Tidal Flushing Restores the Physiological Condition of Fish Residing in Degraded Salt Marshes

Roads, bridges, and dikes constructed across salt marshes can restrict tidal flow, degrade habitat quality for nekton, and facilitate invasion by non-native plants including Phragmites australis. Introduced P. australis contributes to marsh accretion and eliminates marsh surface pools thereby adversely affecting fish by reducing access to intertidal habitats essential for feeding, reproduction, and refuge. Our study assessed the condition of resident fish populations (Fundulus heteroclitus) at four tidally restricted and four tidally restored marshes in New England invaded by P. australis relative to adjacent reference salt marshes. We used physiological and morphological indicators of fish condition, including proximate body composition (% lipid, % lean dry, % water), recent daily growth rate, age class distributions, parasite prevalence, female gravidity status, length-weight regressions, and a common morphological indicator (Fulton’s K) to assess impacts to fish health. We detected a significant increase in the quantity of parasites infecting fish in tidally restricted marshes but not in those where tidal flow was restored to reduce P. australis cover. Using fish length as a covariate, we found that unparasitized, non-gravid F. heteroclitus in tidally restricted marshes had significantly reduced lipid reserves and increased lean dry (structural) mass relative to fish residing in reference marshes. Fish in tidally restored marshes were equivalent across all metrics relative to those in reference marshes indicating that habitat quality was restored via increased tidal flushing. Reference marshes adjacent to tidally restored sites contained the highest abundance of young fish (ages 0–1) while tidally restricted marshes contained the lowest. Results indicate that F. heteroclitus residing in physically and hydrologically altered marshes are at a disadvantage relative to fish in reference marshes but the effects can be reversed through ecological restoration

The polar expression of ENSO and sea-ice variability as recorded in a South Pole ice core

An annually dated ice core recovered from South Pole (2850 m a.s.l.) in 1995, that covers the period 1487–1992, was analyzed for the marine biogenic sulfur species methanesulfonate (MS). Empirical orthogonal function analysis is used to calibrate the high-resolution MS series with associated environmental series for the period of overlap (1973–92). Utilizing this calibration we present a ~500 year long proxy record of the polar expression of the El Niño–Southern Oscillation (ENSO) and southeastern Pacific sea-ice extent variations. These records reveal short-term periods of increased (1800–50, 1900–40) and decreased sea-ice extent (1550–1610, 1660–1710, 1760–1800). In general, increased (decreased) sea-ice extent is associated with a higher (lower) frequency of El Niño events

Ecology of Phragmites australis and responses to tidal restoration

Tidal Marsh Restoration provides the scientific foundation and practical guidance necessary for coastal zone stewards to initiate salt marsh tidal restoration programs. The book compiles, synthesizes, and interprets the current state of knowledge on the science and practice of salt marsh restoration, bringing together leaders across a range of disciplines in the sciences (hydrology, soils, vegetation, zoology), engineering (hydraulics, modeling), and public policy, with coastal managers who offer an abundance of practical insight and guidance on the development of programs. The book is an essential work for managers, planners, regulators, environmental and engineering consultants, and others engaged in planning, designing, and implementing projects or programs aimed at restoring tidal flow to tide-restricted or diked salt marshes.https://scholarworks.wm.edu/asbookchapters/1065/thumbnail.jp

Short-Term Relapse Quantitation as a Fully Surrogate Endpoint for Long-Term Sustained Progression of Disability in RRMS Patients Treated with Natalizumab

Time to sustained worsening in the expanded disability status scale as the standard for evaluating the accumulation of disability has been used as a measure of clinical efficacy in many relapsing-remitting multiple sclerosis (RRMS) clinical trials. However, this measurement usually requires a large sample and long-term study to demonstrate the treatment effect. Annualized relapse rate or time to first relapse is also widely used as alternative measurements of clinical efficacy. A formal statistical validation of short-term relapse activity as a surrogate endpoint for long-term sustained progression of disability could potentially permit smaller, shorter, and less expensive clinical trials in RRMS. Four statistical validation/evaluation approaches consistently showed that relapse activity through one year of treatment serves as statistically valid surrogate endpoint for time to sustained progression of disability. The analysis demonstrates that long-term sustained progression of disability can be predicted by short-term relapse measures with 4 consistent validations of statistical approaches, including a formal statistical hypothesis test. This was demonstrated in a large phase III trial of natalizumab and showed that the beneficial clinical effect of natalizumab on sustained progression of disability at 2 years in patients with RRMS can be predicted by the total number of relapses at 1 year

Phenotopic Plasticity of Leaf Shape Along a Temperature Gradient in \u3cem\u3eAcer Rubrum\u3c/em\u3e

