Optimizing Distributed Tensor Contractions using Node-Aware Processor Grids

We propose an algorithm that aims at minimizing the inter-node communication volume for distributed and memory-efficient tensor contraction schemes on modern multi-core compute nodes. The key idea is to define processor grids that optimize intra-/inter-node communication volume in the employed contraction algorithms. We present an implementation of the proposed node-aware communication algorithm into the Cyclops Tensor Framework (CTF). We demonstrate that this implementation achieves a significantly improved performance for matrix-matrix-multiplication and tensor-contractions on up to several hundreds modern compute nodes compared to conventional implementations without using node-aware processor grids. Our implementation shows good performance when compared with existing state-of-the-art parallel matrix multiplication libraries (COSMA and ScaLAPACK). In addition to the discussion of the performance for matrix-matrix-multiplication, we also investigate the performance of our node-aware communication algorithm for tensor contractions as they occur in quantum chemical coupled-cluster methods. To this end we employ a modified version of CTF in combination with a coupled-cluster code (Cc4s). Our findings show that the node-aware communication algorithm is also able to improve the performance of coupled-cluster theory calculations for real-world problems running on tens to hundreds of compute nodes.Comment: 15 pages, 4 figure

Cross-Inhibition of Norrin and TGF-beta Signaling Modulates Development of Retinal and Choroidal Vasculature

PURPOSE. Norrin is essential for the formation of the retinal vasculature during development and promotes its repair after damage via activation of Wnt/beta-catenin signaling. Since retinal TGF-beta signaling has essentially opposite effects on the retinal vasculature we investigated if and how Norrin inhibits TGF-beta signaling, and vice versa. METHODS. Eyes from transgenic mice with an overexpression of Norrin (beta Bl-Norrin) and/or active TGF-beta (beta B1-TGF-beta 1) in the lens were generated and analyzed by light microscopy, immunohistochemistry, and TUNEL. Further on, protein as well as mRNA levels were investigated by Western blot analyses and real-time RT-PCR, respectively. RESULTS. In beta B1-TGF-beta l mice, the lack of retinal vascular development and choriocapillaris maintenance was rescued when transgenic Norrin was additionally overexpressed in the eye. In addition, retinal Wnt/beta-catenin signaling and the levels of SMAD7, an inhibitor of the canonical TGF-beta pathway, were substantially suppressed in retinae of beta B1-TGF-beta 1 mice. In contrast, Norrin normalized Wnt/beta-catenin signaling and SMAD7 levels in double transgenic mice. Moreover, in retinae of beta B1-TGF-beta 1 mice, the amounts of phosphorylated SMAD3, a downstream mediator of TGF-beta signaling, were increased compared to those of beta B1-Norrin/ beta B1-TGF-beta 1 mice. In vitro, Norrin substantially reduced the TGF-beta-mediated induction of target genes, an effect that was blocked by Dickkopf-1, a specific inhibitor of Wnt/beta-catenin signaling. CONCULSIONS. High amounts of TGF-beta in the eye cause a substantial reduction in the activity of Wnt/beta-catenin signaling. This effect is inhibited in the presence of high amounts of Norrin, which further induce the expression of SMAD7 to inhibit TGF-beta signaling

Electron microscopy analysis of femtosecond laser-assisted capsulotomy before and after lens fragmentation

Studying anterior lens capsule cutting edge profiles from femtosecond laser-assisted capsulotomy procedures performed before and after lens fragmentation. Twenty eyes (10 patients) with age-related cataract underwent femtosecond laser-assisted surgery (FLACS) using the Ziemer Z8 platform. First step of laser surgery was either capsulotomy (group first) or fragmentation (group second). One eye of each patient was assigned randomly, the second eye treated with the different sequence of procedures. After anterior capsule removal, tissue was fixed in cacodylate-buffered solution and cutting-edge profiles were analysed using scanning electron microscopy (SEM). All cases had cataract grade 2 and 3 based on LOCS III grading. SEM analysis showed more smooth edges in the first group, especially in cases with pseudoexfoliation (P = 0.037); more tags and bridges and a significant number of staggered cutting patterns (7 out of 10 cases) in the second group. All cases evolved the same microgroves with \textquotedblvalleys and mountains \textquotedbl as signs of the photodisruption process. Femtosecond laser capsulotomy should be performed before lens fragmentation minimizing the rate of cutting errors. Especially in eyes with advanced cataract, as intracapsular pressure may increase due to lens fragmentation without anterior capsular opening

