Nutrient Estimation from 24-Hour Food Recalls Using Machine Learning and Database Mapping: A Case Study with Lactose.

The Automated Self-Administered 24-Hour Dietary Assessment Tool (ASA24) is a free dietary recall system that outputs fewer nutrients than the Nutrition Data System for Research (NDSR). NDSR uses the Nutrition Coordinating Center (NCC) Food and Nutrient Database, both of which require a license. Manual lookup of ASA24 foods into NDSR is time-consuming but currently the only way to acquire NCC-exclusive nutrients. Using lactose as an example, we evaluated machine learning and database matching methods to estimate this NCC-exclusive nutrient from ASA24 reports. ASA24-reported foods were manually looked up into NDSR to obtain lactose estimates and split into training (n = 378) and test (n = 189) datasets. Nine machine learning models were developed to predict lactose from the nutrients common between ASA24 and the NCC database. Database matching algorithms were developed to match NCC foods to an ASA24 food using only nutrients ("Nutrient-Only") or the nutrient and food descriptions ("Nutrient + Text"). For both methods, the lactose values were compared to the manual curation. Among machine learning models, the XGB-Regressor model performed best on held-out test data (R2 = 0.33). For the database matching method, Nutrient + Text matching yielded the best lactose estimates (R2 = 0.76), a vast improvement over the status quo of no estimate. These results suggest that computational methods can successfully estimate an NCC-exclusive nutrient for foods reported in ASA24

The fecal resistome of dairy cattle is associated with diet during nursing.

Antimicrobial resistance is a global public health concern, and livestock play a significant role in selecting for resistance and maintaining such reservoirs. Here we study the succession of dairy cattle resistome during early life using metagenomic sequencing, as well as the relationship between resistome, gut microbiota, and diet. In our dataset, the gut of dairy calves serves as a reservoir of 329 antimicrobial resistance genes (ARGs) presumably conferring resistance to 17 classes of antibiotics, and the abundance of ARGs declines gradually during nursing. ARGs appear to co-occur with antibacterial biocide or metal resistance genes. Colostrum is a potential source of ARGs observed in calves at day 2. The dynamic changes in the resistome are likely a result of gut microbiota assembly, which is closely associated with diet transition in dairy calves. Modifications in the resistome may be possible via early-life dietary interventions to reduce overall antimicrobial resistance

Tolerability and safety of the intake of bovine milk oligosaccharides extracted from cheese whey in healthy human adults.

Mechanistic research suggests a unique evolutionary relationship between complex milk oligosaccharides and cognate bifidobacteria enriched in breast-fed infants. Bovine milk oligosaccharides (BMO) were recently identified as structurally and functionally similar to human milk oligosaccharides. The present single-blind three-way crossover study is the first to determine the safety and tolerability of BMO consumption by healthy human participants (n 12) and its effects on faecal microbiota and microbial metabolism. Participants consumed each supplement (placebo-control; low- and high-BMO doses) for eleven consecutive days, followed by a 2-week washout period prior to initiating the next supplement arm. Low and high BMO doses were consumed as 25 and 35 % of each individual's daily fibre intake, respectively. Safety and tolerability were measured using standardised questionnaires on gut and stomach discomfort and stool consistency. Faecal extracts were profiled for bacterial populations by next-generation sequencing (NGS) and bifidobacteria presence was confirmed using quantitative PCR. Urine was analysed for changes in microbial metabolism using nuclear magnetic resonance spectroscopy (1H-NMR). Consumption of both the low and high BMO doses was well tolerated and did not change stool consistency from baseline. Multivariate analysis of the NGS results demonstrated no change in faecal microbiota phyla among the placebo-control and BMO supplement groups. In conclusion, BMO supplementation was well tolerated in healthy adults and has the potential to shift faecal microbiota toward beneficial strains as part of a synbiotic treatment with probiotic cultures that selectively metabolise oligosaccharides

Convective Term and Transversely Driven Charge-Density Waves

We derive the convective terms in the damping which determine the structure of the moving charge-density wave (CDW), and study the effect of a current flowing transverse to conducting chains on the CDW dynamics along the chains. In contrast to a recent prediction we find that the effect is orders of magnitude smaller, and that contributions from transverse currents of electron- and hole-like quasiparticles to the force exerted on the CDW along the chains act in the opposite directions. We discuss recent experimental verification of the effect and demonstrate experimentally that geometry effects might mimic the transverse current effect.Comment: RevTeX, 9 pages, 1 figure, accepted for publications in PR

Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants.

