bluuebunny/crossref_metadata_2025 huggingface dataset:
The Prescription of Vitamin K Antagonists in a Very Old Population: A Cross-Sectional Study of 8696 Ambulatory Subjects Aged Over 85 Years
Authors: Manckoundia Patrick , Rosay Clémentine , Menu Didier , Nuss Valentine , Mihai Anca-Maria , Vovelle Jérémie , Nuémi Gilles , d’Athis Philippe , Putot Alain , Barben Jérémy
Published: September 2020

We compared very elderly people taking vitamin K antagonists (VKA) and those not taking VKA (noVKA). Individuals were included in the noVKA group if there was no VKA on their reimbursed prescriptions during the study period. We also compared three subgroups, constituted by VKA type (fluindione, warfarin, or acenocoumarol). We included individuals aged over 85 years, affiliated to Mutualité Sociale Agricole of Burgundy, who were refunded for prescribed VKA in September 2017. The VKA and noVKA groups were compared in terms of demographic conditions, registered chronic diseases (RCD), number of drugs per prescription and cardiovascular medications. The three VKA subgroups were compared for the same items plus laboratory monitoring, novel and refill VKA prescriptions, and prescriber specialty. Of the 8696 included individuals, 1157 (13.30%) were prescribed VKA. Mean age was 90 years. The noVKA group had fewer women (53.67 vs 66.08%), more RCD (93.43 vs. 71.96%) and more drugs per prescription (6.65 vs. 5.18) than the VKA group (all p < 0.01). Except for direct oral anticoagulants and platelet aggregation inhibitors, the VKA group took significantly more cardiovascular medications. The most commonly prescribed VKA was fluindione (59.46%). Mean age was higher in the warfarin (90.42) than in the acenocoumarol (89.83) or fluindione (89.71) subgroups (p < 0.01). No differences were observed for sex (women were predominant) or RCD. 13% of subjects in this population had a VKA prescription. Fluindione was the most commonly prescribed VKA.
Mapping Brick Kilns to Support Environmental Impact Studies around Delhi Using Sentinel-2
Authors: Misra Prakhar , Imasu Ryoichi , Hayashida Sachiko , Arbain Ardhi Adhary , Avtar Ram , Takeuchi Wataru
Published: September 2020

Cities lying in the Indo-Gangetic plains of South Asia have the world’s worst anthropogenic air pollution, which is often attributed to urban growth. Brick kilns, facilities for producing fired clay-bricks for construction are often found at peri-urban region of South Asian cities. Although brick kilns are significant air pollutant emitters, their contribution in under-represented in air pollution emission inventories due to unavailability of their distribution. This research overcomes this gap by proposing publicly available remote sensing dataset based approach for mapping brick-kiln locations using object detection and pixel classification. As brick kiln locations are not permanent, an open-dataset based methodology is advantageous for periodically updating their locations. Brick kilns similar to Bull Trench Kilns were identified using the Sentinel-2 imagery around the state of Delhi in India. The unique geometric and spectral features of brick kilns distinguish them from other classes such as built-up, vegetation and fallow-land even in coarse resolution imagery. For object detection, transfer learning was used to overcome the requirement of huge training datasets, while for pixel-classification random forest algorithm was used. The method achieved a recall of 0.72, precision of 0.99 and F1 score of 0.83. Overall 1564 kilns were detected, which are substantially higher than what was reported in an earlier study over the same region. We find that brick kilns are located outside urban areas in proximity to outwardly expanding built-up areas and tall built structures. Duration of brick kiln operation was also estimated by analyzing the time-series of normalized difference vegetation index (NDVI) over the brick kiln locations. The brick kiln locations can be further used for updating land-use emission inventories to assess particulate matter and black carbon emissions.
Drift Invariant Metric Quality Control of Construction Sites Using BIM and Point Cloud Data
Authors: Bassier Maarten , Vincke Stan , De Winter Heinder , Vergauwen Maarten
Published: September 2020

Construction site monitoring is currently performed through visual inspections and costly selective measurements. Due to the small overhead in construction projects, additional resources are scarce to frequently conduct a metric quality assessment of the constructed objects. However, contradictory, construction projects are characterised by high failure costs which are often caused by erroneously constructed structural objects. With the upcoming use of periodic remote sensing during the different phases of the building process, new possibilities arise to advance from a selective quality analysis to an in-depth assessment of the full construction site. In this work, a novel methodology is presented to rapidly evaluate a large number of built objects on a construction site. Given a point cloud and a set of as-design BIM elements, our method evaluates the deviations between both datasets and computes the positioning errors of each object. Unlike the current state of the art, our method computes the error vectors regardless of drift, noise, clutter and (geo)referencing errors, leading to a better detection rate. The main contributions are the efficient matching of both datasets, the drift invariant metric evaluation and the intuitive visualisation of the results. The proposed analysis facilitates the identification of construction errors early on in the process, hence significantly lowering the failure costs. The application is embedded in native BIM software and visualises the objects by a simple color code, providing an intuitive indicator for the positioning accuracy of the built objects.
Electrophile-Induced Conformational Switch of the Human TRPA1 Ion Channel Detected by Mass Spectrometry
Authors: Moparthi Lavanya , Kjellström Sven , Kjellbom Per , Filipovic Milos R. , Zygmunt Peter M. , Johanson Urban
Published: September 2020

