Segregation Across Neighborhoods in a Small City

Social segregation has profound impacts on socioeconomic outcomes. Using anonymized GPS records for Singapore which we spatially join to census records, we examine daily movement across geographically-refined neighborhoods. We show that the GPS-derived data detect segregation by poverty, even with an imperfect proxy, and in the presence of targeted urban policies aimed at social integration. The findings bode well for the use of GPS data in general to measure social segregation

Model-Independent Determination of H0H_0 and ΩK,0\Omega_{K,0} using Time-Delay Galaxy Lenses and Gamma-Ray Bursts

Combining the `time-delay distance' ($D_{\Delta t}$) measurements from galaxy lenses and other distance indicators provides model-independent determinations of the Hubble constant ($H_0$) and spatial curvature ($\Omega_{K,0}$), only based on the validity of the Friedmann-Lema\^itre-Robertson-Walker (FLRW) metric and geometrical optics. To take the full merit of combining $D_{\Delta t}$ measurements in constraining $H_0$, we use gamma-ray burst (GRB) distances to extend the redshift coverage of lensing systems much higher than that of Type Ia Supernovae (SNe Ia) and even higher than quasars, whilst the general cosmography with a curvature component is implemented for the GRB distance parametrizations. Combining Lensing+GRB yields $H_0=71.5^{+4.4}_{-3.0}$~km s$^{-1}$Mpc$^{-1}$ and $\Omega_{K,0} = -0.07^{+0.13}_{-0.06}$ (1$\sigma$). A flat-universe prior gives slightly an improved $H_0 = 70.9^{+4.2}_{-2.9}$~km s$^{-1}$Mpc$^{-1}$. When combining Lensing+GRB+SN Ia, the error bar $\Delta H_0$ falls by 25\%, whereas $\Omega_{K,0}$ is not improved due to the degeneracy between SN Ia absolute magnitude, $M_B$, and $H_0$ along with the mismatch between the SN Ia and GRB Hubble diagrams at $z\gtrsim 1.4$. Future increment of GRB observations can help to moderately eliminate the $M_B-H_0$ degeneracy in SN Ia distances and ameliorate the restrictions on cosmographic parameters along with $\Omega_{K,0}$ when combining Lensing+SN Ia+GRB. We conclude that there is no evidence of significant deviation from a (an) flat (accelerating) universe and $H_0$ is currently determined at 3\% precision. The measurements show great potential to arbitrate the $H_0$ tension between the local distance ladder and cosmic microwave background measurements and provide a relevant consistency test of the FLRW metric.Comment: Accepted for publication in MNRA

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations

We conducted a joint (pooled) analysis of three genome-wide association studies (GWAS) 1-3 of esophageal squamous cell carcinoma (ESCC) in ethnic Chinese (5,337 ESCC cases and 5,787 controls) with 9,654 ESCC cases and 10,058 controls for follow-up. In a logistic regression model adjusted for age, sex, study, and two eigenvectors, two new loci achieved genome-wide significance, marked by rs7447927 at 5q31.2 (per-allele odds ratio (OR) = 0.85, 95% CI 0.82-0.88; P=7.72x10−20) and rs1642764 at 17p13.1 (per-allele OR= 0.88, 95% CI 0.85-0.91; P=3.10x10−13). rs7447927 is a synonymous single nucleotide polymorphism (SNP) in TMEM173 and rs1642764 is an intronic SNP in ATP1B2, near TP53. Furthermore, a locus in the HLA class II region at 6p21.32 (rs35597309) achieved genome-wide significance in the two populations at highest risk for ESSC (OR=1.33, 95% CI 1.22-1.46; P=1.99x10−10). Our joint analysis identified new ESCC susceptibility loci overall as well as a new locus unique to the ESCC high risk Taihang Mountain region

One-pot synthesis of α-Fe2O3 nanoparticles-decorated reduced graphene oxide for efficient nonenzymatic H2O2 biosensor

Hematite nanoparticles (α-Fe2O3) are successfully decorated on the reduced graphene oxide (rGO) sheets through a simple, one-step, hydrothermal method without addition of other reducing agents. The α-Fe2O3/rGO hybrid was characterized by scanning electron micrographs, X-ray diffraction, X-ray photoelectron spectroscopy, and Raman spectroscopy. This α-Fe2O3/rGO hybrid has been successfully applied in the catalytic performance toward the reduction of H2O2. The nonenzymatic sensor demonstrates a linear relationship over a wide concentration range of 5.0–4495.0 μM (R = 0.9998), a low detection limit of 1.0 μM, and a high sensitivity of 126.9 μA cm−2 mM−1 to the detection of H2O2

The Physiological Responses of Escherichia coli Triggered by Phosphoribulokinase (PrkA) and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco)

Phosphoribulokinase (PrkA) and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) have been proposed to create a heterologous Rubisco-based engineered pathway in Escherichia coli for in situ CO2 recycling. While the feasibility of a Rubisco-based engineered pathway has been shown, heterologous expressions of PrkA and Rubisco also induced physiological responses in E. coli that may compete with CO2 recycling. In this study, the metabolic shifts caused by PrkA and Rubisco were investigated in recombinant strains where ppc and pta genes (encodes phosphoenolpyruvate carboxylase and phosphate acetyltransferase, respectively) were deleted from E. coli MZLF (E. coli BL21(DE3) Δzwf, ΔldhA, Δfrd). It has been shown that the demand for ATP created by the expression of PrkA significantly enhanced the glucose consumptions of E. coli CC (MZLF Δppc) and E. coli CA (MZLF Δppc, Δpta). The accompanying metabolic shift is suggested to be the mgsA route (the methylglyoxal pathway) which results in the lactate production for reaching the redox balance. The overexpression of Rubisco not only enhanced glucose consumption but also bacterial growth. Instead of the mgsA route, the overproduction of the reducing power was balanced by the ethanol production. It is suggested that Rubisco induces a high demand for acetyl-CoA which is subsequently used by the glyoxylate shunt. Therefore, Rubisco can enhance bacterial growth. This study suggests that responses induced by the expression of PrkA and Rubisco will reach a new energy balance profile inside the cell. The new profile results in a new distribution of the carbon flow and thus carbons cannot be majorly directed to the Rubisco-based engineered pathway

A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans

In metazoans, Piwi-related Argonaute proteins engage piRNAs (Piwi-interacting small RNAs) to defend the genome against invasive nucleic acids, such as transposable elements. Yet many organisms-including worms and humans-express thousands of piRNAs that do not target transposons, suggesting that piRNA function extends beyond genome defense. Here, we show that the X chromosome-derived piRNA 21ux-1 downregulates XOL-1 (XO Lethal), a master regulator of X chromosome dosage compensation and sex determination in Caenorhabditis elegans. Mutations in 21ux-1 and several Piwi-pathway components sensitize hermaphrodites to dosage compensation and sex determination defects. We show that the piRNA pathway also targets xol-1 in C. briggsae, a nematode species related to C. elegans. Our findings reveal physiologically important piRNA-mRNA interactions, raising the possibility that piRNAs function broadly to ensure robust gene expression and germline development