BackgroundIndividuals with inactive alleles of the fucosyltransferase 2 gene (FUT2; termed the 'secretor' gene) are common in many populations. Some members of the genus Bifidobacterium, common infant gut commensals, are known to consume 2'-fucosylated glycans found in the breast milk of secretor mothers. We investigated the effects of maternal secretor status on the developing infant microbiota with a special emphasis on bifidobacterial species abundance.ResultsOn average, bifidobacteria were established earlier and more often in infants fed by secretor mothers than in infants fed by non-secretor mothers. In secretor-fed infants, the relative abundance of the Bifidobacterium longum group was most strongly correlated with high percentages of the order Bifidobacteriales. Conversely, in non-secretor-fed infants, Bifidobacterium breve was positively correlated with Bifidobacteriales, while the B. longum group was negatively correlated. A higher percentage of bifidobacteria isolated from secretor-fed infants consumed 2'-fucosyllactose. Infant feces with high levels of bifidobacteria had lower milk oligosaccharide levels in the feces and higher amounts of lactate. Furthermore, feces containing different bifidobacterial species possessed differing amounts of oligosaccharides, suggesting differential consumption in situ.ConclusionsInfants fed by non-secretor mothers are delayed in the establishment of a bifidobacteria-laden microbiota. This delay may be due to difficulties in the infant acquiring a species of bifidobacteria able to consume the specific milk oligosaccharides delivered by the mother. This work provides mechanistic insight into how milk glycans enrich specific beneficial bacterial populations in infants and reveals clues for enhancing enrichment of bifidobacterial populations in at risk populations - such as premature infants

Role of osmotic and hydrostatic pressures in bacteriophage genome ejection

A critical step in the bacteriophage life cycle is genome ejection into host bacteria. The ejection process for double-stranded DNA phages has been studied thoroughly \textit{in vitro}, where after triggering with the cellular receptor the genome ejects into a buffer. The experimental data have been interpreted in terms of the decrease in free energy of the densely packed DNA associated with genome ejection. Here we detail a simple model of genome ejection in terms of the hydrostatic and osmotic pressures inside the phage, a bacterium, and a buffer solution/culture medium. We argue that the hydrodynamic flow associated with the water movement from the buffer solution into the phage capsid and further drainage into the bacterial cytoplasm, driven by the osmotic gradient between the bacterial cytoplasm and culture medium, provides an alternative mechanism for phage genome ejection \textit{in vivo}; the mechanism is perfectly consistent with phage genome ejection \textit{in vitro}.Comment: 5 pages, 2 figures, references update

Noise Stabilization of Self-Organized Memories

We investigate a nonlinear dynamical system which ``remembers'' preselected values of a system parameter. The deterministic version of the system can encode many parameter values during a transient period, but in the limit of long times, almost all of them are forgotten. Here we show that a certain type of stochastic noise can stabilize multiple memories, enabling many parameter values to be encoded permanently. We present analytic results that provide insight both into the memory formation and into the noise-induced memory stabilization. The relevance of our results to experiments on the charge-density wave material $NbSe_3$ is discussed.Comment: 29 pages, 6 figures, submitted to Physical Review

Spin-orbit coupling and ESR theory for carbon nanotubes

A theoretical description of ESR in 1D interacting metals is given, with primary emphasis on carbon nanotubes. The spin-orbit coupling is derived, and the resulting ESR spectrum is analyzed by field theory and exact diagonalization. Drastic differences in the ESR spectra of single-wall and multi-wall nanotubes are found. For single-wall tubes, the predicted double peak spectrum could reveal spin-charge separation.Comment: 4 pages, 1 figure, final version to appear in PR

Defects, order, and hysteresis in driven charge-density waves

We model driven two-dimensional charge-density waves in random media via a modified Swift-Hohenberg equation, which includes both amplitude and phase fluctuations of the condensate. As the driving force is increased, we find that the defect density first increases and then decreases. Furthermore, we find switching phenomena, due to the formation of channels of dislocations. These results are in qualitative accord with recent dynamical x-ray scattering experiments by Ringlandet al. and transport experiments by Lemay et al.Comment: Accepted to Phys. Rev. Lett. Click here for "http://www-theory.mpip-mainz.mpg.de/~karttune/CDW/", movies of driven CDW