The Residual GEM technique and its application to the southwestern Japan/East Sea

The standard gravest empirical mode (GEM) technique for utilizing hydrography in concert with integral ocean measurements performs poorly in the southwestern Japan/East Sea (JES) because of a spatially variable seasonal signal and a shallow thermocline. This paper presents a new method that combines the U.S. Navy\u27s Modular Ocean Data Assimilation System (MODAS) static climatology (which implicitly contains the mean seasonal signal) with historical hydrography to construct a “residual GEM” from which profiles of such parameters as temperature (T) and specific volume anomaly (δ) can be estimated from measurements of an integral quantity such as geopotential height or acoustic echo time (τ). This is called the residual GEM technique. In a further refinement, sea surface temperature (SST) measurements are included in the profile determinations. In the southwestern JES, profiles determined by the standard GEM technique capture 70% of the T variance and 64% of the δ variance, while the residual GEM technique using SST captures 89% of the T variance and 84% of the δ variance. The residual GEM technique was applied to optimally interpolated τ measurements from a two-dimensional array of pressure-gauge-equipped inverted echo sounders moored from June 1999 to July 2001 in the southwestern JES, resulting in daily 3D estimated fields of T and δ throughout the region. These estimates are compared with those from direct measurements and good agreement is found between them

A Multi-Index GEM Technique and Its Application to the Southwestern Japan/East Sea

This paper demonstrates a new gravest empirical mode (GEM) technique that constructs multi-index lookup tables of temperature (T) and specific volume anomalies (δ) using historical hydrocasts as a function of three indices: round-trip travel time (τ) from sea floor to the surface, sea surface temperature, and pressure. Moreover, the historical hydrocasts are separated into non-mixed-layer (NML) and mixed-layer (ML) groups, and a single GEM field is constructed for each group. This is called the MI-GEM technique. The appropriate dates for MI-GEM fields are determined by the monthly distribution of the number of NML and ML profiles in the historical hydrocasts, which are also well correlated with the strength of the winds during the 2 yr of observations. The T and δ profiles that are determined by this MI-GEM technique capture 92% and 88% of the T and δ variances in the depth range of 0–200 db. These values reduce by about one-third of the unexplained error variance of the residual GEM, which was recently developed and applied to the optimal interpolated τ data in the southwestern Japan/East Sea (JES) by Mitchell et al. Comparisons with the in situ CTD casts demonstrate that the MI-GEM technique almost always produces improved full water column profiles of T and δ. Whereas the residual GEM estimates had exhibited qualitatively erroneous features like T inversions in the near–surface layer and too thin or thick intermediate water layers in some regions, the MI-GEM estimates avoid those problems, which were inherent to the residual GEM technique in the southwestern JES

Toca 511 gene transfer and treatment with the prodrug, 5-fluorocytosine, promotes durable antitumor immunity in a mouse glioma model.

BackgroundToca 511 (vocimagene amiretrorepvec) is a retroviral replicating vector encoding an optimized yeast cytosine deaminase (CD). Tumor-selective expression of CD converts the prodrug, 5-fluorocytosine (5-FC), into the active chemotherapeutic, 5-fluorouracil (5-FU). This therapeutic approach is being tested in a randomized phase II/III trial in recurrent glioblastoma and anaplastic astrocytoma (NCT0241416). The aim of this study was to identify the immune cell subsets contributing to antitumor immune responses following treatment with 5-FC in Toca 511-expressing gliomas in a syngeneic mouse model.MethodsFlow cytometry was utilized to monitor and characterize the immune cell infiltrate in subcutaneous Tu-2449 gliomas in B6C3F1 mice treated with Toca 511 and 5-FC.ResultsTumor-bearing animals treated with Toca 511 and 5-FC display alterations in immune cell populations within the tumor that result in antitumor immune protection. Attenuated immune subsets were exclusive to immunosuppressive cells of myeloid origin. Depletion of immunosuppressive cells temporally preceded a second event which included expansion of T cells which were polarized away from Th2 and Th17 in the CD4+ T cell compartment with concomitant expansion of interferon gamma-expressing CD8+ T cells. Immune alterations correlated with clearance of Tu-2449 subcutaneous tumors and T cell-dependent protection from future tumor challenge.ConclusionsTreatment with Toca 511 and 5-FC has a concentrated effect at the site of the tumor which causes direct tumor cell death and alterations in immune cell infiltrate, resulting in a tumor microenvironment that is more permissive to establishment of a T cell mediated antitumor immune response

In vitro biosynthetic studies of bottromycin expand the enzymatic capabilities of the YcaO superfamily

The bottromycins belong to the ribosomally synthesized and posttranslationally modified peptide (RiPP) family of natural products. Bottromycins exhibit unique structural features, including a hallmark macrolactamidine ring and thiazole heterocycle for which divergent members of the YcaO superfamily have been biosynthetically implicated. Here we report the in vitro reconstitution of two YcaO proteins, BmbD and BmbE, responsible for the ATP-dependent cyclodehydration reactions that yield thiazoline- and macrolactamidine-functionalized products, respectively. We also establish the substrate tolerance for BmbD and BmbE and systematically dissect the role of the follower peptide, which we show serves a purpose similar to canonical leader peptides in directing the biosynthetic enzymes to the substrate. Lastly, we leverage the expanded capabilities of YcaO proteins to conduct an extensive bioinformatic survey to classify known YcaO chemistry. This analysis predicts new functions remain to be uncovered within the superfamily

Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury.

