Deep RNA sequencing of muscle tissue reveals absence of viral signatures in dermatomyositis

Objective: To explore a possible connection between active viral infections and manifestation of Dermatomyositis (DM). Methods: Skeletal muscle biopsies were analyzed from patients diagnosed with juvenile (n=10) and adult (n=12) DM. Adult DM patients harbored autoantibodies against either TIF-1γ (n=7) or MDA5 (n=5). Additionally, we investigated skeletal muscle biopsies from non-diseased controls (NDC, n=5). We used an unbiased high-throughput sequencing (HTS) approach to detect viral sequences. To further increase sequencing depth, a host depletion approach was applied. Results: In this observational study, no relevant viral sequences were detected either by native sequencing or after host depletion. The absence of detectable viral sequences makes an active viral infection of the muscle tissue unlikely to be the cause of DM in our cohorts. Discussion: Type I interferons (IFN) play a major role in the pathogenesis of both juvenile and adult dermatomyositis (DM). The IFN response is remarkably conserved between DM subtypes classified by specific autoantibodies. Certain acute viral infections are accompanied by a prominent type I IFN response involving similar downstream mechanisms as in DM. Aiming to elucidate the pathogenesis of DM in skeletal muscle tissue, we used an untargeted high-throughput sequencing and a host depletion approach to detect possible causative viruses

What Is the Added Value of Negative Links in Online Social Networks?

We investigate the“negative link”feature of social networks that allows users to tag other users as foes or as distrusted in addition to the usual friend and trusted links. To answer the question whether negative links have an added value for an online social network, we investigate the machine learning problem of predicting the negative links of such a network using only the positive links as a basis, with the idea that if this problem can be solved with high accuracy, then the “negative link ” feature is redundant. In doing so, we also present a general methodology for assessing the added value of any new link type in online social networks. Our evaluation is performed on two social networks that allow negative links: The technology news website Slashdot and the product review site Epinions. In experiments with these two datasets, we come to the conclusion that a combination of centrality-based and proximity-based link prediction functions can be used to predict the negative edges in the networks we analyse. We explain this result by an application of the models of preferential attachment and balance theory to our learning problem, and show that the “negative link ” feature has a small but measurable added value for these social networks

Structural Dynamics of Knowledge Networks

We investigate the structural patterns of the appearance and disappearance of links in dynamic knowledge networks. Human knowledge is nowadays increasingly created and curated online, in a collaborative and highly dynamic fashion. The knowledge thus created is interlinked in nature, and an important open task is to understand its temporal evolution. In this paper, we study the underlying mechanisms of changes in knowledge networks which are of structural nature, i.e., which are a direct result of a knowledge network’s structure. Concretely, we ask whether the appearance and disappearance of interconnections between concepts (items of a knowledge base) can be predicted using information about the network formed by these interconnections. In contrast to related work on this problem, we take into account the disappearance of links in our study, to account for the fact that the evolution of collaborative knowledge bases includes a high proportion of removals and reverts. We perform an empirical study on the best-known and largest collaborative knowledge base, Wikipedia, and show that traditional indicators of structural change used in the link analysis literature can be classified into four classes, which we show to indicate growth, decay, stability and instability of links. We finally use these methods to identify the underlying reasons for individual additions and removals of knowledge links.

Class II resin composite restorations—tunnel vs. box-only in vitro and in vivo

Purpose!#!In a combined in vitro/in vivo approach, tunnel vs. box-only resin composite restorations should be evaluated using thermomechanical loading (TML) in vitro and a restrospective clinical trial in vivo.!##!Materials and methods!#!For the in vitro part, box-only and tunnel cavities were prepared in 32 extracted human third molars under simulated intraoral conditions in a phantom head. Specimens were randomly assigned to four groups (n = 8; 16 box-only/16 tunnel) and received bonded resin composite restorations with Amelogen Plus (box A/tunnel A) or lining with Ultraseal and Amelogen plus (box B/tunnel B) both bonded using PQ1 (all Ultradent). Specimens were subjected to a standardized aging protocol, 1-year water storage (WS) followed by TML (100,000 × 50 N; 2500 × + 5/+ 55 °C). Initially and after aging, marginal qualities were evaluated using replicas at × 200 magnification (SEM). For the corresponding in vivo observational study, 229 patients received 673 proximal resin composite restorations. From 371 tunnel restorations, 205 cavities were filled without flowable lining (tunnel A), and 166 tunnels were restored using UltraSeal as lining (tunnel B). A total of 302 teeth received conventional box-only fillings. Restorations were examined according to modified USPHS criteria during routine recalls up to 5 years of clinical service.!##!Results!#!In vitro, all initial results showed 100% gap-free margins when a flowable lining was used. Tunnels without lining exhibited some proximal shortcomings already before TML and even more pronounced after TML (p < 0.05). After TML, percentages of gap-free margins dropped to 87-90% in enamel with lining and 70-79% without lining (p < 0.05). In vivo, annual failure rates for box-only were 2.2%, for tunnel A 6.1%, and for tunnel B 1.8%, respectively (p < 0.05). Tunnels had significantly more sufficient proximal contact points than box-only restorations (p < 0.05). Flowable lining was highly beneficial for clinical outcome of tunnel-restorations (p < 0.05).!##!Conclusions!#!With a flowable lining, tunnel restorations proved to be a good alternative to box-only resin composite restorations.!##!Clinical relevance!#!Class II tunnel restorations showed to be a viable alternative for box-only restorations, however, only when flowable resin composite was used as adaptation promotor for areas being difficult to access

