binGroup2: Statistical Tools for Infection Identification via Group Testing.

Group testing is the process of testing items as an amalgamation, rather than separately, to determine the binary status for each item. Its use was especially important during the COVID-19 pandemic through testing specimens for SARS-CoV-2. The adoption of group testing for this and many other applications is because members of a negative testing group can be declared negative with potentially only one test. This subsequently leads to significant increases in laboratory testing capacity. Whenever a group testing algorithm is put into practice, it is critical for laboratories to understand the algorithm's operating characteristics, such as the expected number of tests. Our paper presents the binGroup2 package that provides the statistical tools for this purpose. This R package is the first to address the identification aspect of group testing for a wide variety of algorithms. We illustrate its use through COVID-19 and chlamydia/gonorrhea applications of group testing.

The influence of perceived stress on the human microbiome.

OBJECTIVE: Microbial dysbiosis, a shift from commensal to pathogenic microbiota, is often associated with mental health and the gut-brain axis, where dysbiosis in the gut may be linked to dysfunction in the brain. Many studies focus on dysbiosis induced by clinical events or traumatic incidents; however, many professions in austere or demanding environments may encounter continuously compounded stressors. This study seeks to explore the relationship between microbial populations and stress, both perceived and biochemical. RESULTS: Eight individuals enrolled in the study to provide a longitudinal assessment of the impact of stress on gut health, with four individuals providing enough samples for analysis. Eleven core microbial genera were identified, although the relative abundance of these genera and other members of the microbial population shifted over time. Although our results indicate a potential relationship between perceived stress and microbial composition of the gut, no association with biochemical stress was observed. Increases in perceived stress seem to elucidate a change in potentially beneficial Bacteroides, with a loss in Firmicutes phyla. This shift occurred in multiple individuals, whereas using cortisol as a stress biomarker showed contradictory responses. These preliminary data provide a potential mechanism for gut monitoring, while identifying targets for downstream modulation.

Maternal obesity alters placental lysophosphatidylcholines, lipid storage, and the expression of genes associated with lipid metabolism‡.

Dyslipidemia is a characteristic of maternal obesity and previous studies have demonstrated abnormalities in fatty acid oxidation and storage in term placentas. However, there is little information about the effect of pre-pregnancy obesity on placental lipid metabolism during early pregnancy. The objective of this study was to determine the relationship between lipid profiles and markers of metabolism in placentas from obese and lean dams at midgestation. Mice were fed a western diet (WD) or normal diet (ND) and lysophosphatidylcholines (LPCs) and/or phosphatidylcholines (PCs) were measured in dam circulation and placenta sections using liquid chromatography-tandem mass spectrometry and mass spectrometry imaging, respectively. In WD dam, circulating LPCs containing 16:1, 18:1, 20:0, and 20:3 fatty acids were increased and 18:2 and 20:4 were decreased. In WD placenta from both sexes, LPC 18:1 and PC 36:1 and 38:3 were increased. Furthermore, there were moderate to strong correlations between LPC 18:1, PC 36:1, and PC 38:3. Treatment-, spatial-, and sex-dependent differences in LPC 20:1 and 20:3 were also detected. To identify genes that may regulate diet-dependent differences in placenta lipid profiles, the expression of genes associated with lipid metabolism and nutrient transport was measured in whole placenta and isolated labyrinth using droplet digital PCR and Nanostring nCounter assays. Several apolipoproteins were increased in WD placentas. However, no differences in nutrient transport or fatty acid metabolism were detected. Together, these data indicate that lipid storage is increased in midgestation WD placentas, which may lead to lipotoxicity, altered lipid metabolism and transport to the fetus later in gestation.

The objective function controversy for group testing: Much ado about nothing?

Group testing is an indispensable tool for laboratories when testing high volumes of clinical specimens for infectious diseases. An important decision that needs to be made prior to implementation is determining what group sizes to use. In best practice, an objective function is chosen and then minimized to determine an optimal set of these group sizes, known as the optimal testing configuration (OTC). There are a few options for objective functions, and they differ based on how the expected number of tests, assay characteristics, and testing constraints are taken into account. These varied options have led to a recent controversy in the literature regarding which of two different objective functions is better. In our paper, we examine these objective functions over a number of realistic situations for infectious disease testing. We show that this controversy may be much ado about nothing because the OTCs and corresponding results (eg, number of tests and accuracy) are largely the same for standard testing algorithms in a wide variety of situations.

Spatial variation in western corn rootworm (Coleoptera: Chrysomelidae) susceptibility to Cry3 toxins in Nebraska.

Repeated use of field corn (Zea mays L.) hybrids expressing the Cry3Bb1 and mCry3A traits in Nebraska has selected for field-evolved resistance in some western corn rootworm (WCR; Diabrotica virgifera virgifera LeConte) populations. Therefore, this study was conducted to characterize spatial variation in local WCR susceptibility to Cry3Bb1 and mCry3A traits in Keith and Buffalo counties, Nebraska, and determine the relationship between past management practices and current WCR susceptibility. Adult WCR populations were collected from sampling grids during 2015 and 2016 and single-plant larval bioassays conducted with F1 progeny documented significant variation in WCR susceptibility to Cry3Bb1 and mCry3A on different spatial scales in both sampling grids. At the local level, results revealed that neighboring cornfields may support WCR populations with very different susceptibility levels, indicating that gene flow of resistant alleles from high trait survival sites is not inundating large areas. A field history index, comprised of additive and weighted variables including past WCR management tactics and agronomic practices, was developed to quantify relative selection pressure in individual fields. The field history index-Cry3 trait survivorship relationship from year 1 data was highly predictive of year 2 Cry3 trait survivorship when year 2 field history indices were inserted into the year 1 base model. Sensitivity analyses indicated years of trait use and associated selection pressure at the local level were the key drivers of WCR susceptibility to Cry3 traits in this system. Retrospective case histories from this study will inform development of optimal resistance management programs and increase understanding of plant-insect interactions that may occur when transgenic corn is deployed in the landscape. Results from this study also support current recommendations to slow or mitigate the evolution of resistance by using a multi-tactic approach to manage WCR densities in individual fields within an integrated pest management framework.