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

Bradycardia in a patient with lung cancer

10.47102/annals-acadmedsg.20218ANNALS ACADEMY OF MEDICINE SINGAPORE507593-59

Transmembrane and Coiled-Coil Domain Family 1 Is a Novel Protein of the Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a continuous membrane network in eukaryotic cells comprising the nuclear envelope, the rough ER, and the smooth ER. The ER has multiple critical functions and a characteristic structure. In this study, we identified a new protein of the ER, TMCC1 (transmembrane and coiled-coil domain family 1). The TMCC family consists of at least 3 putative proteins (TMCC1-3) that are conserved from nematode to human. We show that TMCC1 is an ER protein that is expressed in diverse human cell lines. TMCC1 contains 2 adjacent transmembrane domains near the C-terminus, in addition to coiled-coil domains. TMCC1 was targeted to the rough ER through the transmembrane domains, whereas the N-terminal region and C-terminal tail of TMCC1 were found to reside in the cytoplasm. Moreover, the cytosolic region of TMCC1 formed homo-or hetero-dimers or oligomers with other TMCC proteins and interacted with ribosomal proteins. Notably, overexpression of TMCC1 or its transmembrane domains caused defects in ER morphology. Our results suggest roles of TMCC1 in ER organization

Ten-year progression of coronary artery, carotid artery, and aortic calcification in patients with rheumatoid arthritis

© 2017, International League of Associations for Rheumatology (ILAR). Rheumatoid arthritis (RA) is associated with increased vascular calcification, although the rate of progress of calcification is uncertain. The aim of the study was to evaluate the progression of and the predictors for calcification in different vascular beds over 10 years. The 10-year actual coronary calcium score (CS) and 10-year predicted coronary CS, based on the pattern of the general population, were compared. Calcification of the coronary and carotid artery and the aorta was assessed by multi-detector computed tomography. Significant CS progression was determined by the difference between the square root of baseline and square root of follow-up calcium score (i.e., SQRT method). The 10-year predicted coronary CS was based on the mathematical formula derived by the Heinz Nixdorf Recall Study. A total of 49 patients (54 ± 11 years, 90% female) had a follow-up scan after 10.0 ± 0.2 years. The CS in all vascular beds was significantly increased; 55% of the patients had a significant progression of CS in the coronary, 29% in the carotid, and 80% in the aorta. Age and systolic blood pressure (SBP) were independently associated with calcification progression in all vascular beds. Importantly, the absolute increase in 10-year actual coronary CS was significantly higher than that predicted. In patients with RA, calcification in all vascular beds significantly increased over 10 years and was independently associated with age and SBP. Importantly, the absolute increase in 10-year actual coronary CS progression was significantly higher than that predicted.Link_to_subscribed_fulltex

Sequence alignment of TMCC proteins.

<p>(A) Human TMCC family members. (B) Domain structures of human TMCC proteins. (C) TMCC1 in various organisms. Hs, <i>Homo sapiens</i>; Mm, <i>Mus musculus</i>; Gg, <i>Gallus gallus</i>; Xl, <i>Xenopus laevis</i>; Dr, <i>Danio rerio</i>; Dm, <i>Drosophila melanogaster</i>; Ce, <i>Caenorhabditis elegans</i>.</p

Homo- or hetero-dimerization or oligomerization of TMCC proteins.

<p>(A) HEK293T cells were co-transfected with plasmids encoding GFP-TMCC1 and FLAG-tagged TMCC1 fragments; 24 h post-transfection, cell lysates were collected for anti-FLAG immunoprecipitation to test for interactions between FLAG- and GFP-tagged proteins by performing western blotting. A schematic representation of the TMCC1 constructs is presented alongside the blots. Vector, pFLAG-CMV2 vector. FL, full-length TMCC1. (B) HEK293T cells were transfected with GFP-tagged TMCC1(571–653), TMCC2, or TMCC3 plasmids; 24 h post-transfection, cell lysates were prepared for TMCC1 immunoprecipitation to test for interaction between TMCC1 and exogenous proteins. TMCC1 and GFP-tagged proteins were analyzed by western blotting.</p