Background:Recent studies have demonstrated the vital influence of commensal microbial communities on human health. The central role of the gut in the response to injury is well described; however, no prior studies have used culture-independent profiling techniques to characterize the gut microbiome after severe trauma. We hypothesized that in critically injured patients, the gut microbiome would undergo significant compositional changes in the first 72 hours after injury. Methods:Trauma stool samples were prospectively collected via digital rectal examination at the time of presentation (0 hour). Patients admitted to the intensive care unit (n=12) had additional stool samples collected at 24 hours and/or 72 hours. Uninjured patients served as controls (n=10). DNA was extracted from stool samples and 16S rRNA-targeted PCR amplification was performed; amplicons were sequenced and binned into operational taxonomic units (OTUs; 97% sequence similarity). Diversity was analyzed using principle coordinates analyses, and negative binomial regression was used to determine significantly enriched OTUs. Results:Critically injured patients had a median Injury Severity Score of 27 and suffered polytrauma. At baseline (0 hour), there were no detectable differences in gut microbial community diversity between injured and uninjured patients. Injured patients developed changes in gut microbiome composition within 72 hours, characterized by significant alterations in phylogenetic composition and taxon relative abundance. Members of the bacterial orders Bacteroidales, Fusobacteriales and Verrucomicrobiales were depleted during 72 hours, whereas Clostridiales and Enterococcus members enriched significantly. Discussion:In this initial study of the gut microbiome after trauma, we demonstrate that significant changes in phylogenetic composition and relative abundance occur in the first 72 hours after injury. This rapid change in intestinal microbiota represents a critical phenomenon that may influence outcomes after severe trauma. A better understanding of the nature of these postinjury changes may lead to the ability to intervene in otherwise pathological clinical trajectories. Level of evidence:III. Study type:Prognostic/epidemiological

Temporal dissociation of phencyclidine: Induced locomotor and social alterations in rats using an automated homecage monitoring system – implications for the 3Rs and preclinical drug discovery

Background: Rodent behavioural assays are widely used to delineate the mechanisms of psychiatric disorders and predict the efficacy of drug candidates. Conventional behavioural paradigms are restricted to short time windows and involve transferring animals from the homecage to unfamiliar apparatus which induces stress. Additionally, factors including environmental perturbations, handling and the presence of an experimenter can impact behaviour and confound data interpretation. To improve welfare and reproducibility these issues must be resolved. Automated homecage monitoring offers a more ethologically relevant approach with reduced experimenter bias. Aim: To evaluate the effectiveness of an automated homecage system at detecting locomotor and social alterations induced by phencyclidine (PCP) in group-housed rats. PCP is an NMDA receptor antagonist commonly utilised to model aspects of schizophrenia. Methods: Rats housed in groups of 3 were implanted with radio frequency identification (RFID) tags. Each homecage was placed over a RFID reader baseplate for the automated monitoring of the social and locomotor activity of each individual rat. For all rats, we acquired homecage data for 24 h following administration of both saline and PCP (2.5 mg/kg). Results: PCP resulted in significantly increased distance travelled from 15 to 60 min post injection. Furthermore, PCP significantly enhanced time spent isolated from cage-mates and this asociality lasted from 60 to 105 min post treatment. Conclusions: Unlike conventional assays, in-cage monitoring captures the temporal duration of drug effects on multiple behaviours in the same group of animals. This approach could benefit psychiatric preclinical drug discovery though improved welfare and increased between-laboratory replicability

Iterative Learning Control of Single Point Incremental Sheet Forming Process using Digital Image Correlation

Single Point Incremental Sheet Forming (SPIF) is a versatile forming process that has gained significant traction over the past few decades. Its increased formability, quick part adaption, and reduced set-up costs make it an economical choice for small batch and rapid prototype forming applications when compared to traditional stamping processes. However, a common problem with the SPIF process is its tendency to produce high geometric error due to the lack of supporting dies and molds. While geometric error has been a primary focus of recent research, it is still significantly larger for SPIF than traditional forming processes. In this paper, the convergence behavior and the ability to reduce geometric error using a simple Iterative Learning Control (ILC) algorithm is studied with two different forming methods. For both methods a tool path for the desired reference geometry is generated and a part is formed. A Digital Image Correlation (DIC) system takes a measurement and the geometric error along the tool path is calculated. The ILC algorithm then uses the geometric error to alter the tool path for the next forming iteration. The first method, the Single Sheet Forming (SSF) method, performs each iteration on the same sheet. The second method, the Multi Sheet Forming (MSF) method, performs each iteration on a newly replaced sheet. Multiple experiments proved the capability of each method at reducing geometric error. It was concluded that using the MSF method allows for negative corrections to the forming part and, therefore, leads to better final part accuracy. However, this method is less cost effective and more time consuming than using the standard SSF methodology. In addition, it was found that in order to effectively correct a part with an ILC algorithm, steps must be taken to increase the controllability of the part geometry

Analysis of Geometric Accuracy and Thickness Reduction in Multistage Incremental Sheet Forming using Digital Image Correlation

Incremental Sheet Forming (ISF) is a freeform manufacturing method whereby a 3D geometry is created by progressively deforming a metal sheet with a single point tool following a defined trajectory. The thickness distribution of a formed part is a major consideration of the process and is believed to be improved by forming the geometry in multiple stages. This paper describes a series of experiments in which truncated cone geometries were formed using two multistage methods and compared to the same geometry formed using the traditional single stage method. The geometric accuracy and thickness distributions, including 3D thickness distribution plots, of each are examined using digital image correlation (DIC). The data collected indicate that multistage forming, compared to single stage forming, has a significant effect on the geometric accuracy of the processed sheets. Moreover, the results of the experiments conducted in this paper show that sheets processed with multistage forming do not have a uniform sheet thickness reduction, rather they have a parabolic-like thickness distribution in the processed region