Analysis of Microbial Diversity and Metabolites in Sauerkraut Products with and without Microorganism Addition.

The microbial compositions and metabolites of fermented sauerkraut with and without the addition of microorganisms have been compared. The OTU clustering, nonvolatile compounds, volatile compounds and associations between bacterial taxa and metabolites were analyzed by 16S rRNA high-throughput sequencing technology, ultra performance liquid chromatography (UPLC), gas chromatography ion mobility mass spectrometry (GC-IMS) and the O2PLS model studies. The results showed that at the phylum level, the microbial species in the four sauerkraut types consisted mainly of the phyla Firmicutes and Proteobacteria, but different modes of microbial addition formed their own unique microbial communities. There were significant differences in the microbial communities among different northeast China sauerkraut samples, and different microbial communities exerted similar effects to inhibit Firmicutes production. At the genus level, sauerkraut without added microorganisms had the lowest microbial diversity. A total of 26 amino acids and 11 organic acids were identified and were more abundant in nonmicrobially fermented sauerkraut; 88 volatile organic compounds were identified in the 4 types of sauerkraut, with the microbially fermented sauerkraut being richer in alcohols, esters and acids. Different brands of sauerkraut contain their own unique flavor compounds. Cystine and tyrosine, ascorbic acid and acetic acid, and alcohols and esters are closely related to a wide range of microorganisms in sauerkraut. Elucidating the correlations among microbiota and metabolites will help guide future improvements in sauerkraut fermentation processes.

Large-scale prediction of stream water quality using an interpretable deep learning approach.

Deep learning methods, which have strong capabilities for mapping highly nonlinear relationships with acceptable calculation speed, have been increasingly applied for water quality prediction in recent studies. However, it is argued that the practicality of deep learning methods is limited due to the lack of physical mechanics to explain the prediction results of water quality changes. A knowledge gap exists in rationalizing the deep learning results for water quality predictions. To address this gap, an interpretable deep learning framework was established to predict the spatiotemporal variations of water quality parameters in a large spatial region. Mereological, land-use, and socioeconomic variables were adopted to predict the daily variations of stream water quality parameters across 138 sub-catchments in a total of over 575,250 km2 in southern China. The coefficients of determination of chemical oxygen demand (COD), total phosphorus (TP), and total nitrogen (TN) predictions were over 0.80, suggesting a satisfactory prediction performance. The model performance in terms of prediction accuracy could be improved by involving land-use and socioeconomic predictors in addition to hydrological variables. The SHapley Additive exPlanations method used in this study was demonstrated to be effective for interpreting the prediction results by identifying the significant variables and reasoning their influencing directions on the variation of each water quality parameter. The air temperature, proportion of forest area, grain production, population density, and proportion of urban area in each sub-catchment as well as the accumulated rainfall within the previous 3 days were identified as the most significant variables affecting the variations of dissolved oxygen, COD, ammoniacal nitrogen(NH3-N), TN, TP, and turbidity in the stream water in the case area, respectively.

Flood impacts on urban road connectivity in southern China.

Effective measures to improve road accessibility during storms are required as traffic congestion caused by storm floods increasingly constrains the efficiency of urban commuting. However, flood impacts on urban road connectivity are not yet well assessed due to inaccurate simulation of flood processes in urban areas where high-resolution data for drainage networks and gauged hydrological data are insufficient. Thus, this study assesses flood impacts on road network connectivity in an urban area of southern China through joint modeling of 1-D hydrodynamic processes in drainage networks and 2-D flood inundation processes on roads using MIKE Urban and MIKE 21. High-resolution DEM images of 5 m and a drainage network of 5635 pipelines were used for urban hydrological simulation. Flood depths were gauged for model calibration and validation by recruited volunteers in the context of citizen science. The results show that road network connectivity decreases as rainfall increases. More than 40% of road connectivity is lost in the study area when a 1-in-100-year return period rainfall occurs. The study results can help to inform more adaptive strategies for local flood control. The study methods are also applicable to improving urban hydrological modeling in broader regions.

Design Method of Multiwavelength EMATs Based on Spatial Domain Harmonic Control.

