Miracle-dz/UniFAR-FTUs huggingface dataset:
Semantic Segmentation of Brain Tumors in MRI Data Without any Labels

Brain MR images are one of the most important instruments for diagnosing neurological disorders such as tumors, infections or trauma. In particular, grade I-IV brain tumors are a well-studied subject for supervised deep learning approaches. However, for a clinical use of these approaches, a very large annotated database that covers all of the occurring variance is necessary. As MR scanners are not quantitative, it is unclear how good supervised approaches, trained on a speciﬁc database, will actually perform on a new set of images that may stem from a yet other scanner. We propose a new method for brain tumor segmentation, that can not only identify abnormal regions, but can also delineate brain tumors into three characteristic radiological areas: The edema, the enhancing core, and the non-enhancing and necrotic tissue. Our concept is based on FLAIR and T1CE MRI sequences, where abnormalities are detected with a variational autoencoder trained on healthy examples. The detected areas are ﬁnally postprocessed via Gaussian Mixture Models and ﬁnally classiﬁed according to the three deﬁned labels. We show results on the BraTS2018 dataset and compare these to previously published unsupervised segmentation results as well as to the results of the BraTS challenge 2018. Our developed unsupervised anomaly detection approach is on par with previously published methods. Meanwhile, the semantic segmentation - a new and unique model - shows encouraging results.
Generalized Sparse Convolutional Neural Networks for Semantic Segmentation of Point Clouds Derived from Tri-Stereo Satellite Imagery

We studied the applicability of point clouds derived from tri-stereo satellite imagery for semantic segmentation for generalized sparse convolutional neural networks by the example of an Austrian study area. We examined, in particular, if the distorted geometric information, in addition to color, influences the performance of segmenting clutter, roads, buildings, trees, and vehicles. In this regard, we trained a fully convolutional neural network that uses generalized sparse convolution one time solely on 3D geometric information (i.e., 3D point cloud derived by dense image matching), and twice on 3D geometric as well as color information. In the first experiment, we did not use class weights, whereas in the second we did. We compared the results with a fully convolutional neural network that was trained on a 2D orthophoto, and a decision tree that was once trained on hand-crafted 3D geometric features, and once trained on hand-crafted 3D geometric as well as color features. The decision tree using hand-crafted features has been successfully applied to aerial laser scanning data in the literature. Hence, we compared our main interest of study, a representation learning technique, with another representation learning technique, and a non-representation learning technique. Our study area is located in Waldviertel, a region in Lower Austria. The territory is a hilly region covered mainly by forests, agriculture, and grasslands. Our classes of interest are heavily unbalanced. However, we did not use any data augmentation techniques to counter overfitting. For our study area, we reported that geometric and color information only improves the performance of the Generalized Sparse Convolutional Neural Network (GSCNN) on the dominant class, which leads to a higher overall performance in our case. We also found that training the network with median class weighting partially reverts the effects of adding color. The network also started to learn the classes with lower occurrences. The fully convolutional neural network that was trained on the 2D orthophoto generally outperforms the other two with a kappa score of over 90% and an average per class accuracy of 61%. However, the decision tree trained on colors and hand-crafted geometric features has a 2% higher accuracy for roads.
Evaluation of sanitizers for their efficacy in killing Bacillus cereus, Bacillus thuringiensis, and Pseudomonas

The ability of pathogenic and spoilage organisms to survive and grow on foods and foodcontact surfaces raises interest in evaluating the lethality of sanitizers commonly used in the food industry. Chlorine, chlorine dioxide, a peroxyacetic acid-based sanitizer, and a commercial produce sanitizer were evaluated for their effectiveness in killing Bacillus cereus, Bacillus thuringiensis, and Pseudomonas. The sensitivity of B. cereus and B. thuringiensis spores to sanitizers was similar. Treatment of Bacillus spores in suspension with chlorine dioxide followed by heat treatment significantly increased lethality. The effectiveness of chlorine dioxide was significantly reduced when cells or spores were suspended in 0.5% horse serum and spot-inoculated on coupons. Chlorine was effective in killing cells and spores spot-inoculated on coupons but when combined with the commercial produce sanitizer, the lethality was significantly reduced. Chlorine and chlorine dioxide were equally effective in killing Bacillus spores on apples. INDEX WORDS: Chlorine, chlorine dioxide, peroxyacetic acid-based sanitizer, commercial produce sanitizer, sublethal heat treatment, spores, Bacillus cereus, Bacillus thuringiensis, Pseudomonas, stainless steel, apples, dishwashing detergent EVALUATION OF SANITIZERS FOR THEIR EFFICACY IN KILLING BACILLUS CEREUS, BACILLUS THURINGIENSIS, AND PSEUDOMONAS
MedUse: A Visual Analysis Tool for Medication Use Data in the ABCD Study

