House and home

If asked to imagine home, most of us will come to think of a particular house or building. And, for many of us, the quintessential image of home remains the place we grew up in. This close association between house and home has long marked anthropological literature. And yet, when we imagine home, it is often not the structures themselves but the feelings, practices, and relationships within familiar spaces which give home a powerful sense of belonging. Home may be the scent of a grandmother’s cooking, the familiar fuzz of a worn cushion, the seemingly defiant thrill of hanging posters on the wall as a teenager, or the knot of tension in the stomach of a child listening to an argument in the adjoining room. Recent anthropological studies have hence looked beyond physical structures to understand home in terms of a diverse array of practices, meaningful and imaginative forms, and feelings which surround a sense of groundedness within the world. Understood in such terms, home becomes something much less solid than a structure of stone or wood. It tends to be contestable and fragile, a domain not only of belonging but also of potential alienation when attempts to make home fail or are subverted. This flourishing literature increasingly suggests that while physical shelter may be a basic existential need, it is houses and homes, wrapped up in the desire and struggle for belonging, which underpin human sociality

A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates

Motivation Clusters of extremely conserved non-coding elements (CNEs) mark genomic regions devoted to cis-regulation of key developmental genes in Metazoa. We have recently shown that their span coincides with that of topologically associating domains (TADs), making them useful for estimating conserved TAD boundaries in the absence of Hi-C data. The standard approach—detecting CNEs in genome alignments and then establishing the boundaries of their clusters—requires tuning of several parameters and breaks down when comparing closely related genomes. Results We present a novel, kurtosis-based measure of pairwise non-coding conservation that requires no pre-set thresholds for conservation level and length of CNEs. We show that it performs robustly across a large span of evolutionary distances, including across the closely related genomes of primates for which standard approaches fail. The method is straightforward to implement and enables detection and comparison of clusters of CNEs and estimation of underlying TADs across a vastly increased range of Metazoan genomes. Availability and implementation The data generated for this study, and the scripts used to generate the data, can be found at https://github.com/alexander-nash/kurtosis_conservation. Supplementary information Supplementary data are available at Bioinformatics online.publishedVersio

Philosophical Perspectives on Earth System Modeling: Truth, Adequacy, and Understanding

We explore three questions about Earth system modeling that are of both scientific and philosophical interest: What kind of understanding can be gained via complex Earth system models? How can the limits of understanding be bypassed or managed? How should the task of evaluating Earth system models be conceptualized

The hopeful labour of begging – Homeless people’s struggles for a better life in Paris

Both in public imagination and scholarship, begging is often associated with passivity, waiting, inactivity and as such defined as the opposite of ‘real work’. During two years of fieldwork with people sleeping rough in Paris, I observed my informants to the contrary describe begging as their occupation. In this paper, I present an ethnographically grounded argument that the people experiencing homelessness I accompanied over the course of two years experienced begging as labour which involved constructing and supporting emotional narratives of neediness, deservingness and personal connections in scripts, stories and hustles. My interlocutors often understood this labour to be a hopeful one, one that structured their day (and thoughts) but also one that enabled their projets de vies, their struggles into the future. In the wake of overwhelming suffering and structural violence, I observed begging not only a short-term fix for consumption but also as keeping the future open – the more long-term future of eventually leaving the street behind.</jats:p

Evaluating an analytical model to predict subsurface LNAPL distributions and transmissivity from current and historic fluid levels in groundwater wells: Comparing results to numerical simulations

A recent analytical model predicts free, entrapped, and residual LNAPL saturations and the LNAPL transmissivity in the subsurface from current and historic fluid levels in groundwater wells. As such, the model accounts for effects of fluid level fluctuations in a well. The model was developed to predict LNAPL specific volumes and transmissivities from current fluid level measurements in wells and either recorded historic fluid level fluctuations in wells or estimates. An assumption is made in the model that the predictions are not dependent on whether the historic highest or lowest fluid level elevations in a well occur first. To test the assumption, we conduct two simulations with a modified multiphase flow numerical code TMVOC that incorporates relative permeability-saturation-capillary head relations employed in the model. In one simulation, the initial condition is for fluid levels in a well at the historic highest elevations. In the other simulation, the initial condition is for fluid levels in a well at the historic lowest elevations. We change the boundary conditions so both historical conditions occur followed by generating the current condition. Results from the numerical simulations are compared to model predictions and show the assumption in the analytical model is reasonable. The analytical model can be used to develop/refine conceptual site models and for assessing potential LNAPL recovery endpoints, especially on sites with fluctuating fluid levels in wells

