Lung Pattern Classification for Interstitial Lung Diseases Using a Deep Convolutional Neural Network

Automated tissue characterization is one of the most crucial components of a computer aided diagnosis (CAD) system for interstitial lung diseases (ILDs). Although much research has been conducted in this field, the problem remains challenging. Deep learning techniques have recently achieved impressive results in a variety of computer vision problems, raising expectations that they might be applied in other domains, such as medical image analysis. In this paper, we propose and evaluate a convolutional neural network (CNN), designed for the classification of ILD patterns. The proposed network consists of 5 convolutional layers with 2×2 kernels and LeakyReLU activations, followed by average pooling with size equal to the size of the final feature maps and three dense layers. The last dense layer has 7 outputs, equivalent to the classes considered: healthy, ground glass opacity (GGO), micronodules, consolidation, reticulation, honeycombing and a combination of GGO/reticulation. To train and evaluate the CNN, we used a dataset of 14696 image patches, derived by 120 CT scans from different scanners and hospitals. To the best of our knowledge, this is the first deep CNN designed for the specific problem. A comparative analysis proved the effectiveness of the proposed CNN against previous methods in a challenging dataset. The classification performance (~85.5%) demonstrated the potential of CNNs in analyzing lung patterns. Future work includes, extending the CNN to three-dimensional data provided by CT volume scans and integrating the proposed method into a CAD system that aims to provide differential diagnosis for ILDs as a supportive tool for radiologists.

Virulence-associated gene pattern of porcine and human Yersinia enterocolitica biotype 4 isolates.

Yersinia enterocolitica 4/O:3 is the most important human pathogenic bioserotype in Europe and the predominant pathogenic bioserotype in slaughter pigs. Although many studies on the virulence of Y. enterocolitica strains have showed a broad spectrum of detectable factors in pigs and humans, an analysis based on a strict comparative approach and serving to verify the virulence capability of porcine Y. enterocolitica as a source for human yersiniosis is lacking. Therefore, in the present study, strains of biotype (BT) 4 isolated from Swiss slaughter pig tonsils and feces and isolates from human clinical cases were compared in terms of their spectrum of virulence-associated genes (yadA, virF, ail, inv, rovA, ymoA, ystA, ystB and myfA). An analysis of the associated antimicrobial susceptibility pattern completed the characterization. All analyzed BT 4 strains showed a nearly similar pattern, comprising the known fundamental virulence-associated genes yadA, virF, ail, inv, rovA, ymoA, ystA and myfA. Only ystB was not detectable among all analyzed isolates. Importantly, neither the source of the isolates (porcine tonsils and feces, humans) nor the serotype (ST) had any influence on the gene pattern. From these findings, it can be concluded that the presence of the full complement of virulence genes necessary for human infection is common among porcine BT 4 strains. Swiss porcine BT 4 strains not only showed antimicrobial susceptibility to chloramphenicol, cefotaxime, ceftazidime, ciprofloxacin, colistin, florfenicol, gentamicin, kanamycin, nalidixic acid, sulfamethoxazole, streptomycin, tetracycline and trimethoprim but also showed 100% antibiotic resistance to ampicillin. The human BT 4 strains revealed comparable results. However, in addition to 100% antibiotic resistance to ampicillin, 2 strains were resistant to chloramphenicol and nalidixic acid. Additionally, 1 of these strains was resistant to sulfamethoxazole. The results demonstrated that Y. enterocolitica BT 4 isolates from porcine tonsils, as well as from feces, show the same virulence-associated gene pattern and antibiotic resistance properties as human isolates from clinical cases, consistent with the etiological role of porcine BT 4 in human yersiniosis. Thus, cross-contamination of carcasses and organs at slaughter with porcine Y. enterocolitica BT 4 strains, either from tonsils or feces, must be prevented to reduce human yersiniosis.

