Miracle-dz/UniFAR-FTUs huggingface dataset:
Food Weight Estimation using Smartphone and Cutlery

In this era of Internet of Things (IoT), the healthcare system is one of the fields that has received a lot of attention from researchers. Daily-life things and objects such as mobile phones, watches, or shoes are coupled with sensors to make health systems for monitoring, and managing people heath. Recently, some methods have been focused on using food photography and associated image-processing techniques to assess food nutrients to control calorie intake. However, one of the critical issues in such image-based dietary assessment tools is the accuracy and consistent estimation of the sizes and weights of the food portion in the image. In this paper, we propose a system that uses eating tools (cutlery) such as spoon, fork or chopsticks to measure the weight of a food in a picture, in order to estimate the calorie content of that food, for diet assessment and obesity prevention. Our system requires the user to take only a single image from the top with the cutlery in the picture. Using several image processing techniques and the EXIF metadata of the image, the system automatically estimates the diameter and the height of the food container and derives the food volume. Then, given the food type, the system combines the information about the container diameter, height and the food type to provide the weight of the food in the image. Our experiments show tenable results from the system which achieved an average relative error rate of 6.87% for the weight estimation, over the testing food images.
Quick WAVE Screener: A Tool to Address Weight, Activity, Variety, and Excess

t lack of time is a potential barrier that may prevent primary care providers from addressing nutrition and physical activity with their patients who are at risk for or have diabetes. The acronym WAVE was developed to represent key themes (weight, activity, variety, and excess) that need to be addressed to combat the increasing obesity rates and concomitant increase in diabetes, cardiovascular disease, and other obesity-related health problems.
In-hospital mortality following surgical lung biopsy for interstitial lung disease in the USA : 2000-2011

Rationale: Surgical lung biopsy can help to determine a specific diagnosis in interstitial lung disease, but has associated risks. Most currently available mortality data are derived from case series and may not be generalizable to broader populations. Objectives: We aimed to assess in-hospital mortality following surgical lung biopsy for interstitial lung disease in a national secondary care dataset from the United States. Methods: Data were obtained from the 2000-2011 Nationwide Inpatient Sample. Cases were identified using International Classification of Diseases (ICD-9-CM) codes for interstitial lung disease and surgical lung biopsies. Lung resections and cases of lung cancer were excluded. Weighted data were used to estimate numbers of biopsies nationwide and in-hospital mortality, and multivariable logistic regression was used to adjust for sex, age, geographic region, co-morbidity, type of operation and provisional diagnosis. Measurements and Main Results: We estimated there to be around 12,000 surgical lung biopsies performed annually for interstitial lung disease in the United States, two-thirds of which were performed electively. In-hospital mortality was 1.7% for elective procedures, but significantly higher for non-elective procedures (16.0%). Male sex, increasing age, increasing co-morbidity, open surgery and a provisional diagnosis of idiopathic pulmonary fibrosis or connective tissue disease related interstitial lung disease were risk factors for increased mortality.
Low humoral responses to human cytomegalovirus is associated with immunological treatment failure among HIV infected patients on highly active antiretroviral therapy

Human cytomegalovirus (HCMV) is one of the opportunistic infections associated with significant morbidity and mortality among HIV/AIDS patients especially before introduction of antiretroviral therapy (ART). Little is known regarding the humoral immune response against HCMV in relation to CD4 counts among HIV infected individuals. A total of 90 achieved sera from HIV infected patients attending Bugando Medical centre care and treatment centre (CTC) aged 18 years and above were retrieved and analyzed. Sociodemographic data were collected using structured data collection tool. Detection of specific HCMV antibodies was done using Indirect Enzyme Linked Immunosorbent Assay (ELISA). Data were analyzed by using STATA version 11. A total of 90 HIV infected patients were enrolled in the study whereby 36(40%) had immunological treatment failure. The mean age of the study participants was 39±12.3 years. The Prevalence of specific HCMV IgG antibodies was 84(93.3%, 95% CI: 88-98.5) while the prevalence of specific HCMV IgM antibodies was 2(2.3% 95% CI: 0.8-5.4). The median CD4 counts at 6 months and 12 months on HAART were significantly high in treatment success group. At 12 months of HAART as CD4 counts increases the HCMV IgG index value was also found to increase significantly, p=0.04. Significant proportion of HIV infected individuals was infected with HCMV. Higher median HCMV IgG titers were observed among patients with immunological treatment success. There is a need to investigate humoral immune responses in HIV infected individuals in relation to CD4 counts against various infectious diseases in developing countries where most of these infections are endemic.
Radiotherapy planning using MRI

