Management Strategy Evaluation for the Atlantic Surfclam (Spisula solidissima) Using a Spatially Explicit, Vessel-Based Fisheries Model

The commercially valuable Atlantic surfclam (Spisula solidissima) is harvested along the northeastern continental shelf of the United States. Its range has contracted and shifted north, driven by warmer bottom water temperatures. Declining landings per unit of effort (LPUE) in the Mid-Atlantic Bight (MAB) is one result. Declining stock abundance and LPUE suggest that overfishing may be occurring off New Jersey. A management strategy evaluation (MSE) for the Atlantic surfclam is implemented to evaluate rotating closures to enhance Atlantic surfclam productivity and increase fishery viability in the MAB. Active agents of the MSE model are individual fishing vessels with performance and quota constraints influenced by captains\u27 behavior over a spatially varying population. Management alternatives include 2 rules regarding closure locations and 3 rules regarding closure durations. Simulations showed that stock biomass increased, up to 17%, under most alternative strategies in relation to estimated stock biomass under present- day management, and LPUE increased under most alternative strategies, by up to 21%. When incidental mortality caused by the fishery increased, the benefits seen under the alternative management were enhanced. These outcomes suggest that area management involving rotating closures could be valuable in insulating the stock and the commercial fishery from further declines as a northerly shift in range proceeds

Photometric Decomposition of Barred Galaxies

We present a non-parametric method for decomposition of the light of disk galaxies into disk, bulge and bar components. We have developed and tested the method on a sample of 68 disk galaxies for which we have acquired I-band photometry. The separation of disk and bar light relies on the single assumption that the bar is a straight feature with a different ellipticity and position angle from that of the projected disk. We here present the basic method, but recognise that it can be significantly refined. We identify bars in only 47% of the more nearly face-on galaxies in our sample. The fraction of light in the bar has a broad range from 1.3% to 40% of the total galaxy light. If low-luminosity galaxies have more dominant halos, and if halos contribute to bar stability, the luminosity functions of barred and unbarred galaxies should differ markedly; while our sample is small, we find only a slight difference of low significance.Comment: Accepted to appear in AJ, 36 pages, 9 figures, full on-line figures available at http://www.physics.rutgers.edu/~sellwood/Reese.htm

Why do networks have inhibitory/negative connections?

Why do brains have inhibitory connections? Why do deep networks have negative weights? We propose an answer from the perspective of representation capacity. We believe representing functions is the primary role of both (i) the brain in natural intelligence, and (ii) deep networks in artificial intelligence. Our answer to why there are inhibitory/negative weights is: to learn more functions. We prove that, in the absence of negative weights, neural networks with non-decreasing activation functions are not universal approximators. While this may be an intuitive result to some, to the best of our knowledge, there is no formal theory, in either machine learning or neuroscience, that demonstrates why negative weights are crucial in the context of representation capacity. Further, we provide insights on the geometric properties of the representation space that non-negative deep networks cannot represent. We expect these insights will yield a deeper understanding of more sophisticated inductive priors imposed on the distribution of weights that lead to more efficient biological and machine learning.Comment: ICCV2023 camera-read

Modeling to Mars: a NASA Model Based Systems Engineering Pathfinder Effort

The NASA Engineering Safety Center (NESC) Systems Engineering (SE) Technical Discipline Team (TDT) initiated the Model Based Systems Engineering (MBSE) Pathfinder effort in FY16. The goals and objectives of the MBSE Pathfinder include developing and advancing MBSE capability across NASA, applying MBSE to real NASA issues, and capturing issues and opportunities surrounding MBSE. The Pathfinder effort consisted of four teams, with each team addressing a particular focus area. This paper focuses on Pathfinder team 1 with the focus area of architectures and mission campaigns. These efforts covered the timeframe of February 2016 through September 2016. The team was comprised of eight team members from seven NASA Centers (Glenn Research Center, Langley Research Center, Ames Research Center, Goddard Space Flight Center IV&V Facility, Johnson Space Center, Marshall Space Flight Center, and Stennis Space Center). Collectively, the team had varying levels of knowledge, skills and expertise in systems engineering and MBSE. The team applied their existing and newly acquired system modeling knowledge and expertise to develop modeling products for a campaign (Program) of crew and cargo missions (Projects) to establish a human presence on Mars utilizing In-Situ Resource Utilization (ISRU). Pathfinder team 1 developed a subset of modeling products that are required for a Program System Requirement Review (SRR)/System Design Review (SDR) and Project Mission Concept Review (MCR)/SRR as defined in NASA Procedural Requirements. Additionally, Team 1 was able to perform and demonstrate some trades and constraint analyses. At the end of these efforts, over twenty lessons learned and recommended next steps have been identified

Enhanced insulin sensitivity associated with provision of mono and polyunsaturated fatty acids in skeletal muscle cells involves counter modulation of PP2A

