On the design and implementation of broadcast and global combine operations using the postal model

There are a number of models that were proposed in recent years for message passing parallel systems. Examples are the postal model and its generalization the LogP model. In the postal model a parameter λ is used to model the communication latency of the message-passing system. Each node during each round can send a fixed-size message and, simultaneously, receive a message of the same size. Furthermore, a message sent out during round r will incur a latency of hand will arrive at the receiving node at round r + λ - 1. Our goal in this paper is to bridge the gap between the theoretical modeling and the practical implementation. In particular, we investigate a number of practical issues related to the design and implementation of two collective communication operations, namely, the broadcast operation and the global combine operation. Those practical issues include, for example, 1) techniques for measurement of the value of λ on a given machine, 2) creating efficient broadcast algorithms that get the latency hand the number of nodes n as parameters and 3) creating efficient global combine algorithms for parallel machines with λ which is not an integer. We propose solutions that address those practical issues and present results of an experimental study of the new algorithms on the Intel Delta machine. Our main conclusion is that the postal model can help in performance prediction and tuning, for example, a properly tuned broadcast improves the known implementation by more than 20%

Bio‐Metamaterials for Mechano‐Regulation of Mesenchymal Stem Cells

Cell behaviors significantly depend on the elastic properties of the microenvironments, which are distinct from commonly used polymer-based substrates. Artificial elastic materials called metamaterials offer large freedom to adjust their effective elastic properties as experienced by cells, provided (i) the metamaterial unit cell is sufficiently small compared to the biological cell size and (ii) the metamaterial is sufficiently soft to deform by the active cell contraction. Thus, metamaterials targeting bio-applications (bio-metamaterials) appear as a promising path toward the mechanical control of stem cells. Herein, human mesenchymal stem cells (hMSCs) are cultured on three different types of planar periodic elastic metamaterials. To fulfill the above two key requirements, microstructured bio-metamaterials have been designed and manufactured based on a silicon elastomer-like photoresist and two-photon laser printing. In addition to the conventional morphometric and immunocytochemical analysis, the traction force that hMSCs exert on metamaterials are inferred by converting the measured displacement-vector fields into force-vector fields. The differential responses of hMSCs, both on the cellular level and the sub-cellular level, correlate with the calculated effective elastic properties of the bio-metamaterials, suggesting the potential of bio-metamaterials toward mechanical regulation of cell behaviors by the arrangement of unit cells

Juvenile Green Sturgeon (\u3ci\u3eAcipenser medirostris\u3c/i\u3e) and White Sturgeon (\u3ci\u3eAcipenser transmontanus\u3c/i\u3e) Behavior Near Water-Diversion Fish Screens: Experiments in a Laboratory Swimming Fume

Water diversions that extract fresh water for urban, industrial, and agricultural uses, as well as export to southern California, are prevalent throughout the Sacramento–San Joaquin watershed. Many water diversions are fitted with fish-exclusion screens designed to prevent fish from entrainment (i.e., being drawn in). The impact of fish screens on the behavior of migrating juvenile fishes remains largely unknown, especially for threatened species such as sturgeon. We placed individual juvenile green (Acipenser medirostris) or white (Acipenser transmontanus) sturgeon in a laboratory swimming flume in the presence of standard fish screens (2 mm bar spacing) at two field-relevant water velocities (20.4 ± 0.1 and 37.3 ± 0.3 cm·s−1). Fish were tested at 18°C for 15 min during the day or night and in the presence of possible behavioral deterrents. Behavioral responses, including screen contacts, impingements, and time spent near screens were quantified. Green sturgeon contacted and impinged upon the screens twice as frequently as white sturgeon and also differed in how their behaviors were altered by water velocities and time of day. Our results are informative in developing effective management strategies to mitigate the impacts of water diversions on sturgeon populations and suggest that effective restoration strategies for both species should be considered separately

The effect of size on juvenile green sturgeon (\u3ci\u3eAcipenser medirostris\u3c/i\u3e) behavior near water-diversion fish screens

Anthropogenic water management projects and facilities that alter the local and regional hydrology of riverine environments greatly influence the behavior, physiology, and survival of native fishes. To mitigate for losses of native fishes at these structures, many are outfitted with fish-exclusion screens to reduce entrainment. The effect of fish size and age on behavior near fish screens, however, is largely unknown. Therefore, we tested two size classes of juvenile green sturgeon (Acipenser medirostris; small, early juveniles: 9.2 ± 0.2 cm fork length [FL], 6.9 ± 0.3 g; intermediate juveniles: 18.8 ± 0.2 cm FL, 36.9 ± 0.8 g) near fish-exclusion screens in a laboratory swimming flume. Although size was a significant factor influencing the way in which fish contacted the screens (i.e., proportion of body contacts, p = 2.5×10−9), it did not significantly influence the number of times fish contacted screens or the amount of time fish spent near screens. We also compared the performance of these two size classes to that of older and larger sturgeon that were tested previously (29.6 ± 0.2 cm FL, 147.1 ± 3.1 g), and documented a clear difference in the behavior of the fish that resulted in disparities in how the large fish contacted screens relative to small- or intermediate-sized juveniles (p = 0.005, 5.4 × 10−4, respectively). Our results further our understanding of how ontogeny affects fish behavior near anthropogenic devices, and are informative for managers seeking to identify the most susceptible size and age class of juvenile green sturgeon to water-diversion structures to potentially develop size-specific conservation strategies

