Learning to Segment Breast Biopsy Whole Slide Images

We trained and applied an encoder-decoder model to semantically segment breast biopsy images into biologically meaningful tissue labels. Since conventional encoder-decoder networks cannot be applied directly on large biopsy images and the different sized structures in biopsies present novel challenges, we propose four modifications: (1) an input-aware encoding block to compensate for information loss, (2) a new dense connection pattern between encoder and decoder, (3) dense and sparse decoders to combine multi-level features, (4) a multi-resolution network that fuses the results of encoder-decoders run on different resolutions. Our model outperforms a feature-based approach and conventional encoder-decoders from the literature. We use semantic segmentations produced with our model in an automated diagnosis task and obtain higher accuracies than a baseline approach that employs an SVM for feature-based segmentation, both using the same segmentation-based diagnostic features.Comment: Added more WSI images in appendi

Oral Health and Primary Care: Exploring Integration Models and Their Implications for Dental Hygiene Practice

Background: Historically, the oral health care system has been separated both administratively and clinically from the larger health care delivery system. Despite this historical separation, providing oral health care services lies within the scope of all health care professionals' practices. Current efforts to shift the compartmentalized American health care system to a total patient care model provide an opportunity to integrate oral health care with primary care in order to improve the population's oral health. This article seeks to acquaint dental hygienists, the oral health care professionals focused on disease prevention, with new and emerging models of oral health care delivery and interprofessional collaborative practice in the hope that they soon will participate in and expand the implementation of these practice models. Methods: This study focused on five health centers, all of which have been identified as organizational leaders in the development and implementation of models designed to support the integration of oral health care with primary care. Quantitative information on each health center was derived from annual reports submitted to the Uniform Data System (UDS) and information on the integration models was obtained through structured key informant interviews. Results: Each organization has incorporated oral health risk assessment, clinical assessments, education, preventive interventions, and dental care coordination into primary care services. One organization provides oral health care as part of its outreach services and programs. The health care team members involved in integration vary. Some of the health centers primarily call on doctors to implement integration of oral health care while others employ dental hygienists, nurses, medical assistants, and outreach team members. Interprofessional collaboration was observed in each organization but took on different forms. Conclusions: Although their methods of integrating oral health care with primary care differed, the five health centers described in this study successfully used integration to improve the delivery of oral health care services to their patients. All of these organizations placed a high value on interprofessional collaboration regardless of the particular collaborative model employed and identified a champion tasked with overseeing the improvement of oral health care delivery.The development of this article was supported by the National Association of Community Health Centers through funding provided by the DentaQuest Foundation

The Cross-correlation of MgII Absorption and Galaxies in BOSS

We present a measurement of the cross-correlation of MgII absorption and massive galaxies, using the DR11 main galaxy sample of the Baryon Oscillation Spectroscopic Survey of SDSS-III (CMASS galaxies), and the DR7 quasar spectra of SDSS-II. The cross-correlation is measured by stacking quasar absorption spectra shifted to the redshift of galaxies that are within a certain impact parameter bin of the quasar, after dividing by a quasar continuum model. This results in an average MgII equivalent width as a function of impact parameter from a galaxy, ranging from 50 kpc to more than 10 Mpc in proper units, which includes all MgII absorbers. We show that special care needs to be taken to use an unbiased quasar continuum estimator, to avoid systematic errors in the measurement of the mean stacked MgII equivalent width. The measured cross-correlation follows the expected shape of the galaxy correlation function, although measurement errors are large. We use the cross-correlation amplitude to derive the bias factor of MgII absorbers, finding bMgII = 2.33 \pm? 0.19, where the error accounts only for the statistical uncertainty in measuring the mean equivalent width. This bias factor is larger than that obtained in previous studies and may be affected by modeling uncertainties that we discuss, but if correct it suggests that MgII absorbers at redshift z \simeq 0:5 are spatially distributed on large scales similarly to the CMASS galaxies in BOSS. Keywords: galaxies: haloes, galaxies: formation, quasars: absorption lines, large-scale structure of universeComment: Accepted for publication to MNRAS. Accepted 2014 December 12. Received 2014 November 29; in original form 2014 February

Fungal Colonists of Maize Grain Conditioned at Constant Temperatures and Humidities

Fungal colonization of shelled maize (Pioneer 3320) harvested from a field near Furman, South Carolina, in 1992 was determined after 348 and 751 days of continuous storage at each of seven temperatures (10, 15, 20, 25, 30, 35, or 40°C) and four constant relative humidities, giving equilibrium grain moisture contents ranging from 9.4% to 17.5% m.c. in 28 grain conditioning environments. Twenty fungal species infected surface sterilized seeds and were recorded from these conditioned grain treatments, including species commonly found in preharvest maize [e.g. Acremonium zeae, Aspergillus flavus, Fusarium moniliforme (syn. F. verticillioides), Penicillium pinophilum (syn. P. funiculosum), etc.]. Eupenicillium cinnamopurpureum and Monascus ruber were recorded only from conditioned grain treatments. Eurotium chevalieri colonized 50-96% of the kernels from grain conditioning treatments with the highest moisture content for each incubation temperature. Grain samples with \u3e33% E. chevalieri infection had a decreased occurrence of F. moniliforme and A. zeae, and no kernels from these samples germinated. No fungi colonized more than 50% of the kernels conditioned at 30-40°C and 9.4-14.2% m.c. The results of this study indicate that individual patterns of fungal colonization during grain conditioning were a function of the survival rates for preharvest fungal colonists and their potential replacement by E. chevalieri