The human Transient Receptor Potential A1 (hTRPA1) ion channel, also known as the wasabi receptor, acts as a biosensor of various potentially harmful stimuli. It is activated by a wide range of chemicals, including the electrophilic compound N-methylmaleimide (NMM), but the mechanism of activation is not fully understood. Here, we used mass spectrometry to map and quantify the covalent labeling in hTRPA1 at three different concentrations of NMM. A functional truncated version of hTRPA1 (Δ1-688 hTRPA1), lacking the large N-terminal ankyrin repeat domain (ARD), was also assessed in the same way. In the full length hTRPA1, the labeling of different cysteines ranged from nil up to 95% already at the lowest concentration of NMM, suggesting large differences in reactivity of the thiols. Most important, the labeling of some cysteine residues increased while others decreased with the concentration of NMM, both in the full length and the truncated protein. These findings indicate a conformational switch of the proteins, possibly associated with activation or desensitization of the ion channel. In addition, several lysines in the transmembrane domain and the proximal N-terminal region were labeled by NMM, raising the possibility that lysines are also key targets for electrophilic activation of hTRPA1.
Therapeutic Effects of Lactoferrin in Ocular Diseases: From Dry Eye Disease to Infections
Authors: Vagge Aldo , Senni Carlotta , Bernabei Federico , Pellegrini Marco , Scorcia Vincenzo , Traverso Carlo E , Giannaccare Giuseppe
Published: September 2020

Lactoferrin is a naturally occurring iron-binding glycoprotein, produced and secreted by mucosal epithelial cells and neutrophils in various mammalian species, including humans. It is typically found in fluids like saliva, milk and tears, where it reaches the maximum concentration. Thanks to its unique anti-inflammatory, antioxidant and antimicrobial activities, topical application of lactoferrin plays a crucial role in the maintenance of a healthy ocular surface system. The present review aims to provide a comprehensive evaluation of the clinical applications of lactoferrin in ocular diseases. Besides the well-known antibacterial effect, novel interest has been rising towards its potential application in the field of dry eye and viral infections. A growing body of evidence supports the antimicrobial efficacy of lactoferrin, which is not limited to its iron-chelating properties but also depends on its capability to directly interact with pathogen particles while playing immunomodulatory effects. Nowadays, lactoferrin antiviral activity is of special interest, since lactoferrin-based eye drops could be adopted to treat/prevent the new severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection, which has conjunctivitis among its possible clinical manifestations. In the future, further data from randomized controlled studies are desirable to confirm the efficacy of lactoferrin in the wide range of ocular conditions where it can be used.
Interaction Modes of Microsomal Cytochrome P450s with Its Reductase and the Role of Substrate Binding
Authors: Esteves Francisco , Urban Philippe , Rueff José , Truan Gilles , Kranendonk Michel
Published: September 2020

The activity of microsomal cytochromes P450 (CYP) is strictly dependent on the supply of electrons provided by NADPH cytochrome P450 oxidoreductase (CPR). The variant nature of the isoform-specific proximal interface of microsomal CYPs implies that the interacting interface between the two proteins is degenerated. Recently, we demonstrated that specific CPR mutations in the FMN-domain (FD) may induce a gain in activity for a specific CYP isoform. In the current report, we confirm the CYP isoform dependence of CPR’s degenerated binding by demonstrating that the effect of four of the formerly studied FD mutants are indeed exclusive of a specific CYP isoform, as verified by cytochrome c inhibition studies. Moreover, the nature of CYP’s substrate seems to have a modulating role in the CPR:CYP interaction. In silico molecular dynamics simulations of the FD evidence that mutations induces very subtle structural alterations, influencing the characteristics of residues formerly implicated in the CPR:CYP interaction or in positioning of the FMN moiety. CPR seems therefore to be able to form effective interaction complexes with its structural diverse partners via a combination of specific structural features of the FD, which are functional in a CYP isoform dependent manner, and dependent on the substrate bound.
Mouse Ataxin-2 Expansion Downregulates CamKII and Other Calcium Signaling Factors, Impairing Granule—Purkinje Neuron Synaptic Strength
Authors: Arsović Aleksandar , Halbach Melanie Vanessa , Canet-Pons Júlia , Esen-Sehir Dilhan , Döring Claudia , Freudenberg Florian , Czechowska Nicoletta , Seidel Kay , Baader Stephan L. , Gispert Suzana , Sen Nesli-Ece , Auburger Georg
Published: September 2020

Spinocerebellar ataxia type 2 (SCA2) is caused by polyglutamine expansion in Ataxin-2 (ATXN2). This factor binds RNA/proteins to modify metabolism after stress, and to control calcium (Ca2+) homeostasis after stimuli. Cerebellar ataxias and corticospinal motor neuron degeneration are determined by gain/loss in ATXN2 function, so we aimed to identify key molecules in this atrophic process, as potential disease progression markers. Our Atxn2-CAG100-Knock-In mouse faithfully models features observed in patients at pre-onset, early and terminal stages. Here, its cerebellar global RNA profiling revealed downregulation of signaling cascades to precede motor deficits. Validation work at mRNA/protein level defined alterations that were independent of constant physiological ATXN2 functions, but specific for RNA/aggregation toxicity, and progressive across the short lifespan. The earliest changes were detected at three months among Ca2+ channels/transporters (Itpr1, Ryr3, Atp2a2, Atp2a3, Trpc3), IP3 metabolism (Plcg1, Inpp5a, Itpka), and Ca2+-Calmodulin dependent kinases (Camk2a, Camk4). CaMKIV–Sam68 control over alternative splicing of Nrxn1, an adhesion component of glutamatergic synapses between granule and Purkinje neurons, was found to be affected. Systematic screening of pre/post-synapse components, with dendrite morphology assessment, suggested early impairment of CamKIIα abundance together with the weakening of parallel fiber connectivity. These data reveal molecular changes due to ATXN2 pathology, primarily impacting excitability and communication.
Aldehyde Dehydrogenase 2 Ameliorates Chronic Alcohol Consumption-Induced Atrial Fibrillation through Detoxification of 4-HNE
Authors: Hsu Lung-An , Tsai Feng-Chun , Yeh Yung-Hsin , Chang Chi-Jen , Kuo Chi-Tai , Chen Wei-Jan , Tsai Hsin-Yi , Chang Gwo-Jyh
Published: September 2020

