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A New Approach to Monitoring Coastal Marshes for Persistent Flooding

Many areas in coastal Louisiana are below sea level and protected from flooding by a system of natural and man-made levees. Flooding is common when the levees are overtopped by storm surge or rising rivers. Many levees in this region are further stressed by erosion and subsidence. The floodwaters can become constricted by levees and trapped, causing prolonged inundation. Vegetative communities in coastal regions, from fresh swamp forest to saline marsh, can be negatively affected by inundation and changes in salinity. As saltwater persists, it can have a toxic effect upon marsh vegetation causing die off and conversion to open water types, destroying valuable species habitats. The length of time the water persists and the average annual salinity are important variables in modeling habitat switching (cover type change). Marsh type habitat switching affects fish, shellfish, and wildlife inhabitants, and can affect the regional ecosystem and economy. There are numerous restoration and revitalization projects underway in the coastal region, and their effects on the entire ecosystem need to be understood. For these reasons, monitoring persistent saltwater intrusion and inundation is important. For this study, persistent flooding in Louisiana coastal marshes was mapped using MODIS (Moderate Resolution Imaging Spectroradiometer) time series of a Normalized Difference Water Index (NDWI). The time series data were derived for 2000 through 2009, including flooding due to Hurricane Rita in 2005 and Hurricane Ike in 2008. Using the NDWI, duration and extent of flooding can be inferred. The Time Series Product Tool (TSPT), developed at NASA SSC, is a suite of software developed in MATLAB(R) that enables improved-quality time series images to be computed using advanced temporal processing techniques. This software has been used to compute time series for monitoring temporal changes in environmental phenomena, (e.g. NDVI times series from MODIS), and was modified and used to compute the NDWI indices and also the Normalized Difference Soil Index (NDSI). Coastwide Reference Monitoring System (CRMS) water levels from various hydrologic monitoring stations and aerial photography were used to optimize thresholds for MODIS-derived time series of NDWI and to validate resulting flood maps. In most of the profiles produced for post-hurricane assessment, the increase in the NDWI index (from storm surge) is accompanied by a decrease in the vegetation index (NDVI) and then a period of declining water. The NDSI index represents non-green or dead vegetation and increases after the hurricane s destruction of the marsh vegetation. Behavior of these indices over time is indicative of which areas remain flooded, which areas recover to their former levels of vegetative vigor, and which areas are stressed or in transition. Tracking these indices over time shows the recovery rate of vegetation and the relative behavior to inundation persistence. The results from this study demonstrated that identification of persistent marsh flooding, utilizing the tools developed in this study, provided an approximate 70-80 percent accuracy rate when compared to the actual days flooded at the CRMS stations.

Kalcic, M. T.↗

Distributed metadata servers for cluster file systems using shared low latency persistent key-value metadata store

A cluster file system is provided having a plurality of distributed metadata servers with shared access to one or more shared low latency persistent key-value metadata stores. A metadata server comprises an abstract storage interface comprising a software interface module that communicates with at least one shared persistent key-value metadata store providing a key-value interface for persistent storage of key-value metadata. The software interface module provides the key-value metadata to the at least one shared persistent key-value metadata store in a key-value format. The shared persistent key-value metadata store is accessed by a plurality of metadata servers. A metadata request can be processed by a given metadata server independently of other metadata servers in the cluster file system. A distributed metadata storage environment is also disclosed that comprises a plurality of metadata servers having an abstract storage interface to at least one shared persistent key-value metadata store.

97 MATHEMATICS AND COMPUTING↗

The Computational Complexity of Multidimensional Persistence

We present findings on the computational complexity of computing multidimensional persistent homology. We first show that the worst-case computational complexity of multidimensional persistence is exponential. We then present an algorithm for computing multidimensional persistence which extends the algorithm given by Zomorodian and Carlsson for computing one-dimensional persistence. The computational complexity of our algorithm is polynomial in the size of the persistence module and exponential in the persistence dimension.