Conventional electromagnetic acoustic transducers (EMATs) are generally only used to generate and detect guided waves with a single wavelength, which increases their sensitivity at that particular wavelength but limits their application scenarios and the accuracy of defect assessment. This article proposes a design method for multiwavelength EMATs based on spatial-domain harmonic control. First, the EMAT model is analyzed, where it is then outlined that the eddy-current density distribution of the specimen is equivalent to the spatial low-pass filtering of the coil-current density distribution. This shows that the multiwavelength guided waves can be achieved as long as the spatial distribution of the coil-current density contains those multiple harmonics that are desired. It is then proposed that the structure of the EMAT coil is equivalent to the spatial sampled pulse sequences of a spatial signal. The coil parameter design based on pulse modulation technology is proposed. Taking a dual-wavelength EMAT design for Lamb waves as an example, details of the coil parameter design are presented. The simulation and experiment with the dual-wavelength EMAT proved the correctness of the proposed method. Finally, an experiment with a three-wavelength EMAT demonstrated the feasibility of the proposed method in designing multiwavelength EMATs.

Impact of Breast Density Legislation on Breast Cancer Risk Assessment and Supplemental Screening: A Survey of 110 Radiology Facilities.

Breast density notification laws, passed in 19 states as of October 2014, mandate that patients be informed of their breast density. The purpose of this study is to assess the impact of this legislation on radiology practices, including performance of breast cancer risk assessment and supplemental screening studies. A 20-question anonymous web-based survey was emailed to radiologists in the Society of Breast Imaging between August 2013 and March 2014. Statistical analysis was performed using Fisher's exact test. Around 121 radiologists from 110 facilities in 34 USA states and 1 Canadian site responded. About 50% (55/110) of facilities had breast density legislation, 36% of facilities (39/109) performed breast cancer risk assessment (one facility did not respond). Risk assessment was performed as a new task in response to density legislation in 40% (6/15) of facilities in states with notification laws. However, there was no significant difference in performing risk assessment between facilities in states with a law and those without (p < 0.831). In anticipation of breast density legislation, 33% (16/48), 6% (3/48), and 6% (3/48) of facilities in states with laws implemented handheld whole breast ultrasound (WBUS), automated WBUS, and tomosynthesis, respectively. The ratio of facilities offering handheld WBUS was significantly higher in states with a law than in states without (p < 0.001). In response to breast density legislation, more than 33% of facilities are offering supplemental screening with WBUS and tomosynthesis, and many are performing formal risk assessment for determining patient management.

Quantitatively defining washout in hepatocellular carcinoma.

OBJECTIVE: Washout on delayed phase (or equilibrium phase) imaging of an arterially hyperenhancing lesion is an excellent predictor of hepatocellular carcinoma (HCC). The purpose of our study was to quantitatively define washout in pathologically proven HCC. A quantitative definition of HCC may minimize interobserver variability and facilitate more accurate diagnosis. MATERIALS AND METHODS: We identified 47 liver lesions that were hyperenhancing in the arterial phase from 24 patients who underwent triphasic MDCT as part of preoperative evaluation for liver transplantation. All HCCs were pathologically proven. Regions of interest were obtained of lesions and areas of adjacent liver on arterial, portal venous, and delayed phase images. Enhancement profiles were assessed by three radiologists. RESULTS: Of the 47 hypervascular lesions, 14 HCCs were identified. There was a statistically significant difference in percentage attenuation ratio (defined as 100 × ratio of attenuation of adjacent liver to that of the lesion) between lesions that were HCC (median percentage attenuation ratio, 121) and those that were not (median percentage attenuation ratio, 101) on delayed phase. Percentage attenuation ratio ≥ 107 on delayed phase imaging achieved maximal sensitivity (100%) with good specificity (75.8%), positive predictive value (PPV) (63.6%), and negative predictive value (NPV) (100%) in HCC detection. Percentage attenuation ratio also correlated well with radiologists' assessments of enhancement profiles of lesions (multinomial logistic regression McFadden R(2), 0.72; chi-square p, < 0.01). CONCLUSION: Our analysis of simple CT attenuation measurements indicates that percentage attenuation ratio offers excellent sensitivity, specificity, PPV, and NPV for HCC detection and very good correlation with radiologists' assessments of washout.

