Shortcuts through Colocation Facilities

Network overlays, running on top of the existing Internet substrate, are of perennial value to Internet end-users in the context of, e.g., real-time applications. Such overlays can employ traffic relays to yield path latencies lower than the direct paths, a phenomenon known as Triangle Inequality Violation (TIV). Past studies identify the opportunities of reducing latency using TIVs. However, they do not investigate the gains of strategically selecting relays in Colocation Facilities (Colos). In this work, we answer the following questions: (i) how Colo-hosted relays compare with other relays as well as with the direct Internet, in terms of latency (RTT) reductions; (ii) what are the best locations for placing the relays to yield these reductions. To this end, we conduct a large-scale one-month measurement of inter-domain paths between RIPE Atlas (RA) nodes as endpoints, located at eyeball networks. We employ as relays Planetlab nodes, other RA nodes, and machines in Colos. We examine the RTTs of the overlay paths obtained via the selected relays, as well as the direct paths. We find that Colo-based relays perform the best and can achieve latency reductions against direct paths, ranging from a few to 100s of milliseconds, in 76% of the total cases; 75% (58% of total cases) of these reductions require only 10 relays in 6 large Colos.Comment: In Proceedings of the ACM Internet Measurement Conference (IMC '17), London, GB, 201

Use of novel casing in sucuk production: Antimicrobials incorporated into multilayer plastic film

In this study, effects of novel casing, antimicrobials (chitosan and AgZeo) incorporated into multilayer polyethylene casing, on chemical and microbial attributes of sucuks were followed through 3 days of fermentation and 12 days of storage after heat treatment. Microbial growth was reduced by chitosan incorporated casing. Aerobic plate count (APC) of 8.81 log CFU g–1 on the 3rd day of fermentation was reduced to 2.60 log CFU g–1 by the end of storage. APC and lactic acid bacteria (LAB) were decreased significantly (P<0.05) by antimicrobial casings. The lowest concentrations of histamine and tyramine were observed (P<0.05) in sucuks stuffed into chitosan incorporated casing. These results show that antimicrobial casing could be used in sucuk production to improve its safety and quality

Kratkotrajno očuvanje sperme potočne pastrmke (salmo trutta macrostigma): delovanje ekstendera na pokretljivost

Cilj eksperimenta je bila procena spermatoloških parametara kratkotrajno čuvane sperme potočne pastrmke (Salmo trutta macrostigma) korišćenjem različitih ekstendera. Mleč je uzorkovan od odraslih mužjaka istiskanjem rukom, bez anestezije. Po određivanju najvažnijih karakteristika sperme (volumen, pokretljivost, trajanje pokretljivosti, gustina, pH) uzorci sperme koji su pokazali >80 pokretljivosti su prikupljeni i razblaženi u odnosu 1:3 sa tri različita ekstendera. Razblažena sperma je čuvana 72 sata na 4°C. Tokom čuvanja na svaka 24 h je procenjivan motilitet spermatozoida (%). U zaključku, rezultati studije su pokazali da se ekstender I pokazao boljim od druga 2 za kratkotrajno očuvanje sperme potočne pastrmke

Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders

Extracting insight from the enormous quantity of data generated from molecular simulations requires the identification of a small number of collective variables whose corresponding low-dimensional free-energy landscape retains the essential features of the underlying system. Data-driven techniques provide a systematic route to constructing this landscape, without the need for extensive a priori intuition into the relevant driving forces. In particular, autoencoders are powerful tools for dimensionality reduction, as they naturally force an information bottleneck and, thereby, a low-dimensional embedding of the essential features. While variational autoencoders ensure continuity of the embedding by assuming a unimodal Gaussian prior, this is at odds with the multi-basin free-energy landscapes that typically arise from the identification of meaningful collective variables. In this work, we incorporate this physical intuition into the prior by employing a Gaussian mixture variational autoencoder (GMVAE), which encourages the separation of metastable states within the embedding. The GMVAE performs dimensionality reduction and clustering within a single unified framework, and is capable of identifying the inherent dimensionality of the input data, in terms of the number of Gaussians required to categorize the data. We illustrate our approach on two toy models, alanine dipeptide, and a challenging disordered peptide ensemble, demonstrating the enhanced clustering effect of the GMVAE prior compared to standard VAEs. The resulting embeddings appear to be promising representations for constructing Markov state models, highlighting the transferability of the dimensionality reduction from static equilibrium properties to dynamics

