Analysis of NVMe over fabrics with SCinet DTN-as-a-Service

Supporting transfers of science big data over Wide Area Networks (WANs) with Data Transfer Nodes (DTNs) requires optimizing multiple parameters within the underlying infrastructure. New solutions for such data movement require new paradigms and technologies, such as NVMe over Fabrics, which provides high-performance data movement with direct remote NVMe device access over traditional fabrics. However, recent NVMe over Fabrics studies have been limited to local storage fabrics. To support increasing demands for the large volume of science data movement during Supercomputing (SC) conferences, we proposed a SCinet DTN-as-a-Service framework orchestrating the desired optimization to meet users, applications, and providers’ requirements. Furthermore, we extend the SCinet DTN-as-a-Service framework to incorporate new techniques, solve optimization issues in data-intensive science and evaluate NVMe over Fabrics with multiple WAN testbeds to examine its performance and discover new opportunities for optimization.

     

Using spotlight observations to predict resource selection and abundance for white-tailed deer

Spotlight surveys for white-tailed deer (Odocoileus virginianus) can yield large presence-only datasets applicable to a variety of resource selection modeling procedures. By understanding how populations distribute according to a given resource for a reference area, density and abundance can be predicted across new areas assuming the relationship between habitat quality (measured by an index of selection) and species distribution are equivalent. Habitat-based density estimators have been applied to wildlife species and are useful for addressing conservation and management concerns. Although achieving reliable population estimates is a primary goal for spotlighting studies, presence-only models have yet to be applied to spotlight data for estimating habitat selection and abundance for deer. From 2012 to 2017, we conducted spring spotlight surveys in each of 99 counties in Iowa, USA, and collected spatial locations for 20,149 groups of deer (n = 71,323 individuals). We used a resource selection function (RSF) based on deer locations to predict the relative probability of use for deer at the population level and to estimate statewide abundance. The number of deer observed statewide increased significantly with increasing RSF value for all years and the mean RSF value along survey transects explained 59% of the variability in county-level deer counts, indicating that a functional response between habitat quality and deer distribution existed at landscape scales. We applied our RSF to a habitat-based density estimator (extrapolation) and zero-inflated Poisson (ZIP) and negative binomial (ZINB) count models to predict statewide abundance from spotlight counts. Population estimates for 2012 were variable, indicating that atypical weather conditions may affect spotlight counts and population estimates in some years. For 2013–2017, we predicted a mean population of 439,129 (95% CI ∼ ± 55,926), 440,360 (∼ ± 43,676), and 465,959 (∼ ± 51,242) deer across years for extrapolation, ZIP, and ZINB models, respectively. Estimates from all models were not significantly different than estimates from an existing deer population accounting model in Iowa for 2013 and 2016, and differed by <76,000 deer for all models from 2013–2017. Extrapolation and ZIP models performed similarly and differed by <2,897 deer across all years, whereas ZINB models showed inconsistencies in model convergence and precision of estimates. Our results indicate that presence-only models are capable of producing reliable and precise estimates of resource selection and abundance for deer at broad landscape scales in Iowa and provide a tool for estimating deer abundance in a spatially explicit manner. © 2019 The Wildlife Society.     

The non-flavonoid inducible nodA3 and the flavonoid regulated nodA1 genes of Rhizobium tropici CIAT 899 guarantee nod factor production and nodulation of different host legumes

Plant and Soil - Previous studies have shown that pH, rather than calcium (Ca), is the main reason why some Lupinus species are sensitive to nutrient solutions mimicking calcareous soils; however,...     

