Unhappy Cities

There are persistent differences in self-reported subjective well-being across US metropolitan areas, and residents of declining cities appear less happy than others. Yet some people continue to move to these areas, and newer residents appear to be as unhappy as longer-term residents. While historical data on happiness are limited, the available facts suggest that cities that are now declining were also unhappy in their more prosperous past. These facts support the view that individuals do not maximize happiness alone but include it in the utility function along with other arguments. People may trade off happiness against other competing objectives

Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors.

Genome-wide association studies have identified over 70 single-nucleotide polymorphisms (SNPs) associated with breast cancer. A subset of these SNPs are associated with quantitative expression of nearby genes, but the functional effects of the majority remain unknown. We hypothesized that some risk SNPs may regulate alternative splicing. Using RNA-sequencing data from breast tumors and germline genotypes from The Cancer Genome Atlas, we tested the association between each risk SNP genotype and exon-, exon-exon junction- or transcript-specific expression of nearby genes. Six SNPs were associated with differential transcript expression of seven nearby genes at FDR < 0.05 (BABAM1, DCLRE1B/PHTF1, PEX14, RAD51L1, SRGAP2D and STXBP4). We next developed a Bayesian approach to evaluate, for each SNP, the overlap between the signal of association with breast cancer and the signal of association with alternative splicing. At one locus (SRGAP2D), this method eliminated the possibility that the breast cancer risk and the alternate splicing event were due to the same causal SNP. Lastly, at two loci, we identified the likely causal SNP for the alternative splicing event, and at one, functionally validated the effect of that SNP on alternative splicing using a minigene reporter assay. Our results suggest that the regulation of differential transcript isoform expression is the functional mechanism of some breast cancer risk SNPs and that we can use these associations to identify causal SNPs, target genes and the specific transcripts that may mediate breast cancer risk

A Comparison of Gulf Stream Sea Surface Height Fields Derived from Geosat Altimeter Data and Those Derived from Sea Surface Temperature Data

Two types of satellite data, Geosat altimeter data and sea surface temperature data (SST), are compared and evaluated for their usefulness in assimilation into a numerical model of the Gulf Stream region. Synoptic sea surface height (SSH) fields are derived from the SST data in the following way: first three-dimensional temperature and salinity analysis fields are obtained through the Optimum Thermal Interpolation System (OTIS), and then SSH fields are calculated using a primitive equation, free-surface, numerical model running in a diagnostic mode. The aforementioned SSH fields are compared with SSH fields obtained from the Geosat altimeter data. Use of Geosat data requires an estimate of the cream SSH field relative to the earth geoid. Three different methods to obtain the mean SSH field are demonstrated. The first method uses altimetry and SST data, the second uses a diagnostic calculation with climatological data; and the third uses prognostic numerical calculations. The three estimates compared favorably with each other and with estimates obtained elsewhere. The comparison of the synoptic SSH fields derived from both data types reveals similarity in the Gulf Stream meanders and some mesoscale features, but shows differences in strength of eddies and in variability far from the Gulf Stream. Due to the smoothed nature of the OTIS analysis fields, the SSH derived from altimetry data has larger variability amplitudes compared to that derived from SST data. The statistical interpolation method, which is used to interpolate altimetry data from satellite tracks onto the model grid, is also evaluated for its filtering effect and its sensitivity to different parameters. The SSH variability of the Gulf Stream was calculated from two years of the exact repeat mission of the Geosat satellite, where altimeter data were interpolated daily onto the model grid. It is suggested here that some of the underestimation of mesoscale variations by statistical interpolation methods, as indicated by previous studies, may be explained by the filtering effect of the scheme

Practical Evaluation of Lempel-Ziv-78 and Lempel-Ziv-Welch Tries

We present the first thorough practical study of the Lempel-Ziv-78 and the Lempel-Ziv-Welch computation based on trie data structures. With a careful selection of trie representations we can beat well-tuned popular trie data structures like Judy, m-Bonsai or Cedar

Comparison of standardised versus non-standardised methods for testing the in vitro potency of oxytetracycline against mannheimia haemolytica and pasteurella multocida

The in vitro pharmacodynamics of oxytetracycline was established for six isolates of each of the calf pneumonia pathogens Mannheimia haemolytica and Pasteurella multocida. Minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and bacterial time-kill curves were determined in two matrices, Mueller Hinton broth (MHB) and calf serum. Geometric mean MIC ratios, serum:MHB, were 25.2:1 (M. haemolytica) and 27.4:1 (P. multocida). The degree of binding of oxytetracycline to serum protein was 52.4%. Differences between serum and broth MICs could not be accounted for by oxytetracycline binding to serum protein. In vitro time-kill data suggested a co-dependent killing action of oxytetracycline. The in vitro data indicate inhibition of the killing action of oxytetracycline by serum factor(s). The nature of the inhibition requires further study. The outcome of treatment with oxytetracycline of respiratory tract infections in calves caused by M. haemolytica and P. multocida may not be related solely to a direct killing action