Immunohistochemical study on roe deer haemal nodes

Background: The aim of this study was to investigate the immunohistochemical characteristics of the haemal nodes located in the abdominal and thoracic cavities in roe deer (Capreolus capreolus). Materials and methods: In this study, 2 adult male and 2 adult female roe deers in addition to 2 roe deer foetuses at the late foetal stages were used. The avidin-biotin-peroxidase technique was applied to anti-CD3, anti-CD79acy, anti­-macrophage, anti-S100 primary antibodies. Results: Positive results were gained for all the antibodies used. Many CD3 positive T-lymphocytes were seen in the lymphoid tissue areas of the foetal haemal nodes, in the germinal centre of the lymph follicles of the adult haemal nodes and in their lymphatic cords. CD79acy positive cells were less in number while S-100 protein was positive in both lymph follicles and in sinuses of the adult haemal nodes. In foetal haemal nodes, cells positive for S-100 protein were more prevalent in the sinuses. For the MAC387 primary antibody, there were positive macrophages seen in the capsule and trabeculae of the haemal nodes, located denser in males. Macrophage cells in the lymphoid structures and granulocytes in the sinuses of the haemal nodes of both adults and foetuses were positive for MAC387. Conclusions: This study is the first one to define the detailed structural features immunohistochemically in the haemal nodes of the roe deer. Even it’s concluded that the results were similar with the other ruminants, it’s also pointed out that there are certain differences among the foetal, adult male and female haemal nodes of the roe deer. (Folia Morphol 2018; 77, 2: 266–271

Complications in children with ventricular assist devices: systematic review and meta-analyses

Heart failure is a significant cause of mortality in children with cardiovascular diseases. Treatment of heart failure depends on patients’ symptoms, age, and severity of their condition, with heart transplantation required when other treatments are unsuccessful. However, due to lack of fitting donor organs, many patients are left untreated, or their transplant is delayed. In these patients, ventricular assist devices (VADs) are used to bridge to heart transplant. However, VAD support presents various complications in patients. The aim of this study was to compile, review, and analyse the studies reporting risk factors and aetiologies of complications of VAD support in children. Random effect risk ratios (RR) with 95% confidence intervals were calculated to analyse relative risk of thrombosis (RR = 3.53 [1.04, 12.06] I2 = 0% P = 0.04), neurological problems (RR = 0.95 [0.29, 3.15] I2 = 53% P = 0.93), infection (RR = 0.31 [0.05, 2.03] I2 = 86% P = 0.22), bleeding (RR = 2.57 [0.76, 8.66] I2 = 0% P = 0.13), and mortality (RR = 2.20 [1.36, 3.55] I2 = 0% P = 0.001) under pulsatile-flow and continuous-flow VAD support, relative risk of mortality (RR = 0.45 [0.15, 1.37] I2 = 36% P = 0.16) under left VAD and biVAD support, relative risk of thrombosis (RR = 1.72 [0.46, 6.44] I2 = 0% P = 0.42), infection (RR = 1.77 [0.10, 32.24] I2 = 46% P = 0.70) and mortality (RR = 0.92 [0.14, 6.28] I2 = 45% P = 0.93) in children with body surface area  1.2 m2 under VAD support, relative risk of mortality in children supported with VAD and diagnosed with cardiomyopathy and congenital heart diseases (RR = 1.31 [0.10, 16.61] I2 = 73% P = 0.84), and cardiomyopathy and myocarditis (RR = 0.91 [0.13, 6.24] I2 = 58% P = 0.92). Meta-analyses results show that further research is necessary to reduce complications under VAD support

