Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Oncotype DX Recurrence Score by Histologic Types of Breast Carcinoma.

CONTEXT Oncotype DX (ODX) is a widely used commercial assay that estimates the risk of distant recurrence and may predict the benefit of chemotherapy in a subset of breast cancers. Some studies have shown the ability to predict Oncotype DX recurrence score (ODXRS), based on routinely reported pathologic features; however, there are limited data correlating specific histologic type of breast cancer to ODXRS. OBJECTIVE To compare ODXRS to specific histologic types of breast cancer. DESIGN One hundred eighty-four cases were sent for ODXRS testing and the results were compared with histologic type and grade. RESULTS The highest average ODXRS was seen in invasive ductal carcinoma with micropapillary features (29) followed by invasive ductal carcinoma not otherwise specified (mean = 19.4, SD = 11.6), invasive mucinous carcinoma (mean = 17.2, SD = 5.9), invasive lobular carcinoma (mean = 15.7, SD = 7.2), mixed ductal and lobular carcinoma (mean = 14.1, SD = 7.7), tubular carcinoma (10.0), and mixed ductal and mucinous carcinoma (mean = 8.0, SD = 4.2). Most tumors that had a high ODXRS were grade 3 invasive ductal carcinoma, representing 13 of a total of 20 cases (65%). Interestingly, 3 of the 4 cases of pure invasive mucinous carcinoma had an intermediate ODXRS. CONCLUSIONS Although the numbers are small, our findings raise further awareness of the significance between histologic type and grade, and RS in breast cancer. In some special histologic types of breast cancer, particularly those considered to follow either an excellent or poor clinical course by histology alone, it is unclear whether the ODXRS results are as meaningful as in carcinomas of no special type. Further investigation with higher numbers and outcome data is needed.
ZO Proteins Redundantly Regulate the Transcription Factor DbpA/ZONAB*

Background: ZO-1 overexpression inhibits DbpA/ZONAB overactivation, suggesting that ZO-1 sequesters DbpA at junctions. Results: Simultaneous depletion of ZO-1, ZO-2, and ZO-3 is required to decrease DbpA localization at junctions. Conclusion: The junctional localization of DbpA is regulated redundantly by ZO proteins. Significance: Clarifying how junctional transcription factors are regulated is essential to understand epithelial proliferation. The localization and activities of DbpA/ZONAB and YAP transcription factors are in part regulated by the density-dependent assembly of epithelial junctions. DbpA activity and cell proliferation are inhibited by exogenous overexpression of the tight junction (TJ) protein ZO-1, leading to a model whereby ZO-1 acts by sequestering DbpA at the TJ. However, mammary epithelial cells and mouse tissues knock-out for ZO-1 do not show increased proliferation, as predicted by this model. To address this discrepancy, we examined the localization and activity of DbpA and YAP in Madin-Darby canine kidney cells depleted either of ZO-1, or one of the related proteins ZO-2 and ZO-3 (ZO proteins), or all three together. Depletion of only one ZO protein had no effect on DbpA localization and activity, whereas depletion of ZO-1 and ZO-2, which is associated with reduced ZO-3 expression, resulted in increased DbpA localization in the cytoplasm. Only depletion of ZO-2 reduced the nuclear import of YAP. Mammary epithelial (Eph4) cells KO for ZO-1 showed junctional DbpA, demonstrating that ZO-1 is not required to sequester DbpA at junctions. However, further depletion of ZO-2 in Eph4 ZO-1KO cells, which do not express ZO-3, caused decreased junctional localization and expression of DbpA, which were rescued by the proteasome inhibitor MG132. In vitro binding assays showed that full-length ZO-1 does not interact with DbpA. These results show that ZO-2 is implicated in regulating the nuclear shuttling of YAP, whereas ZO proteins redundantly control the junctional retention and stability of DbpA, without affecting its shuttling to the nucleus.
Grid-based pavement crack analysis using deep learning

