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https://www.readbyqxmd.com/read/29767365/current-and-future-methods-for-mrna-analysis-a-drive-toward-single-molecule-sequencing
#1
Anthony Bayega, Somayyeh Fahiminiya, Spyros Oikonomopoulos, Jiannis Ragoussis
The transcriptome encompasses a range of species including messenger RNA, and other noncoding RNA such as rRNA, tRNA, and short and long noncoding RNAs. Due to the huge role played by mRNA in development and disease, several methods have been developed to sequence and characterize mRNA, with RNA sequencing (RNA-Seq) emerging as the current method of choice particularly for large high-throughput studies. Short-read RNA-Seq which involves sequencing of short cDNA fragments and computationally assembling them to reconstruct the transcriptome, or aligning them to a reference is the most widely used approach...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29767360/transcript-profiling-using-long-read-sequencing-technologies
#2
Anthony Bayega, Yu Chang Wang, Spyros Oikonomopoulos, Haig Djambazian, Somayyeh Fahiminiya, Jiannis Ragoussis
RNA sequencing using next-generation sequencing (NGS, RNA-Seq) technologies is currently the standard approach for gene expression profiling, particularly for large-scale high-throughput studies. NGS technologies comprise short-read RNA-Seq (dominated by Illumina) and long-read RNA-Seq technologies provided by Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT). Although short-read sequencing technologies are the most widely used, long-read technologies are increasingly becoming the standard approach for de novo transcriptome assembly and isoform expression quantification due to the complex nature of the transcriptome which consists of variable lengths of transcripts and multiple alternatively spliced isoforms for most genes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29758854/bioelectrochemically-assisted-anaerobic-digestion-system-for-biogas-upgrading-and-enhanced-methane-production
#3
Zeou Dou, Christy M Dykstra, Spyros G Pavlostathis
The objective of this study was to evaluate the effect of biofilm and external voltage on the performance and microbial community composition of batch-fed, combined anaerobic digestion-bioelectrochemical cell (AD-BEC) systems under different operational conditions. A dextrin/peptone mixture was fed at a range of organic loading rates (0.34 to 1.37g COD/L-d). The hybrid system with both suspended biomass and biofilm without any external potential application achieved a substantially higher initial soluble COD consumption (53...
August 15, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29751047/identification-of-novel-bioinspired-synthetic-mosquito-repellents-by-combined-ligand-based-screening-and-obp-structure-based-molecular-docking
#4
Trias Thireou, Georgia Kythreoti, Katerina E Tsitsanou, Konstantinos Koussis, Christina E Drakou, Julie Kinnersley, Thomas Kröber, Patrick M Guerin, Jing-Jiang Zhou, Kostas Iatrou, Elias Eliopoulos, Spyros E Zographos
In this work we report a fast and efficient virtual screening protocol for discovery of novel bioinspired synthetic mosquito repellents with lower volatility and, in all likelihood, increased protection time as compared with their plant-derived parental compounds. Our screening protocol comprises two filtering steps. The first filter is based on the shape and chemical similarity to known plant-derived repellents, whereas the second filter is based on the predicted similarity of the ligand's binding mode to the Anopheles gambiae odorant binding protein (AgamOBP1) relative to that of DEET and Icaridin to the same OBP...
May 8, 2018: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29748717/ethical-challenges-in-resuscitation
#5
REVIEW
Spyros D Mentzelopoulos, Anne-Marie Slowther, Zoe Fritz, Claudio Sandroni, Theodoros Xanthos, Clifton Callaway, Gavin D Perkins, Craig Newgard, Eleni Ischaki, Robert Greif, Erwin Kompanje, Leo Bossaert
PURPOSE: A rapidly evolving resuscitation science provides more effective treatments to an aging population with multiple comorbidites. Concurrently, emergency care has become patient-centered. This review aims to describe challenges associated with the application of key principles of bioethics in resuscitation and post-resuscitation care; propose actions to address these challenges; and highlight the need for evidence-based ethics and consensus on ethical principles interpretation. METHODS: Following agreement on the article's outline, subgroups of 2-3 authors provided narrative reviews of ethical issues concerning autonomy and honesty, beneficence/nonmaleficence and dignity, justice, specific practices/circumstances such as family presence during resuscitation, and emergency research...