Analysis of expansin-induced morphogenesis on the apical meristem of tomato

Our previous work has shown that localised activity of the cell-wall-loosening protein expansin is sufficient to induce primordia on the apical meristem of tomato, consistent with the hypothesis that tissue expansion plays a key role in leaf initiation. In this paper we describe the earliest morphogenic events visible on the surface of the apical meristem of tomato (Lycopersicon esculentum Mill.) following treatment with expansin and report on the spectrum of final structures formed. Our observations are consistent with a proposed primary function of expansin effecting morphogenesis via altered biophysical stress patterns in the meristem. The primordia induced by expansin do not complete the full program of leaf development. We present data indicating that one reason for this might be the inability of exogenous expansin to mimic the endogenous pattern of expansin activity in the meristem. These data provide the first detailed analysis at the cellular level of expansin action on living tissue, the first description of the spectrum of structures induced by expansin on the apical meristem, and give an insight into a potentially fundamental mechanism in plant development.

Biodiversity and Ecosystem Function in the Gulf of Maine: Pattern and Role of Zooplankton and Pelagic Nekton

This paper forms part of a broader overview of biodiversity of marine life in the Gulf of Maine area (GoMA), facilitated by the GoMA Census of Marine Life program. It synthesizes current data on species diversity of zooplankton and pelagic nekton, including compilation of observed species and descriptions of seasonal, regional and cross-shelf diversity patterns. Zooplankton diversity in the GoMA is characterized by spatial differences in community composition among the neritic environment, the coastal shelf, and deep offshore waters. Copepod diversity increased with depth on the Scotian Shelf. On the coastal shelf of the western Gulf of Maine, the number of higher-level taxonomic groups declined with distance from shore, reflecting more nearshore meroplankton. Copepod diversity increased in late summer, and interdecadal diversity shifts were observed, including a period of higher diversity in the 1990s. Changes in species diversity were greatest on interannual scales, intermediate on seasonal scales, and smallest across regions, in contrast to abundance patterns, suggesting that zooplankton diversity may be a more sensitive indicator of ecosystem response to interannual climate variation than zooplankton abundance. Local factors such as bathymetry, proximity of the coast, and advection probably drive zooplankton and pelagic nekton diversity patterns in the GoMA, while ocean-basin-scale diversity patterns probably contribute to the increase in diversity at the Scotian Shelf break, a zone of mixing between the cold-temperate community of the shelf and the warm-water community offshore. Pressing research needs include establishment of a comprehensive system for observing change in zooplankton and pelagic nekton diversity, enhanced observations of "underknown'' but important functional components of the ecosystem, population and metapopulation studies, and development of analytical modeling tools to enhance understanding of diversity patterns and drivers. Ultimately, sustained observations and modeling analysis of biodiversity must be effectively communicated to managers and incorporated into ecosystem approaches for management of GoMA living marine resources.

Penalty Enhancement for Hate Crimes: An Economic Analysis

The issue of bias-motivated crimes has attracted consderable attention in recent years. In this paper, we develop an economic framework to analyze penalty enhancements for bias-motivated crimes. We extend the standard model by introducing two different groups of potential victims of crime, and assume that a potential offender's benefits from a crime depend on the group to which the victim belongs. We begin with the assumption that the harm to an individual victim from a bias-motivated crime is identical to that from an equivalent non-hate crime. Nonetheless, we derive the result that a pattern of crimes disproportionately targeting an identifiable group leads to greater social harm. This conclusion follows both from a model where disparities in groups' victimization probabilities lead to social losses due to fairness concerns, as well as a model where potential victims have the opportunity to undertake socially costly victimization avoidance activities. In particular, penalty enhancements can reduce the incentives for avoidance activity, and thereby protect the networks of profitable interactions that link members of different groups. We also argue that those groups that are covered by hate crime statutes tend to be those whose characteristics make it especially likely that penalty enhancement is socially optimal. Finally, we consider a number of other issues related to hate crimes, including teh choice of sanctions from behind a Rawlsian 'veil of ignorance' concerning group identity.

