Nutrient Limitation of Periphyton in a Spring-Fed, Coastal Stream in Florida, USA.

There is strong evidence to suggest that ground-water nitrate concentrations have increased in recent years and further increases are expected along portions of the central Gulf coast of Florida. Much of the nitrate enriched groundwater is discharged into surface waters through numerous freshwater springs that are characteristic of the area and the potential for eutrophication of their receiving waters is a legitimate concern. To test the potential effects of elevated nutrient concentrations on the periphyton community an in situ nutrient addition experiment was conducted in the spring-fed Chassahowitzka River, FL, USA, during the summer of 1999. Plastic tubes housing arrays of glass microscope slides were suspended in the stream. Periphyton colonizing the microscope slides was subjected to artificial increases in nitrogen, phosphorus or a combination of both. Slides from each tube were collected at 3- to 4- day intervals and the periphyton communities were measured for chlorophyll concentration. The addition of approximately 10 μg/L of phosphate above ambient concentrations significantly increased the amount of periphyton on artificial substrates relative to controls; the addition of approximately 100 μg/L of nitrate above ambient concentrations did not. The findings from this experiment implicated phosphorus, rather than nitrogen, as the nutrient that potentially limits periphyton growth in this system.(PDF contains 4 pages.

Dynamical Realization of Macroscopic Superposition States of Cold Bosons in a Tilted Double Well

We present exact expressions for the quantum sloshing of Bose-Einstein condensates in a tilted two-well potential. Tunneling is suppressed by a small potential difference between wells, or tilt. However, tunneling resonances occur for critical values of the tilt when the barrier is high. At resonance, tunneling times on the order of 10-100 ms are possible. Furthermore, such tilted resonances lead to a dynamical scheme for creating few-body NOON-like macroscopic superposition states which are protected by the many body wavefunction against potential fluctuations.Comment: 6 pages, 5 figures, final version, only minor changes from previous arXiv versio

Identification and correction of systematic error in high-throughput sequence data

A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads. The implications of such errors are application specific, ranging from minor informatics nuisances to major problems affecting biological inferences. Recently developed “next-gen” sequencing technologies have greatly reduced the cost of sequencing, but have been shown to be more error prone than previous technologies. Both position specific (depending on the location in the read) and sequence specific (depending on the sequence in the read) errors have been identified in Illumina and Life Technology sequencing platforms. We describe a new type of _systematic_ error that manifests as statistically unlikely accumulations of errors at specific genome (or transcriptome) locations. We characterize and describe systematic errors using overlapping paired reads form high-coverage data. We show that such errors occur in approximately 1 in 1000 base pairs, and that quality scores at systematic error sites do not account for the extent of errors. We identify motifs that are frequent at systematic error sites, and describe a classifier that distinguishes heterozygous sites from systematic error. Our classifier is designed to accommodate data from experiments in which the allele frequencies at heterozygous sites are not necessarily 0.5 (such as in the case of RNA-Seq). Systematic errors can easily be mistaken for heterozygous sites in individuals, or for SNPs in population analyses. Systematic errors are particularly problematic in low coverage experiments, or in estimates of allele-specific expression from RNA-Seq data. Our characterization of systematic error has allowed us to develop a program, called SysCall, for identifying and correcting such errors. We conclude that correction of systematic errors is important to consider in the design and interpretation of high-throughput sequencing experiments

Rituximab with chemotherapy in children and adolescents with central nervous system and/or bone marrow-positive Burkitt lymphoma/leukaemia: a childrens oncology group report

pre-printApproximately 1 in 4 children and adolescents with de-novo mature and Burkitt lymphoma (BL) present with high-risk disease that is either mature B-cell leukaemia (bone marrow ≥ 25% blasts [BM]) and/or have central nervous system (CNS) involvement. Both the Berlin-Frankfurt- Münster (BFM) and French-American-British (FAB) international cooperative studies have unsuccessfully attempted to reduce the overall burden of chemotherapy in this high risk group of patients. In the FAB 96 study, a randomized attempt to reduce the dose of cytarabine during consolidation and eliminate three final cycles of maintenance was halted early due to inferior event-free survival (EFS) (Cairo, et al 2012, Cairo, et al concluded that reducing the infusion duration of methotrexate from 24 to 4 hours led to significantly inferior EFS in high risk (R3/R4) patients.(Woessmann, et al 2005) Subsets of children with BL, such as those with poor response to initial reduction, complex karyotypes, and those with combined BM and CNS disease, have a significantly worse prognosis (Cairo, et al 2012, Cairo, et al 2007, Poirel, et al 2009)

Measurement of dynamic Stark polarizabilities by analyzing spectral lineshapes of forbidden transitions

We present a measurement of the dynamic scalar and tensor polarizabilities of the excited state 3D1 in atomic ytterbium. The polarizabilities were measured by analyzing the spectral lineshape of the 408-nm 1S0->3D1 transition driven by a standing wave of resonant light in the presence of static electric and magnetic fields. Due to the interaction of atoms with the standing wave, the lineshape has a characteristic polarizability-dependent distortion. A theoretical model was used to simulate the lineshape and determine a combination of the polarizabilities of the ground and excited states by fitting the model to experimental data. This combination was measured with a 13% uncertainty, only 3% of which is due to uncertainty in the simulation and fitting procedure. The scalar and tensor polarizabilities of the state 3D1 were measured for the first time by comparing two different combinations of polarizabilities. We show that this technique can be applied to similar atomic systems.Comment: 13 pages, 7 figures, submitted to PR

The Aphids (Homoptera: Aphididae) of British Columbia: 21. Further Additions

Seven species are added to the aphid fauna of British Columbia. Sixty-five of the 113 new aphid-host associations of plant species are newly recorded

Semi-analytic approximations for production of atmospheric muons and neutrinos

Simple approximations for fluxes of atmospheric muons and muon neutrinos are developed which display explicitly how the fluxes depend on primary cosmic ray energy and on features of pion production. For energies of approximately 10 GeV and above the results are sufficiently accurate to calculate response functions and to use for estimates of systematic uncertainties.Comment: 15 pages with 8 figure

Observation of a Large Atomic Parity Violation Effect in Ytterbium

Atomic parity violation has been observed in the 6s^2 1S0 - 5d6s 3D1 408-nm forbidden transition of ytterbium. The parity-violating amplitude is found to be two orders of magnitude larger than in cesium, where the most precise experiments to date have been performed. This is in accordance with theoretical predictions and constitutes the largest atomic parity-violating amplitude yet observed. This also opens the way to future measurements of neutron skins and anapole moments by comparing parity-violating amplitudes for various isotopes and hyperfine components of the transition