97 MATHEMATICS AND COMPUTING↗

Persistent Supercooled Drizzle at Temperatures Below -25 °C Observed at McMurdo Station, Antarctica

The rarity of reports in the literature of brief and spatially limited observations of drizzle at temperatures below -20 degrees C suggest that riming and other temperature-dependent cloud microphysical processes such as heterogeneous ice nucleation and ice crystal depositional growth prevent drizzle persistence in cold environments. In this study, we report on a persistent drizzle event observed by ground-based remote sensing measurements at McMurdo Station, Antarctica. The temperatures in the drizzle-producing cloud were below -25 degrees C and the drizzle persisted for a period exceeding 7.5 hr. Using ground-based, satellite, and reanalysis data, we conclude that drizzle was likely present in parts of a widespread cloud field, which stretched more than similar to 1,000 km along the Ross Ice Shelf coast. Parameter space sensitivity tests using two-moment bulk microphysics in large eddy simulations constrained by the observations suggest that activated ice freezing nuclei and accumulation-mode aerosol number concentrations aloft during this persistent drizzle period were likely on the order of 0.2 L-1 and 20 cm -3 , respectively. In such constrained simulations, the drizzle moisture flux through cloud base exceeds that of ice. The simulations also indicate that drizzle can lead to the formation of multiple peaks in cloud water content profiles. This study suggests that persistent drizzle at these low temperatures may be common at the low aerosol concentrations typical of the Antarctic and Southern Ocean atmospheres.

54 ENVIRONMENTAL SCIENCES↗

MOSIQS: Persistent Memory Object Storage With Metadata Indexing and Querying for Scientific Computing

Scientific applications often require high-bandwidth shared storage to perform joint simulations and collaborative data analytics. Shared memory pools provide a chance to satisfy such needs. Recently, a high-speed network such as Gen-Z utilizing persistent memory (PM) offers an opportunity to create a shared memory pool connected to compute nodes. However, there are several challenges to use scientific applications on the shared memory pool directly such as scalability, failure-atomicity, and lack of scientific metadata-based search and query. In this paper, we propose MOSIQS, a persistent memory object storage framework with metadata indexing and querying for scientific computing. We design MOSIQS based on the key idea that memory objects on PM pool can live beyond the application lifetime and can become the sharing currency for applications and scientists. MOSIQS provides an aggregate memory pool atop an array of persistent memory devices to store and access memory objects to accelerate scientific computing. MOSIQS uses a lightweight persistent memory key-value store to manage the metadata of memory objects, which enables memory object sharing. To facilitate metadata search and query over millions of memory objects resident on memory pool, we introduce Group Split and Merge (GSM), a novel persistent index data structure designed primarily for scientific datasets. GSM splits and merges dynamically to minimize the query search space and maintains low query processing time while overcoming the index storage overhead. MOSIQS is implemented on top of PMDK. We evaluate the proposed approach on many-core server with an array of real PM devices. Experimental results show that MOSIQS gains a 100% write performance improvement and executes multi-attribute queries efficiently with 2.7× less index storage overhead offering significant potential to speed up scientific computing applications.

97 MATHEMATICS AND COMPUTING↗

Malicious Cyber Activity Detection using Zigzag Persistence

In this study we synthesize zigzag persistence from topological data analysis with autoencoder-based approaches to detect malicious cyber activity, and derive analytic insights. Cybersecurity aims to safeguard computers, networks, and servers from various forms of malicious attacks, including network damage, data theft, and activity monitoring. We focus on the cybersecurity domain and investigate the detection of malicious activity using log data. We consider the dynamics of the log data and explore the changing topology of a hypergraph representation of this data to gain insights into the underlying activity. These hypergraphs capture complex interactions between processes, together with their temporal information. To study the changing topology we use zigzag persistence, which captures how topological features persist at multiple dimensions over time. We observe that this detects malicious activity in a cyber data set. To automate this detection we implement an autoencoder trained on a vectorization of the resulting zigzag persistence barcodes. Our experimental results demonstrate the effectiveness of the autoencoder in detecting malicious activity. Overall, this study highlights the potential of zigzag persistence and its combination with temporal hypergraphs for analyzing cybersecurity log data and detecting malicious behavior.

