this microalga in submerged condition and analyze its physiological state. Also in this case, Scenedesmus vacuolatus shows positive outcomes: it has a good ability of attachment and the adhesion process is scarcely influenced by the kind of carrier used. Eventually, by studying growth of Scenedesmus vacuolatus on a on a porous substrate bioreactor (the Twin Layer system), the performances of Scenedesmus vacuolatus in liquid systems are shown lower than that ones in attached cultivation and also in this case the addition of CO2 is necessary to increase the productivity. Comparison with data obtained from other organisms in other experiments on porous substrate bioreactor shows that immobilized cultivation of Scenedesmus vacuolatus based on Twin-layer system allows to achieve very good values of biomass productivity and light yield and confirms that also in immobilized cultivation Scenedesmus vacuolatus is a good candidate for industrial uses.
Multi‐probe FISH Analysis of Immunophenotyped Chronic Lymphocytic Leukemia by Imaging Flow Cytometry

Imaging flow cytometry is an automated method that enables cells and fluorescent signals to be visualized and quantified. Here, we describe a new imaging flow cytometry method whereby fluorescence in situ hybridization (FISH) is integrated with cell phenotyping. The method, called “immuno‐flowFISH,” provides an exciting new dimension for the analysis of genomic changes in cytological samples (e.g., blood, bone marrow). Cells are analyzed in suspension without any requirement for prior cell isolation or separation. Multiple antibodies and FISH probes, each with a unique fluorophore, can be added and many thousands of cells analyzed. Specific cell populations are identified by their antigenic profile and then analyzed for the presence of chromosomal defects. Immuno‐flowFISH was applied to the assessment of chronic lymphocytic leukemia (CLL), a mature B‐cell neoplasm where chromosomal abnormalities predict prognosis and treatment requirements. This integrated immunophenotyping and multi‐probe FISH strategy could detect both structural and numerical chromosomal changes involving chromosomes 12 and 17 in CLL cells. Given that many thousands of cells were analyzed and the leukemic cells were positively identified by their immunophenotype, this multi‐probe method adds precision to the cytogenomic analysis of CLL. © 2021 Wiley Periodicals LLC.
COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases

Abstract Summary The global response to the COVID-19 pandemic has led to a rapid increase of scientific literature on this deadly disease. Extracting knowledge from biomedical literature and integrating it with relevant information from curated biological databases is essential to gain insight into COVID-19 etiology, diagnosis and treatment. We used Semantic Web technology RDF to integrate COVID-19 knowledge mined from literature by iTextMine, PubTator and SemRep with relevant biological databases and formalized the knowledge in a standardized and computable COVID-19 Knowledge Graph (KG). We published the COVID-19 KG via a SPARQL endpoint to support federated queries on the Semantic Web and developed a knowledge portal with browsing and searching interfaces. We also developed a RESTful API to support programmatic access and provided RDF dumps for download. Availability and implementation The COVID-19 Knowledge Graph is publicly available under CC-BY 4.0 license at https://research.bioinformatics. udel.edu/covid19kg/. Supplementary information Supplementary data are available at Bioinformatics online.
Agomelatine might be more appropriate for elderly, depressed, type 2 diabetes mellitus patients than paroxetine/fluoxetine

Agomelatine was a novel and melatonergic antidepressant. The present study was conducted to find out whether age was an important factor for agomelatine in treating depressed type 2 diabetes mellitus (T2DM) patients. In total, 193 depressed T2DM patients were included. There were 84 patients ranged from 27 years old to 49 years old (age phase I) (n = 44 receiving agomelatine, n = 40 receiving paroxetine or fluoxetine), and 109 patients ranged from 50 years old to 70 years old (age phase II) (n = 56 receiving agomelatine, n = 53 receiving paroxetine or fluoxetine). The Hamilton Depression Rating Scale (HDRS) score, Hamilton Anxiety Rating Scale (HARS) score, fasting plasma glucose (FPG), hemoglobin A1c (HbA1c) level and body mass index (BMI) were assessed after 12 weeks treatment. After treatment, we found that among patients in age phase I, there were no significant differences in final average HDRS score, HARS score, FPG, HbA1c level, BMI, response rate and remission rate between the two groups. However, among patients in age phase II, compared to patients receiving paroxetine or fluoxetine, patients receiving agomelatine had the significantly lower average HDRS score, HARS score, HbA1c level and BMI, and significantly higher response rate and remission rate. The incidence of treatment-related adverse events was similar between the two groups in both age phases. These results suggested that age was an important factor for agomelatine in treating depressed T2DM patients. Compared to paroxetine/fluoxetine, agomelatine might be more appropriate for elderly depressed T2DM patients.
Correlation between experimentally indicated and atomistically simulated roles of EGFR N-glycosylation*