Both phenotypic plasticity and genetic determination can be important for understanding how plants respond to environmental change. However, little is known about the plastic response of leaf teeth and leaf dissection to temperature. This gap is critical because these leaf traits are commonly used to reconstruct paleoclimate from fossils, and such studies tacitly assume that traits measured from fossils reflect the environment at the time of their deposition, even during periods of rapid climate change. We measured leaf size and shape in Acer rubrum derived from four seed sources with a broad temperature range and grown for two years in two gardens with contrasting climates (Rhode Island and Florida). Leaves in the Rhode Island garden have more teeth and are more highly dissected than leaves in Florida from the same seed source. Plasticity in these variables accounts for at least 6–19 % of the total variance, while genetic differences among ecotypes probably account for at most 69–87 %. This study highlights the role of phenotypic plasticity in leaf-climate relationships. We suggest that variables related to tooth count and leaf dissection in A. rubrum can respond quickly to climate change, which increases confidence in paleoclimate methods that use these variables

DNA assays for genetic discrimination of three Phragmites australis subspecies in the United States

Premise: To genetically discriminate subspecies of the common reed (Phragmites australis), we developed real-time quantitative (qPCR) assays for identifying P. australis subsp. americanus, P. australis subsp. australis, and P. australis subsp. berlandieri. Methods and Results: Utilizing study-generated chloroplast DNA sequences, we developed three novel qPCR assays. Assays were verified on individuals of each subspecies and against two non-target species, Arundo donax and Phalaris arundinacea. One assay amplifies only P. australis subsp. americanus, one amplifies P. australis subsp. australis and/or P. australis subsp. berlandieri, and one amplifies P. australis subsp. americanus and/or P. australis subsp. australis. This protocol enhances currently available rapid identification methods by providing genetic discrimination of all three subspecies. Conclusions: The newly developed assays were validated using P. australis samples from across the United States. Application of these assays outside of this geographic range should be preceded by additional testing

Parameterized Complexity of the k-anonymity Problem

The problem of publishing personal data without giving up privacy is becoming increasingly important. An interesting formalization that has been recently proposed is the $k$-anonymity. This approach requires that the rows of a table are partitioned in clusters of size at least $k$ and that all the rows in a cluster become the same tuple, after the suppression of some entries. The natural optimization problem, where the goal is to minimize the number of suppressed entries, is known to be APX-hard even when the records values are over a binary alphabet and $k=3$, and when the records have length at most 8 and $k=4$ . In this paper we study how the complexity of the problem is influenced by different parameters. In this paper we follow this direction of research, first showing that the problem is W[1]-hard when parameterized by the size of the solution (and the value $k$). Then we exhibit a fixed parameter algorithm, when the problem is parameterized by the size of the alphabet and the number of columns. Finally, we investigate the computational (and approximation) complexity of the $k$-anonymity problem, when restricting the instance to records having length bounded by 3 and $k=3$. We show that such a restriction is APX-hard.Comment: 22 pages, 2 figure

Calibrating genomic and allelic coverage bias in single-cell sequencing

Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1–10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (∼0.1 × ) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples.National Cancer Institute (U.S.) (Grant P30-CA14051

Nuclear Factor I/B is an Oncogene in Small Cell Lung Cancer

Small cell lung cancer (SCLC) is an aggressive cancer often diagnosed after it has metastasized. Despite the need to better understand this disease, SCLC remains poorly characterized at the molecular and genomic levels. Using a genetically engineered mouse model of SCLC driven by conditional deletion of Trp53 and Rb1 in the lung, we identified several frequent, high-magnitude focal DNA copy number alterations in SCLC. We uncovered amplification of a novel, oncogenic transcription factor, Nuclear factor I/B (Nfib), in the mouse SCLC model and in human SCLC. Functional studies indicate that NFIB regulates cell viability and proliferation during transformation.National Cancer Institute (U.S.) (grant P30-CA14051)David H. Koch Institute for Integrative Cancer Research at MIT (Ludwig Center for Molecular Oncology)Howard Hughes Medical InstituteAlfred P. Sloan Foundation (Research Fellowship)International Association for the Study of Lung Cance

Sectoral Impacts of Invasive Species in the United States and Approaches to Management

Invasive species have a major effect on many sectors of the U.S. economy and on the well-being of its citizens. Their presence impacts animal and human health, military readiness, urban vegetation and infrastructure, water, energy and transportations systems, and indigenous peoples in the United States (Table 9.1). They alter bio-physical systems and cultural practices and require significant public and private expenditure for control. This chapter provides examples of the impacts to human systems and explains mechanisms of invasive species’ establishment and spread within sectors of the U.S. economy. The chapter is not intended to be comprehensive but rather to provide insight into the range and severity of impacts. Examples provide context for ongoing Federal programs and initiatives and support State and private efforts to prevent the introduction and spread of invasive species and eradicate and control established invasive species