The RxNorm vocabulary is a yearly-published biomedical resource providing normalized names for medications. It is used to capture medication use in the Adolescent Brain Cognitive Development (ABCD) study, an active and publicly available longitudinal research study following 11,800 children over 10 years. In this work, we present medUse, a visual tool allowing researchers to explore and analyze the relationship of drug category to cognitive or imaging derived measures using ABCD study data. Our tool provides position-based context for tree traversal and selection granularity of both study participants and drug category. Developed as part of the Data Exploration and Analysis Portal (DEAP), medUse is available to more than 600 ABCD researchers world-wide. By integrating medUse into an actively used research product we are able to reach a wide audience and increase the practical relevance of visualization for the biomedical ﬁeld.
Testing a Smartphone App (Young with Diabetes) to Improve Self-Management of Diabetes Over 12 Months: Randomized Controlled Trial

Background Young people often struggle to self-manage type 1 diabetes during the transition from childhood to adulthood. Mobile health (mHealth) apps may have the potential to support self-management, but evidence is limited and randomized controlled trials are needed. Objective We assessed whether the mHealth app “Young with Diabetes” improved young people’s self-management measured by glycated hemoglobin (HbA1c) and three self-reported psychometric scales. Methods Young people (14-22 years) with inadequate glycemic control and their parents were enrolled in a randomized controlled trial and assigned either to Young with Diabetes and usual care (Young with Diabetes group) or to usual care alone (control). Young with Diabetes use was monitored; functions included a chat room, contact the health care provider, reminders, tips, information about the diabetes department and type 1 diabetes topics, carbohydrate counting, and a parents’ section. Outcomes included HbA1c and three self-reported psychometric scales: Perceived Competence in Diabetes Scale; Health Care Climate Questionnaire; and Problem Areas In Diabetes care survey. Data were collected at baseline and at 2, 7, and 12 months. Results A total of 151 young people were randomized (Young with Diabetes group=76, control=75) and 49 parents agreed to participate. At 12 months, HbA1c was significantly higher (4.1 mmol/mol; 0.4 %) in the Young with Diabetes group, compared to the control group (P=.04); this finding did not occur when comparing app users (Young with Diabetes use ≥5 days) with nonusers. Young people used Young with Diabetes on a mean of 10.5 days. They spent the most time chatting about alcohol and searching for information about sex. Most young people and half of the parents reported that Young with Diabetes helped them. More than 80% would recommend Young with Diabetes to peers. Conclusions Young with Diabetes did not improve HbA1c, but it may be a useful complement to self-management. Qualitative evaluation is needed to explore benefits and shortcomings of Young with Diabetes. Health care providers should address young peoples’ knowledge about sensitive topics, provide them with peer support, and be aware of parents’ need for information about how to support Trial Registration ClinicalTrials.gov NCT02632383; https://clinicaltrials.gov/ct2/show/NCT02632383 (Archived by WebCite at http://www.webcitation.org/6zCK2u7xM)
Examining the Adoption and Abandonment of Security, Privacy, and Identity Theft Protection Practices

Users struggle to adhere to expert-recommended security and privacy practices. While prior work has studied initial adoption of such practices, little is known about the subsequent implementation and abandonment. We conducted an online survey (n=902) examining the adoption and abandonment of 30 commonly recommended practices. Security practices were more widely adopted than privacy and identity theft protection practices. Manual and fully automatic practices were more widely adopted than practices requiring recurring user interaction. Participants' gender, education, technical background, and prior negative experience are correlated with their levels of adoption. Furthermore, practices were abandoned when they were perceived as low-value, inconvenient, or when users overrode them with subjective judgment. We discuss how security, privacy, and identity theft protection recommendations and tools can be better aligned with user needs.
Involvement of Cell Surface Carbohydrates in the Sexual Cell Fusion of Dictyostelium discoideum