Aldehyde dehydrogenase 2 (ALDH2) is an enzyme that detoxifies reactive oxygen species (ROS)-generated aldehyde adducts such as 4-hydroxy-trans-2-nonenal (4-HNE). Previous meta-analyses have shown an increase in the risk of atrial fibrillation (AF) in patients with chronic alcohol consumption. ALDH2*2, a common dysfunctional polymorphism in the ALDH2 gene, has been linked to an increased risk of cancer and heart disease. We tested the effect of ALDH2 deficiency on alcohol-induced AF in a murine model of chronic-binge ethanol feeding, with ALDH2*2 knock-in (KI) mice generated by a CRISPR/CAS9 system. In addition, right atrial appendages were obtained from eight patients with AF undergoing open heart surgery. The results showed that burst atrial pacing induced a greater susceptibility to AF in ALDH2*2 KI mice exposed to chronic ethanol intoxication than in wild-type mice, resulting from a higher degree of 4-HNE accumulation and collagen deposition in their atria. Alda-1 attenuated transforming growth factor beta 1 (TGF-β1) expression and collagen deposition in the atria and reduced AF inducibility. Patients with AF and the ALDH2*2 allele exhibited greater oxidative stress and substrate remodeling in their atria than non-carriers. In conclusion, ALDH2 deficiency may increase the risk of chronic alcohol and tachypacing-induced AF through the accumulation of 4-HNE and increased ROS production.
Extracellular Vesicles in Bone Metastasis: Key Players in the Tumor Microenvironment and Promising Therapeutic Targets
Authors: Tamura Takaaki , Yoshioka Yusuke , Sakamoto Shinichi , Ichikawa Tomohiko , Ochiya Takahiro
Published: September 2020

Extracellular vesicles (EVs) are lipid membranous vesicles that are released from every type of cell. It has become clear that EVs are involved in a variety of biological phenomena, including cancer progression, and play critical roles in intracellular communication through the horizontal transfer of cellular cargoes such as proteins, DNA fragments, RNAs including mRNA and non-coding RNAs (microRNA, piRNA, and long non-coding RNA) and lipids. The most common cause of death associated with cancer is metastasis. Recent investigations have revealed that EVs are deeply associated with metastasis. Bone is a preferred site of metastasis, and bone metastasis is generally incurable and dramatically affects patient quality of life. Bone metastasis can cause devastating complications, including hypercalcemia, pathological fractures, spinal compression, and bone pain, which result in a poor prognosis. Although the mechanisms underlying bone metastasis have yet to be fully elucidated, increasing evidence suggests that EVs in the bone microenvironment significantly contribute to cancer progression and cancer bone tropism. Emerging evidence on EV functions in bone metastasis will facilitate the discovery of novel treatments. In this review, we will discuss the remarkable effects of EVs, especially on the tumor microenvironment in bone.
The Hidden Fragility in the Heart of the Athletes: A Review of Genetic Biomarkers
Authors: Barretta Ferdinando , Mirra Bruno , Monda Emanuele , Caiazza Martina , Lombardo Barbara , Tinto Nadia , Scudiero Olga , Frisso Giulia , Mazzaccara Cristina
Published: September 2020

Sudden cardiac death (SCD) is a devastating event which can also affect people in apparent good health, such as young athletes. It is known that intense and continuous exercise along with a genetic background that predisposes a person to the risk of fatal arrhythmias is a trigger for SCD. Therefore, knowledge of the athlete’s genetic conditions underlying the onset of SCD must be extended, in order to develop new effective prevention and/or therapeutic strategies. Arrhythmic features occur across a broad spectrum of cardiac diseases, sometimes presenting with overlapping phenotypes. The genetic basis of arrhythmogenic disorders has been greatly highlighted in the last 30 years, and has shown marked heterogeneity. The advent of next-generation sequencing has constantly updated our understanding of the genetic basis of arrhythmogenic diseases and is laying the foundation for precision medicine. With the exception of a few clinical cases involving a single athlete showing a highly suspected phenotype for the presence of a heart disease, there are few studies to date that analysed the applicability of genetic testing on cohorts of athletes. This evidence shows that genetic testing can contribute to the diagnosis of up to 13% of athletes; however, the presence of clinical markers is essential. This review aims to provide a reference collection on current knowledge of the genetic basis of sudden cardiac death in athletes and to review updated evidence on the effectiveness of genetic testing in early identification of athletes at risk for SCD.
Characterization of Rat Cardiovascular System by Anacrotic/Dicrotic Notches in the Condition of Increase/Decrease of NO Bioavailability
Authors: Tomasova Lenka , Misak Anton , Kurakova Lucia , Grman Marian , Ondrias Karol
Published: September 2020