hypergraphs, temporal hypergraph, topological data↗

SmpB down-regulates proton-motive force for the persister tolerance to aminoglycosides in Aeromonas veronii

Highlights: • The smpB deletion exhibited a higher susceptibility to aminoglycosides in A. veronii. • The expression level of SmpB was enhanced by gentamicin challenge. • The effect of SmpB on persistence formation was eliminated by PMF inhibition. • The smpB deletion downregulated proton-motive force-related metabolic genes. Bacterial persisters comprise a small fraction of phenotypically heterogeneous variants with transient capability for survival when exposed to high concentrations of antibiotic. In aquatic pathogenic bacteria Aeromonas veronii, Small Protein B (SmpB), the core factor of trans-translation system, was identified as a new persistence-related gene. The SmpB deletion exhibited a higher susceptibility and lower persister cell formation under aminoglycosides antibiotics pressure compared with wild type. The transcriptional and translational activities of smpB gene were significantly enhanced by the gentamicin challenge in exponential phase, but not changed in stationary phase. The transcriptomic analysis revealed that the smpB deletion stimulated the production of proton-motive force (PMF). The cell survival induced by carbonyl cyanide m-chlorophenyl hydrazone (CCCP) further verified that SmpB variation affected the quantities of PMF. Taken together, these results uncovered a novel mechanism of persister formation mediated by SmpB under aminoglycosides treatments.

60 APPLIED LIFE SCIENCES↗

Effect of retrapping on the persistent luminescence in strontium silicate orange–yellow phosphor

The orange–yellow long persistent luminescence in Sr{sub 3}SiO{sub 5}:Eu{sup 2+}, Er{sup 3+} with the chromaticity coordination of (0.48, 0.49) can persist for over 20 h above the recognizable intensity level (≥0.32 mcd/m{sup 2}) because of retrapping carriers by the deep traps. The incorporation of Er{sup 3+} into Sr{sub 3}SiO{sub 5}:Eu{sup 2+} generates a large number of shallow traps responsible for the fast decay component as well as deep traps responsible for the decay tail of the LPL. It demonstrates that the retrapping of the carrier released from a trap plays an important role in the persistent luminescence process. - Graphical abstract: LPL decay curves of Sr{sub 3−x−y}SiO{sub 5}:xEu{sup 2+}, yEr{sup 3+} (x=0.0025, y=0, 0.0025). Inset: Orange–yellow emission images recorded using a classic Reflex digital camera with exposure times varying with the persistent luminescence times. Display Omitted - Highlights: • The persistence time of Sr{sub 3}SiO{sub 5}:Eu{sup 2+}, Er{sup 3+} lasts over 20 h above the recognizable intensity level. • The incorporation of Er{sup 3+} into Sr{sub 3}SiO{sub 5}:Eu{sup 2+} generates a large number of shallow traps. • The experimental results provide an evidence for the retrapping process in LPL processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Biomolecular budget of persistent, microbial-derived soil organic carbon: The importance of underexplored pools

The details of how soil microorganisms contribute to stable soil organic carbon pools are a pressing knowledge gap with direct implications for soil health and climate mitigation. It is now recognized that microbial necromass contributes substantially to the formation of stable soil carbon. However, the quantification of necromass in soils has largely been limited to model molecules such as aminosugar biomarkers. The abundance and chemical composition of other persistent microbial residues remain unresolved, particularly concerning how these pools may vary with microbial community structure, soil texture, and management practices. We use yearlong soil incubation experiments with an isotopic tracer to quantify the composition of persistent residues derived from microbial communities inhabiting sand or silt dominated soil with annual (corn) or perennial (switchgrass) monocultures. Persistent microbial residues were recovered in diverse soil biomolecular pools including metabolites, proteins, lipids, and mineral-associated organic matter (MAOM). The relative abundances of microbial contributions to necromass pools were consistent across cropping systems and soil textures. The greatest residue accumulation was not recovered in MAOM but in the light density fraction of soil debris that persisted after extraction by chemical fractionation using organic solvents. Necromass abundance was positively correlated with microbial biomass abundance and revealed a possible role of cell wall morphology in enhancing microbial carbon persistence; while gram-negative bacteria accounted for the greatest contribution to microbial-derived carbon by mass at one year, residues from gram-positive Actinobacteria and Firmicutes showed greater durability. Together these results offer a quantitative assessment of the relative importance of diverse molecular classes for generating durable soil carbon.