Carbon, Metals, and Grain Size Correlate with Bacterial Community Structure in Sediments of a High Arsenic Aquifer

Bacterial communities can exert significant influence on the biogeochemical cycling of arsenic (As). This has globally important implications since As in drinking water affects the health of over 100 million people worldwide, including in the Ganges–Brahmaputra Delta region of Bangladesh where geogenic arsenic in groundwater can reach concentrations of more than 10 times the World Health Organization’s limit. Thus, the goal of this research was to investigate patterns in bacterial community composition across gradients in sediment texture and chemistry in an aquifer with elevated groundwater As concentrations in Araihazar, Bangladesh. We characterized the bacterial community by pyrosequencing 16S rRNA genes from aquifer sediment samples collected at three locations along a groundwater flow path at a range of depths between 1.5 and 15 m. We identified significant differences in bacterial community composition between locations in the aquifer. In addition, we found that bacterial community structure was significantly related to sediment grain size, and sediment carbon (C), manganese (Mn), and iron (Fe) concentrations. Deltaproteobacteria and Chloroflexi were found in higher proportions in silty sediments with higher concentrations of C, Fe, and Mn. By contrast, Alphaproteobacteria and Betaproteobacteria were in higher proportions in sandy sediments with lower concentrations of C and metals. Based on the phylogenetic affiliations of these taxa, these results may indicate a shift to more Fe-, Mn-, and humic substance-reducers in the high C and metal sediments. It is well-documented that C, Mn, and Fe may influence the mobility of groundwater arsenic, and it is intriguing that these constituents may also structure the bacterial community

Reversible Host–Guest Crosslinks in Supramolecular Hydrogels for On‐Demand Mechanical Stimulation of Human Mesenchymal Stem Cells

Stem cells are regulated not only by biochemical signals but also by biophysical properties of extracellular matrix (ECM). The ECM is constantly monitored and remodeled because the fate of stem cells can be misdirected when the mechanical interaction between cells and ECM is imbalanced. A well-defined ECM model for bone marrow-derived human mesenchymal stem cells (hMSCs) based on supramolecular hydrogels containing reversible host–guest crosslinks is fabricated. The stiffness (Young\u27s modulus E) of the hydrogels can be switched reversibly by altering the concentration of non-cytotoxic, free guest molecules dissolved in the culture medium. Fine-adjustment of substrate stiffness enables the authors to determine the critical stiffness level E* at which hMSCs turn the mechano-sensory machinery on or off. Next, the substrate stiffness across E* is switched and the dynamic adaptation characteristics such as morphology, traction force, and YAP/TAZ signaling of hMSCs are monitored. These data demonstrate the instantaneous switching of traction force, which is followed by YAP/TAZ signaling and morphological adaptation. Periodical switching of the substrate stiffness across E* proves that frequent applications of mechanical stimuli drastically suppress hMSC proliferation. Mechanical stimulation across E* level using dynamic hydrogels is a promising strategy for the on-demand control of hMSC transcription and proliferation

Chloride channel gene expression in the rabbit cornea

Purpose: The maintenance of stromal hydration by the corneal endothelium relies on active transendothelial anion transport, with bicarbonate and chloride the major anions carrying the current. However, the ion transport pathways that operate to maintain stromal hydration have yet to be fully elucidated. Methods: We used RT-PCR to identify the gene expression profile of members of the ClC family of chloride channels in freshly isolated samples of rabbit corneal endothelium, stroma, and epithelium. The expression of a separate group of genes was also examined to confirm the purity of the sample collection protocol. The expression of the ClC-2 and ClC-3 channel protein in the cornea was also evaluated by light and electron microscopic immunolabelling. Results: The mRNA for ClC-2, ClC-3, ClC-5, ClC-6, and ClC-7 were expressed in both the corneal epithelium and endothelium, and in the stroma. The mRNA for the skeletal muscle specific channel ClC-1 and the kidney specific chloride channel ClC-Ka were not detectable. ClC-4 mRNA was not detected in any rabbit tissue examined. The expression pattern of the mRNAs for collagens V, VI, VII, and VIII demonstrated the absence of contamination in epithelial and endothelial samples. ClC-2 and ClC-3 immunolabelling confirmed the presence of these proteins in corneal endothelium, stroma, and epithelium. Conclusions: Together with cystic fibrosis transmembrane conductance regulator (CFTR) and calcium activated chloride channel-1 (CLCA1), these results bring the number of chloride channel genes known to be expressed in the corneal endothelium and epithelium to seven. These channels are likely to be important for the maintenance of corneal transparency