Numerical Observation of a Tubular Phase in Anisotropic Membranes

We provide the first numerical evidence for the existence of a tubular phase, predicted by Radzihovsky and Toner (RT), for anisotropic tethered membranes without self-avoidance. Incorporating anisotropy into the bending rigidity of a simple model of a tethered membrane with free boundary conditions, we show that the model indeed has two phase transitions corresponding to the flat-to-tubular and tubular-to-crumpled transitions. For the tubular phase we measure the Flory exponent $\nu_F$ and the roughness exponent $\zeta$. We find $\nu_F=0.305(14)$ and $\zeta=0.895(60)$, which are in reasonable agreement with the theoretical predictions of RT --- $\nu_F=1/4$ and $\zeta=1$.Comment: 8 pages, LaTeX, REVTEX, final published versio

Estimating the mean manifold of a deformable object from noisy observations

Assume we have a set of noisy observations (for example, images) of different objects, each undergoing a different geometric deformation, yet all the deformations belong to the same family. As a result of the action of these deformations, the set of different observations on each object is generally a manifold in the ambient space of observations. It has been shown, [1], that in the absence of noise, in those cases where the set of deformations admits a finite-dimensional representation, the universal manifold embedding (UME) provides a mapping from the space of observations to a low dimensional linear space. The manifold corresponding to each object is mapped to a distinct linear subspace of Euclidean space, and the dimension of the subspace is the same as that of the manifold. In the presence of noise, different observations are mapped to different subspaces. In this paper we derive a method for “averaging” the different subspaces, obtained from different observations made on the same object, in order to estimate the mean representation of the object manifold. The mean manifold representation is then employed to minimize the effects of noise in matched manifold detectors and to improve the separability of data sets in the context of object detection and classification

Sudden Drops in the Loss: Syntax Acquisition, Phase Transitions, and Simplicity Bias in MLMs

Most interpretability research in NLP focuses on understanding the behavior and features of a fully trained model. However, certain insights into model behavior may only be accessible by observing the trajectory of the training process. We present a case study of syntax acquisition in masked language models (MLMs) that demonstrates how analyzing the evolution of interpretable artifacts throughout training deepens our understanding of emergent behavior. In particular, we study Syntactic Attention Structure (SAS), a naturally emerging property of MLMs wherein specific Transformer heads tend to focus on specific syntactic relations. We identify a brief window in pretraining when models abruptly acquire SAS, concurrent with a steep drop in loss. This breakthrough precipitates the subsequent acquisition of linguistic capabilities. We then examine the causal role of SAS by manipulating SAS during training, and demonstrate that SAS is necessary for the development of grammatical capabilities. We further find that SAS competes with other beneficial traits during training, and that briefly suppressing SAS improves model quality. These findings offer an interpretation of a real-world example of both simplicity bias and breakthrough training dynamics.Comment: ICLR 2024 camera-read

Dynamic Fluctuation Phenomena in Double Membrane Films

Dynamics of double membrane films is investigated in the long-wavelength limit including the overdamped squeezing mode. We demonstrate that thermal fluctuations essentially modify the character of the mode due to its nonlinear coupling to the transversal shear hydrodynamic mode. The corresponding Green function acquires as a function of the frequency a cut along the imaginary semi-axis. Fluctuations lead to increasing the attenuation of the squeezing mode it becomes larger than the `bare' value.Comment: 7 pages, Revte

Analysis of the uncertainty in the monetary valuation of ecosystem services - a case study at the river basin scale

Ecosystem services provide multiple benefits to human wellbeing and are increasingly considered by 18 policy-makers in environmental management. However, the uncertainty related with the monetary 19 valuation of these benefits is not yet adequately defined or integrated by policy-makers. Given this 20 background, our aim was to quantify different sources of uncertainty when performing monetary 21 valuation of ecosystem services, in order to provide a series of guidelines to reduce them. With an 22 example of 4 ecosystem services (i.e., water provisioning, waste treatment, erosion protection, and 23 habitat for species) provided at the river basin scale, we quantified the uncertainty associated with 24 the following sources: (1) the number of services considered, (2) the number of benefits considered 25 for each service, (3) the valuation metrics (i.e. valuation methods) used to value benefits, and (4) the 26 uncertainty of the parameters included in the valuation metrics. Results indicate that the highest 27 uncertainty was caused by the number of services considered, as well as by the number of benefits 28 considered for each service, whereas the parametric uncertainty was similar to the one related to the 29 selection of valuation metric, thus suggesting that the parametric uncertainty, which is the only 30 uncertainty type commonly considered, was less critical than the structural uncertainty, which is in 31 turn mainly dependent on the decision-making context. Given the uncertainty associated to the 32 valuation structure, special attention should be given to the selection of services, benefits and 33 metrics according to a given context