A compendium of multi-omics data illuminating host responses to lethal human virus infections.

Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology.

Low-frequency electrically induced exercise after spinal cord injury: Physiologic challenge to skeletal muscle and feasibility for long-term use.

CONTEXT: Skeletal muscle has traditionally been considered a "force generator": necessary for purposes of locomotion, but expendable for non-ambulators who use wheelchairs, such as people with a spinal cord injury (SCI). Active skeletal muscle plays an indispensable role in regulating systemic metabolic functions, even in people with paralysis, but because of severe osteoporosis, high tetanic muscle forces induced with high frequency electrical stimulation may be risky for some individuals. The purpose of this study was to compare the physiologic muscle properties incurred by two low force/low frequency repetitive stimulation protocols (1 and 3 Hz); and, to assess the acceptability of each protocol among people with SCI. METHODS: Ten individuals with chronic SCI (12.9 years) and 11 individuals without SCI (NonSCI) participated in the study. Participants received either 1 or 3 Hz stimulation to the quadriceps muscle on Day 1, then the converse on Day 2. Each session consisted of 1000 stimulus pulses. RESULTS: The initial and maximum forces were similar for the 1 and 3 Hz frequencies. The fatigue index (FI) for SCI and NonSCI groups were lower (P < 0.007) for 3 Hz than for 1 Hz (0.34 ± 0.17 versus 0.65 ± 0.16 and 0.72 ± 0.14 versus 0.87 ± 0.07, respectively). CONCLUSION: The 3 Hz stimulation offered the greatest physiological challenge and was perceived as more acceptable for long term use among people with SCI.

Computational tools and algorithms for ion mobility spectrometry-mass spectrometry.

Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.

Regulation of ß-cell death by ADP-ribosylhydrolase ARH3 via lipid signaling in insulitis.

BACKGROUND: Lipids are regulators of insulitis and ß-cell death in type 1 diabetes development, but the underlying mechanisms are poorly understood. Here, we investigated how the islet lipid composition and downstream signaling regulate ß-cell death. METHODS: We performed lipidomics using three models of insulitis: human islets and EndoC-ßH1 ß cells treated with the pro-inflammatory cytokines interlukine-1ß and interferon-γ, and islets from pre-diabetic non-obese mice. We also performed mass spectrometry and fluorescence imaging to determine the localization of lipids and enzyme in islets. RNAi, apoptotic assay, and qPCR were performed to determine the role of a specific factor in lipid-mediated cytokine signaling. RESULTS: Across all three models, lipidomic analyses showed a consistent increase of lysophosphatidylcholine species and phosphatidylcholines with polyunsaturated fatty acids and a reduction of triacylglycerol species. Imaging assays showed that phosphatidylcholines with polyunsaturated fatty acids and their hydrolyzing enzyme phospholipase PLA2G6 are enriched in islets. In downstream signaling, omega-3 fatty acids reduce cytokine-induced ß-cell death by improving the expression of ADP-ribosylhydrolase ARH3. The mechanism involves omega-3 fatty acid-mediated reduction of the histone methylation polycomb complex PRC2 component Suz12, upregulating the expression of Arh3, which in turn decreases cell apoptosis. CONCLUSIONS: Our data provide insights into the change of lipidomics landscape in ß cells during insulitis and identify a protective mechanism by omega-3 fatty acids. Video Abstract.

Mapping microhabitats of lignocellulose decomposition by a microbial consortium.