Dynamic Smile Analysis : Changes with Age

Introduction: The objective of this study was to define age-related changes in the human smile. The areas of interest were: upper lip length at smile and repose, upper lip thickness at smile and repose, maxillary incisal display at smile, interlabial gap height at smile, smile index, percent buccal corridors, intercommissural width at rest, smile height, and smile arc. A secondary objective was to study the perioral changes from rest to smile and compare them on the basis of age. Materials and Method: Video equipment was used to capture video for 261 subjects. Two frames for each subject were selected; one frame representing the lips and rest and the second representing the widest smile. After excluding 40 subjects the data for the remaining 221 subjects was analyzed. Results: There was a decrease of 1.5 to 2 mm in the maxillary incisor display during smile, with increase in age. Smile index significantly increased with increase in age. Most (78%) subjects displayed an average smile height. No subjects in the 50 and over age group displayed a high smile while no subjects in the 15-19 year old age group presented with a low smile. All the dynamic measures indicated there was a pattern of decreasing change from rest to smile especially evident after the 30-39 year old age group. Conclusions: This study helps to establish age related dynamic norms. As the person ages the smile gets narrower vertically and wider transversely. The dynamic measures indicate that the muscles' ability to create a smile decreases with increasing age.

A coalescent analysis for modeling the mutation process in colorectal cancer

Colorectal cancer is the forth most common diagnosed cancer in the United States. Every year about a hundred forty-seven thousand people will be diagnosed with colorectal cancer and fifty-six thousand people lose their lives due to this disease. Most of the hereditary nonpolyposis colorectal cancer (HNPCC) and 12% of the sporadic colorectal cancer show microsatellite instability. Colorectal cancer is a multistep progressive disease. It starts from a mutation in a normal colorectal cell and grows into a clone of cells that further accumulates mutations and finally develops into a malignant tumor. In terms of molecular evolution, the process of colorectal tumor progression represents the acquisition of sequential mutations. ^ Clinical studies use biomarkers such as microsatellite or single nucleotide polymorphisms (SNPs) to study mutation frequencies in colorectal cancer. Microsatellite data obtained from single genome equivalent PCR or small pool PCR can be used to infer tumor progression. Since tumor progression is similar to population evolution, we used an approach known as coalescent, which is well established in population genetics, to analyze this type of data. Coalescent theory has been known to infer the sample's evolutionary path through the analysis of microsatellite data. ^ The simulation results indicate that the constant population size pattern and the rapid tumor growth pattern have different genetic polymorphic patterns. The simulation results were compared with experimental data collected from HNPCC patients. The preliminary result shows the mutation rate in 6 HNPCC patients range from 0.001 to 0.01. The patients' polymorphic patterns are similar to the constant population size pattern which implies the tumor progression is through multilineage persistence instead of clonal sequential evolution. The results should be further verified using a larger dataset. ^

Secondary data analysis of a pilot study of use of an instructional video for dietary assessment

Introduction. Food frequency questionnaires (FFQ) are used study the association between dietary intake and disease. An instructional video may potentially offer a low cost, practical method of dietary assessment training for participants thereby reducing recall bias in FFQs. There is little evidence in the literature of the effect of using instructional videos on FFQ-based intake. Objective. This analysis compared the reported energy and macronutrient intake of two groups that were randomized either to watch an instructional video before completing an FFQ or to view the same instructional video after completing the same FFQ. Methods. In the parent study, a diverse group of students, faculty and staff from Houston Community College were randomized to two groups, stratified by ethnicity, and completed an FFQ. The "video before" group watched an instructional video about completing the FFQ prior to answering the FFQ. The "video after" group watched the instructional video after completing the FFQ. The two groups were compared on mean daily energy (Kcal/day), fat (g/day), protein (g/day), carbohydrate (g/day) and fiber (g/day) intakes using descriptive statistics and one-way ANOVA. Demographic, height, and weight information was collected. Dietary intakes were adjusted for total energy intake before the comparative analysis. BMI and age were ruled out as potential confounders. Results. There were no significant differences between the two groups in mean daily dietary intakes of energy, total fat, protein, carbohydrates and fiber. However, a pattern of higher energy intake and lower fiber intake was reported in the group that viewed the instructional video before completing the FFQ compared to those who viewed the video after. Discussion. Analysis of the difference between reported intake of energy and macronutrients showed an overall pattern, albeit not statistically significant, of higher intake in the video before versus the video after group. Application of instructional videos for dietary assessment may require further research to address the validity of reported dietary intakes in those who are randomized to watch an instructional video before reporting diet compared to a control groups that does not view a video.^