In order to analyze the molecular mechanism of sexual cell fusion between cells of HM1 and NC4 (opposite mating type strains in Dictyostelium discoideum), monoclonal antibodies were raised against partially‐purified gp 70, a fusion‐related protein of HM1 cells. The antibodies were screened for activity to inhibit cell fusion and 9 hybridoma clones were obtained. One of the fusion‐blocking monoclonal antibodies, mAb1G7, was used for further analysis. It recognized nearly ten bands in an immunoblot of fusion competent HM1 cells, but no bands when HM1 membrane proteins had been deglycosylated. These results suggest the importance of carbohydrates in the cell fusion process. To confirm this possibility, effects of sugars or lectins on cell fusion were examined. Although inhibition by the sugars was incomplete, Con A, WGA, LCA, strongly inhibited cell fusion. Furthermore, tunicamycin inhibited the acquisition of fusion competence in HM1 cells, indicating the importance of N‐linked glycosylation of proteins in cell fusion. All above results suggest that N‐linked carbohydrates on HM1 cell surface are involved in the sexual cell fusion of D. discoideum.
Barriers and Facilitators to Cervical Cancer Prevention in Mbuji-Mayi, Democratic Republic of Congo: A Qualitative Study

Background: Cervical cancer is undoubtedly a worrying public health problem, the heaviest burden of which is borne by developing countries such as the Democratic Republic of Congo. These countries are still struggling to put in place coherent programs capable of reducing the incidence of the disease because of the many challenges they face. The present study aims to document the knowledge, attitudes and practices of women and healthcare workers in Mbuji-Mayi on cervical cancer in order to plan educational needs. Methods: We opted for a descriptive qualitative approach by focus groups around the three main themes (knowledge, attitudes and practices) and by individual interviews with a semi-structured questionnaire around the same themes. Results: Knowledge of cervical cancer was poor in the community (women interviewed). The nurses were mainly informed on a few aspects of the disease. The practitioners had acceptable theoretical knowledge, but the practice remained very rudimentary. An attitude of resignation with sometimes superstitious and supernatural considerations was observed regarding the disease by the community (women interviewed). Conclusion: The practice of prevention, whether primary or secondary, against cervical cancer was almost nonexistent in Mbuji-Mayi.
Association between Diabetic Neuropathy and Neutrophil Lymphocyte Ratio amongst Type 2 Diabetics

Original Research Article Background: The study aimed to evaluate the relationship between Diabetic neuropathy and neutrophil lymphocyte ratio amongst patients with type 2 diabetes. Methodology: The study was conducted as a cross sectional study in outpatient Department of Medicine, Hamidia Hospital Bhopal for a period of 6 months. All the 100 known cases of type 2 diabetes belonging to age group of 18 to 80 years and giving consent were included in the study. Detailed data regarding sociodemographic variables, diabetes duration and treatment was obtained and entered in questionnaire. Height, weight, BMI was recorded. CBC, FBS, PPBS and HbA1c was also conducted. Results: The present study observed no statistically significant association between various baseline variables and Neutrophil to lymphocyte ratio (p>0.05). Neutrophil to lymphocyte ratio were significantly associated with duration of diabetes and presence of neuropathy i.e. NLR were significantly higher in patients with neuropathy and patients with longer duration of diabetes (p<0.05). Diabetic neuropathy was observed to be significantly correlated with neutrophil to lymphocyte ratio and duration of diabetes (p<0.01). Conclusion: Higher neutrophil to lymphocyte ratio may be considered as a prognostic indicator of diabetic neuropathy. This is a cost effective marker that is easily available and can be used in community settings as well as resource poor settings.
EFFECT OF EXTRAORAL AGING CONDITIONS ON MECHANICAL PROPERTIES OF FACIAL SILICONE ELASTOMER REINFORCED WITH TITANIUM-OXIDE NANOPARTICLES (IN VITRO STUDY)