Isoquinoline-Based Biaryls as a Robust Scaffold for Microtubule Inhibitors

We here report the discovery of isoquinoline-based biaryls as a new scaffold for colchicine domain tubulin inhibitors. Colchicine domain inhibitors comprise a structurally diverse class of compounds offering highly desirable cytotoxic and vascular disrupting bioactivities. Current research on colchicine domain inhibitors is focused on improving in vivo robustness and tolerability: properties that are inextricably linked to the scaffold structure employed. The isoquinoline-based biaryl scaffold we now report offers high-potency tubulin inhibition with excellent robustness and druglikeness, allowing solubility, in vivo tolerability and facile late-stage structural diversification through a tolerant synthetic route. We have confirmed the tubulin-binding properties and mechanism of these isoquinoline-based biaryls through a series of cellular tests and established safe in vivo dosing parameters in mice. By addressing several problems facing the current families of inhibitors, we thus expect that this new scaffold will find a range of powerful in vivo applications towards translational use in cancer therapy. </div

Type I Interferon response in olfactory bulb, the site of tick-borne flavivirus accumulation, is primarily regulated by IPS-1

Background: Although type I interferons (IFNs)—key effectors of antiviral innate immunity are known to be induced via different pattern recognition receptors (PRRs), the cellular source and the relative contribution of different PRRs in host protection against viral infection is often unclear. IPS-1 is a downstream adaptor for retinoid-inducible gene I (RIG-I)-like receptor signaling. In this study, we investigate the relative contribution of IPS-1 in the innate immune response in the different brain regions during infection with tick-borne encephalitis virus (TBEV), a flavivirus that causes a variety of severe symptoms like hemorrhagic fevers, encephalitis, and meningitis in the human host. Methods: IPS-1 knockout mice were infected with TBEV/Langat virus (LGTV), and viral burden in the peripheral and the central nervous systems, type I IFN induction, brain infiltrating cells, and inflammatory response was analyzed. Results: We show that IPS-1 is indispensable for controlling TBEV and LGTV infections in the peripheral and central nervous system. Our data indicate that IPS-1 regulates neuropathogenicity in mice. IFN response is differentially regulated in distinct regions of the central nervous system (CNS) influencing viral tropism, as LGTV replication was mainly restricted to olfactory bulb in wild-type (WT) mice. In contrast to the other brain regions, IFN upregulation in the olfactory bulb was dependent on IPS-1 signaling. IPS-1 regulates basal levels of antiviral interferon-stimulated genes (ISGs) like viperin and IRF-1 which contributes to the establishment of early viral replication which inhibits STAT1 activation. This diminishes the antiviral response even in the presence of high IFN-β levels. Consequently, the absence of IPS-1 causes uncontrolled virus replication, in turn resulting in apoptosis, activation of microglia and astrocytes, elevated proinflammatory response, and recruitment of inflammatory cells into the CNS. Conclusions: We show that LGTV replication is restricted to the olfactory bulb and that IPS-1 is a very important player in the olfactory bulb in shaping the innate immune response by inhibiting early viral replication and viral spread throughout the central nervous system. In the absence of IPS-1, higher viral replication leads to the evasion of antiviral response by inhibiting interferon signaling. Our data suggest that the local microenvironment of distinct brain regions is critical to determine virus permissiveness

Additional file 2: Figure S2. of Type I Interferon response in olfactory bulb, the site of tick-borne flavivirus accumulation, is primarily regulated by IPS-1

Effect of IPS-1 signaling on BBB permeability upon LGTV infection. WT and IPS-1 −/− mice were mock or intraperitoneally infected with 104 FFU of LGTV (n = 3). Mice were intravenously injected with 100 μl 2 % Evans blue (Sigma) in PBS 4 and 7 dpi. After 1 h, animals were transcardially perfused with 20 ml PBS and the brains were removed. The brains were weighted and homogenized in 50 % TCA, and absorbance was measured at 610 nm. The absorbance was divided by the weight of the sample and normalized to mock infected samples. (PDF 42.5 KB

Additional file 5: Figure S4. of Type I Interferon response in olfactory bulb, the site of tick-borne flavivirus accumulation, is primarily regulated by IPS-1

Enhanced viral replication in olfactory bulb of IPS-1 −/− mice 4 dpi. WT and IPS-1 deficient mice were infected intraperitoneal with LGTV and olfactory bulb, cerebrum, cerebellum and brain stem was collected 4 dpi. LGTV RNA levels were quantified with the NS3 real-time qPCR assay (detection limit 10 copies). Asterisks indicates statistical significance between IPS-1 −/− olfactory bulb compared to other brain regions and calculated by Mann-Whitney test. Number sign indicates not detectable. (PDF 45.6 KB

Additional file 1: Figure S1. of Type I Interferon response in olfactory bulb, the site of tick-borne flavivirus accumulation, is primarily regulated by IPS-1

IPS-1 −/− mice have lower IFN-α levels in serum after LGTV infection compared to WT mice. WT and IPS-1 −/− mice were infected intraperitoneally with 104 FFU of LGTV, and serum samples were collected at indicated time points (n = 5–10). The amount of IFN-α in the mouse serum was determined by enzyme linked immunosorbent assay (ELISA) according to the manufacturer’s instructions (PBL). Significance was calculated with student’s T test, *p < 0.05. (PDF 53.6 KB