Hypoxia induces the activation of the phosphatidylinositol 3-kinase/Akt cell survival pathway in PC12 cells: protective role in apoptosis

Hypoxia is a common environmental stress that influences signaling pathways and cell function. Several cell types, including neuroendocrine chromaffin cells, have evolved to sense oxygen levels and initiate specific adaptive responses to hypoxia. Here we report that under hypoxic conditions, rat pheochromocytoma PC12 cells are resistant to apoptosis induced by serum withdrawal and chemotherapy treatment. This effect is also observed after treatment with deferoxamine, a compound that mimics many of the effects of hypoxia. The hypoxia-dependent protection from apoptosis correlates with activation of the phosphatidylinositol 3-kinase (PI3K)/Akt pathway, which is detected after 3-4 h of hypoxic or deferoxamine treatment and is sustained while hypoxic conditions are maintained. Hypoxia-induced Akt activation can be prevented by treatment with cycloheximide or actinomycin D, suggesting that de novo protein synthesis is required. Finally, inhibition of PI3K impairs both the protection against apoptosis and the activation of Akt in response to hypoxia, suggesting a functional link between these two phenomena. Thus, reduced oxygen tension regulates apoptosis in PC12 cells through activation of the PI3K/Akt survival pathway.     

Electronic characterization of the oxidized state of the blue copper protein rusticyanin by 1H NMR: is the axial methionine the dominant influence for the high redox potential?

The oxidized state of rusticyanin, the blue copper protein with the highest redox potential in its class, has been investigated through (1)H nuclear magnetic resonance applied to its cobalt(II) derivative. The assignment of the protons belonging to the coordinated residues has been performed. Many other amino acids situated in the vicinity of the metal ion, including six hydrophobic residues (isoleucine140 and five phenylalanines) have also been identified. The orientation of the main axes of the magnetic susceptibility tensor for the cobalt(II)-rusticyanin as well as its axial, Deltachi(ax), and rhombic, Deltachi(rh), magnetic susceptibility anisotropy components have been determined. A comparison of the present results with those previously obtained for cobalt(II)azurin [Donaire, A., Salgado, J., Moratal, J. M. (1998) Biochemistry 37, 8659-8673] allows us to provide further insights into the reasons for the high redox potential of this protein. According to our results, the interaction between the metal ion and the thioether Sdelta of the axial methionine is not as influential as the strong destabilizing effect that the hydrophobic residues close to the metal ion undergo in the oxidized state.     

Monogeneans in introduced and native cichlids in México: evidence for transfer

We examined 2 cichlid fish species native to México, Cichlasoma callolepis and C. fenestratum, and 2 introduced African cichlids, Oreochromis aureus and O. niloticus, from 3 localities in southeastern México for monogeneans. Six monogenean species infected the African cichlids: Cichlidogyrus haplochromii, C. dossoui, C. longicornis longicornis, C. sclerosus, C. tilapiae, and Enterogyrus malmbergi. We found all these parasite species, except C. haplochromii and C. dossoui, on the native C. fenestratum and C. callolepis. Prevalences of Cichlidogyrus spp. were 3-10% and abundances ranged from 0.03 +/- 0.2 to 0.1 +/- 0.3 for native cichlids. We only recovered a single E. malmbergi from 1 C. callolepis. We found Sciadicleithrum bravohollisae, a monogenean of native Cichlasoma spp., on the gills of the introduced O. aureus from Lake Catemaco (prevalence 3%, abundance 0.03 +/- 0.2). Although prevalence and abundance in atypical hosts were fairly low, the present findings provide evidence of monogenean transfer from African to American cichlids and vice versa. This is the first record of exotic monogeneans in the genus Cichlidogyrus and Enterogyrus infecting native American cichlid fish. It is also the first record from southeastern México of a native American monogenean infecting introduced African cichlids.     

Arabidopsis ammonium transporters,AtAMT1;1 and AtAMT1;2, have different biochemical properties and functional roles