The role of informatics in health care reform.

Improving health care quality while simultaneously reducing cost has become a high priority of health care reform. Informatics is crucial in tackling this challenge. The American Recovery and Reinvestment Act of 2009 mandates adaptation and "meaningful use " of health information technology. In this review, we will highlight several areas in which informatics can make significant contributions, with a focus on radiology. We also discuss informatics related to the increasing imperatives of state and local regulations (such as radiation dose tracking) and quality initiatives.

Multidetector computed tomography triphasic evaluation of the liver before transplantation: importance of equilibrium phase washout and morphology for characterizing hypervascular lesions.

OBJECTIVE: We aim to identify the sensitivity and positive predictive value (PPV) of arterial phase imaging in detecting hepatocellular carcinoma (HCC) and determine the added value of portal venous and equilibrium phase imaging and lesion morphology characterization. METHODS: We reviewed all patients who underwent liver transplantation at our institution that had a triphasic multidetector computed tomography examination within 6 months of transplantation. Forty-seven hypervascular lesions were identified in 24 patients. Imaging findings were correlated with explant pathologic correlation. RESULTS: Hypervascularity in the arterial phase resulted in sensitivity of 87.5% and PPV of 29.8%. The presence of washout in the equilibrium phase increased the PPV to 92.9% with a slight decrease in sensitivity (81.3%). The negative predictive value of hypervascular lesions without washout in the equilibrium phase was 97.1%. There was significant correlation between larger lesions and HCC and between round lesions and HCC. CONCLUSIONS: The presence of washout in the equilibrium phase is a better indicator of malignancy.

Abdominal complications of chemotherapy: findings at computed tomography.

Modern chemotherapy may result in an array of complications that can produce computed tomography (CT) findings in the hepatobiliary, gastrointestinal and urinary systems. This article describes the CT findings that may be seen in abdominal complications of contemporary chemotherapy. Knowledge of the varying CT appearances that can be encountered may facilitate both diagnosis and management in such cases.

A bayesian network for differentiating benign from malignant thyroid nodules using sonographic and demographic features.

OBJECTIVE: The objective of our study was to create a Bayesian network (BN) that incorporates a multitude of imaging features and patient demographic characteristics to guide radiologists in assessing the likelihood of malignancy in suspicious-appearing thyroid nodules. MATERIALS AND METHODS: We built a BN to combine multiple indicators of the malignant potential of thyroid nodules including both imaging and demographic factors. The imaging features and conditional probabilities relating those features to diagnoses were compiled from an extensive literature review. To evaluate our network, we randomly selected 54 benign and 45 malignant nodules from 93 adult patients who underwent ultrasound-guided biopsy. The final diagnosis in each case was pathologically established. We compared the performance of our network with that of two radiologists who independently evaluated each case on a 5-point scale of suspicion for malignancy. Probability estimates of malignancy from the BN and radiologists were compared using receiver operating characteristic (ROC) analysis. RESULTS: The network performed comparably to the two expert radiologists. Using each radiologist's assessment of the imaging features as input to the network, the differences between the area under the ROC curve (A(z)) for the BN and for the radiologists were -0.03 (BN vs radiologist 1, 0.85 vs 0.88) and -0.01 (BN vs radiologist 2, 0.76 vs 0.77). CONCLUSION: We created a BN that incorporates a range of sonographic and demographic features and provides a probability about whether a thyroid nodule is benign or malignant. The BN distinguished between benign and malignant thyroid nodules as well as the expert radiologists did.

Hypervascular liver lesions.