We characterized modes of action of NO-donor S-nitrosoglutathione (GSNO) and NO-synthase inhibitor l-NAME derived from dicrotic (DiN) and anacrotic (AnN) notches of rat arterial pulse waveform (APW) in the condition of increased/decreased NO bioavailability. The cross-relationship patterns of DiN and AnN with 34 hemodynamic parameters (HPs) induced by GSNO and l-NAME are presented. After GSNO bolus administration, approximate non-hysteresis relationships were observed in the difference between DiN–AnN (mmHg) blood pressure (BP) and other 19 HPs, suggesting that these HPs, i.e., their signaling pathways, responding to NO concentration, are directly connected. Hysteresis relationships were observed between DiN-AnN (mmHg) and other 14 HPs, suggesting that signaling pathways of these HPs are indirectly connected. The hysteresis relationships were only observed between the time interval DiN-AnN (ms) and other 34 HPs, indicating no direct connection of signaling pathways. The cross-relationship patterns of DiN-AnN (mmHg), but not DiN-AnN (ms), induced by l-NAME were in accordance to the increased NO bioavailability induced by GSNO. In conclusion, we found the non-hysteresis/hysteresis cross-relationship “patterns” of DiN-AnN intervals to other HPs in the presence of GSNO that revealed their direct or indirect signaling pathways connections. This may contribute to our understanding of biological effects of natural substances that modulate NO production and/or NO signaling pathways.
Predicting Nonalcoholic Fatty Liver Disease through a Panel of Plasma Biomarkers and MicroRNAs in Female West Virginia Population
Authors: Pillai Sneha S. , Lakhani Hari Vishal , Zehra Mishghan , Wang Jiayan , Dilip Anum , Puri Nitin , O’Hanlon Kathleen , Sodhi Komal
Published: September 2020

(1) Background: Nonalcoholic fatty liver disease (NAFLD) is primarily characterized by the presence of fatty liver, hepatic inflammation and fibrogenesis eventually leading to nonalcoholic steatohepatitis (NASH) or cirrhosis. Obesity and diabetes are common risk factors associated with the development and progression of NAFLD, with one of the highest prevalence of these diseased conditions in the West Virginia population. Currently, the diagnosis of NAFLD is limited to radiologic studies and biopsies, which are not cost-effective and highly invasive. Hence, this study aimed to develop a panel and assess the progressive levels of circulatory biomarkers and miRNA expression in patients at risk for progression to NASH to allow early intervention strategies. (2) Methods: In total, 62 female patients were enrolled and blood samples were collected after 8–10 h of fasting. Computed tomography was performed on abdomen/pelvis following IV contrast administration. The patients were divided into the following groups: Healthy subjects with normal BMI and normal fasting blood glucose (Control, n = 20), Obese with high BMI and normal fasting blood glucose (Obese, n = 20) and Obese with high fasting blood glucose (Obese + DM, n = 22). Based on findings from CT, another subset was created from Obese + DM group with patients who showed signs of fatty liver infiltration (Obese + DM(FI), n = 10). ELISA was performed for measurement of plasma biomarkers and RT-PCR was performed for circulating miRNA expression. (3) Results: Our results show significantly increased levels of plasma IL-6, Leptin and FABP-1, while significantly decreased level of adiponectin in Obese, Obese + DM and Obese + DM(FI) group, as compared to healthy controls. The level of CK-18 was significantly increased in Obese + DM(FI) group as compared to control. Subsequently, the expression of miR-122, miR-34a, miR-375, miR-16 and miR-21 was significantly increased in Obese + DM and Obese + DM(FI) group as compared to healthy control. Our results also show distinct correlation of IL-6, FABP-1 and adiponectin levels with the expression of miRNAs in relation to the extent of NAFLD progression. (4) Conclusion: Our results support the clinical application of these biomarkers and miRNAs in monitoring the progression of NAFLD, suggesting a more advanced diagnostic potential of this panel than conventional methods. This panel may provide an appropriate method for early prognosis and management of NAFLD and subsequent adverse hepatic pathophysiology, potentially reducing the disease burden on the West Virginia population.
Intra-Tumoral Angiogenesis Is Associated with Inflammation, Immune Reaction and Metastatic Recurrence in Breast Cancer
Authors: Oshi Masanori , Newman Stephanie , Tokumaru Yoshihisa , Yan Li , Matsuyama Ryusei , Endo Itaru , Nagahashi Masayuki , Takabe Kazuaki
Published: September 2020

Angiogenesis is one of the hallmarks of cancer. We hypothesized that intra-tumoral angiogenesis correlates with inflammation and metastasis in breast cancer patients. To test this hypothesis, we generated an angiogenesis pathway score using gene set variation analysis and analyzed the tumor transcriptome of 3999 breast cancer patients from The Cancer Genome Atlas Breast Cancer (TCGA-BRCA), Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), GSE20194, GSE25066, GSE32646, and GSE2034 cohorts. We found that the score correlated with expression of various angiogenesis-, vascular stability-, and sphingosine-1-phosphate (S1P)-related genes. Surprisingly, the angiogenesis score was not associated with breast cancer subtype, Nottingham pathological grade, clinical stage, response to neoadjuvant chemotherapy, or patient survival. However, a high score was associated with a low fraction of both favorable and unfavorable immune cell infiltrations except for dendritic cell and M2 macrophage, and with Leukocyte Fraction, Tumor Infiltrating Lymphocyte Regional Fraction and Lymphocyte Infiltration Signature scores. High-score tumors had significant enrichment for unfavorable inflammation-related gene sets (interleukin (IL)6, and tumor necrosis factor (TNF)α- and TGFβ-signaling), as well as metastasis-related gene sets (epithelial mesenchymal transition, and Hedgehog-, Notch-, and WNT-signaling). High score was significantly associated with metastatic recurrence particularly to brain and bone. In conclusion, using the angiogenesis pathway score, we found that intra-tumoral angiogenesis is associated with immune reaction, inflammation and metastasis-related pathways, and metastatic recurrence in breast cancer.
Identification, Characterization, and Genomic Analysis of Novel Serratia Temperate Phages from a Gold Mine
Authors: Bujak Katarzyna , Decewicz Przemyslaw , Kaminski Jerzy , Radlinska Monika
Published: September 2020