The use of magnetic resonance imaging (MRI) in radiotherapy (RT) planning is rapidly expanding. We review the wide range of image contrast mechanisms available to MRI and the way they are exploited for RT planning. However a number of challenges are also considered: the requirements that MR images are acquired in the RT treatment position, that they are geometrically accurate, that effects of patient motion during the scan are minimized, that tissue markers are clearly demonstrated, that an estimate of electron density can be obtained. These issues are discussed in detail, prior to the consideration of a number of specific clinical applications. This is followed by a brief discussion on the development of real-time MRI-guided RT.
Improving the Testability of Code Generation for Microsoft DSL Tools

There are noticeable issues related to the traditional meth od for software engineering, perhaps the most significant being the current cost and t ime to market of software systems. Microsoft’s Software Factories (SF) confront the se problems. A tool that supports creating SFs is the Microsoft Tools for Domain-Specifi c Languages (DSL Tools), which allows developers to define a modeling language, gener ate visual designers and transform models, that are described in custom modeling lan u ges, to code. It does not provide any means for testing the transformation proces s from model to code, so that testing boils down to repeatedly executing the code gen eration with a variety of input. A proposed method for improving the testing process i s to build a tool that provides support for testing the code generation process. In th is report, we describe how we built a tool that automatically builds input testmodels f or SFs, optimizes generated test sets based on predicted test quality, supplies tests to a SF and generates a log-file based on the results of the testing process. Then, several me thods for qualifying the quality of generated tests are proposed, which are based on c overage criteria. After that, we illustrate the results of a case study where the effe ctiveness of the automated test generation approach is tested, as well as the performan ce of coverage criteria in predicting test set quality. Twelve errors were exposed in t he SF under test, most of these being robustness errors which appear difficult to find u sing traditional testing approaches. In addition, testing the performance of coverage criteria indicated that there was a relation between metamodel coverage and the number of e rrors found and that, of all proposed coverage criteria, average metamodel cover age was the best predictor for test quality. Finally, we conclude that automated test g eneration is a promising approach for improving the testing process for SFs.
Identification of the Differential Expression Profiles of Serum and Tissue Proteins During Rat Hepatocarcinogenesis

The pathogenesis of hepatocellular carcinoma is complex and not fully known yet. This study aims to screen and identify the differentially expressed proteins in peripheral blood and liver tissue samples from rat hepatocellular carcinoma and to further clarify the pathogenesis and discover the specific tumor markers and molecular targets of hepatocellular carcinoma. The hepatocellular carcinoma model of Wistar rats were induced by chemical carcinogen. The serum and liver tissue samples were obtained after induction for 2, 4, 8, 14, 18, and 21 weeks. The results showed that the clusterin (IPI00198667), heat shock protein a8 (IPI00208205), and N-myc downstream-regulated gene-2 (IPI00382069) being closely related to hepatocarcinogenesis were eventually identified from the 30 different proteins. As the time progressed, the serum levels of clusterin and heat shock protein a8 increased gradually during induced liver cancer in rats. However, the serum N-myc downstream-regulated gene 2 level in induced liver cancer in rats underwent biphasic changes, and the serum N-myc downstream-regulated gene 2 level decreased at the 8th week, increased at the 14th week, and then decreased significantly. Statistical difference occurred in protein expression of clusterin and heat shock protein a8 in liver tissues at the different time points. In the liver tissues, the N-myc downstream-regulated gene 2 level decreased gradually at the 8th week, increased gradually at the 14th week, and then decreased significantly after 14 weeks. The study demonstrated that heat shock protein a8, clusterin, and N-myc downstream-regulated gene 2 participated in the process of abnormal cell division, proliferation, and carcinogenesis of liver cells during hepatocarcinogenesis.
The STOPPA Twin Study Explains the Exhaled Nitric Oxide and Asthma Link by Genetics and Sensitization