A descriptive and exploratory analysis of occupational injuries at a chemical manufacturing facility

A retrospective study of 1353 occupational injuries occurring at a chemical manufacturing facility in Houston, Texas from January, 1982 through May, 1988 was performed to investigate the etiology of the occupational injury process. Injury incidence rates were calculated for various sub-populations of workers to determine differences in the risk of injury for various groups. Linear modeling techniques were used to determine the association between certain collected independent variables and severity of an injury event. Finally, two sub-groups of the worker population, shiftworkers and injury recidivists, were examined. An injury recidivist as defined is any worker experiencing one or more injury per year. Overall, female shiftworkers evidenced the highest average injury incidence rate compared to all other worker groups analyzed. Although the female shiftworkers were younger and less experienced, the etiology of their increased risk of injury remains unclear, although the rigors of performing shiftwork itself or ergonomic factors are suspect. In general, females were injured more frequently than males, but they did not incur more severe injuries. For all workers, many injuries were caused by erroneous or foregone training, and risk taking behaviors. Injuries of these types are avoidable. The distribution of injuries by severity level was bimodal; either injuries were of minor or major severity with only a small number of cases falling in between. Of the variables collected, only the type of injury incurred and the worker's titlecode were statistically significantly associated with injury severity. Shiftworkers did not sustain more severe injuries than other worker groups. Injury to shiftworkers varied as a 24-hour pattern; the greatest number occurred between 1200-1230 hours, (p = 0.002) by Cosinor analysis. Recidivists made up 3.3% of the population (23 males and 10 females), yet suffered 17.8% of the injuries. Although past research suggests that injury recidivism is a random statistical event, analysis of the data by logistic regression implicates gender, area worked, age and job titlecode as being statistically significantly related to injury recidivism at this facility. ^

ECONOMIC ANALYSIS OF THE DEMAND FOR PRESCRIPTION MEDICINE IN THE UNITED STATES

The purpose of this study was to understand the role of principle economic, sociodemographic and health status factors in determining the likelihood and volume of prescription drug use. Econometric demand regression models were developed for this purpose. Ten explanatory variables were examined: family income, coinsurance rate, age, sex, race, household head education level, size of family, health status, number of medical visits, and type of provider seen during medical visits. The economic factors (family income and coinsurance) were given special emphasis in this study.^ The National Medical Care Utilization and Expenditure Survey (NMCUES) was the data source. The sample represented the civilian, noninstitutionalized residents of the United States in 1980. The sample method used in the survey was a stratified four-stage, area probability design. The sample was comprised of 6,600 households (17,123 individuals). The weighted sample provided the population estimates used in the analysis. Five repeated interviews were conducted with each household. The household survey provided detailed information on the United States health status, pattern of health care utilization, charges for services received, and methods of payments for 1980.^ The study provided evidence that economic factors influenced the use of prescription drugs, but the use was not highly responsive to family income and coinsurance for the levels examined. The elasticities for family income ranged from -.0002 to -.013 and coinsurance ranged from -.174 to -.108. Income has a greater influence on the likelihood of prescription drug use, and coinsurance rates had an impact on the amount spent on prescription drugs. The coinsurance effect was not examined for the likelihood of drug use due to limitations in the measurement of coinsurance. Health status appeared to overwhelm any effects which may be attributed to family income or coinsurance. The likelihood of prescription drug use was highly dependent on visits to medical providers. The volume of prescription drug use was highly dependent on the health status, age, and whether or not the individual saw a general practitioner. ^

A comparison of two statistical methods for analysis of day of the week effect on births from 2005-2007 in Harris County of Texas

The pattern of the births during the week has been reported by many studies. The births occurred in weekends are found consistently less then births occurred in weekdays. This study employed two statistical methods, two-way ANOVA and two-way Friedman's test to analyse the daily variations in amount of births of 222,735 births from 2005-2007 in Harris County, Texas. The two methods were compared on their assumptions, procedures and results. Both of the tests showed a significant result which indicated that the births through the week are not uniformly distributed. The result of multiple comparison demonstrated the births occurring on weekends were significantly different than the births occurring on weekdays with least amount on Sundays.^