May 10, 2018: Intensive Care Medicine
https://www.readbyqxmd.com/read/29741498/formation-of-nanoporous-si-upon-self-organized-growth-of-al-and-si-nanostructures
#6
Annett Thøgersen, Ingvild J T Jensen, Marit Stange, Torunn Kjeldstad, Diego Martinez-Martinez, Ole Martin Lovvik, Alexander G Ulyashin, Spyros Diplas
Nanostructured materials offer unique electronic and optical properties compared to their bulk counterparts. The challenging part of the synthesis is to balance between control of design, size limitations, up-scalability and contamination. In this work we show that self organized Al nanowires in amorphous Si can be produced at room temperature by magnetron co-sputtering using two individual targets. Nanoporous Si, containing nanotunnels with dimensions within the quantum confinement regime, were then made by selective etching of Al...
May 9, 2018: Nanotechnology
https://www.readbyqxmd.com/read/29740042/evidence-of-cd4-t-cell-mediated-immune-pressure-on-the-hepatitis-c-virus-genome
#7
Michaela Lucas, Pooja Deshpande, Ian James, Andri Rauch, Katja Pfafferott, Elouise Gaylard, Shahzma Merani, Anne Plauzolles, Andrew Lucas, Wyatt McDonnell, Spyros Kalams, Mark Pilkinton, Cody Chastain, Louise Barnett, Amy Prosser, Simon Mallal, Karen Fitzmaurice, Heidi Drummer, M Azim Ansari, Vincent Pedergnana, Ellie Barnes, Mina John, Dermot Kelleher, Paul Klenerman, Silvana Gaudieri
Hepatitis C virus (HCV)-specific T cell responses are critical for immune control of infection. Viral adaptation to these responses, via mutations within regions of the virus targeted by CD8+ T cells, is associated with viral persistence. However, identifying viral adaptation to HCV-specific CD4+ T cell responses has been difficult although key to understanding anti-HCV immunity. In this context, HCV sequence and host genotype from a single source HCV genotype 1B cohort (n = 63) were analyzed to identify viral changes associated with specific human leucocyte antigen (HLA) class II alleles, as these variable host molecules determine the set of viral peptides presented to CD4+ T cells...
May 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29734516/dermal-capillary-rarefaction-as-a-marker-of-microvascular-damage-in-patients-with-rheumatoid-arthritis-association-with-inflammation-and-disorders-of-the-macrocirculation
#8
Panagiota Anyfanti, Eugenia Gkaliagkousi, Areti Triantafyllou, Xenophon Zabulis, Panagiotis Dolgyras, Vasiliki Galanopoulou, Spyros Aslanidis, Stella Douma
OBJECTIVE: Capillary rarefaction is observed in various cardiovascular diseases, yet it remains understudied in RA, a chronic inflammatory disease accompanied by excess cardiovascular risk. We quantified capillary density in RA patients and explored potential associations with macrocirculatory disorders, inflammation and cardiovascular risk. METHODS: Dermal capillary density was assessed with nailfold capillaroscopy in RA and non-RA individuals, using specifically designed semiautomated software...
May 7, 2018: Microcirculation: the Official Journal of the Microcirculatory Society, Inc
https://www.readbyqxmd.com/read/29730677/early-post-interventional-sonographic-evaluation-of-prostatic-artery-embolization-a-promising-role-for-contrast-enhanced-ultrasonography-ceus
#9
Hippocrates Moschouris, Konstantinos Stamatiou, Mariana Kalokairinou Motogna, Spyros Vrakas, Michail Kiltenis, Konstantinos Kladis-Kalentzis, Avraam Tsavdaroglou, Nikolaos Papadogeorgopoulos, Kyriaki Marmaridou, Katerina Malagari
AIMS: To assess the feasibility, findings and potential value of early post-interventional, contrast-enhanced ultrasonographic (CEUS) study of prostate artery embolization (PAE). MATERIAL AND METHODS: Fourteen patients treated with PAE for symptomatic benign prostatic hyperplasia were prospectively included in the study. Sonographic evaluation of the prostate included: 1) baseline transabdominal and transrectal CEUS (ta-CEUS and tr-CEUS, respectively) 1-3 days prior to PAE; 2) early post PAE CEUS, with ta-CEUS immediately post PAE and tr-CEUS 3 days post PAE; and 3) follow-up with ta-CEUS and tr-CEUS 3 months post PAE...
