Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis

The genetics of an individual is a crucial factor in understanding the risk of developing the neurodegenerative disease amyotrophic lateral sclerosis (ALS). There is still a large proportion of the heritability of ALS, particularly in sporadic cases, to be understood. Among others, active transposable elements drive inter-individual variability, and in humans long interspersed element 1 (LINE1, L1), Alu and SINE-VNTR-Alu (SVA) retrotransposons are a source of polymorphic insertions in the population. We undertook a pilot study to characterise the landscape of non-reference retrotransposon insertion polymorphisms (non-ref RIPs) in 15 control and 15 ALS individuals’ whole genomes from Project MinE, an international project to identify potential genetic causes of ALS. The combination of two bioinformatics tools (mobile element locator tool (MELT) and TEBreak) identified on average 1250 Alu, 232 L1 and 77 SVA non-ref RIPs per genome across the 30 analysed. Further PCR validation of individual polymorphic retrotransposon insertions showed a similar level of accuracy for MELT and TEBreak. Our preliminary study did not identify a specific RIP or a significant difference in the total number of non-ref RIPs in ALS compared to control genomes. The use of multiple bioinformatic tools improved the accuracy of non-ref RIP detection and our study highlights the potential importance of studying these elements further in ALS

Spontaneous magnetization of aluminum nanowires deposited on the NaCl(100) surface

We investigate electronic structures of Al quantum wires, both unsupported and supported on the (100) NaCl surface, using the density-functional theory. We confirm that unsupported nanowires, constrained to be linear, show magnetization when elongated beyond the equilibrium length. Allowing ions to relax, the wires deform to zig-zag structures with lower magnetization but no dimerization occurs. When an Al wire is deposited on the NaCl surface, a zig-zag geometry emerges again. The magnetization changes moderately from that for the corresponding unsupported wire. We analyse the findings using electron band structures and simple model wires.Comment: submitted to PHys. Rev.

Clinical Heterogeneity in Patients With FOXP3 Mutations Presenting With Permanent Neonatal Diabetes

OBJECTIVE—Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is caused by FOXP3 mutations. We aimed to determine the prevalence, genetics, and clinical phenotype of FOXP3 mutations in a large cohort with permanent neonatal diabetes (PNDM)

The role of occupied d states in the relaxation of hot electrons in Au

We present first-principles calculations of electron-electron scattering rates of low-energy electrons in Au. Our full band-structure calculations indicate that a major contribution from occupied d states participating in the screening of electron-electron interactions yields lifetimes of electrons in Au with energies of $1.0-3.0 {\rm eV}$ above the Fermi level that are larger than those of electrons in a free-electron gas by a factor of $\sim 4.5$. This prediction is in agreement with a recent experimental study of ultrafast electron dynamics in Au(111) films (J. Cao {\it et al}, Phys. Rev. B {\bf 58}, 10948 (1998)), where electron transport has been shown to play a minor role in the measured lifetimes of hot electrons in this material.Comment: 4 pages, 2 figures, to appear in Phys. Rev.

Theta-point behavior of diluted polymer solutions: Can one observe the universal logarithmic corrections predicted by field theory?

In recent large scale Monte-Carlo simulations of various models of Theta-point polymers in three dimensions Grassberger and Hegger found logarithmic corrections to mean field theory with amplitudes much larger than the universal amplitudes of the leading logarithmic corrections calculated by Duplantier in the framework of tricritical O(n) field theory. To resolve this issue we calculate the universal subleading correction of field theory, which turns out to be of the same order of magnitude as the leading correction for all chain lengths available in present days simulations. Borel resummation of the renormalization group flow equations also shows the presence of such large corrections. This suggests that the published simulations did not reach the asymptotic regime. To further support this view, we present results of Monte-Carlo simulations on a Domb-Joyce like model of weakly interacting random walks. Again the results cannot be explained by keeping only the leading corrections, but are in fair accord with our full theoretical result. The corrections found for the Domb-Joyce model are much smaller than those for other models, which clearly shows that the effective corrections are not yet in the asymptotic regime. All together our findings show that the existing simulations of Theta-polymers are compatible with tricritical field theory since the crossover to the asymptotic regime is very slow. Similar results were found earlier for self avoiding walks at their upper critical dimension d=4.Comment: 15 pages,6 figure

Glyphosate, Other Herbicides, And Transformation Products In Midwestern Streams, 2002