Anti-angiogenic properties of rapamycin on human retinal pericytes in an in vitro model of neovascular AMD via inhibition of the mTOR pathway

Purpose Choroidal neovascularizations (CNV) are partially stabilized through a coverage of pericytes leading to a partial anti-VEGF resistence. Drugs licensed for neovascular AMD (nAMD) do not take this mechanical and growth factor-driven CNV stability into account. The purpose of this work was to see if inhibiting the mammalian target of rapamycin (mTOR) may successfully block angiogenic cellular pathways in primary human retinal pericytes in an in vitro model of nAMD. Methods The mTOR inhibitor rapamycin was used to treat human retinal pericytes (HRP) at doses ranging from 0.005 to 15 g/ml. A modified metabolism-based XTT-Assay was used to assess toxicity and anti-proliferative effects. A scratch wound experiment showed the effects on migration. On Cultrex basement membrane gels, the influence of rapamycin on the development of endothelial cell capillary-like structures by human umbilical vein vascular endothelial cells (HUVEC) in the absence and presence of pericytes was investigated. Results Rapamycin showed no signs of toxicity within its range of solubility. The drug showed dose dependent anti-proliferative activity and inhibited migration into the scratch wound. Endothelial cell tube formation in a HUVEC monoculture was effectively inhibited at 45%. A co-culture of HUVEC with pericytes on Cultrex induced endothelial tube stabilization but was disrupted by the addition of rapamycin leading to degradation of 94% of the tubes. Conclusions Rapamycin allows for an efficient modulation of aspects of angiogenesis in pericytes via mTOR-modulation in vitro. Further studies are needed to elucidate whether rapamycin may have an impact on CNV in nAMD in vivo

Ex vivo excimer laser ablation of cornea guttata and ROCK inhibitor‐aided endothelial recolonization of ablated central cornea

Purpose To determine whether excimer laser ablation of guttae is a viable strategy for removal of diseased tissue in Fuchs' endothelial corneal dystrophy (FECD) on excised human Descemet membranes and whether an excimer laser‐created wound on healthy human corneas ex vivo is recolonized with corneal endothelial cells. Methods Descemet membranes of FECD patients and corneal endothelium of normal human corneas were ablated ex vivo using an excimer laser licensed for glaucoma surgery. Specimens were kept in cell culture medium supplemented with 10 μm of rho‐kinase inhibitor ripasudil. Corneal endothelial cell regeneration was observed using light and electron scanning microscopy. Furthermore, the whole corneal samples were evaluated by haematoxylin/eosin staining and immunohistochemical analysis using antibodies against Na+/K+‐ATPase. Results Guttae and corneal endothelium could be ablated with an excimer laser without total ultrastructural damage to the Descemet membrane or stroma. Nearly complete endothelial wound closure was accomplished after 26–38 days in treated corneas. Light and electron scanning microscopy suggested the establishment of a layer of flat endothelial cells. Additionally, Na+/K+‐ATPase expression could only be observed on the inner side of the Descemet membrane. Conclusion Our proof of concept study demonstrated that excimer lasers can be used to ablate diseased tissue from excised FECD Descemet membranes ex vivo. Additionally, corneal endothelial cells recolonize a previously ablated endothelial area in healthy human corneas ex vivo under treatment with ripasudil. Thus, our results are the first experimental basis to further investigate the feasibility of an excimer laser ablation as a graftless FECD treatment option

