QoS monitoring in real-time streaming overlays based on lock-free data structures

AbstractPeer-to-peer streaming is a well-known technology for the large-scale distribution of real-time audio/video contents. Delay requirements are very strict in interactive real-time scenarios (such as synchronous distance learning), where playback lag should be of the order of seconds. Playback continuity is another key aspect in these cases: in presence of peer churning and network congestion, a peer-to-peer overlay should quickly rearrange connections among receiving nodes to avoid freezing phenomena that may compromise audio/video understanding. For this reason, we designed a QoS monitoring algorithm that quickly detects broken or congested links: each receiving node is able to independently decide whether it should switch to a secondary sending node, called "fallback node". The architecture takes advantage of a multithreaded design based on lock-free data structures, which improve the performance by avoiding synchronization among threads. We will show the good responsiveness of the proposed approach on machines with different computational capabilities: measured times prove both departures of nodes and QoS degradations are promptly detected and clients can quickly restore a stream reception. According to PSNR and SSIM, two well-known full-reference video quality metrics, QoE remains acceptable on receiving nodes of our resilient overlay also in presence of swap procedures

The Satellite Reliable Distribution Protocol (SRDP)

The Satellite Reliable Distribution Protocol (SRDP) is proposed and discussed. SRDP is designed for satellite-based data broadcasting and aims at transmitting reliably multicast via satellite Internet applications’ data in an efficient and scalable way. SRDP operates in three steps, called phases. In phase 1 the sender transmits a file through the satellite internet adding a reasonable degree of redundancy. In phase 2 the sender retransmits a set of new redundant packets to recover some packets that were lost during phase 1. Phase 3 allows each receiver to request all its missing packets by a TCP connection to the sender. In order to evaluate the performance of the SRDP, we have considered two different types of loss behaviours: random and burst. Our results show how to choose the amount of redundancy in order to optimize the performance of the SRDP

Kajian Perbedaan Konsentrasi Larutan Garam Pada Perendaman Rgh Dan Vaksin Terhadap Kelulushidupan Dan Pertumbuhan Benih Ikan Lele Sangkuriang (Clarias Gariepinus)

