Single-File Diffusion of Externally Driven Particles

We study 1-D diffusion of $N$ hard-core interacting Brownian particles driven by the space- and time-dependent external force. We give the exact solution of the $N$-particle Smoluchowski diffusion equation. In particular, we investigate the nonequilibrium energetics of two interacting particles under the time-periodic driving. The hard-core interaction induces entropic repulsion which differentiates the energetics of the two particles. We present exact time-asymptotic results which describe the mean energy, the accepted work and heat, and the entropy production of interacting particles and we contrast these quantities against the corresponding ones for the non-interacting particles

De relatie tussen waterkwaliteit en welzijn bij Afrikaanse meerval en tong op Nederlandse viskwekerijen

Het doel van deze literatuurstudie is het beschrijven van de mogelijke knelpunten in de relatie tussen het welzijn van vissen en de waterkwaliteit in recirculatiesystemen (RAS), gespecificeerd op de Afrikaanse meerval (Clarias gariepinus) en tong (Solea solea). Hiernaast is bij een tongkwekerij en bij twee meervalkwekerijen een studie uitgevoerd naar de waterkwaliteit. De resultaten tonen aan dat de temperatuur, pH en zuurstofconcentratie van het water constant zijn. Het TAN-niveau (Total Ammonia Nitrogen) laat een variabel beeld zien bij de meervalkwekerijen, bij de tongkwekerij is het TAN-niveau constant laag

{TADA}: {T}axonomy Adaptive Domain Adaptation

Traditional domain adaptation addresses the task of adapting a model to a novel target domain under limited or no additional supervision. While tackling the input domain gap, the standard domain adaptation settings assume no domain change in the output space. In semantic prediction tasks, different datasets are often labeled according to different semantic taxonomies. In many real-world settings, the target domain task requires a different taxonomy than the one imposed by the source domain. We therefore introduce the more general taxonomy adaptive domain adaptation (TADA) problem, allowing for inconsistent taxonomies between the two domains. We further propose an approach that jointly addresses the image-level and label-level domain adaptation. On the label-level, we employ a bilateral mixed sampling strategy to augment the target domain, and a relabelling method to unify and align the label spaces. We address the image-level domain gap by proposing an uncertainty-rectified contrastive learning method, leading to more domain-invariant and class discriminative features. We extensively evaluate the effectiveness of our framework under different TADA settings: open taxonomy, coarse-to-fine taxonomy, and partially-overlapping taxonomy. Our framework outperforms previous state-of-the-art by a large margin, while capable of adapting to target taxonomies

The funhouse mirror: the I in personalised healthcare

Precision Medicine is driven by the idea that the rapidly increasing range of relatively cheap and efficient self-tracking devices make it feasible to collect multiple kinds of phenotypic data. Advocates of N = 1 research emphasize the countless opportunities personal data provide for optimizing individual health. At the same time, using biomarker data for lifestyle interventions has shown to entail complex challenges. In this paper, we argue that researchers in the field of precision medicine need to address the performative dimension of collecting data. We propose the fun-house mirror as a metaphor for the use of personal health data; each health data source yields a particular type of image that can be regarded as a ‘data mirror’ that is by definition specific and skewed. This requires competence on the part of individuals to adequately interpret the images thus provided

Characterising ChIP-seq binding patterns by model-based peak shape deconvolution

BACKGROUND: Chromatin immunoprecipitation combined with massive parallel sequencing (ChIP-seq) is widely used to study protein-chromatin interactions or chromatin modifications at genome-wide level. Sequence reads that accumulate locally at the genome (peaks) reveal loci of selectively modified chromatin or specific sites of chromatin-binding factors. Computational approaches (peak callers) have been developed to identify the global pattern of these sites, most of which assess the deviation from background by applying distribution statistics. RESULTS: We have implemented MeDiChISeq, a regression-based approach, which--by following a learning process--defines a representative binding pattern from the investigated ChIP-seq dataset. Using this model MeDiChISeq identifies significant genome-wide patterns of chromatin-bound factors or chromatin modification. MeDiChISeq has been validated for various publicly available ChIP-seq datasets and extensively compared with other peak callers. CONCLUSIONS: MeDiChI-Seq has a high resolution when identifying binding events, a high degree of peak-assessment reproducibility in biological replicates, a low level of false calls and a high true discovery rate when evaluated in the context of gold-standard benchmark datasets. Importantly, this approach can be applied not only to 'sharp' binding patterns--like those retrieved for transcription factors (TFs)--but also to the broad binding patterns seen for several histone modifications. Notably, we show that at high sequencing depths, MeDiChISeq outperforms other algorithms due to its powerful peak shape recognition capacity which facilitates discerning significant binding events from spurious background enrichment patterns that are enhanced with increased sequencing depths