Photonuclear reactions with Zinc: A case for clinical linacs

The use of bremsstrahlung photons produced by a linac to induce photonuclear reactions is wide spread. However, using a clinical linac to produce the photons is a new concept. We aimed to induce photonuclear reactions on zinc isotopes and measure the subsequent transition energies and half-lives. For this purpose, a bremsstrahlung photon beam of 18 MeV endpoint energy produced by the Philips SLI-25 linac has been used. The subsequent decay has been measured with a well-shielded single HPGe detector. The results obtained for transition energies are in good agreement with the literature data and in many cases surpass these in accuracy. For the half-lives, we are in agreement with the literature data, but do not achieve their precision. The obtained accuracy for the transition energies show what is achievable in an experiment such as ours. We demonstrate the usefulness and benefits of employing clinical linacs for nuclear physics experiments

Modulation of plant autophagy during pathogen attack

In plants, the highly conserved catabolic process of autophagy has long been known as a means of maintaining cellular homeostasis and coping with abiotic stress conditions. Accumulating evidence has linked autophagy to immunity against invading pathogens, regulating plant cell death, and antimicrobial defences. In turn, it appears that phytopathogens have evolved ways not only to evade autophagic clearance but also to modulate and co-opt autophagy for their own benefit. In this review, we summarize and discuss the emerging discoveries concerning how pathogens modulate both host and self-autophagy machineries to colonize their host plants, delving into the arms race that determines the fate of interorganismal interaction.Fil: Leary, Alexandre Y. Imperial College London; Reino UnidoFil: Sanguankiattichai, Nattapong. University of Oxford; Reino UnidoFil: Duggan, Cian. Imperial College London; Reino UnidoFil: Tumtas, Yasin. Imperial College London; Reino UnidoFil: Pandey, Pooja. Imperial College London; Reino UnidoFil: Segretin, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Salguero Linares, Jose. Imperial College London; Reino UnidoFil: Savage, Zachary D. Imperial College London; Reino UnidoFil: Yow, Rui Jin. Imperial College London; Reino UnidoFil: Bozkurt, Tolga O.. Imperial College London; Reino Unid

AlphaFold2-multimer guided high-accuracy prediction of typical and atypical ATG8-binding motifs

Macroautophagy/autophagy is an intracellular degradation process central to cellular homeostasis and defense against pathogens in eukaryotic cells. Regulation of autophagy relies on hierarchical binding of autophagy cargo receptors and adaptors to ATG8/LC3 protein family members. Interactions with ATG8/LC3 are typically facilitated by a conserved, short linear sequence, referred to as the ATG8/LC3 interacting motif/region (AIM/LIR), present in autophagy adaptors and receptors as well as pathogen virulence factors targeting host autophagy machinery. Since the canonical AIM/LIR sequence can be found in many proteins, identifying functional AIM/LIR motifs has proven challenging. Here, we show that protein modelling using Alphafold-Multimer (AF2-multimer) identifies both canonical and atypical AIM/LIR motifs with a high level of accuracy. AF2-multimer can be modified to detect additional functional AIM/LIR motifs by using protein sequences with mutations in primary AIM/LIR residues. By combining protein modelling data from AF2-multimer with phylogenetic analysis of protein sequences and protein-protein interaction assays, we demonstrate that AF2-multimer predicts the physiologically relevant AIM motif in the ATG8-interacting protein 2 (ATI-2) as well as the previously uncharacterized noncanonical AIM motif in ATG3 from potato (Solanum tuberosum). AF2-multimer also identified the AIM/LIR motifs in pathogen-encoded virulence factors that target ATG8 members in their plant and human hosts, revealing that cross-kingdom ATG8-LIR/AIM associations can also be predicted by AF2-multimer. We conclude that the AF2-guided discovery of autophagy adaptors/receptors will substantially accelerate our understanding of the molecular basis of autophagy in all biological kingdoms