The leaf-cutter ant fungal garden ecosystem is a naturally evolved model system for efficient plant biomass degradation. Degradation processes mediated by the symbiotic fungus Leucoagaricus gongylophorus are difficult to characterize due to dynamic metabolisms and spatial complexity of the system. Herein, we performed microscale imaging across 12-µm-thick adjacent sections of Atta cephalotes fungal gardens and applied a metabolome-informed proteome imaging approach to map lignin degradation. This approach combines two spatial multiomics mass spectrometry modalities that enabled us to visualize colocalized metabolites and proteins across and through the fungal garden. Spatially profiled metabolites revealed an accumulation of lignin-related products, outlining morphologically unique lignin microhabitats. Metaproteomic analyses of these microhabitats revealed carbohydrate-degrading enzymes, indicating a prominent fungal role in lignocellulose decomposition. Integration of metabolome-informed proteome imaging data provides a comprehensive view of underlying biological pathways to inform our understanding of metabolic fungal pathways in plant matter degradation within the micrometer-scale environment.

Deciphering ApoE Genotype-Driven Proteomic and Lipidomic Alterations in Alzheimer's Disease Across Distinct Brain Regions.

Alzheimer's disease (AD) is a neurodegenerative disease with a complex etiology influenced by confounding factors such as genetic polymorphisms, age, sex, and race. Traditionally, AD research has not prioritized these influences, resulting in dramatically skewed cohorts such as three times the number of Apolipoprotein E (APOE) ε4-allele carriers in AD relative to healthy cohorts. Thus, the resulting molecular changes in AD have previously been complicated by the influence of apolipoprotein E disparities. To explore how apolipoprotein E polymorphism influences AD progression, 62 post-mortem patients consisting of 33 AD and 29 controls (Ctrl) were studied to balance the number of ε4-allele carriers and facilitate a molecular comparison of the apolipoprotein E genotype. Lipid and protein perturbations were assessed across AD diagnosed brains compared to Ctrl brains, ε4 allele carriers (APOE4+ for those carrying 1 or 2 ε4s and APOE4- for non-ε4 carriers), and differences in ε3ε3 and ε3ε4 Ctrl brains across two brain regions (frontal cortex (FCX) and cerebellum (CBM)). The region-specific influences of apolipoprotein E on AD mechanisms showcased mitochondrial dysfunction and cell proteostasis at the core of AD pathophysiology in the post-mortem brains, indicating these two processes may be influenced by genotypic differences and brain morphology.

A fast and sensitive size-exclusion chromatography method for plasma extracellular vesicle proteomic analysis.

Extracellular vesicles (EVs) carry diverse biomolecules derived from their parental cells, making their components excellent biomarker candidates. However, purifying EVs is a major hurdle in biomarker discovery since current methods require large amounts of samples, are time-consuming and typically have poor reproducibility. Here we describe a simple, fast, and sensitive EV fractionation method using size exclusion chromatography (SEC) on a fast protein liquid chromatography (FPLC) system. Our method uses a Superose 6 Increase 5/150, which has a bed volume of 2.9 mL. The FPLC system and small column size enable reproducible separation of only 50 µL of human plasma in 15 minutes. To demonstrate the utility of our method, we used longitudinal samples from a group of individuals that underwent intense exercise. A total of 838 proteins were identified, of which, 261 were previously characterized as EV proteins, including classical markers, such as cluster of differentiation (CD)9 and CD81. Quantitative analysis showed low technical variability with correlation coefficients greater than 0.9 between replicates. The analysis captured differences in relevant EV-proteins involved in response to physical activity. Our method enables fast and sensitive fractionation of plasma EVs with low variability, which will facilitate biomarker studies in large clinical cohorts.

Assessment of Beverage Trends and Replacing Nondairy Caloric Beverages with Milk at Meals across Childhood Improves Intake of Key Nutrients at Risk of Inadequate Consumption: An NHANES Modeling Study.