Bacteria of the genus Serratia inhabit a variety of ecological niches like water, soil, and the bodies of animals, and have a wide range of lifestyles. Currently, the complete genome sequences of 25 Serratia phages are available in the NCBI database. All of them were isolated from nutrient-rich environments like sewage, with the use of clinical Serratia strains as hosts. In this study, we identified a novel Serratia myovirus named vB_SspM_BZS1. Both the phage and its host Serratia sp. OS31 were isolated from the same oligotrophic environment, namely, an abandoned gold mine (Zloty Stok, Poland). The BZS1 phage was thoroughly characterized here in terms of its genomics, morphology, and infection kinetics. We also demonstrated that Serratia sp. OS31 was lysogenized by mitomycin-inducible siphovirus vB_SspS_OS31. Comparative analyses revealed that vB_SspM_BZS1 and vB_SspS_OS31 were remote from the known Serratia phages. Moreover, vB_SspM_BZS1 was only distantly related to other viruses. However, we discovered similar prophage sequences in genomes of various bacteria here. Additionally, a protein-based similarity network showed a high diversity of Serratia phages in general, as they were scattered across nineteen different clusters. In summary, this work broadened our knowledge on the diverse relationships of Serratia phages.
Molecular Alterations in Spermatozoa of a Family Case Living in the Land of Fires—A First Look at Possible Transgenerational Effects of Pollutants
Authors: Lettieri Gennaro , Marra Federica , Moriello Claudia , Prisco Marina , Notari Tiziana , Trifuoggi Marco , Giarra Antonella , Bosco Liana , Montano Luigi , Piscopo Marina
Published: September 2020

In our previous work, we reported alterations in protamines/histones ratio, in DNA binding of these proteins and their involvement in DNA oxidative damage in 84% of the young men living in the Land of Fires. In the present work, we extended our findings, evaluating any alterations in spermatozoa of a family case, a father and son, living in this area, to also give a first look at the possibility of transgenerational inherited effects of environmental contaminants on the molecular alterations of sperm nuclear basic proteins (SNBP), DNA and semen parameters. In the father and son, we found a diverse excess of copper and chromium in the semen, different alterations in SNBP content and low DNA binding affinity of these proteins. In addition, DNA damage, in the presence of CuCl2 and H2O2, increased by adding both the father and son SNBP. Interestingly, son SNBP, unlike his father, showed an unstable DNA binding and were able to produce DNA damage even without external addition of CuCl2, in line with a lower seminal antioxidant activity than the father. The peculiarity of some characteristics of son semen could be a basis for possible future studies on transgenerational effects of pollutants on fertility.
Age and Sex-Dependent ADNP Regulation of Muscle Gene Expression Is Correlated with Motor Behavior: Possible Feedback Mechanism with PACAP
Authors: Kapitansky Oxana , Sragovich Shlomo , Jaljuli Iman , Hadar Adva , Giladi Eliezer , Gozes Illana
Published: September 2020

The activity-dependent neuroprotective protein (ADNP), a double-edged sword, sex-dependently regulates multiple genes and was previously associated with the control of early muscle development and aging. Here we aimed to decipher the involvement of ADNP in versatile muscle gene expression patterns in correlation with motor function throughout life. Using quantitative RT-PCR we showed that Adnp+/− heterozygous deficiency in mice resulted in aberrant gastrocnemius (GC) muscle, tongue and bladder gene expression, which was corrected by the Adnp snippet, drug candidate, NAP (CP201). A significant sexual dichotomy was discovered, coupled to muscle and age-specific gene regulation. As such, Adnp was shown to regulate myosin light chain (Myl) in the gastrocnemius (GC) muscle, the language acquisition gene forkhead box protein P2 (Foxp2) in the tongue and the pituitary-adenylate cyclase activating polypeptide (PACAP) receptor PAC1 mRNA (Adcyap1r1) in the bladder, with PACAP linked to bladder function. A tight age regulation was observed, coupled to an extensive correlation to muscle function (gait analysis), placing ADNP as a muscle-regulating gene/protein.
Analyzing Gene Expression Profiles from Ataxia and Spasticity Phenotypes to Reveal Spastic Ataxia Related Pathways
Authors: Kakouri Andrea C. , Votsi Christina , Tomazou Marios , Minadakis George , Karatzas Evangelos , Christodoulou Kyproula , Spyrou George M.
Published: September 2020