Pavement crack detected plays an important role in pavement maintenance. Image recognition is a traditional way for pavement crack detected. Recently, deep learning is a state-of-the-art method for target detection. CNN (convolutional neural network), a significant method in deep learning, is widely used in image target detection and brings about breakthroughs. However, CNN has not been applied to pavement crack detection. In this paper, we apply CNN to detect pavement crack and PCA (Principal Component Analysis) to classify the detected pavement cracks. Firstly, two databases are obtained by using two different scales of grid (32×32, 64×64) to segment pavement images. Each database has 30000 images for training set. We obtain two kinds of trained CNN. Each CNN is trained by one training set, which is part of each scale databases. We use trained CNN to detect the existence of pavement crack in corresponding scale grids. We confirm the scale of segment grid by comparing the results of pavement crack detected. Secondly, we only keep the grids containing crack and achieve the skeleton of crack in a pavement image. Lastly, we use PCA to analyse the skeleton of crack. The classification of crack can be obtained. The F-measure for crack detection is 94.7%. Meanwhile, the proposed method achieves 97.2%, 97.6% and 90.1% correct rate of classification for longitudinal crack, transverse crack and alligator crack, respectively. The results show proposed method can detect the pavement crack and evaluate the type of crack precisely.
The emerging epidemic of skin cancer

Summary A study of the incidence of skin cancer over a 14‐year period in the North Humberside area of the U.K. indicates a steady rise in the numbers of the four most common types of skin cancer. A steep increase in the incidence of squamous cell carcinoma of the skin compared with that of internal squamous cell carcinoma was also detected.
Characterization of antimicrobial photodynamic therapy-treated Streptococci mutans: an atomic force microscopy study.

UNLABELLED Abstract Objective: The aim of the present study was to examine the size and shape of Streptococcus mutans bacterial cells of infected dentin substrate subjected to photodynamic therapy (PDT) using atomic force microscopy (AFM). BACKGROUND DATA New trends in the application of AFM have been developed in the field of dentistry, making AFM a useful technique in high resolution imaging of biological structures and processes. MATERIALS AND METHODS PDT was completed using an efficient light-emitting diode source (LED - λ=620-660 nm) with total light dose of 94 J/cm(2) in the presence of the photosensitizer toluidine blue O (TBO). Dentin specimens were immersed in brain heart infusion (BHI) broth inoculated with S. mutans for 5 days to induce caries in vitro. After demineralization, the samples were subjected to a series of treatments in which carious dentin infected by S. mutans was exposed to 0.9% sodium chlorite (NaCl) solution (control) for 10 min, or subjected to PDT-TBO photosensitizer followed by light exposure (energy density of 94 J/cm(2)). RESULTS Three-dimensional (3-D) images and cross-sectional measurements showed rod and diplococcic cell shapes. Photoinactivated bacterial cells did not differ from the control with respect to their cross-sectional shape, but they did show a reduction in size. CONCLUSIONS Photodynamic therapy decreased the diameter of S. mutans cells and AFM may be used as a technique for bacterial cell analysis.
Evaluation of a Partnership Approach to Translating Research on Breast Cancer and the Environment

Background: The growing literature on community-based participatory research (CBPR) suggests that a participatory approach benefits science in important ways. However there have been few formal evaluations of a CBPR approach itself, and few standards developed to assist in such efforts. Objectives: This evaluation used CBPR guidelines developed by Green and colleagues to evaluate the participatory approach of the Community Outreach and Translation Core (COTC) of the Bay Area Breast Cancer and the Environment Research Center (BABCERC) in translating scientific findings from two key projects to the public. Method: To assess key stakeholders’ perceptions of alignment between the projects and the guidelines, four COTC members, four researchers, and four community members rated the projects on each of the 26 guidelines. These data were triangulated with transcripts from interviews with the same participants and a focus group with a subset of the participants. Results: The participatory approach by the COTC resulted in many important benefits including improved relationships among diverse stakeholders, knowledge generation, increased sensitivity and propriety of the research, and increased community support of research. However, several atypical features of this collaboration—for example, the basic and etiological nature of the science being undertaken, and the multiple communities (lay and activist/advocate) involved—resulted in different levels and qualities of participation among stakeholders. Conclusions: Further research should focus on the adaptation of participatory research principles for different kinds of community partners and on the development and refinement of standards and tools to assist in evaluating the process and outcome of participatory research.
Integrating copper toxicity and climate change to understand extinction risk to two species of pond-breeding anurans.