Hypervascular hepatocellular lesions include both benign and malignant etiologies. In the benign category, focal nodular hyperplasia and adenoma are typically hypervascular. In addition, some regenerative nodules in cirrhosis may be hypervascular. Malignant hypervascular primary hepatocellular lesions include hepatocellular carcinoma, fibrolamellar carcinoma, and peripheral cholangiocarcinoma. Vascular liver lesions often appear hypervascular because they tend to follow the enhancement of the blood pool; these include hemangiomas, arteriovenous malformations, angiosarcomas, and peliosis. While most gastrointestinal malignancies that metastasize to the liver will appear hypovascular on arterial and portal-venous phase imaging, certain cancers such as metastatic neuroendocrine tumors (including pancreatic neuroendocrine tumors, carcinoid, and gastrointestinal stromal tumors) tend to produce hypervascular metastases due to the greater recruitment of arterial blood supply. Finally, rare hepatic lesions such as glomus tumor and inflammatory pseudotumor may have a hypervascular appearance.

The "etiome": identification and clustering of human disease etiological factors.

BACKGROUND: Both genetic and environmental factors contribute to human diseases. Most common diseases are influenced by a large number of genetic and environmental factors, most of which individually have only a modest effect on the disease. Though genetic contributions are relatively well characterized for some monogenetic diseases, there has been no effort at curating the extensive list of environmental etiological factors. RESULTS: From a comprehensive search of the MeSH annotation of MEDLINE articles, we identified 3,342 environmental etiological factors associated with 3,159 diseases. We also identified 1,100 genes associated with 1,034 complex diseases from the NIH Genetic Association Database (GAD), a database of genetic association studies. 863 diseases have both genetic and environmental etiological factors available. Integrating genetic and environmental factors results in the "etiome", which we define as the comprehensive compendium of disease etiology. Clustering of environmental factors may alert clinicians of the risks of added exposures, or synergy in interventions to alter these factors. Clustering of both genetic and environmental etiological factors puts genes in the context of environment in a quantitative manner. CONCLUSION: In this paper, we obtained a comprehensive list of associations between disease and environmental factors using MeSH annotation of MEDLINE articles. It serves as a summary of current knowledge between etiological factors and diseases. By combining the environmental etiological factors and genetic factors from GAD, we computed the "etiome" profile for 863 diseases. Comparing diseases across these profiles may have utility for clinical medicine, basic science research, and population-based science.

A Controlled Vocabulary to Represent Sonographic Features of the Thyroid and its application in a Bayesian Network to Predict Thyroid Nodule Malignancy.

It is challenging to distinguish benign from malignant thyroid nodules on high resolution ultrasound. Many ultrasound features have been studied individually as predictors for thyroid malignancy, none with a high degree of accuracy, and there is no consistent vocabulary used to describe the features. Our hypothesis is that a standard vocabulary will advance accuracy. We performed a systemic literature review and identified all the sonographic features that have been well studied in thyroid cancers. We built a controlled vocabulary for describing sonographic features and to enable us to unify data in the literature on the predictive power of each feature. We used this terminology to build a Bayesian network to predict thyroid malignancy. Our Bayesian network performed similar to or slightly better than experienced radiologists. Controlled terminology for describing thyroid radiology findings could be useful to characterize thyroid nodules and could enable decision support applications.

A Bayesian classifier for differentiating benign versus malignant thyroid nodules using sonographic features.

Thyroid nodules are a common, yet challenging clinical problem. The vast majority of these nodules are benign; however, deciding which nodule should undergo biopsy is difficult because the imaging appearance of benign and malignant thyroid nodules overlap. High resolution ultrasound is the primary imaging modality for evaluating thyroid nodules. Many sonographic features have been studied individually as predictors for thyroid malignancy. There has been little work to create predictive models that combine multiple predictors, both imaging features and demographic factors. We have created a Bayesian classifier to predict whether a thyroid nodule is benign or malignant using sonographic and demographic findings. Our classifier performed similar to or slightly better than experienced radiologists when evaluated using 41 thyroid nodules with known pathologic diagnosis. This classifier could be helpful in providing practitioners an objective basis for deciding whether to biopsy suspicious thyroid nodules.

Comparison of one-day versus one-hour application of topical gatifloxacin in eliminating conjunctival bacterial flora.