Spastic ataxia (SA) is a group of rare neurodegenerative diseases, characterized by mixed features of generalized ataxia and spasticity. The pathogenetic mechanisms that drive the development of the majority of these diseases remain unclear, although a number of studies have highlighted the involvement of mitochondrial and lipid metabolism, as well as calcium signaling. Our group has previously published the GBA2 c.1780G > C (p.Asp594His) missense variant as the cause of spastic ataxia in a Cypriot consanguineous family, and more recently the biochemical characterization of this variant in patients’ lymphoblastoid cell lines. GBA2 is a crucial enzyme of sphingolipid metabolism. However, it is unknown if GBA2 has additional functions and therefore additional pathways may be involved in the disease development. The current study introduces bioinformatics approaches to better understand the pathogenetic mechanisms of the disease. We analyzed publicly available human gene expression datasets of diseases presented with ‘ataxia’ or ‘spasticity’ in their clinical phenotype and we performed pathway analysis in order to: (a) search for candidate perturbed pathways of SA; and (b) evaluate the role of sphingolipid signaling pathway and sphingolipid metabolism in the disease development, through the identification of differentially expressed genes in patients compared to controls. Our results demonstrate consistent differential expression of genes that participate in the sphingolipid pathways and highlight alterations in the pathway level that might be associated with the disease phenotype. Through enrichment analysis, we discuss additional pathways that are connected to sphingolipid pathways, such as PI3K-Akt signaling, MAPK signaling, calcium signaling, and lipid and carbohydrate metabolism as the most enriched for ataxia and spasticity phenotypes.
Pathogenic Mechanisms of Myeloma Bone Disease and Possible Roles for NRF2
Authors: Yen Chia-Hung , Hsu Chin-Mu , Hsiao Samuel Yien , Hsiao Hui-Hua
Published: September 2020

Osteolytic bone lesions are one of the central features of multiple myeloma (MM) and lead to bone pain, fractures, decreased quality of life, and decreased survival. Dysfunction of the osteoclast (OC)/osteoblast (OB) axis plays a key role in the development of myeloma-associated osteolytic lesions. Many signaling pathways and factors are associated with myeloma bone diseases (MBDs), including the RANKL/OPG and NF-κB pathways. NRF2, a master regulator of inflammatory signaling, might play a role in the regulation of bone metabolism via anti-inflammatory signaling and decreased reactive oxygen species (ROS) levels. The loss of NRF2 expression in OCs reduced bone mass via the RANK/RANKL pathway and other downstream signaling pathways that affect osteoclastogenesis. The NRF2 level in OBs could interfere with interleukin (IL)-6 expression, which is associated with bone metabolism and myeloma cells. In addition to direct impact on OCs and OBs, the activity of NRF2 on myeloma cells and mesenchymal stromal cells influences the inflammatory stress/ROS level in these cells, which has an impact on OCs, OBs, and osteocytes. The interaction between these cells and OCs affects the osteoclastogenesis of myeloma bone lesions associated with NRF2. Therefore, we have reviewed the effects of NRF2 on OCs and OBs in MBDs.
C-Terminal Extensions of Ku70 and Ku80 Differentially Influence DNA End Binding Properties
Authors: Inagawa Takabumi , Wennink Thomas , Lebbink Joyce H. G. , Keijzers Guido , Florea Bogdan I. , Verkaik Nicole S. , van Gent Dik C.
Published: September 2020

The Ku70/80 heterodimer binds to DNA ends and attracts other proteins involved in the non-homologous end-joining (NHEJ) pathway of DNA double-strand break repair. We developed a novel assay to measure DNA binding and release kinetics using differences in Förster resonance energy transfer (FRET) of the ECFP-Ku70/EYFP-Ku80 heterodimer in soluble and DNA end bound states. We confirmed that the relative binding efficiencies of various DNA substrates (blunt, 3 nucleotide 5′ extension, and DNA hairpin) measured in the FRET assay reflected affinities obtained from direct measurements using surface plasmon resonance. The FRET assay was subsequently used to investigate Ku70/80 behavior in the context of a DNA-dependent kinase (DNA-PK) holocomplex. As expected, this complex was much more stable than Ku70/80 alone, and its stability was influenced by DNA-PK phosphorylation status. Interestingly, the Ku80 C-terminal extension contributed to DNA-PK complex stability but was not absolutely required for its formation. The Ku70 C-terminal SAP domain, on the other hand, was required for the stable association of Ku70/80 to DNA ends, but this effect was abrogated in DNA-PK holocomplexes. We conclude that FRET measurements can be used to determine Ku70/80 binding kinetics. The ability to do this in complex mixtures makes this assay particularly useful to study larger NHEJ protein complexes on DNA ends.
In Vitro Innovation of Tendon Tissue Engineering Strategies
Authors: Citeroni Maria Rita , Ciardulli Maria Camilla , Russo Valentina , Della Porta Giovanna , Mauro Annunziata , El Khatib Mohammad , Di Mattia Miriam , Galesso Devis , Barbera Carlo , Forsyth Nicholas R. , Maffulli Nicola , Barboni Barbara
Published: September 2020

Tendinopathy is the term used to refer to tendon disorders. Spontaneous adult tendon healing results in scar tissue formation and fibrosis with suboptimal biomechanical properties, often resulting in poor and painful mobility. The biomechanical properties of the tissue are negatively affected. Adult tendons have a limited natural healing capacity, and often respond poorly to current treatments that frequently are focused on exercise, drug delivery, and surgical procedures. Therefore, it is of great importance to identify key molecular and cellular processes involved in the progression of tendinopathies to develop effective therapeutic strategies and drive the tissue toward regeneration. To treat tendon diseases and support tendon regeneration, cell-based therapy as well as tissue engineering approaches are considered options, though none can yet be considered conclusive in their reproduction of a safe and successful long-term solution for full microarchitecture and biomechanical tissue recovery. In vitro differentiation techniques are not yet fully validated. This review aims to compare different available tendon in vitro differentiation strategies to clarify the state of art regarding the differentiation process.
Whole-Genome Sequencing Analysis of Quorum Quenching Bacterial Strain Acinetobacter lactucae QL-1 Identifies the FadY Enzyme for Degradation of the Diffusible Signal Factor
Authors: Ye Tian , Zhou Tian , Xu Xudan , Zhang Wenping , Fan Xinghui , Mishra Sandhya , Zhang Lianhui , Zhou Xiaofan , Chen Shaohua
Published: September 2020