Chemical contamination is often suggested as an important contributing factor to amphibian population declines, but direct links are rarely reported. Population modeling provides a quantitative method to integrate toxicity data with demographic data to understand the long-term effects of contaminants on population persistence. In this study we use laboratory-derived embryo and larval toxicity data for two anuran species to investigate the potential for toxicity to contribute to population declines. We use the southern toad (Anaxyrus terrestris) and the southern leopard frog (Lithobates sphenocephalus) as model species to investigate copper (Cu) toxicity. We use matrix models to project populations through time and quantify extinction risk (the probability of quasi-extinction in 35 yr). Life-history parameters for toads and frogs were obtained from previously published literature or unpublished data from a long-term (>35 yr) data set. In addition to Cu toxicity, we investigate the role of climate change on amphibian populations by including the probability of early pond drying that results in catastrophic reproductive failure (CRF, i.e., complete mortality of all larval individuals). Our models indicate that CRF is an important parameter for both species as both were unable to persist when CRF probability was >50% for toads or 40% for frogs. Copper toxicity alone did not result in significant effects on extinction risk unless toxicity was very high (>50% reduction in survival parameters). For toads, Cu toxicity and high probability of CRF both resulted in high extinction risk but no synergistic (or greater than additive) effects between the two stressors occurred. For leopard frogs, in the absence of CRF survival was high even under Cu toxicity, but with CRF Cu toxicity increased extinction risk. Our analyses highlight the importance of considering multiple stressors as well as species differences in response to those stressors. Our models were consistently most sensitive to juvenile and adult survival, further suggesting the importance of terrestrial stages to population persistence. Future models will incorporate multiple wetlands with different combinations of stressors to understand if our results for a single wetland result in a population sink within the landscape.
The dependencies of fronto‐parietal BOLD responses evoked by covert visual search suggest eye‐centred coding

Visual scenes explored covertly are initially represented in a retinal frame of reference (FOR). On the other hand, ‘later’ stages of the cortical network allocating spatial attention most probably use non‐retinal or non‐eye‐centred representations as they may ease the integration of different sensory modalities for the formation of supramodal representations of space. We tested if the cortical areas involved in shifting covert attention are based on eye‐centred or non‐eye‐centred coding by using functional magnetic resonance imaging. Subjects were scanned while detecting a target item (a regularly oriented ‘L’) amidst a set of distractors (rotated ‘L's). The array was centred either 5° right or left of the fixation point, independent of eye‐gaze orientation, the latter varied in three steps: straight relative to the head, 10° left or 10° right. A quantitative comparison of the blood‐oxygen‐level‐dependent (BOLD) responses for the three eye‐gaze orientations revealed stronger BOLD responses in the right intraparietal sulcus (IPS) and the right frontal eye field (FEF) for search in the contralateral (i.e. left) eye‐centred space, independent of whether the array was located in the right or left head‐centred hemispace. The left IPS showed the reverse pattern, i.e. an activation by search in the right eye‐centred hemispace. In other words, the IPS and the right FEF, members of the cortical network underlying covert search, operate in an eye‐centred FOR.
Counterproductive Work Behaviours in an Organization and Their Measurement upon the Example of Research Conducted among Employees in the Public Administration Sector in Poland