Background: Milk is a key source of important nutrients including the nutrients of public health concern. However, most Americans do not meet current (dairy) United States Department of Agriculture (USDA) dietary guideline recommendations, and the intake has been declining. Objective: The aim of this study was to investigate milk and beverage intake trends and nutrient intakes from these products in United States children aged 6-18 y and to model the effect of isocaloric substitution of nondairy beverages with milk. Methods: Data from National Health and Nutrition Examination Survey (NHANES) 2001-2018 for children age 6-8 (N = 4696), 9-13 (N = 8117) and 14-18 y (N = 8514) were used with milk and other beverage intakes determined from the first 24-h in-person dietary recall. Nutrient intake was determined using the NHANES cycle-specific total nutrient intake files. Nutrient modeling was performed by isocaloric substitution with milk of all nondairy beverages consumed during lunch and dinner meals combined. Sample-weighted analyses were performed using SAS 9.4. Results: Between ages 6-8 and 14-18 y, daily intake of milk and flavored milk decreased by 10% and 62%, respectively, while daily intake of caloric beverages excluding milk increased by 96%. Daily intake from caloric beverages and milk combined decreased for fiber, protein, fat, saturated fat, calcium, magnesium, potassium, vitamin A, and vitamin D and increased for energy, carbohydrates, added sugars, and folate between ages 6-8 y and 14-18 y. Isocaloric substitution of all caloric nondairy beverages at meals with milk (using nutrient contribution of USDA milk, not further specified (NFS)) resulted in increases in protein, fat, saturated fat, calcium, magnesium, potassium, sodium, vitamin A, folate, vitamin B12, and vitamin D and decreases in carbohydrate, fiber, and added sugar. Conclusion: These findings provide additional evidence to support dietary recommendations for milk, and efforts should be made on behalf of leading health professionals and childhood meal programs to highlight milk as a beverage of choice in children and adolescents.

Impact of breast density on diagnostic accuracy in digital breast tomosynthesis versus digital mammography: results from a European screening trial.

BACKGROUND: The diagnostic accuracy of digital breast tomosynthesis (DBT) and digital mammography (DM) in breast cancer screening may vary per breast density subgroup. The purpose of this study was to evaluate which women, based on automatically assessed breast density subgroups, have the greatest benefit of DBT compared with DM in the prospective Malmö Breast Tomosynthesis Screening Trial. MATERIALS AND METHODS: The prospective European, Malmö Breast Tomosynthesis Screening Trial (n = 14,848, Jan. 27, 2010-Feb. 13, 2015) compared one-view DBT and two-view DM, with consensus meeting before recall. Breast density was assessed in this secondary analysis with the automatic software Laboratory for Individualized Breast Radiodensity Assessment. DBT and DM's diagnostic accuracies were compared by breast density quintiles of breast percent density (PD) and absolute dense area (DA) with confidence intervals (CI) and McNemar's test. The association between breast density and cancer detection was analyzed with logistic regression, adjusted for ages < 55 and ≥ 55 years and previous screening participation. RESULTS: In total, 14,730 women (median age: 58 years; inter-quartile range = 16) were included in the analysis. Sensitivity was higher and specificity lower for DBT compared with DM for all density subgroups. The highest breast PD quintile showed the largest difference in sensitivity and specificity at 81.1% (95% CI 65.8-90.5) versus 43.2% (95% CI 28.7-59.1), p < .001 and 95.5% (95% CI 94.7-96.2) versus 97.2% (95% CI 96.6-97.8), p < 0.001, respectively. Breast PD quintile was also positively associated with cancer detected via DBT at odds ratio 1.24 (95% CI 1.09-1.42, p = 0.001). CONCLUSION: Women with the highest breast density had the greatest benefit from digital breast tomosynthesis compared with digital mammography with increased sensitivity at the cost of slightly lower specificity. These results may influence digital breast tomosynthesis's use in an individualized screening program stratified by, for instance, breast density. TRIAL REGISTRATION: Trial registration at https://www. CLINICALTRIALS: gov : NCT01091545, registered March 24, 2010.

Elucidating regulatory processes of intense physical activity by multi-omics analysis.