The diffusible signal factor (DSF) is a fatty acid signal molecule and is widely conserved in various Gram-negative bacteria. DSF is involved in the regulation of pathogenic virulence in many bacterial pathogens, including Xanthomonas campestris pv. campestris (Xcc). Quorum quenching (QQ) is a potential approach for preventing and controlling DSF-mediated bacterial infections by the degradation of the DSF signal. Acinetobacter lactucae strain QL-1 possesses a superb DSF degradation ability and effectively attenuates Xcc virulence through QQ. However, the QQ mechanisms in strain QL-1 are still unknown. In the present study, whole-genome sequencing and comparative genomics analysis were conducted to identify the molecular mechanisms of QQ in strain QL-1. We found that the fadY gene of QL-1 is an ortholog of XccrpfB, a known DSF degradation gene, suggesting that strain QL-1 is capable of inactivating DSF by QQ enzymes. The results of site-directed mutagenesis indicated that fadY is required for strain QL-1 to degrade DSF. The determination of FadY activity in vitro revealed that the fatty acyl-CoA synthetase FadY had remarkable catalytic activity. Furthermore, the expression of fadY in transformed Xcc strain XC1 was investigated and shown to significantly attenuate bacterial pathogenicity on host plants, such as Chinese cabbage and radish. This is the first report demonstrating a DSF degradation enzyme from A. lactucae. Taken together, these findings shed light on the QQ mechanisms of A. lactucae strain QL-1, and provide useful enzymes and related genes for the biocontrol of infectious diseases caused by DSF-dependent bacterial pathogens.
Noncanonical Constitutive Androstane Receptor Signaling in Gene Regulation
Authors: Pustylnyak Yuliya A. , Gulyaeva Lyudmila F. , Pustylnyak Vladimir O.
Published: September 2020

The constitutive androstane receptor (CAR, NR1I3) is extremely important for the regulation of many physiological processes, especially xenobiotic (drug) metabolism and transporters. CAR differs from steroid hormone receptors in that it can be activated using structurally unrelated chemicals, both through direct ligand-binding and ligand-independent (indirect) mechanisms. By binding to specific responsive elements on DNA, CAR increases the expression of its target genes encoding drug-metabolizing enzymes and transporters. Therefore, CAR is mainly characterized as a ligand-dependent or ligand-independent transcription factor, and the induction of gene expression is considered the canonical mode of CAR action. Consistent with its central role in xenobiotic metabolism, CAR signaling includes a collection of mechanisms that are employed alongside the core transcriptional machinery of the receptor. These so-called noncanonical CAR pathways allow the receptor to coordinate the regulation of many aspects of cell biology. In this mini-review, we review noncanonical CAR signaling, paying special attention to the role of CAR in energy homeostasis and cell proliferation.
A Web-Based Honeypot in IPv6 to Enhance Security
Authors: Wang Keyong , Tong Mengyao , Yang Dequan , Liu Yuhang
Published: September 2020

IPv6 is a next-generation IP protocol that replaces IPv4. It not only expands the number of network address resources but also solves the problem of multiple access devices connected to the Internet. While IPv6 has brought excellent convenience to the public, related security issues have gradually emerged, and an assessment of the security situation in IPv6 has also become more important. Unlike passive defense, the honeypot is a security device for active defense. The real network application and the fake network application, disguised by the honeypot, are located on a similar subnet, and provide a network application service; but, in both cases, behavior logs from unauthorized users are caught. In this manner, and to protect web-based applications from attacks, this article introduces the design and implementation of a web-based honeypot that includes a weak password module and an SQL inject module, which supports the IPv6 network to capture unauthorized access behavior. We also propose the Security Situation Index (SSI), which can measure the security situation of the network application environment. The value of SSI is established according to the different parameters that are based on honeypots. There is a firewall outside the test system environment, so the obtained data should be used as the real invasion data, and the captured behavior is not a false positive. Threats can be spotted smartly by deploying honeypots; this paper demonstrates that the honeypot is an excellent method of capturing malicious requests and can be measured with the SSI of the whole system. According to the information, the administrator can modify the current security policy, which can improve the security level of a whole IPv6 network system.
De Novo Transcriptomic and Metabolomic Analyses Reveal the Ecological Adaptation of High-Altitude Bombus pyrosoma
Authors: Liu Yanjie , Zhao Huiyue , Luo Qihua , Yang Yadong , Zhang Guangshuo , Zhou Zhiyong , Naeem Muhammad , An Jiandong
Published: September 2020

Bombus pyrosoma is one of the most abundant bumblebee species in China, with a distribution range of very varied geomorphology and vegetation, which makes it an ideal pollinator species for research into high-altitude adaptation. Here, we sequenced and assembled transcriptomes of B. pyrosoma from the low-altitude North China Plain and the high-altitude Tibet Plateau. Subsequent comparative analysis of de novo transcriptomes from the high- and low-altitude groups identified 675 common upregulated genes (DEGs) in the high-altitude B. pyrosoma. These genes were enriched in metabolic pathways and corresponded to enzyme activities involved in energy metabolism. Furthermore, according to joint analysis with comparative metabolomics, we suggest that the metabolism of coenzyme A (CoA) and the metabolism and transport of energy resources contribute to the adaptation of high-altitude B. pyrosoma. Meanwhile, we found many common upregulated genes enriched in the Toll and immune deficiency (Imd)signaling pathways that act as important immune defenses in insects, and hypoxia and cold temperatures could induce the upregulation of immune genes in insects. Therefore, we suppose that the Toll and Imd signaling pathways also participated in the high-altitude adaptation of B. pyrosoma. Like other organisms, we suggest that the high-altitude adaptation of B. pyrosoma is controlled by diverse mechanisms.
Modelling of Boiling Flows for Nuclear Thermal Hydraulics Applications—A Brief Review
Authors: Giustini Giovanni
Published: September 2020