Background: The link between asthma and exhaled nitric oxide (FENO) is not completely understood. The aim of this study was to estimate the association between FENO and asthma, taking genetics, sensitization, and inhaled corticosteroids (ICS) into account. Methods: A total of 681 twins (53% monozygotic [MZ] and 47% dizygotic [DZ]) from the population-based STOPPA study (mean age 12.6 years) were recruited and information on FENO (parts per billion), parental report of current asthma, sensitization to airborne allergens (Phadiatop; IgE ≥0.35 kUA/l), and ICS-treatment was collected. We estimated the association between FENO and asthma, sensitization, and ICS in all twins and within pairs (DZ and MZ) to address shared genetic and environmental factors. Linear regression of log-transformed FENO was used and results presented as exponentiated regression coefficients (exp[β]), with 95% confidence interval (CI). Results: We found an association between asthma and FENO in all twins, exp(β) 1.31 [1.11, 1.54]. In within-pairs analysis, the association was stronger within DZ pairs discordant for FENO, exp(β) 1.50 [1.19, 1.89], compared to MZ pairs, exp(β) 1.07 [0.84, 1.37], p = . 049. There was no difference in FENO in non-sensitized children with asthma, compared to children with neither asthma nor sensitization, exp(β) 0.89 [0.77, 1.03]. However, increased FENO was associated with sensitization, exp(β) 1.48 [1.30, 1.69], and with sensitization together with asthma, exp(β) 1.98 [1.57, 2.51], in all twins and within DZ pairs discordant for FENO, but not in MZ pairs. The FENO asthma association remained in DZ pairs without regular ICS-treatment. Conclusions: The association between FENO and asthma is explained by genetics and sensitization.
Two-Stream 3D Convolutional Neural Network for Skeleton-Based Action Recognition

It remains a challenge to efficiently extract spatialtemporal information from skeleton sequences for 3D human action recognition. Although most recent action recognition methods are based on Recurrent Neural Networks which present outstanding performance, one of the shortcomings of these methods is the tendency to overemphasize the temporal information. Since 3D convolutional neural network(3D CNN) is a powerful tool to simultaneously learn features from both spatial and temporal dimensions through capturing the correlations between three dimensional signals, this paper proposes a novel two-stream model using 3D CNN. To our best knowledge, this is the first application of 3D CNN in skeleton-based action recognition. Our method consists of three stages. First, skeleton joints are mapped into a 3D coordinate space and then encoding the spatial and temporal information, respectively. Second, 3D CNN models are seperately adopted to extract deep features from two streams. Third, to enhance the ability of deep features to capture global relationships, we extend every stream into multitemporal version. Extensive experiments on the SmartHome dataset and the large-scale NTU RGB-D dataset demonstrate that our method outperforms most of RNN-based methods, which verify the complementary property between spatial and temporal information and the robustness to noise.
Deletion of the rodent malaria ortholog for falcipain-1 highlights differences between hepatic and blood stage merozoites