The article discusses primarily the issues of counterproductive work behaviour in the organization. The author focused on measurement of such behaviours using one of the most frequently used scale to measure these behaviours (Counterproductive Work Behaviour Checklist; CWB-C). The aim of the article was also to present preliminary results of a research conducted in 2016 using CWB-C among employees of local government units in Poland. The results show that the scale of involvement of employees is small and the behaviours are rather directed against the organization than the co-workers or supervisors. What is more, they are less serious rather than serious abuses.
Automatic repositioning of MRSI voxels in longitudinal studies: Impact on reproducibility of metabolite concentration measurements

To study an automatic repositioning method to reduce variability in longitudinal MRSI exams based on a priori image registration. Longitudinal proton MR spectroscopic imaging (1H MRSI) exams to study the effects of disease or treatment are becoming increasingly common. However, one source of variability in such exams arises from imperfect relocalization of the MRSI grid in the follow‐up exams.
Usefulness of tacrolimus for refractory adult-onset still's disease: Report of six cases

Six patients with refractory adult-onset Still's disease (AOSD) were treated with tacrolimus (TAC). Patient 1 was pregnant, for whom high-dose corticosteroid (CS) monotherapy did not achieve clinical remission, whereas TAC concomitant with CS was successful, and her baby had no apparent abnormalities. Patient 2 had hemophagocytic syndrome (HPS), for whom high-dose CS monotherapy did not achieve clinical remission, whereas TAC improved HPS, and a complete clinical remission was achieved with concomitant administration of TAC and methotrexate (MTX) with CS. Cases 3–5 could not have reduced CS doses due to repeated recurrences and other disease-modifying antirheumatic drugs, including MTX, Cyclosporine A, and tumor necrosis factor alpha inhibitors, did not control disease activity. TAC administration allowed for reduced CS doses. Case 6 experienced adverse effects, and TAC was discontinued due to elevated serum creatinine and potassium levels. TAC was useful for five of six patients, which suggests it as an option for refractory AOSD.
Calcified carotid artery plaques predict cardiovascular outcomes in the elderly

Background: Identifying plaque composition using ultrasound may aid in stratifying patients at high risk for cardiovascular disease (CVD). Calcification is an integral part of plaque progression and may contribute to plaque vulnerability. We investigated the ability of calcified carotid plaques identified using carotid ultrasound to predict cardiovascular outcomes in older adults. Methods: Participants included 187 hypertensive and 187 normotensive adults undergoing a duplex scan to identify the presence of calcified carotid plaques. Hypertensive participants received either blood pressure treatment or placebo, and all participants were followed for incident cardiovascular events and death for a maximum of 11 years. Results: The untreated hypertensive group was significantly associated with a higher time-to-any CVD event [relative risk (RR) 2.97, 95% confidence interval (CI) 2.03–4.35, P < 0.0001] and mortality (RR 3.11, 95% CI 1.92–5.04, P < 0.0001) when compared to the normotensive group. Participants with calcified carotid plaques had higher cardiovascular event rates (RR 6.22, 95% CI 1.97–19.6, P = 0.0018) and mortality (RR 6.30, 95% CI 1.55–25.7, P = 0.010) when compared to those without plaque. After controlling for age, male sex, blood pressure status, glucose, and IMT, the presence of calcified carotid plaques remained predictive of CVD events (RR 2.35, 95% CI 1.5–3.8, P = 0.0005) and mortality (RR 2.72, 95% CI 1.4–5.2, P = 0.0021). Conclusion: Calcified carotid plaques may predict mortality and cardiovascular outcomes independent of traditional CVD risk factors and may serve as an additional CVD risk assessment in the elderly.
EXPERIMENTAL TRANSMISSION OF ENTEROMYXUM SCOPHTHALMI (MYXOZOA), AN ENTERIC PARASITE OF TURBOT SCOPHTHALMUS MAXIMUS