PURPOSE: To compare efficacies of 1-day, 1-hour, and combined 1-day/1-hour preoperative topical gatifloxacin in eliminating conjunctival bacterial flora. DESIGN: Prospective, comparative case series. PARTICIPANTS: Sixty patients (120 eyes) scheduled to undergo anterior segment intraocular surgery at Stanford University Medical Center. METHODS: Cultures were collected from the palpebral conjunctival sac at baseline and after 1 day (4 doses), 1 hour (3 doses), and 1 day/1 hour (7 doses) of gatifloxacin use. MAIN OUTCOME MEASURES: Incidence of positive bacterial samples collected pre- and post-antibiotic treatment and number of colony forming units (CFUs). RESULTS: SeptiChek (Becton Dickinson, Franklin Lakes, NJ) positive cultures significantly decreased from 67% growth at baseline to 28% (P<0.0001) after 1 day and from 60% at baseline to 37% (P = 0.018) after 1 hour of gatifloxacin use. Reductions of 44% growth at baseline to 12% (P = 0.0001) after 1 day and 32% at baseline to 13% (P = 0.029) after 1 hour of gatifloxacin use were observed on blood agar. Surgical eyes that received both 1-day and 1-hour preoperative gatifloxacin had reductions from 67% growth at baseline to 18% posttreatment (P<0.0001) and 45% at baseline to 7% posttreatment (P<0.0001) on SeptiChek and blood agar media, respectively. In addition to a lower frequency of positive cultures, a significantly lower CFU count was found after 1-day (P = 0.004) and 1-hour (P = 0.049) gatifloxacin use compared with pretreatment levels. Combined 1-day/1-hour doses of gatifloxacin were associated with a greater reduction in CFUs (P = 0.001) when compared with 1-hour treatment alone. CONCLUSIONS: Both 1-hour and 1-day topical gatifloxacin use are effective in reducing the frequency of conjunctival bacterial growth and the overall bacterial load as measured by CFUs, relative to baseline. Although a 1-hour pretreatment is associated with a reduction in bacterial growth, the combination of 1-day and 1-hour preoperative gatifloxacin dosing results in an even lower overall bacterial load, suggesting that the latter might be the preferred preoperative regimen for eyes undergoing anterior segment surgery.

Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans.

We used mRNA tagging to identify genes expressed in the intestine of C. elegans. Animals expressing an epitope-tagged protein that binds the poly-A tail of mRNAs (FLAG::PAB-1) from an intestine-specific promoter (ges-1) were used to immunoprecipitate FLAG::PAB-1/mRNA complexes from the intestine. A total of 1938 intestine-expressed genes (P<0.001) were identified using DNA microarrays. First, we compared the intestine-expressed genes with those expressed in the muscle and germline, and identified 510 genes enriched in all three tissues and 624 intestine-, 230 muscle- and 1135 germ line-enriched genes. Second, we showed that the 1938 intestine-expressed genes were physically clustered on the chromosomes, suggesting that the order of genes in the genome is influenced by the effect of chromatin domains on gene expression. Furthermore, the commonly expressed genes showed more chromosomal clustering than the tissue-enriched genes, suggesting that chromatin domains may influence housekeeping genes more than tissue-specific genes. Third, in order to gain further insight into the regulation of intestinal gene expression, we searched for regulatory motifs. This analysis found that the promoters of the intestine genes were enriched for the GATA transcription factor consensus binding sequence. We experimentally verified these results by showing that the GATA motif is required in cis and that GATA transcription factors are required in trans for expression of these intestinal genes.

A suite of web-based programs to search for transcriptional regulatory motifs.

The identification of regulatory motifs is important for the study of gene expression. Here we present a suite of programs that we have developed to search for regulatory sequence motifs: (i) BioProspector, a Gibbs-sampling-based program for predicting regulatory motifs from co-regulated genes in prokaryotes or lower eukaryotes; (ii) CompareProspector, an extension to BioProspector which incorporates comparative genomics features to be used for higher eukaryotes; (iii) MDscan, a program for finding protein-DNA interaction sites from ChIP-on-chip targets. All three programs examine a group of sequences that may share common regulatory motifs and output a list of putative motifs as position-specific probability matrices, the individual sites used to construct the motifs and the location of each site on the input sequences. The web servers and executables can be accessed at http://seqmotifs.stanford.edu.