Berdasarkan data KKP (2013), pencapaian produksi ikan lele pada tahun 2013 mampu melampaui target. Ikan lele merupakan ikan yang mudah dibudidayakan, sehingga banyak dilakukan penelitian agar didapatkan benih lele dengan pertumbuhan dan kelulushidupan yang lebih baik, serta tahan terhadap serangan penyakit. Penelitian ini bertujuan untuk mengetahui pengaruh konsentrasi larutan garam yang berbeda dan konsentrasi yang terbaik pada perendaman rGH dan vaksin terhadap kelulushidupan dan pertumbuhan benih lele sangkuriang. Penelitian ini dilaksanakan pada tanggal 13 November 2014 – 15 Februari 2015 di Satuan Kerja Pembenihan dan Budidaya Ikan Air Tawar (SATKER PBIAT), Siwarak, Ungaran, Semarang. Ikan uji yang digunakan adalah benih lele sangkuriang umur 12 hari. Metode yang digunakan adalah eksperimental dengan rancangan acak lengkap (RAL) 4 perlakuan dan 3 ulangan, yaitu: (A) perlakuan tanpa larutan garam, (B) konsentrasi 0,5%, (C) konsentrasi 1,0% dan (D) konsentrasi 1,5%. Pemeliharaan ikan dilakukan selama 42 hari. Variabel data yang diamati meliputi kelulushidupan, SGR, panjang mutlak, FCR, EPP dan kelulushidupan setelah uji tantang. Analisa data dengan menggunakan anova untuk mengetahui pengaruh perlakuan yang berbeda nyata, apabila hasil yang didapatkan berbeda nyata, maka dilanjutkan dengan uji duncan untuk mengetahui perlakuan yang terbaik. Hasil penelitian menunjukkan perlakuan terbaik adalah perlakuan C, dengan nilai kelulushidupan (87,00±1,00%), SGR (7,79±0,03%), nilai panjang mutlak (6,75±0,15cm), nilai FCR (0,71±0,01) dan nilai EPP (140,28±1,25%), sedangkan untuk kelulushidupan setelah uji tantang didapatkan hasil yang tidak berbeda nyata, dimana: A (93,33±5,77%), B (96,67±5,77%), C (96,67±5,77%) dan D (96,67±5,77%). Kesimpulan dari penelitian ini ialah pemberian konsentrasi larutan garam yang berbeda berpengaruh sangat nyata terhadap kelulushidupan, SGR, panjang mutlak, FCR dan EPP, namun tidak berpengaruh nyata terhadap kelulushidupan setelah uji tantang. Konsentrasi larutan garam terbaik pada penelitian ini adalah 1,0%. Based on data from KKP (2013), the achievement of the production of catfish in 2013 was able of exceeding the target. Catfish is a fish that easily cultivated, so a lot of research done to get catfish\u27s seed with better survival and growth, and it can resistant to attack of deseases. This research was aimed to find out the effect of different salt solution concentrations and the best concentration from immersion of rGH and vaccine for survival rate and growth of sangkuriang catfish\u27s seed. This research was conducted on November 13th, 2014 – February 15th, 2015 at Satuan Kerja Pembenihan dan Budidaya Ikan Air Tawar (SATKER PBIAT), Siwarak, Ungaran, Semarang. The fish that used for this research is sangkuriang catfish\u27s seed aged 12 days. Completely randomized design (CRD) was used in this research with four treatments and three replication, which treatments are: (A) without salt solution concentration, (B) Using concentration 0.5%, (C) Concentration 1.0% and (D) Concentration 1.5%. The Fishes are maintained for 42 days. Observational variable are survival rate, SGR, absolute length, FCR, EPP and survival rate after challenge test. Data analysis using anova to know the effect of treatment is significantly different, if the result is significantly different, then continue with duncan test to know the best treatment. The best result is treatment C, with survival rate (87.00±1.00%), SGR (7.79±0.03%), absolute length (6.75±0.15cm), FCR (0.71±0.01), EPP (140.28±1.25%), and for survival rate after challenge test are not significantly different, where: treatment A (93.33±5.77%), B (96.67±5.77%), C (96.67±5.77%) and D (96.67±5.77%). The conclusion of this research is giving of salt solution with different concentration take significantly effect for survival rate, SGR, absolute length, FCR and EPP, but did not take significantly effect for survival rate after challenge test. The best salt solution concentration is 1.0%

Long non-coding RNAs and cancer: a new frontier of translational research?

Author manuscriptTiling array and novel sequencing technologies have made available the transcription profile of the entire human genome. However, the extent of transcription and the function of genetic elements that occur outside of protein-coding genes, particularly those involved in disease, are still a matter of debate. In this review, we focus on long non-coding RNAs (lncRNAs) that are involved in cancer. We define lncRNAs and present a cancer-oriented list of lncRNAs, list some tools (for example, public databases) that classify lncRNAs or that scan genome spans of interest to find whether known lncRNAs reside there, and describe some of the functions of lncRNAs and the possible genetic mechanisms that underlie lncRNA expression changes in cancer, as well as current and potential future applications of lncRNA research in the treatment of cancer.RS is supported as a fellow of the TALENTS Programme (7th R&D Framework Programme, Specific Programme: PEOPLE—Marie Curie Actions—COFUND). MIA is supported as a PhD fellow of the FCT (Fundação para a Ciência e Tecnologia), Portugal. GAC is supported as a fellow by The University of Texas MD Anderson Cancer Center Research Trust, as a research scholar by The University of Texas System Regents, and by the Chronic Lymphocytic Leukemia Global Research Foundation. Work in GAC’s laboratory is supported in part by the NIH/ NCI (CA135444); a Department of Defense Breast Cancer Idea Award; Developmental Research Awards from the Breast Cancer, Ovarian Cancer, Brain Cancer, Multiple Myeloma and Leukemia Specialized Programs of Research Excellence (SPORE) grants from the National Institutes of Health; a 2009 Seena Magowitz–Pancreatic Cancer Action Network AACR Pilot Grant; the Laura and John Arnold Foundation and the RGK Foundation