AbstractEpidermal Growth Factor Receptor (EGFR) is a glycosylated tyrosine kinase receptor associated with several cancers. EGFR plays an important role in cancer therapy and inspired several experimental and computational (molecular dynamics simulation) studies to investigate its function and dynamics. N-glycosylation is a critical aspect of EGFR functioning that was mainly unexplained until recently due to the challenges in obtaining and analysis of the structural data involving the glycan moieties. Latest simulations of glycosylated EGFR suggest atomistic mechanisms underlying the experimentally proposed functions of N-glycans in: EGFR increased ligand binding, reduced flexibility and arrangement within the cell membrane. It was shown that the increase in the ligand binding of glycosylated EGFR is mediated by the interaction between the two glycans attached to the growth factor binding subdomains resulting in stabilization of the growth factor binding site. Persistent hydrogen bonds’ formation between .
“Let’s Talk about Skin Cancer”: Examining Association between Family Communication about Skin Cancer, Perceived Risk, and Sun Protection Behaviors

Family communication about skin cancer risk may motivate protective behaviors. However, it is unclear how widespread such communication might be. In this study, we describe prevalence and patterns (across environmental, personal, and behavioral factors) of family communication about skin cancer across N = 600 diverse (79% female, 48% Hispanic, 44% non-Hispanic White) primary care patients from Albuquerque, New Mexico, a geographical location with year-round sun exposure. Over half reported discussing general cancer (77%) and skin cancer risks (66%) with their families. The most frequent target of skin cancer risk communication included doctors (54%), followed by friends/coworkers (49%), spouse/partner (43%), other family members (38%), sisters (36%), mothers (36%), daughters (33%), sons (32%), father (24%), and brothers (22%). On average, participants reported having talked to three family members about skin cancer risks. The most frequently discussed content of skin cancer risk communication was the use of sun protection (89%), followed by the personal risk of skin cancer (68%), who had skin cancer in the family (60%), family risk of skin cancer (59%), time of sun exposure (57%), and skin cancer screening (57%). A family or personal history of cancer, higher perceived risk, higher health literacy, being non-Hispanic, having higher education or income, and proactive sun protective behavior were associated with greater family communication about general cancer and skin cancer risks. These study findings have implications for interventions that encourage discussions about skin cancer risk, sun protection, and skin cancer screening that lead to adoption of sun-safe behaviors.
KLF9 (Kruppel Like Factor 9) induced PFKFB3 (6-Phosphofructo-2-Kinase/Fructose-2, 6-Biphosphatase 3) downregulation inhibits the proliferation, metastasis and aerobic glycolysis of cutaneous squamous cell carcinoma cells

ABSTRACT Cutaneous squamous cell carcinoma (CSCC) is the second most common skin cancer in humans with increasing incidence. In this paper, we focused on the effects of krueppel-like factor 9 (KLF9) on the progression of CSCC cells by binding to PFKFB3. mRNA and protein expressions of KLF9 and PFKFB3 in human HaCaT and CSCC cells were, respectively, examined by RT-qPCR analysis and Western blot. The viability, proliferation, invasion and migration of A431 cells after transfection were analyzed with MTT, clone formation, transwell and wound healing assays. The levels of glucose, lactic acid and ATP in transfected A431 cells were detected by their commercial kits. Ki-67 expression in transfected A431 cells was determined using immunofluorescence analysis and in tumor tissues was analyzed by immunohistochemistry. The levels of migration, EMT and aerobic glycolysis-related proteins were tested with Western blot. The combination of KLF9 and PFKFB3 was confirmed by dual-luciferase reporter assay and ChIP. As a result, PFKFB3 expression was elevated in CSCC cells compared with HaCaT. Knockdown of PFKFB3 restrained the proliferation, metastasis, and aerobic glycolysis of CSCC cells. In addition, KLF9 could bind to PFKFB3. Downregulation of KLF9 crippled the inhibitory effect of knockdown of PFKFB3 on the proliferation, metastasis, and aerobic glycolysis of CSCC cells. In conclusion, PFKFB3 was transcriptionally regulated by KLF9, and PFKFB3 silencing inhibits the proliferation, metastasis, and aerobic glycolysis of cutaneous squamous cell carcinoma cells.
Dose of Cardiac Rehabilitation to Reduce Mortality and Morbidity: A Population‐Based Study