BACKGROUND: Physiological and biochemical processes across tissues of the body are regulated in response to the high demands of intense physical activity in several occupations, such as firefighting, law enforcement, military, and sports. A better understanding of such processes can ultimately help improve human performance and prevent illnesses in the work environment. METHODS: To study regulatory processes in intense physical activity simulating real-life conditions, we performed a multi-omics analysis of three biofluids (blood plasma, urine, and saliva) collected from 11 wildland firefighters before and after a 45 min, intense exercise regimen. Omics profiles post- versus pre-exercise were compared by Student's t-test followed by pathway analysis and comparison between the different omics modalities. RESULTS: Our multi-omics analysis identified and quantified 3835 proteins, 730 lipids and 182 metabolites combining the 3 different types of samples. The blood plasma analysis revealed signatures of tissue damage and acute repair response accompanied by enhanced carbon metabolism to meet energy demands. The urine analysis showed a strong, concomitant regulation of 6 out of 8 identified proteins from the renin-angiotensin system supporting increased excretion of catabolites, reabsorption of nutrients and maintenance of fluid balance. In saliva, we observed a decrease in 3 pro-inflammatory cytokines and an increase in 8 antimicrobial peptides. A systematic literature review identified 6 papers that support an altered susceptibility to respiratory infection. CONCLUSION: This study shows simultaneous regulatory signatures in biofluids indicative of homeostatic maintenance during intense physical activity with possible effects on increased infection susceptibility, suggesting that caution against respiratory diseases could benefit workers on highly physical demanding jobs.

Identification of a specific exporter that enables high production of aconitic acid in Aspergillus pseudoterreus.

Aconitic acid is an unsaturated tricarboxylic acid that is attractive for its potential use in manufacturing biodegradable and biocompatible polymers, plasticizers, and surfactants. Previously Aspergillus pseudoterreus was engineered as a platform to produce aconitic acid by deleting the cadA (cis-aconitic acid decarboxylase) gene in the itaconic acid biosynthetic pathway. In this study, the aconitic acid transporter gene (aexA) was identified using comparative global discovery proteomics analysis between the wild-type and cadA deletion strains. The protein AexA belongs to the Major Facilitator Superfamily (MFS). Deletion of aexA almost abolished aconitic acid secretion, while its overexpression led to a significant increase in aconitic acid production. Transportation of aconitic acid across the plasma membrane is a key limiting step in its production. In vitro, proteoliposome transport assay further validated AexA's function and substrate specificity. This research provides new approaches to efficiently pinpoint and characterize exporters of fungal organic acids and accelerate metabolic engineering to improve secretion capability and lower the cost of bioproduction.

The Accuracy of Ankle Eccentric Torque Control Explains Dynamic Postural Control During the Y-Balance Test.

Background: The Y-Balance Test (YBT), especially the posteromedial (PM) reach direction (PM-YBT), is able to identify dynamic postural control deficits in those who have ankle instability. However, there still exists a need to understand how sensorimotor function at the ankle explains the performance during the PM-YBT. Hypothesis/Purpose: The purpose of this study was to determine whether the ability to accurately control eccentric ankle torque explained PM-YBT performance. It was hypothesized that eccentric dorsiflexion/plantarflexion torque control would be positively related to the maximum reach distance (MRD) of PM-YBT. Study Design: Cross-sectional study. Methods: Twelve healthy subjects performed the PM-YBT, maximum voluntary isometric contractions (MVIC) for both dorsiflexion and plantarflexion muscle strength, and then the torque control testing of the ankle. The torque control testing provided a target torque level on a screen in front of the subject and passive rotations of the ankle joint in the sagittal plane at 10 deg/sec between plantarflexion to dorsiflexion. Subjects were then instructed to eccentrically contract the dorsiflexors and plantar flexors to generate torque while the ankle joint rotated. The accuracy of torque control during eccentric dorsiflexion and plantarflexion by calculating absolute errors, the area between the target torque and the produced torque were evaluated. Tibialis anterior and soleus muscle activities were simultaneously recorded during testing. A step-wise linear regression model was used to determine the best model predicted the MRD of the PM-YBT (PM-MRD). Results: A step-wise linear regression developed a model explaining only eccentric dorsiflexion torque control predicted higher PM-MRD score (R2 = 44%, F1,10 = 7.94, ß = -0.67, p = 0.02). Conclusion: The accuracy of torque control during eccentric dorsiflexion predicts better performance in the PM-YBT. Level of Evidence: 3b.

