1st INCF Workshop on Genetic Animal Models for Brain Diseases

The INCF Secretariat organized a workshop to focus on the “role of neuroinformatics in the processes of building, evaluating, and using genetic animal models for brain diseases” in Stockholm, December 13–14, 2009. Eight scientists specialized in the fields of neuroinformatics, database, ontologies, and brain disease participated together with two representatives of the National Institutes of Health and the European Union, as well as three observers of the national INCF nodes of Norway, Poland, and the United Kingdom

Where is the USA Corn Belt, and how is it changing?

The “Corn Belt” is a commonly used term, but often referenced as a vaguely defined region in the Midwest USA. A few key studies have delineated synoptic maps of the Corn Belt boundaries going back to the early 20th century, but a modern flexible and accessible framework for mapping the Corn Belt in space and time is needed. New tools provide reference maps for the Corn Belt in the 21st century and the ability to quantify space-time changes in corn cropping patterns. The Land use and Agricultural Management Practices web-Service (LAMPS) was used to estimate the average corn (maize, Zea mays L.) area in each county of the contiguous 48 USA states for the years 2010–2016. LAMPS provides a modified areal Fraction of corn (Fc) used to map the Corn Belt at three intensity levels, for example. The resulting patterns illustrate a mostly contiguous Midwest Corn Belt surrounded by more scattered regions, including southern and eastern regions. We also mapped irrigated areas and temporal changes in Fc. Mapped patterns have the potential to help researchers study issues related to food, feed, biofuel, and water security

No evidence of microplastic ingestion in emperor penguin chicks (Aptenodytes forsteri) from the Atka Bay colony (Dronning Maud Land, Antarctica)

Microplastic (500 μm using Attenuated Total Reflection Fourier-transform Infrared (ATR-FTIR) spectroscopy. A total of 85 putative particles, mostly in the shape of fibers (65.9 %), were sorted. However, none of the particles were identified as MP applying state-of-the-art methodology. Sorted fibers were further evidenced to originate from contamination during sample processing and analyses. We find that MP concentrations in the local food web of the Weddell Sea and Dronning Maud Land coastal and marginal sea-ice regions; the feeding grounds to chick-rearing emperor penguin adults, are currently at such low levels that no detectable biomagnification is occurring via trophic transfer. Being in contrast to MP studies on other Antarctic and sub-Antarctic penguin species, our comparative discussion including these studies, highlights the importance for standardized procedures for sampling, sample processing and analyses to obtain comparable results. We further discuss other stomach contents and their potential role for MP detection, as well as providing a baseline for the long-term monitoring of MP in apex predator species from this region

Efficient algorithms for electrostatic interactions including dielectric contrasts

Coarse grained models of soft matter are usually combined with implicit solvent models that take the electrostatic polarizability into account via a dielectric background. In biophysical or nanoscale simulations that include water, this constant can vary greatly within the system. Performing molecular dynamics or other simulations that need compute exact electrostatic interactions between charges in those systems is computationally demanding. We review here several algorithms developped by us that perform exactly this task. For planar dielectric surfaces in partial periodic boundary conditions, the arising image charges can be either treated with the MMM2D algorithm in a very efficient and accurate way, or with the ELC term that enables the user to use his favorite 3D periodic Coulomb solver . Arbitrarily shaped interfaces can be dealt with using induced surface charges with the ICC algorithm. Finally, the local electrostatics algorithm MEMD (Maxwell Equations Molecular Dynamics) allows even to employ a smoothly varying dielectric constant in the systems. We introduce the concepts of these three algorithms, and an extension for the inclusion of boundaries that are to be held fixed at constant potential (metal conditions). For each method, we present a showcase application to highlight the importance of dielectric interfaces

Simulational study of anomalous tracer diffusion in hydrogels

In this article, we analyze different factors that affect the diffusion behavior of small tracer particles (as they are used e.g.in fluorescence correlation spectroscopy (FCS)) in the polymer network of a hydrogel and perform simulations of various simplified models. We observe, that under certain circumstances the attraction of a tracer particle to the polymer network strands might cause subdiffusive behavior on intermediate time scales. In theory, this behavior could be employed to examine the network structure and swelling behavior of weakly crosslinked hydrogels with the help of FCS.Comment: 11 pages, 11 figure

Contralateral lymph node metastases in patients with vulvar cancer and unilateral sentinel lymph node metastases

Introduction The risk of contralateral lymph node metastases following unilateral sentinel lymph node (SLN) metastases in patients with vulvar cancer(s) remains to be systematically assessed. Material and methods We performed a multicenter, retrospective registry-based study of 476 patients with vulvar cancer. The primary outcome measure was the rate of contralateral non-SLN metastases in the case of positive unilateral SLN. Results Out of 476 patients with primary vulvar cancer, 202 received SLN biopsy: 58 unilateral and 144 bilateral. Out of 66 patients with unilateral metastatic SLN, 62 (93.9%) received contralateral lymphadenectomy—18 after unilateral and 44 after bilateral SLN biopsy. In the study group, 132 SLN were assessed with a median number of 2 (range 1–4) per patient and 76 of these were positive. Lymph node-positivity was associated with advanced tumor stage, as well as lymph and vascular space invasion. In the group of patients with bilateral inguino-femoral lymphadenectomy, 1004 lymph nodes were resected with a median number of 15 (range 10–29) per patient. After full dissection of the inguino-femoral lymph nodes, no contralateral non-SLN metastases were found. Conclusions The risk of contralateral non-SLN metastases in patients with unilateral SLN metastases was low. Therefore, the impact of contralateral lymphadenectomy on patient survival should be investigated in further studies