The Cockayne syndrome B protein, involved in transcription-coupled DNA repair, resides in an RNA polymerase II-containing complex

Transcription-coupled repair (TCR), a subpathway of nucleotide excision repair (NER) defective in Cockayne syndrome A and B (CSA and CSB), is responsible for the preferential removal of DNA lesions from the transcribed strand of active genes, permitting rapid resumption of blocked transcription. Here we demonstrate by microinjection of antibodies against CSB and CSA gene products into living primary fibroblasts, that both proteins are required for TCR and for recovery of RNA synthesis after UV damage in vivo but not for basal transcription itself. Furthermore, immunodepletion showed that CSB is not required for in vitro NER or transcription. Its central role in TCR suggests that CSB interacts with other repair and transcription proteins. Gel filtration of repair- and transcription-competent whole cell extracts provided evidence that CSB and CSA are part of large complexes of different sizes. Unexpectedly, there was no detectable association of CSB with several candidate NER and transcription proteins. However, a minor but significant portion (10-15%) of RNA polymerase II was found to be tightly associated with CSB. We conclude that within cell-free extracts, CSB is not stably associated with the majority of core NER or transcription components, but is part of a distinct complex involving RNA polymerase II. These findings suggest that CSB is implicated in, but not essential for, transcription, and support the idea that Cockayne syndrome is due to a combined repair and transcription deficiency

Transient parkinsonism in isolated extrapontine myelinolysis

Extrapontine myelinolysis (EPM) is a rare cause of parkinsonism. In this case report, we describe a 63-year-old woman with parkinsonism due to EPM after correction of hyponatremia. During a 4-year follow-up, both the clinical features of parkinsonism and the changes on magnetic resonance imaging resolved. Parkinsonism due to EPM should be recognized as it has a good prognosis

The importance of both setting and intensity of physical activity in relation to non-clinical anxiety and depression

Physical activity is associated with good physical and mental health. Current recommendations suggest that people should achieve 30 minutes of moderate-intensity activity most days of the week to gain health benefits. This activity may be accumulated in leisure time, in active commuting, at work or in the home. Here we look at the cross-sectional relationship between physical activity and mental health as measured by the HADS anxiety and depression scores in a sample of 1,742 participants from a Scottish general population survey. The participants were men and women in three age cohorts aged around 24, 44 and 64 years who, in 1995, were interviewed face to face and also self-completed the HADS depression and anxiety scale. Respondents reported their levels of physical activity at work, in the home and in leisure time; the intensities of activity were also determined. Physical activity was related to depression scores but not to anxiety scores. There was no relationship between work physical activity and depression score. Among women, depression score increased with each additional episode of vigorous home activity. In both sexes, depression score decreased with each additional episode of vigorous leisure activity, but among men the decrease in depression score with moderate leisure activity was reversed if a lot of moderate activity was undertaken. We have found a variable relationship between depression scores and various settings for physical activity. Researchers, policymakers and practitioners who are interested in the relationship between physical activity and mental health should take into account the setting for activity as well as frequency, duration and intensity of activity

Nucleic Acids Res

The absence of a quality control (QC) system is a major weakness for the comparative analysis of genome-wide profiles generated by next-generation sequencing (NGS). This concerns particularly genome binding/occupancy profiling assays like chromatin immunoprecipitation (ChIP-seq) but also related enrichment-based studies like methylated DNA immunoprecipitation/methylated DNA binding domain sequencing, global run on sequencing or RNA-seq. Importantly, QC assessment may significantly improve multidimensional comparisons that have great promise for extracting information from combinatorial analyses of the global profiles established for chromatin modifications, the bindings of epigenetic and chromatin-modifying enzymes/machineries, RNA polymerases and transcription factors and total, nascent or ribosome-bound RNAs. Here we present an approach that associates global and local QC indicators to ChIP-seq data sets as well as to a variety of enrichment-based studies by NGS. This QC system was used to certify >5600 publicly available data sets, hosted in a database for data mining and comparative QC analyses