Introduction: Investigators have been searching for ideal maxillofacial prosthetic materials in order to gain patient acceptance and can be fabricated easily in the dental setting. Objectives: To evaluate the influence of adding different concentrations of titanium oxide nanoparticles (TiO2 NPs) on the mechanical properties of facial silicone elastomer (SE) after different extra-oral aging methods. Materials and methods: TiO2 nanoparticles were mixed with MED-4210 maxillofacial silicone elastomer at 1.5 %, 2% and 2.5 % weight percentage (w/w). Unmodified silicone was served as control group. Each of the above groups were evaluated to mechanical properties before aging conditions. Control & 2.5% nano-TiO2 silicone elastomers groups were subjected to six equal aging conditions groups as follow. Dry storage in dark for 6 months, storage in simulated sebum solution for 6 months, storage in simulated acidic perspiration for 6 months, accelerated artificial daylight weathering for 360 hours, storage in antimicrobial silicone-cleaning solution for 30 hours and mixed aging of sebum under UV light for 360 hours. After aging exposures, they were evaluated to the mechanical properties. Data were analyzed using the Kolmogorov-Smirnov test, F-test (ANOVA) and Post-hoc pair-wise test. Results:TiO2 nanoparticles addition improved the mechanical properties in terms of tensile strength and percentage elongation, tear strength and shore A hardness of MED-4210 maxillofacial silicon elastomer before and after extra-oral aging conditions (P < 0.05). Pair-wise comparison between control group and 2.5% nano-TiO2 silicone elastomers composite exhibited significant differences according to the mechanical properties after aging. Conclusions: Reinforcement of MED-4210 maxillofacial silicon elastomer with TiO2 nanoparticles introduces a favorable material with physical and anti-ageing properties in our in vitro study.
Effects of foliar and root application of epsom salt on aquaponics beetroot (Beta vulgaris) production in confined condition

The study was conducted to evaluate the impact of epsom salt, rich in magnesium and sulfur content beneficial to plant, on beetroot production in aquaponics system. Media based aquaponics systems (nine units) were employed for beetroot and tilapia culture where three treatments T1, T2 and T0 were applied with three replications (R1, R2, and R3) each. Epsom salt was applied in T1 as foliar spray in the form of 5% solution in each replication, whereas same amount of epsom salt (5 g) was directly applied on vegetable bed in T2 as root application. But in control (T0) no epsom salt was used. Beetroot saplings were planted in retrospect at a rate of two saplings per growbed (replication). After thirty days, plants grew enough to support the water clarification in aquaponics, ten tilapia fry were stocked per tank (90 L) in each replication. Fish were fed commercial floating feed containing 30% protein. Although the fish growth parameters in three treatments were statistically similar, the highest mean length gain, weight gain, specific growth rate and fish production were found 5.11±1.64 cm, 30.16±0.11 g, 0.39±0.01 %/day and 26.27±2.47 tons/ha/60 days respectively in T1 followed by T2 and T0. However, response of beetroots to different treatments was statistically different. The highest average leaf area (69.79 ± 0.48 cm), length of root (31.03±0.43 cm), weight of root (21.17±1.92 g), and production of beetroot 8.67±1.54 tons/ha/90 days were found in T1 followed by T2 and T0. Harvesting time was also reduced in epsom salt based aquaponics system. The overall production of beetroot and tilapia was higher in T1 (foliar spray) than T2 (root application) and T0 (control). Thus, the study signifies the potentialities of epsom salt in aquaponics vegetable production. However, further research is needed to verify the dose response to epsom salt in aquaponics system.
Responses of pomegranates to ethylene treatment and storage temperature