Background There is wide variability in cardiac rehabilitation (CR) dose (ie, number of sessions) delivered, and no evidence‐based recommendations regarding what dose to prescribe. We aimed to test what CR dose impacts major adverse cardiovascular events (MACEs). Methods and Results This is an historical cohort study of all patients who had coronary artery disease and who initiated supervised CR between 2002 and 2012 from a single major CR center. CR dose was defined as number of visits including exercise and patient education. Follow‐up was performed using record linkage from the Rochester Epidemiology Project. MACEs included acute myocardial infarction, unstable angina, ventricular arrhythmias, stroke, revascularization, or all‐cause mortality. Dose was analyzed in several ways, including tertiles, categories, and as a continuous variable. Cox models were adjusted for factors associated with dose and MACE. The cohort consisted of 2345 patients, who attended a mean of 12.5±11.1 of 36 prescribed sessions. After a mean follow‐up of 6 years, 695 (29.65%) patients had a MACE, including 231 who died. CR dose was inversely associated with MACE (hazard ratio, 0.66 [95% CI]; 0.55–0.91) in those completing ≥20 sessions, when compared with those not exposed to formal exercise sessions (≤1 session; log‐rank P=0.007). We did not find evidence of nonlinearity (P≥0.050), suggesting no minimal threshold nor ceiling. Each additional session was associated with a lower rate of MACE (fully adjusted hazard ratio, 0.98 [95% CI, 0.97–0.99]). Greater session frequency was also associated with lower MACE risk (fully adjusted hazard ratio, 0.74 [95% CI, 0.58–0.94]). Conclusions CR reduces MACEs, but the benefit appears to be linear, with greater risk reduction with higher doses, and no upper threshold.
Honey in wound healing: An updated review

Abstract Wound healing is a complex process with many interdependent pathophysiological and immunological mediators to restore the cellular integrity of damaged tissue. Cutaneous wound healing is the repair response to a multitude of pathologies induced by trauma, surgery, and burn leading to the restoration and functionality of the compromised cells. Many different methods have been employed to treat acute and chronic wounds, such as antimicrobial therapy, as most wounds are susceptible to infection from microbes and are difficult to treat. However, many antimicrobial agents have become ineffective in wound treatment due to the emergence of multiple drug-resistant bacteria, and failures in current wound treatment methods have been widely reported. For this reason, alternative therapies have been sought, one of which is the use of honey as a wound treatment agent. The use of honey has recently gained clinical popularity for possible use in wound treatment and regenerative medicine. With this high demand, a better delivery and application procedure is required, as well as research aiming at its bioactivity. Honey is a safe natural substance, effective in the inhibition of bacterial growth and the treatment of a broad range of wound types, including burns, scratches, diabetic boils (Skin abscesses associated with diabetic), malignancies, leprosy, fistulas, leg ulcers, traumatic boils, cervical and varicose ulcers, amputation, burst abdominal wounds, septic and surgical wounds, cracked nipples, and wounds in the abdominal wall. Honey comprises a wide variety of active compounds, including flavonoids, phenolic acid, organic acids, enzymes, and vitamins, that may act to improve the wound healing process. Tissue-engineered scaffolds have recently attracted a great deal of attention, and various scaffold fabrication techniques are being researched. Some incorporate honey to improve their delivery during wound treatment. Hence, the aim of this review is to summarize recent studies on the wound healing properties of honey.
"The Small Decisions Are What Makes it Interesting"

Games and play research at CHI employs psychological theory to investigate the ways that varied qualities of people, videogames, and play contexts contribute to nuances in player experience (PX). Play is often characterised as self-endorsed and freely chosen behaviour, and self-determination theory (SDT) proposes that this autonomous quality contributes to wellbeing restoration. However, prior research has produced only inconsistent support for this claim. In this study, 148 participants experienced an autonomy-satisfying or -frustrating puzzle before playing Spore, a videogame likely to satisfy autonomy. Need-frustrated participants showed comparatively greater improvement in autonomy, vitality, and intrinsic motivation when playing Spore, and in-game autonomy satisfaction was shown to index post-play wellbeing outcomes. However, further results were mixed, and only competence frustration was found to predict ill-being outcomes. These findings are contextualised by post-study interviews that investigate the ways that autonomy, wellbeing, and motivation emerge in and through play in daily life.
Faster R-CNN based on Optimized SqueezeNet for Liver Lesion Detection from DeepLesion Dataset

Computed tomography (CT) images have been widely used by radiologists and doctors to diagnose patients with liver cancer. However, liver lesion detection from CT images can be difficult due to the similar characteristics of the lesion region and the surrounding region. The recent developments in deep learning methods including deep learning object detection models, such as Faster Region with Convolutional Neural Network (Faster R-CNN) has shed light on whether it can contribute to liver lesion detection from CT images. Until recently, the pre-trained deep neural networks, ResNet50 and ResNet101, are applied as the feature extractors for Faster R-CNN to detect liver lesions in CT images. Nevertheless, Faster R-CNN with ResNet50 and ResNet101 have produced a very low average precision (AP) and large network size due to their massive number of parameters. In this research, a lightweight architecture has been implemented based on SqueezeNet and Faster R-CNN (Squeeze-Faster R-CNN) to detect liver lesions from CT images. The architecture of SqueezeNet has been optimized by reducing the depth of the network from 18 to 15, the number of filters has been decreased from 96 to 64, and the size of the filters was reduced from 7 × 7 to 3 × 3 in the first convolutional layer. This has improved the AP from 42.7 to 63.8 and has further reduced the number of parameters from around 1.24 million to 0.53 million. This optimized framework can be beneficial for lesion detection on embedded devices with limited memory.
Compressed Sensing Spare Reconstruction Optimization based on the NNIA

