ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of millions of protein sequences, requires minimal computational resources, and is open source, multi-platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative proteomic data derived from patient-derived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples

The Plant Propagation Algorithm on Timetables: First Results

One Stochastic HillClimber and two implementations of the Plant Propagation Algorithm (PPA-1 and PPA-2) are applied to an instance of the University Course Timetabling Problem from the Univer- sity of Amsterdam. After completing 10 runs of 200,000 objective function evaluations each, results show that PPA-1 outperforms the HillClimber, but PPA-2 makes the best timetables

Role of Visual Dysfunction in Postural Control in Children With Cerebral Palsy

Introduction: Deficient postural control is one of the key problems in cerebral palsy (CP). Little, however, is known about the specific nature of postural problems of children with CP, nor of the relation between abnormal posture and dysfunction of the visual system. Aim of the study: To provide additional information on the association of abnormalities in postural control and visual dysfunction of the anterior or posterior part of the visual system. Methods: Data resulting from ophthalmologic, orthoptic, neurological, neuro-radiological, and ethological investigations of more than 313 neurologically impaired children were retrospectively analyzed. Results: Abnormal postural control related to ocular and ocular motor disorders consisted of anomalous head control and subsequent abnormal head posture and torticollis. The abnormal postural control related to retrochiasmatical damage of the visual system consisted of a torticollis combined with adjustment of the upper part of the body, as if at the same time adapting to a combination of defects and optimizing residual visual functions. Conclusion: Visual dysfunctions play a distinct role in the postural control of children with CP

Understanding and Finding Solutions to the Problem of Sedimentation in the National Wildlife Refuge System

The National Wildlife Refuge System (Refuge System) is a collection of public lands maintained by the U.S. Fish and Wildlife Service for migratory birds and other wildlife. Wetlands on individual National Wildlife Refuges (Refuges) may be at risk of increased sedimentation because of land use and water management practices. Increased sedimentation can reduce wetland habitat quality by altering hydrologic function, degrading water quality, and inhibiting growth of vegetation and invertebrates. On Refuges negatively affected by increased sedimentation, managers have to address complex questions about how to best remediate and mitigate the negative effects. The best way to account for these complexities is often not clear. On other Refuges, managers may not know whether sedimentation is a problem. Decision makers in the Refuge System may need to allocate resources to studying which Refuges could be at risk. Such analyses would help them understand where to direct support for managing increased sedimentation. In this paper, we summarize a case study demonstrating the use of decision-analytic tools in the development of a sedimentation management plan for Agassiz National Wildlife Refuge, Minnesota. Using what we learned from that process, we surveyed other Refuges in U.S. Fish and Wildlife Service Region 3 (an area encompassing the states of Illinois, Indiana, Iowa, Ohio, Michigan, Minnesota, Missouri, and Wisconsin) and Region 6 (an area encompassing the states of Colorado, Kansas, Montana, Nebraska, North Dakota, South Dakota, Utah, and Wyoming) about whether they experience sediment-related impacts to management. Our results show that cases of management being negatively affected by increased sedimentation are not isolated. We suggest that the Refuge System conduct a comprehensive and systematic assessment of increased sedimentation among Refuges to understand the importance of sedimentation in context with other management problems that Refuges face. The results of such an assessment could guide how the Refuge System allocates resources to studying and managing widespread stressors

A stochastic view on surface inhomogeneity of nanoparticles

The interactions between and with nanostructures can only be fully understood when the functional group distribution on their surfaces can be quantified accurately. Here we apply a combination of direct stochastic optical reconstruction microscopy (dSTORM) imaging and probabilistic modelling to analyse molecular distributions on spherical nanoparticles. The properties of individual fluorophores are assessed and incorporated into a model for the dSTORM imaging process. Using this tailored model, overcounting artefacts are greatly reduced and the locations of dye labels can be accurately estimated, revealing their spatial distribution. We show that standard chemical protocols for dye attachment lead to inhomogeneous functionalization in the case of ubiquitous polystyrene nanoparticles. Moreover, we demonstrate that stochastic fluctuations result in large variability of the local group density between particles. These results cast doubt on the uniform surface coverage commonly assumed in the creation of amorphous functional nanoparticles and expose a striking difference between the average population and individual nanoparticle coverage

Resistively-shunted superconducting quantum point contacts

We have studied the Josephson dynamics of resistively-shunted ballistic superconducting quantum point contacts at finite temperatures and arbitrary number of conducting modes. Compared to the classical Josephson dynamics of tunnel junctions, dynamics of quantum point contacts exhibits several new features associated with temporal fluctuations of the Josephson potential caused by fluctuations in the occupation of the current-carrying Andreev levels.Comment: 5 pages, RevTex, 3 postscript figures include

Non-equilibrium current noise in mesoscopic disordered SNS junctions

Current noise in superconductor-normal metal-superconductor (SNS) junctions is calculated within the scattering theory of multiple Andreev reflections (MAR). It is shown that the noise exhibits subharmonic gap singularities at $eV=2\Delta/n$, $n=1,2,...$ both in single-mode junctions with arbitrary transparency $D$ and in multi-mode disordered junctions. The subharmonic structure is superimposed with monotonic increase of the effective transferred charge $q^*=S_I(0)/2I$ with decreasing bias voltage. Other features of the noise include a step-like increase of $q^*$ in junctions with small $D$, and a divergence $S_I(0) \propto V^{-1/2}$ at small voltages and excess noise $S_{ex} = 2eI_{ex}$, where $I_{ex}$ is the excess current, at large voltages, in junctions with diffusive transport.Comment: 5 page

Size and depth of residual tumor after neoadjuvant chemoradiotherapy in rectal cancer – implications for the development of new imaging modalities for response assessment

With the shift towards organ preserving treatment strategies in rectal cancer it has become increasingly important to accurately discriminate between a complete and good clinical response after neoadjuvant chemoradiotherapy (CRT). Standard of care imaging techniques such as CT and MRI are well equipped for initial staging of rectal tumors, but discrimination between a good clinical and complete response remains difficult due to their limited ability to detect small residual vital tumor fragments. To identify new promising imaging techniques that could fill this gap, it is crucial to know the size and invasion depth of residual vital tumor tissue since this determines the requirements with regard to the resolution and imaging depth of potential new optical imaging techniques. We analyzed 198 pathology slides from 30 rectal cancer patients with a Mandard tumor regression grade 2 or 3 after CRT that underwent surgery. For each patient we determined response pattern, size of the largest vital tumor fragment or bulk and the shortest distance from the vital tumor to the luminal surface. The response pattern was shrinkage in 14 patients and fragmentation in 16 patients. For both groups combined, the largest vital tumor fragment per patient was smaller than 1mm for 38% of patients, below 0.2mm for 12% of patients and for one patient as small as 0.06mm. For 29% of patients the vital tumor remnant was present within the first 0.01mm from the luminal surface and for 87% within 0.5mm. Our results explain why it is difficult to differentiate between a good clinical and complete response in rectal cancer patients using endoscopy and MRI, since in many patients submillimeter tumor fragments remain below the luminal surface. To detect residual vital tumor tissue in all patients included in this study a technique with a spatial resolution of 0.06mm and an imaging depth of 8.9mm would have been required. Optical imaging techniques offer the possibility of detecting majority of these cases due to the potential of both high-resolution imaging and enhanced contrast between tissue types. These techniques could thus serve as a complimentary tool to conventional methods for rectal cancer response assessment.</p