54 ENVIRONMENTAL SCIENCES↗

Acute lung injury and persistent small airway disease in a rabbit model of chlorine inhalation

Chlorine is a pulmonary toxicant to which humans can be exposed through accidents or intentional releases. Acute effects of chlorine inhalation in humans and animal models have been well characterized, but less is known about persistent effects of acute, high-level chlorine exposures. In particular, animal models that reproduce the long-term effects suggested to occur in humans are lacking. Here, we report the development of a rabbit model in which both acute and persistent effects of chlorine inhalation can be assessed. Male New Zealand White rabbits were exposed to chlorine while the lungs were mechanically ventilated. After chlorine exposure, the rabbits were extubated and were allowed to survive for up to 24 h after exposure to 800 ppm chlorine for 4 min to study acute effects or up to 7 days after exposure to 400 ppm for 8 min to study longer term effects. Acute effects observed 6 or 24 h after inhalation of 800 ppm chlorine for 4 min included hypoxemia, pulmonary edema, airway epithelial injury, inflammation, altered baseline lung mechanics, and airway hyperreactivity to inhaled methacholine. Seven days after recovery from inhalation of 400 ppm chlorine for 8 min, rabbits exhibited mild hypoxemia, increased area of pressure–volume loops, and airway hyperreactivity. Lung histology 7 days after chlorine exposure revealed abnormalities in the small airways, including inflammation and sporadic bronchiolitis obliterans lesions. Immunostaining showed a paucity of club and ciliated cells in the epithelium at these sites. These results suggest that small airway disease may be an important component of persistent respiratory abnormalities that occur following acute chlorine exposure. This non-rodent chlorine exposure model should prove useful for studying persistent effects of acute chlorine exposure and for assessing efficacy of countermeasures for chlorine-induced lung injury. - Highlights: • A novel rabbit model of chlorine-induced lung disease was developed. • Acute effects of chlorine were pulmonary edema, hypoxemia and impaired lung function. • Persistent small airway disease developed following recovery from acute injury. • Small airway disease included inflammation and bronchiolitis obliterans lesions. • The model should be useful for studying chlorine lung injury and testing treatments.

60 APPLIED LIFE SCIENCES↗

Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition

Gut microbiome succession affects infant development. However, it remains unclear what factors promote persistence of initial bacterial colonizers in the developing gut. Here, we perform strain-resolved analyses to compare gut colonization of preterm and full-term infants throughout the first year of life and evaluate associations between strain persistence and strain origin as well as genetic potential. Analysis of fecal metagenomes collected from 13 full-term and 9 preterm infants reveals that infants' initially distinct microbiomes converge by age 1 year. Approximately 11% of early colonizers, primarily Bacteroides and Bifidobacterium, persist during the first year of life, and those are more prevalent in full-term, compared with preterm infants. Examination of 17 mother-infant pairs reveals maternal gut strains are significantly more likely to persist in the infant gut than other strains. Enrichment in genes for surface adhesion, iron acquisition, and carbohydrate degradation may explain persistence of some strains through the first year of life.