With the development of big data artificial intelligence, compressed sensing spare reconstruction (CSSR) problem has always been a research hotspot in the field of signal processing. To deal with the problem, the CSSR problem is first viewed as a multi-objective optimization algorithm. And a multi-objective CSSR model is explained by considering the factor of reconstruction error and sparsity degree. To solve the optimization model, an immune algorithm based on neighborhood selection is employed. And the value of reconstruction error and sparsity degree could be optimized by using the nondominated neighbor immune algorithm method to obtain the minimize value. Meanwhile, to verify the performance of sparse reconstruction four one-dimensional sparse signals are adopted. The simulation result show that the reconstruction error of the nondominated neighbor immune algorithm obtains the best result on the whole and the performance improve rate of can reach 40.00% at most on sparse signal F1-F4.
Bacterial Outer Membrane Vesicles as Nano‐Scale Bioreactors: A Fatty Acid Conversion Case Study

Bacterial outer membrane vesicles (OMVs) are small unilamellar proteoliposomes, involved in various functions including cell‐to‐cell signalling and protein excretion. We have engineered the OMVs of Escherichia coli to nano‐scaled bioreactors for the biotransformation of fatty acids by targeting a fatty acid double bond hydratase of Stentrophomonas maltophilia (SmOhyA) and/or a photoactivated fatty acid decarboxylase from Chlorella variabilis NC64 A (CvFAP) into OMVs. Engineered OMVs containing both SmOhyA and CvFAP were able to catalyse the transformation of oleic acid ((Z)‐octadec‐9‐enoic acid) into 9‐hydroxyheptadecane via (R)‐10‐hydroxyoctadecanoic acid. The specific biotransformation rates of oleic acid reached 8.0×10−12 μmol/min per OMV.
Genome-wide mapping of Vibrio cholerae VpsT binding identifies a mechanism for c-di-GMP homeostasis

Many bacteria use cyclic dimeric guanosine monophosphate (c-di-GMP) to control changes in lifestyle. The molecule, synthesised by proteins having diguanylate cyclase activity, is often a signal to transition from motile to sedentary behaviour. In Vibrio cholerae, c-di-GMP can exert its effects via the transcription factors VpsT and VpsR. Together, these proteins activate genes needed for V. cholerae to form biofilms. In this work, we have mapped the genome-wide distribution of VpsT in a search for further regulatory roles. We show that VpsT binds 23 loci and recognises a degenerate DNA palindrome having the consensus 5’-W-5R-4[CG]-3Y-2W-1W+1R+2[GC]+3Y+4W+5-3’. Most genes targeted by VpsT encode functions related to motility, biofilm formation, or c-di-GMP metabolism. Most notably, VpsT activates expression of the vpvABC operon that encodes a diguanylate cyclase. This creates a positive feedback loop needed to maintain intracellular levels of c-di-GMP. Mutation of the key VpsT binding site, upstream of vpvABC, severs the loop and c-di-GMP levels fall accordingly. Hence, as well as relaying the c-di-GMP signal, VpsT impacts c-di-GMP homeostasis.
A sensitized genetic screen to identify regulators of C. elegans germline stem cells

Germline stem cells (GSCs) in Caenorhabditis elegans are maintained by GLP-1/Notch signaling from the niche and by a downstream RNA regulatory network. Loss of the GLP-1 receptor causes GSCs to precociously undergo meiotic differentiation, the “Glp” phenotype, due to a failure to self-renew. lst-1 and sygl-1 are functionally redundant direct targets of GLP-1 signaling whose gene products work with PUF RNA binding proteins to promote GSC self-renewal. Whereas single loss-of-function mutants are fertile, lst-1 sygl-1 double mutants are sterile and Glp. We set out to identify genes that function redundantly with either lst-1 or sygl-1 to maintain GSCs. To this end, we conducted forward genetic screens for Glp mutants in genetic backgrounds lacking functional copies of either lst-1 or sygl-1. The screens generated nine glp-1 alleles, two lst-1 alleles, and one allele of pole-1, which encodes the catalytic subunit of DNA polymerase ε. Three glp-1 alleles reside in Ankyrin (ANK) repeats not previously mutated. pole-1 single mutants have a low penetrance Glp that is enhanced by loss of either lst-1 or sygl-1. Thus, the screen uncovered one locus that interacts genetically with both lst-1 and sygl-1 and generated useful mutations for further studies of GSC regulation.