Retrospective analysis of Methicillin-Resistant Staphylococcus Aureus (MRSA) skin and Soft-Tissue Infections (SSTI) in a university hospital emergency department (ED)

Study Objective: Identify the most frequent risk factors of Community Acquired-MRSA (CA-MRSA) Skin and Soft-tissue Infections (SSTIs) using a case series of patients and characterize them by age, race/ethnicity, gender, abscess location, druguse and intravenous drug-user (IVDU), underlying medical conditions, homelessness, treatment resistance, sepsis, those whose last healthcare visit was within the last 12 months, and describe the susceptibility pattern from this central Texas population that have come into the University Medical Center Brackenridge (UMCB) Emergency Department (ED). ^ Methods: This study was a retrospective case-series medical record review involving a convenience sample of patients in 2007 from an urban public hospital's ED in Texas that had a SSTI that tested positive for MRSA. All positive MRSA cultures underwent susceptibility testing to determine antibiotic resistance. The demographic and clinical variables that were independently associated with MRSA were determined by univariate and multivariate analysis using logistic regression to calculate odds ratios (OR), 95% confidence intervals, and significance (p≤ 0.05). ^ Results: In 2007, there were 857 positive MRSA cultures. The demographics were: males 60% and females 40%, with the average age of 36.2 (std. dev. =13) the study population consisted of non-Hispanic white (42%), Hispanics (38%), and non-Hispanic black (18.8%). Possible risk factors addressed included using recreational drugs (not including IVDU) (27%) homelessness (13%), diabetes status (12.6%) or having an infectious disease, and IVDU (10%). The most frequent abscess location was the leg (26.6%), followed by the arm and torso (both 13.7%). Eighty-three percent of patients had one prominent susceptibility pattern that had a susceptibility rate for the following antibiotics: trimethoprim/sulfamethoxazole (TMP-SMX) and vancomycin had 100%, gentamicin 99%, clindamycin 96%, tetracycline 96%, and erythromycin 56%. ^ Conclusion: The ED is becoming an important area for disease transmission between the sterile hospital environment and the outside environment. As always, it is important to further research in the ED in an effort to better understand MRSA transmission and antibiotic resistance, as well as to keep surveillance for the introduction of new opportunistic pathogens into the population. ^

Chemical analysis and argon geochronology from dive SAR_1 on Cornacya seamount of the Sardinia Channel

Sarcya 1 dive explored a previously unknown 12 My old submerged volcano, labelled Cornacya. A well developed fracturation is characterised by the following directions: N 170 to N-S, N 20 to N 40, N 90 to N 120, N 50 to N 70, which corresponds to the fracturation pattern of the Sardinian margin. The sampled lavas exhibit features of shoshonitic suites of intermediate composition and include amphibole-and mica-bearing lamprophyric xenoliths which are geochemically similar to Ti-poor lamproites. Mica compositions reflect chemical exchanges between the lamprophyre and its shoshonitic host rock suggesting their simultaneous emplacement. Nd compositions of the Cornacya K-rich suite indicate that continental crust was largely involved in the genesis of these rocks. The spatial association of the lamprophyre with the shoshonitic rocks is geochemically similar to K-rich and TiO2-poor igneous suites, emplaced in post-collisional settings. Among shoshonitic rocks, sample SAR 1-01 has been dated at 12.6±0.3 My using the 40Ar/39Ar method with a laser microprobe on single grains. The age of the Cornacya shoshonitic suite is similar to that of the Sisco lamprophyre from Corsica, which similarly is located on the western margin of the Tyrrhenian Sea. Thus, the Cornacya shoshonitic rocks and their lamprophyric xenolith and the Sisco lamprophyre could represent post-collisional suites emplaced during the lithospheric extension of the Corsica-Sardinia block, just after its rotation and before the Tyrrhenian sea opening. Drilling on the Sardinia margin (ODP Leg 107) shows that the upper levels of the present day margin (Hole 654) suffered tectonic subsidence before the lower part (Hole 652). The structure of this lower part is interpreted as the result of an eastward migration of the extension during Late Miocene and Early Pliocene times. Data of Cornacya volcano are in good agreement with this model and provide good chronological constraints for the beginning of the phenomenon.