Time course metabolome of Roux-en-Y gastric bypass confirms correlation between leptin, body weight and the microbiome

Roux-en-Y gastric bypass (RYGB) is an effective way to lose weight and reverse type 2 dia- betes. We profiled the metabolome of 18 obese patients (nine euglycemic and nine diabet- ics) that underwent RYGB surgery and seven lean subjects. Plasma samples from the obese patients were collected before the surgery and one week and three months after the surgery. We analyzed the metabolome in association to five hormones (Adiponectin, Insulin, Ghrelin, Leptin, and Resistin), four peptide hormones (GIP, Glucagon, GLP1, and PYY), and two cytokines (IL-6 and TNF). PCA showed samples cluster by surgery time and many microbially driven metabolites (indoles in particular) correlated with the three months after the surgery. Network analysis of metabolites revealed a connection between carbohydrate (mannosamine and glucosamine) and glyoxylate and confirms glyoxylate association to dia- betes. Only leptin and IL-6 had a significant association with the measured metabolites. Lep- tin decreased immediately after RYGB (before significant weight loss), whereas IL-6 showed no consistent response to RYGB. Moreover, leptin associated with tryptophan in support of the possible role of leptin in the regulation of serotonin synthesis pathways in the gut. These results suggest a potential link between gastric leptin and microbial-derived metabolites in the context of obesity and diabetes

New Approach to Silver Halide Photography Using Radical Cation Chemistry

A new mechanism for spectral sensitization of silver halide is described, which can potentially double the sensitivity of photographic emulsions. The photooxidized sensitizing dye is trapped using an organic donor molecule, which fragments to form a cation and a reducing radical, which injects an electron into the conduction band of the silver halide. In this way, two conduction-band electrons can be produced for each absorbed photon

MOODS: fast search for position weight matrix matches in DNA sequences

Summary: MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online matching algorithms, achieving considerably faster scanning speed than with a simple brute-force search. MOODS is written in C++, with bindings for the popular BioPerl and Biopython toolkits. It can easily be adapted for different purposes and integrated into existing workflows. It can also be used as a C++ library

Measurement and simulation of one-dimensional transient three phase flow for monotonic liquid drainage

Simultaneous movement of oil, water, and air in a sandy porous medium was investigated experimentally under transient flow conditions and results were compared to numerical simulations employing a finite element multiphase flow code. The liquid hydrocarbon was Soltrol 170, a low-density branched alkane mixture. Liquid saturations were measured using a collinear dual-energy gamma radiation apparatus and liquid pressures were measured using hydrophilic (untreated) and hydrophobic (treated) ceramic tensiometers connected to pressure transducers. The experimental regime was selected to impose monotonically draining water and total liquid saturation paths to avoid hysteretic effects. Measured saturations and pressures are compared to values obtained from numerical simulations of the experiment using a finite element solution of the governing multiphase flow equations assuming negligible gas pressure gradients. Functional relationships between permeabilitiesk, saturations S, and capillary pressures P employed in the numerical model were estimated by two calibration methods which require different degrees of experimental effort. Measured transient water saturation versus oil-water capillary head data agreed well with predictions from static air-water S-P relations and interfacial tension data. Transient total liquid saturation versus air-oil capillary head data deviated more severely from the scaled air-water S-P data, possibly reflecting noncompliance with the assumption of negligible gas pressure gradients. Reasonably good agreement was observed between measured and numerically simulated water and oil saturations and pressures in space and time. Sensitivity of the numerical results to calibration method was not great

A new generation of JASPAR, the open-access repository for transcription factor binding site profiles

JASPAR is the most complete open-access collection of transcription factor binding site (TFBS) matrices. In this new release, JASPAR grows into a meta-database of collections of TFBS models derived by diverse approaches. We present JASPAR CORE—an expanded version of the original, non-redundant collection of annotated, high-quality matrix-based transcription factor binding profiles, JASPAR FAM—a collection of familial TFBS models and JASPAR phyloFACTS—a set of matrices computationally derived from statistically overrepresented, evolutionarily conserved regulatory region motifs from mammalian genomes. JASPAR phyloFACTS serves as a non-redundant extension to JASPAR CORE, enhancing the overall breadth of JASPAR for promoter sequence analysis. The new release of JASPAR is available at