Almost all 'the commercial production of pomegranates in the United States is in California. The fruit is large, deep purple-red in color, and glossy in appearance, and the edible portion, the pulp around each seed (aril), is eaten fresh or used in making juice, jelly, grenadine, and wine. Harvesting of the most widely grown cultivar of pomegranate, Punica granatum 'Wonderful', usually begins in the middl ptember and continues unti1 m'd-Oct ber. Currently used indices of 0 um maturity are titratable acidity (less than 1.85 percent acid content) and intensity of red color of the juice. Pomegranates may be stored for several weeks to extend their marketing season, but very little information is available on their postharvest physiology and optimum storage conditions. Our objectives were to investigate responses of pomegranates to ethylene treatments and to storage temperature and duration. During the 1979 to seasons, we obtained fruits of t 'Wonderful' ltivar from a packinghou a indsay, California. We used medium-size (about 230-gram) fruits in all experiments except when investigating the relationship between fruit size and composition. Respiration and ethylene production were measured on five individual fruits (replicates) per treatment. Studies of weight loss, compositional changes, and chilling injury used three replicates of five fruits each per treatment. Quality evaluations included external skin color as well as color, soluble solids content, pH, and titratable acidity of the juice extracted from the arils.
Reframing water governance praxis: Does reflection on metaphors have a role?

Action for adaptation is needed in the face of anthropogenic climate change. The record of adaptation in the field of freshwater governance is poor to date, as it is apparently constrained by operational frameworks. Analyses based on the Contemporary Theory of Metaphor can reveal underlying, often institutionally reified, operational frameworks. We present a desktop metaphor mapping study of one UK and one Australian water management planning document. This mapping demonstrates the potential of metaphor analysis, with further methodological and praxis development, to support the new ways of thinking and acting that are needed to challenge deeply held social and cultural norms of linear, rather than systemic, causality. We suggest that metaphor has the potential to help practitioners expose and examine reified operational frameworks and practices, and to change those that hinder adaptive and systemic praxis.
Diagnostic value of contrast enhanced computed tomography in detection of renal sinus fat invasion in renal cell carcinoma patients taking histopathology as gold standard

Introduction: Renal sinus fat invasion is one of the most common stage T3a finding in renal cell carcinoma. The detection of renal sinus fat invasion is important as it is helps in planning the treatment modality. Multidetector contrast enhancement CT scan is one of the most common modalities used for staging purpose in RCC. Objective: In our study we aim to determine the diagnostic value of multidetector CT scan in in detection of renal sinus fat invasion in RCC patients taking histopathology as gold standard. Material and Methods: All the patients with diagnosed RCC (stage T1a, T1b, T2 and T3a) were included in our study. The preoperative CT scans of all the patients were assessed for the presence of renal sinus fat invasion by two experienced radiologists. The results were evaluated for sensitivity, specificity, positive and negative predictive value taking histopathology as gold standard. Results: A total 143/284 (51.4%) patients were at stage T3a out of which renal sinus fat invasion was seen in 117/143 (82%) patients. The multidetector enhancement Ct scan findings for renal sinus fat invasion by two radiologists depicted a mean sensitivity of 88%, specificity 73%, 52% positive predictive value and 95% negative predictive value. The size, laterality and polarity did not show a significant correlation (p>0.05) Conclusion: MDCT is a useful tool in the exclusion of renal sinus fat invasion owing to its high negative predictive value. Although it has a good sensitivity for renal sinus fat involvement however due to low specificity and positive predictive value it cannot be totally relied upon for invasion. Other factors like size, irregular tumor margins, nodular enhancement of renal sinus fat and location of tumor lesion should also be correlated.
Light reacclimatization of lower leaves in C4 maize canopies grown at two planting densities

C4 plants have high photosynthetic capacity but are inefficient under low light. In a canopy, lower leaves developed under high light are progressively shaded. To elucidate how lower leaves in a C4 canopy reacclimatize to low light, we investigated maize canopies differing in light environment grown at standard and low planting densities (SPD, LPD). Although upper leaves at SPD and both upper and lower leaves at LPD had light-response curves of photosynthesis of sun leaves, lower leaves at SPD had that of shade leaves. All leaves at both densities had anatomical framework of sun leaves, but the chloroplast content in mesophyll and bundle-sheath cells of lower leaves at SPD was greatly reduced to reacclimatize to low light. This study demonstrates that lower leaves at SPD reacclimatize to low light by adjusting their physiological and chloroplast traits while maintaining anatomical framework, whereas those at LPD behave as sun leaves.