May 2, 2018: Medical Ultrasonography
https://www.readbyqxmd.com/read/29726775/parietal-association-deficits-in-patients-harboring-parietal-lobe-gliomas-a-prospective-study
#10
Evangelia Liouta, George Stranjalis, Aristotelis V Kalyvas, Christos Koutsarnakis, Stavroula Pantinaki, Faidon Liakos, Spyros Komaitis, Lampis C Stavrinou
OBJECTIVE Although the parietal lobe is a common site for glioma formation, current literature is scarce, consists of retrospective studies, and lacks consistency with regard to the incidence, nature, and severity of parietal association deficits (PADs). The aim of this study was to assess the characteristics and incidence of PADs in patients suffering from parietal lobe gliomas through a prospective study and a battery of comprehensive neuropsychological tests. METHODS Between 2012 and 2016 the authors recruited 38 patients with glioma confined in the parietal lobe...
May 4, 2018: Journal of Neurosurgery
https://www.readbyqxmd.com/read/29710603/assessing-the-sustainability-of-acid-mine-drainage-amd-treatment-in-south-africa
#11
Vhahangwele Masindi, Efthalia Chatzisymeon, Ioannis Kortidis, Spyros Foteinis
The environmental sustainability of acid mine drainage (AMD) treatment at semi-industrial scale is examined by means of the life cycle assessment (LCA) methodology. An integrated process which includes magnesite, lime, soda ash and CO2 bubbling treatment was employed to effectively treat, at semi-industrial scale, AMD originating from a coal mine in South Africa. Economic aspects are also discussed. AMD is a growing problem of emerging concern that cause detrimental effects to the environment and living organisms, including humans, and impose on development, health, access to clean water, thus also affect economic growth and cause social instability...
April 20, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29709050/acrometastasis-due-to-lung-adenocarcinoma
#12
Vasiliki Apollonatou, Stelios Loukides, Andriana I Papaioannou, Spyros Papiris
We are presenting a case of acrometastasis in a male patient with lung adenocarcinoma. Acrometastases accumulate for 0.1% of all metastatic bone lesions and can be the first manifestation of cancer in approximately 10% of cases. The main clinical manifestations are tenderness, intermittent pain, functional impairment, erythema, heat and swelling of the affected part. Lung cancer is the main primary malignancy which causes acrometastases. Although the lesions can be recognized in x-rays or CT scans, the gold standard for the diagnosis is MRI scan in which the full extension of the tumor can be evaluated...
2018: Advances in Respiratory Medicine
https://www.readbyqxmd.com/read/29707183/an-investigation-of-the-morphology-of-the-petrotympanic-fissure-using-cone-beam-computed-tomography
#13
Spyros Damaskos, Konstantinos Syriopoulos, Rogier L Sens, Constantinus Politis
Objectives: The purpose of the present study was: a) to examine the visibility and morphology of the petrotympanic fissure on cone-beam computed tomography images, and b) to investigate whether the petrotympanic fissure morphology is significantly affected by gender and age, or not. Material and Methods: Using Newtom VGi (QR Verona, Italy), 106 cone-beam computed tomography examinations (212 temporomandibular joint areas) of both genders were retrospectively and randomly selected...
January 2018: Journal of Oral & Maxillofacial Research
https://www.readbyqxmd.com/read/29696605/assessment-of-the-virological-quality-of-marine-and-running-surface-waters-in-nw-greece-a-case-study
#14
Petros Kokkinos, Hera Karayanni, Alexandra Meziti, Ria Feidaki, Spyros Paparrodopoulos, Apostolos Vantarakis
The virological quality of surface marine and running water samples collected from Igoumenitsa gulf and Kalamas river (NW Greece) was assessed from October 2012 to September 2013. Sampling sites were exposed to different land and/or anthropogenic effects. Seawater samples were collected monthly from five sampling stations (new harbor, old harbor, wastewater treatment plant outlet, protected Natura area, Drepano beach). Viral targets included human adenoviruses (hAdVs), as index human viruses, while noroviruses (NoVs) and hepatitis A virus (HAV) were also studied...
April 25, 2018: Food and Environmental Virology
https://www.readbyqxmd.com/read/29678075/an-analytical-method-for-multimorbidity-management-using-bayesian-networks
#15
Stéphane Deparis, Alessandra Pascale, Pierpaolo Tommasi, Spyros Kotoulas
This paper describes an application of Bayesian Networks to mo-del persons with multimorbidity using measurements of vital signs and lifestyle assessments. The model was developed as part of a project on the use of wearable and home sensors and tablet applications to help persons with multimorbidity and their carers manage their conditions in daily life. The training data was extracted from TILDA, an open dataset collected from a longitudinal health study of the older Irish population. A categorical BN structure was learnt using a score-based approach, with constraints on the ordering of variables...