Direct Transverse Sinus Puncture for Transvenous Coil Embolization of Vein of Galen Malformations: Innovating Existing Techniques.

BACKGROUND AND IMPORTANCE: Vein of Galen malformations (VOGMs) are complex arteriovenous malformations in neonates and young children. Recent advances in endovascular interventions have drastically improved treatment and clinical outcomes in what was previously high-morbidity, high-mortality disease. The high-flow shunt pathophysiology in VOGMs can lead to dynamic changes in the malformation angioarchitecture, and over time patients can develop jugular bulb stenosis. In the setting of inaccessible transvenous access to the malformation for endovascular embolization in cases where transarterial embolization is inadequate, a combined surgical and endovascular technique must be used. We present the first successful modern-day application of direct puncture through transverse sinus for transvenous embolization of a VOGM. CLINICAL PRESENTATION: We present 2 unique cases of complex VOGM malformations in patients who had previously undergone staged endovascular embolization for reduction of flow within the malformation. On follow-up, in both cases, there was development of severe sigmoid sinus and jugular bulb stenosis, increasing intracranial venous congestion and causing marked clinical deterioration. The stenosis prevented traditional transvenous access and treatment. We describe a direct puncture transverse sinus access using a burr hole approach for endovascular transvenous embolization in both cases with successful clinical outcomes. CONCLUSION: Direct access using burr hole craniotomy to the transverse sinus for transvenous endovascular embolization is a safe approach in the setting of severe jugular bulb stenosis for treatment of VOGMs. This technique can be done efficiently to achieve complete flow elimination in the malformation, in cases where that is called for, without significant risks or complications related to the approach.

Exercise Prescription Principles among Physicians and Physical Therapists for Patients with Impaired Glucose Control: A Cross-Sectional Study.

Exercise confers a multitude of benefits with limited adverse side effects, making it a powerful "medication" for a plethora of diseases. In people living with uncontrolled glucose levels, exercise can be an effective "medication" to assist in the management of hyperglycemia. We sought to survey healthcare providers (physicians and physical therapists) to determine the current state of exercise recommendation for people with glucose control issues. Healthcare providers were surveyed from six academic medical centers in the Midwest to determine the recommended exercise parameters (type, frequency, duration, intensity, and timing) for patients with glucose control issues. Data from 209 practitioners who completed the survey were used for analysis. Chi-square tests were used to determine differences in exercise recommendations between physical therapists (PTs) and physicians (MD/DOs). PTs and MD/DOs recommended similar exercise parameters. Of all respondents, 78.9% recommended exercise to patients with glucose control issues. Respondents who considered themselves to be active exercisers were more likely to recommend exercise than those who were not exercisers. Only 6.1% of all respondents recommended post-meal exercise. Healthcare providers overwhelmingly recommended exercise for people with glucose control issues, but the "timing" is not congruent with best practice recommendations.

Impaired Glucose Tolerance and Visceral Adipose Tissue Thickness among Lean and Non-Lean People with and without Spinal Cord Injury.

After spinal cord injury (SCI), multiple adaptations occur that influence metabolic health and life quality. Prolonged sitting and inactivity predispose people with SCI to body composition changes, such as increased visceral adipose tissue (VAT) thickness, which is often associated with impaired glucose tolerance. Our goal is to understand whether VAT is an index of leanness, and, secondarily, whether mobility methods influence glucose tolerance for people living with SCI. A total of 15 people with SCI and 20 people without SCI had fasting oral glucose tolerance tests (OGTT) and VAT thickness (leanness) measured during a single session. Glucose was 51% and 67% greater for individuals with SCI relative to those without SCI after 60 and 120 min of an OGTT (p < 0.001). Glucose area under the curve (AUC) was 28%, 34%, and 60% higher for non-lean people with SCI than lean people with SCI and non-lean and lean people without SCI, respectively (p = 0.05, p = 0.009, p < 0.001). VAT was associated with glucose AUC (R2 = 0.23, p = 0.004). Taken together, these findings suggest that leanness, as estimated from VAT, may be an important consideration when developing rehabilitation programs to influence metabolism among people with SCI.

Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts.

Efficient conversion of pentose sugars remains a significant barrier to the replacement of petroleum-derived chemicals with plant biomass-derived bioproducts. While the oleaginous yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) has a relatively robust native metabolism of pentose sugars compared to other wild yeasts, faster assimilation of those sugars will be required for industrial utilization of pentoses. To increase the rate of pentose assimilation in R. toruloides, we leveraged previously reported high-throughput fitness data to identify potential regulators of pentose catabolism. Two genes were selected for further investigation, a putative transcription factor (RTO4_12978, Pnt1) and a homolog of a glucose transceptor involved in carbon catabolite repression (RTO4_11990). Overexpression of Pnt1 increased the specific growth rate approximately twofold early in cultures on xylose and increased the maximum specific growth by 18% while decreasing accumulation of arabitol and xylitol in fast-growing cultures. Improved growth dynamics on xylose translated to a 120% increase in the overall rate of xylose conversion to fatty alcohols in batch culture. Proteomic analysis confirmed that Pnt1 is a major regulator of pentose catabolism in R. toruloides. Deletion of RTO4_11990 increased the growth rate on xylose, but did not relieve carbon catabolite repression in the presence of glucose. Carbon catabolite repression signaling networks remain poorly characterized in R. toruloides and likely comprise a different set of proteins than those mainly characterized in ascomycete fungi.

Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine-Exocrine Signaling Sphere of Influence.

The need for a clinically accessible method with the ability to match protein activity within heterogeneous tissues is currently unmet by existing technologies. Our proteomics sample preparation platform, named microPOTS (Microdroplet Processing in One pot for Trace Samples), can be used to measure relative protein abundance in micron-scale samples alongside the spatial location of each measurement, thereby tying biologically interesting proteins and pathways to distinct regions. However, given the smaller pixel/voxel number and amount of tissue measured, standard mass spectrometric analysis pipelines have proven inadequate. Here we describe how existing computational approaches can be adapted to focus on the specific biological questions asked in spatial proteomics experiments. We apply this approach to present an unbiased characterization of the human islet microenvironment comprising the entire complex array of cell types involved while maintaining spatial information and the degree of the islet's sphere of influence. We identify specific functional activity unique to the pancreatic islet cells and demonstrate how far their signature can be detected in the adjacent tissue. Our results show that we can distinguish pancreatic islet cells from the neighboring exocrine tissue environment, recapitulate known biological functions of islet cells, and identify a spatial gradient in the expression of RNA processing proteins within the islet microenvironment.

Perspective: The Benefits of Including Flavored Milk in Healthy Dietary Patterns.

The Dietary Guidelines for Americans recommend two-and-a-half cup equivalents of low-fat and fat-free dairy foods per day for children 4-8 y and 3 cup equivalents per day for adolescents aged 9-18 and adults. Currently, the Dietary Guidelines for Americans recognizes 4 nutrients as being of public concern because of suboptimal levels in the diet. These include calcium, dietary fiber, potassium, and vitamin D. In the American diet, dairy foods are leading contributors of calcium, vitamin D, and potassium. Milk, because of its unique nutrient package that provides shortfall nutrients to the diets of children and adolescents, remains an underpinning of dietary recommendations and is included with school meals. Despite this, milk consumption is declining, and >80% of Americans do not meet recommendations for dairy. Data indicate that children and adolescents who consume flavored milk are more likely to consume more dairy and adhere to healthier overall dietary patterns. Flavored milk, however, receives more scrutiny than plain milk because of its contribution of added sugar and calories to the diet and concerns over childhood obesity. Therefore, the purpose of this narrative review is to describe trends in beverage consumption in children and adolescents aged 5-18 y and highlight the science that has examined the impact of including flavored milk in overall healthy dietary patterns within this population.