The boiling process is utterly fundamental to the design and safety of water-cooled fission reactors. Both boiling water reactors and pressurised water reactors use boiling under high-pressure subcooled liquid flow conditions to achieve high surface heat fluxes required for their operation. Liquid water is an excellent coolant, which is why water-cooled reactors can have such small sizes and high-power densities, yet also have relatively low component temperatures. Steam is in contrast a very poor coolant. A good understanding of how liquid water coolant turns into steam is correspondingly vital. This need is particularly pressing because heat transfer by water when it is only partially steam (‘nucleate boiling’ regime) is particularly effective, providing a great incentive to operate a plant in this regime. Computational modelling of boiling, using computational fluid dynamics (CFD) simulation at the ‘component scale’ typical of nuclear subchannel analysis and at the scale of the single bubbles, is a core activity of current nuclear thermal hydraulics research. This paper gives an overview of recent literature on computational modelling of boiling. The knowledge and capabilities embodied in the surveyed literature entail theoretical, experimental and modelling work, and enabled the scientific community to improve its current understanding of the fundamental heat transfer phenomena in boiling fluids and to develop more accurate tools for the prediction of two-phase cooling in nuclear systems. Data and insights gathered on the fundamental heat transfer processes associated with the behaviour of single bubbles enabled us to develop and apply more capable modelling tools for engineering simulation and to obtain reliable estimates of the heat transfer rates associated with the growth and departure of steam bubbles from heated surfaces. While results so far are promising, much work is still needed in terms of development of fundamental understanding of the physical processes and application of improved modelling capabilities to industrially relevant flows.
Nitric Oxide Stroke Volume Index as a New Hemodynamic Prognostic Parameter for Patients with Pulmonary Arterial Hypertension
Authors: Barańska-Pawełczak Karolina , Wojciechowska Celina , Opara Mariusz , Jacheć Wojciech
Published: September 2020

The aim of the study was to determine the prognostic value of hemodynamic parameters measured during initial diagnostic right heart catheterization (RHC) in standard conditions and using a nitric oxide reversibility test. A retrospective observational study of 62 patients with pulmonary arterial hypertension (PAH) was performed. Clinical, biochemical, echocardiographic, and hemodynamic data obtained at the time of the PAH diagnosis were precisely analyzed. Patients were followed for five years. Death or lung transplantation was considered as a primary endpoint. The mean follow-up period was 1090 ± 703 days and the median age was 46.84 years. In the studied group, 25 patients survived, 36 patients died, and one underwent a lung transplantation. From all the examined parameters, only stroke volume index during reversibility test with iNO (SVI(NO test)) (HR = 0.910; 95% confidence interval 0.878–0.944; p < 0.001) and initial arterial oxygen saturation (SaO2) (HR = 0.910; 95% confidence interval 0.843–0.982; p = 0.015) have been established as independent predictors of death or lung transplantation in the five-year follow–up. An SVI(NO test) value above 39.86 mL/m2 was associated with 100% five-year survival rate (AUC = 0.956; 95% confidence interval 0.899–1.000; p < 0.001; specificity/sensitivity: 100/84%). The results of the analysis suggest that the SVI(NO test) measured during the initial diagnostic RHC could be a very valuable prognostic factor in the PAH patients.
The Efficacy of the Mineralcorticoid Receptor Antagonist Canrenone in COVID-19 Patients
Authors: Vicenzi Marco , Ruscica Massimiliano , Iodice Simona , Rota Irene , Ratti Angelo , Di Cosola Roberta , Corsini Alberto , Bollati Valentina , Aliberti Stefano , Blasi Francesco
Published: September 2020

Background: In COVID-19 patients, aldosterone via angiotensin-converting enzyme-2 deregulation may be responsible for systemic and pulmonary vasoconstriction, inflammation, and oxidative organ damage. Aim: To verify retrospectively the impact of the mineralcorticoid receptor antagonist canrenone i.v. on the need of invasive ventilatory support and/or all-cause in-hospital mortality. Methods: Sixty-nine consecutive COVID-19 patients, hospitalized for moderate to severe respiratory failure at Fondazione Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico of Milan, received two different therapeutic approaches in usual care according to the personal skills and pharmacological management experience of the referral medical team. Group A (n = 39) were given vasodilator agents or renin–angiotensin–aldosterone system (RAAS) inhibitors and group B (n = 30) were given canrenone i.v. Results: Among the 69 consecutive COVID-19 patients, those not receiving canrenone i.v. (group A) had an event-free rate of 51% and a survival rate of 64%. Group B (given a mean dose of 200 mg/q.d. of canrenone for at least two days of continuous administration) showed an event-free rate of 80% with a survival rate of 87%. Kaplan–Meier analysis for composite outcomes and mortality showed log rank statistics of 0.0004 and 0.0052, respectively. Conclusions: The novelty of our observation relies on the independent positive impact of canrenone on the all-cause mortality and clinical improvement of COVID-19 patients ranging from moderate to severe diseases.