Proteases have been implicated in a variety of developmental processes during the malaria parasite lifecycle. In particular, invasion and egress of the parasite from the infected hepatocyte and erythrocyte, critically depend on protease activity. Although falcipain-1 was the first cysteine protease to be characterized in P. falciparum, its role in the lifecycle of the parasite has been the subject of some controversy. While an inhibitor of falcipain-1 blocked erythrocyte invasion by merozoites, two independent studies showed that falcipain-1 disruption did not affect growth of blood stage parasites. To shed light on the role of this protease over the entire Plasmodium lifecycle, we disrupted berghepain-1, its ortholog in the rodent parasite P. berghei. We found that this mutant parasite displays a pronounced delay in blood stage infection after inoculation of sporozoites. Experiments designed to pinpoint the defect of berghepain-1 knockout parasites found that it was not due to alterations in gliding motility, hepatocyte invasion or liver stage development and that injection of berghepain-1 knockout merosomes replicated the phenotype of delayed blood stage growth after sporozoite inoculation. We identified an additional role for berghepain-1 in preparing blood stage merozoites for infection of erythrocytes and observed that berghepain-1 knockout parasites exhibit a reticulocyte restriction, suggesting that berghepain-1 activity broadens the erythrocyte repertoire of the parasite. The lack of berghepain-1 expression resulted in a greater reduction in erythrocyte infectivity in hepatocyte-derived merozoites than it did in erythrocyte-derived merozoites. These observations indicate a role for berghepain-1 in processing ligands important for merozoite infectivity and provide evidence supporting the notion that hepatic and erythrocytic merozoites, though structurally similar, are not identical.
Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study

Motivation: Molecular pathways and networks play a key role in basic and disease biology. An emerging notion is that networks encoding patterns of molecular interplay may themselves differ between contexts, such as cell type, tissue or disease (sub)type. However, while statistical testing of differences in mean expression levels has been extensively studied, testing of network differences remains challenging. Furthermore, since network differences could provide important and biologically interpretable information to identify molecular subgroups, there is a need to consider the unsupervised task of learning subgroups and networks that define them. This is a nontrivial clustering problem, with neither subgroups nor subgroup‐specific networks known at the outset. Results: We leverage recent ideas from high‐dimensional statistics for testing and clustering in the network biology setting. The methods we describe can be applied directly to most continuous molecular measurements and networks do not need to be specified beforehand. We illustrate the ideas and methods in a case study using protein data from The Cancer Genome Atlas (TCGA). This provides evidence that patterns of interplay between signalling proteins differ significantly between cancer types. Furthermore, we show how the proposed approaches can be used to learn subtypes and the molecular networks that define them. Availability and implementation: As the Bioconductor package nethet. Contact: staedler.n@gmail.com or sach.mukherjee@dzne.de Supplementary information: Supplementary data are available at Bioinformatics online.
Systems-Level Feedbacks of NRF2 Controlling Autophagy upon Oxidative Stress Response

Although the primary role of autophagy-dependent cellular self-eating is cytoprotective upon various stress events (such as starvation, oxidative stress, and high temperatures), sustained autophagy might lead to cell death. A transcription factor called NRF2 (nuclear factor erythroid-related factor 2) seems to be essential in maintaining cellular homeostasis in the presence of either reactive oxygen or nitrogen species generated by internal metabolism or external exposure. Accumulating experimental evidence reveals that oxidative stress also influences the balance of the 5′ AMP-activated protein kinase (AMPK)/rapamycin (mammalian kinase target of rapamycin or mTOR) signaling pathway, thereby inducing autophagy. Based on computational modeling here we propose that the regulatory triangle of AMPK, NRF2 and mTOR guaranties a precise oxidative stress response mechanism comprising of autophagy. We suggest that under conditions of oxidative stress, AMPK is crucial for autophagy induction via mTOR down-regulation, while NRF2 fine-tunes the process of autophagy according to the level of oxidative stress. We claim that the cellular oxidative stress response mechanism achieves an incoherently amplified negative feedback loop involving NRF2, mTOR and AMPK. The mTOR-NRF2 double negative feedback generates bistability, supporting the proper separation of two alternative steady states, called autophagy-dependent survival (at low stress) and cell death (at high stress). In addition, an AMPK-mTOR-NRF2 negative feedback loop suggests an oscillatory characteristic of autophagy upon prolonged intermediate levels of oxidative stress, resulting in new rounds of autophagy stimulation until the stress events cannot be dissolved. Our results indicate that AMPK-, NRF2- and mTOR-controlled autophagy induction provides a dynamic adaptation to altering environmental conditions, assuming their new frontier in biomedicine.
Example‐Based Fractured Appearance