An explainable model of host genetic interactions linked to COVID-19 severity

We employed a multifaceted computational strategy to identify the genetic factors contributing to increased risk of severe COVID-19 infection from a Whole Exome Sequencing (WES) dataset of a cohort of 2000 Italian patients. We coupled a stratified k-fold screening, to rank variants more associated with severity, with the training of multiple supervised classifiers, to predict severity based on screened features. Feature importance analysis from tree-based models allowed us to identify 16 variants with the highest support which, together with age and gender covariates, were found to be most predictive of COVID-19 severity. When tested on a follow-up cohort, our ensemble of models predicted severity with high accuracy (ACC = 81.88%; AUCROC = 96%; MCC = 61.55%). Our model recapitulated a vast literature of emerging molecular mechanisms and genetic factors linked to COVID-19 response and extends previous landmark Genome-Wide Association Studies (GWAS). It revealed a network of interplaying genetic signatures converging on established immune system and inflammatory processes linked to viral infection response. It also identified additional processes cross-talking with immune pathways, such as GPCR signaling, which might offer additional opportunities for therapeutic intervention and patient stratification. Publicly available PheWAS datasets revealed that several variants were significantly associated with phenotypic traits such as "Respiratory or thoracic disease", supporting their link with COVID-19 severity outcome.A multifaceted computational strategy identifies 16 genetic variants contributing to increased risk of severe COVID-19 infection from a Whole Exome Sequencing dataset of a cohort of Italian patients

The polymorphism L412F in TLR3 inhibits autophagy and is a marker of severe COVID-19 in males

The polymorphism L412F in TLR3 has been associated with several infectious diseases. However, the mechanism underlying this association is still unexplored. Here, we show that the L412F polymorphism in TLR3 is a marker of severity in COVID-19. This association increases in the sub-cohort of males. Impaired macroautophagy/autophagy and reduced TNF/TNFα production was demonstrated in HEK293 cells transfected with TLR3L412F-encoding plasmid and stimulated with specific agonist poly(I:C). A statistically significant reduced survival at 28 days was shown in L412F COVID-19 patients treated with the autophagy-inhibitor hydroxychloroquine (p = 0.038). An increased frequency of autoimmune disorders such as co-morbidity was found in L412F COVID-19 males with specific class II HLA haplotypes prone to autoantigen presentation. Our analyses indicate that L412F polymorphism makes males at risk of severe COVID-19 and provides a rationale for reinterpreting clinical trials considering autophagy pathways. Abbreviations: AP: autophagosome; AUC: area under the curve; BafA1: bafilomycin A1; COVID-19: coronavirus disease-2019; HCQ: hydroxychloroquine; RAP: rapamycin; ROC: receiver operating characteristic; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; TLR: toll like receptor; TNF/TNF-α: tumor necrosis factor

Carriers of ADAMTS13 Rare Variants Are at High Risk of Life-Threatening COVID-19

Thrombosis of small and large vessels is reported as a key player in COVID-19 severity. However, host genetic determinants of this susceptibility are still unclear. Congenital Thrombotic Thrombocytopenic Purpura is a severe autosomal recessive disorder characterized by uncleaved ultra-large vWF and thrombotic microangiopathy, frequently triggered by infections. Carriers are reported to be asymptomatic. Exome analysis of about 3000 SARS-CoV-2 infected subjects of different severities, belonging to the GEN-COVID cohort, revealed the specific role of vWF cleaving enzyme ADAMTS13 (A disintegrin-like and metalloprotease with thrombospondin type 1 motif, 13). We report here that ultra-rare variants in a heterozygous state lead to a rare form of COVID-19 characterized by hyper-inflammation signs, which segregates in families as an autosomal dominant disorder conditioned by SARS-CoV-2 infection, sex, and age. This has clinical relevance due to the availability of drugs such as Caplacizumab, which inhibits vWF-platelet interaction, and Crizanlizumab, which, by inhibiting P-selectin binding to its ligands, prevents leukocyte recruitment and platelet aggregation at the site of vascular damage

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types