Several experiments were designed to elucidate the modes of transmission of the myxozoan parasite Enteromyxum scophthalmi to turbot Scophthalmus maximus. Direct transmission of the infections was achieved by cohabitation of infected and test fish, through waterborne contamination from the effluent of a tank containing infected fish, and via the oral route using parasite-infected intestines. The transmission of the turbot enteromyxosis was successful in all the fish exposed to the parasite by the 3 routes; accumulated mortality reached 100% at the end of most experiments. The progress of the infections was monitored by study of the histopathology. Influence of the mode of exposure was observed, with the oral route the fastest to initiate the parasite infections. The temperature also affected the course of the infections, which were established earlier at higher water temperature. Direct fish-to-fish transmission of the disease explains the rapid spreading of the turbot enteromyxosis in farms.
Exploiting 3D geometric primitives for multicamera pedestrian detection

In this paper, we present an approach for multicamera pedestrian detection exploiting the concepts of multiview geometry and the shapes of 3D geometric primitives. Multicamera occupancy maps provide peak responses corresponding to the object detection but suffer from several false detections known as ghosts. The novelty of this paper is the introduction of shape patterns which can model the objects, such as pedestrians, by defining a kernel function in the projected occupancy space. This kernel depends upon the geometry of the 3D primitives and also varies in relation to their position with respect to the cameras in the real world configuration. For multiple objects visible across several cameras, we define a formation model which is the convolution of this spatially varying kernel with the set of possible object locations. The locations corresponding to detections can thus be obtained through a deconvolution process. For efficient computations, we further propose an estimated deconvolution process specific to our kernel responses which can also be heavily parallelized. We show the application of this process towards pedestrian detection by studying various 3D cylindrical primitives. Experiments on two public dataset sequences, including comparison with another approach, show the efficiency of the proposed method in terms of pedestrian detection and ghost pruning, including in adverse and challenging conditions.
Global Environmental Education using Squeak and Field Servers

We are promoting projects in combination with Squeak eToys, visual programming software for children and Field Server, remote monitoring system for edible vegetation. We developed a Squeak interface with Field Servers, the remote environment monitoring equipments developed by the National Agricultural Research Center of Japan and installed throughout the world. The interface allows children to create Squeak eToys Programs easily that can monitor remote environment. We are preparing an educational program that encourage children to develop such Squeak eToys Programs and to discuss environmental issues with overseas peers using Picton, the picture language developed by Pangaea, the Japan-based nonprofit activity. Our project is backed by the Japanese Ministry of Education, Culture, Sports, Science and Technology.
Gaussian mixture models improve fMRI-based image reconstruction

New computational models have made it possible to reconstruct perceived images from BOLD responses in visual cortex. We expand a linear Gaussian framework for percept decoding with Gaussian mixture models to better represent the prior distribution of images. In our setup, different mixture components correspond to different letter categories. Our framework not only leads to more accurate reconstructions, but also automatically infers semantic categories from low-level visual areas of the human brain.
OrganDots – an organotypic 3D tissue culture platform for drug development

Introduction: There is an urgent need for preclinical testing systems that more accurately reflect responses in human target organs. The use of ex vivo tissues taken out of the human body and kept alive for sufficient time to perform testing has until recently been limited by tissue availability and by the length of time tissues can be kept alive outside the body, however, recent advances in tissue handling and tissue culture techniques have now made it possible to envisage using such tissues for drug discovery on a scale that is of value for the evaluation of compounds prior to testing in humans. Areas covered: The article presents a method for generating 3D microtissues at the air–liquid interface ‘OrganDots’ which are formed by reaggregating primary tissues or stem cell-based material which may be useful in drug discovery and development. The article compares this method with other methods for obtaining ex vivo tissues and looks at their uses as surrogates to testing compounds in humans. Expert opinion: Reconstituting tissues in vitro has now reached a point where they can be used to profile the activity of compounds prior to in vivo testing. The ability to reconstitute tissues from primary material and the ability to synthesize new tissues in vitro from stem cells may lead to new testing systems that better reflect human pathophysiology and may allow individual differences to be expressed in vitro. These new drug testing systems should lead to more predictable in vitro drug testing systems in the near future.