Sedimentation rate calculations and isotopic analysis on sediment cores along the IODP Expedition 311 transect

The oceanographic and tectonic conditions of accretionary margins are well-suited for several potential processes governing methane generation, storage and release. To identify the relevant methane evolution pathways in the northern Cascadia accretionary margin, a four-site transect was drilled during Integrated Ocean Drilling Program Expedition 311. The d13C values of methane range from a minimum value of -82.2 per mil on an uplifted ridge of accreted sediment near the deformation front (Site U1326, 1829 mbsl, meters below sea level) to a maximum value of -39.5 per mil at the most landward location within an area of steep canyons near the shelf edge (Site U1329, 946 mbsl). An interpretation based solely on methane isotope values might conclude the 13C-enrichment of methane indicates a transition from microbially- to thermogenically-sourced methane. However, the co-existing CO2 exhibits a similar trend of 13C-enrichment along the transect with values ranging from -22.5 per mil to +25.7 per mil. The magnitude of the carbon isotope separation between methane and CO2 (Ec = 63.8 ± 5.8) is consistent with isotope fractionation during microbially mediated carbonate reduction. These results, in conjunction with a transect-wide gaseous hydrocarbon content composed of > 99.8% (by volume) methane and uniform dDCH4 values (-172 per mil ± 8) that are distinct from thermogenic methane at a seep located 60 km from the Expedition 311 transect, suggest microbial CO2 reduction is the predominant methane source at all investigated sites. The magnitude of the intra-site downhole 13C-enrichment of CO2 within the accreted ridge (Site U1326) and a slope basin nearest the deformation front (Site U1325, 2195 mbsl) is ~ 5 per mil. At the mid-slope site (Site U1327, 1304 mbsl) the downhole 13C-enrichment of the CO2 is ~ 25 per mil and increases to ~ 40 per mil at the near-shelf edge Site U1329. This isotope fractionation pattern is indicative of more extensive diagenetic alteration at sites with greater 13C-enrichment. The magnitude of the 13C-enrichment of CO2 correlates with decreasing sedimentation rates and a diminishing occurrence of stratigraphic gas hydrate. We suggest the decreasing sedimentation rates increase the exposure time of sedimentary organic matter to aerobic and anaerobic degradation, during burial, thereby reducing the availability of metabolizable organic matter available for methane production. This process is reflected in the occurrence and distribution of gas hydrate within the northern Cascadia margin accretionary prism. Our observations are relevant for evaluating methane production and the occurrence of stratigraphic gas hydrate within other convergent margins.

Sporomorphs and quantitative analysis of the Eocene record from IODP Hole 318-U1356A

The early Eocene epoch was characterized by extreme global warmth, which in terrestrial settings was characterized by an expansion of near-tropical vegetation belts into the high latitudes. During the middle to late Eocene, global cooling caused the retreat of tropical vegetation to lower latitudes. In high-latitude settings, near-tropical vegetation was replaced by temperate floras. This floral change has recently been traced as far south as Antarctica, where along the Wilkes Land margin paratropical forests thrived during the early Eocene and temperate Nothofagus forests developed during the middle Eocene. Here we provide both qualitative and quantitative palynological data for this floral turnover based on a sporomorph record recovered at Integrated Ocean Drilling Program (IODP) Site U1356 off the Wilkes Land margin. Following the nearest living relative concept and based on a comparison with modern vegetation types, we examine the structure and diversity patterns of the Eocene vegetation along the Wilkes Land margin. Our results indicate that the early Eocene forests along the Wilkes Land margin were characterized by a diverse canopy composed of plants that today occur in tropical settings; their richness pattern was similar to that of present-day forests from New Caledonia. The middle Eocene forests were characterized by a canopy dominated by Nothofagus and exhibited richness patterns similar to modern Nothofagus forests from New Zealand.