False-positive recalls in the prospective Malmö Breast Tomosynthesis Screening Trial.

OBJECTIVES: To evaluate the total number of false-positive recalls, including radiographic appearances and false-positive biopsies, in the Malmö Breast Tomosynthesis Screening Trial (MBTST). METHODS: The prospective, population-based MBTST, with 14,848 participating women, was designed to compare one-view digital breast tomosynthesis (DBT) to two-view digital mammography (DM) in breast cancer screening. False-positive recall rates, radiographic appearances, and biopsy rates were analyzed. Comparisons were made between DBT, DM, and DBT + DM, both in total and in trial year 1 compared to trial years 2 to 5, with numbers, percentages, and 95% confidence intervals (CI). RESULTS: The false-positive recall rate was higher with DBT, 1.6% (95% CI 1.4; 1.8), compared to screening with DM, 0.8% (95% CI 0.7; 1.0). The proportion of the radiographic appearance of stellate distortion was 37.3% (91/244) with DBT, compared to 24.0% (29/121) with DM. The false-positive recall rate with DBT during trial year 1 was 2.6% (95% CI 1.8; 3.5), then stabilized at 1.5% (95% CI 1.3; 1.8) during trial years 2 to 5. The percentage of stellate distortion with DBT was 50% (19/38) trial year 1 compared to 35.0% (72/206) trial years 2 to 5. CONCLUSIONS: The higher false-positive recall rate with DBT compared to DM was mainly due to an increased detection of stellate findings. The proportion of these findings, as well as the DBT false-positive recall rate, was reduced after the first trial year. CLINICAL RELEVANCE STATEMENT: Assessment of false-positive recalls gives information on potential benefits and side effects in DBT screening. KEY POINTS: • The false-positive recall rate in a prospective digital breast tomosynthesis screening trial was higher compared to digital mammography, but still low compared to other trials. • The higher false-positive recall rate with digital breast tomosynthesis was mainly due to an increased detection of stellate findings; the proportion of these findings was reduced after the first trial year.

Engineering Rhodosporidium toruloides for production of 3-hydroxypropionic acid from lignocellulosic hydrolysate.

Microbial production of valuable bioproducts is a promising route towards green and sustainable manufacturing. The oleaginous yeast, Rhodosporidium toruloides, has emerged as an attractive host for the production of biofuels and bioproducts from lignocellulosic hydrolysates. 3-hydroxypropionic acid (3HP) is an attractive platform molecule that can be used to produce a wide range of commodity chemicals. This study focuses on establishing and optimizing the production of 3HP in R. toruloides. As R. toruloides naturally has a high metabolic flux towards malonyl-CoA, we exploited this pathway to produce 3HP. Upon finding the yeast capable of catabolizing 3HP, we then implemented functional genomics and metabolomic analysis to identify the catabolic pathways. Deletion of a putative malonate semialdehyde dehydrogenase gene encoding an oxidative 3HP pathway was found to significantly reduce 3HP degradation. We further explored monocarboxylate transporters to promote 3HP transport and identified a novel 3HP transporter in Aspergillus pseudoterreus by RNA-seq and proteomics. Combining these engineering efforts with media optimization in a fed-batch fermentation resulted in 45.4 g/L 3HP production. This represents one of the highest 3HP titers reported in yeast from lignocellulosic feedstocks. This work establishes R. toruloides as a host for 3HP production from lignocellulosic hydrolysate at high titers, and paves the way for further strain and process optimization towards enabling industrial production of 3HP in the future.