The use of glyphosate has increased rapidly, and there is limited understanding of its environmental fate. The objective of this study was to document the occurrence of glyphosate and the transformation product aminomethylphosphonic acid (AMPA) in Midwestern streams and to compare their occurrence with that of more commonly measured herbicides such as acetochlor, atrazine, and metolachlor. Water samples were collected at sites on 51 streams in nine Midwestern states in 2002 during three runoff events: after the application of pre-emergence herbicides, after the application of post-emergence herbicides, and during harvest season. All samples were analyzed for glyphosate and 20 other herbicides using gas chromatography/mass spectrometry or high performance liquid chromatography/mass spectrometry. The frequency of glyphosate and AMPA detection, range of concentrations in runoff samples, and ratios of AMPA to glyphosate concentrations did not vary throughout the growing season as substantially as for other herbicides like atrazine, probably because of different seasonal use patterns. Glyphosate was detected at or above 0.1 μg/l in 35 percent of pre-emergence, 40 percent of post-emergence, and 31 percent of harvest season samples, with a maximum concentration of 8.7 μg/l. AMPA was detected at or above 0.1 μg/l in 53 percent of pre-emergence, 83 percent of post-emergence, and 73 percent of harvest season samples, with a maximum concentration of 3.6 μg/l. Glyphosate was not detected at a concentration at or above the U.S. Environmental Protection Agency’s maximum contamination level (MCL) of 700 μg/l in any sample. Atrazine was detected at or above 0.1 μg/l in 94 percent of pre-emergence, 96 percent of postemergence, and 57 percent of harvest season samples, with a maximum concentration of 55 μg/l. Atrazine was detected at or above its MCL (3 μg/l) in 57 percent of pre-emergence and 33 percent of postemergence samples

Analysis of transcription factors key for mouse pancreatic development establishes NKX2-2 and MNX1 mutations as causes of neonatal diabetes in man

notes: PMCID: PMC3887257This is a freely-available open access publication. Please cite the published version which is available via the DOI link in this record.Understanding transcriptional regulation of pancreatic development is required to advance current efforts in developing beta cell replacement therapies for patients with diabetes. Current knowledge of key transcriptional regulators has predominantly come from mouse studies, with rare, naturally occurring mutations establishing their relevance in man. This study used a combination of homozygosity analysis and Sanger sequencing in 37 consanguineous patients with permanent neonatal diabetes to search for homozygous mutations in 29 transcription factor genes important for murine pancreatic development. We identified homozygous mutations in 7 different genes in 11 unrelated patients and show that NKX2-2 and MNX1 are etiological genes for neonatal diabetes, thus confirming their key role in development of the human pancreas. The similar phenotype of the patients with recessive mutations and mice with inactivation of a transcription factor gene support there being common steps critical for pancreatic development and validate the use of rodent models for beta cell development.Wellcome TrustDiabetes UKEuropean Community’s Seventh Framework Programme (FP7/2007-2013

Oncoplastic Breast Consortium consensus conference on nipple-sparing mastectomy

Purpose Indications for nipple-sparing mastectomy (NSM) have broadened to include the risk reducing setting and locally advanced tumors, which resulted in a dramatic increase in the use of NSM. The Oncoplastic Breast Consortium consensus conference on NSM and immediate reconstruction was held to address a variety of questions in clinical practice and research based on published evidence and expert panel opinion. Methods The panel consisted of 44 breast surgeons from 14 countries across four continents with a background in gynecology, general or reconstructive surgery and a practice dedicated to breast cancer, as well as a patient advocate. Panelists presented evidence summaries relating to each topic for debate during the in-person consensus conference. The iterative process in question development, voting, and wording of the recommendations followed the modified Delphi methodology. Results Consensus recommendations were reached in 35, majority recommendations in 24, and no recommendations in the remaining 12 questions. The panel acknowledged the need for standardization of various aspects of NSM and immediate reconstruction. It endorsed several oncological contraindications to the preservation of the skin and nipple. Furthermore, it recommended inclusion of patients in prospective registries and routine assessment of patient-reported outcomes. Considerable heterogeneity in breast reconstruction practice became obvious during the conference. Conclusions In case of conflicting or missing evidence to guide treatment, the consensus conference revealed substantial disagreement in expert panel opinion, which, among others, supports the need for a randomized trial to evaluate the safest and most efficacious reconstruction techniques