A common weathering effect is the appearance of cracks due to material fractures. Previous exemplar‐based aging and weathering methods have either reused images or sought to replicate observed patterns exactly. We introduce a new approach to exemplar‐based modeling that creates weathered patterns on synthetic objects by matching the statistics of fracture patterns in a photograph. We present a user study to determine which statistics are correlated to visual similarity and how they are perceived by the user. We then describe a revised physically‐based fracture model capable of producing a wide range of crack patterns at interactive rates. We demonstrate how a Bayesian optimization method can determine the parameters of this model so it can produce a pattern with the same key statistics as an exemplar. Finally, we present results using our approach and various exemplars to produce a variety of fracture effects in synthetic renderings of complex environments. The speed of the fracture simulation allows interactive previews of the fractured results and its application on large scale environments.
Targeting the centriolar replication factor STIL synergizes with DNA damaging agents for treatment of ovarian cancer

Advanced ovarian cancer is an incurable disease. Thus, novel therapies are required. We wished to identify new therapeutic targets for ovarian cancer. ShRNA screen performed in 42 ovarian cancer cell lines identified the centriolar replication factor STIL as an essential gene for ovarian cancer cells. This was verified in-vivo in orthotopic human ovarian cancer mouse models. STIL depletion by administration of siRNA in neutral liposomes resulted in robust anti-tumor effect that was further enhanced in combination with cisplatin. Consistent with this finding, STIL depletion enhanced the extent of DNA double strand breaks caused by DNA damaging agents. This was associated with centrosomal depletion, ongoing genomic instability and enhanced formation of micronuclei. Interestingly, the ongoing DNA damage was not associated with reduced DNA repair. Indeed, we observed that depletion of STIL enhanced canonical homologous recombination repair and increased BRCA1 and RAD51 foci in response to DNA double strand breaks. Thus, inhibition of STIL significantly enhances the efficacy of DNA damaging chemotherapeutic drugs in treatment of ovarian cancer.
Intraoperative Transpedicular Onyx Injection to Reduce Vascularity of a Thoracic Hemangiopericytoma After Unsuccessful Preoperative Endovascular Embolization: a Technical Report.

BACKGROUND AND IMPORTANCE Hemangiopericytoma is a rare vascular tumor with central nervous system involvement representing only 1% of central nervous system tumors. They rarely affect the vertebral column. Complete surgical resection is the treatment of choice for hemangiopericytoma given their high rates of local recurrence. However, the high vascularity of such tumors with the risk of massive bleeding during surgery represents a significant challenge to surgeons. Therefore, preoperative endovascular embolization via the transarterial route has been advocated. CLINICAL PRESENTATION In the current study, we present a case of a T12 hemangiopericytoma that was managed by a 2-stage surgical resection, with the use of intraoperative transpedicular onyx injection to reduce intraoperative blood loss following an unsuccessful trial of preoperative endovascular embolization. CONCLUSION Preoperative endovascular embolization is not feasible in some cases due to the location of the segmental or radiculomedullary arteries in relation to tumor feeders and, rarely, small size of these arterial feeders. Percutaneous injection of onyx is an option. In this case report, we discuss direct intraoperative injection via a transpedicular route as a safe and effective method for decreasing the vascularity of some lesions and improving intraoperative blood loss.