Importance of collection in gene set enrichment analysis of drug response in cancer cell lines

Gene set enrichment analysis (GSEA) associates gene sets and phenotypes, its use is predicated on the choice of a pre-defined collection of sets. The defacto standard implementation of GSEA provides seven collections yet there are no guidelines for the choice of collections and the impact of such choice, if any, is unknown. Here we compare each of the standard gene set collections in the context of a large dataset of drug response in human cancer cell lines. We define and test a new collection based on gene co-expression in cancer cell lines to compare the performance of the standard collections to an externally derived cell line based collection. The results show that GSEA findings vary significantly depending on the collection chosen for analysis. Henceforth, collections should be carefully selected and reported in studies that leverage GSEA

A model for atomic and molecular interstellar gas: The Meudon PDR code

We present the revised ``Meudon'' model of Photon Dominated Region (PDR code), presently available on the web under the Gnu Public Licence at: http://aristote.obspm.fr/MIS. General organisation of the code is described down to a level that should allow most observers to use it as an interpretation tool with minimal help from our part. Two grids of models, one for low excitation diffuse clouds and one for dense highly illuminated clouds, are discussed, and some new results on PDR modelisation highlighted.Comment: accepted in ApJ sup

Splitting Strong and Electromagnetic Interactions in K(L4) Decays

We recently considered $K_{\ell 4}$ decays in the framework of chiral perturbation theory based on the effective Lagrangian including mesons, photons, and leptons. There, we published analytic one-loop-level expressions for form factors $f$ and $g$ corresponding to the mixed process, $K^0\to\pi^0\pi^-\ell^+\nu_{\ell}$. We propose here a possible splitting between strong and electromagnetic parts allowing analytic (and numerical) evaluation of Isospin breaking corrections. The latter are sensitive to the infrared divergence subtraction scheme and are sizeable near the $\pi\pi$ production threshold. Our results should be used for the extraction of the $P$-wave iso-vector $\pi\pi$ phase shift from the outgoing data of the currently running KTeV experiment at FNAL.Comment: 47 pages, LaTeX, 6 postscript figure

Mental health trajectories among the general population and higher-risk groups following the COVID-19 pandemic in Switzerland, 2021-2023.

Mental health deteriorated in the early stages of the COVID-19 pandemic, but improved relatively quickly as restrictions were eased, suggesting overall resilience. However, longer-term follow-up of mental health in the general population is scarce. We examined mental health trajectories in 5624 adults (58 % women; aged 18-97 years) from the Specchio-COVID19 cohort, using the Generalized Anxiety Disorder scale-2 and the Patient Health Questionnaire-2, administered each month from February to June 2021, and in Spring 2022 and 2023. Depressive and anxiety symptoms declined during a pandemic wave from February to May 2021 (β = -0.06 [-0.07, -0.06]; -0.06 [-0.07, -0.05]), and remained lower at longer-term follow-up than at the start of the wave. Loneliness also declined over time, with the greatest decline during the pandemic wave (β = -0.25 [-0.26, -0.24]). Many higher-risk groups, including socioeconomically disadvantaged individuals, those with a chronic condition, and those living alone had poorer mental health levels throughout the study period. Women and younger individuals had a faster improvement in mental health during the pandemic wave. Loneliness trajectories were associated with mental health trajectories throughout the study period. We cannot definitively conclude that the observed changes in mental health were due to experiences of the pandemic. While there was a need for additional mental health support during stricter policy responses to COVID-19, overall, mental health improved relatively soon after measures were eased. Nevertheless, the persistence of mental health disparities highlights the need for further efforts from the government and healthcare practitioners to support vulnerable groups beyond the pandemic

Energy and decay width of the pi-K atom

The energy and decay width of the pi-K atom are evaluated in the framework of the quasipotential-constraint theory approach. The main electromagnetic and isospin symmetry breaking corrections to the lowest-order formulas for the energy shift from the Coulomb binding energy and for the decay width are calculated. They are estimated to be of the order of a few per cent. We display formulas to extract the strong interaction S-wave pi-K scattering lengths from future experimental data concerning the pi-K atom.Comment: 37 pages, 5 figures, uses Axodra

Development and Evaluation of a Trapping System for Anoplophora glabripennis (Coleoptera: Cerambycidae) in the United States

Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae), commonly known as the Asian longhorned beetle, is an invasive wood-boring pest that infests a number of hardwood species and causes considerable economic losses in North America, several countries in Europe, and in its native range in Asia. The success of eradication efforts may depend on early detection of introduced populations; however, detection has been limited to identification of tree damage (oviposition pits and exit holes), and the serendipitous collection of adults, often by members of the public. Here we describe the development, deployment, and evaluation of semiochemical-baited traps in the greater Worcester area in Massachusetts. Over 4 yr of trap evaluation (2009-2012), 1013 intercept panel traps were deployed, 876 of which were baited with three different families of lures. The families included lures exhibiting different rates of release of the male-produced A. glabripennis pheromone, lures with various combinations of plant volatiles, and lures with both the pheromone and plant volatiles combined. Overall, 45 individual beetles were captured in 40 different traps. Beetles were found only in traps with lures. In several cases, trap catches led to the more rapid discovery and management of previously unknown areas of infestation in the Worcester county regulated area. Analysis of the spatial distribution of traps and the known infested trees within the regulated area provides an estimate of the relationship between trap catch and beetle pressure exerted on the traps. Studies continue to optimize lure composition and trap placemen

Isospin breaking corrections to low-energy pi-K scattering

We evaluate the matrix elements for the processes pi^0 K^0 -> pi^0 K^0 and pi^- K^+ -> pi^0 K^0 in the presence of isospin breaking terms at leading and next-to-leading order. As a direct application the releveant combination of the S-wave scattering lengths involved in the pion-kaon atom lifetime is determined. We discuss the sensitivity of the results with respect to the input parameters.Comment: 33 pages, plain latex, 2 figure

Importance of Preoperative Imaging in Acetabular Revision Surgery - A Case Report

Acetabular defects, particularly as a result of protrusion of acetabular components into the hemipelvis, may cause serious complications during revision procedures as a result of iatrogenic injury to surrounding anatomical structures. In these challenging cases, we advocate the utilisation of preoperative three dimensional imaging. MRI and CT- imaging offer superior understanding of the three-dimensional quality of bony defects and the relationship of implants to important anatomical structures. Appropriate preoperative planning may also prevent major complications during the removal of the pre-existing hardware, prior to re-implantation of implants. Potential complications include injury of nerves, blood vessels and other intrapelvic structures

Femoral Shaft Fracture Occurring as a Result of Physical Manipulation: A Case Report

Treatments including physical manipulation maneuvers have been widely used for the management of various pain complaints. These maneuvers, although generally considered safe, can be associated with serious complications. We report the case of a 37-years-old previously healthy male patient, who presented to our emergency department (ED) for severe right thigh pain and inability to bear weight that developed during a chiropractic session. Imaging done at the ED showed a displaced distal femoral shaft fracture. The majority of the complications of manipulation maneuvers can be as simple as sprains, however, can be drastic or life-threatening in certain cases causing cerebrovascular accidents or major orthopedic fractures. Such complications are rare and definitely underreported. A femoral shaft fracture occurring as a result of physical manipulation has not been previously reported in the literature. We report a distal femoral shaft fracture that was induced by forceful chiropractic manipulation. It is the first to be reported in the literature. This complication should be noted, reported, and the necessary precautions are taken to avoid such major adverse events