59 BASIC BIOLOGICAL SCIENCES↗

Targeting Mycobacterium tuberculosis Persistence through Inhibition of the Trehalose Catalytic Shift

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is the leading cause of death worldwide by infectious disease. Treatment of Mtb infection requires a six-month course of multiple antibiotics, an extremely challenging regimen necessitated by Mtb’s ability to form drug-tolerant persister cells. Mtb persister formation is dependent on the trehalose catalytic shift, a stress-responsive metabolic remodeling mechanism in which the disaccharide trehalose is liberated from cell surface glycolipids and repurposed as an internal carbon source to meet energy and redox demands. Here, using a biofilm-persister model, metabolomics, and cryo-electron microscopy (EM), we found that azidodeoxy- and aminodeoxy-d-trehalose analogues block the Mtb trehalose catalytic shift through inhibition of trehalose synthase TreS (Rv0126), which catalyzes the isomerization of trehalose to maltose. Out of a focused eight-member compound panel constructed by chemoenzymatic synthesis, the natural product 2-trehalosamine exhibited the highest potency and significantly potentiated first- and second-line TB drugs in broth culture and macrophage infection assays. We also report the first structure of TreS bound to a substrate analogue inhibitor, obtained via cryo-EM, which revealed conformational changes likely essential for catalysis and inhibitor binding that can potentially be exploited for future therapeutic development. Our results demonstrate that inhibition of the trehalose catalytic shift is a viable strategy to target Mtb persisters and advance trehalose analogues as tools and potential adjunctive therapeutics for investigating and targeting mycobacterial persistence.

60 APPLIED LIFE SCIENCES↗

HIV persistence in tissue macrophages of humanized myeloid-only mice during antiretroviral therapy

Despite years of fully suppressive antiretroviral therapy (ART), HIV persists in its hosts and is never eradicated. One major barrier to eradication is that the virus infects multiple cell types that may individually contribute to HIV persistence. Tissue macrophages are critical contributors to HIV pathogenesis; however, their specific role in HIV persistence during long-term suppressive ART has not been established. Using humanized myeloid-only mice (MoM), we demonstrate that HIV infection of tissue macrophages is rapidly suppressed by ART, as reflected by a rapid drop in plasma viral load and a dramatic decrease in the levels of cell-associated viral RNA and DNA. No viral rebound was observed in the plasma of 67% of the ART-treated animals at 7 weeks after ART interruption, and no replication-competent virus was rescued from the tissue macrophages obtained from these animals. In contrast, in a subset of animals (~33%), a delayed viral rebound was observed that is consistent with the establishment of persistent infection in tissue macrophages. Furthermore, these observations represent the first direct evidence, to our knowledge, of HIV persistence in tissue macrophages in vivo .

59 BASIC BIOLOGICAL SCIENCES↗

Multiresolution persistent homology for excessively large biomolecular datasets

Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Persistent in vivo cytogenetic effects of radioiodine therapy: a 21-year follow-up study using multicolor FISH

Abstract Our previous studies demonstrated the cytogenetic effects in the peripheral blood lymphocytes of a 34-year-old male patient who received ablative radioactive 131iodine therapy (RIT) on two different occasions in 1992 and 1994. Assessment of RIT-induced chromosomal damage by the cytokinesis-blocked micronucleus assay (CBMN) showed the persistence of elevated micronucleus frequency in this patient for more than two decades since the first RIT. Subsequent cytogenetic analysis performed in 2012 revealed both stable and unstable aberrations, whose frequencies were higher than the baseline reported in the literature. Here, we report the findings of our recent cytogenetic analysis peformed in 2015 on this patient using the multicolor fluorescence in situ hybridization (mFISH) technique. Our results showed that both reciprocal and non-reciprocal translocations persisted at higher frequencies in the patient than those reported in 2012. Persistence of structural aberrations for more than two decades indicate that these aberrations might have originated from long-lived T-lymphocytes or hematopoietic stem cells. Our study suggests that the long-term persistence of chromosome translocations in circulating lymphocytes can be useful for monitoring the extent of RIT-induced chromosomal instability several years after exposure and for estimating the cumulative absorbed dose after multiple RITs for retrospective biodosimetry purposes. This is perhaps the first and longest follow-up study documenting the persistence of cytogenetic damage for 21 years after internal radiation exposure.