Mass growth and mergers: direct observations of the luminosity function of LRG satellite galaxies out to z=0.7 from SDSS and BOSS images

We present a statistical study of the luminosity functions of galaxies surrounding luminous red galaxies (LRGs) at average redshifts =0.34 and =0.65. The luminosity functions are derived by extracting source photometry around more than 40,000 LRGs and subtracting foreground and background contamination using randomly selected control fields. We show that at both studied redshifts the average luminosity functions of the LRGs and their satellite galaxies are poorly fitted by a Schechter function due to a luminosity gap between the centrals and their most luminous satellites. We utilize a two-component fit of a Schechter function plus a log-normal distribution to demonstrate that LRGs are typically brighter than their most luminous satellite by roughly 1.3 magnitudes. This luminosity gap implies that interactions within LRG environments are typically restricted to minor mergers with mass ratios of 1:4 or lower. The luminosity functions further imply that roughly 35% of the mass in the environment is locked in the LRG itself, supporting the idea that mass growth through major mergers within the environment is unlikely. Lastly, we show that the luminosity gap may be at least partially explained by the selection of LRGs as the gap can be reproduced by sparsely sampling a Schechter function. In that case LRGs may represent only a small fraction of central galaxies in similar mass halos.Comment: ApJ accepted versio

Prophylactic Laparoscopic Gastrectomy for Hereditary Diffuse Gastric Cancer: A Case Series in a Single Family

This study suggests that a laparoscopic approach for prophylactic total gastrectomy for carriers of CDH1 gene mutation can be performed safely and effectively

Treatment with an anti-CD11d integrin antibody reduces neuroinflammation and improves outcome in a rat model of repeated concussion

Background: Concussions account for the majority of traumatic brain injuries (TBI) and can result in cumulative damage, neurodegeneration, and chronic neurological abnormalities. The underlying mechanisms of these detrimental effects remain poorly understood and there are presently no specific treatments for concussions. Neuroinflammation is a major contributor to secondary damage following more severe TBI, and recent findings from our laboratory suggest it may be involved in the cumulative properties of repeated concussion. We previously found that an anti-CD11d monoclonal antibody that blocks the CD11d/CD18 integrin and adhesion molecule interaction following severe experimental TBI reduces neuroinflammation, oxidative activity, and tissue damage, and improves functional recovery. As similar processes may be involved in repeated concussion, here we studied the effects of the anti-CD11d treatment in a rat model of repeated concussion.Methods: Rats were treated 2 h and 24 h after each of three repeated mild lateral fluid percussion injuries with either the CD11d antibody or an isotype-matched control antibody, 1B7. Injuries were separated by a five-day inter-injury interval. After the final treatment and either an acute (24 to 72 h post-injury) or chronic (8 weeks post-injury) recovery period had elapsed, behavioral and pathological outcomes were examined.Results: The anti-CD11d treatment reduced neutrophil and macrophage levels in the injured brain with concomitant reductions in lipid peroxidation, astrocyte activation, amyloid precursor protein accumulation, and neuronal loss. The anti-CD11d treatment also improved outcome on tasks of cognition, sensorimotor ability, and anxiety.Conclusions: These findings demonstrate that reducing inflammation after repeated mild brain injury in rats leads to improved behavioral outcomes and that the anti-CD11d treatment may be a viable therapy to improve post-concussion outcomes. © 2013 Shultz et al.; licensee BioMed Central Ltd

More scanning, but not zooming, is associated with diagnostic accuracy in evaluating digital breast pathology slides.

Diagnoses of medical images can invite strikingly diverse strategies for image navigation and visual search. In computed tomography screening for lung nodules, distinct strategies, termed scanning and drilling, relate to both radiologists clinical experience and accuracy in lesion detection. Here, we examined associations between search patterns and accuracy for pathologists (N = 92) interpreting a diverse set of breast biopsy images. While changes in depth in volumetric images reveal new structures through movement in the z-plane, in digital pathology changes in depth are associated with increased magnification. Thus, drilling in radiology may be more appropriately termed zooming in pathology. We monitored eye-movements and navigation through digital pathology slides to derive metrics of how quickly the pathologists moved through XY (scanning) and Z (zooming) space. Prior research on eye-movements in depth has categorized clinicians as either scanners or drillers. In contrast, we found that there was no reliable association between a clinicians tendency to scan or zoom while examining digital pathology slides. Thus, in the current work we treated scanning and zooming as continuous predictors rather than categorizing as either a scanner or zoomer. In contrast to prior work in volumetric chest images, we found significant associations between accuracy and scanning rate but not zooming rate. These findings suggest fundamental differences in the relative value of information types and review behaviors across two image formats. Our data suggest that pathologists gather critical information by scanning on a given plane of depth, whereas radiologists drill through depth to interrogate critical features