International audienceAims/Hypothesis: Reduced skeletal muscle insulin sensitivity is a feature associated with sustained exposure to excess saturated fatty acids (SFA), whereas mono and polyunsaturated fatty acids (MUFA and PUFA) not only improve insulin sensitivity but blunt SFA-induced insulin resistance. The mechanisms by which MUFAs and PUFAs institute these favourable changes remain unclear, but may involve stimulating insulin signalling by counter-modulation/repression of protein phosphatase 2A (PP2A). This study investigated the effects of oleic acid (OA; a MUFA), linoleic acid (LOA; a PUFA) and palmitate (PA; a SFA) in cultured myotubes and determined whether changes in insulin signalling can be attributed to PP2A regulation. Principal Findings: We treated cultured skeletal myotubes with unsaturated and saturated fatty acids and evaluated insulin signalling, phosphorylation and methylation status of the catalytic subunit of PP2A. Unlike PA, sustained incubation of rat or human myotubes with OA or LOA significantly enhanced Akt-and ERK1/2-directed insulin signalling. This was not due to heightened upstream IRS1 or PI3K signalling nor to changes in expression of proteins involved in proximal insulin signalling, but was associated with reduced dephosphorylation/inactivation of Akt and ERK1/2. Consistent with this, PA reduced PP2Ac demethylation and tyrosine 307 phosphorylation-events associated with PP2A activation. In contrast, OA and LOA strongly opposed these PA-induced changes in PP2Ac thus exerting a repressive effect on PP2A.Conclusions/Interpretation: Beneficial gains in insulin sensitivity and the ability of unsaturated fatty acids to oppose palmitate-induced insulin resistance in muscle cells may partly be accounted for by counter-modulation of PP2A

Dual Chromatin and Cytoskeletal Remodeling by SETD2

Posttranslational modifications (PTMs) of tubulin specify microtubules for specialized cellular functions and comprise what is termed a "tubulin code." PTMs of histones comprise an analogous "histone code," although the "readers, writers, and erasers" of the cytoskeleton and epigenome have heretofore been distinct. We show that methylation is a PTM of dynamic microtubules and that the histone methyltransferase SET-domain-containing 2 (SETD2), which is responsible for H3 lysine 36 trimethylation (H3K36me3) of histones, also methylates α-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules. Methylation of microtubules occurs during mitosis and cytokinesis and can be ablated by SETD2 deletion, which causes mitotic spindle and cytokinesis defects, micronuclei, and polyploidy. These data now identify SETD2 as a dual-function methyltransferase for both chromatin and the cytoskeleton and show a requirement for methylation in maintenance of genomic stability and the integrity of both the tubulin and histone codes

Exome Sequencing of a Multigenerational Human Pedigree

Over the next few years, the efficient use of next-generation sequencing (NGS) in human genetics research will depend heavily upon the effective mechanisms for the selective enrichment of genomic regions of interest. Recently, comprehensive exome capture arrays have become available for targeting approximately 33 Mb or ∼180,000 coding exons across the human genome. Selective genomic enrichment of the human exome offers an attractive option for new experimental designs aiming to quickly identify potential disease-associated genetic variants, especially in family-based studies. We have evaluated a 2.1 M feature human exome capture array on eight individuals from a three-generation family pedigree. We were able to cover up to 98% of the targeted bases at a long-read sequence read depth of ≥3, 86% at a read depth of ≥10, and over 50% of all targets were covered with ≥20 reads. We identified up to 14,284 SNPs and small indels per individual exome, with up to 1,679 of these representing putative novel polymorphisms. Applying the conservative genotype calling approach HCDiff, the average rate of detection of a variant allele based on Illumina 1 M BeadChips genotypes was 95.2% at ≥10x sequence. Further, we propose an advantageous genotype calling strategy for low covered targets that empirically determines cut-off thresholds at a given coverage depth based on existing genotype data. Application of this method was able to detect >99% of SNPs covered ≥8x. Our results offer guidance for “real-world” applications in human genetics and provide further evidence that microarray-based exome capture is an efficient and reliable method to enrich for chromosomal regions of interest in next-generation sequencing experiments

A semiquantitative metric for evaluating clinical actionability of incidental or secondary findings from genome-scale sequencing

As genome-scale sequencing is increasingly applied in clinical scenarios, a wide variety of genomic findings will be discovered as secondary or incidental findings, and there is debate about how they should be handled. The clinical actionability of such findings varies, necessitating standardized frameworks for a priori decision making about their analysis

Pancreatic Fistula Following Pancreaticoduodenectomy: Clinical Predictors and Patient Outcomes

Pancreatic fistula continues to be a common complication following PD. This study seeks to identify clinical factors which may predict pancreatic fistula (PF) and evaluate the effect of PF on outcomes following pancreaticoduodenectomy (PD). We performed a retrospective analysis of a clinical database at an academic tertiary care hospital with a high volume of pancreatic surgery. Five hundred ten consecutive patients underwent PD, and PF occurred in 46 patients (9%). Perioperative mortality of patients with PF was 0%. Forty-five of 46 PF (98%) closed without reoperation with a mean time to closure of 34 days. Patients who developed PF showed a higher incidence of wound infection, intra-abdominal abscess, need for reoperation, and hospital length of stay. Multivariate analysis demonstrated an invaginated pancreatic anastomosis and closed suction intraperitoneal drainage were associated with PF whereas a diagnosis of chronic pancreatitis and endoscopic stenting conferred protection. Development of PF following PD in this series was predicted by gender, preoperative stenting, pancreatic anastomotic technique, and pancreas pathology. Outcomes in patients with PF are remarkable for a higher rate of septic complications, longer hospital stays, but in this study, no increased mortality