micronuclei↗

Relation between photon thermal Hall effect and persistent heat current in nonreciprocal radiative heat transfer

In this work, we study the photon thermal Hall effect and the persistent heat current in radiative heat transfer. We show that the photon thermal Hall effect is not a uniquely nonreciprocal effect; it can arise in some reciprocal systems with broken-mirror symmetry. This is in contrast with the persistent heat current, which is a uniquely nonreciprocal effect that cannot exist in any reciprocal system. Nevertheless, for a specific class of systems with C 4 rotational symmetry, we note that the photon thermal Hall effect is uniquely nonreciprocal, and moreover there is a direct connection between the persistent heat current and the photon thermal Hall effect. In the near-equilibrium regime, the magnitude of the photon thermal Hall effect is proportional to the temperature derivative of the persistent heat current in such systems. Therefore, the persistent heat current as predicted for the equilibrium situation can be probed by the photon thermal Hall effect away from equilibrium.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Drought Reduces Formation, but Enhances Persistence, of Mineral‐Associated Organic Matter in a Grassland Soil

Drought effects are pervasive in terrestrial ecosystems, yet there is limited understanding of how drought impacts the transformation of plant carbon (C) inputs to mineral-associated organic matter (MAOM)—the largest and slowest-cycling pool of soil organic carbon (SOC). In a 12-week 13 C-CO 2 greenhouse labeling experiment, we tracked the formation of MAOM derived from the two dominant sources of plant C input to the mineral soil—living root inputs ( 13 C-rhizodeposits) and decaying root inputs ( 13 C-root detritus)—under normal moisture and droughted conditions in a semiarid grassland soil. At the end of the 12-week period, we also measured the persistence of 13 C-MAOM formed from rhizodeposits versus root detritus via a subsequent persistence assay. Drought reduced the formation of MAOM derived from living roots by decreasing rhizodeposits, reducing microbial growth rates, and altering the composition of organic matter, lipids, and metabolites. Drought initially delayed the formation of MAOM derived from root detritus by slowing the early stages of root litter decomposition (week 4–8), but did not decrease total MAOM formation by the end of the 12-week period. Notably, drought enhanced the persistence of MAOM derived from root detritus, but did not influence the persistence of MAOM derived from rhizodeposits. Our results provide some of the first direct evidence that drought can reduce the formation of MAOM in a grassland soil, but may enhance its persistence, based on the source of plant input from which MAOM is derived.

13C- labeling↗

Long-Term Efficacy of Lymph Node Reoperation for Persistent Papillary Thyroid Cancer: 13-Year Follow-Up

Background: Current recommendations for persistent or recurrent locoregional papillary thyroid cancer (PTC) include consideration of surgical resection versus active surveillance. The purpose of this study is to determine long-term outcomes after surgical resection of recurrent or persistent metastatic PTC in cervical lymph nodes after failure of initial surgery and radioactive iodine therapy using newer validated clinical outcomes measures. Methods: Outcomes of 70 patients who underwent cervical lymphadenectomy (n = 110) from 1999 to 2013 for recurrent or persistent locoregional PTC metastases were reviewed. Measures included biochemical remission (BCR) based on Tg levels, American Thyroid Association classifications for response to treatment [biochemical incomplete response (BIR), structural incomplete response (SIR), indeterminate response (IR), and excellent response (ER)], need for reoperation, surgical complications, disease progression, and death. Results: The median follow-up was 13.1 years, with only two additional reoperations since 2010, one of which had no metastasis on pathology with the other developing anaplastic thyroid cancer in background PTC. ER was achieved in 31 (44%) patients, all of whom remained in ER at time of last follow-up (median 14.1 years). There were no structural recurrences in patients with persistent BIR or IR after reoperation. Patients with SIR had stable disease, except for one who died due to anaplastic thyroid cancer. Conclusions: Patients who achieved ER after reoperation had no need for further treatment. Patients with persistent detectable Tg levels after reoperation rarely developed structural recurrence. ATA outcomes can be safely used to guide treatment decisions over a decade after reoperation for PTC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