2018: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/29675748/association-between-obesity-and-depressive-symptoms-in-mexican-population
#16
Gerardo A Zavala, Spyros Kolovos, Alessandro Chiarotto, Judith E Bosmans, Maiza Campos-Ponce, Jorge L Rosado, Olga P Garcia
PURPOSE: Obesity and depression are among the leading causes of disability in Mexico, but their association has not been explored yet. The aim of the current study was to investigate the association between obesity and depression in Mexican population. METHODS: We used data from the health and nutrition survey (ENSANUT 2012), which is representative of the Mexican population. Obesity was determined using the body mass index (BMI) and abdominal obesity by measuring waist circumference...
April 19, 2018: Social Psychiatry and Psychiatric Epidemiology
https://www.readbyqxmd.com/read/29673760/tumor-suppressive-functions-of-4-mu-on-breast-cancer-cells-of-different-er-status-regulation-of-hyaluronan-has2-cd44-and-specific-matrix-effectors
#17
Theodoros T Karalis, Paraskevi Heldin, Demitrios H Vynios, Thomas Neill, Simone Buraschi, Renato V Iozzo, Nikos K Karamanos, Spyros S Skandalis
The malignant phenotype of various cancers is linked to enhanced expression of hyaluronan, a pro-angiogenic glycosaminoglycan whose expression is suppressed by 4-methylumbelliferone (4-MU), a non-toxic oral agent used as a dietary supplement to improve health and combat prostate cancer. However, little is known about the effects of hyaluronan inhibition by 4-MU on breast cancer cells. In this study, we investigated the role of 4-MU in mammary carcinoma cells with distinct malignant phenotypes and estrogen receptor (ER) status, a major prognostic factor in the clinical management of breast cancers...
April 16, 2018: Matrix Biology: Journal of the International Society for Matrix Biology
https://www.readbyqxmd.com/read/29667320/flotillin-1-interacts-with-the-serotonin-transporter-and-modulates-chronic-corticosterone-response
#18
Sonali N Reisinger, Eryan Kong, Barbara Molz, Thomas Humberg, Spyros Sideromenos, Ana Cicvaric, Thomas Steinkellner, Jae-Won Yang, Maureen Cabatic, Francisco J Monje, Harald H Sitte, Benjamin J Nichols, Daniela D Pollak
Aberrant serotonergic neurotransmission in the brain is considered at the core of the pathophysiological mechanisms involved in neuropsychiatric disorders. Gene by environment interactions contribute to the development of depression and involve modulation of the availability and functional activity of the serotonin transporter (SERT). Using behavioral and in vivo electrophysiological approaches together with biochemical, molecular-biological and molecular imaging tools we establish Flotillin-1 (Flot1) as a novel protein interacting with SERT and demonstrate its involvement in the response to chronic corticosterone (CORT) treatment...
April 18, 2018: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/29662879/abnormal-elongations-of-hox-gene-clusters-may-cause-cancer
#19
Spyros Papageorgiou
No abstract text is available yet for this article.
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29661874/characterization-of-extensively-or-pandrug-resistant-st147-and-st101-oxa-48-producing-klebsiella-pneumoniae-isolates-causing-bloodstream-infections-in-icu-patients
#20
Kalliope Avgoulea, Vincenzo Di Pilato, Olympia Zarkotou, Samanta Sennati, Leda Politi, Antonio Cannatelli, Katerina Themeli-Digalaki, Tommaso Giani, Athanassios Tsakris, Gian Maria Rossolini, Spyros Pournaras
Carbapenem-resistant Klebsiella pneumoniae cause important healthcare-associated infections worldwide. An outbreak of ST11 OXA-48-producing K. pneumoniae isolates (OXA-48-Kp) occurred in Tzaneio Hospital in 2012 and was contained until 2014, when OXA-48-Kp reemerged. The present study involved 19 bloodstream infection (BSI) OXA-48-Kp recovered from 19 ICU patients hospitalized between August 2014 and July 2016. MICs were determined by broth microdilution. β-lactamase genes were detected by PCR. All isolates were typed by PFGE/MLST and 10 representative isolates by next generation sequencing (NGS)...
April 16, 2018: Antimicrobial Agents and Chemotherapy
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