Gravitational wave emission from dynamical stellar interactions

We are witnessing the dawn of gravitational wave (GW) astronomy. With currently available detectors, observations are restricted to GW frequencies in the range between ${\sim} 10\,\mathrm{Hz}$ and $10\,\mathrm{kHz}$, which covers the signals from mergers of compact objects. The launch of the space observatory LISA will open up a new frequency band for the detection of stellar interactions at lower frequencies. In this work, we predict the shape and strength of the GW signals associated with common-envelope interaction and merger events in binary stars, and we discuss their detectability. Previous studies estimated these characteristics based on semi-analytical models. In contrast, we used detailed three-dimensional magnetohydrodynamic simulations to compute the GW signals. We show that for the studied models, the dynamical phase of common-envelope events and mergers between main-sequence stars lies outside of the detectability band of the LISA mission. We find, however, that the final stages of common-envelope interactions leading to mergers of the stellar cores fall into the frequency band in which the sensitivity of LISA peaks, making them promising candidates for detection. These detections can constrain the enigmatic common-envelope dynamics. Furthermore, future decihertz observatories such as DECIGO or BBO would also be able to observe this final stage and the post-merger signal, through which we might be able to detect the formation of Thorne-\.Zytkow objects.Comment: Accepted for publication in A&A, 12 pages, 8 figure

Decorin—An Antagonist of TGF-β in Astrocytes of the Optic Nerve

During the pathogenesis of glaucoma, optic nerve (ON) axons become continuously damaged at the optic nerve head (ONH). This often is associated with reactive astrocytes and increased transforming growth factor (TGF-β) 2 levels. In this study we tested the hypothesis if the presence or absence of decorin (DCN), a small leucine-rich proteoglycan and a natural inhibitor of several members of the TGF family, would affect the expression of the TGF-βs and connective tissue growth factor (CTGF/CCN2) in human ONH astrocytes and murine ON astrocytes. We found that DCN is present in the mouse ON and is expressed by human ONH and murine ON astrocytes. DCN expression and synthesis was significantly reduced after 24 h treatment with 3 nM CTGF/CCN2, while treatment with 4 pM TGF-β2 only reduced expression of DCN significantly. Conversely, DCN treatment significantly reduced the expression of TGF-β1, TGF-β2 and CTGF/CCN2 vis-a-vis untreated controls. Furthermore, DCN treatment significantly reduced expression of fibronectin (FN) and collagen IV (COL IV). Notably, combined treatment with DCN and triciribine, a small molecule inhibitor of protein kinase B (AKT), attenuated effects of DCN on CTGF/CCN2, TGF-β1, and TGF-β2 mRNA expression. We conclude (1) that DCN is an important regulator of TGF-β and CTGF/CCN2 expression in astrocytes of the ON and ONH, (2) that DCN thereby regulates the expression of extracellular matrix (ECM) components and (3) that DCN executes its negative regulatory effects on TGF-β and CTGF/CCN2 via the pAKT/AKT signaling pathway in ON astrocytes

Distribution of Gold Nanoparticles in the Anterior Chamber of the Eye after Intracameral Injection for Glaucoma Therapy

In glaucoma therapy, nanoparticles (NPs) are a favorable tool for delivering drugs to the outflow tissues of the anterior chamber of the eye where disease development and progression take place. In this context, a prerequisite is an efficient enrichment of NPs in the trabecular meshwork with minimal accumulation in off-target tissues such as the cornea, lens, iris and ciliary body. We evaluated the optimal size for targeting the trabecular meshwork by using gold NPs of 5, 60, 80 and 120 nm with a bare surface (AuNPs) or coated with hyaluronic acid (HA-AuNPs). NPs were compared regarding their colloidal stability, distribution in the anterior chamber of the eye ex vivo and cellular uptake in vitro. HA-AuNPs demonstrated an exceptional colloidal stability. Even after application into porcine eyes ex vivo, the HA coating prevented an aggregation of NPs inside the trabecular meshwork. NPs with a diameter of 120 nm exhibited the highest volume-based accumulation in the trabecular meshwork. Off-target tissues in the anterior chamber demonstrated an exceptionally low gold content. Our findings are particularly important for NPs with encapsulated anti-glaucoma drugs because a higher particle volume would be accompanied by a higher drug payload