We have compared the biochemical properties of two different Arabidopsis ammonium transporters, AtAMT1;1 and AtAMT1;2, expressed in yeast, with the biophysical properties of ammonium transport in planta. Expression of the AtAMT1;1 gene in Arabidopsis roots increased approximately four-fold in response to nitrogen deprivation. This coincided with a similar increase in high-affinity ammonium uptake by these plants. The biophysical characteristics of this high-affinity system (K_m for ammonium and methylammonium of 8 M and 31 M, respectively) matched those of AtAMT1;1 expressed in yeast (K_m for methylammonium of 32 M and K_i for ammonium of 1–10 M). The same transport system was present, although less active, in nitrate-fed roots. Ammonium-fed plants exhibited the lowest rates of ammonium uptake and appeared to deploy a different transporter (K_m for ammonium of 46 M). Expression of AtAMT1;2 in roots was insensitive to changes in nitrogen nutrition. In contrast to AtAMT1;1, AtAMT1;2 expressed in yeast exhibited biphasic kinetics for methylammonium uptake: in addition to a high-affinity phase with a K_m of 36 M, a low-affinity phase with a K_m for methylammonium of 3.0 mM was measured. Despite the presence of a putative chloroplast transit peptide in AtAMT1;2, the protein was not imported into chloroplasts in vitro. The electrophysiological data for roots, together with the biochemical properties of AtAMT1;1 and Northern blot analysis indicate a pre-eminent role for AtAMT1;1 in ammonium uptake across the plasma membrane of nitrate-fed and nitrogen-deprived root cells.     

The mitotic centromeric protein MEI-S332 and its role in sister-chromatid cohesion

Faithful segregation of sister chromatids during cell division requires properly regulated cohesion between the sister centromeres. The sister chromatids are attached along their lengths, but particularly tightly in the centromeric regions. Therefore specific cohesion proteins may be needed at the centromere. Here we show that Drosophila MEI-S332 protein localizes to mitotic metaphase centromeres. Both overexpression and mutation of MEI-S332 increase the number of apoptotic cells. In mei-S332 mutants the ratio of metaphase to anaphase figures is lower than wild type, but it is higher if MEI-S332 is overexpressed. In chromosomal squashes centromeric attachments appear weaker in mei-S332 mutants than wild type and tighter when MEI-S332 is overexpressed. These results are consistent with MEI-S332 contributing to centromeric sister-chromatid cohesion in a dose-dependent manner. MEI-S332 is the first member identified of a predicted class of centromeric proteins that maintain centromeric cohesion. Received: 11 December 1998; in revised form: 4 August 1999 / Accepted: 13 August 1999     

Cytologic features of malignant peripheral nerve sheath tumor

OBJECTIVE: To study the cytomorphologic features of malignant peripheral nerve sheath tumor (MPNST), including the epithelioid cell variant, and to establish differential diagnostic features with benign neurogenic tumors and other sarcomas. STUDY DESIGN: Cytologic smears from primary, recurrent and metastatic tumors in 10 patients with MPNST were reviewed. Three patients had neurofibromatosis 1 (NF1), and in two others the tumor arose from a preexisting neurofibroma. Immunocytochemical evaluation of S-100 protein was performed in four cases. A complete pathologic study was available in all cases. To assess the validity of morphologic recognition, a blinded study, including eight cases of spindle MPNST among smears from histologically proven schwannomas, synovial sarcomas, leiomyosarcomas, malignant fibrous histiocytomas and liposarcomas, was performed. RESULTS: Neurogenic differentiation was recognizable in four cases (differentiated), while the other four (anaplastic) were indistinguishable from other pleomorphic sarcomas. The presence of elongated, slender, often wavy nuclei and less commonly a delicate, fibrillary metachromatic stroma were features suggestive of nerve sheath differentiation. Other cytologic, as well as clinical, features permitted their identification as malignant. Two cases of epithelioid MPNST disclosed large, polygonal to plasmocytoid tumor cells without specific cytologic features. S-100 immunoexpression was positive in two of the four cytologic samples tested. CONCLUSION: Although no morphologic findings are specific to MPNST, the above-mentioned cytologic features may suggest, in differentiated cases, its neurogenic differentiation. On the basis of morphologic features alone, the diagnosis of anaplastic and epithelioid MPNST is not possible, and immunocytochemical and ultrastructural studies are necessary. A specific cytodiagnosis is possible in recurrences, metastases and cases of NF1 or a preexisting neurofibroma.